Fix shieldclock crash in dycore_only

[JosephMouallem]

shieldClock timer starts in update_atmos_pre_radiation and ends in update_atmos_physics.
This causes a crash when compiling shield and running with dycore_only since update_atmos_physics is not called in update_atmos_radiation_physics, mpp_clock_begin is called again before calling mpp_clock_end.

In this commit both mpp_clock_begin and mpp_clock_end are moved to update_atmos_radiation_physics.

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules
• New check tests, if applicable, are included

[JosephMouallem]

@bensonr

[laurenchilutti]

Merging #34 would fix this bug. So we can probable close this and merge #34