[WIP] Modifications to acceptance ratio from Moves #112
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This PR allows the Move class the option to directly impact the acceptance ratio of a move by the
Move.acceptance_ratioattribute. This can potentially come into effect in a variety of circumstances for example, due to dart overlap in Smart Darting. The log of theMove.acceptance_ratiois added to the protocol work to get the overall acceptance ratio during theacceptRejectNCMC()portion of the simulation.Also in the case when
Move.acceptance_ratio == 0at either the beginning of the NCMC iteration, or after theMove.move()method takes place, the entire NCMC portion is automatically rejected. This can come up in numerous places as well, like @khburley's dihedral rotational moves within specific regions where you wouldn't want to continue calculations if the dihedral ends up outside those regions.