[Numpy-discussion] huge array calculation speed

Charles R Harris charlesr.harris@gmail....
Thu Jul 10 12:35:41 CDT 2008

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.

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