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# In this script the Virtual Crystal approximation is used to model
# a stronger affinity for positive charge on the H atoms.
# This could model interaction with other molecules not explicitly
# handled.
import numpy as np
from ase.calculators.siesta import Siesta
from ase.calculators.siesta.parameters import Species
from ase.optimize import QuasiNewton
from ase import Atoms
atoms = Atoms('CH4', np.array([
[0.000000, 0.000000, 0.000000],
[0.682793, 0.682793, 0.682793],
[-0.682793, -0.682793, 0.682790],
[-0.682793, 0.682793, -0.682793],
[0.682793, -0.682793, -0.682793]]))
siesta = Siesta(
species=[
Species(symbol='H', excess_charge=0.1)])
atoms.calc = siesta
dyn = QuasiNewton(atoms, trajectory='h.traj')
dyn.run(fmax=0.02)
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