Move calculation of sncovr from FV3/io/FV3GFS_io.F90 to ccpp/physics/physics/GFS_phys_time_vary.XYZ.F90

[grantfirl]

This moves the calculation of the Sfcprop%sncovr variable from sfc_prop_restart_read subroutine in the FV3GFS_io.F90 file to GFS_phys_time_vary.XYZ.F90 in ccpp-physics. This was flagged as a problem by @climbfuji, and seemed to interfere with the NoahMP work (related to namelist_soilveg.F existing in both the CCPP and non-CCPP physics repos).

Work done:
(FV3)

• Only calculate Sfcprop%sncovr in FV3GFS_io.F90 for the non-CCPP build using directives
• namelist_soilveg is no longer needed in the non-CCPP physics makefile for the CCPP build
• Remove the call for set_soilveg in GFS_driver.F90 since it is no longer needed (happens as part of the CCPP physics-init stage)
• edit the non-CCPP physics makefile for the CCPP build to remove these two files

(ccpp-physics)

• put the calculation of Sfcprop%sncovr in the GFS_phys_time_vary_run subroutine of GFS_phys_time_vary.XYZ.F90 (makes use of the first_time_step flag since it is initialization-related but must happen after the ccpp_physics_init stage)

NOTE: As far as I can tell, this code needs to go in GFS_phys_time_vary_run for the following reasons:

• the FV3GFS_restart_read call where the code had been executed happened after the CCPP physics_init stage, and it is possible to read in values for Sfcprop%sncovr in this routine.
• although it is related to the initialization of surface properties and this might belong in GFS_surface_generic_pre, it is expected to have already been initialized in rrtmg_lw_pre_run, which gets called before LSMs

[grantfirl]

Associated PR:
https://github.com/NCAR/FV3/pull/201

[grantfirl]

These PRs were provisionally tested (PASSED) on Cheyenne/Intel (due to Theia maintenance) using only the fv3_control test for (IPD repro/prod) and CCPP (repro/prod). It should undergo full testing later, but I will be using this in my NoahMP debugging in the meantime.

[grantfirl]

The code changes in this PR are included in PR #305 .