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 test_slab_generator(self):
"""Test that no exception is raised when running SlabGenerator."""
atoms = bulk('Pd', 'fcc', cubic=True)
SlabGenerator(atoms, miller_index=(1, 1, 1), layers=6, vacuum=4)
SlabGenerator(atoms, miller_index=(1, 1, 0), layers=6, vacuum=4)
SlabGenerator(atoms, miller_index=(1, 0, 0), layers=6, vacuum=4)
SlabGenerator(atoms, miller_index=(0, 0, 0, 1), layers=6)
def test_terminations(self):
"""Test termination finding on fcc(211)."""
atoms = bulk('Pd', 'fcc', a=4, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(atoms, miller_index=(2, 1, 1), layers=8, vacuum=4)
gen.get_slab(iterm=1)
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 create_slab_from_bulk_tmp(atoms=None, facet=None):
"""
"""
#| - create_slab_from_bulk
# SG = SlabGenerator(
# atoms, facet, 20, vacuum=15,
# fixed=None, layer_type='ang',
# attach_graph=True,
# standardize_bulk=True,
# primitive=True, tol=1e-03)
SG = SlabGenerator(
atoms,
facet,
20,
vacuum=15,
fixed=None,
layer_type="sym",
attach_graph=True,
standardize_bulk=True,
primitive=True,
tol=1e-03,
)
# print("TEMP", "SlabGenerator:", SlabGenerator)
slab_i = SG.get_slab()
slab_i.set_pbc([True, True, True])
# #############################################
# Write slab to file ##########################
directory = "out_data"
if not os.path.exists(directory):
os.makedirs(directory)
assert False, "Fix os.makedirs"
# TEMP write to file
path_i = os.path.join("out_data", "temp.cif")
slab_i.write(path_i)
# Rereading the structure file to get it back into ase format
slab_i = io.read(path_i)
# data_dict_i["slab_0"] = slab_i
return(slab_i)
def test_no_standardization(self):
"""Test that the slab generator functions if not standardized."""
atoms = bulk('Pd', 'fcc', cubic=True)
SlabGenerator(atoms,
miller_index=(1, 1, 1),
layer_type='trim',
layers=3,
standardize_bulk=True)
def test_surface_generator():
atoms = bulk('Pd', 'fcc', a=4, cubic=True)
# A variety of slab tests
gen = SlabGenerator(atoms, miller_index=(1, 0, 0), layers=6, vacuum=4)
gen = SlabGenerator(atoms, miller_index=(1, 1, 0), layers=6, vacuum=4)
gen = SlabGenerator(atoms, miller_index=(0, 0, 1), layers=6, vacuum=4)
# Test automatic termination finding
atoms = bulk('Pd', 'fcc', a=4, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(atoms, miller_index=(2, 1, 1), min_width=10, vacuum=4)
gen.get_slab(iterm=1)
def create_slab_from_bulk(atoms=None, facet=None, layers=20):
"""Create slab from bulk atoms object and facet.
Args:
atoms (ASE atoms object): ASE atoms object of bulk structure.
facet (str): Facet cut
layers (int): Number of layers
"""
#| - create_slab_from_bulk
SG = SlabGenerator(
atoms,
facet,
layers,
vacuum=15,
# atoms, facet, 20, vacuum=15,
fixed=None,
layer_type='ang',
attach_graph=True,
standardize_bulk=True,
primitive=True,
tol=1e-03)
# print("TEMP", "SlabGenerator:", SlabGenerator)
slab_i = SG.get_slab()
slab_i.set_pbc([True, True, True])
# #############################################
# Write slab to file ##########################
# directory = "out_data"
directory = os.path.join(os.environ["PROJ_irox_oer"],
"workflow/creating_slabs", "out_data")
# assert False, "Fix os.makedirs"
if not os.path.exists(directory):
os.makedirs(directory)
path_i = os.path.join("out_data", "temp.cif")
slab_i.write(path_i)
# Rereading the structure file to get it back into ase format
slab_i = io.read(path_i)
# data_dict_i["slab_0"] = slab_i
return (slab_i)
def test_adsorption_examples(self):
"""Test adsorption structure examples."""
atoms = bulk('Pd', 'fcc', a=5, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(atoms, miller_index=(1, 1, 1), layer_type='trim',
layers=3, vacuum=4)
atoms = gen.get_slab()
sites = AdsorptionSites(atoms)
sites.plot('./Pd3Cu-adsorption-sites.png')
atoms = bulk('Pd', 'fcc', a=5, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(atoms, miller_index=(3, 2, 1), layers=8, vacuum=5)
atoms = gen.get_slab()
sites = AdsorptionSites(atoms)
coordinates = sites.get_coordinates()
assert (len(coordinates) == 56)
connectivity = sites.get_connectivity()
test_connectivity = np.array([
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4])
np.testing.assert_allclose(connectivity, test_connectivity)
topology = sites.get_topology()
assert (len(topology) == 56)
periodic = sites.get_periodic_sites()
symmetric = sites.get_symmetric_sites()
np.testing.assert_allclose(symmetric, periodic)
atoms = bulk('Pd', 'fcc', a=5, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(atoms, miller_index=(2, 1, 1), layers=8, vacuum=5)
atoms = gen.get_slab()
sites = AdsorptionSites(atoms)
coordinates = sites.get_coordinates()
vectors = sites.get_adsorption_vectors(unique=False)
assert (len(vectors) == 32)
def test_gcd_miller_index(self):
"""Test that miller indices are properly reduces to their
greatest common divisor.
"""
atoms = bulk('Pd', 'fcc')
gen = SlabGenerator(atoms,
miller_index=(3, 3, 3),
layers=3,
layer_type='trim')
np.testing.assert_array_equal(gen.miller_index, [1, 1, 1])
def test_matrix_notation_search(self):
"""Test the matrix notation algorithm."""
atoms = bulk('Pd', 'fcc', cubic=True)
gen = SlabGenerator(atoms, miller_index=(1, 1, 1), layers=6)
gen.get_slab(size=1)
gen.get_slab(size=[[1, 0], [0, 1]])
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)
sizes = [(3, 4, 1), (3, 3, 1), (3, 3, 1), (2, 2, 1), (2, 2, 1), (2, 2, 1),
(3, 2, 1)]
vacuum = 14
primitive = []
bare = []
coordinates = []
connectivity = []
Cu_N_ads = {}
for idx, term in enumerate(terminations):
gen = SlabGenerator(atoms_bulk,
miller_index=miller_indices[idx],
layers=layers[idx],
fixed=fixed[idx],
vacuum=10,
standardize_bulk=True,
layer_type="trim")
prim = gen.get_slab()
supercell = prim.repeat(sizes[idx])
#print(supercell.get_cell())
primitive.append(prim)
bare.append(supercell)
coords_tmp, connect_tmp = gen.adsorption_sites(prim)
coordinates.append(coords_tmp)
connectivity.append(connect_tmp)
list_ads = next_ads(bare[-1], [1, 1], primitive[-1].get_cell(),
coordinates[-1])
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
from catkit.gen.surface import SlabGenerator
from ase.build import bulk
from ase.visualize import view
from ase import Atom, Atoms
import numpy as np
atoms_bulk = bulk(name='Cu', crystalstructure='fcc', a=3.6302862146117354, cubic=True)
gen = SlabGenerator(atoms_bulk,
miller_index = (2,1,0),
layers = 8,
fixed = 4,
vacuum = 10,
standardize_bulk = True,
layer_type = "trim")
primitive = gen.get_slab()
#supercell = primitive.repeat(2,3)
supercell_1 = gen.get_slab( size=2 )
supercell_2 = gen.get_slab( size=(2,2) )
supercell_3 = gen.get_slab( size=np.array([[2,0],[0,2]]))
view(primitive)
view(supercell_3)
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 test_adsorption_examples():
atoms = bulk('Pd', 'fcc', a=5, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(atoms, miller_index=(1, 1, 1), layers=3, vacuum=4)
atoms = gen.get_slab(primitive=True)
atoms.set_surface_atoms([8, 9, 10, 11])
sites = AdsorptionSites(atoms)
sites.plot('./Pd3Cu-adsorption-sites.png')
atoms = bulk('Pd', 'fcc', a=5, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(atoms, miller_index=(3, 2, 1), layers=13, vacuum=5)
atoms = gen.get_slab(primitive=True)
top, _ = gen.get_voronoi_surface_atoms(atoms)
atoms.set_surface_atoms(top)
sites = AdsorptionSites(atoms)
coordinates = sites.get_coordinates()
assert (len(coordinates) == 56)
connectivity = sites.get_connectivity()
test_connectivity = np.array([
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 4, 4
])
np.testing.assert_allclose(connectivity, test_connectivity)
topology = sites.get_topology()
assert (len(topology) == 56)
periodic = sites.get_periodic_sites()
symmetric = sites.get_symmetric_sites()
print(periodic)
np.testing.assert_allclose(symmetric, periodic)
atoms = bulk('Pd', 'fcc', a=5, cubic=True)
atoms[3].symbol = 'Cu'
gen = SlabGenerator(atoms, miller_index=(2, 1, 1), layers=10, vacuum=5)
atoms = gen.get_slab(primitive=True)
top, _ = gen.get_voronoi_surface_atoms(atoms, attach_graph=False)
atoms.set_surface_atoms(top)
sites = AdsorptionSites(atoms)
coordinates = sites.get_coordinates()
vectors = sites.get_adsorption_vectors(unique=False)
assert (len(vectors) == 32)
#calc = Vasp(encut=400,
# ismear=2,
# sigma=0.2,
# gga='PE',
# xc='PBE')
#label = "CarbonMonoxide"
#co2 = copy.deepcopy(co)
#calc2 = Vasp2(label=label,
# encut=400,
# ismear=2,
# sigma=0.2,
# gga='PE',
# xc='PBE')
#co.set_calculator(calc)
#co.get_potential_energy()
atoms_bulk = bulk(name='Cu',
crystalstructure='fcc',
a=3.6302862146117354,
cubic=True)
gen = SlabGenerator(atoms_bulk,
miller_index=[2, 1, 0],
layers=8,
fixed=4,
vacuum=10,
standardize_bulk=True,
layer_type="trim")
bare = gen.get_slab(size=[2, 2])
view(bare)