def initialize_sampler(**kwargs):
"""Initialize a multistate sampler.
Parameters
----------
test : TestSystem object
sampler_class : MultiStateSampler-derived class
timestep : Quantity
Simulation timestep
state_update_steps : int
Len of an iteration (in time steps).
States are updated at each iteration.
platform : string
Valid values are: 'Reference', 'CPU', 'CUDA', 'OpenGL'
reference_thermodynamic_state
thermodynamic_states
metadata
pressure : Quantity or None
checkpoint_iterations : int
Stride for checkpoint print (in iterations)
ms_container : pathlib.Path
Path to multistate trajectory container
Returns
-------
sampler
"""
prms = SimpleNamespace(**kwargs)
# initialize sampler
smp = prms.sampler_class(number_of_iterations=0,
mcmc_moves=propagator(
timestep=prms.timestep,
n_steps=prms.state_update_steps,
platform=prms.platform),
online_analysis_interval=None)
# set sampler states and positions
smp.from_testsystem(prms.test,
reference_state=prms.reference_thermodynamic_state,
thermodynamic_states=prms.thermodynamic_states,
pressure=prms.pressure,
stride=prms.checkpoint_iterations,
storage=prms.ms_container,
metadata=prms.metadata)
smp.minimize()
return smp
def initialize_sampler():
"""Initialize a multistate sampler."""
# initialize sampler
smp = SAMSSampler(number_of_iterations=burnin_iterations,
mcmc_moves=propagator(timestep=timestep,
n_steps=state_update_steps),
online_analysis_interval=None)
# set sampler states and positions
smp.from_testsystem(test,
temperatures=temperatures,
pressure=pressure,
stride=checkpoint_iterations,
storage=ms_container)
return smp