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Reduce memory usage in egbond_hb
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@Thomas3R
Thomas3R committed Mar 14, 2024
1 parent e13cbfb commit f467c74
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Showing 5 changed files with 48 additions and 7 deletions.
13 changes: 8 additions & 5 deletions src/gfnff/gfnff_eg.f90
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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
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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
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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
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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(:)
logical, allocatable:: isABH(:)
integer :: hb_mapNAB
integer :: hb_mapNH

integer, allocatable :: ispinsyst(:,:)
integer, allocatable :: nspinsyst(:)
Expand Down
8 changes: 8 additions & 0 deletions src/restart.f90
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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

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