Singular film supercell transformation matrix when calling get_interfaces for CoherentInterfaceBuilder

[tfhughes]

Python version

Python 3.11.4

Pymatgen version

2023.9.10

Operating system version

Mac Tahoe 26.2 (25C56)

Current behavior

Not sure if this is a known pymatgen issue when building interfaces but I can’t find a GitHub issue for it. Printing some information from CoherentInterfaceBuilder.get_interfaces shows the following:

film_shift 0.08333336181879059
sub_shift 0.12499996873087585
film_slab.lattice.matrix[:2]
[[-1.96204495 5.88613486 -6.26018476]
[ 5.88613486 5.88613486 6.26018476]]
match.film_sl_vectors
[[ -7.84817982 0. 0. ]
[ -3.92408991 -11.77226973 -12.52036953]]
super_film_transform
[[ 0 0 0]
[ 0 -2 0]
[ 0 0 1]]

I think that last transform, a film supercell transform, is the issue since there should never be a zero along the diagonal.

Here is a script to reproduce the issue:

import numpy
from pymatgen.analysis.interfaces.zsl import ZSLGenerator
from pymatgen.core.structure import Structure as PMGStructure
from pymatgen.analysis.interfaces.coherent_interfaces import CoherentInterfaceBuilder

pbc1 = [
    [3.816817045211792, 0.0, 0.0],
    [0.0, 3.816817045211792, 0.0],
    [0.0, 0.0, 3.816817045211792]]
ans1 = [57, 27, 8, 8, 8]
xyz1 = numpy.array([
    [1.908409, 1.908409, 1.908409],
    [0.0, 0.0, 0.0],
    [1.908409, 0.0, 0.0],
    [0.0, 1.908409, 0.0],
    [0.0, 0.0, 1.908409]])
sub_st = PMGStructure(pbc1, ans1, xyz1, charge=0,
    validate_proximity=False, to_unit_cell=False,
    coords_are_cartesian=True, site_properties=None)

pbc2 = [
    [3.9240899085998535, 0.0, 0.0],
    [0.0, 3.9240899085998535, 0.0],
    [0.0, 0.0, 12.520369529724121]]
ans2 = [57, 57, 57, 57, 28, 28, 8, 8, 8, 8, 8, 8, 8, 8]
xyz2 = numpy.array([
    [0.0, 0.0, 4.550816],
    [1.962045, 1.962045, 1.709368],
    [1.962045, 1.962045, 10.811001],
    [0.0, 0.0, 7.969553],
    [0.0, 0.0, 0.0],
    [1.962045, 1.962045, 6.260185],
    [0.0, 0.0, 2.241059],
    [1.962045, 1.962045, 4.019126],
    [1.962045, 0.0, 0.0],
    [0.0, 1.962045, 0.0],
    [1.962045, 1.962045, 8.501243],
    [0.0, 0.0, 10.279311],
    [0.0, 1.962045, 6.260185],
    [1.962045, 0.0, 6.260185]])
film_st = PMGStructure(pbc2, ans2, xyz2, charge=0,
    validate_proximity=False, to_unit_cell=False,
    coords_are_cartesian=True, site_properties=None)

kwargs = {'max_area': 450.0}
film_hkl = (3, 2, 3)
sub_hkl = (2, 1, 0)
term = ('La_C2/m_1', 'CoO2_P2/m_3')

zslgen = ZSLGenerator(**kwargs)
builder = CoherentInterfaceBuilder(sub_st, film_st, film_hkl, sub_hkl, zslgen=zslgen)
inters = builder.get_interfaces(term, gap=1.0, vacuum_over_film=10.0,
    film_thickness=4.0, substrate_thickness=4.0, in_layers=True)
print(len(list(inters)))

Throws the following traceback:

Traceback (most recent call last):
  File "/Users/hughes/pymatgen_test/test.py", line 54, in <module>
    print(len(list(inters)))
              ^^^^^^^^^^^^
  File "/Users/hughes/scr/bld_26-3/internal/lib/python3.11/site-packages/pymatgen/analysis/interfaces/coherent_interfaces.py", line 200, in get_interfaces
    film_sl_slab.make_supercell(super_film_transform)
  File "/Users/hughes/scr/bld_26-3/internal/lib/python3.11/site-packages/pymatgen/core/structure.py", line 4115, in make_supercell
    supercell = struct * scaling_matrix
                ~~~~~~~^~~~~~~~~~~~~~~~
  File "/Users/hughes/scr/bld_26-3/internal/lib/python3.11/site-packages/pymatgen/core/structure.py", line 1320, in __mul__
    f_lat = lattice_points_in_supercell(scale_matrix)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/hughes/scr/bld_26-3/internal/lib/python3.11/site-packages/pymatgen/util/coord.py", line 295, in lattice_points_in_supercell
    frac_points = np.dot(all_points, np.linalg.inv(supercell_matrix))
                                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<__array_function__ internals>", line 200, in inv
  File "/Users/hughes/scr/bld_26-3/internal/lib/python3.11/site-packages/numpy/linalg/linalg.py", line 538, in inv
    ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/hughes/scr/bld_26-3/internal/lib/python3.11/site-packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular
    raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix

Expected Behavior

I expect to get an interface back with no traceback.

Minimal example

Relevant files to reproduce this bug

No response