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Fix Wrong Oriented Cell When Calling SlabGenerator.get_slab #24

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Fix Wrong Oriented Cell When Calling SlabGenerator.get_slab #24

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7 changes: 6 additions & 1 deletion src/pymatgen/core/structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2558,6 +2558,7 @@ def get_primitive_structure(
tolerance: float = 0.25,
use_site_props: bool = False,
constrain_latt: list | dict | None = None,
reduce: bool = True,
) -> Self | Structure:
"""Find a smaller unit cell than the input. Sometimes it doesn't
find the smallest possible one, so this method is recursively called
Expand All @@ -2577,6 +2578,8 @@ def get_primitive_structure(
preserve, e.g. ["alpha", "c"] or dict with the lattice
parameter names as keys and values we want the parameters to
be e.g. {"alpha": 90, "c": 2.5}.
reduce (bool): Whether get_reduced_structure is called prior to
checking lattice constraints and returning structure.

Returns:
The most primitive structure found.
Expand Down Expand Up @@ -2745,7 +2748,9 @@ def factors(n: int):
tolerance=tolerance,
use_site_props=use_site_props,
constrain_latt=constrain_latt,
).get_reduced_structure()
)
if reduce:
primitive = primitive.get_reduced_structure()
if not constrain_latt:
return primitive

Expand Down
59 changes: 43 additions & 16 deletions src/pymatgen/core/surface.py
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Original file line number Diff line number Diff line change
Expand Up @@ -133,7 +133,6 @@ def __init__(
fractional_coords. Defaults to None for no properties.
energy (float): A value for the energy.
"""
self.oriented_unit_cell = oriented_unit_cell
self.miller_index = miller_index
self.shift = shift
self.reconstruction = reconstruction
Expand All @@ -154,6 +153,30 @@ def __init__(
lattice.gamma,
)

oriented_unit_cell = copy.deepcopy(oriented_unit_cell)
ouc_lattice = oriented_unit_cell.lattice
ouc_lattice = Lattice.from_parameters(
ouc_lattice.a,
ouc_lattice.b,
ouc_lattice.c,
ouc_lattice.alpha,
ouc_lattice.beta,
ouc_lattice.gamma,
)

self.oriented_unit_cell = Structure(
ouc_lattice,
oriented_unit_cell.species,
oriented_unit_cell.frac_coords,
charge=oriented_unit_cell.charge,
coords_are_cartesian=False,
site_properties=oriented_unit_cell.site_properties,
labels=oriented_unit_cell.labels,
properties=oriented_unit_cell.properties,
)
else:
self.oriented_unit_cell = oriented_unit_cell

super().__init__(
lattice,
species,
Expand Down Expand Up @@ -1152,31 +1175,35 @@ def get_slab(
if self.center_slab:
struct = center_slab(struct)

ouc = self.oriented_unit_cell.copy()

# Reduce to primitive cell
if self.primitive:
prim_slab = struct.get_primitive_structure(tolerance=tol)
struct = prim_slab
prim_slab = struct.get_primitive_structure(tolerance=tol, reduce=False)

if energy is not None:
energy *= prim_slab.volume / struct.volume

# Reorient the lattice to get the correctly reduced cell
ouc = self.oriented_unit_cell.copy()
if self.primitive:
# Find a reduced OUC
slab_l = struct.lattice
ouc = ouc.get_primitive_structure(
prim_slab_l = prim_slab.lattice
prim_ouc = ouc.get_primitive_structure(
constrain_latt={
"a": slab_l.a,
"b": slab_l.b,
"alpha": slab_l.alpha,
"beta": slab_l.beta,
"gamma": slab_l.gamma,
}
"a": prim_slab_l.a,
"b": prim_slab_l.b,
"alpha": prim_slab_l.alpha,
"beta": prim_slab_l.beta,
"gamma": prim_slab_l.gamma,
},
reduce=False,
)

# Ensure lattice a and b are consistent between the OUC and the Slab
ouc = ouc if (slab_l.a == ouc.lattice.a and slab_l.b == ouc.lattice.b) else self.oriented_unit_cell
# Ensure lattice a and b are consistent between the OUC and the slab
a_b_consistent = np.isclose(prim_slab_l.a, prim_ouc.lattice.a) and np.isclose(
prim_slab_l.b, prim_ouc.lattice.b
)
if a_b_consistent:
struct = prim_slab
ouc = prim_ouc

return Slab(
struct.lattice,
Expand Down
30 changes: 28 additions & 2 deletions tests/core/test_surface.py
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Original file line number Diff line number Diff line change
Expand Up @@ -436,6 +436,32 @@ def test_get_slab(self):
assert np.dot(a_vec, gen._normal) == approx(0)
assert np.dot(b_vec, gen._normal) == approx(0)

def test_get_slab_oriented_unit_cell_obeys_constrained_lattice(self):
bulk = Structure.from_spacegroup(
"Fm-3m",
Lattice.cubic(4.194),
["Mg", "O"],
[[0, 0, 0], [0.5, 0.5, 0.5]],
)
slab = SlabGenerator(
initial_structure=bulk,
miller_index=(1, 1, 1),
min_slab_size=10,
min_vacuum_size=20,
primitive=True,
lll_reduce=False,
center_slab=False,
max_normal_search=None,
).get_slab(shift=0)

slab_l = slab.lattice
ouc_l = slab.oriented_unit_cell.lattice
assert ouc_l.a == approx(slab_l.a)
assert ouc_l.b == approx(slab_l.b)
assert ouc_l.alpha == approx(slab_l.alpha)
assert ouc_l.beta == approx(slab_l.beta)
assert ouc_l.gamma == approx(slab_l.gamma)

def test_normal_search(self):
fcc = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Fe"], [[0, 0, 0]])
for miller in [(1, 0, 0), (1, 1, 0), (1, 1, 1), (2, 1, 1)]:
Expand Down Expand Up @@ -630,8 +656,8 @@ def test_bonds_broken(self):
# expect 2 and 6 bonds broken so we check for this.
# Number of broken bonds are floats due to primitive
# flag check and subsequent transformation of slabs.
assert slabs[0].energy == approx(8.0)
assert slabs[1].energy == approx(24.0)
assert slabs[0].energy == approx(2.0)
assert slabs[1].energy == approx(6.0)


class TestReconstructionGenerator(MatSciTest):
Expand Down
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