bug: corrected some bugs on valid shifts

Author: pfebrer

sisl/geom/nanoribbon.py

@@ -406,7 +406,7 @@ def _parse_shift(self, shift, prev, align):
             self._junction_error(prev, "LONE ATOMS: Previous odd section, which has an open end,"
                 " is wider than the incoming one. A wider odd section must always"
                 " have a closed end. You can solve this by making the previous section"
-                " one unit smaller or larger (L = L +- 1).", "raise"
+                " one unit smaller or larger (L = L +- 1).", self.on_lone_atom
             )
 
         # Get the difference in width between the previous and this ribbon section
@@ -415,8 +415,8 @@ def _parse_shift(self, shift, prev, align):
         # on 1, 2, 3 or 4 atoms. After that, the cycle just repeats (e.g. 5 == 1, etc).
         diff_mod = W_diff % 4
 
-        # Now, we need to calculate the offset that we have to apply to the incoming
-        # section depending on several factors.
+        # Calculate the shifts that are valid (don't leave atoms with less than 2 bonds)
+        # This depends on several factors.
         if diff_mod % 2 == 0 and W % 2 == 1:
             # Both sections are odd
 
@@ -445,7 +445,7 @@ def _parse_shift(self, shift, prev, align):
 
                 # Update the valid shift limits if the sections are aligned on any of the edges.
                 shift_offset = self._offset_from_center(align, prev)
-                valid_shifts += shift_offset
+                valid_shifts -= shift_offset
             elif prev.W == W:
                 valid_shifts = np.array([0])
             else:
@@ -469,7 +469,7 @@ def _parse_shift(self, shift, prev, align):
                 shift_offset = self._offset_from_center(align, prev)
 
                 # Apply the offsets and calculate the maximum and minimum shifts.
-                min_shift, max_shift = -shift_lim + shift_offset, shift_lim + shift_offset
+                min_shift, max_shift = -shift_lim - shift_offset, shift_lim - shift_offset
 
                 valid_shifts = np.arange(min_shift, max_shift + 1, 2)
         else:

sisl/geom/tests/test_geom.py

@@ -118,9 +118,18 @@ def test_graphene_heteroribbon():
 
 def test_graphene_heteroribbon_errors():
     # 7-open with 9 can only be perfectly aligned.
-    graphene_heteroribbon([(7,1), (9,1)], align="center", on_lone_atom="raise")
+    # Let's test it from the center
+    graphene_heteroribbon([(7, 1), (9, 1)], align="center", on_lone_atom="raise")
     with pytest.raises(ValueError):
-        graphene_heteroribbon([(7,1), (9,1,-1)], align="center", on_lone_atom="raise")
+        graphene_heteroribbon([(7, 1), (9, 1, -1)], align="center", on_lone_atom="raise")
+    # From the bottom
+    graphene_heteroribbon([(7, 1), (9, 1, -1)], align="bottom", on_lone_atom="raise")
+    with pytest.raises(ValueError):
+        graphene_heteroribbon([(7, 1), (9, 1, 0)], align="bottom", on_lone_atom="raise")
+    # And from the top
+    graphene_heteroribbon([(7, 1), (9, 1, 1)], align="top", on_lone_atom="raise")
+    with pytest.raises(ValueError):
+        graphene_heteroribbon([(7, 1), (9, 1, -1)], align="top", on_lone_atom="raise")
 
     grap_heteroribbon = partial(
         graphene_heteroribbon, align="auto", shift_quantum=True