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 - 12:30:02 PDT
