def shrinkUniverse(universe, temperature=300.*Units.K, trajectory=None,
scale_factor=0.95):
"""Shrinks |universe|, which must have been scaled up by
Function:MMTK.Solvation.addSolvent, back to its original size.
The compression is performed in small steps, in between which
some energy minimization and molecular dynamics steps are executed.
The molecular dynamics is run at the given |temperature|, and
an optional |trajectory| (a MMTK.Trajectory.Trajectory object or
a string, interpreted as a file name) can be specified in which
intermediate configurations are stored.
"""
# Set velocities and initialize trajectory output
universe.initializeVelocitiesToTemperature(temperature)
if trajectory is not None:
if type(trajectory) == type(''):
trajectory = Trajectory(universe, trajectory, "w",
"solvation protocol")
close_trajectory = 1
else:
close_trajectory = 0
actions = [TrajectoryOutput(trajectory, ["configuration"], 0, None, 1)]
snapshot = SnapshotGenerator(universe, actions=actions)
snapshot()
# Do some minimization and equilibration
minimizer = SteepestDescentMinimizer(universe, step_size = 0.05*Units.Ang)
actions = [VelocityScaler(temperature, 0.01*temperature, 0, None, 1),
TranslationRemover(0, None, 20)]
integrator = VelocityVerletIntegrator(universe, delta_t = 0.5*Units.fs,
actions = actions)
for i in range(5):
minimizer(steps = 40)
integrator(steps = 200)
# Scale down the system in small steps
i = 0
while universe.scale_factor > 1.:
if trajectory is not None and i % 1 == 0:
snapshot()
i = i + 1
step_factor = max(scale_factor, 1./universe.scale_factor)
for object in universe:
object.translateTo(step_factor*object.position())
universe.scaleSize(step_factor)
universe.scale_factor = universe.scale_factor*step_factor
for i in range(3):
minimizer(steps = 10)
integrator(steps = 50)
del universe.scale_factor
if trajectory is not None:
snapshot()
if close_trajectory:
trajectory.close()
