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When examining subdaily output from the PTM, @melofton noticed that water quality diagnostic variable jump depths at the end of the day and end of the simulation. They look reasonable at other times and the water quality states are fine. I determined that it is due to water quality diagnostics not receiving the same treatment as water quality variables in the check_layer_thinkness() function call. This PR fixes the issue.

Added handling for WQD_Vars in volume calculations.
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