context = openmm.Context(testsystem.system, integrator)
context.setPositions(testsystem.positions)
openmm.LocalEnergyMinimizer.minimize(context)
testsystem.positions = context.getState(getPositions=True).getPositions()
del context, integrator
# Benchmark integrators.
for integrator_name in integrators_to_benchmark:
if integrator_name == 'VerletIntegrator':
integrator = openmm.VerletIntegrator(timestep)
elif integrator_name == 'VelocityVerletIntegrator':
integrator = integrators.VelocityVerletIntegrator(timestep)
elif integrator_name == 'VVVRIntegrator':
integrator = integrators.VVVRIntegrator(temperature=temperature, collision_rate=collision_rate, timestep=timestep)
elif integrator_name == 'GHMCIntegrator':
integrator = integrators.GHMCIntegrator(temperature=temperature, collision_rate=collision_rate, timestep=timestep)
# Create system.
context = openmm.Context(testsystem.system, integrator)
context.setPositions(testsystem.positions)
# Run one step.
integrator.step(1)
# Perform timing trials.
elapsed_time = np.zeros([ntrials], np.float64)
for trial in range(ntrials):
initial_time = time.time()
integrator.step(nsteps)
final_time = time.time()
elapsed_time[trial] = final_time - initial_time
hmc_integrators.guess_force_groups(system, nonbonded=1, fft=1, others=0)
groups = [(0, 2), (1, 1)]
idict = {
"verlet":
mm.VerletIntegrator(timestep),
"langevin":
mm.LangevinIntegrator(temperature, collision_rate, timestep),
"vv":
integrators.VelocityVerletIntegrator(timestep),
"vvvr":
integrators.VelocityVerletIntegrator(timestep),
"ghmc10":
integrators.GHMCIntegrator(temperature=temperature,
collision_rate=collision_rate,
timestep=timestep,
steps_per_hmc=10),
"ghmc20":
integrators.GHMCIntegrator(temperature=temperature,
collision_rate=collision_rate,
timestep=timestep,
steps_per_hmc=20),
"ghmcrespa20":
integrators.GHMCRESPA(temperature,
steps_per_hmc=20,
timestep=timestep,
collision_rate=collision_rate,
groups=groups)
}
factors = {"ghmc10": 10, "ghmc20": 20, "ghmcrespa20": 20}
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
>>> from openmmtools 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