Merge pull request #485 from kamronald/fix_cluster_gen

Update creation of Cluster instances
CederGroupHub · Aug 14, 2024 · b818a2a · b818a2a
2 parents 4d77c98 + 5230e87
commit b818a2a
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diff --git a/smol/cofe/space/cluster.py b/smol/cofe/space/cluster.py
@@ -58,7 +58,7 @@ def __init__(self, site_spaces, frac_coords, lattice):
  self._centroid = centroid - shift
  self._frac_coords = frac_coords - shift
  self._sites = tuple(
- Site(site_space, coords)
+ Site(site_space.composition, coords)
  for site_space, coords in zip(
  site_spaces, lattice.get_cartesian_coords(frac_coords)
  )

diff --git a/tests/test_cofe/test_cluster.py b/tests/test_cofe/test_cluster.py
@@ -36,7 +36,7 @@ def test_diameter(cluster):
 def test_periodicity(cluster, rng):
  new_coords = cluster.frac_coords.copy()
  new_coords += rng.integers(-5, 5)
- site_spaces = [s.species for s in cluster.sites]
+ site_spaces = get_site_spaces(cluster)
  assert Cluster(site_spaces, new_coords, cluster.lattice) == cluster
  new_coords[0] += 0.005 + rng.random()
  assert Cluster(site_spaces, new_coords, cluster.lattice) != cluster