On Thu, Jul 10, 2008 at 10:38 AM, Dan Lussier <dtlussier@gmail.com> wrote:

Hello,

I am relatively new to numpy and am having trouble with the speed of
a specific array based calculation that I'm trying to do.

What I'm trying to do is to calculate the total total potential
energy and coordination number of each atom within a relatively large
simulation. Each atom is at a position (x,y,z) given by a row in a
large array (approximately 1e6 by 3) and presently I have no
information about its nearest neighbours so each its position must be
checked against all others before cutting the list down prior to
calculating the energy.

This looks to be O(n^2) and might well be the bottle neck. There are various ways to speed up such things but more information would help determine the method, i.e., is this operation within a loop so that the values change a lot. However, one quick thing to try is a sort on one of the coordinates so you only need to check a subset of the vectors. Searchsorted could be useful here also.

Chuck