changes to GFS_phys_time_vary.scm.F90 (SCM ONLY) to match FV3-based counterpart#643
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…#643) * clean up output_1st_tstep_rst and fix diag time at GEFS restart * change logf file to atm.logf
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This is an addendum to the GFS_phys_time_vary.fv3.F90 changes in #623.
Required for compilation with NCAR/ccpp-scm#240. FV3 regression tests should not be required since this file is never used in FV3.