def __init__(self, atoms, timestep, temperature, friction, fixcm=True,
trajectory=None, communicator=gpaw_world):
MolecularDynamics.__init__(self, atoms, timestep, trajectory)
self.temp = temperature
self.frict = friction
self.fixcm = fixcm # will the center of mass be held fixed?
self.communicator = communicator
self.updatevars()
def __init__(self, atoms,
timestep, temperature, externalstress, ttime, pfactor,
mask=None, trajectory=None):
MolecularDynamics.__init__(self, atoms, timestep, trajectory)
#self.atoms = atoms
#self.timestep = timestep
self.zero_center_of_mass_momentum(verbose=1)
self.temperature = temperature
self.set_stress(externalstress)
self.set_mask(mask)
self.eta = zeros((3,3), float)
self.zeta = 0.0
self.zeta_integrated = 0.0
self.initialized = 0
self.ttime = ttime
self.pfactor_given = pfactor
self._calculateconstants()
self.timeelapsed = 0.0
self.frac_traceless = 1
def attach_atoms(self, atoms):
"""Assign atoms to a restored dynamics object.
This function must be called to set the atoms immediately after the
dynamics object has been read from a trajectory.
"""
try:
self.atoms
except AttributeError:
pass
else:
raise RuntimeError, "Cannot call attach_atoms on a dynamics which already has atoms."
MolecularDynamics.__init__(self, atoms, self.dt)
####self.atoms = atoms
limit = 1e-6
h = self._getbox()
if max(abs((h - self.h).ravel())) > limit:
raise RuntimeError, "The unit cell of the atoms does not match the unit cell stored in the file."
self.inv_h = linalg.inv(self.h)
self._make_special_q_arrays()
self.q[:] = dot(self.atoms.get_positions(),
self.inv_h) - 0.5
self._calculate_q_past_and_future()
self.initialized = 1
def __init__(self, atoms, dt, trajectory=None):
MolecularDynamics.__init__(self, atoms, dt, trajectory)