Chimie Théorique » QMX

"""Molecular Dynamics."""

import numpy as np

from ase.optimize.optimize import Dynamics

from ase.data import atomic_masses

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):

        Dynamics.__init__(self, atoms, logfile=None, trajectory=trajectory)

        self.dt = timestep

        self.masses = self.atoms.get_masses()

        self.masses.shape = (-1, 1)

        if logfile:

            self.attach(MDLogger(dyn=self, atoms=atoms, logfile=logfile),

                        interval=loginterval)

    def run(self, steps=50):

        """Integrate equation of motion."""

        f = self.atoms.get_forces()

        if not self.atoms.has('momenta'):

            self.atoms.set_momenta(np.zeros_like(f))

        for step in xrange(steps):

            f = self.step(f)

            self.nsteps += 1

            self.call_observers()

    def get_time(self):

        return self.nsteps * self.dt