fix lattice bug

MaterSim · Jan 15, 2022 · 99c593c · 99c593c
1 parent 9908cc2
commit 99c593c
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Showing 2 changed files with 12 additions and 8 deletions.
diff --git a/pyxtal/__init__.py b/pyxtal/__init__.py
@@ -1506,9 +1506,10 @@ def _get_alternative(self, wyc_sets, index, ref_cell=None):
             if pos1 is not None:
                 new_struc.atom_sites[i] = atom_site(wp, pos1, site.specie)
             else:
-                print(pos)
-                print(wp)
-                raise RuntimeError("Cannot find the right pos")
+                return None
+                #print(pos)
+                #print(wp)
+                #raise RuntimeError("Cannot find the right pos")
 
         new_struc.source = "Alt. Wyckoff Set [{:d}]: {:s}".format(index, xyz_string)
         new_struc.wyc_set_id = index
@@ -2035,7 +2036,7 @@ def get_transition_by_path(self, ref_struc, path, d_tol, d_tol2=0.5, N_images=2)
                     for label in site:
                         try:
                             index = string.ascii_lowercase.index(label[-1])
-                        except ValueError: #8A
+                        except ValueError: #'8A'
                             index = 26
                         _site.extend(relation[index])
                     _sites0.append(_site)

diff --git a/pyxtal/lattice.py b/pyxtal/lattice.py
@@ -223,10 +223,13 @@ def search_transformation(self, lat_ref, d_tol=1.0, f_tol=0.1):
 
             for j, tran2 in enumerate(trans2):
                 tmp = np.dot(tran2, lat0.matrix)
-                cell2 = Lattice.from_matrix(tmp, l_type=self.ltype).matrix
-                diff = np.abs(cell1-cell2).flatten()
-                id = np.argmax(diff)
-                d_tol1, f_tol1 = diff[id], diff[id]/abs(cell1.flatten()[id])
+                try:
+                    cell2 = Lattice.from_matrix(tmp, l_type=self.ltype).matrix
+                    diff = np.abs(cell1-cell2).flatten()
+                    id = np.argmax(diff)
+                    d_tol1, f_tol1 = diff[id], diff[id]/abs(cell1.flatten()[id])
+                except:
+                    d_tol1, f_tol1 = 10, 1.0
                 tols[j, :] = [d_tol1, f_tol1]
                 #print([d_tol1, f_tol1])
             #print(tols)