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from ase.build import add_adsorbate, fcc111
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.db import connect
from ase.optimize import BFGS
db1 = connect('bulk.db')
db2 = connect('ads.db')
def run(symb, a, n, ads):
atoms = fcc111(symb, (1, 1, n), a=a)
add_adsorbate(atoms, ads, height=1.0, position='fcc')
# Constrain all atoms except the adsorbate:
fixed = list(range(len(atoms) - 1))
atoms.constraints = [FixAtoms(indices=fixed)]
atoms.calc = EMT()
opt = BFGS(atoms, logfile=None)
opt.run(fmax=0.01)
return atoms
for row in db1.select():
a = row.cell[0, 1] * 2
symb = row.symbols[0]
for n in [1, 2, 3]:
for ads in 'CNO':
atoms = run(symb, a, n, ads)
db2.write(atoms, layers=n, surf=symb, ads=ads)
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