Actually, I don't think you need to deal w/ the extra points at all if you
do netfrc right after PME gradsum. Just do the total accumulate and get rid
of the resulting net forces for all atoms (including extra points). The
forces on extra points will be transferred to nearby heavy atoms (hence
become zero) in a later stage.
The results could be tiny different though. But theoretically I believe it
is OK.
Taisung
-----Original Message-----
From: Scott Le Grand [mailto:varelse2005.gmail.com]
Sent: Friday, May 22, 2020 4:31 PM
To: AMBER Developers Mailing List <amber-developers.ambermd.org>
Subject: Re: [AMBER-Developers] Faster NetFrc
So if I accumulate them from the extra points in gradsum, but then only
apply to atoms that are not extra points, we are good?
On Fri, May 22, 2020 at 1:29 PM David Cerutti <dscerutti.gmail.com> wrote:
> Our emails may have crossed in writing, but it appears that in both
> CPU and GPU codes the netfrc is being subtracted after extra points
> have had their forces transmitted to their massive frame atoms. The
> solutions to dealing with the pollution that netfrc correction causes
> with extra points differ in each code.
>
> Dave
>
>
> On Fri, May 22, 2020 at 4:27 PM Scott Le Grand <varelse2005.gmail.com>
> wrote:
>
> > Cool, and if it's an extra point should I or should I not subtract
> > the netfrc? Dumb questions asked upfront to save time later?
> >
> > On Fri, May 22, 2020 at 1:20 PM <cancersimulation.gmail.com> wrote:
> >
> > > It is static. Usually, it should be the same as "numextra" here
> > >
> > > use prmtop_dat_mod, only : numextra
> > >
> > > I believe Dave Cerutti has implemented some extra-point stuff and
> > > I
> don't
> > > know if the above statement still holds with his stuff.
> > >
> > > Taisung
> > >
> > > -----Original Message-----
> > > From: Scott Le Grand [mailto:varelse2005.gmail.com]
> > > Sent: Friday, May 22, 2020 3:02 PM
> > > To: AMBER Developers Mailing List <amber-developers.ambermd.org>
> > > Subject: Re: [AMBER-Developers] Faster NetFrc
> > >
> > > So also...
> > >
> > > I would assume the value of "ignored" is static. How do I
> > > calculate it
> a
> > > priori? And it looks like I don't apply it to the extra points.
> > > Feel
> free
> > > to
> > > describe off-list, but I want to drill down deep and get this
> > > right on
> > the
> > > first swing...
> > >
> > > On Thu, May 21, 2020 at 6:08 PM Scott Le Grand
> > > <varelse2005.gmail.com>
> > > wrote:
> > >
> > > > Excellent, that makes this much more straightforward. Should
> > > > have something by early next week.
> > > >
> > > > On Thu, May 21, 2020 at 6:04 PM <taisung.gmail.com> wrote:
> > > >
> > > >> The force thresholds are for those "dummies" (not the
> > > >> alchemical dummies but something like lone-pair points of water
> > > >> models). The forces of those atoms are "transferred" to other
> > > >> real atoms at the final force collection stage--and hence need
> > > >> to be kept to zero during the netfrc stage. Of course, you may
> > > >> find better ways to do things. For example, as Scott
> > > >> mentioned, the only non-conserved force part is PME reciprocal
> > > >> part. If the netfrc is done in the PME reciprocal part, there is
no need to have such force thresholds.
> > > >>
> > > >> Taisung
> > > >>
> > > >> -----Original Message-----
> > > >> From: David Cerutti [mailto:dscerutti.gmail.com]
> > > >> Sent: Thursday, May 21, 2020 8:37 PM
> > > >> To: AMBER Developers Mailing List
> > > >> <amber-developers.ambermd.org>
> > > >> Subject: Re: [AMBER-Developers] Faster NetFrc
> > > >>
> > > >> As implied, the GTI code is the revision that introduced this.
> > > >> Taisung can comment more on his logic, but the presence of this
> > > >> "small" term reminds me of something he's got in the non-bonded
> inner
> > > >> loop as well. I'm not sure we ever determined why these
> conditionals
> > > >> were needed; I think the one in the non-bonded loop should just
> > > >> go away after some other revisions I made, but I'll wait for
> > > >> more
> input.
> > > >>
> > > >> Dave
> > > >>
> > > >>
> > > >> On Thu, May 21, 2020 at 8:29 PM Scott Le Grand
> > > >> <varelse2005.gmail.com>
> > > >> wrote:
> > > >>
> > > >> > Hey guys,
> > > >> > Back as an AMBER developer and one of the first things I'd
> > > >> > like to do is optimize netfrc.
> > > >> >
> > > >> > Fixed point conservative forces have no net force. They
> > > >> > automagically cancel out 100%. So we can ignore everything
> > > >> > except non-conserved
> > > >> forces.
> > > >> >
> > > >> > The only non-conserved force I know of is the Ewald Gradient Sum.
> > > >> > So if I add up the net force there, and handle it upon either
> force
> > > >> > reduction or update, I can eliminate two passes on memory and
> > > >> > the two kernels currently dedicated to adding and then
> > > >> > subtracting
> them.
> > > >> >
> > > >> > But... Are there any other non-conserved forces?
> > > >> >
> > > >> > And... It looks like the FORTRAN and the CUDA code do
> > > >> > different
> > > things.
> > > >> > FORTRAN simply averages the forces and subtracts. But CUDA
> > > >> > only averages over atoms with force thresholds above a
> > > >> > predefined small amount. What's up with that?
> > > >> >
> > > >> > pme_ene.F90:
> > > >> > if (netfrc .gt. 0 .and. onstep) then
> > > >> >
> > > >> > if (ti_mode .eq. 0) then
> > > >> > do i = 1, atm_cnt
> > > >> > net_frcs(:) = net_frcs(:) + frc(:, i)
> > > >> > end do
> > > >> >
> > > >> > ! Now do the correction:
> > > >> >
> > > >> > net_frcs(:) = net_frcs(:) / dble(atm_cnt - numextra)
> > > >> >
> > > >> > do i = 1, atm_cnt
> > > >> > frc(:, i) = frc(:, i) - net_frcs(:)
> > > >> > end do
> > > >> > else
> > > >> > do i = 1, atm_cnt
> > > >> > ti_net_frcs(1, :) = ti_net_frcs(1, :) +
> > > >> > ti_nb_frc(1, :,
> i)
> > > >> > ti_net_frcs(2, :) = ti_net_frcs(2, :) +
> > > >> > ti_nb_frc(2, :,
> i)
> > > >> > end do
> > > >> >
> > > >> > ti_net_frcs(1,:) =
> > > >> > ti_net_frcs(1,:)/dble(ti_atm_cnt(1)-ti_numextra_pts(1))
> > > >> > ti_net_frcs(2,:) =
> > > >> > ti_net_frcs(2,:)/dble(ti_atm_cnt(2)-ti_numextra_pts(2))
> > > >> > net_frcs(:) = ti_net_frcs(1,:) + ti_net_frcs(2,:)
> > > >> >
> > > >> > do i = 1, atm_cnt
> > > >> > ! This matches how sander removes netfrcs in TI runs
> > > >> > if (ti_lst(1,i) .ne. 0) then
> > > >> > frc(:, i) = frc(:, i) - ti_net_frcs(1,:)
> > > >> > else if (ti_lst(2,i) .ne. 0) then
> > > >> > frc(:, i) = frc(:, i) - ti_net_frcs(2,:)
> > > >> > else
> > > >> > frc(:, i) = frc(:, i) - net_frcs(:)
> > > >> > end if
> > > >> > end do
> > > >> > end if
> > > >> > ! Any extra points must have their 0.d0 forces reset...
> > > >> >
> > > >> > if (numextra .gt. 0 .and. frameon .ne. 0) &
> > > >> > call zero_extra_pnts_vec(frc, ep_frames,
> > > >> > gbl_frame_cnt)
> > > >> >
> > > >> > end if
> > > >> >
> > > >> >
> > > >> > GTI path:
> > > >> > while (pos < cSim.atoms) {
> > > >> > PMEFloat fx = converter(pX[pos], ONEOVERFORCESCALE);
> > > >> > PMEFloat fy = converter(pY[pos], ONEOVERFORCESCALE);
> > > >> > PMEFloat fz = converter(pZ[pos], ONEOVERFORCESCALE);
> > > >> > if (abs(fx) > small || abs(fy) > small || abs(fz) > small) {
> > > >> > pX[pos] -= nfX;
> > > >> > pY[pos] -= nfY;
> > > >> > pZ[pos] -= nfZ;
> > > >> > }
> > > >> > pos += increment;
> > > >> > }
> > > >> >
> > > >> > Scott
> > > >> > _______________________________________________
> > > >> > AMBER-Developers mailing list AMBER-Developers.ambermd.org
> > > >> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > > >> >
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Received on Fri May 22 2020 - 14:30:02 PDT
