fix the translation vec

pyxtal/wyckoff_site.py

@@ -106,6 +106,7 @@ def _get_coords_and_species(self, absolute=False, add_PBC=False, first=False):
         coord0 = self.mol.cart_coords.dot(self.orientation.matrix.T)  #
         wp_atomic_sites = []
         wp_atomic_coords = None
+
         for point_index, op2 in enumerate(self.wp.ops):
             # Obtain the center in absolute coords
             center_relative = op2.operate(self.position)
@@ -115,8 +116,10 @@ def _get_coords_and_species(self, absolute=False, add_PBC=False, first=False):
             #op2_m = self.wp.generators_m[point_index]
             op2_m = self.wp.generators_m[point_index]
             rot = op2_m.affine_matrix[0:3][:, 0:3].T
-            #tau = op2_m.affine_matrix[0:3][:, 3]
-            tau = op2.translation_vector
+            if self.diag and self.wp.index > 0:
+                tau = op2.translation_vector
+            else:
+                tau = op2_m.affine_matrix[0:3][:, 3]
             tmp = np.dot(coord0, rot) + tau
             # Add absolute center to molecule
             tmp += center_absolute