def __init__(self, engine): descriptor = SnapshotDescriptor.construct( snapshot_class=engine.InternalizedSnapshotClass, snapshot_dimensions=engine.descriptor._dimensions) self.engine = engine super(_InternalizedEngineProxy, self).__init__(options={}, descriptor=descriptor)
def setup(self): self.descriptor = SnapshotDescriptor.construct( snapshot_class=ToySnapshot, snapshot_dimensions={ 'n_spatial': 1, 'n_atoms': 1 }) slow_options = { 'n_frames_max': 10000, 'engine_sleep': 100, 'name_prefix': "test", 'engine_directory': engine_dir } fast_options = { 'n_frames_max': 10000, 'engine_sleep': 0, 'name_prefix': "test", 'engine_directory': engine_dir } self.template = peng.toy.Snapshot(coordinates=np.array([[0.0]]), velocities=np.array([[1.0]])) self.slow_engine = ExampleExternalEngine(slow_options, self.descriptor, self.template) self.fast_engine = ExampleExternalEngine(fast_options, self.descriptor, self.template) self.ensemble = paths.LengthEnsemble(5)
def __init__(self, sequences, sleep_ms=0): self.sequences = sequences self.sleep_ms = sleep_ms self.descriptor = SnapshotDescriptor.construct( snapshot_class=ExternalMDSnapshot, snapshot_dimensions={ 'n_spatial': 2, 'n_atoms': 1 }) self.internalized_engine = _InternalizedEngineProxy(self)
def __init__(self, gro): traj = md.load(gro) self.topology = MDTrajTopology(traj.topology) n_atoms = self.topology.n_atoms n_spatial = self.topology.n_spatial descriptor = SnapshotDescriptor.construct( snapshot_class=ExternalMDSnapshot, snapshot_dimensions={ 'n_spatial': n_spatial, 'n_atoms': n_atoms }) super(GroFileEngine, self).__init__(options={}, descriptor=descriptor, template=None)