Source code for openpathsampling.engines.openmm.snapshot


@author: JD Chodera
@author: JH Prinz

from openpathsampling.engines import BaseSnapshot, SnapshotFactory
from . import features

[docs] @features.base.attach_features([ features.velocities, features.coordinates, features.box_vectors, features.engine ]) class MDSnapshot(BaseSnapshot): """ A fast MD snapshot, which does not proxy the coordinates/velocities. """
# The following code does the same as above # # MDSnapshot = SnapshotFactory( # name='MDSnapshot', # features=[ # features.velocities, # features.coordinates, # features.box_vectors, # features.engine # ], # description="A fast MDSnapshot", # base_class=BaseSnapshot # )
[docs] @features.base.attach_features([ features.statics, features.kinetics, features.masses, features.instantaneous_temperature, features.engine, features.traj_quantities, ]) class Snapshot(BaseSnapshot): """ The standard snapshot for MD, based on statics and kinetics proxies. """ StaticContainer = features.StaticContainer KineticContainer = features.KineticContainer @staticmethod def construct( coordinates=None, box_vectors=None, velocities=None, statics=None, kinetics=None, engine=None): """ Construct a new snapshot from numpy arrays This will create the container objects and return a Snapshot object. Mostly a helper to allow for easier creation. You can either use coordinates and velocities and/or statics and kinetics objects. If both are present the more complex (statics and kinetics) will be used Parameters ---------- coordinates : numpy.array, shape ``(n_atoms, n_spatial)`` the atomic coordinates box_vectors : numpy.array, shape ``(n_spatial, n_spatial)`` the box vectors velocities : numpy.array, shape ``(n_atoms, n_spatial)`` the atomic velocities statics : `openpathsampling.engines.openmm.StaticContainer` the statics container if it already exists kinetics : `openpathsampling.engines.openmm.KineticContainer` the kinetics container if it already exists engine : :obj:`openpathsampling.engines.DynamicsEngine` the engine that should be referenced as the one used to generate the object Returns ------- :obj:`Snapshot` the created `Snapshot` object """ if statics is None: statics = Snapshot.StaticContainer( coordinates=coordinates, box_vectors=box_vectors, engine=engine ) if kinetics is None: kinetics = Snapshot.KineticContainer( velocities=velocities, engine=engine ) return Snapshot( engine=engine, statics=statics, kinetics=kinetics ) @property def topology(self): return self.engine.topology