def test_autoneb(asap3):
EMT = asap3.EMT
fmax = 0.02
# Pt atom adsorbed in a hollow site:
slab = fcc211('Pt', size=(3, 2, 2), vacuum=4.0)
add_adsorbate(slab, 'Pt', 0.5, (-0.1, 2.7))
# Fix second and third layers:
slab.set_constraint(FixAtoms(range(6, 12)))
# Use EMT potential:
slab.calc = EMT()
# Initial state:
qn = QuasiNewton(slab, trajectory='neb000.traj')
qn.run(fmax=fmax)
# Final state:
slab[-1].x += slab.get_cell()[0, 0]
slab[-1].y += 2.8
qn = QuasiNewton(slab, trajectory='neb001.traj')
qn.run(fmax=fmax)
# Stops PermissionError on Win32 for access to
# the traj file that remains open.
del qn
def attach_calculators(images):
for i in range(len(images)):
images[i].calc = EMT()
autoneb = AutoNEB(attach_calculators,
prefix='neb',
optimizer='BFGS',
n_simul=3,
n_max=7,
fmax=fmax,
k=0.5,
parallel=False,
maxsteps=[50, 1000])
autoneb.run()
nebtools = NEBTools(autoneb.all_images)
assert abs(nebtools.get_barrier()[0] - 0.937) < 1e-3
def test_surface():
import numpy as np
from ase import Atoms, Atom
from ase.build import fcc111, fcc211, add_adsorbate, bulk, surface
import math
atoms = fcc211('Au', (3, 5, 8), vacuum=10.)
assert len(atoms) == 120
atoms = atoms.repeat((2, 1, 1))
assert np.allclose(atoms.get_distance(0, 130), 2.88499566724)
atoms = fcc111('Ni', (2, 2, 4), orthogonal=True)
add_adsorbate(atoms, 'H', 1, 'bridge')
add_adsorbate(atoms, Atom('O'), 1, 'fcc')
add_adsorbate(atoms, Atoms('F'), 1, 'hcp')
# The next test ensures that a simple string of multiple atoms cannot be used,
# which should fail with a KeyError that reports the name of the molecule due
# to the string failing to work with Atom().
failed = False
try:
add_adsorbate(atoms, 'CN', 1, 'ontop')
except KeyError as e:
failed = True
assert e.args[0] == 'CN'
assert failed
# This test ensures that the default periodic behavior remains unchanged
cubic_fcc = bulk("Al", a=4.05, cubic=True)
surface_fcc = surface(cubic_fcc, (1,1,1), 3)
assert list(surface_fcc.pbc) == [True, True, False]
assert surface_fcc.cell[2][2] == 0
# This test checks the new periodic option
cubic_fcc = bulk("Al", a=4.05, cubic=True)
surface_fcc = surface(cubic_fcc, (1,1,1), 3, periodic=True)
assert (list(surface_fcc.pbc) == [True, True, True])
expected_length = 4.05*3**0.5 #for FCC with a=4.05
assert math.isclose(surface_fcc.cell[2][2], expected_length)
from ase.build import fcc211, add_adsorbate
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton
from ase.neb import NEBTools
from ase.autoneb import AutoNEB
# Pt atom adsorbed in a hollow site:
slab = fcc211('Pt', size=(3, 2, 2), vacuum=4.0)
add_adsorbate(slab, 'Pt', 0.5, (-0.1, 2.7))
# Fix second and third layers:
slab.set_constraint(FixAtoms(range(6, 12)))
# Use EMT potential:
slab.set_calculator(EMT())
# Initial state:
qn = QuasiNewton(slab, trajectory='neb000.traj')
qn.run(fmax=0.05)
# Final state:
slab[-1].x += slab.get_cell()[0, 0]
slab[-1].y += 2.8
qn = QuasiNewton(slab, trajectory='neb001.traj')
qn.run(fmax=0.05)
# Stops PermissionError on Win32 for access to
# the traj file that remains open.
del qn
def opt_fcc211(self) -> None:
''' Optimize fcc211 slab '''
slab = fcc211(self.symbol, self.repeats_surface, self.a, self.vacuum)
self.prepare_slab_opt(slab)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Run with even number of cores
from gpaw import GPAW, Mixer, PoissonSolver
import ase.parallel as mpi
from ase.build import fcc211, add_adsorbate
from ase.constraints import FixAtoms
from ase.optimize import QuasiNewton
from ase.neb import NEBtools
from ase.autoneb import AutoNEB
size = mpi.world.size
rank = mpi.world.rank
slab = fcc211('Ag', size=(3, 2, 1), vacuum=3.0)
add_adsorbate(slab, 'Ag', 0.5, (-0.1, 2.7))
slab.set_constraint(FixAtoms(range(6)))
slab.pbc = 1
def getcalc(**kwargs):
kwargs1 = dict(
xc='oldLDA',
gpts=(32, 24, 32),
setups={'Ag': '11'},
#h=0.24,
poissonsolver=PoissonSolver(relax='GS'),
mixer=Mixer(0.5, 5, 50.0),
mode='lcao',
from ase.build import fcc211, add_adsorbate
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton
from ase.neb import NEBTools
from ase.autoneb import AutoNEB
# Pt atom adsorbed in a hollow site:
slab = fcc211('Pt', size=(3, 2, 2), vacuum=4.0)
add_adsorbate(slab, 'Pt', 0.5, (-0.1, 2.7))
# Fix second and third layers:
slab.set_constraint(FixAtoms(range(6, 12)))
# Use EMT potential:
slab.set_calculator(EMT())
# Initial state:
qn = QuasiNewton(slab, trajectory='neb000.traj')
qn.run(fmax=0.05)
# Final state:
slab[-1].x += slab.get_cell()[0, 0]
slab[-1].y += 2.8
qn = QuasiNewton(slab, trajectory='neb001.traj')
qn.run(fmax=0.05)
# Stops PermissionError on Win32 for access to
# the traj file that remains open.
del qn
import numpy as np
from ase import Atoms, Atom
from ase.build import fcc111, fcc211, add_adsorbate, bulk, surface
import math
atoms = fcc211('Au', (3, 5, 8), vacuum=10.)
assert len(atoms) == 120
atoms = atoms.repeat((2, 1, 1))
assert np.allclose(atoms.get_distance(0, 130), 2.88499566724)
atoms = fcc111('Ni', (2, 2, 4), orthogonal=True)
add_adsorbate(atoms, 'H', 1, 'bridge')
add_adsorbate(atoms, Atom('O'), 1, 'fcc')
add_adsorbate(atoms, Atoms('F'), 1, 'hcp')
# The next test ensures that a simple string of multiple atoms cannot be used,
# which should fail with a KeyError that reports the name of the molecule due
# to the string failing to work with Atom().
failed = False
try:
add_adsorbate(atoms, 'CN', 1, 'ontop')
except KeyError as e:
failed = True
assert e.args[0] == 'CN'
assert failed
# This test ensures that the default periodic behavior remains unchanged
cubic_fcc = bulk("Al", a=4.05, cubic=True)
surface_fcc = surface(cubic_fcc, (1,1,1), 3)
import numpy as np
from ase import Atoms, Atom
from ase.build import fcc111, fcc211, add_adsorbate
atoms = fcc211('Au', (3, 5, 8), vacuum=10.)
assert len(atoms) == 120
atoms = atoms.repeat((2, 1, 1))
assert np.allclose(atoms.get_distance(0, 130), 2.88499566724)
atoms = fcc111('Ni', (2, 2, 4), orthogonal=True)
add_adsorbate(atoms, 'H', 1, 'bridge')
add_adsorbate(atoms, Atom('O'), 1, 'fcc')
add_adsorbate(atoms, Atoms('F'), 1, 'hcp')
# The next test ensures that a simple string of multiple atoms cannot be used,
# which should fail with a KeyError that reports the name of the molecule due
# to the string failing to work with Atom().
failed = False
try:
add_adsorbate(atoms, 'CN', 1, 'ontop')
except KeyError as e:
failed = True
assert e.args[0] == 'CN'
assert failed