[BUG/ISSUE] Non-species restart variables not set in mid-run GCHP checkpoint files

[lizziel]

What institution are you from?

Harvard University

Description of the problem

Some of the non-species fields in GCHP mid-run checkpoint (restart) files are all zero. This will cause small differences when restarting a run from a mid-point checkpoint file, which can happen if, for example, a long run fails in the middle.

GEOS-Chem version

All GCHP versions.

Description of modifications

The solution is to update the internal state pointers for these fields every timestep rather than just in the first timestep (for use during restart) and the last timestep for outputting the end-of-run file. The area field need only be updated in the first timestep (it is currently only set at the end of the run).