Re: PMEGridSize

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Oct 13 2003 - 13:34:44 CDT

Hi,

PMEGridSize[XYZ] should be the nearest integer roundup of cellBasisVector
for which a fast fourier transform (FFT) can be efficiently performed.
This typically means that the grid size will have only factors of 2,3,5.

The FFT algorithm converts an order N^2 fourier transform to order N log N
by exploiting a factorization of the transform, originally based on powers
of 2, but later extended to other factors. The speed of the transform
will be limited by the largest prime factor in the input dimension.
Therefore, grid sizes of the form 2^a * 3^b * 5^c are most efficient, for
example, 30, 32, 36, 40, 45, 48, 50, 54, 60, 64, 72, 75, 80, 81, and 90
are all good grid sizes.

-Jim

On Fri, 10 Oct 2003, Peter Jones wrote:

> Hello,
>
> I am trying to find out the relationship between cellBasisVector and
> PMEGridSize for PME simulations. I thought that maybe for a periodic
> box with sides defined along the x,y,z axes, and a 1 grid,
> PMEGridSize is set to the nearest integer roundup (or down?) of
> cellBasisVector in the corresponding dimension, but after looking at
> various config files on your website, I think there's something I'm not
> getting. Can you please explain this or direct me to an appropriate
> reference?
>
>
> thankyou,
>
> regards,
>
> Peter.
>
> Peter Jones Ph.D.
> Research Fellow
> Department of Cell and Molecular Biology
> University of Technology Sydney
> Westbourne Street
> Gore Hill N.S.W. 2065
> Australia
>
> Tel: 61-2-95190524
> FAX: 61-2-9514 4026
> email: Peter.Jones-2_at_uts.edu.a
>
>
>
> UTS CRICOS Provider Code: 00099F
>
> DISCLAIMER
> ========================================================================
> This email message and any accompanying attachments may contain
> confidential information. If you are not the intended recipient, do not
> read, use, disseminate, distribute or copy this message or attachments.
> If you have received this message in error, please notify the sender
> immediately and delete this message. Any views expressed in this message
> are those of the individual sender, except where the sender expressly,
> and with authority, states them to be the views the University of
> Technology Sydney. Before opening any attachments, please check them for
> viruses and defects.
> ========================================================================
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:03 CST