def cut_slab_catkit(
bulk,
facet,
slab_thickness=6,
vacuum=8.,
):
"""Cut slab from bulk using CatKit.
Args:
bulk:
facet:
"""
# | - cut_slab_catkit
gen = SlabGenerator_catkit(
bulk,
miller_index=facet,
layers=slab_thickness,
vacuum=vacuum,
fixed=2,
layer_type='ang',
# attach_graph=True,
standardize_bulk=False,
tol=1e-8
)
terminations = gen.get_unique_terminations()
images = []
for i, t in enumerate(terminations):
images += [gen.get_slab(iterm=i, size=1)]
# view(images)
return(images)
def get_struct(symbol='Ag2Au2', adsorbate='OH', SB_symbol='L10', a=4, c=3):
"""It returns the structure generated with catkit
using the keyword given."""
size = (1, 1)
layers = 3
miller = (1, 1, 1)
vacuum = 10
get_height = dict([('C', 1.0), ('O', 1.0), ('N', 1.0), ('S', 1.0),
('H', 1.0)])
if adsorbate in ['CH', 'OH', 'NH', 'SH']:
tags = [-1, -2]
n_atoms = 14
elif adsorbate in ['CH2', 'OH2']:
tags = [-1, -2, -2]
n_atoms = 15
elif adsorbate == 'CH3':
tags = [-1, -2, -2, -2]
n_atoms = 16
else:
tags = [-1]
n_atoms = 13
data = np.load('bulk_data.npy')[()]
if '2' in symbol:
m1, m2, _ = symbol.split('2')
b = bulk(m1, cubic=True, crystalstructure='fcc', a=a, c=c)
b[2].symbol = m2
b[3].symbol = m2
elif '3' in symbol:
m1, m2 = symbol.split('3')
b = bulk(m1, cubic=True, crystalstructure='fcc', a=a, c=c)
b[3].symbol = m2
else:
b = bulk(symbol, cubic=True, crystalstructure='fcc', a=a, c=c)
gen = SlabGenerator(b,
miller_index=miller,
vacuum=vacuum,
layers=layers,
fixed=2,
layer_type='trim',
standardize_bulk=False,
primitive=False)
terminations = gen.get_unique_terminations()
if len(terminations) > 1:
raise IncosistencyError('There are more than one temrination.')
slab = gen.get_slab(size=size, iterm=-1)
mm = {'Fe': 3, 'Ni': 1, 'Co': 1, 'Mn': 1}
slab.set_initial_magnetic_moments(
[mm.get(i, 0) for i in slab.get_chemical_symbols()])
adsorbate = molecule(adsorbate)[0]
adsorbate.set_tags(tags)
builder = Builder(slab)
structures = builder.add_adsorbate(adsorbate, index=-1)
return structures
def test_surface_examples(self):
"""Test surface construction examples."""
atoms = bulk('Pd', 'fcc', a=4, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(
atoms, miller_index=(2, 1, 1), layers=6, fixed=5, vacuum=4)
terminations = gen.get_unique_terminations()
assert (len(terminations) == 2)
for i, t in enumerate(terminations):
slab = gen.get_slab(iterm=i)
assert (len(slab) == 16)
atoms = surface('Pd', size=(3, 3), miller=(1, 1, 1), vacuum=4)
con_matrix = atoms.connectivity
test_con_matrix = np.array([
[0, 3, 3, 1, 1, 1, 0, 0, 0],
[3, 0, 3, 1, 1, 1, 0, 0, 0],
[3, 3, 0, 1, 1, 1, 0, 0, 0],
[1, 1, 1, 0, 3, 3, 1, 1, 1],
[1, 1, 1, 3, 0, 3, 1, 1, 1],
[1, 1, 1, 3, 3, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1, 0, 3, 3],
[0, 0, 0, 1, 1, 1, 3, 0, 3],
[0, 0, 0, 1, 1, 1, 3, 3, 0]])
np.testing.assert_allclose(con_matrix, test_con_matrix)
test_surf_atoms = np.array([6, 7, 8])
np.testing.assert_allclose(atoms.get_surface_atoms(), test_surf_atoms)
atoms = bulk('Pd', 'fcc', a=5, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(
atoms, miller_index=(1, 1, 1), layers=3, layer_type='trim',
fixed=2, vacuum=10)
atoms = gen.get_slab()
coordinates, connectivity = gen.adsorption_sites(atoms)
test_connectivity = np.array([1, 1, 2, 2, 2, 3, 3, 3, 3])
np.testing.assert_allclose(connectivity, test_connectivity)
def test_surface_examples():
atoms = bulk('Pd', 'fcc', a=4, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(atoms,
miller_index=(2, 1, 1),
layers=9,
fixed=5,
vacuum=4)
terminations = gen.get_unique_terminations()
assert (len(terminations) == 2)
for i, t in enumerate(terminations):
slab = gen.get_slab(iterm=i)
assert (len(slab) == 18)
atoms = bulk('Pd', 'hcp', a=3, cubic=True)
gen = SlabGenerator(atoms,
miller_index=(1, 1, 0),
layers=6,
fixed=2,
vacuum=4)
atoms = gen.get_slab()
con_matrix = gen.get_graph_from_bulk(atoms, attach=True)
test_con_matrix = np.array(
[[0.0, 2.0, 2.0, 2.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[2.0, 0.0, 2.0, 2.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[2.0, 2.0, 0.0, 2.0, 2.0, 2.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[2.0, 2.0, 2.0, 0.0, 2.0, 2.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
[1.0, 0.0, 2.0, 2.0, 0.0, 2.0, 2.0, 2.0, 1.0, 0.0, 0.0, 0.0],
[0.0, 1.0, 2.0, 2.0, 2.0, 0.0, 2.0, 2.0, 0.0, 1.0, 0.0, 0.0],
[0.0, 0.0, 1.0, 0.0, 2.0, 2.0, 0.0, 2.0, 2.0, 2.0, 1.0, 0.0],
[0.0, 0.0, 0.0, 1.0, 2.0, 2.0, 2.0, 0.0, 2.0, 2.0, 0.0, 1.0],
[0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 2.0, 2.0, 0.0, 2.0, 2.0, 2.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 2.0, 2.0, 2.0, 0.0, 2.0, 2.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 2.0, 2.0, 0.0, 2.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 2.0, 2.0, 2.0, 0.0]])
np.testing.assert_allclose(con_matrix, test_con_matrix)
# We can identify both top and bottom sites.
top, bottom = gen.get_voronoi_surface_atoms(atoms)
atoms.set_surface_atoms(top)
test_surf_atoms = np.array([8, 9, 10, 11])
np.testing.assert_allclose(top, test_surf_atoms)
atoms = bulk('Pd', 'fcc', a=5, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(atoms,
miller_index=(1, 1, 1),
layers=3,
fixed=2,
vacuum=10)
atoms = gen.get_slab(primitive=True)
coordinates, connectivity = gen.adsorption_sites(atoms)
test_connectivity = np.array([1, 1, 2, 2, 2, 3, 3, 3, 3])
np.testing.assert_allclose(connectivity, test_connectivity)
def get_struct(symbol='Ag2Au2',
adsorbate='C',
site='hollow',
site_type='Ag_Ag_Au|FCC',
SB_symbol='L10'):
"""It returns the structure generated with catkit
using the keyword given."""
size = (1, 1)
layers = 3
miller = (1, 1, 1)
vacuum = 10
get_height = dict([('C', 1.0), ('O', 1.0), ('N', 1.0), ('S', 1.0),
('H', 1.0)])
if adsorbate in ['CH', 'OH', 'NH', 'SH']:
tags = [-1, -2]
n_atoms = 14
elif adsorbate in ['CH2', 'OH2']:
tags = [-1, -2, -2]
n_atoms = 15
elif adsorbate == 'CH3':
tags = [-1, -2, -2, -2]
n_atoms = 16
else:
tags = [-1]
n_atoms = 13
data = np.load('bulk_data.npy')[()]
try:
a = data[symbol]['a']
c = data[symbol]['c']
except KeyError:
if '2' in symbol:
m1, m2, _ = symbol.split('2')
try:
a = data[m1 + '2' + m2 + '2']['a']
c = data[m1 + '2' + m2 + '2']['c']
except KeyError:
a = data[m2 + '2' + m1 + '2']['a']
c = data[m2 + '2' + m1 + '2']['c']
if '2' in symbol:
m1, m2, _ = symbol.split('2')
name = m1 + '2' + m2 + '2'
b = Atoms(name,
scaled_positions=[(0, 0, 0), (0.5, 0.5, 0), (0.5, 0, 0.5),
(0, 0.5, 0.5)],
cell=[a, a, c],
pbc=True)
b.set_pbc((1, 1, 1))
elif '3' in symbol:
m1, m2 = symbol.split('3')
b = bulk(m1, cubic=True, crystalstructure='fcc', a=a, c=c)
b[3].symbol = m2
else:
b = bulk(symbol, cubic=True, crystalstructure='fcc', a=a, c=c)
gen = SlabGenerator(b,
miller_index=miller,
vacuum=vacuum,
layers=layers,
fixed=2,
layer_type='trim',
standardize_bulk=False,
primitive=False)
terminations = gen.get_unique_terminations()
if len(terminations) > 1:
raise IncosistencyError('There are more than one temrination.')
slab = gen.get_slab(size=size, iterm=-1)
mm = {'Fe': 3, 'Ni': 1, 'Co': 1, 'Mn': 1}
slab.set_initial_magnetic_moments(
[mm.get(i, 0) for i in slab.get_chemical_symbols()])
ads_slab = slab.copy()
coords, conn = gen.adsorption_sites(slab)
if site == 'top':
si = 1
if site == 'bridge':
si = 2
if site == 'hollow':
si = 3
adsorbate = molecule(adsorbate)[0]
adsorbate.set_tags(tags)
builder = Builder(slab)
structures = builder.add_adsorbate(adsorbate, index=-1)
ads_slab = None
for struct in structures:
connectivity = struct.connectivity
connectivity = connectivity[~(connectivity == 0).all(1)]
if n_atoms == 13:
ads_conn = np.array(connectivity[:, -1]).reshape(n_atoms).sum()
ads_site = [
i
for i, j in zip(struct.get_chemical_symbols(),
np.array(connectivity[:, -1]).reshape(n_atoms))
if j == 1
]
if n_atoms == 14:
ads_conn = np.array(connectivity[:, -2]).reshape(n_atoms).sum() - 1
ads_site = [
i for i, j in zip(
struct.get_chemical_symbols(),
np.array(connectivity[:, -2]).reshape(n_atoms)[:13])
if j == 1
]
if n_atoms == 15:
ads_conn = np.array(connectivity[:, -3]).reshape(n_atoms).sum() - 2
ads_site = [
i for i, j in zip(
struct.get_chemical_symbols(),
np.array(connectivity[:, -3]).reshape(n_atoms)[:13])
if j == 1
]
if n_atoms == 16:
ads_conn = np.array(connectivity[:, -4]).reshape(n_atoms).sum() - 3
ads_site = [
i for i, j in zip(
struct.get_chemical_symbols(),
np.array(connectivity[:, -4]).reshape(n_atoms)[:13])
if j == 1
]
if si != ads_conn:
continue
if SB_symbol == 'A1':
if si == 1 or si == 2:
ads_slab = struct
else:
if get_under_hollow(struct[:13]) == site_type.split('|')[1]:
ads_slab = struct
else:
if si == 1:
if ads_site[0] == site_type:
ads_slab = struct
elif si == 3:
hol = get_under_hollow(struct[:13])
a, b = site_type.split('|')
a = a.split('_')
if Counter(ads_site) == Counter(a) and b == hol:
ads_slab = struct
else:
if SB_symbol == 'L10':
if '|' not in site_type:
if len(set(ads_site)) == 1:
if ads_site[0] == site_type:
ads_slab = struct
else:
if not len(set(ads_site)) == 2:
continue
if get_under_bridge(
struct[:13]) == site_type.split('|')[1]:
ads_slab = struct
else:
if '|' in site_type and len(set(ads_site)) == 1:
if get_under_bridge(
struct[:13]) == site_type.split('|')[1]:
ads_slab = struct
else:
ads_slab = struct
return slab, ads_slab