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Allow for setting termination_ftol for film and substrate slabs separately #4498

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Allow for setting termination_ftol for film and substrate slabs separately #4498

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allows for setting termination_ftol for film and substrate slabs sepa…
jinlhr542 Sep 16, 2025
7d2e9bc
termination_ftol test
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Update coherent_interfaces.py
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21 changes: 13 additions & 8 deletions src/pymatgen/analysis/interfaces/coherent_interfaces.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ def __init__(
film_miller: tuple[int, int, int],
substrate_miller: tuple[int, int, int],
zslgen: ZSLGenerator | None = None,
termination_ftol: float = 0.25,
termination_ftol: float | tuple[float, float] = 0.25,
label_index: bool = False, # necessary to add index to termination
filter_out_sym_slabs: bool = True,
):
Expand All @@ -43,7 +43,7 @@ def __init__(
film_miller (tuple[int, int, int]): miller index for the film layer
substrate_miller (tuple[int, int, int]): miller index for the substrate layer
zslgen (ZSLGenerator | None): BiDirectionalZSL if you want custom lattice matching tolerances for coherency.
termination_ftol (float): tolerance to distinguish different terminating atomic planes.
termination_ftol (float): tolerances (film, substrate) to distinguish different terminating atomic planes.
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@DanielYang59 DanielYang59 Sep 17, 2025 •
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I'm not very familiar with the use case of CoherentInterfaceBuilder but I assume it's reasonable to allow more fine-grained control over the film and substrate. In this case I guess: either you allow termination_ftol to be float | tuple[float, float] but you should update the docstring accordingly (currently it's still float), or you could deprecate this arg with two args like film/substrate_termination_tol.

label_index (bool): If True add an extra index at the beginning of the termination label.
filter_out_sym_slabs (bool): If True filter out identical slabs with different terminations.
This might need to be set as False to find more non-identical terminations because slab
Expand Down Expand Up @@ -133,24 +133,29 @@ def _find_terminations(self):
reorient_lattice=False, # This is necessary to not screw up the lattice
)

film_slabs = film_sg.get_slabs(ftol=self.termination_ftol, filter_out_sym_slabs=self.filter_out_sym_slabs)
sub_slabs = sub_sg.get_slabs(ftol=self.termination_ftol, filter_out_sym_slabs=self.filter_out_sym_slabs)
if type(self.termination_ftol) is not tuple:
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should use isinstance here as type() is would only allow exact tuple but not subclasses

self.termination_ftol = (self.termination_ftol, self.termination_ftol)
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@DanielYang59 DanielYang59 Sep 17, 2025 •
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I guess it's more readable to unpack within __init__ instead of accessing with index, something like:

if isinstance(termination_ftol, tuple):
    self.film_termination_ftol, self.substrate_termination_ftol = termination_ftol
else:
    self.film_termination_ftol = self.substrate_termination_ftol = termination_ftol

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Daniel, many thanks for these helpful suggestions. I have commited these changes.


film_slabs = film_sg.get_slabs(ftol=self.termination_ftol[0], filter_out_sym_slabs=self.filter_out_sym_slabs)
sub_slabs = sub_sg.get_slabs(ftol=self.termination_ftol[1], filter_out_sym_slabs=self.filter_out_sym_slabs)
film_shifts = [slab.shift for slab in film_slabs]

if self.label_index:
film_terminations = [
label_termination(slab, self.termination_ftol, t_idx) for t_idx, slab in enumerate(film_slabs, start=1)
label_termination(slab, self.termination_ftol[0], t_idx)
for t_idx, slab in enumerate(film_slabs, start=1)
]
else:
film_terminations = [label_termination(slab, self.termination_ftol) for slab in film_slabs]
film_terminations = [label_termination(slab, self.termination_ftol[0]) for slab in film_slabs]

sub_shifts = [slab.shift for slab in sub_slabs]
if self.label_index:
sub_terminations = [
label_termination(slab, self.termination_ftol, t_idx) for t_idx, slab in enumerate(sub_slabs, start=1)
label_termination(slab, self.termination_ftol[1], t_idx)
for t_idx, slab in enumerate(sub_slabs, start=1)
]
else:
sub_terminations = [label_termination(slab, self.termination_ftol) for slab in sub_slabs]
sub_terminations = [label_termination(slab, self.termination_ftol[1]) for slab in sub_slabs]

self._terminations = {
(film_label, sub_label): (film_shift, sub_shift)
Expand Down
21 changes: 18 additions & 3 deletions tests/analysis/interfaces/test_coherent_interface.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ def setup_method(self):
def test_termination_searching(self):
sub_analyzer = SubstrateAnalyzer()
matches = list(sub_analyzer.calculate(substrate=self.substrate, film=self.film))
cib = CoherentInterfaceBuilder(
cib1 = CoherentInterfaceBuilder(
film_structure=self.film,
substrate_structure=self.substrate,
film_miller=matches[0].film_miller,
Expand All @@ -69,9 +69,24 @@ def test_termination_searching(self):
label_index=True,
filter_out_sym_slabs=False,
)
assert cib.terminations == [
cib2 = CoherentInterfaceBuilder(
film_structure=self.film,
substrate_structure=self.substrate,
film_miller=matches[0].film_miller,
substrate_miller=matches[0].substrate_miller,
zslgen=sub_analyzer,
termination_ftol=(2, 0.1),
label_index=True,
filter_out_sym_slabs=False,
)
assert cib1.terminations == [
("1_Ge_P4/mmm_1", "1_Si_P4/mmm_1"),
("1_Ge_P4/mmm_1", "2_Si_P4/mmm_1"),
("2_Ge_P4/mmm_1", "1_Si_P4/mmm_1"),
("2_Ge_P4/mmm_1", "2_Si_P4/mmm_1"),
], "termination results wrong"
], "cib1 termination results wrong"

assert cib2.terminations == [
("1_Ge_C2/m_2", "1_Si_P4/mmm_1"),
("1_Ge_C2/m_2", "2_Si_P4/mmm_1"),
], "cib2 termination results wrong"
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