Chimie Théorique » QMX

import numpy as np

from ase.optimize.optimize import Dynamics

from ase.optimize.fire import FIRE

from ase.units import kB

from ase.parallel import world

from ase.io.trajectory import PickleTrajectory

class BasinHopping(Dynamics):

    """Basin hopping algorythm.

    After Wales and Doye, J. Phys. Chem. A, vol 101 (1997) 5111-5116"""

    def __init__(self, atoms,

                 temperature=100 * kB,

                 optimizer=FIRE,

                 fmax=0.1,

                 dr=.1,

                 logfile='-', 

                 trajectory='lowest.traj',

                 optimizer_logfile='-',

                 local_minima_trajectory='local_minima.traj',

                 adjust_cm=True):

        Dynamics.__init__(self, atoms, logfile, trajectory)

        self.kT = temperature

        self.optimizer = optimizer

        self.fmax = fmax

        self.dr = dr

        if adjust_cm:

            self.cm = atoms.get_center_of_mass()

        else:

            self.cm = None

        self.optimizer_logfile = optimizer_logfile

        self.lm_trajectory = local_minima_trajectory

        if isinstance(local_minima_trajectory, str):

            self.lm_trajectory = PickleTrajectory(local_minima_trajectory,

                                                  'w', atoms)

        self.initialize()

    def initialize(self):

        self.positions = 0. * self.atoms.get_positions()

        self.Emin = self.get_energy(self.atoms.get_positions())

        self.rmin = self.atoms.get_positions()

        self.positions = self.atoms.get_positions()

        self.call_observers()

        self.log(-1, self.Emin, self.Emin)

    def run(self, steps):

        """Hop the basins for defined number of steps."""

        ro = self.positions

        Eo = self.get_energy(ro)

        for step in range(steps):

            rn = self.move(ro)

            En = self.get_energy(rn)

            if En < self.Emin:

                # new minimum found

                self.Emin = En

                self.rmin = self.atoms.get_positions()

                self.call_observers()

                rn = self.rmin

            self.log(step, En, self.Emin)

            accept = np.exp((Eo - En) / self.kT) > np.random.uniform()

            if accept:

                ro = rn

                Eo = En

    def log(self, step, En, Emin):

        if self.logfile is None:

            return

        name = self.__class__.__name__

        self.logfile.write('%s: step %d, energy %15.6f, emin %15.6f\n'

                           % (name, step, En, self.Emin))

        self.logfile.flush()

    def move(self, ro):

        atoms = self.atoms

        # displace coordinates

        disp = np.random.uniform(-1., 1., (len(atoms), 3))

        rn = ro + self.dr * disp

        atoms.set_positions(rn)

        if self.cm is not None:

            cm = atoms.get_center_of_mass()

            atoms.translate(self.cm - cm)

        rn = atoms.get_positions()

        if world is not None:

            world.broadcast(rn, 0)

        atoms.set_positions(rn)

        return atoms.get_positions()

    def get_minimum(self):

        atoms = self.atoms.copy()

        atoms.set_positions(self.rmin)

        return self.Emin, atoms

    def get_energy(self, positions):

        """Return the energy of the nearest local minimum."""

        if np.sometrue(self.positions != positions):

            self.positions = positions

            self.atoms.set_positions(positions)

            try:

                opt = self.optimizer(self.atoms, logfile=self.optimizer_logfile)

                opt.run(fmax=self.fmax)

                if self.lm_trajectory is not None:

                    self.lm_trajectory.write(self.atoms)

                self.energy = self.atoms.get_potential_energy()

            except:

                # the atoms are probably to near to each other

                self.energy = 1.e32

        return self.energy