Remove starting offset

aiida_kkr/tools/tools_STM_scan.py

@@ -71,19 +71,26 @@ def get_r_offset(clust1, clust2, host_structure, add_position):
         pos2 = np.array(host_structure.sites[ilayer2].position)
         r_out_of_plane = pos2 - pos1
 
+    # convert from Ang to alat units (used internally in KKR)
+    alat = get_alat_from_bravais(np.array(host_structure.cell), host_structure.pbc[2])
+    r_out_of_plane /= alat
+
+    # remove spurious offsets that might be there due to the choice of the unit cell positions
+    r_out_of_plane = np.round(r_out_of_plane, 7)
+    r_out_of_plane[:2] %= 1  # modulo 1 for x and y coordinate
+
     # calculate in-plane vector from da, db inputs
     da = add_position.get_dict().get('da', 0)
     db = add_position.get_dict().get('db', 0)
     cell = np.array(host_structure.cell)
     r_in_plane = da * cell[0] + db * cell[1]
 
+    # convert from Ang to alat units (used internally in KKR)
+    r_in_plane /= alat
+
     # combine to offset vector
     r_offset = r_out_of_plane + r_in_plane
 
-    # convert from Ang to alat units (used internally in KKR)
-    alat = get_alat_from_bravais(np.array(host_structure.cell), host_structure.pbc[2])
-    r_offset /= alat
-
     return r_offset