Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Reduce memory usage in egbond_hb for GFN-FF #994

Merged
merged 8 commits into from
Mar 21, 2024
Merged

Reduce memory usage in egbond_hb for GFN-FF #994

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
f73ba08
Add dependecies in meson build
Thomas3R Mar 13, 2024
1045447
fix gfnff restart
Thomas3R Mar 14, 2024
ced2985
Merge branch 'main' of https://github.com/Thomas3R/xtb into main
Thomas3R Mar 14, 2024
b50eda6
GFNFF: Update ntrans in latPoint
Thomas3R Mar 14, 2024
e13cbfb
Merge branch 'main' of https://github.com/Thomas3R/xtb into main
Thomas3R Mar 14, 2024
f467c74
Reduce memory usage in egbond_hb
Thomas3R Mar 14, 2024
0af518f
Merge branch 'main' of https://github.com/Thomas3R/xtb into main
Thomas3R Mar 14, 2024
8cd5947
Add comments in topology.f90
Thomas3R Mar 20, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 8 additions & 5 deletions src/gfnff/gfnff_eg.f90
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -555,7 +555,7 @@ subroutine gfnff_eg(env,mol,pr,n,ichrg,at,xyz,sigma,g,etot,res_gff, &
endif
deallocate(dcn, dcndr)
allocate(dEdcn(n),source=0.0_wp)
allocate(considered_ABH(n,n,n), source=.false.)
allocate(considered_ABH(topo%hb_mapNAB,topo%hb_mapNAB,topo%hb_mapNH), source=.false.)

!$omp parallel do default(none) reduction(+:g, ebond, sigma, dEdcn) &
!$omp shared(grab0, topo, neigh, param, rab0, rabdcn, xyz, at, hb_cn, hb_dcn, n, dhbcndL, considered_ABH) &
Expand Down Expand Up @@ -1038,7 +1038,7 @@ subroutine egbond_hb(i,iat,jat,iTr,rab,rij,drij,drijdcn,hb_cn,hb_dcn,n,at,xyz,e,
real*8,intent(in) :: hb_cn(n)
real*8,intent(in) :: hb_dcn(3,n,n)
real(wp), intent(in) :: dhbcndL(3,3,n)
logical, intent(inout) :: considered_ABH(n,n,n) ! only consider ABH triplets once; indep of iTr
logical, intent(inout) :: considered_ABH(topo%hb_mapNAB,topo%hb_mapNAB,topo%hb_mapNH)! only consider ABH triplets once; indep of iTr
real*8,intent(inout) :: e
real*8,intent(inout) :: g(3,n)
real*8,intent(inout) :: sigma(3,3)
Expand All @@ -1048,12 +1048,12 @@ subroutine egbond_hb(i,iat,jat,iTr,rab,rij,drij,drijdcn,hb_cn,hb_dcn,n,at,xyz,e,
integer j,k
integer jA,jH,iTrA,iTrH,iTrB
integer hbH,hbB,hbA
integer mapA,mapB,mapH
real*8 dr,dum
real*8 dx,dy,dz,vrab(3),dg(3)
real*8 yy,zz
real*8 t1,t4,t5,t6,t8


if (at(iat).eq.1) then
hbH=iat
hbA=jat
Expand Down Expand Up @@ -1128,8 +1128,11 @@ subroutine egbond_hb(i,iat,jat,iTr,rab,rij,drij,drijdcn,hb_cn,hb_dcn,n,at,xyz,e,
hbB = topo%bond_hb_B(1,k,j)
iTrB= topo%bond_hb_B(2,k,j)
! only add gradient one time per ABH triple (independent of iTrB)
if(.not.considered_ABH(hbA,hbB,hbH)) then
considered_ABH(hbA,hbB,hbH)=.true.
mapA=topo%hb_mapABH(hbA)
mapB=topo%hb_mapABH(hbB)
mapH=topo%hb_mapABH(hbH)
if(.not.considered_ABH(mapA,mapB,mapH)) then
considered_ABH(mapA,mapB,mapH)=.true.
dg=hb_dcn(:,hbB,hbH)*zz
g(:,hbB)=g(:,hbB)-dg
endif
Expand Down
24 changes: 23 additions & 1 deletion src/gfnff/gfnff_ini.f90
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1422,6 +1422,7 @@ integer function itabrow6(i)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

!Set up fix hblist just like for the HB term
allocate(topo%isABH(mol%n), source=.false.)
call bond_hbset0(mol%n,mol%at,mol%xyz,mol%npbc,bond_hbn,topo,neigh,hbthr1,hbthr2)
allocate(bond_hbl(6,bond_hbn))
allocate(neigh%nr_hb(neigh%nbond), source=0)
Expand All @@ -1430,12 +1431,33 @@ integer function itabrow6(i)
!Set up AH, B and nr. of B list
call bond_hb_AHB_set0(mol%n,mol%at,neigh%nbond,bond_hbn,bond_hbl,AHB_nr,neigh)
allocate( lin_AHB(4,0:AHB_nr), source=0 )
call bond_hb_AHB_set1(mol%n,mol%at,neigh%nbond,bond_hbn,bond_hbl,AHB_nr,lin_AHB,topo%bond_hb_nr,topo%b_max,neigh)
call bond_hb_AHB_set1(mol%n,mol%at,neigh%nbond,bond_hbn,bond_hbl,AHB_nr,lin_AHB,topo%bond_hb_nr,topo%b_max,topo,neigh)
allocate( topo%bond_hb_AH(4,topo%bond_hb_nr), source = 0 )
allocate( topo%bond_hb_B(2,topo%b_max,topo%bond_hb_nr), source = 0 )
allocate( topo%bond_hb_Bn(topo%bond_hb_nr), source = 0 )
call bond_hb_AHB_set(mol%n,mol%at,neigh%nbond,bond_hbn,bond_hbl,AHB_nr,lin_AHB,topo,neigh)

! create mapping from atom index to hb index, for AB and H seperately
allocate(topo%hb_mapABH(mol%n), source=0)
j=0 ! H counter
k=0 ! AB counter
do i=1, mol%n
! check if atom i is A,B, or H
if (topo%isABH(i)) then
! check if it is H
if (mol%at(i).eq.1) then
j = j + 1
topo%hb_mapABH(i) = j
! then it is A or B
else
k = k + 1
topo%hb_mapABH(i) = k
end if
end if
end do
topo%hb_mapNAB=k
topo%hb_mapNH=j

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! bend
Expand Down
6 changes: 5 additions & 1 deletion src/gfnff/gfnff_ini2.f90
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1107,12 +1107,13 @@ subroutine bond_hb_AHB_set(n,at,numbond,bond_hbn,bond_hbl,tot_AHB_nr,lin_AHB,top

end subroutine bond_hb_AHB_set

subroutine bond_hb_AHB_set1(n,at,numbond,bond_hbn,bond_hbl,tot_AHB_nr,lin_AHB,AH_count,bmax,neigh)
subroutine bond_hb_AHB_set1(n,at,numbond,bond_hbn,bond_hbl,tot_AHB_nr,lin_AHB,AH_count,bmax,topo,neigh)
use xtb_gfnff_param
use xtb_gfnff_neighbor
implicit none
!Dummy
type(TNeigh), intent(inout) :: neigh
type(TGFFTopology), intent(inout) :: topo
integer,intent(in) :: n
integer,intent(in) :: numbond
integer,intent(in) :: at(n)
Expand Down Expand Up @@ -1172,6 +1173,7 @@ subroutine bond_hb_AHB_set1(n,at,numbond,bond_hbn,bond_hbl,tot_AHB_nr,lin_AHB,AH
lin_AHB(2,tot_count) = hbH
lin_AHB(3,tot_count) = iTrA
lin_AHB(4,tot_count) = iTrH
topo%isABH(Bat)=.true.
if (lin_AHB(1,tot_count)-lin_AHB(1,tot_count-1).eq.0.and.&
&lin_AHB(2,tot_count)-lin_AHB(2,tot_count-1).eq.0) then
lin_diff=0
Expand All @@ -1190,6 +1192,8 @@ subroutine bond_hb_AHB_set1(n,at,numbond,bond_hbn,bond_hbl,tot_AHB_nr,lin_AHB,AH
cycle
end if
end do
topo%isABH(hbA)=.true.
topo%isABH(hbH)=.true.
neigh%nr_hb(i) = B_count
end if
end do
Expand Down
4 changes: 4 additions & 0 deletions src/gfnff/topology.f90
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,10 @@ module xtb_gfnff_topology
real(wp),allocatable:: qfrag (:) ! fragment charge (for EEQ)
real(wp),allocatable:: hbbas (:) ! HB donor atom basicity
real(wp),allocatable:: hbaci (:) ! HB acceptor atom acidity
integer, allocatable:: hb_mapABH(:) ! mapping of indices from all atoms to only AB and H separately
logical, allocatable:: isABH(:) ! logical set to true if the atom is part of a hydrogen bond
integer :: hb_mapNAB ! number of AB atoms that are part of a hydrogen bond
integer :: hb_mapNH ! number of H atoms that are part of a hydrogen bond

integer, allocatable :: ispinsyst(:,:)
integer, allocatable :: nspinsyst(:)
Expand Down
8 changes: 8 additions & 0 deletions src/restart.f90
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -125,11 +125,14 @@ subroutine read_restart_gff(env,fname,n,version,success,verbose,topo,neigh)
& topo%natxbAB,topo%nbatm,topo%nfrag,topo%nsystem,topo%maxsystem
read(ich) topo%nbond_blist,topo%nbond_vbond,topo%nangl_alloc,topo%ntors_alloc,topo%bond_hb_nr,topo%b_max
read(ich) neigh%numnb, neigh%numctr, neigh%nbond, neigh%iTrDim
read(ich) topo%hb_mapNAB, topo%hb_mapNH
topo%nbond = neigh%nbond
call gfnff_param_alloc(topo,neigh, n)
if (.not.allocated(topo%ispinsyst)) allocate( topo%ispinsyst(n,topo%maxsystem), source = 0 )
if (.not.allocated(topo%nspinsyst)) allocate( topo%nspinsyst(topo%maxsystem), source = 0 )
if (.not.allocated(neigh%nr_hb)) allocate(neigh%nr_hb(neigh%nbond))
if (.not.allocated(topo%hb_mapABH)) allocate(topo%hb_mapABH(n))
if (.not.allocated(topo%isABH)) allocate(topo%isABH(n))
read(ich) neigh%blist
read(ich) topo%alist
read(ich) topo%tlist
Expand All @@ -145,6 +148,8 @@ subroutine read_restart_gff(env,fname,n,version,success,verbose,topo,neigh)
read(ich) topo%bond_hb_B
read(ich) topo%bond_hb_Bn
read(ich) neigh%nr_hb
read(ich) topo%hb_mapABH
read(ich) topo%isABH
read(ich) topo%vangl,topo%vtors,topo%chieeq, &
& topo%gameeq,topo%alpeeq,topo%alphanb,topo%qa, &
& topo%xyze0,topo%zetac6,&
Expand Down Expand Up @@ -214,6 +219,7 @@ subroutine write_restart_gff(env,fname,nat,version,topo,neigh)
& topo%natxbAB,topo%nbatm,topo%nfrag,topo%nsystem, topo%maxsystem
write(ich) topo%nbond_blist,topo%nbond_vbond,topo%nangl_alloc,topo%ntors_alloc,topo%bond_hb_nr,topo%b_max
write(ich) neigh%numnb, neigh%numctr, neigh%nbond, neigh%iTrDim
write(ich) topo%hb_mapNAB, topo%hb_mapNH
!Arrays Integers
write(ich) neigh%blist
write(ich) topo%alist
Expand All @@ -230,6 +236,8 @@ subroutine write_restart_gff(env,fname,nat,version,topo,neigh)
write(ich) topo%bond_hb_B
write(ich) topo%bond_hb_Bn
write(ich) neigh%nr_hb
write(ich) topo%hb_mapABH
write(ich) topo%isABH
!Arrays Reals
write(ich) topo%vangl,topo%vtors,topo%chieeq,&
& topo%gameeq,topo%alpeeq,topo%alphanb,topo%qa, &
Expand Down
Loading