Update initialization of surface related variables

[grantfirl]

This PR accomplishes the following:

• Addresses issues Transient in surface temperature when using LSM (even with UFS ICs) #209 and Setting surface temperature from forcing file even with UFS ICs #210.
• Also addresses bug report by @wangevine related to specified surface fluxes being zero as long as used with new ccpp-physics PR that fixes gmtb_scm_sfc_flux_spec scheme.
• Updates SCM to use latest master branches of ccpp-physics/framework

This represents a major rewrite of surface variable initialization to address the above issues and make future maintenance easier.

UFS_IC_generator.py

• reads in ALL variables from surface file (as opposed to only some) following what is done in FV3GFS_io.F90; if variables are not present in the file, it will still write out the variable with values equal to a user-configurable missing value
• handles all Noah LSM, RUC LSM, NoahMP LSM, and NSST variables
• handles new fractional landmask and lake variables in the 'oro' files
• outputs all variables (including missing ones)

gmtb_scm_input.F90

• reads in all new variables output by UFS_IC_generator.py
• utilizes new NetCDF_read_var module to handle missing data

gmtb_scm_type_defs.F90

• removes redundant variables in the 'state' DDT introduced when UFS ICs were originally added
• adds new variables to 'input' DDT only
• new "set" type-bound procedure for the physics DDT (should be used only for initialization of physics variables that doesn't happen in the ccpp_physics_init stage; should NOT be used for variables that are associated with pointers that can be modified/forced outside of the physics by the SCM)
• updated "associate" type-bound procedure of physics DDT to only have pointer association for variables that get modified/forced by SCM (specifically surface temperature logic)
• new "set" routine conditionally sets Sfcprop variables, depending on missing data (will STOP if variables are required but missing)
• includes logic from FV3/io/FV3GFS_io.F90 to deriving surface variables (related to fractional landmask, lake, NSST, NoahMP, and RUC LSM)
• includes NoahMP "cold start" logic when NoahMP is active and Noah LSM input data is present, but NoahMP input data is missing

gmtb_scm_utils.F90

• new NetCDF read module with generic interfaces for reading variables or setting to missing
• new module for quality controlling variables or stopping if encountering missing values for required variables

gmtb_scm.F90

• includes call to new physics%set routine after the physics%associate call

[grantfirl]

Testing was done for:

• existing specified surface flux cases (fixes issue noticed by @wangevine)
• existing cases with simple ocean
• existing UFS IC cases (also tested with IC files that have fractional landmask and lake data, but not RUC data yet)

Note to GSL folks @climbfuji @tanyasmirnova This PR should pave the way for testing with the RUC LSM. If there are FV3 IC files somewhere (after processing by global_chgres) that have RUC LSM variables, I could test it.

[climbfuji]

RUC can be / is usually initialized from ICs that were created with Noah LSM - but both should work.

…

On Dec 7, 2020, at 2:09 PM, grantfirl ***@***.***> wrote: Testing was done for: existing specified surface flux cases (fixes issue noticed by @wangevine <https://github.com/wangevine>) existing cases with simple ocean existing UFS IC cases (also tested with IC files that have fractional landmask and lake data, but not RUC data yet) Note to GSL folks @climbfuji <https://github.com/climbfuji> @tanyasmirnova <https://github.com/tanyasmirnova> This PR should pave the way for testing with the RUC LSM. If there are FV3 IC files somewhere (after processing by global_chgres) that have RUC LSM variables, I could test it. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#217 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB5C2RNLLHRPVKEV7MMYXBLSTVAAHANCNFSM4UMIGTCA>.

[climbfuji]

I don't claim to understand or to have reviewed line by line the surface initialization, but at least I didn't see anything obviously wrong. Some of the new netCDF routines could have been collapsed into fewer by using elemental functions/subroutines, but the current implementation is fine.