perses.rjmc.geometry.GeometryEngine¶

class perses.rjmc.geometry.GeometryEngine(metadata=None, storage=None)[source]¶

This is the base class for the geometry engine.

Methods

`logp_reverse`(top_proposal, new_coordinates, …)	Calculate the logp for the given geometry proposal
`propose`(top_proposal, current_positions, beta)	Make a geometry proposal for the appropriate atoms.

__init__(metadata=None, storage=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`([metadata, storage])	Initialize self.
`logp_reverse`(top_proposal, new_coordinates, …)	Calculate the logp for the given geometry proposal
`propose`(top_proposal, current_positions, beta)	Make a geometry proposal for the appropriate atoms.

logp_reverse(top_proposal, new_coordinates, old_coordinates, beta)[source]¶

Calculate the logp for the given geometry proposal

Returns:	logp : float The log probability of the proposal for the given transformation

propose(top_proposal, current_positions, beta)[source]¶

Make a geometry proposal for the appropriate atoms.

Returns:	new_positions : [n, 3] ndarray The new positions of the system

perses