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I spent some time thinking about this during the weekend and I think I found the solution:
Lets say I have 10 simulation runs using my known system (using different initial conditions for each run) and each run includes 52 timesteps, i.e. 520 in total.
If I choose nbatch=10 (1 batch for 1 simulation run) and nsteps=52 (prediction horizon in the objective function), each simulation run (i.e. system trajectory) is independently evaluated in the objective function. This way, no data point from one trajectory slips into the evaluation of a different trajectory in the objective function. This is probably obvious for most people, but I am quite new to training neural nets and for me it took a l…

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