From 99c593c3279a130db2d95276fc0cc57eeecfc987 Mon Sep 17 00:00:00 2001
From: qzhu <qzhu@cms-2.physics.unlv.edu>
Date: Fri, 14 Jan 2022 18:54:40 -0800
Subject: [PATCH] fix lattice bug

---
 pyxtal/__init__.py |  9 +++++----
 pyxtal/lattice.py  | 11 +++++++----
 2 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/pyxtal/__init__.py b/pyxtal/__init__.py
index a57635f2..e60dd642 100644
--- 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
index 86746d6b..993fb2f5 100644
--- 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)