def __init__(self, config_: Config, old_sampler_state=None):
"""
:param systemLoader:
:param config:
"""
self._times = None
self.config = config_
self.logger = make_message_writer(self.config.verbose, self.__class__.__name__)
if self.config.systemloader.system is None:
self.system = self.config.systemloader.get_system(self.config.parameters.createSystem)
self.topology = self.config.systemloader.topology
positions, velocities = self.config.systemloader.get_positions(), None
else:
self.system = self.config.systemloader.system
self.topology = self.config.systemloader.topology
positions, velocities = self.config.systemloader.get_positions(), None
self.topology = self.config.systemloader.topology
self.explicit = self.config.systemloader.explicit
integrator = integrators.GeodesicBAOABIntegrator(temperature=self.config.parameters.integrator_params['temperature'],
timestep=self.config.parameters.integrator_params['timestep'],
collision_rate=self.config.parameters.integrator_params[
'collision_rate'],
constraint_tolerance=self.config.parameters.integrator_setConstraintTolerance)
self.simulation = app.Simulation(self.topology, self.system, integrator,
self.config.parameters.platform, self.config.parameters.platform_config)
self.simulation.context.setPositions(self.config.systemloader.positions)
self.simulation.minimizeEnergy(self.config.parameters.minMaxIters)
self.simulation.context.setVelocitiesToTemperature(self.config.parameters.integrator_params['temperature'])
def _get_default_integrator(temperature):
"""Return a new instance of the default integrator."""
# Use a likely-to-be-used Integrator.
return integrators.GeodesicBAOABIntegrator(temperature=temperature)