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"""Molecular Dynamics."""
import warnings
import numpy as np
from ase.optimize.optimize import Dynamics
from ase.md.logger import MDLogger
class MolecularDynamics(Dynamics):
"""Base-class for all MD classes."""
def __init__(self, atoms, timestep, trajectory, logfile=None,
loginterval=1):
self.dt = timestep
Dynamics.__init__(self, atoms, logfile=None, trajectory=trajectory)
self.masses = self.atoms.get_masses()
if 0 in self.masses:
warnings.warn('Zero mass encountered in atoms; this will '
'likely lead to errors if the massless atoms '
'are unconstrained.')
self.masses.shape = (-1, 1)
if logfile:
self.attach(MDLogger(dyn=self, atoms=atoms, logfile=logfile),
interval=loginterval)
def todict(self):
return {'type': 'molecular-dynamics',
'md-type': self.__class__.__name__,
'timestep': self.dt}
def run(self, steps=50):
"""Integrate equation of motion."""
f = self.atoms.get_forces(md=True)
if not self.atoms.has('momenta'):
self.atoms.set_momenta(np.zeros_like(f))
for step in range(steps):
f = self.step(f)
self.nsteps += 1
self.call_observers()
def get_time(self):
return self.nsteps * self.dt
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