h_matrix = [ [1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0] ]
positions = [ [0.0, 0.0, 0.0],
[0.5, 0.5, 0.0],
[0.5, 0.0, 0.5],
[0.0, 0.5, 0.5] ]
https://www.saylor.org/content/cubic_neighbors/cubic_near_neighbors.html