fixed tests and prevent symmetrically_remove_atoms() from removing at…

…oms on the same layer

pymatgen/core/surface.py

@@ -673,7 +673,8 @@ def symmetrically_remove_atoms(self, indices):
             for i2 in eq_indices:
                 if i2 == i1:
                     continue
-
+                if slabcopy[i2].frac_coords[2] == slabcopy[i1].frac_coords[2]:
+                    continue
                 # Test site remove to see if it results in symmetric slab
                 s = self.copy()
                 s.remove_sites([i1, i2])
@@ -1475,7 +1476,7 @@ def build_slabs(self):
                 for p in pts_to_rm:
                     p[2] = slab.lattice.get_fractional_coords([top_site[0], top_site[1],
                                                                top_site[2]+p[2]*d])[2]
-                    cart_point = self.lattice.get_cartesian_coords(p)
+                    cart_point = slab.lattice.get_cartesian_coords(p)
                     dist = [site.distance_from_point(cart_point) for site in slab]
                     site1 = dist.index(min(dist))
                     slab.symmetrically_remove_atoms([site1])

pymatgen/core/tests/slab.cif

@@ -0,0 +1,38 @@
+# generated using pymatgen
+data_Ti5O
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   4.60000000
+_cell_length_b   4.60000000
+_cell_length_c   22.56000000
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   120.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Ti5O
+_chemical_formula_sum   'Ti10 O2'
+_cell_volume   413.41420059
+_cell_formula_units_Z   2
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Ti  Ti1  1  0.000000  0.000000  0.093750  1
+  Ti  Ti2  1  0.000000  0.000000  0.218750  1
+  Ti  Ti3  1  0.333333  0.666667  0.156250  1
+  Ti  Ti4  1  0.666667  0.333333  0.156250  1
+  Ti  Ti5  1  0.000000  0.000000  0.343750  1
+  Ti  Ti6  1  0.333333  0.666667  0.281250  1
+  Ti  Ti7  1  0.666667  0.333333  0.281250  1
+  Ti  Ti8  1  0.000000  0.000000  0.468750  1
+  Ti  Ti9  1  0.333333  0.666667  0.406250  1
+  Ti  Ti10  1  0.666667  0.333333  0.406250  1
+  O  O11  1  0.000000  0.000000  0.568750  1
+  O  O12  1  0.000000  0.000000  -0.006250  1