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
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>
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Received on Thu May 21 2020 - 18:00:02 PDT
