I believe thermal layers are modelled in SH3 for the same reason StandingCow states.
Thermal Layers are Very Dynamic. Weather has a huge impact on where they are or if they exist at all. There can actually be multiple thermal layers in the same area (existing at certain depths of course). From my experience in SH3 (and i pre-ordered and still play it a lot) is that the Dev Team may have even modelled the "Afternoon Effect". The afternoon effect is a layer created right around periscope depth on very sunny days. The sun warms the surface of the water creating a very shallow layer. On afternoon attacks on bright days, I have sometimes gottn away undetected by staying at periscope depth and slinking away--even 1942 and later...
Layers work because the rapid temperature differential creates a dense Salinity layer. It's the layer of dense salt that reflects sound, not temperature itself.
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Past Hatteras the convoys sail,
It seems the Allies will prevail.
Churchill and Franklin share a grin,
They know who's gonna win this sim.
Finback
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