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 - 13:30:01 PDT
