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reax_connect.F
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**********************************************************************
* *
* REAXFF Reactive force field program *
* *
* Developed and written by Adri van Duin, duin@wag.caltech.edu *
* *
* Copyright (c) 2001-2010 California Institute of Technology *
* *
* This is an open-source program. Feel free to modify its *
* contents. Please keep me informed of any useful modification *
* or addition that you made. Please do not distribute this *
* program to others; if people are interested in obtaining *
* a copy of this program let them contact me first. *
* *
**********************************************************************
**********************************************************************
subroutine srtatom
**********************************************************************
#include "cbka.blk"
#include "cbkatomcoord.blk"
#include "cbkff.blk"
#include "cbkia.blk"
#include "cbkqa.blk"
#include "control.blk"
#include "opt.blk"
#include "small.blk"
**********************************************************************
* *
* Determine atom types in system *
* *
**********************************************************************
* Requires the following variables
* ndebug - opt.blk; determines whether to debug or not; everywhere
* xmasmd - cbka.blk; some sort of atmoic mass?; srtatom, reac.f
* molin - opt.blk; keeps info on?; srtatom
* nso - cbka.blk; number of atoms?; srtatom, inout.f
* nprob - cbka.blk; does?; connect.f, inout.f, reac.f
* nasort - cbka.blk; a sorting array; srtatom
* ia - cbka.blk; atom numbers?; poten.f, inout.f, connect.f, charges.f
* iag - cbka.blk; ; connect.f, inout.f, poten.f, reac.f
* xmasat - cbka.blk; does?; srtatom, reac.f
* amas - cbka.blk; ? ; srtatom, ffinpt, molanal, ovcor
* qa - cbka.blk; some sort of error statement variable?; srtatom, srtbon1, inout.f, radbo
*
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In srtatom'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
xmasmd=0.0
do i1=1,nso
molin(nprob,i1)=0
nasort(i1)=0
end do
do i1=1,na
ia(i1,1)=0
iag(i1,1)=0
do i2=1,nso
if (qa(i1).eq.qas(i2)) then
ia(i1,1)=i2
iag(i1,1)=i2
molin(nprob,i2)=molin(nprob,i2)+1
xmasat(i1)=amas(i2)
xmasmd=xmasmd+amas(i2)
nasort(i2)=nasort(i2)+1
end if
end do
if (ia(i1,1).eq.0) then
write (*,*)'Unknown atom type: ',qa(i1)
stop 'Unknown atom type'
end if
end do
return
end
**********************************************************************
**********************************************************************
subroutine molec
**********************************************************************
#include "cbka.blk"
#include "cbkdcell.blk"
#include "cbkff.blk"
#include "cbkia.blk"
#include "cbkmolec.blk"
#include "cbknmolat.blk"
#include "control.blk"
#include "small.blk"
dimension nmolo2(nat),iseen(nmolmax),isee2(nmolmax)
**********************************************************************
* *
* Determine changes in molecules *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In molec'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
npreac=0
do i1=1,nmolo
natmol=0
do i2=1,na
if (ia(i2,3+mbond).eq.i1) then
natmol=natmol+1
nmolat(i1,natmol+1)=i2
end if
end do
nmolat(i1,1)=natmol
end do
if (nmolo5.lt.nmolo5o) nradcount=0 !reset reaction counter
do i1=1,nmolo5
natmol=0
do i2=1,na
if (iag(i2,3+mbond).eq.i1) then
natmol=natmol+1
nmolat2(i1,natmol+1)=i2
end if
end do
nmolat2(i1,1)=natmol
end do
nmolo5o=nmolo5
do i1=nmolo+1,nmoloold
do i2=1,nmolat(i1,1)
nmolat(i1,1+i2)=0
end do
nmolat(i1,1)=0
end do
do i1=1,nmolo
elmol(i1)=0.0
do i2=1,nmolat(i1,1)
ihu=nmolat(i1,i2+1)
ity=ia(ihu,1)
elmol(i1)=elmol(i1)+stlp(ity)
end do
end do
do i1=1,nmolo5
elmol2(i1)=0.0
do i2=1,nmolat2(i1,1)
ihu=nmolat2(i1,i2+1)
ity=iag(ihu,1)
elmol2(i1)=elmol2(i1)+stlp(ity)
end do
end do
return
end
**********************************************************************
**********************************************************************
subroutine dista2 (n1,n2,dista,dx,dy,dz)
**********************************************************************
#include "cbka.blk"
#include "cbkc.blk"
**********************************************************************
* *
* Determine interatomic distances *
* *
**********************************************************************
c$$$* if (ndebug.eq.1) then
c$$$C* open (65,file='fort.65',status='unknown',access='append')
c$$$* write (65,*) 'In dista2'
c$$$* call timer(65)
c$$$* close (65)
c$$$* end if
dx=c(n1,1)-c(n2,1)
dy=c(n1,2)-c(n2,2)
dz=c(n1,3)-c(n2,3)
dista=sqrt(dx*dx+dy*dy+dz*dz)
return
end
**********************************************************************
**********************************************************************
subroutine srtbon1(lprune,lhb,hbcut_in,lhbnew_in,ltripstaball_in)
**********************************************************************
#include "cbka.blk"
#include "cbkabo.blk"
#include "cbkbo.blk"
#include "cbkbosi.blk"
#include "cbkbopi.blk"
#include "cbkbopi2.blk"
#include "cbkc.blk"
#include "cbkch.blk"
#include "cbkconst.blk"
#include "cbkdbopidc.blk"
#include "cbkdrdc.blk"
#include "cbkia.blk"
#include "cbknubon2.blk"
#include "cbknvlbo.blk"
#include "cbkpairs.blk"
#include "cbknvlown.blk"
#include "cbkqa.blk"
#include "cbkrbo.blk"
#include "cellcoord.blk"
#include "control.blk"
#include "small.blk"
#include "cbkdbodc.blk"
#include "cbksrtbon1.blk"
#include "cbkff.blk"
#include "cbksrthb.blk"
#include "cbkcovbon.blk"
logical found
integer nboncol(nboallmax)
integer iball(nboallmax,3)
**********************************************************************
* *
* Determine connections within the molecule *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In srtbon1'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
c Transfer hbcut, lhbnew, and ltripstaball from C++ calling function
hbcut = hbcut_in
lhbnew = lhbnew_in
ltripstaball = ltripstaball_in
do i1=1,na
abo(i1)=0.0d0
end do
nbonall=0
nbon2=0
nsbmax=0
nsbma2=0
if (imolde.eq.0) then
nmolo=0
nmolo5=0
end if
if (imolde.eq.0) then
do i1=1,na
do i2=2,mbond+3
ia(i1,i2)=0
iag(i1,i2)=0
end do
end do
else
do i1=1,na
do i2=2,mbond+2
ia(i1,i2)=0
iag(i1,i2)=0
end do
end do
end if
do i1=1,na
do i2=1,mbond
nubon1(i1,i2)=0
nubon2(i1,i2)=0
end do
end do
* First detect all bonds and create preliminary list
do 11 ivl=1,nvpair
if (nvlbo(ivl).eq.0) goto 11 !not in bond order range
i1=nvl1(ivl)
i2=nvl2(ivl)
call dista2(i1,i2,dis,dxm,dym,dzm)
ih1=ia(i1,1)
ih2=ia(i2,1)
disdx=dxm/dis
disdy=dym/dis
disdz=dzm/dis
itype=0
if (ih1.gt.ih2) then
ih1=ia(i2,1)
ih2=ia(i1,1)
end if
do i3=1,nboty2
if (ih1.eq.nbs(i3,1).and.ih2.eq.nbs(i3,2)) itype=i3
end do
if (itype.eq.0.and.rat(ih1).gt.zero.and.rat(ih2).gt.zero) then
c$$$ call mdsav(1,qfile(nprob))
write (*,*)qa(i1),'-',qa(i2),'Fatal: Unknown bond in molecule'
stop
end if
rhulp=dis/rob1(ih1,ih2)
**********************************************************************
* *
* Determine bond orders *
* *
**********************************************************************
rh2=zero
rh2p=zero
rh2pp=zero
ehulp=zero
ehulpp=zero
ehulppp=zero
if (rapt(ih1).gt.zero.and.rapt(ih2).gt.zero) then
rhulp2=dis/rob2(ih1,ih2)
rh2p=rhulp2**ptp(itype)
ehulpp=exp(pdp(itype)*rh2p)
end if
if (vnq(ih1).gt.zero.and.vnq(ih2).gt.zero) then
rhulp3=dis/rob3(ih1,ih2)
rh2pp=rhulp3**popi(itype)
ehulppp=exp(pdo(itype)*rh2pp)
end if
if (rat(ih1).gt.zero.and.rat(ih2).gt.zero) then
rh2=rhulp**bop2(itype)
ehulp=(1.0+cutoff)*exp(bop1(itype)*rh2)
end if
bor=ehulp+ehulpp+ehulppp
j1=i1
j2=i2
**********************************************************************
* *
* Determine bond orders *
* *
**********************************************************************
if (bor.gt.cutoff) then
nbonall=nbonall+1
if (nbonall.gt.nboallmax) then
write (6,*)'nbonall = ',nbonall,
$ ' reax_defs.h::NBOALLMAXDEF = ',NBOALLMAXDEF,
$ ' after',ivl, ' of ',nvpair,' pairs completed.'
stop 'Too many bonds; maybe wrong cell parameters.'
end if
iball(nbonall,1)=itype
iball(nbonall,2)=j1
iball(nbonall,3)=j2
ia(i1,2)=ia(i1,2)+1
if (ia(i1,2).gt.mbond) then
write (6,*)'ia(i1,2) = ',ia(i1,2),
$ ' reax_defs.h::MBONDDEF = ',MBONDDEF,
$ ' after',ivl, ' of ',nvpair,' pairs completed.'
stop 'Too many bonds on atom. Increase MBONDDEF'
end if
if (i1.ne.i2) then
ia(i2,2)=ia(i2,2)+1
if (ia(i2,2).gt.mbond) then
write (6,*)'ia(i1,2) = ',ia(i1,2),
$ ' reax_defs.h::MBONDDEF = ',MBONDDEF,
$ ' after',ivl, ' of ',nvpair,' pairs completed.'
stop 'Too many bonds on atom. Increase MBONDDEF'
end if
endif
ia(i1,ia(i1,2)+2)=i2
ia(i2,ia(i2,2)+2)=i1
if (abs(de1(iball(nbonall,1))).gt.-0.01) then
nubon2(i1,ia(i1,2))=nbonall
nubon2(i2,ia(i2,2))=nbonall
else
nbonall=nbonall-1 !Inorganics
end if
end if
11 continue
**********************************************************************
* *
* lprune controls level of bond-pruning performed to increase *
* performance. For correct results, it should be set to 4. *
* However, making it smaller can speed up *
* force calculation and may not have a big effect on forces. *
* Setting it to 0 turns off pruning, useful for debugging. *
* *
**********************************************************************
*********************************************************************
* *
* lhb controls whether or not to unprune ghost bonds that *
* may possibly form ghost hydrogen bonds. *
* Setting it to 1 causes unpruning, and so is the safe option. *
* If lprune = 0, then pruning is not used, results are exact *
* and lhb has no effect. *
* *
**********************************************************************
if (lprune .gt. 0) then
**********************************************************************
* *
* Eliminate bonds that are not in 1-6 interaction *
* with local atom, or closer. *
* Need additional sweep to catch possible hydrogen bonds *
* *
**********************************************************************
ntmp0 = 0
ntmp1 = 0
ntmp2 = 0
ntmp3 = 0
ntmp4 = 0
ntmp5 = 0
ntmp6 = 0
ntmphb = 0
* color 1 are bonds with two local atoms
* color 2 are bonds with one local atom
* color 3 are bonds adjacent to bond with one local atom
do i1 = 1,nbonall
if (iball(i1,2).le.na_local) then
if (iball(i1,3).le.na_local) then
nboncol(i1) = 1
ntmp1 = ntmp1+1
else
nboncol(i1) = 2
ntmp2 = ntmp2+1
endif
else if (iball(i1,3).le.na_local) then
nboncol(i1) = 2
ntmp2 = ntmp2+1
else
nboncol(i1) = 0
endif
end do
if (lprune .ge. 3) then
do i1 = 1,nbonall
if (nboncol(i1).eq.2) then
if (iball(i1,2).le.na_local) then
i3=iball(i1,3)
else
i3=iball(i1,2)
endif
do i4 = 1,ia(i3,2)
i5=nubon2(i3,i4)
if (nboncol(i5).eq.0) then
nboncol(i5)=3
ntmp3 = ntmp3+1
endif
end do
endif
end do
endif
* color 4 bonds are part of a 1-4 interaction with local atom
if (lprune .ge. 4) then
do i1 = 1,nbonall
if (nboncol(i1).eq.3) then
* One end definitely has a bond of color 2
* Find it and color bonds on other end 4
i3=iball(i1,2)
i3b=0
do i4 = 1,ia(i3,2)
i5=nubon2(i3,i4)
if (nboncol(i5).eq.2) then
i3b=iball(i1,3)
endif
end do
if (i3b.eq.0) then
i3=iball(i1,3)
i3b=0
do i4 = 1,ia(i3,2)
i5=nubon2(i3,i4)
if (nboncol(i5).eq.2) then
i3b=iball(i1,2)
endif
end do
endif
if (i3b.eq.0) then
stop 'Could not find color 2 from color 3 bond'
endif
do i4 = 1,ia(i3b,2)
i5=nubon2(i3b,i4)
if (nboncol(i5).eq.0) then
nboncol(i5)=4
ntmp4 = ntmp4+1
endif
end do
endif
end do
endif
* color 5 bonds are part of a 1-5 interaction with local atom
if (lprune .ge. 5) then
do i1 = 1,nbonall
if (nboncol(i1).eq.4) then
* One end definitely has a bond of color 3
* Find it and color bonds on other end 5
i3=iball(i1,2)
i3b=0
do i4 = 1,ia(i3,2)
i5=nubon2(i3,i4)
if (nboncol(i5).eq.3) then
i3b=iball(i1,3)
endif
end do
if (i3b.eq.0) then
i3=iball(i1,3)
i3b=0
do i4 = 1,ia(i3,2)
i5=nubon2(i3,i4)
if (nboncol(i5).eq.3) then
i3b=iball(i1,2)
endif
end do
endif
if (i3b.eq.0) then
stop 'Could not find color 3 from color 4 bond'
endif
do i4 = 1,ia(i3b,2)
i5=nubon2(i3b,i4)
if (nboncol(i5).eq.0) then
nboncol(i5)=5
ntmp5 = ntmp5+1
endif
end do
endif
end do
endif
* color 6 bonds are part of a 1-6 interaction with local atom
if (lprune .ge. 6) then
do i1 = 1,nbonall
if (nboncol(i1).eq.5) then
* One end definitely has a bond of color 4
* Find it and color bonds on other end 6
i3=iball(i1,2)
i3b=0
do i4 = 1,ia(i3,2)
i5=nubon2(i3,i4)
if (nboncol(i5).eq.4) then
i3b=iball(i1,3)
endif
end do
if (i3b.eq.0) then
i3=iball(i1,3)
i3b=0
do i4 = 1,ia(i3,2)
i5=nubon2(i3,i4)
if (nboncol(i5).eq.4) then
i3b=iball(i1,2)
endif
end do
endif
if (i3b.eq.0) then
stop 'Could not find color 4 from color 5 bond'
endif
do i4 = 1,ia(i3b,2)
i5=nubon2(i3b,i4)
if (nboncol(i5).eq.0) then
nboncol(i5)=6
ntmp6 = ntmp6+1
endif
end do
endif
end do
endif
* Catch all the possible hydrogen bonds
* This section replicates the logic used in srthb()
if (lhb .eq. 1) then
c Outer loop must be Verlet list, because ia() does not store Verlet entries,
c but it does store bond entries in nubon2()
do ivl=1,nvpair !Use Verlet-list to find donor-acceptor pairs
j1=nvl1(ivl)
j2=nvl2(ivl)
ihhb1=nphb(ia(j1,1))
ihhb2=nphb(ia(j2,1))
if (ihhb1.gt.ihhb2) then !Make j1 donor(H) atom and j2 acceptor(O) atom
j2=nvl1(ivl)
j1=nvl2(ivl)
ihhb1=nphb(ia(j1,1))
ihhb2=nphb(ia(j2,1))
end if
* Only need to compute bonds where j1 is local
if (j1 .le. na_local) then
if (ihhb1.eq.1.and.ihhb2.eq.2) then
call dista2(j1,j2,dishb,dxm,dym,dzm)
if (dishb.lt.hbcut) then
do i23=1,ia(j1,2) !Search for acceptor atoms bound to donor atom
if (nboncol(nubon2(j1,i23)).eq.0) then
j3=ia(j1,2+i23)
if (nphb(ia(j3,1)).eq.2.and.j3.ne.j2) then
nboncol(nubon2(j1,i23))=-1
ntmphb = ntmphb+1
endif
endif
end do
end if
end if
end if
end do
end if
* Compact the list, removing all uncolored bonds
nbon = 0
do i1 = 1,nbonall
if (nboncol(i1).eq.0) then
ntmp0=ntmp0+1
else
nbon = nbon+1
if (nbon.gt.nbomax) then
write (6,*)nbon,nbomax
write (6,*)'nbon = ',nbon,' reax_defs.h::NBOMAXDEF = ',
$ NBOMAXDEF,' after',i1, ' of ',nbonall,
$ ' initial bonds completed.'
stop 'Too many pruned bonds; increase NBOMAXDEF'
end if
ib(nbon,1) = iball(i1,1)
ib(nbon,2) = iball(i1,2)
ib(nbon,3) = iball(i1,3)
endif
end do
**********************************************************************
* *
* Do not perform ghost-bond pruning *
* *
**********************************************************************
else
nbon = 0
do i1 = 1,nbonall
nbon = nbon+1
if (nbon.gt.nbomax) then
write (6,*)nbon,nbomax
write (6,*)'nbon = ',nbon,' reax_defs.h::NBOMAXDEF = ',
$ NBOMAXDEF,' after',i1, ' of ',nbonall,
$ ' initial bonds completed.'
stop 'Too many pruned bonds; increase NBOMAXDEF'
end if
ib(nbon,1) = iball(i1,1)
ib(nbon,2) = iball(i1,2)
ib(nbon,3) = iball(i1,3)
end do
endif
do i1=1,na
do i2=2,mbond+2
ia(i1,i2)=0
iag(i1,i2)=0
end do
end do
* Generate full set of bond data structures
do 10 i0 = 1,nbon
i1 = ib(i0,2)
i2 = ib(i0,3)
call dista2(i1,i2,dis,dxm,dym,dzm)
* do 10 i1=1,na-1
* do 10 i2=i1+1,na
* call dista2(i1,i2,dis,dxm,dym,dzm)
ih1=ia(i1,1)
ih2=ia(i2,1)
* if (dis.gt.5.0*rob) goto 10
disdx=dxm/dis
disdy=dym/dis
disdz=dzm/dis
itype=0
if (ih1.gt.ih2) then
ih1=ia(i2,1)
ih2=ia(i1,1)
end if
do i3=1,nboty2
if (ih1.eq.nbs(i3,1).and.ih2.eq.nbs(i3,2)) itype=i3
end do
if (itype.eq.0.and.rat(ih1).gt.zero.and.rat(ih2).gt.zero) then
c$$$ call mdsav(1,qfile(nprob))
write (*,*)qa(i1),'-',qa(i2),'Fatal: Unknown bond in molecule'
stop
end if
rhulp=dis/rob1(ih1,ih2)
**********************************************************************
* *
* Determine bond orders *
* *
**********************************************************************
rh2=zero
rh2p=zero
rh2pp=zero
ehulp=zero
ehulpp=zero
ehulppp=zero
if (rapt(ih1).gt.zero.and.rapt(ih2).gt.zero) then
rhulp2=dis/rob2(ih1,ih2)
rh2p=rhulp2**ptp(itype)
ehulpp=exp(pdp(itype)*rh2p)
end if
if (vnq(ih1).gt.zero.and.vnq(ih2).gt.zero) then
rhulp3=dis/rob3(ih1,ih2)
rh2pp=rhulp3**popi(itype)
ehulppp=exp(pdo(itype)*rh2pp)
end if
if (rat(ih1).gt.zero.and.rat(ih2).gt.zero) then
rh2=rhulp**bop2(itype)
ehulp=(1.0+cutoff)*exp(bop1(itype)*rh2)
end if
bor=ehulp+ehulpp+ehulppp
borsi=ehulp
borpi=ehulpp
borpi2=ehulppp
dbordrob=bop2(itype)*bop1(itype)*rh2*(1.0/dis)*ehulp+
$ptp(itype)*pdp(itype)*rh2p*(1.0/dis)*ehulpp+
$popi(itype)*pdo(itype)*rh2pp*(1.0/dis)*ehulppp
dborsidrob=bop2(itype)*bop1(itype)*rh2*(1.0/dis)*ehulp
dborpidrob=ptp(itype)*pdp(itype)*rh2p*(1.0/dis)*ehulpp
dborpi2drob=popi(itype)*pdo(itype)*rh2pp*(1.0/dis)*ehulppp
nbon2=nbon2+1
j1=i1
j2=i2
**********************************************************************
* *
* Determine bond orders *
* *
**********************************************************************
ib(i0,1)=itype
ib(i0,2)=j1
ib(i0,3)=j2
ibsym(i0)=ivl
drdc(i0,1,1)=disdx
drdc(i0,2,1)=disdy
drdc(i0,3,1)=disdz
drdc(i0,1,2)=-disdx
drdc(i0,2,2)=-disdy
drdc(i0,3,2)=-disdz
abo(i1)=abo(i1)+bor-cutoff
if (i1.ne.i2) abo(i2)=abo(i2)+bor-cutoff
bo(i0)=bor-cutoff
bos(i0)=bor-cutoff
bosi(i0)=borsi-cutoff
bopi(i0)=borpi
bopi2(i0)=borpi2
rbo(i0)=dis
dbodr(i0)=dbordrob
* dbosidr(i0)=dborsidrob
dbopidr(i0)=dborpidrob
dbopi2dr(i0)=dborpi2drob
dbodc(i0,1,1)=dbodr(i0)*drdc(i0,1,1)
dbodc(i0,2,1)=dbodr(i0)*drdc(i0,2,1)
dbodc(i0,3,1)=dbodr(i0)*drdc(i0,3,1)
dbodc(i0,1,2)=dbodr(i0)*drdc(i0,1,2)
dbodc(i0,2,2)=dbodr(i0)*drdc(i0,2,2)
dbodc(i0,3,2)=dbodr(i0)*drdc(i0,3,2)
* dbosidc(i0,1,1)=dbosidr(i0)*drdc(i0,1,1)
* dbosidc(i0,2,1)=dbosidr(i0)*drdc(i0,2,1)
* dbosidc(i0,3,1)=dbosidr(i0)*drdc(i0,3,1)
* dbosidc(i0,1,2)=dbosidr(i0)*drdc(i0,1,2)
* dbosidc(i0,2,2)=dbosidr(i0)*drdc(i0,2,2)
* dbosidc(i0,3,2)=dbosidr(i0)*drdc(i0,3,2)
dbopidc(i0,1,1)=dbopidr(i0)*drdc(i0,1,1)
dbopidc(i0,2,1)=dbopidr(i0)*drdc(i0,2,1)
dbopidc(i0,3,1)=dbopidr(i0)*drdc(i0,3,1)
dbopidc(i0,1,2)=dbopidr(i0)*drdc(i0,1,2)
dbopidc(i0,2,2)=dbopidr(i0)*drdc(i0,2,2)
dbopidc(i0,3,2)=dbopidr(i0)*drdc(i0,3,2)
dbopi2dc(i0,1,1)=dbopi2dr(i0)*drdc(i0,1,1)
dbopi2dc(i0,2,1)=dbopi2dr(i0)*drdc(i0,2,1)
dbopi2dc(i0,3,1)=dbopi2dr(i0)*drdc(i0,3,1)
dbopi2dc(i0,1,2)=dbopi2dr(i0)*drdc(i0,1,2)
dbopi2dc(i0,2,2)=dbopi2dr(i0)*drdc(i0,2,2)
dbopi2dc(i0,3,2)=dbopi2dr(i0)*drdc(i0,3,2)
ia(i1,2)=ia(i1,2)+1
if (i1.ne.i2) ia(i2,2)=ia(i2,2)+1
ia(i1,ia(i1,2)+2)=i2
ia(i2,ia(i2,2)+2)=i1
if (ia(i1,2).gt.nsbma2) nsbma2=ia(i1,2)
if (ia(i2,2).gt.nsbma2) nsbma2=ia(i2,2)
if (bor.gt.cutof3) then
iag(i1,2)=iag(i1,2)+1
iag(i2,2)=iag(i2,2)+1
iag(i1,iag(i1,2)+2)=i2
iag(i2,iag(i2,2)+2)=i1
nubon1(i1,iag(i1,2))=i0
nubon1(i2,iag(i2,2))=i0
if (iag(i1,2).gt.nsbmax) nsbmax=iag(i1,2)
if (iag(i2,2).gt.nsbmax) nsbmax=iag(i2,2)
end if
nubon2(i1,ia(i1,2))=i0
nubon2(i2,ia(i2,2))=i0
10 continue
**********************************************************************
* *
* Sort molecules *
* *
**********************************************************************
imolde = 1
if (imolde.eq.1) return !fixed molecular definitions
FOUND=.FALSE.
DO 31 K1=1,NA
IF (IA(K1,3+mbond).EQ.0) FOUND=.TRUE.
31 IF (IA(K1,3+mbond).GT.NMOLO) NMOLO=IA(K1,3+mbond)
IF (.NOT.FOUND) GOTO 32
************************************************************************
* *
* Molecule numbers are assigned. No restrictions are made for the *
* sequence of the numbers in the connection table. *
* *
************************************************************************
N3=1
34 N2=N3
NMOLO=NMOLO+1
if (nmolo.gt.nmolmax) then
write (*,*)nmolmax
write (*,*)'Too many molecules in system; increase nmolmax'
write (*,*)'nmolmax = ',nmolmax
write (*,*)'nmolo = ',nmolo
write (*,*)'n2 = ',n2
stop 'Too many molecules in system'
end if
IA(N2,3+mbond)=NMOLO
37 FOUND=.FALSE.
DO 36 N1=N2+1,NA
IF (IA(N1,3+mbond).NE.0) GOTO 36
DO 35 L=1,mbond
IF (IA(N1,l+2).EQ.0) GOTO 36
IF (IA(IA(N1,l+2),3+mbond).EQ.NMOLO) THEN
FOUND=.TRUE.
IA(N1,3+mbond)=NMOLO
GOTO 36
ENDIF
35 CONTINUE
36 CONTINUE
IF (FOUND) GOTO 37
DO 33 N3=N2+1,NA
33 IF (IA(N3,3+mbond).EQ.0) GOTO 34
************************************************************************
* *
* The assigned or input molecule numbers are checked for their *
* consistency. *
* *
************************************************************************
32 FOUND=.FALSE.
DO 42 N1=1,NA
DO 41 L=1,mbond
IF (IA(N1,L+2).EQ.0) GOTO 42
IF (IA(IA(N1,L+2),3+mbond).NE.IA(N1,3+mbond)) THEN
FOUND=.TRUE.
ENDIF
41 CONTINUE
42 CONTINUE
IF (FOUND) THEN
write (7,1000)NA,qmol
do i1=1,NA
write (7,1100)i1,ia(i1,1),(ia(i1,2+i2),i2=1,nsbmax),
$ia(i1,3+mbond)
end do
write (7,*)tm11,tm22,tm33,angle(1),angle(2),angle(3)
STOP' Mol.nrs. not consistent; maybe wrong cell parameters'
end if
**********************************************************************
* *
* Sort molecules again *
* This sort is on iag, enforces bond order cutoff *
* *
**********************************************************************
FOUND=.FALSE.
DO 61 K1=1,NA
IF (IAG(K1,3+mbond).EQ.0) FOUND=.TRUE.
61 IF (IAG(K1,3+mbond).GT.NMOLO5) NMOLO5=IAG(K1,3+mbond)
IF (.NOT.FOUND) GOTO 62
************************************************************************
* *
* Molecule numbers are assigned. No restrictions are made for the *
* sequence of the numbers in the connection table. *
* *
************************************************************************
N3=1
64 N2=N3
NMOLO5=NMOLO5+1
if (nmolo5.gt.nmolmax) stop 'Too many molecules in system'
IAG(N2,3+mbond)=NMOLO5
67 FOUND=.FALSE.
DO 66 N1=N2+1,NA
IF (IAG(N1,3+mbond).NE.0) GOTO 66
DO 65 L=1,mbond
IF (IAG(N1,l+2).EQ.0) GOTO 66
IF (IAG(IAG(N1,l+2),3+mbond).EQ.NMOLO5) THEN
FOUND=.TRUE.
IAG(N1,3+mbond)=NMOLO5
GOTO 66
ENDIF
65 CONTINUE
66 CONTINUE
IF (FOUND) GOTO 67
DO 63 N3=N2+1,NA
63 IF (IAG(N3,3+mbond).EQ.0) GOTO 64
************************************************************************
* *
* The assigned or input molecule numbers are checked for their *
* consistency. *
* *
************************************************************************
62 FOUND=.FALSE.
DO 72 N1=1,NA
DO 71 L=1,mbond
IF (IAG(N1,L+2).EQ.0) GOTO 72
IF (IAG(IAG(N1,L+2),3+mbond).NE.IAG(N1,3+mbond)) THEN
FOUND=.TRUE.
ENDIF
71 CONTINUE
72 CONTINUE
IF (FOUND) THEN
write (7,1000)NA,qmol
do i1=1,NA
write (7,1100)i1,iag(i1,1),(iag(i1,2+i2),i2=1,nsbmax),
$iag(i1,3+mbond)
end do
write (7,*)tm11,tm22,tm33,angle(1),angle(2),angle(3)
STOP' Mol.nrs. not consistent; maybe wrong cell parameters'
ENDIF
**********************************************************************
* *
* Format part *
* *
**********************************************************************
1000 format (i3,2x,a60)
1100 format (8i3)
end
**********************************************************************
**********************************************************************
subroutine srtang
**********************************************************************
#include "cbka.blk"
#include "cbkbo.blk"
#include "cbknubon2.blk"
#include "cbkff.blk"
#include "cbkia.blk"
#include "cbkrbo.blk"
#include "cbkvalence.blk"
#include "cellcoord.blk"
#include "control.blk"
#include "small.blk"
dimension a(3),b(3),j(3)
dimension ityva(100)
**********************************************************************
* *
* Find valency angles in molecule *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In srtang'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
nval=0
if (nvaty.eq.0) return
do iindexatom=1,na
inumbonds=ia(iindexatom,2)
do jindexbond=1,inumbonds-1
jindexbondlist = nubon2(iindexatom,jindexbond)
if (bo(jindexbondlist).lt.cutof2) goto 51
k4=ib(jindexbondlist,2)
k5=ib(jindexbondlist,3)
do kindexbond=jindexbond+1,inumbonds
kindexbondlist = nubon2(iindexatom,kindexbond)
iju=0
if (bo(kindexbondlist).lt.cutof2) goto 50
if (bo(jindexbondlist)*bo(kindexbondlist).lt.0.001) goto 50
k7=ib(kindexbondlist,2)
k8=ib(kindexbondlist,3)
* Exclude angles that have no local atoms.
* Angles with non-local center atom are not needed for angle
* energies, but are needed to construct torsions.
if ( k4 .le. na_local .or.
$ k5 .le. na_local .or.
$ k7 .le. na_local .or.
$ k8 .le. na_local) then
if (k4.eq.k7.and.k5.eq.k8.and.k4.ne.k8.and.k5.ne.k7) then
nval=nval+1
iv(nval,2)=k5
iv(nval,3)=k4
iv(nval,4)=k8
iv(nval,5)=jindexbondlist
iv(nval,6)=kindexbondlist
nval=nval+1
iv(nval,2)=k4
iv(nval,3)=k5
iv(nval,4)=k7
iv(nval,5)=jindexbondlist
iv(nval,6)=kindexbondlist
iju=2
write(6,*) 'Aaaah!'
end if
if (iju.eq.2) goto 50
if (k4.eq.k8.and.k5.eq.k7.and.k4.ne.k7.and.k5.ne.k8) then
nval=nval+1
iv(nval,2)=k5
iv(nval,3)=k4
iv(nval,4)=k7
iv(nval,5)=jindexbondlist
iv(nval,6)=kindexbondlist
nval=nval+1
iv(nval,2)=k4
iv(nval,3)=k5
iv(nval,4)=k8
iv(nval,5)=jindexbondlist
iv(nval,6)=kindexbondlist
iju=2
write(6,*) 'Aaaah!'
end if
if (iju.eq.2) goto 50
if (k4.eq.k7) then
nval=nval+1
iv(nval,2)=k5
iv(nval,3)=k4
iv(nval,4)=k8
iv(nval,5)=jindexbondlist
iv(nval,6)=kindexbondlist
iju=1
end if
if (iju.eq.1) goto 50
if (k4.eq.k8) then
nval=nval+1
iv(nval,2)=k5
iv(nval,3)=k4
iv(nval,4)=k7
iv(nval,5)=jindexbondlist
iv(nval,6)=kindexbondlist
iju=1
end if
if (iju.eq.1) goto 50
if (k5.eq.k7) then
nval=nval+1
iv(nval,2)=k4
iv(nval,3)=k5
iv(nval,4)=k8
iv(nval,5)=jindexbondlist
iv(nval,6)=kindexbondlist
iju=1
end if
if (iju.eq.1) goto 50
if (k5.eq.k8) then
nval=nval+1
iv(nval,2)=k4
iv(nval,3)=k5
iv(nval,4)=k7
iv(nval,5)=jindexbondlist
iv(nval,6)=kindexbondlist
iju=1
end if
if (iju.eq.1) goto 50
write (6,*)'nval = ',nval,
$ ' after',iindexatom, ' of ',na,' atoms completed.'
stop 'Adjacent bonds did not make an angle'
endif
50 continue
if (nval.gt.nvamax) then
write (6,*)'nval = ',nval,' reax_defs.h::NVAMAXDEF = ',
$ NVAMAXDEF,
$ ' after',iindexatom, ' of ',na,' atoms completed.'
stop 'Too many valency angles. Increase NVAMAXDEF'
endif
if (iju.gt.0) then
**********************************************************************
* *
* Determine force field types of angles *
* *
**********************************************************************
ityva(1)=0
ih1=ia(iv(nval,2),1)
ih2=ia(iv(nval,3),1)
ih3=ia(iv(nval,4),1)
if (ih3.lt.ih1) then
ih3=ia(iv(nval,2),1)
ih2=ia(iv(nval,3),1)
ih1=ia(iv(nval,4),1)
end if
nfound=0
do i3=1,nvaty
if (ih1.eq.nvs(i3,1).and.ih2.eq.nvs(i3,2).and.
$ih3.eq.nvs(i3,3)) then
nfound=nfound+1
ityva(nfound)=i3
end if
end do
if (ityva(1).eq.0.or.abs(vka(ityva(1))).lt.0.001) then !Valence angle does not exist in force field;ignore
nval=nval-1
ihul=0
else
iv(nval,1)=ityva(1)
ihul=1
do i3=1,nfound-1 !Found multiple angles of the same type
nval=nval+1
iv(nval,1)=ityva(i3+1)
do i4=2,6
iv(nval,i4)=iv(nval-1,i4)
end do
end do
end if
if (iju.eq.2) then
ityva(1)=0
ih1=ia(iv(nval-ihul,2),1)
ih2=ia(iv(nval-ihul,3),1)
ih3=ia(iv(nval-ihul,4),1)
if (ih3.lt.ih1) then
ih3=ia(iv(nval-ihul,2),1)
ih2=ia(iv(nval-ihul,3),1)
ih1=ia(iv(nval-ihul,4),1)
end if
nfound=0
do i3=1,nvaty
if (ih1.eq.nvs(i3,1).and.ih2.eq.nvs(i3,2).and.
$ih3.eq.nvs(i3,3)) then
nfound=nfound+1
ityva(nfound)=i3
end if
end do
if (ityva(1).eq.0.or.abs(vka(ityva(1))).lt.0.001) then !Valence angle does not exist in force field;ignore
if (ihul.eq.1) then
do i3=1,6
iv(nval-1,i3)=iv(nval,i3)
end do
end if
nval=nval-1
else
iv(nval-ihul,1)=ityva(1)
do i3=1,nfound-1 !Found multiple angles of the same type
nval=nval+1
iv(nval,1)=ityva(i3+1)
do i4=2,6
iv(nval,i4)=iv(nval-1,i4)
end do
end do
end if
end if
end if
end do
51 continue
end do
end do
nbonop=0
return
end
**********************************************************************
**********************************************************************
subroutine srttor
**********************************************************************
#include "cbka.blk"
#include "cbkc.blk"
#include "cbkbo.blk"
#include "cbkrbo.blk"
#include "cbkia.blk"
#include "cbktorsion.blk"
#include "cbkvalence.blk"
#include "cellcoord.blk"
#include "control.blk"
#include "small.blk"
#include "cbknubon2.blk"
**********************************************************************
* *
* Find torsion angles in molecule *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$ open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In srttor'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
ntor=0
if (ntoty.eq.0) return
do 61 i1=1,nbon
k2=ib(i1,2)
k3=ib(i1,3)
c Only compute interaction if both atoms local
c are local or else flip a coin
if (k2 .gt. na_local) go to 61
if (k3 .gt. na_local) then
if (itag(k2) .lt. itag(k3)) go to 61
if (itag(k2) .eq. itag(k3)) then
if(c(k2,3) .gt. c(k3,3)) go to 61
if(c(k2,3) .eq. c(k3,3) .and.
$ c(k2,2) .gt. c(k3,2)) go to 61
if(c(k2,3) .eq. c(k3,3) .and.
$ c(k2,2) .eq. c(k3,2) .and.
$ c(k2,1) .gt. c(k3,1)) go to 61
endif
endif
iob1=ia(k2,2)
iob2=ia(k3,2)
do 60 i2=1,iob1 !Atoms connected to k2
k4=ia(k2,2+i2)
ibo2=nubon2(k2,i2)
do 60 i3=1,iob2 !Atoms connected to k3
k5=ia(k3,2+i3)
ibo3=nubon2(k3,i3)
bopr=bo(i1)*bo(ibo2)*bo(ibo3)
if (bopr.gt.cutof2.and.k2.ne.k5.and.k3.ne.k4.and.k4.ne.k5) then
ntor=ntor+1
it(ntor,2)=k4
it(ntor,3)=k2
it(ntor,4)=k3
it(ntor,5)=k5
it(ntor,6)=ibo2
it(ntor,7)=i1
it(ntor,8)=ibo3
**********************************************************************
* *
* Determine force field types of torsion angles *
* *
**********************************************************************
ity=0
ih1=ia(it(ntor,2),1)
ih2=ia(it(ntor,3),1)
ih3=ia(it(ntor,4),1)
ih4=ia(it(ntor,5),1)
if (ih2.gt.ih3) then
ih1=ia(it(ntor,5),1)
ih2=ia(it(ntor,4),1)
ih3=ia(it(ntor,3),1)
ih4=ia(it(ntor,2),1)
end if
if (ih2.eq.ih3.and.ih4.lt.ih1) then
ih1=ia(it(ntor,5),1)
ih2=ia(it(ntor,4),1)
ih3=ia(it(ntor,3),1)
ih4=ia(it(ntor,2),1)
end if
do i4=1,ntoty
if (ih1.eq.nts(i4,1).and.ih2.eq.nts(i4,2).and.ih3.eq.nts(i4,3)
$.and.ih4.eq.nts(i4,4)) ity=i4
end do
if (ity.eq.0) then
do i4=1,ntoty
if (nts(i4,1).eq.0.and.ih2.eq.nts(i4,2).and.ih3.eq.nts(i4,3)
$.and.nts(i4,4).eq.0) ity=i4
end do
end if
if (ity.eq.0) then
ntor=ntor-1 !Torsion angle does not exist in force field: ignore
else
it(ntor,1)=ity
end if
end if
60 continue
61 continue
if (ntor.gt.ntomax) stop 'Too many torsion angles'
* do i1=1,ntor
* write (41,'(20i4)')i1,it(i1,1),it(i1,2),it(i1,3),
* $it(i1,4),it(i1,5),it(i1,6),it(i1,7),it(i1,8)
* end do
return
end
**********************************************************************
**********************************************************************
subroutine srtoop
**********************************************************************
#include "cbka.blk"
#include "cbkbo.blk"
#include "cbkrbo.blk"
#include "cbkvalence.blk"
#include "control.blk"
#include "small.blk"
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In srtoop'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
**********************************************************************
* *
* Find out of plane angles in molecule *
* *
**********************************************************************
noop=0
do i1=1,nval
k2=iv(i1,2)
k3=iv(i1,3)
k4=iv(i1,4)
k5=iv(i1,5)
k6=iv(i1,6)
do i2=1,nbon
k7=ib(i2,2)
k8=ib(i2,3)
if (bo(i2).gt.cutof2) then
if (k7.eq.k3.and.k8.ne.k4.and.k8.ne.k2) then
noop=noop+1
ioop(noop,2)=k8
ioop(noop,3)=k3
ioop(noop,4)=k2
ioop(noop,5)=k4
ioop(noop,6)=i2
ioop(noop,7)=iv(i1,5)
ioop(noop,8)=iv(i1,6)
ioop(noop,9)=i1
end if
if (k8.eq.k3.and.k7.ne.k4.and.k7.ne.k2) then
noop=noop+1
ioop(noop,2)=k7
ioop(noop,3)=k3
ioop(noop,4)=k2
ioop(noop,5)=k4
ioop(noop,6)=i2
ioop(noop,7)=iv(i1,5)
ioop(noop,8)=iv(i1,6)
ioop(noop,9)=i1
end if
end if
end do
end do
do i1=1,noop
call caltor(ioop(i1,2),ioop(i1,3),ioop(i1,4),ioop(i1,5),hoop)
end do
**********************************************************************
return
end
**********************************************************************
**********************************************************************
subroutine srthb
**********************************************************************
#include "cbka.blk"
#include "cbkc.blk"
#include "cbkbo.blk"
#include "cbkconst.blk"
#include "cbkia.blk"
#include "cbkrbo.blk"
#include "cbksrthb.blk"
#include "control.blk"
#include "small.blk"
#include "cbkpairs.blk"
#include "cbknvlown.blk"
#include "cbknubon2.blk"
**********************************************************************
* *
* Find hydrogen bonds in molecule *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$ open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In srthb'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
nhb=0
**********************************************************************
* *
* Locate donor/acceptor bonds *
* *
**********************************************************************
c Outer loop must be Verlet list, because ia() does not store Verlet entries,
c but it does store bond entries in nubon2()
c
c The problem with using the nvlown ownership criterion
c is that it would require that we unprune every bond that is within
c certain distance, as well as its first and second neighbor bonds.
c
c For the ownership criterion based on H atom location no unpruning is required.
c Apparently lprune=4 is sufficient here, implying that we need to capture first and
c second neighbor bonds of the O-H bond, and of course we need to include all hydrogen
c bond partners within hbcut.
c
do 20 ivl=1,nvpair !Use Verlet-list to find donor-acceptor pairs
j1=nvl1(ivl)
j2=nvl2(ivl)
ity1=ia(j1,1)
ity2=ia(j2,1)
ihhb1=nphb(ia(j1,1))
ihhb2=nphb(ia(j2,1))
if (ihhb1.gt.ihhb2) then !Make j1 donor(H) atom and j2 acceptor(O) atom
j2=nvl1(ivl)
j1=nvl2(ivl)
ity1=ia(j1,1)
ity2=ia(j2,1)
ihhb1=nphb(ia(j1,1))
ihhb2=nphb(ia(j2,1))
end if
* Only need to compute bonds where j1 is local
if (j1 .le. na_local) then
if (ihhb1.eq.1.and.ihhb2.eq.2) then
call dista2(j1,j2,dishb,dxm,dym,dzm)
if (dishb.lt.hbcut) then
do 10 i23=1,ia(j1,2) !Search for acceptor atoms bound to donor atom
j3=ia(j1,2+i23)
ity3=ia(j3,1)
nbohb=nubon2(j1,i23)
if (nphb(ity3).eq.2.and.j3.ne.j2.and.bo(nbohb).gt.0.01) then
**********************************************************************
* *
* Accept hydrogen bond and find hydrogen bond type *
* *
**********************************************************************
nhb=nhb+1
if (nhb.gt.nhbmax) then
write (*,*)nhb,nhbmax
write (*,*)'Maximum number of hydrogen bonds exceeded'
stop 'Maximum number of hydrogen bonds exceeded'
end if
ihb(nhb,1)=0
do i3=1,nhbty
if (ity3.eq.nhbs(i3,1).and.ity1.eq.nhbs(i3,2).and.ity2.eq.
$nhbs(i3,3)) ihb(nhb,1)=i3
end do
if (ihb(nhb,1).eq.0) then !Hydrogen bond not in force field
nhb=nhb-1
* write (*,*)'Warning: added hydrogen bond ',ity3,ity1,ity2
* nhbty=nhbty+1
* nhbs(nhbty,1)=ity3
* nhbs(nhbty,2)=ity1
* nhbs(nhbty,3)=ity2
* rhb(nhbty)=2.70
* dehb(nhbty)=zero
* vhb1(nhbty)=5.0
* vhb2(nhbty)=20.0
* ihb(nhb,1)=nhbty
end if
ihb(nhb,2)=j3
ihb(nhb,3)=j1
ihb(nhb,4)=j2
ihb(nhb,5)=nbohb
ihb(nhb,6)=k1
ihb(nhb,7)=k2
ihb(nhb,8)=k3
* write (64,*)nhb,ihb(nhb,1),j3,j1,j2,nbohb,k1,k2,k3,bo(nbohb),
* $dishb
end if
10 continue
end if
end if
end if
20 end do
* stop 'end in srthb'
return
end
**********************************************************************

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