Set _pre_run_state attribribute in Sire dynamics#141
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This PR is a companion to OpenBioSim/sire#420. It sets the
_pre_run_stateattribute of theDynamicsDataobject, allowing correct recovery during a crash. The state is set after each repex swap, then conditionally again following any MC sampling move that updates atom positions. The PR also exposes theauto_fix_minimisedynamics option, allowing it to be disabled if crash recovery isn't desired.