Okay, I can provide two examples given below.
I wouldn't be surprised if it's not a bug and I'm missing something obvious, e.g. my neighbour cut-off is wrong. I've tried a few different values and can sometimes get it to work for graphs of certain sizes, but it then breaks when I try a graph of a different size. It's perplexing because I've used these same points and boundaries in a different context and they seem to be correct.
This example works (vertices corresponding to a 3x3x3 repeated hexagonal-close-packed lattice), the ratio of edges to vertices is 6.0 as expected:
g,pos = gt.geometric_graph(points_working, 1.00000001,
[(0, 3.0), (0, 5.196152422706632), (0, 4.8989794855663558)])
While this one (vertices corresponding to a 4x4x4 repeated hexagonal-close-packed lattice) doesn't work, and the ratio of edges to vertices is 5.625:
g,pos = gt.geometric_graph(points_not_working, 1.00000001,
[(0, 4.0), (0, 6.9282032302755088), (0, 6.5319726474218083)])
where points_working =
[[ 0. 0. 0. ]
[ 0.5 0.8660254 0. ]
[ 0.5 0.28867513 0.81649658]
[ 0. 1.15470054 0.81649658]
[ 0. 0. 1.63299316]
[ 0.5 0.8660254 1.63299316]
[ 0.5 0.28867513 2.44948974]
[ 0. 1.15470054 2.44948974]
[ 0. 0. 3.26598632]
[ 0.5 0.8660254 3.26598632]
[ 0.5 0.28867513 4.0824829 ]
[ 0. 1.15470054 4.0824829 ]
[ 0. 1.73205081 0. ]
[ 0.5 2.59807621 0. ]
[ 0.5 2.02072594 0.81649658]
[ 0. 2.88675135 0.81649658]
[ 0. 1.73205081 1.63299316]
[ 0.5 2.59807621 1.63299316]
[ 0.5 2.02072594 2.44948974]
[ 0. 2.88675135 2.44948974]
[ 0. 1.73205081 3.26598632]
[ 0.5 2.59807621 3.26598632]
[ 0.5 2.02072594 4.0824829 ]
[ 0. 2.88675135 4.0824829 ]
[ 0. 3.46410162 0. ]
[ 0.5 4.33012702 0. ]
[ 0.5 3.75277675 0.81649658]
[ 0. 4.61880215 0.81649658]
[ 0. 3.46410162 1.63299316]
[ 0.5 4.33012702 1.63299316]
[ 0.5 3.75277675 2.44948974]
[ 0. 4.61880215 2.44948974]
[ 0. 3.46410162 3.26598632]
[ 0.5 4.33012702 3.26598632]
[ 0.5 3.75277675 4.0824829 ]
[ 0. 4.61880215 4.0824829 ]
[ 1. 0. 0. ]
[ 1.5 0.8660254 0. ]
[ 1.5 0.28867513 0.81649658]
[ 1. 1.15470054 0.81649658]
[ 1. 0. 1.63299316]
[ 1.5 0.8660254 1.63299316]
[ 1.5 0.28867513 2.44948974]
[ 1. 1.15470054 2.44948974]
[ 1. 0. 3.26598632]
[ 1.5 0.8660254 3.26598632]
[ 1.5 0.28867513 4.0824829 ]
[ 1. 1.15470054 4.0824829 ]
[ 1. 1.73205081 0. ]
[ 1.5 2.59807621 0. ]
[ 1.5 2.02072594 0.81649658]
[ 1. 2.88675135 0.81649658]
[ 1. 1.73205081 1.63299316]
[ 1.5 2.59807621 1.63299316]
[ 1.5 2.02072594 2.44948974]
[ 1. 2.88675135 2.44948974]
[ 1. 1.73205081 3.26598632]
[ 1.5 2.59807621 3.26598632]
[ 1.5 2.02072594 4.0824829 ]
[ 1. 2.88675135 4.0824829 ]
[ 1. 3.46410162 0. ]
[ 1.5 4.33012702 0. ]
[ 1.5 3.75277675 0.81649658]
[ 1. 4.61880215 0.81649658]
[ 1. 3.46410162 1.63299316]
[ 1.5 4.33012702 1.63299316]
[ 1.5 3.75277675 2.44948974]
[ 1. 4.61880215 2.44948974]
[ 1. 3.46410162 3.26598632]
[ 1.5 4.33012702 3.26598632]
[ 1.5 3.75277675 4.0824829 ]
[ 1. 4.61880215 4.0824829 ]
[ 2. 0. 0. ]
[ 2.5 0.8660254 0. ]
[ 2.5 0.28867513 0.81649658]
[ 2. 1.15470054 0.81649658]
[ 2. 0. 1.63299316]
[ 2.5 0.8660254 1.63299316]
[ 2.5 0.28867513 2.44948974]
[ 2. 1.15470054 2.44948974]
[ 2. 0. 3.26598632]
[ 2.5 0.8660254 3.26598632]
[ 2.5 0.28867513 4.0824829 ]
[ 2. 1.15470054 4.0824829 ]
[ 2. 1.73205081 0. ]
[ 2.5 2.59807621 0. ]
[ 2.5 2.02072594 0.81649658]
[ 2. 2.88675135 0.81649658]
[ 2. 1.73205081 1.63299316]
[ 2.5 2.59807621 1.63299316]
[ 2.5 2.02072594 2.44948974]
[ 2. 2.88675135 2.44948974]
[ 2. 1.73205081 3.26598632]
[ 2.5 2.59807621 3.26598632]
[ 2.5 2.02072594 4.0824829 ]
[ 2. 2.88675135 4.0824829 ]
[ 2. 3.46410162 0. ]
[ 2.5 4.33012702 0. ]
[ 2.5 3.75277675 0.81649658]
[ 2. 4.61880215 0.81649658]
[ 2. 3.46410162 1.63299316]
[ 2.5 4.33012702 1.63299316]
[ 2.5 3.75277675 2.44948974]
[ 2. 4.61880215 2.44948974]
[ 2. 3.46410162 3.26598632]
[ 2.5 4.33012702 3.26598632]
[ 2.5 3.75277675 4.0824829 ]
[ 2. 4.61880215 4.0824829 ]]
and points_not_working =
[[ 0. 0. 0. ]
[ 0.5 0.8660254 0. ]
[ 0.5 0.28867513 0.81649658]
[ 0. 1.15470054 0.81649658]
[ 0. 0. 1.63299316]
[ 0.5 0.8660254 1.63299316]
[ 0.5 0.28867513 2.44948974]
[ 0. 1.15470054 2.44948974]
[ 0. 0. 3.26598632]
[ 0.5 0.8660254 3.26598632]
[ 0.5 0.28867513 4.0824829 ]
[ 0. 1.15470054 4.0824829 ]
[ 0. 0. 4.89897949]
[ 0.5 0.8660254 4.89897949]
[ 0.5 0.28867513 5.71547607]
[ 0. 1.15470054 5.71547607]
[ 0. 1.73205081 0. ]
[ 0.5 2.59807621 0. ]
[ 0.5 2.02072594 0.81649658]
[ 0. 2.88675135 0.81649658]
[ 0. 1.73205081 1.63299316]
[ 0.5 2.59807621 1.63299316]
[ 0.5 2.02072594 2.44948974]
[ 0. 2.88675135 2.44948974]
[ 0. 1.73205081 3.26598632]
[ 0.5 2.59807621 3.26598632]
[ 0.5 2.02072594 4.0824829 ]
[ 0. 2.88675135 4.0824829 ]
[ 0. 1.73205081 4.89897949]
[ 0.5 2.59807621 4.89897949]
[ 0.5 2.02072594 5.71547607]
[ 0. 2.88675135 5.71547607]
[ 0. 3.46410162 0. ]
[ 0.5 4.33012702 0. ]
[ 0.5 3.75277675 0.81649658]
[ 0. 4.61880215 0.81649658]
[ 0. 3.46410162 1.63299316]
[ 0.5 4.33012702 1.63299316]
[ 0.5 3.75277675 2.44948974]
[ 0. 4.61880215 2.44948974]
[ 0. 3.46410162 3.26598632]
[ 0.5 4.33012702 3.26598632]
[ 0.5 3.75277675 4.0824829 ]
[ 0. 4.61880215 4.0824829 ]
[ 0. 3.46410162 4.89897949]
[ 0.5 4.33012702 4.89897949]
[ 0.5 3.75277675 5.71547607]
[ 0. 4.61880215 5.71547607]
[ 0. 5.19615242 0. ]
[ 0.5 6.06217783 0. ]
[ 0.5 5.48482756 0.81649658]
[ 0. 6.35085296 0.81649658]
[ 0. 5.19615242 1.63299316]
[ 0.5 6.06217783 1.63299316]
[ 0.5 5.48482756 2.44948974]
[ 0. 6.35085296 2.44948974]
[ 0. 5.19615242 3.26598632]
[ 0.5 6.06217783 3.26598632]
[ 0.5 5.48482756 4.0824829 ]
[ 0. 6.35085296 4.0824829 ]
[ 0. 5.19615242 4.89897949]
[ 0.5 6.06217783 4.89897949]
[ 0.5 5.48482756 5.71547607]
[ 0. 6.35085296 5.71547607]
[ 1. 0. 0. ]
[ 1.5 0.8660254 0. ]
[ 1.5 0.28867513 0.81649658]
[ 1. 1.15470054 0.81649658]
[ 1. 0. 1.63299316]
[ 1.5 0.8660254 1.63299316]
[ 1.5 0.28867513 2.44948974]
[ 1. 1.15470054 2.44948974]
[ 1. 0. 3.26598632]
[ 1.5 0.8660254 3.26598632]
[ 1.5 0.28867513 4.0824829 ]
[ 1. 1.15470054 4.0824829 ]
[ 1. 0. 4.89897949]
[ 1.5 0.8660254 4.89897949]
[ 1.5 0.28867513 5.71547607]
[ 1. 1.15470054 5.71547607]
[ 1. 1.73205081 0. ]
[ 1.5 2.59807621 0. ]
[ 1.5 2.02072594 0.81649658]
[ 1. 2.88675135 0.81649658]
[ 1. 1.73205081 1.63299316]
[ 1.5 2.59807621 1.63299316]
[ 1.5 2.02072594 2.44948974]
[ 1. 2.88675135 2.44948974]
[ 1. 1.73205081 3.26598632]
[ 1.5 2.59807621 3.26598632]
[ 1.5 2.02072594 4.0824829 ]
[ 1. 2.88675135 4.0824829 ]
[ 1. 1.73205081 4.89897949]
[ 1.5 2.59807621 4.89897949]
[ 1.5 2.02072594 5.71547607]
[ 1. 2.88675135 5.71547607]
[ 1. 3.46410162 0. ]
[ 1.5 4.33012702 0. ]
[ 1.5 3.75277675 0.81649658]
[ 1. 4.61880215 0.81649658]
[ 1. 3.46410162 1.63299316]
[ 1.5 4.33012702 1.63299316]
[ 1.5 3.75277675 2.44948974]
[ 1. 4.61880215 2.44948974]
[ 1. 3.46410162 3.26598632]
[ 1.5 4.33012702 3.26598632]
[ 1.5 3.75277675 4.0824829 ]
[ 1. 4.61880215 4.0824829 ]
[ 1. 3.46410162 4.89897949]
[ 1.5 4.33012702 4.89897949]
[ 1.5 3.75277675 5.71547607]
[ 1. 4.61880215 5.71547607]
[ 1. 5.19615242 0. ]
[ 1.5 6.06217783 0. ]
[ 1.5 5.48482756 0.81649658]
[ 1. 6.35085296 0.81649658]
[ 1. 5.19615242 1.63299316]
[ 1.5 6.06217783 1.63299316]
[ 1.5 5.48482756 2.44948974]
[ 1. 6.35085296 2.44948974]
[ 1. 5.19615242 3.26598632]
[ 1.5 6.06217783 3.26598632]
[ 1.5 5.48482756 4.0824829 ]
[ 1. 6.35085296 4.0824829 ]
[ 1. 5.19615242 4.89897949]
[ 1.5 6.06217783 4.89897949]
[ 1.5 5.48482756 5.71547607]
[ 1. 6.35085296 5.71547607]
[ 2. 0. 0. ]
[ 2.5 0.8660254 0. ]
[ 2.5 0.28867513 0.81649658]
[ 2. 1.15470054 0.81649658]
[ 2. 0. 1.63299316]
[ 2.5 0.8660254 1.63299316]
[ 2.5 0.28867513 2.44948974]
[ 2. 1.15470054 2.44948974]
[ 2. 0. 3.26598632]
[ 2.5 0.8660254 3.26598632]
[ 2.5 0.28867513 4.0824829 ]
[ 2. 1.15470054 4.0824829 ]
[ 2. 0. 4.89897949]
[ 2.5 0.8660254 4.89897949]
[ 2.5 0.28867513 5.71547607]
[ 2. 1.15470054 5.71547607]
[ 2. 1.73205081 0. ]
[ 2.5 2.59807621 0. ]
[ 2.5 2.02072594 0.81649658]
[ 2. 2.88675135 0.81649658]
[ 2. 1.73205081 1.63299316]
[ 2.5 2.59807621 1.63299316]
[ 2.5 2.02072594 2.44948974]
[ 2. 2.88675135 2.44948974]
[ 2. 1.73205081 3.26598632]
[ 2.5 2.59807621 3.26598632]
[ 2.5 2.02072594 4.0824829 ]
[ 2. 2.88675135 4.0824829 ]
[ 2. 1.73205081 4.89897949]
[ 2.5 2.59807621 4.89897949]
[ 2.5 2.02072594 5.71547607]
[ 2. 2.88675135 5.71547607]
[ 2. 3.46410162 0. ]
[ 2.5 4.33012702 0. ]
[ 2.5 3.75277675 0.81649658]
[ 2. 4.61880215 0.81649658]
[ 2. 3.46410162 1.63299316]
[ 2.5 4.33012702 1.63299316]
[ 2.5 3.75277675 2.44948974]
[ 2. 4.61880215 2.44948974]
[ 2. 3.46410162 3.26598632]
[ 2.5 4.33012702 3.26598632]
[ 2.5 3.75277675 4.0824829 ]
[ 2. 4.61880215 4.0824829 ]
[ 2. 3.46410162 4.89897949]
[ 2.5 4.33012702 4.89897949]
[ 2.5 3.75277675 5.71547607]
[ 2. 4.61880215 5.71547607]
[ 2. 5.19615242 0. ]
[ 2.5 6.06217783 0. ]
[ 2.5 5.48482756 0.81649658]
[ 2. 6.35085296 0.81649658]
[ 2. 5.19615242 1.63299316]
[ 2.5 6.06217783 1.63299316]
[ 2.5 5.48482756 2.44948974]
[ 2. 6.35085296 2.44948974]
[ 2. 5.19615242 3.26598632]
[ 2.5 6.06217783 3.26598632]
[ 2.5 5.48482756 4.0824829 ]
[ 2. 6.35085296 4.0824829 ]
[ 2. 5.19615242 4.89897949]
[ 2.5 6.06217783 4.89897949]
[ 2.5 5.48482756 5.71547607]
[ 2. 6.35085296 5.71547607]
[ 3. 0. 0. ]
[ 3.5 0.8660254 0. ]
[ 3.5 0.28867513 0.81649658]
[ 3. 1.15470054 0.81649658]
[ 3. 0. 1.63299316]
[ 3.5 0.8660254 1.63299316]
[ 3.5 0.28867513 2.44948974]
[ 3. 1.15470054 2.44948974]
[ 3. 0. 3.26598632]
[ 3.5 0.8660254 3.26598632]
[ 3.5 0.28867513 4.0824829 ]
[ 3. 1.15470054 4.0824829 ]
[ 3. 0. 4.89897949]
[ 3.5 0.8660254 4.89897949]
[ 3.5 0.28867513 5.71547607]
[ 3. 1.15470054 5.71547607]
[ 3. 1.73205081 0. ]
[ 3.5 2.59807621 0. ]
[ 3.5 2.02072594 0.81649658]
[ 3. 2.88675135 0.81649658]
[ 3. 1.73205081 1.63299316]
[ 3.5 2.59807621 1.63299316]
[ 3.5 2.02072594 2.44948974]
[ 3. 2.88675135 2.44948974]
[ 3. 1.73205081 3.26598632]
[ 3.5 2.59807621 3.26598632]
[ 3.5 2.02072594 4.0824829 ]
[ 3. 2.88675135 4.0824829 ]
[ 3. 1.73205081 4.89897949]
[ 3.5 2.59807621 4.89897949]
[ 3.5 2.02072594 5.71547607]
[ 3. 2.88675135 5.71547607]
[ 3. 3.46410162 0. ]
[ 3.5 4.33012702 0. ]
[ 3.5 3.75277675 0.81649658]
[ 3. 4.61880215 0.81649658]
[ 3. 3.46410162 1.63299316]
[ 3.5 4.33012702 1.63299316]
[ 3.5 3.75277675 2.44948974]
[ 3. 4.61880215 2.44948974]
[ 3. 3.46410162 3.26598632]
[ 3.5 4.33012702 3.26598632]
[ 3.5 3.75277675 4.0824829 ]
[ 3. 4.61880215 4.0824829 ]
[ 3. 3.46410162 4.89897949]
[ 3.5 4.33012702 4.89897949]
[ 3.5 3.75277675 5.71547607]
[ 3. 4.61880215 5.71547607]
[ 3. 5.19615242 0. ]
[ 3.5 6.06217783 0. ]
[ 3.5 5.48482756 0.81649658]
[ 3. 6.35085296 0.81649658]
[ 3. 5.19615242 1.63299316]
[ 3.5 6.06217783 1.63299316]
[ 3.5 5.48482756 2.44948974]
[ 3. 6.35085296 2.44948974]
[ 3. 5.19615242 3.26598632]
[ 3.5 6.06217783 3.26598632]
[ 3.5 5.48482756 4.0824829 ]
[ 3. 6.35085296 4.0824829 ]
[ 3. 5.19615242 4.89897949]
[ 3.5 6.06217783 4.89897949]
[ 3.5 5.48482756 5.71547607]
[ 3. 6.35085296 5.71547607]]
The points themselves are generated from a hexagonal-close-packed basis set of vertices (given here in fractional co-ordinates):
[[ 0. , 0. , 0. ],
[ 0.5 , 0.5 , 0. ],
[ 0.5 , 0.16666667, 0.5 ],
[ 0. , 0.66666667, 0.5 ]]
and the boundary conditions from the ideal (scaled) lattice parameters, which are 1.0, sqrt(3), and sqrt(8/3.)
Thanks for your help.
Matthew
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