Example #1
0
File: mcmc.py Project: swails/repex
    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
Example #2
0
File: mcmc.py Project: swails/repex
    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
        >>> import testsystems
        >>> test = testsystems.AlanineDipeptideVacuum()
        >>> # Create a Context.
        >>> import simtk.openmm as mm
        >>> import simtk.unit as u
        >>> integrator = mm.VerletIntegrator(1.0 * u.femtoseconds)
        >>> platform = mm.Platform.getPlatformByName('Reference')
        >>> context = mm.Context(test.system, integrator, platform)
        >>> # Set positions and velocities.
        >>> context.setPositions(test.positions)
        >>> context.setVelocitiesToTemperature(298 * u.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
Example #3
0
File: mcmc.py Project: swails/repex
    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
        >>> import testsystems
        >>> test = testsystems.AlanineDipeptideVacuum()
        >>> # Create a Context.
        >>> import simtk.openmm as mm
        >>> import simtk.unit as u
        >>> integrator = mm.VerletIntegrator(1.0 * u.femtoseconds)
        >>> platform = mm.Platform.getPlatformByName('Reference')
        >>> context = mm.Context(test.system, integrator, platform)
        >>> # Set positions and velocities.
        >>> context.setPositions(test.positions)
        >>> context.setVelocitiesToTemperature(298 * u.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
Example #4
0
File: mcmc.py Project: swails/repex
    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