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] <[email protected]> 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>>
>
>
> _______________________________________________
> graph-tool mailing list
> [hidden email] <http:///user/SendEmail.jtp?type=node&node=4026229&i=1>
> http://lists.skewed.de/mailman/listinfo/graph-tool
>
> *signature.asc* (836 bytes) Download Attachment
> <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/attachment/4026229/0/signature.asc>
> --
> Tiago de Paula Peixoto <[email protected]>
>
>
> ------------------------------
> If you reply to this email, your message will be added to the discussion
> below:
>
> http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/Geometric-graph-generation-possible-bug-difficult-to-re-produce-tp4026228p4026229.html
> To unsubscribe from Geometric graph generation: possible bug, difficult to
> re-produce, click here
> <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4026228&code=bS5rLmhvcnRvbkBnbWFpbC5jb218NDAyNjIyOHwxMjc5MTUzNDA3>
> .
> NAML
> <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>
--
View this message in context:
http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/Geometric-graph-generation-possible-bug-difficult-to-re-produce-tp4026228p4026230.html
Sent from the Main discussion list for the graph-tool project mailing list
archive at Nabble.com.
_______________________________________________
graph-tool mailing list
[email protected]
http://lists.skewed.de/mailman/listinfo/graph-tool
