change neighbours for cuboid mesh with periodic boundary conditions

Author: Weiwei Wang

fidimag/common/cuboid_mesh.py

@@ -147,21 +147,24 @@ def init_neighbours(self):
                         self.index(k, j, i + 1),  # over
                     ]]
 
-                    n_neighbours = [other for other in [
+                    nngbs = [other for other in [
                         self.index(k - 2, j, i),  # left
                         self.index(k + 2, j, i),  # right
                         self.index(k, j - 2, i),  # behind
                         self.index(k, j + 2, i),  # in front
                         self.index(k, j, i - 2),  # under
                         self.index(k, j, i + 2),  # over
                     ]]
+                    
+                    # July 1st, 2016 Weiwei: I think it's okay for a cell with its neighbour is itself 
+                    # if periodic boundary conditions are used. For example, if we only have cell and enable 
+                    # periodic boundary condition in x-direction, then we got a rod.
+                    # therefore, I commented two lines below.
                     # no cell should be its own neighbour
-                    neighbours = [other if other != cell
-                                  else -1 for other in ngbs]
-                    next_neighbours = [other if other != cell
-                                  else -1 for other in n_neighbours]
-                    connectivity.append(neighbours)
-                    connectivity_next.append(next_neighbours)
+                    # neighbours = [other if other != cell
+                    #              else -1 for other in ngbs]
+                    connectivity.append(ngbs)
+                    connectivity_next.append(nngbs)
 
         return np.array(connectivity, dtype=np.int32), np.array(connectivity_next, dtype=np.int32)
 

fidimag/common/cuboid_mesh_test.py

@@ -125,7 +125,8 @@ def test_neighbours_x_periodic_all():
 
     """
     mesh = CuboidMesh(1, 1, 1, 2, 1, 1, periodicity=(True, True, True))
-    assert allclose(mesh.neighbours, np.array(((1, 1, -1, -1, -1, -1), (0, 0, -1, -1, -1, -1))))
+    #assert allclose(mesh.neighbours, np.array(((1, 1, -1, -1, -1, -1), (0, 0, -1, -1, -1, -1))))
+    assert allclose(mesh.neighbours, np.array(((1, 1, 0, 0, 0, 0), (0, 0, 1, 1, 1, 1))))
 
 
 def test_neighbours_y():