Fix Cannot extract the right mapping from spglib #228

qzhu2017 · Aug 28, 2023 · 56aa415 · 56aa415
1 parent d813fc4
commit 56aa415
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Showing 2 changed files with 9 additions and 4 deletions.
diff --git a/pyxtal/miscellaneous/bug_spglib.py b/pyxtal/miscellaneous/bug_spglib.py
@@ -0,0 +1,5 @@
+from pyxtal import pyxtal
+
+c = pyxtal()
+c.from_seed('pyxtal/database/cifs/c_bug.vasp'); print(c)
+c.from_seed('pyxtal/database/cifs/c_bug2.vasp'); print(c)
diff --git a/pyxtal/util.py b/pyxtal/util.py
@@ -104,7 +104,7 @@ def symmetrize(pmg, tol=1e-3, a_tol=5.0, style='pyxtal', hn=None):
  pos = dataset['std_positions']
  numbers = dataset['std_types']
 
- return Structure(cell, numbers, pos)
+ return Structure(cell, numbers, pos), hn
 
 def get_symmetrized_pmg(pmg, tol=1e-3, a_tol=5.0, style='pyxtal', hn=None):
  """
@@ -123,11 +123,11 @@ def get_symmetrized_pmg(pmg, tol=1e-3, a_tol=5.0, style='pyxtal', hn=None):
  pymatgen structure with symmetrized lattice
  """
 
- pmg = symmetrize(pmg, tol, a_tol=a_tol, style=style, hn=hn)
+ pmg, hn = symmetrize(pmg, tol, a_tol=a_tol, style=style, hn=hn)
  s = sga(pmg, symprec=tol, angle_tolerance=a_tol)
  # make sure that the coordinates are in standard setting
- if hn is None:
- hn = Hall(s._space_group_data['number'], style=style).hall_default
+ #if hn is None:
+ # hn = Hall(s._space_group_data['number'], style=style).hall_default
  if hn != s._space_group_data["hall_number"]:
  s._space_group_data = get_symmetry_dataset(s._cell, tol,
  angle_tolerance=a_tol,