def minimize(self, tolerance=None, maxIterations=None, platform=None):
"""
Minimize the current configuration.
Parameters
----------
tolerance : simtk.unit.Quantity compatible with kilocalories_per_mole/anstroms, optional, default = 1*kilocalories_per_mole/anstrom
Tolerance to use for minimization termination criterion.
maxIterations : int, optional, default = 100
Maximum number of iterations to use for minimization.
platform : simtk.openmm.Platform, optional
Platform to use for minimization.
Examples
--------
>>> # Create a test system
>>> import testsystems
>>> test = testsystems.AlanineDipeptideVacuum()
>>> # Create a sampler state.
>>> sampler_state = SamplerState(system=test.system, positions=test.positions)
>>> # Minimize
>>> sampler_state.minimize()
"""
timer = Timer()
if (tolerance is None):
tolerance = 1.0 * u.kilocalories_per_mole / u.angstroms
if (maxIterations is None):
maxIterations = 100
# Use LocalEnergyMinimizer
from simtk.openmm import LocalEnergyMinimizer
timer.start("Context creation")
context = self.createContext(platform=platform)
logger.debug("LocalEnergyMinimizer: platform is %s" %
context.getPlatform().getName())
logger.debug("Minimizing with tolerance %s and %d max. iterations." %
(tolerance, maxIterations))
timer.stop("Context creation")
timer.start("LocalEnergyMinimizer minimize")
LocalEnergyMinimizer.minimize(context, tolerance, maxIterations)
timer.stop("LocalEnergyMinimizer minimize")
# Retrieve data.
sampler_state = SamplerState.createFromContext(context)
self.positions = sampler_state.positions
self.potential_energy = sampler_state.potential_energy
self.total_energy = sampler_state.total_energy
del context
timer.report_timing()
return
def minimize(self, tolerance=None, maxIterations=None, platform=None):
"""
Minimize the current configuration.
Parameters
----------
tolerance : simtk.unit.Quantity compatible with kilocalories_per_mole/anstroms, optional, default = 1*kilocalories_per_mole/anstrom
Tolerance to use for minimization termination criterion.
maxIterations : int, optional, default = 100
Maximum number of iterations to use for minimization.
platform : simtk.openmm.Platform, optional
Platform to use for minimization.
Examples
--------
>>> # Create a test system
>>> import testsystems
>>> test = testsystems.AlanineDipeptideVacuum()
>>> # Create a sampler state.
>>> sampler_state = SamplerState(system=test.system, positions=test.positions)
>>> # Minimize
>>> sampler_state.minimize()
"""
timer = Timer()
if (tolerance is None):
tolerance = 1.0 * u.kilocalories_per_mole / u.angstroms
if (maxIterations is None):
maxIterations = 100
# Use LocalEnergyMinimizer
from simtk.openmm import LocalEnergyMinimizer
timer.start("Context creation")
context = self.createContext(platform=platform)
logger.debug("LocalEnergyMinimizer: platform is %s" % context.getPlatform().getName())
logger.debug("Minimizing with tolerance %s and %d max. iterations." % (tolerance, maxIterations))
timer.stop("Context creation")
timer.start("LocalEnergyMinimizer minimize")
LocalEnergyMinimizer.minimize(context, tolerance, maxIterations)
timer.stop("LocalEnergyMinimizer minimize")
# Retrieve data.
sampler_state = SamplerState.createFromContext(context)
self.positions = sampler_state.positions
self.potential_energy = sampler_state.potential_energy
self.total_energy = sampler_state.total_energy
del context
timer.report_timing()
return
def apply(self, thermodynamic_state, sampler_state, platform=None):
"""
Apply the GHMC MCMC move.
Parameters
----------
thermodynamic_state : ThermodynamicState
The thermodynamic state to use when applying the MCMC move
sampler_state : SamplerState
The sampler state to apply the move to
platform : simtk.openmm.Platform, optional, default = None
If not None, the specified platform will be used.
Returns
-------
updated_sampler_state : SamplerState
The updated sampler state
Examples
--------
>>> # Create a test system
>>> import testsystems
>>> test = testsystems.AlanineDipeptideVacuum()
>>> # Create a sampler state.
>>> sampler_state = SamplerState(system=test.system, positions=test.positions)
>>> # Create a thermodynamic state.
>>> from thermodynamics import ThermodynamicState
>>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin)
>>> # Create a LangevinDynamicsMove
>>> move = GHMCMove(nsteps=10, timestep=1.0*u.femtoseconds, collision_rate=20.0/u.picoseconds)
>>> # Perform one update of the sampler state.
>>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)
"""
timer = Timer()
# Create integrator.
integrator = integrators.GHMCIntegrator(temperature=thermodynamic_state.temperature, collision_rate=self.collision_rate, timestep=self.timestep)
# Random number seed.
seed = np.random.randint(_RANDOM_SEED_MAX)
integrator.setRandomNumberSeed(seed)
# Create context.
timer.start("Context Creation")
context = sampler_state.createContext(integrator, platform=platform)
timer.stop("Context Creation")
# TODO: Enforce constraints?
#tol = 1.0e-8
#context.applyConstraints(tol)
#context.applyVelocityConstraints(tol)
# Run dynamics.
timer.start("step()")
integrator.step(self.nsteps)
timer.stop("step()")
# Get updated sampler state.
timer.start("update_sampler_state")
updated_sampler_state = SamplerState.createFromContext(context)
timer.start("update_sampler_state")
# Accumulate acceptance statistics.
ghmc_global_variables = { integrator.getGlobalVariableName(index) : index for index in range(integrator.getNumGlobalVariables()) }
naccepted = integrator.getGlobalVariable(ghmc_global_variables['naccept'])
nattempted = integrator.getGlobalVariable(ghmc_global_variables['ntrials'])
self.naccepted += naccepted
self.nattempted += nattempted
# DEBUG.
#print " GHMC accepted %d / %d (%.1f%%)" % (naccepted, nattempted, float(naccepted) / float(nattempted) * 100.0)
# Clean up.
del context
timer.report_timing()
return updated_sampler_state
def apply(self, thermodynamic_state, sampler_state, platform=None):
"""
Apply the Langevin dynamics MCMC move.
Parameters
----------
thermodynamic_state : ThermodynamicState
The thermodynamic state to use when applying the MCMC move
sampler_state : SamplerState
The sampler state to apply the move to
platform : simtk.openmm.Platform, optional, default = None
If not None, the specified platform will be used.
Returns
-------
updated_sampler_state : SamplerState
The updated sampler state
Examples
--------
Alanine dipeptide in vacuum.
>>> # Create a test system
>>> import testsystems
>>> test = testsystems.AlanineDipeptideVacuum()
>>> # Create a sampler state.
>>> sampler_state = SamplerState(system=test.system, positions=test.positions)
>>> # Create a thermodynamic state.
>>> from thermodynamics import ThermodynamicState
>>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin)
>>> # Create a LangevinDynamicsMove
>>> move = LangevinDynamicsMove(nsteps=10, timestep=0.5*u.femtoseconds, collision_rate=20.0/u.picoseconds)
>>> # Perform one update of the sampler state.
>>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)
Ideal gas.
>>> # Create a test system
>>> import testsystems
>>> test = testsystems.IdealGas()
>>> # Add a MonteCarloBarostat.
>>> barostat = mm.MonteCarloBarostat(1*u.atmospheres, 298*u.kelvin, 25)
>>> force_index = test.system.addForce(barostat)
>>> # Create a sampler state.
>>> sampler_state = SamplerState(system=test.system, positions=test.positions)
>>> # Create a thermodynamic state.
>>> from thermodynamics import ThermodynamicState
>>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin)
>>> # Create a LangevinDynamicsMove
>>> move = LangevinDynamicsMove(nsteps=500, timestep=0.5*u.femtoseconds, collision_rate=20.0/u.picoseconds)
>>> # Perform one update of the sampler state.
>>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)
"""
timer = Timer()
# Check if the system contains a barostat.
system = sampler_state.system
forces = { system.getForce(index).__class__.__name__ : system.getForce(index) for index in range(system.getNumForces()) }
barostat = None
if 'MonteCarloBarostat' in forces:
barostat = forces['MonteCarloBarostat']
barostat.setTemperature(thermodynamic_state.temperature)
parameter_name = barostat.Pressure()
# Create integrator.
integrator = mm.LangevinIntegrator(thermodynamic_state.temperature, self.collision_rate, self.timestep)
# Random number seed.
seed = np.random.randint(_RANDOM_SEED_MAX)
integrator.setRandomNumberSeed(seed)
# Create context.
timer.start("Context Creation")
context = sampler_state.createContext(integrator, platform=platform)
timer.stop("Context Creation")
logger.debug("LangevinDynamicMove: Context created, platform is %s" % context.getPlatform().getName())
# Set pressure, if barostat is included.
if barostat is not None:
context.setParameter(parameter_name, thermodynamic_state.pressure)
if self.reassign_velocities:
# Assign Maxwell-Boltzmann velocities.
context.setVelocitiesToTemperature(thermodynamic_state.temperature)
# Run dynamics.
timer.start("step()")
integrator.step(self.nsteps)
timer.stop("step()")
# Get updated sampler state.
timer.start("update_sampler_state")
updated_sampler_state = SamplerState.createFromContext(context)
timer.start("update_sampler_state")
# Clean up.
del context
timer.report_timing()
return updated_sampler_state
def apply(self, thermodynamic_state, sampler_state, platform=None):
"""
Apply the MCMC move.
Parameters
----------
thermodynamic_state : ThermodynamicState
The thermodynamic state to use when applying the MCMC move
sampler_state : SamplerState
The sampler state to apply the move to
platform : simtk.openmm.Platform, optional, default = None
If not None, the specified platform will be used.
Returns
-------
updated_sampler_state : SamplerState
The updated sampler state
Examples
--------
>>> # Create a test system
>>> import testsystems
>>> test = testsystems.LennardJonesFluid()
>>> # Create a sampler state.
>>> sampler_state = SamplerState(system=test.system, positions=test.positions, box_vectors=test.system.getDefaultPeriodicBoxVectors())
>>> # Create a thermodynamic state.
>>> from thermodynamics import ThermodynamicState
>>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin, pressure=1*u.atmospheres)
>>> # Create a Monte Carlo Barostat move.
>>> move = MonteCarloBarostatMove(nattempts=5)
>>> # Perform one update of the sampler state.
>>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)
"""
timer = Timer()
# Make sure system contains a barostat.
system = sampler_state.system
forces = { system.getForce(index).__class__.__name__ : system.getForce(index) for index in range(system.getNumForces()) }
old_barostat_frequency = None
if 'MonteCarloBarostat' in forces:
force = forces['MonteCarloBarostat']
force.setTemperature(thermodynamic_state.temperature)
old_barostat_frequency = force.getFrequency()
force.setFrequency(1)
parameter_name = force.Pressure()
else:
# Add MonteCarloBarostat.
force = mm.MonteCarloBarostat(thermodynamic_state.pressure, thermodynamic_state.temperature, 1)
system.addForce(force)
parameter_name = force.Pressure()
# Create integrator.
integrator = integrators.DummyIntegrator()
# Random number seed.
seed = np.random.randint(_RANDOM_SEED_MAX)
force.setRandomNumberSeed(seed)
# Create context.
timer.start("Context Creation")
context = sampler_state.createContext(integrator, platform=platform)
timer.stop("Context Creation")
# Set pressure.
context.setParameter(parameter_name, thermodynamic_state.pressure)
# Run update.
# Note that ONE step of this integrator is equal to self.nsteps of velocity Verlet dynamics followed by Metropolis accept/reject.
timer.start("step(1)")
integrator.step(self.nattempts)
timer.stop("step(1)")
# Get sampler state.
timer.start("update_sampler_state")
updated_sampler_state = SamplerState.createFromContext(context)
timer.stop("update_sampler_state")
# DEBUG
#print thermodynamics.volume(updated_sampler_state.box_vectors)
# Clean up.
del context
# Restore frequency of barostat.
if old_barostat_frequency:
force.setFrequency(old_barostat_frequency)
timer.report_timing()
# Return updated sampler state.
return updated_sampler_state
def apply(self, thermodynamic_state, sampler_state, platform=None):
"""
Apply the MCMC move.
Parameters
----------
thermodynamic_state : ThermodynamicState
The thermodynamic state to use when applying the MCMC move
sampler_state : SamplerState
The sampler state to apply the move to
platform : simtk.openmm.Platform, optional, default = None
If not None, the specified platform will be used.
Returns
-------
updated_sampler_state : SamplerState
The updated sampler state
Examples
--------
>>> # Create a test system
>>> import testsystems
>>> test = testsystems.AlanineDipeptideVacuum()
>>> # Create a sampler state.
>>> sampler_state = SamplerState(system=test.system, positions=test.positions)
>>> # Create a thermodynamic state.
>>> from thermodynamics import ThermodynamicState
>>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin)
>>> # Create an HMC move.
>>> move = HMCMove(nsteps=10, timestep=0.5*u.femtoseconds)
>>> # Perform one update of the sampler state.
>>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)
"""
timer = Timer()
# Create integrator.
integrator = integrators.HMCIntegrator(temperature=thermodynamic_state.temperature, timestep=self.timestep, nsteps=self.nsteps)
# Random number seed.
seed = np.random.randint(_RANDOM_SEED_MAX)
integrator.setRandomNumberSeed(seed)
# Create context.
timer.start("Context Creation")
context = sampler_state.createContext(integrator, platform=platform)
timer.stop("Context Creation")
# Run dynamics.
# Note that ONE step of this integrator is equal to self.nsteps of velocity Verlet dynamics followed by Metropolis accept/reject.
timer.start("HMC integration")
integrator.step(1)
timer.stop("HMC integration")
# Get sampler state.
timer.start("updated_sampler_state")
updated_sampler_state = SamplerState.createFromContext(context)
timer.stop("updated_sampler_state")
# Clean up.
del context
timer.report_timing()
# Return updated sampler state.
return updated_sampler_state
def apply(self, thermodynamic_state, sampler_state, platform=None):
"""
Apply the GHMC MCMC move.
Parameters
----------
thermodynamic_state : ThermodynamicState
The thermodynamic state to use when applying the MCMC move
sampler_state : SamplerState
The sampler state to apply the move to
platform : simtk.openmm.Platform, optional, default = None
If not None, the specified platform will be used.
Returns
-------
updated_sampler_state : SamplerState
The updated sampler state
Examples
--------
>>> # Create a test system
>>> import testsystems
>>> test = testsystems.AlanineDipeptideVacuum()
>>> # Create a sampler state.
>>> sampler_state = SamplerState(system=test.system, positions=test.positions)
>>> # Create a thermodynamic state.
>>> from thermodynamics import ThermodynamicState
>>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin)
>>> # Create a LangevinDynamicsMove
>>> move = GHMCMove(nsteps=10, timestep=1.0*u.femtoseconds, collision_rate=20.0/u.picoseconds)
>>> # Perform one update of the sampler state.
>>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)
"""
timer = Timer()
# Create integrator.
integrator = integrators.GHMCIntegrator(
temperature=thermodynamic_state.temperature,
collision_rate=self.collision_rate,
timestep=self.timestep)
# Random number seed.
seed = np.random.randint(_RANDOM_SEED_MAX)
integrator.setRandomNumberSeed(seed)
# Create context.
timer.start("Context Creation")
context = sampler_state.createContext(integrator, platform=platform)
timer.stop("Context Creation")
# TODO: Enforce constraints?
#tol = 1.0e-8
#context.applyConstraints(tol)
#context.applyVelocityConstraints(tol)
# Run dynamics.
timer.start("step()")
integrator.step(self.nsteps)
timer.stop("step()")
# Get updated sampler state.
timer.start("update_sampler_state")
updated_sampler_state = SamplerState.createFromContext(context)
timer.start("update_sampler_state")
# Accumulate acceptance statistics.
ghmc_global_variables = {
integrator.getGlobalVariableName(index): index
for index in range(integrator.getNumGlobalVariables())
}
naccepted = integrator.getGlobalVariable(
ghmc_global_variables['naccept'])
nattempted = integrator.getGlobalVariable(
ghmc_global_variables['ntrials'])
self.naccepted += naccepted
self.nattempted += nattempted
# DEBUG.
#print " GHMC accepted %d / %d (%.1f%%)" % (naccepted, nattempted, float(naccepted) / float(nattempted) * 100.0)
# Clean up.
del context
timer.report_timing()
return updated_sampler_state
def apply(self, thermodynamic_state, sampler_state, platform=None):
"""
Apply the Langevin dynamics MCMC move.
Parameters
----------
thermodynamic_state : ThermodynamicState
The thermodynamic state to use when applying the MCMC move
sampler_state : SamplerState
The sampler state to apply the move to
platform : simtk.openmm.Platform, optional, default = None
If not None, the specified platform will be used.
Returns
-------
updated_sampler_state : SamplerState
The updated sampler state
Examples
--------
Alanine dipeptide in vacuum.
>>> # Create a test system
>>> import testsystems
>>> test = testsystems.AlanineDipeptideVacuum()
>>> # Create a sampler state.
>>> sampler_state = SamplerState(system=test.system, positions=test.positions)
>>> # Create a thermodynamic state.
>>> from thermodynamics import ThermodynamicState
>>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin)
>>> # Create a LangevinDynamicsMove
>>> move = LangevinDynamicsMove(nsteps=10, timestep=0.5*u.femtoseconds, collision_rate=20.0/u.picoseconds)
>>> # Perform one update of the sampler state.
>>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)
Ideal gas.
>>> # Create a test system
>>> import testsystems
>>> test = testsystems.IdealGas()
>>> # Add a MonteCarloBarostat.
>>> barostat = mm.MonteCarloBarostat(1*u.atmospheres, 298*u.kelvin, 25)
>>> force_index = test.system.addForce(barostat)
>>> # Create a sampler state.
>>> sampler_state = SamplerState(system=test.system, positions=test.positions)
>>> # Create a thermodynamic state.
>>> from thermodynamics import ThermodynamicState
>>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin)
>>> # Create a LangevinDynamicsMove
>>> move = LangevinDynamicsMove(nsteps=500, timestep=0.5*u.femtoseconds, collision_rate=20.0/u.picoseconds)
>>> # Perform one update of the sampler state.
>>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)
"""
timer = Timer()
# Check if the system contains a barostat.
system = sampler_state.system
forces = {
system.getForce(index).__class__.__name__: system.getForce(index)
for index in range(system.getNumForces())
}
barostat = None
if 'MonteCarloBarostat' in forces:
barostat = forces['MonteCarloBarostat']
barostat.setTemperature(thermodynamic_state.temperature)
parameter_name = barostat.Pressure()
# Create integrator.
integrator = mm.LangevinIntegrator(thermodynamic_state.temperature,
self.collision_rate, self.timestep)
# Random number seed.
seed = np.random.randint(_RANDOM_SEED_MAX)
integrator.setRandomNumberSeed(seed)
# Create context.
timer.start("Context Creation")
context = sampler_state.createContext(integrator, platform=platform)
timer.stop("Context Creation")
logger.debug("LangevinDynamicMove: Context created, platform is %s" %
context.getPlatform().getName())
# Set pressure, if barostat is included.
if barostat is not None:
context.setParameter(parameter_name, thermodynamic_state.pressure)
if self.reassign_velocities:
# Assign Maxwell-Boltzmann velocities.
context.setVelocitiesToTemperature(thermodynamic_state.temperature)
# Run dynamics.
timer.start("step()")
integrator.step(self.nsteps)
timer.stop("step()")
# Get updated sampler state.
timer.start("update_sampler_state")
updated_sampler_state = SamplerState.createFromContext(context)
timer.start("update_sampler_state")
# Clean up.
del context
timer.report_timing()
return updated_sampler_state
def apply(self, thermodynamic_state, sampler_state, platform=None):
"""
Apply the MCMC move.
Parameters
----------
thermodynamic_state : ThermodynamicState
The thermodynamic state to use when applying the MCMC move
sampler_state : SamplerState
The sampler state to apply the move to
platform : simtk.openmm.Platform, optional, default = None
If not None, the specified platform will be used.
Returns
-------
updated_sampler_state : SamplerState
The updated sampler state
Examples
--------
>>> # Create a test system
>>> import testsystems
>>> test = testsystems.LennardJonesFluid()
>>> # Create a sampler state.
>>> sampler_state = SamplerState(system=test.system, positions=test.positions, box_vectors=test.system.getDefaultPeriodicBoxVectors())
>>> # Create a thermodynamic state.
>>> from thermodynamics import ThermodynamicState
>>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin, pressure=1*u.atmospheres)
>>> # Create a Monte Carlo Barostat move.
>>> move = MonteCarloBarostatMove(nattempts=5)
>>> # Perform one update of the sampler state.
>>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)
"""
timer = Timer()
# Make sure system contains a barostat.
system = sampler_state.system
forces = {
system.getForce(index).__class__.__name__: system.getForce(index)
for index in range(system.getNumForces())
}
old_barostat_frequency = None
if 'MonteCarloBarostat' in forces:
force = forces['MonteCarloBarostat']
force.setTemperature(thermodynamic_state.temperature)
old_barostat_frequency = force.getFrequency()
force.setFrequency(1)
parameter_name = force.Pressure()
else:
# Add MonteCarloBarostat.
force = mm.MonteCarloBarostat(thermodynamic_state.pressure,
thermodynamic_state.temperature, 1)
system.addForce(force)
parameter_name = force.Pressure()
# Create integrator.
integrator = integrators.DummyIntegrator()
# Random number seed.
seed = np.random.randint(_RANDOM_SEED_MAX)
force.setRandomNumberSeed(seed)
# Create context.
timer.start("Context Creation")
context = sampler_state.createContext(integrator, platform=platform)
timer.stop("Context Creation")
# Set pressure.
context.setParameter(parameter_name, thermodynamic_state.pressure)
# Run update.
# Note that ONE step of this integrator is equal to self.nsteps of velocity Verlet dynamics followed by Metropolis accept/reject.
timer.start("step(1)")
integrator.step(self.nattempts)
timer.stop("step(1)")
# Get sampler state.
timer.start("update_sampler_state")
updated_sampler_state = SamplerState.createFromContext(context)
timer.stop("update_sampler_state")
# DEBUG
#print thermodynamics.volume(updated_sampler_state.box_vectors)
# Clean up.
del context
# Restore frequency of barostat.
if old_barostat_frequency:
force.setFrequency(old_barostat_frequency)
timer.report_timing()
# Return updated sampler state.
return updated_sampler_state
def apply(self, thermodynamic_state, sampler_state, platform=None):
"""
Apply the MCMC move.
Parameters
----------
thermodynamic_state : ThermodynamicState
The thermodynamic state to use when applying the MCMC move
sampler_state : SamplerState
The sampler state to apply the move to
platform : simtk.openmm.Platform, optional, default = None
If not None, the specified platform will be used.
Returns
-------
updated_sampler_state : SamplerState
The updated sampler state
Examples
--------
>>> # Create a test system
>>> import testsystems
>>> test = testsystems.AlanineDipeptideVacuum()
>>> # Create a sampler state.
>>> sampler_state = SamplerState(system=test.system, positions=test.positions)
>>> # Create a thermodynamic state.
>>> from thermodynamics import ThermodynamicState
>>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin)
>>> # Create an HMC move.
>>> move = HMCMove(nsteps=10, timestep=0.5*u.femtoseconds)
>>> # Perform one update of the sampler state.
>>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)
"""
timer = Timer()
# Create integrator.
integrator = integrators.HMCIntegrator(
temperature=thermodynamic_state.temperature,
timestep=self.timestep,
nsteps=self.nsteps)
# Random number seed.
seed = np.random.randint(_RANDOM_SEED_MAX)
integrator.setRandomNumberSeed(seed)
# Create context.
timer.start("Context Creation")
context = sampler_state.createContext(integrator, platform=platform)
timer.stop("Context Creation")
# Run dynamics.
# Note that ONE step of this integrator is equal to self.nsteps of velocity Verlet dynamics followed by Metropolis accept/reject.
timer.start("HMC integration")
integrator.step(1)
timer.stop("HMC integration")
# Get sampler state.
timer.start("updated_sampler_state")
updated_sampler_state = SamplerState.createFromContext(context)
timer.stop("updated_sampler_state")
# Clean up.
del context
timer.report_timing()
# Return updated sampler state.
return updated_sampler_state