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If you want to keep all your user-created clocks in sync with the core one, you can either ask for no maximized DT for the core clock in the render module config section or set the same maximized DT on your user clock with the orxClock_SetModifier() function.
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What I meant is that I don't see why clock desync would affect anything in-game. Or at least I haven't encountered not thought of a case where that would matter.
The time within a clock is consistent. If two clocks have the same settings, the time between those will also be consistent.
As you're using your own clocks, I assume you're not using the core clock (if you are, what is then the point?), and in that case I don't see why desync between your clocks and the core one should matter.
I've a few questions: have you considered using the main clock for everything, and simply 'skipping' clock cycles to achieve each various element's appropriate tick rate? Not the nicest answer but seems a "simple" fix if nothing else is available.
Secondly; if I ever write on this forum with my phone again, please yell at me
Real secondly: are you using a different clock per enemy? Or are the timing issue arising from enemies being spawned by the main clock at 'wrong' time etc?
Let assume you need it, for doing some time stretching for example, all your logic should then be on user clocks and nothing on the core clock, beside orx's internal inputs, rendering, ...
Lastly, do you know why you have slowdowns? The profiler is there for that exact reasion: letting you know why things slow down and where it happens.
So no, I never add similar problems, but by simply removing the maximised DT on the core clock, that should remove your problem for the time being.
I have functions that are responsible for responding to user input, updating time left in the round, etc. In these, I just check the current value of IsInPlay and don't update if false.
What I did in a recent proto is that I add a new clock (a paused one) to all my game objects (ie. not menu ones) that I remove when un-pausing. By default my objects don't have any clock, so it's easy for me.
That's also the strategy I used for slowing down projectiles around the player in Mushroom Stew when the time special weapon is activated.