AgAuAg chain

We consider the linear chain of three atoms AgAuAg here, which we relax in the first step:

# creates: 1scogef.png
from ase import io
from ase.atoms import Atoms
from ase.optimize import FIRE
from ase.calculators.emt import EMT

fmax = 0.01

fname = 'AgAuAg.traj'
try:
    image = io.read(fname)
except FileNotFoundError:
    image = Atoms('AgAuAg', positions=((-1, 0, 0), (0, 0, 0), (1, 0, 0)))
    image.calc = EMT()
    FIRE(image).run(fmax=fmax)
    image.write(fname)

We will stretch this configuration on the two outer atoms.

Symmetric cogef

The standard COGEF pulling script is applied:

# creates: 1scogef.png
from ase import io
from ase.optimize import FIRE
from ase.calculators.emt import EMT

from cogef import COGEF1D

image = io.read('AgAuAg.traj')


def initialize(atoms):
    atoms.calc = EMT()
    return atoms

fmax = 0.01
cogef = COGEF1D(0, 2, initialize=initialize, fmax=fmax)

if not len(cogef.images):  # calculation was done already
    cogef.images = [image]

    stepsize = 0.1
    steps = 50
    cogef.move(stepsize, steps)

which creates the directory cogef1d_0_2 and writes the file cogef1d_0_2/cogef.traj containing the corresponding trajectory.

This produces rather high energies (“symmetric” above) as both AgAu bondlengths are stretched equally.

Symmetry breaking through rattle

We may break symmetry by using rattle:

# creates: 1scogef.png
import numpy as np
from ase import io
from ase.optimize import FIRE
from ase.calculators.emt import EMT

from cogef import COGEF1D

image = io.read('AgAuAg.traj')


def initialize(atoms):
    atoms.calc = EMT()
    atoms.rattle()
    return atoms

fmax = 0.01
cogef = COGEF1D(0, 2, name='rattle', initialize=initialize, fmax=fmax)

if not len(cogef.images):  # calculation was done already
    cogef.images = [image]

    stepsize = 0.1
    steps = 50
    cogef.move(stepsize, steps)

which creates the directory rattle_0_2 and writes the file rattle_0_2/cogef.traj. The symmetry breaking enables one of the bonds to be intact, while the other breaks. The figure shows that this assymmetric configuration is of lower energy.