Fix NumPy array indexing in 32-bit system in `analysis.chemenv.coordi…

…nation_environments` (#4194)

* fix index in 32bit system

* pre-commit auto-fixes

---------

Co-authored-by: Haoyu Yang <yang@debian32bit.lan>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py

@@ -218,7 +218,9 @@ def points_wcs_csc(self, permutation=None):
         """
         if permutation is None:
             return self._points_wcs_csc
-        return np.concatenate((self._points_wcs_csc[:1], self._points_wocs_csc.take(permutation, axis=0)))
+        return np.concatenate(
+            (self._points_wcs_csc[:1], self._points_wocs_csc.take(np.array(permutation, dtype=np.intp), axis=0))
+        )
 
     def points_wocs_csc(self, permutation=None):
         """
@@ -227,7 +229,7 @@ def points_wocs_csc(self, permutation=None):
         """
         if permutation is None:
             return self._points_wocs_csc
-        return self._points_wocs_csc.take(permutation, axis=0)
+        return self._points_wocs_csc.take(np.array(permutation, dtype=np.intp), axis=0)
 
     def points_wcs_ctwcc(self, permutation=None):
         """
@@ -239,7 +241,7 @@ def points_wcs_ctwcc(self, permutation=None):
         return np.concatenate(
             (
                 self._points_wcs_ctwcc[:1],
-                self._points_wocs_ctwcc.take(permutation, axis=0),
+                self._points_wocs_ctwcc.take(np.array(permutation, dtype=np.intp), axis=0),
             )
         )
 
@@ -250,7 +252,7 @@ def points_wocs_ctwcc(self, permutation=None):
         """
         if permutation is None:
             return self._points_wocs_ctwcc
-        return self._points_wocs_ctwcc.take(permutation, axis=0)
+        return self._points_wocs_ctwcc.take(np.array(permutation, dtype=np.intp), axis=0)
 
     def points_wcs_ctwocc(self, permutation=None):
         """
@@ -262,7 +264,7 @@ def points_wcs_ctwocc(self, permutation=None):
         return np.concatenate(
             (
                 self._points_wcs_ctwocc[:1],
-                self._points_wocs_ctwocc.take(permutation, axis=0),
+                self._points_wocs_ctwocc.take(np.array(permutation, dtype=np.intp), axis=0),
             )
         )
 
@@ -273,7 +275,7 @@ def points_wocs_ctwocc(self, permutation=None):
         """
         if permutation is None:
             return self._points_wocs_ctwocc
-        return self._points_wocs_ctwocc.take(permutation, axis=0)
+        return self._points_wocs_ctwocc.take(np.array(permutation, dtype=np.intp), axis=0)
 
     @property
     def cn(self):
@@ -1976,6 +1978,7 @@ def _cg_csm_separation_plane_optim2(
         stop_search = False
         # TODO: do not do that several times ... also keep in memory
         if sepplane.ordered_plane:
+            separation_indices = [arr.astype(np.intp) for arr in separation_indices]
             inp = self.local_geometry.coords.take(separation_indices[1], axis=0)
             if sepplane.ordered_point_groups[0]:
                 pp_s0 = self.local_geometry.coords.take(separation_indices[0], axis=0)