def get_atoms():
atoms = Atoms([
Atom('Pd', [5.078689759346383, 5.410678028467162, 4.000000000000000]),
Atom('Pd', [7.522055777772603, 4.000000000000000, 4.000000000000000]),
Atom('Pd', [7.522055777772603, 6.821356056934325, 4.000000000000000]),
Atom('Pd', [6.707600438297196, 5.410678028467162, 6.303627574066606]),
Atom('N', [4.807604264052752, 5.728625577716107, 5.919407072553396]),
Atom('H', [4.000000000000000, 5.965167390141987, 6.490469524180266]),
])
constraint = FixAtoms(mask=[a.symbol == 'Pd' for a in atoms])
atoms.set_constraint(constraint)
atoms.center(vacuum=4.0)
atoms.set_pbc(False)
return atoms
vscr = os.getenv('VASP_SCRIPT')
if vcmd == None and vscr == None:
raise NotAvailable('Neither VASP_COMMAND nor VASP_SCRIPT defined')
from ase_ext import Atoms
from ase_ext.calculators.vasp import Vasp
import numpy as np
def array_almost_equal(a1, a2, tol=np.finfo(type(1.0)).eps):
"""Replacement for old numpy.testing.utils.array_almost_equal."""
return (np.abs(a1 - a2) < tol).all()
d = 1.14
co = Atoms('CO', positions=[(0, 0, 0), (0, 0, d)],
pbc=True)
co.center(vacuum=5.)
calc = Vasp(
xc = 'PBE',
prec = 'Low',
algo = 'Fast',
ismear= 0,
sigma = 1.,
lwave = False,
lcharg = False)
co.set_calculator(calc)
en = co.get_potential_energy()
assert abs(en + 14.918933) < 1e-4
# Secondly, check that restart from the previously created VASP output works
from gpaw import GPAW
logo = """\
H HH HHH
H H H H
HHH H HH
H H H H
H H HH HHH"""
d = 0.8
atoms = Atoms()
for y, line in enumerate(logo.split('\n')):
for x, c in enumerate(line):
if c == 'H':
atoms.append(Atom('H', [d * x, -d * y, 0]))
atoms.center(vacuum=2.0)
view(atoms)
if 0:
calc = GPAW(nbands=30)
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('ase-logo.gpw')
else:
calc = GPAW('ase-logo.gpw', txt=None)
density = calc.get_pseudo_density()
image = density[..., density.shape[2] // 2]
if 1: # scale colors to wiki background / foreground
import numpy as np
def get_atoms():
cell = (5, 5, 5)
atoms = Atoms('H2', [(0, 0, 0), (0, 0, 1.4)], cell=cell)
atoms.center()
return atoms
