def createFromContext(cls, context):
"""
Create an SamplerState object from the information in a current OpenMM Context object.
Parameters
----------
context : simtk.openmm.Context
The Context object from which to create a sampler state.
Returns
-------
sampler_state : SamplerState
The sampler state containing positions, velocities, and box vectors.
Examples
--------
>>> # Create a test system
>>> test = testsystems.AlanineDipeptideVacuum()
>>> # Create a Context.
>>> import simtk.openmm as mm
>>> import simtk.unit as u
>>> integrator = openmm.VerletIntegrator(1.0 * unit.femtoseconds)
>>> platform = openmm.Platform.getPlatformByName('Reference')
>>> context = openmm.Context(test.system, integrator, platform)
>>> # Set positions and velocities.
>>> context.setPositions(test.positions)
>>> context.setVelocitiesToTemperature(298 * unit.kelvin)
>>> # Create a sampler state from the Context.
>>> sampler_state = SamplerState.createFromContext(context)
>>> # Clean up.
>>> del context, integrator
"""
# Get state.
openmm_state = context.getState(getPositions=True, getVelocities=True, getEnergy=True)
# Create new object, bypassing init.
self = SamplerState.__new__(cls)
# Populate context.
self.system = copy.deepcopy(context.getSystem())
self.positions = openmm_state.getPositions(asNumpy=True)
self.velocities = openmm_state.getVelocities(asNumpy=True)
self.box_vectors = openmm_state.getPeriodicBoxVectors(asNumpy=True)
self.potential_energy = openmm_state.getPotentialEnergy()
self.kinetic_energy = openmm_state.getKineticEnergy()
self.total_energy = self.potential_energy + self.kinetic_energy
self.volume = thermodynamics.volume(self.box_vectors)
return self
def __init__(self, system, positions, velocities=None, box_vectors=None, platform=None):
self.system = copy.deepcopy(system)
self.positions = positions
self.velocities = velocities
self.box_vectors = box_vectors
# Create Context.
context = self.createContext(platform=platform)
# Get state.
openmm_state = context.getState(getPositions=True, getVelocities=True, getEnergy=True)
# Populate context.
self.positions = openmm_state.getPositions(asNumpy=True)
self.velocities = openmm_state.getVelocities(asNumpy=True)
self.box_vectors = openmm_state.getPeriodicBoxVectors(asNumpy=False)
self.potential_energy = openmm_state.getPotentialEnergy()
self.kinetic_energy = openmm_state.getKineticEnergy()
self.total_energy = self.potential_energy + self.kinetic_energy
self.volume = thermodynamics.volume(self.box_vectors)
# Clean up.
del context