Hi,
Rats, a missed opportunity:
But I agree with Bob, dont study this unless you're
waiting for sander to compile.
;:::)))))
better late than never ?
scott
On Tue, Feb 02, 2010 at 06:45:49PM -0500, Scott Brozell wrote:
> Hi,
>
> If you really want to study nfft vs nfftdim then start with
> get_fftdims in ew_fft.f.
> It might also be useful to browse spatial_recip.f and spatial_fft.f
> since that gives a different perspective, and there may be more
> explanations in spatial_fft.f than in the originals.
> I think the reference on this is
> .Article{Crowley97,
> author = {Crowley, M.F. and Darden, T.A. and Cheatham, III, T.E. and Deerfield, II, D.W.},
> title = {{Adventures in improving the scaling and accuracy of a parallel molecular dynamics program}},
> journal = {J. Supercomput.},
> volume = {11},
> pages = {255-278},
> year = {1997} }
>
> But I agree with Bob, dont study this unless your spouse is on a Roman Holiday.
>
> scott
>
> On Tue, Feb 02, 2010 at 05:53:36PM -0500, Robert Duke wrote:
> > The motivation behind using half complex fft's is performance related; Mike
> > Crowley gets credit for this going back to amber 7, and it is a great idea
> > that has been written up and used in various places. I would have to look
> > up some stuff to attempt to explain it, and unless you are a numerical
> > methods weeny, you would not care anyway. The two sets of indices are a
> > convenience, though there is an opportunity to shoot yourself in the foot
> > here, for the uninitiated. I don't know whether Mike or Tom first did it,
> > but there are good reasons for it; it is however indeed not well
> > documented. So I am not doing any criticizing on this one; just trying to
> > make sure there are slightly fewer self-inflicted wounds... ;-)
> > - Bob
> > ----- Original Message -----
> > From: "Mark Williamson" <mjw.sdsc.edu>
> > To: "AMBER Developers Mailing List" <amber-developers.ambermd.org>
> > Sent: Tuesday, February 02, 2010 5:47 PM
> > Subject: Re: [AMBER-Developers] ips.f::aips_sumrc() is not using
> > nfftdim2andnfftdim3
> >
> >
> > >Robert Duke wrote:
> > >>Okay, be careful about dinking with nfft[123] vs nfftdim[123]. I have no
> > >>idea whether this ips code is correct, but this nfft vs. nfftdim stuff
> > >>has caused confusion before in the recip space code (notably, the guys
> > >>doing the pmemd gpu port made some assumptions and renamed some stuff and
> > >>majorly broke some code). I have not refreshed my memory by looking at
> > >>code, but I vaguely remember that these two sets of variables exist due
> > >>to use of half complex fft's in reciprocal space calcs, and you basically
> > >>have to be able to treat different fft-related data structures as if they
> > >>are dimensioned differently (I am sure that is as clear as mud - bottom
> > >>line - don't dink with these variables unless you know what you are
> > >>doing, and as far as I know, Mike Crowley, Tom Darden and I are the only
> > >>folks who have done a lot with this stuff - though looks like ips folks
> > >>waded into it a bit too...).
> > >>Regards - Bob
> > >
> > >Thanks Bob, I was not aware of this. It sounds quite esoteric; I assume
> > >the motivation behind this was performance related? Are there any
> > >documents expanding upon this?
> > >
> > >regards,
> > >
> > >Mark
>
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Received on Tue Feb 02 2010 - 16:00:03 PST
