I don't know if there is a "correct" way to time dives, but i'll tell you the methodology i used.
Only dive time worth measuring (in my opinion), is crash dive. To do that, i set up a test mission where the starting position has you doing 10 kts (or whatever your average cruising speed is), with a preset waypoint, and a windspeed of say, 3 to 5 kts. (heavy winds slow you down, and a perfectly calm day is unrealistic, though i don't think it makes you go any faster)
Anyway, when i start the mission, all i have to do, is hit the return to course command/button/hotkey. Then, i advance time compression for a minute, just to make sure the boat is fully under way, and at the the cruising speed. Then i bring the TC back to normal.
For the purposes of testing, i'll have the unit cam enabled and the camera positioned in such a way where i have a good broadside view of the boat. Now with my stop watch in hand, and the camera set, i'll hit the C key. I start the stop watch as soon as the engine telegraph is all the way into flank. I stop the watch when the CE/DO calls out 40 feet. During this time im watching the boat just to see where the periscope shears are, the angle of the dive, and just how much of the boat is exposed. But 40 feet is usually where i stop the stopwatch.
However you measure it, be consistent.
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