Attempt to understand graph-tool geometric graph generation + possible bug

geometric_graph_test.py

# coding: utf-8

import graph_tool.all as gt
import math
import numpy as np

# basis vectors for hexagonal-close-packed lattice
basis = np.array([[ 0.        ,  0.        ,  0.        ],
                  [ 0.5       ,  0.5       ,  0.        ],
                  [ 0.5       ,  0.16666667,  0.5       ],
                  [ 0.        ,  0.66666667,  0.5       ]])

# unit cell for hexagonal-close-packed lattice
cell = np.array([1.0, math.sqrt(3), math.sqrt(8/3.)])

def make_points(size):
  '''Generates a hexagonal-close-packed lattice of a given size from basis vectors and unit cell.'''
    points = []
    for i in range(size):
        for j in range(size):
            for k in range(size):
                for v in basis:
                    points.append((v+[i,j,k])*cell)
    return np.array(points)

# This example works.
size = 3
points = make_points(size)
g3, pos3 = gt.geometric_graph(points, 1.00000001, [(0,cell[0]*size),(0,cell[1]*size),(0,cell[2]*size)])
print g3
print float(g3.num_edges())/g3.num_vertices() # should be 6.0

# This example doesn't seem to work.
# Note that points array here is a subset of the points array for size=3
size = 4
points = make_points(size)
g4, pos4 = gt.geometric_graph(points, 1.00000001, [(0,cell[0]*size),(0,cell[1]*size),(0,cell[2]*size)])
print g4
print float(g4.num_edges())/g4.num_vertices()