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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Received on Thu May 21 2020 - 17:30:02 PDT
