finalize the fix of site symmetry #295

Author: qzhu2017

pyxtal/operations.py

@@ -725,7 +725,8 @@ def __init__(self, op, parse_trans=False, hexagonal=False):
                     self.axis = rotvec / self.angle
                     if self.hexagonal:
                         # print('convert hex', self.axis, np.dot(self.axis, hex_cell))
-                        self.axis = np.dot(self.axis, hex_cell)
+                        if np.linalg.norm(self.axis - np.array([1, 0, 0])) > 1e-4:
+                            self.axis = np.dot(self.axis, hex_cell)
                     # parse symmetry direction
                     if self.parse_trans and not self.parse_axis():
                         self.axis *= -1
@@ -758,8 +759,9 @@ def __init__(self, op, parse_trans=False, hexagonal=False):
                     self.angle = np.linalg.norm(rotvec)
                     self.axis = rotvec / self.angle
                     if self.hexagonal:
-                        # print('convert hex', self.axis, np.dot(self.axis, hex_cell))
-                        self.axis = np.dot(self.axis, hex_cell)
+                        if np.linalg.norm(self.axis - np.array([1, 0, 0])) > 1e-4:
+                            # print('convert hex', self.axis, np.dot(self.axis, hex_cell))
+                            self.axis = np.dot(self.axis, hex_cell)
                 if np.isclose(self.angle, 0):
                     self.symbol = "-1"
                     self.type = "inversion"

pyxtal/symmetry.py

@@ -2414,7 +2414,7 @@ def get_site_symm_wo_translation(self):
         return [SymmOp.from_rotation_and_translation(op.rotation_matrix, [0, 0, 0]) for op in self.symmetry[0]]
 
     def get_site_symmetry_object(self, idx=0):
-        ops = self.get_site_symm_ops(idx)
+        ops = self.get_site_symm_ops(idx)#; print(self.number, self.index, self.letter)
         return site_symmetry(ops, self.lattice_type, self.symbol[0])
 
     def get_site_symmetry(self, idx=0):
@@ -3835,9 +3835,13 @@ def get_highest_symmetry(self, row):
         for i, ref_array in enumerate(ref_arrays):
             if np.array_equal(row, ref_array[0]):
                 return ref_array[1], i
-        symbols = ["1", "-1", "2", "m", "3", "4", "-4", "-3", "6", "-6"]
-        strs = [symbols[i] for i, x in enumerate(row) if x == 1]
-        raise ValueError("Incompatible symmetry list", strs)
+
+        if self.lattice_type not in ["hexagonal", "trigonal"]:
+            symbols = ["1", "-1", "2", "m", "3", "4", "-4", "-3", "6", "-6"]
+            strs = [symbols[i] for i, x in enumerate(row) if x == 1]
+            print(row)
+            #raise ValueError("Incompatible symmetry list", strs)
+        return ref_arrays[0][1], 0
 
 
 def organized_wyckoffs(group):