implement timestep_init phases and catch up with master of ccpp-physics

[grantfirl]

• Implement the timestep_init/finalize phases in SCM source code
• update to ccpp-physics master as of 2021/01/26
• change build system so that ccpp_prebuild.py writes caps/cmake snippets to build directory rather than src directory (this now works with the default CMakeLists.txt in ccpp-physics)
• change the diagnostic bucket clearing to SCM code
  -- change timing of diagnostic clearing (order of operations was wrong)
  -- allow for diagnostic clearing every timestep
• comment out reading in RUC LSM init variables since changes to ccpp-physics has rendered it obsolete (followup PR needed to read in RUC LSM init data)

[grantfirl]

Associated PR: NCAR/ccpp-physics#562

[grantfirl]

The fix in the CMakeLists.txt for ccpp-physics in NCAR/ccpp-physics@2d8c061#diff-1e7de1ae2d059d21e1dd75d5812d5a34b0222cef273b7c3a2af62eb747f9d20a leads to build issues in the SCM, but it is likely the SCM build system's fault.

[grantfirl]

Also, the RUC LSM code that was commented out needs to be updated following a recent change in that code.

[climbfuji]

Please let me know when you are done with the updates by requesting another review, and I'll take a look. Thanks!

[grantfirl]

Please let me know when you are done with the updates by requesting another review, and I'll take a look. Thanks!

There definitely need to be followup PR(s) to catch up to master, but I'd like to merge this before continuing on.

[climbfuji]

@grantfirl I merged NCAR/ccpp-physics#562 earlier today.

[grantfirl]

@grantfirl I merged NCAR/ccpp-physics#562 earlier today.

Thanks. Did you want to review this PR again?

[grantfirl]

I'll update the submodule pointer for ccpp-physics real quick.

[grantfirl]

I'll update the submodule pointer for ccpp-physics real quick.

Nevermind. Since that PR went into top of master, that will break things. I think that I'll just need to go ahead and update the SCM to the top of master.

[climbfuji]

I'll update the submodule pointer for ccpp-physics real quick.

Nevermind. Since that PR went into top of master, that will break things. I think that I'll just need to go ahead and update the SCM to the top of master.

Yeah, no other choice, unfortunately. Cannot merge it somewhere in between.

[grantfirl]

I'll update the submodule pointer for ccpp-physics real quick.

Nevermind. Since that PR went into top of master, that will break things. I think that I'll just need to go ahead and update the SCM to the top of master.

Yeah, no other choice, unfortunately. Cannot merge it somewhere in between.

Totally fine. The update to top-of-master is long overdue anyway, so now is a good time.

[grantfirl]

Replaced by #239