Chimie Théorique » QMX

import numpy as np

from ase.optimize.optimize import Optimizer

class MDMin(Optimizer):

    def __init__(self, atoms, restart=None, logfile='-', trajectory=None,

                 dt=None):

        Optimizer.__init__(self, atoms, restart, logfile, trajectory)

        if dt is not None:

            self.dt = dt

    def initialize(self):

        self.v = None

        self.dt = 0.2

    def read(self):

        self.v, self.dt = self.load()

    def step(self, f):

        atoms = self.atoms

        if self.v is None:

            self.v = np.zeros((len(atoms), 3))

        else:

            self.v += 0.5 * self.dt * f

            # Correct velocities:

            vf = np.vdot(self.v, f)

            if vf < 0.0:

                self.v[:] = 0.0

            else:

                self.v[:] = f * vf / np.vdot(f, f)

        self.v += 0.5 * self.dt * f

        r = atoms.get_positions()

        atoms.set_positions(r + self.dt * self.v)

        self.dump((self.v, self.dt))