Update internal model to treat depth as positive upwards

[VeckoTheGecko]

Creating a tracking issue for the following review comment.

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Had a discussion with @erikvansebille about this. Having the internal model of Parcels be internally consistent with whether depth is positive downwards/upwards irrespective of the how its defined in the fieldset data is important so that we don't have to worry about it at this point in the code (this is related to #2003). When uses provide their model input it get's converted to Parcels' internal representation.

We decided to go for depth positive upwards, which (mainly for myself since this confuses me) would look like

0 -------------- Ocean surface
        ଳ
-2 
              ଳ
-4        ଳ

...

\_      ___
  \____/   \____

Currently we treat the depth as depth positive downwards (this is also the case in our test data), so I suggest that we keep with this for now, and I'll make an issue to track updating our internal model to be depth positive upwards (as in the diagram). As part of the issue, we will also check the depth on initialisation so no broken state can make its way down this far.

Originally posted by @VeckoTheGecko in #2060 (comment)