ValueErrors in the CoherentInterfaceBuilder

[nightroxide]

Python version

Python 3.12.5

Pymatgen version

2024.8.9

Operating system version

Windows 11

Current behavior

Value error when trying to make interfaces

Expected Behavior

A list of possible homojunction structures

Minimal example

from pymatgen.analysis.interfaces import CoherentInterfaceBuilder
from pymatgen.core.structure import Structure
from mp_api.client import MPRester

id = "mp-13"
mpapi_key="key here"
with MPRester(mpapi_key, mute_progress_bars=True) as mpr:
    # get substrate data
    summary = mpr.materials.summary.search(material_ids=id)[0]
    s = substrate_summary.structure

# make a simple homojunction
cib=CoherentInterfaceBuilder(s,s,(1,0,0),(1,1,1))
homojunctions=cib.get_interfaces(cib.terminations[0],film_thickness=8,substrate_thickness=8)

Relevant files to reproduce this bug

---

ValueError Traceback (most recent call last)
Cell In[7], line 12
9 summary = mpr.materials.summary.search(material_ids=id)[0]
10 s = substrate_summary.structure
---> 12 cib=CoherentInterfaceBuilder(s,s,(1,0,0),(1,1,1))
13 homojunctions=cib.get_interfaces(cib.terminations[0],film_thickness=8,substrate_thickness=8)

File c:\Users\pavarga\AppData\Local\miniconda3\envs\mapi\Lib\site-packages\pymatgen\analysis\interfaces\coherent_interfaces.py:53, in CoherentInterfaceBuilder.init(self, substrate_structure, film_structure, film_miller, substrate_miller, zslgen)
50 self.substrate_miller = substrate_miller
51 self.zslgen = zslgen or ZSLGenerator(bidirectional=True)
---> 53 self._find_matches()
54 self._find_terminations()

File c:\Users\pavarga\AppData\Local\miniconda3\envs\mapi\Lib\site-packages\pymatgen\analysis\interfaces\coherent_interfaces.py:82, in CoherentInterfaceBuilder._find_matches(self)
60 film_sg = SlabGenerator(
61 self.film_structure,
62 self.film_miller,
(...)
68 reorient_lattice=False, # This is necessary to not screw up the lattice
69 )
71 sub_sg = SlabGenerator(
72 self.substrate_structure,
73 self.substrate_miller,
(...)
79 reorient_lattice=False, # This is necessary to not screw up the lattice
80 )
---> 82 film_slab = film_sg.get_slab(shift=0)
83 sub_slab = sub_sg.get_slab(shift=0)
85 film_vectors = film_slab.lattice.matrix

File c:\Users\pavarga\AppData\Local\miniconda3\envs\mapi\Lib\site-packages\pymatgen\core\surface.py:1147, in SlabGenerator.get_slab(self, shift, tol, energy)
1145 # Center the slab layer around the vacuum
1146 if self.center_slab:
-> 1147 struct = center_slab(struct)
1149 # Reduce to primitive cell
1150 if self.primitive:

File c:\Users\pavarga\AppData\Local\miniconda3\envs\mapi\Lib\site-packages\pymatgen\core\surface.py:762, in center_slab(slab)
759 all_indices = list(range(len(slab)))
761 # Get a reasonable cutoff radius to sample neighbors
--> 762 bond_dists = sorted(nn[1] for nn in slab.get_neighbors(slab[0], 10) if nn[1] > 0)
763 # TODO (@DanielYang59): magic number for cutoff radius (would 3 be too large?)
764 cutoff_radius = bond_dists[0] * 3

File c:\Users\pavarga\AppData\Local\miniconda3\envs\mapi\Lib\site-packages\pymatgen\core\structure.py:1662, in IStructure.get_neighbors(self, site, r, include_index, include_image)
1641 def get_neighbors(
1642 self,
1643 site: PeriodicSite,
(...)
1646 include_image: bool = False,
1647 ) -> list[PeriodicNeighbor]:
1648 """Get all neighbors to a site within a sphere of radius r. Excludes the
1649 site itself.
1650
(...)
1660 PeriodicNeighbor
1661 """
-> 1662 return self.get_all_neighbors(r, include_index=include_index, include_image=include_image, sites=[site])[0]

File c:\Users\pavarga\AppData\Local\miniconda3\envs\mapi\Lib\site-packages\pymatgen\core\structure.py:1997, in IStructure.get_all_neighbors(self, r, include_index, include_image, sites, numerical_tol)
1995 if sites is None:
1996 sites = self.sites
-> 1997 center_indices, points_indices, images, distances = self.get_neighbor_list(
1998 r=r, sites=sites, numerical_tol=numerical_tol
1999 )
2000 if len(points_indices) < 1:
2001 return [[]] * len(sites)

File c:\Users\pavarga\AppData\Local\miniconda3\envs\mapi\Lib\site-packages\pymatgen\core\structure.py:1782, in IStructure.get_neighbor_list(self, r, sites, numerical_tol, exclude_self)
1780 lattice_matrix = np.ascontiguousarray(self.lattice.matrix, dtype=float)
1781 pbc = np.ascontiguousarray(self.pbc, dtype=int)
-> 1782 center_indices, points_indices, images, distances = find_points_in_spheres(
1783 cart_coords,
1784 site_coords,
1785 r=r,
1786 pbc=pbc,
1787 lattice=lattice_matrix,
1788 tol=numerical_tol,
1789 )
1790 cond = np.array([True] * len(center_indices))
1791 if exclude_self:

File src\pymatgen\optimization\neighbors.pyx:48, in pymatgen.optimization.neighbors.find_points_in_spheres()

ValueError: Buffer dtype mismatch, expected 'const int64_t' but got 'long'

[DanielYang59]

Hi @nightroxide thanks for reporting this. This is a duplicate of #3990 and has been fixed by #3992.