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 On 13 August 2015 at 09:51, Tiago Peixoto [via Main discussion list for the graph-tool project] <ml-node+s982480n4026229h18@n3.nabble.com> wrote:

On 10.08.2015 18:27, mh wrote:

...

Hello,

I apologise I can't give a better bug report than this, but I've been playing with generating geometric graphs using graph-tool. I think the periodic boundary conditions may not be working properly in some cases, literally I think corner cases, or maybe there's a rounding error of some kind?

I was trying to create a hexagonal close packed-like geometric graph. (I'm fairly new to graph analysis, and I've been struggling to come up with a good example that would show this bug because I'm finding it difficult to track down exactly which edges are missing, but I'm pretty sure something's wrong because I'm not getting the number of edges I expect.) It is difficult to say anything without a specific example of the problem. Please post a small, self-contained code where the issue can be seen.

Best, Tiago

-- Tiago de Paula Peixoto <[hidden email] <http:///user/SendEmail.jtp?type=node&node=4026229&i=0>>

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Hi Tiago, Thanks for the reply. I've written up the example as a github gist, I hope that makes it easier to run. I will try and pinpoint some specific example edges too. https://gist.github.com/mkhorton/aefa5378ec7ec3160876 Thanks, Matthew On 17 August 2015 at 18:02, Tiago Peixoto [via Main discussion list for the graph-tool project] <ml-node+s982480n4026240h59@n3.nabble.com> wrote:

On 13.08.2015 11:28, mh wrote:

...

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)])

Well, can you pinpoint any of the missing edges? It would be much easier to debug if the example contained only two points where a missing edge should have been...

Also, please provide data in a way that is easy to load in a program, at least with copy and paste. If you do print(array), it is not a good idea, since one would need to parse it by hand. Instead do print(repr(array)).

Best, Tiago

-- Tiago de Paula Peixoto <[hidden email] <http:///user/SendEmail.jtp?type=node&node=4026240&i=0>>

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