Logger move task

Currently, the logger writes the particles after the kick1. It means that the velocities are at t + 0.5 dt and the positions are at t. The only place where both are synchronized is after the kick2, therefore this merge request is moving the task after the kick2.

I am also changing runner_do_logger. We are currently writing the particles when they start. I am changing this in order to write them at the end of their step.

@nnrw56 We can discuss it tomorrow.