Populate mid-run checkpoints with non-species data every timeset #1442
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The update in this PR fixes a GCHP bug in which non-species entries in mid-run restart files (aka checkpoint files) were incorrect. All internal state data is now updated every timestep, with the except of area which is only updated in the first timestep since it is time-invariant.
This update will have no impact on GCHP 1-month benchmarks or end-of-run restart files. It will correct a problem in 1-year GCHP benchmarks which used mid-run checkpoint files to retrieve area for generating mass tables. It will also correct error introduced when restarting a GCHP simulation from a previously generated mid-run checkpoint file to continue a series of runs. This would happen if, for example, a run crashed mid-way through the configured run duration due to a compute cluster issue rather than a model issue.