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lammps/lib/reax/reax_inout.F
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reax_inout.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 ffinpt
**********************************************************************
#include "cbka.blk"
#include "cbkboncor.blk"
#include "cbkconst.blk"
#include "cbkcovbon.blk"
#include "cbkff.blk"
#include "cbkfftorang.blk"
#include "cbknonbon.blk"
#include "cbksrthb.blk"
#include "cbktorsion.blk"
#include "cellcoord.blk"
#include "control.blk"
#include "opt.blk"
#include "valang.blk"
#include "cbksrtbon1.blk"
#include "cbkchb.blk"
dimension rcore2(nsort),ecore2(nsort),acore2(nsort)
**********************************************************************
* *
* Read in force field *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In ffinpt'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
open (4,file='ffield.reax',status='old')
rewind (4)
iline=0
read (4,'(a40)',end=990,err=990)qffield
iline=iline+1
**********************************************************************
* *
* Read in general force field parameters *
* *
**********************************************************************
read (4,1100,end=990,err=990)npar
iline=iline+1
do i1=1,npar
read (4,1300,end=990,err=990)vpar(i1)
iline=iline+1
end do
cutoff=0.01*vpar(30)
swa=vpar(12)
if (abs(swa).gt.0.01) write (*,*)
$'Warning: non-zero value for lower Taper-radius cutoff'
swb=vpar(13)
if (swb.lt.zero) stop
$'Negative value for upper Taper-radius cutoff'
if (swb.lt.5.0) write (*,*)
$'Warning: very low value for upper Taper-radius cutoff:',swb
**********************************************************************
* *
* Read in atom type data *
* *
**********************************************************************
read (4,1100,end=990,err=990) nso
iline=iline+1
read (4,*,end=990,err=990)
iline=iline+1
read (4,*,end=990,err=990)
iline=iline+1
read (4,*,end=990,err=990)
iline=iline+1
if (nso.gt.nsort) stop 'Maximum number of atom types exceeded'
do i1=1,nso
read (4,1200,end=990,err=990)qas(i1),rat(i1),aval(i1),amas(i1),
$rvdw(i1),eps(i1),gam(i1),rapt(i1),stlp(i1)
iline=iline+1
read (4,1250,end=990,err=990)alf(i1),vop(i1),valf(i1),
$valp1(i1),valp2(i1),chi(i1),eta(i1),vnphb
iline=iline+1
read (4,1250,end=990,err=990)vnq(i1),vlp1(i1),vincr(i1),
$bo131(i1),bo132(i1),bo133(i1),sigqeq(i1),default
iline=iline+1
read (4,1250,end=990,err=990)vovun(i1),vval1(i1),vrom,
$vval3(i1),vval4(i1),rcore2(i1),ecore2(i1),acore2(i1)
iline=iline+1
idef(i1)=int(default)
nphb(i1)=int(vnphb)
end do
**********************************************************************
* *
* Calculate van der Waals and Coulomb pair-parameters *
* *
**********************************************************************
do i1=1,nso
do i2=1,nso
rcore(i1,i2)=sqrt(rcore2(i1)*rcore2(i2))
ecore(i1,i2)=sqrt(ecore2(i1)*ecore2(i2))
acore(i1,i2)=sqrt(acore2(i1)*acore2(i2))
p1co(i1,i2)=sqrt(4.0*rvdw(i1)*rvdw(i2))
p2co(i1,i2)=sqrt(eps(i1)*eps(i2))
p3co(i1,i2)=sqrt(alf(i1)*alf(i2))
gamwh=sqrt(vop(i1)*vop(i2))
gamwco(i1,i2)=1.0/gamwh**vpar(29)
gamch=sqrt(gam(i1)*gam(i2))
gamcco(i1,i2)=1.0/gamch**3
rob1(i1,i2)=0.50*(rat(i1)+rat(i2))
rob2(i1,i2)=0.50*(rapt(i1)+rapt(i2))
rob3(i1,i2)=0.50*(vnq(i1)+vnq(i2))
end do
end do
**********************************************************************
* *
* Read in bond type data *
* *
**********************************************************************
read (4,1100,end=990,err=990)nboty
iline=iline+1
read (4,*,end=990,err=990)
iline=iline+1
if (2*nboty.gt.nbotym) stop 'Maximum nr. of bond types exceeded'
ih=0
do i1=1,nboty
ih=ih+1
read (4,1400,end=990,err=990)nbs(ih,1),nbs(ih,2),de1(ih),
$de2(ih),de3(ih),psi(ih),pdo(ih),v13cor(ih),popi(ih),vover(ih)
iline=iline+1
read (4,1450,end=990,err=990)psp(ih),pdp(ih),ptp(ih),
$bom(ih),bop1(ih),bop2(ih),ovc(ih),vuncor(ih)
iline=iline+1
if (nbs(ih,1).ne.nbs(ih,2)) then
ih=ih+1
nbs(ih,1)=nbs(ih-1,2)
nbs(ih,2)=nbs(ih-1,1)
de1(ih)=de1(ih-1)
de2(ih)=de2(ih-1)
de3(ih)=de3(ih-1)
psi(ih)=psi(ih-1)
pdo(ih)=pdo(ih-1)
v13cor(ih)=v13cor(ih-1)
vover(ih)=vover(ih-1)
psp(ih)=psp(ih-1)
pdp(ih)=pdp(ih-1)
ptp(ih)=ptp(ih-1)
bop1(ih)=bop1(ih-1)
bop2(ih)=bop2(ih-1)
* bop3(ih)=bop3(ih-1)
* bop4(ih)=bop4(ih-1)
bom(ih)=bom(ih-1)
popi(ih)=popi(ih-1)
ovc(ih)=ovc(ih-1)
end if
end do
nboty2=ih
**********************************************************************
* *
* Read in off-diagonal parameters *
* *
**********************************************************************
read (4,1100,end=990,err=990)nodmty
iline=iline+1
if (nodmty.gt.nodmtym)
$stop 'Maximum nr. of off-diagonal Morse types exceeded'
ih=0
do i1=1,nodmty
ih=ih+1
read (4,1400,end=990,err=990)nodm1,nodm2,deodmh,rodmh,godmh,
$rsig,rpi,rpi2
iline=iline+1
if (rsig.gt.zero) rob1(nodm1,nodm2)=rsig
if (rsig.gt.zero) rob1(nodm2,nodm1)=rsig
if (rpi.gt.zero) rob2(nodm1,nodm2)=rpi
if (rpi.gt.zero) rob2(nodm2,nodm1)=rpi
if (rpi2.gt.zero) rob3(nodm1,nodm2)=rpi2
if (rpi2.gt.zero) rob3(nodm2,nodm1)=rpi2
if (rodmh.gt.zero) p1co(nodm1,nodm2)=2.0*rodmh
if (rodmh.gt.zero) p1co(nodm2,nodm1)=2.0*rodmh
if (deodmh.gt.zero) p2co(nodm1,nodm2)=deodmh
if (deodmh.gt.zero) p2co(nodm2,nodm1)=deodmh
if (godmh.gt.zero) p3co(nodm1,nodm2)=godmh
if (godmh.gt.zero) p3co(nodm2,nodm1)=godmh
end do
**********************************************************************
* *
* Read in valency angle and conjugation type data *
* *
**********************************************************************
read (4,1100,end=990,err=990)nvaty
iline=iline+1
if (nvaty.gt.nvatym)
$stop 'Maximum nr. of valency angle types exceeded'
do i1=1,nvaty
read (4,1500,end=990,err=990)nvs(i1,1),nvs(i1,2),
$nvs(i1,3),th0(i1),vka(i1),vka3(i1),vka8(i1),vkac(i1),vkap(i1),
$vval2(i1)
iline=iline+1
end do
**********************************************************************
* *
* Read in torsion angle type data *
* *
**********************************************************************
read (4,1100,end=990,err=990)ntoty
iline=iline+1
if (ntoty.gt.ntotym)
$stop 'Maximum nr. of torsion angle types exceeded'
do i1=1,ntoty
read (4,1600,end=990,err=990)nts(i1,1),nts(i1,2),nts(i1,3),
$nts(i1,4),v1(i1),
$v2(i1),v3(i1),v4(i1),vconj(i1),v2bo(i1),v3bo(i1)
iline=iline+1
end do
**********************************************************************
* *
* Read in hydrogen bond type data *
* *
**********************************************************************
read (4,1100,end=990,err=990)nhbty
iline=iline+1
if (nhbty.gt.nhbtym)
$stop 'Maximum nr. of hydrogen bond types exceeded'
do i1=1,nhbty
read (4,1500,end=990,err=990)nhbs(i1,1),nhbs(i1,2),
$nhbs(i1,3),rhb(i1),dehb(i1),vhb1(i1),vhb2(i1)
iline=iline+1
end do
**********************************************************************
* *
* Calculate vdWaals interaction parameters *
* *
**********************************************************************
do i1=1,nso
do i2=1,nso
rr=(rvdw(i1)+rvdw(i2))
rr2=rr*rr
eps2=sqrt(eps(i1)*eps(i2))
rr6=rr2*rr2*rr2
pvdw1(i1,i2)=eps2*rr6*rr6
pvdw1(i2,i1)=eps2*rr6*rr6
pvdw2(i1,i2)=2.0*eps2*rr6
pvdw2(i2,i1)=2.0*eps2*rr6
end do
end do
**********************************************************************
* *
* Error part *
* *
**********************************************************************
goto 999
990 write (*,*)'Error or end-of-file reading unit 4 on line:',iline
stop
999 continue
close(4)
**********************************************************************
* *
* Format part *
* *
**********************************************************************
1100 format (i3,2x,a2,3x,3d22.15)
1200 format (1x,a2,10f9.4)
1250 format (3x,10f9.4)
1300 format (f10.4)
1400 format (2i3,8f9.4)
1450 format (6x,8f9.4)
1500 format (3i3,7f9.4)
1600 format (4i3,7f9.4)
return
end
**********************************************************************
***********************************************************************
subroutine mdsav(node)
***********************************************************************
#include "cbka.blk"
#include "cbkabo.blk"
#include "cbkatomcoord.blk"
#include "cbkbo.blk"
#include "cbkc.blk"
#include "cbkch.blk"
#include "cbkconst.blk"
#include "cbkdistan.blk"
#include "cbkenergies.blk"
#include "cbkia.blk"
#include "cbkinit.blk"
#include "cbklonpar.blk"
#include "cbknubon2.blk"
#include "cbkqa.blk"
#include "cbktregime.blk"
#include "cbksrtbon1.blk"
#include "cellcoord.blk"
#include "control.blk"
#include "opt.blk"
#include "small.blk"
dimension idum(mbond+3),bodum(mbond+3),qat2(2)
character*25 qfileh
character*33 qfile2
character*4 qext
character*6 qmdfi
character *7 var
character *3 qat2,pepname
character *1 qrtemp
************************************************************************
* *
* Save coordinates, velocities and accelerations of MD-system *
* *
************************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In mdsav'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
************************************************************************
c
c This is just for test purposes
c
************************************************************************
c$$$ write(6,*) '***************************'
c$$$ write(6,*) 'mdsav node number is ',node
c$$$ write(6,*) '***************************'
return
qfileh='Unknown'
qmdfi='moldyn'
pepname=' '
ipeptide=0
if (ni.eq.2) qmdfi='molsav'
if (iopt.eq.0) then
do i1=1,mbond+3
idum(i1)=nzero
bodum(i1)=zero
end do
C if (napp.eq.1)
C $open (7,file='fort.7',status='unknown',access='append')
if (napp.ne.1)
$open (7,file='fort.7',status='unknown')
nsbmaxh=5*((nsbmax/5)+1)
write (7,100)na,qmol,mdstep,nsbmaxh
if (nbiolab.eq.1) write (67,101)na,qmol
do i1=1,na
bosum=0.0
do i3=1,nsbmax
if (iag(i1,2+i3).gt.0) bosum=bosum+bo(nubon1(i1,i3))
end do
if (nsbmax.lt.5) then
write (7,200)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)),
$(idum(i2),i2=1,5-iag(i1,2)),
$iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)),
$(bodum(i2),i2=1,5-iag(i1,2)),abo(i1),vlp(i1),ch(i1)
if (nbiolab.eq.1) then !Delphi-connection table output
write (67,201)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2))
end if
else if (nsbmax.lt.10) then
write (7,210)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)),
$(idum(i2),i2=1,10-iag(i1,2)),
$iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)),
$(bodum(i2),i2=1,10-iag(i1,2)),abo(i1),vlp(i1),ch(i1)
else if (nsbmax.lt.15) then
write (7,220)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)),
$(idum(i2),i2=1,15-iag(i1,2)),
$iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)),
$(bodum(i2),i2=1,15-iag(i1,2)),abo(i1),vlp(i1),ch(i1)
else if (nsbmax.lt.20) then
write (7,230)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)),
$(idum(i2),i2=1,20-iag(i1,2)),
$iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)),
$(bodum(i2),i2=1,20-iag(i1,2)),abo(i1),vlp(i1),ch(i1)
else if (nsbmax.lt.25) then
write (7,240)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)),
$(idum(i2),i2=1,25-iag(i1,2)),
$iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)),
$(bodum(i2),i2=1,25-iag(i1,2)),abo(i1),vlp(i1),ch(i1)
else if (nsbmax.gt.25) then
write (7,250)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)),
$(idum(i2),i2=1,35-iag(i1,2)),
$iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)),
$(bodum(i2),i2=1,35-iag(i1,2)),abo(i1),vlp(i1),ch(i1)
end if
end do
boss=zero
vlps=0.0
C if (napp.eq.1)
C $open (8,file='fort.8',status='unknown',access='append')
if (napp.ne.1)
$open (8,file='fort.8',status='unknown')
nsbmaxh=5*((nsbma2/5)+1)
write (8,100)na,qmol,mdstep,nsbmaxh
chsum=0.0
do i1=1,na
bosum=0.0
do i3=1,nsbma2
if (ia(i1,2+i3).gt.0) bosum=bosum+bo(nubon2(i1,i3))
end do
if (nsbma2.lt.5) then
write (8,200)i1,ia(i1,1),(ia(i1,2+i2),i2=1,ia(i1,2)),
$(idum(i2),i2=1,5-ia(i1,2)),
$ia(i1,3+mbond),(bo(nubon2(i1,i2)),i2=1,ia(i1,2)),
$(bodum(i2),i2=1,5-ia(i1,2)),abo(i1),vlp(i1),ch(i1)
else if (nsbma2.lt.10) then
write (8,210)i1,ia(i1,1),(ia(i1,2+i2),i2=1,ia(i1,2)),
$(idum(i2),i2=1,10-ia(i1,2)),
$ia(i1,3+mbond),(bo(nubon2(i1,i2)),i2=1,ia(i1,2)),
$(bodum(i2),i2=1,10-ia(i1,2)),abo(i1),vlp(i1),ch(i1)
else if (nsbma2.lt.15) then
write (8,220)i1,ia(i1,1),(ia(i1,2+i2),i2=1,ia(i1,2)),
$(idum(i2),i2=1,15-ia(i1,2)),
$ia(i1,3+mbond),(bo(nubon2(i1,i2)),i2=1,ia(i1,2)),
$(bodum(i2),i2=1,15-ia(i1,2)),abo(i1),vlp(i1),ch(i1)
else if (nsbma2.lt.20) then
write (8,230)i1,ia(i1,1),(ia(i1,2+i2),i2=1,ia(i1,2)),
$(idum(i2),i2=1,20-ia(i1,2)),
$ia(i1,3+mbond),(bo(nubon2(i1,i2)),i2=1,ia(i1,2)),
$(bodum(i2),i2=1,20-ia(i1,2)),abo(i1),vlp(i1),ch(i1)
else if (nsbma2.lt.25) then
write (8,240)i1,ia(i1,1),(ia(i1,2+i2),i2=1,ia(i1,2)),
$(idum(i2),i2=1,25-ia(i1,2)),
$ia(i1,3+mbond),(bo(nubon2(i1,i2)),i2=1,ia(i1,2)),
$(bodum(i2),i2=1,25-ia(i1,2)),abo(i1),vlp(i1),ch(i1)
end if
boss=boss+bosum/2.0
vlps=vlps+vlp(i1)
chsum=chsum+ch(i1)
end do
write (7,*)2.0*boss,vlps,2.0*boss+2.0*vlps,chsum
close(8)
close(7)
end if
if (noutpt.eq.0) then
write (var,'(f7.4)')float(mdstep/nsav)/1d4
if (ni.eq.0) open (unit=67,file=qmdfi//var(3:7),
$status='unknown')
write (67,300)qmol
do i1=1,na
write (67,400)i1,qa(i1),(c(i1,i2),i2=1,3)
end do
write (67,*)
close(67)
end if
if (noutpt.eq.2) then
C open (88,file='moldyn.bgf',status='unknown',access='append')
call writebgf(88)
close (88)
end if
if ((ni.eq.1.and.iopt.eq.0).or.(ni.eq.1.and.iopt.eq.1.and.
$iflga.eq.1)) then
qrtemp=qr
if (qr.eq.'I') qr='C'
if (qfileh.eq.' ') then
write (*,*)'Warning: no file name given; use Unknown'
qfileh='Unknown'
end if
qfile2=qfileh
if (imodfile.eq.0) then
istart=1
qstrana1(1:25)=qfileh
call stranal(istart,iend,vout,iout,1)
qfile2=qfileh(istart:iend-1)//".geo"
end if
call writegeo(98)
if (imodfile.eq.1.or.iopt.eq.0) then
open (88,file=qfile2,status='unknown')
call writegeo(88)
close (88)
end if
qr=qrtemp
if (iopt.eq.0) then
do i1=1,na
write (56,410) i1,ch(i1)
write (55,410) i1,chgbgf(i1)
end do
**********************************************************************
* *
* Write .pdb output file *
* *
**********************************************************************
open (unit=47,file='output.pdb',status='unknown')
do i1=1,na
write (47,412)'ATOM ',i1,qa(i1),pepname,ipeptide,c(i1,1),
$c(i1,2),c(i1,3),1.0,2.2,qa(i1)
end do
write (47,*) 'TER'
write (47,*) 'END'
close (47)
if (nsurp.eq.0) then
if (kx.gt.0.or.ky.gt.0.or.kz.gt.0) then
qrtemp=qr
**********************************************************************
* *
* Write crystal structure including periodic images *
* *
**********************************************************************
* mux=(1+kx+kx)
* muy=(1+ky+ky)
* muz=(1+kz+kz)
* qr='F'
* write (86,'(2x,a1,1x,a60)')qr,qmol
* qr=qrtemp
* write (86,'(3f10.4)')mux*axiss(1),muy*axiss(2),muz*axiss(3)
* write (86,'(3f10.4)')angle(1),angle(2),angle(3)
* do i1=1,na
* write (86,'(i4,1x,a2,3x,3d22.15)')i1,qa(i1),(c(i1,i2),i2=1,3)
* end do
* nhulp=na+1
* do k1=-kx,kx
* do k2=-ky,ky
* do k3=-kz,kz
* if (k1.ne.0.or.k2.ne.0.or.k3.ne.0) then
* do i1=1,na
* cx=c(i1,1)+k1*tm11
* cy=c(i1,2)+k1*tm21+k2*tm22
* cz=c(i1,3)+k1*tm31+k2*tm32+k3*tm33
* write (86,'(i4,1x,a2,3x,3d22.15)')nhulp,qa(i1),cx,cy,cz
* nhulp=nhulp+1
* end do
* end if
* end do
* end do
* end do
* write (86,*)
**********************************************************************
* *
* Write crystal structure with extra unit cells *
* *
**********************************************************************
mux=1+iexx
muy=1+iexy
muz=1+iexz
qr='F'
write (85,'(2x,a1,1x,a60)')qr,qmol
qr=qrtemp
write (85,'(3f10.4)')mux*axiss(1),muy*axiss(2),muz*axiss(3)
write (85,'(3f10.4)')angle(1),angle(2),angle(3)
do i1=1,na
write (85,'(i4,1x,a2,3x,3d22.15)')i1,qa(i1),(c(i1,i2),i2=1,3)
end do
nhulp=na+1
do k1=0,iexx
do k2=0,iexy
do k3=0,iexz
if (k1.ne.0.or.k2.ne.0.or.k3.ne.0) then
do i1=1,na
cx=c(i1,1)+k1*tm11
cy=c(i1,2)+k1*tm21+k2*tm22
cz=c(i1,3)+k1*tm31+k2*tm32+k3*tm33
write (85,'(i4,1x,a2,3x,3d22.15)')nhulp,qa(i1),cx,cy,cz
nhulp=nhulp+1
end do
end if
end do
end do
end do
write (85,*)
end if
end if
end if
end if
if (ni.eq.0.or.ni.eq.2) then
**********************************************************************
* *
* Write ASCII trajectory file *
* *
**********************************************************************
if (ni.eq.0) open(unit=66,file=qmdfi//'.vel',status='unknown')
if (ni.eq.2) then
write (var,'(f7.4)')float(mdstep/nsav3)/1d4
open (unit=66,file=qmdfi//var(3:7),status='unknown')
end if
write (66,500)axis(1),axis(2),axis(3)
write (66,550)angle(1),angle(2),angle(3)
write (66,600)na,((c(i,j),j=1,3),qlabel(i),i=1,na)
write (66,700)((vel(j,i),j=1,3),i=1,na)
write (66,800)((accel(j,i),j=1,3),i=1,na)
write (66,900)((aold(j,i),j=1,3),i=1,na)
write (66,1000)tempmd
write (66,1050)
close (66)
end if
if (ni.ne.2.and.iopt.eq.0) then
C open (unit=68,file='xmolout',status='unknown',access='append')
write (68,1200)na
write (68,1300)qmol,mdstep+nit+nprevrun,estrc,
$axis(1),axis(2),axis(3),angle(1),angle(2),angle(3)
do i1=1,na
if (ixmolo.eq.0) write (68,1400)qa(i1),(c(i1,i2),i2=1,3)
if (ixmolo.eq.1) write (68,1400)qa(i1),(c(i1,i2),i2=1,3),
$(vel(i2,i1)/1e+10,i2=1,3),iag(i1,3+mbond)
if (ixmolo.eq.2) write (68,1401)qa(i1),(c(i1,i2),i2=1,3),
$iag(i1,3+mbond)
end do
close (68)
if (itrout.ne.0) then
C open (unit=69,file='xmolout2',status='unknown',access='append')
write (69,1200)na
write (69,1300)qmol,mdstep+nit+nprevrun,estrc,
$axis(1),axis(2),axis(3),angle(1),angle(2),angle(3)
do i1=1,na
if (ixmolo.eq.0) write (69,1400)qa(i1),(cp(i1,i2),i2=1,3)
if (ixmolo.eq.1) write (69,1400)qa(i1),(cp(i1,i2),i2=1,3),
$(vel(i2,i1)/1e+10,i2=1,3),iag(i1,3+mbond)
if (ixmolo.eq.2) write (68,1401)qa(i1),(c(i1,i2),i2=1,3),
$iag(i1,3+mbond)
end do
close (69)
end if
call molanal
end if
**********************************************************************
* *
* Generate BIOGRAF output-file *
* *
**********************************************************************
if ((ni.eq.1.and.iopt.eq.0).or.(ni.eq.1.and.iopt.eq.1.and.
$iflga.eq.1)) then
if (qfileh.eq.' ') then
write (*,*)'Warning: no file name given; use Unknown'
qfileh='Unknown'
end if
qfile2=qfileh
if (imodfile.eq.0) then
istart=1
qstrana1(1:25)=qfileh
call stranal(istart,iend,vout,iout,1)
qfile2=qfileh(istart:iend-1)//".bgf"
end if
call writebgf(90)
if (imodfile.eq.1.or.iopt.eq.0) then
open (88,file=qfile2,status='unknown')
call writebgf(88)
close (88)
end if
end if
return
**********************************************************************
* *
* Format part *
* *
**********************************************************************
100 format (i4,1x,a40,'Iteration:',i8,' #Bonds:',i4)
101 format (i3,2x,a40)
200 format (8i4,8f7.3)
201 format (8i3)
210 format (13i4,13f7.3)
220 format (18i4,18f7.3)
230 format (23i4,23f7.3)
240 format (28i4,28f7.3)
250 format (38i4,38f7.3)
300 format (2x,a1,1x,a60)
301 format (2x,a1,1x,f6.2,a60)
302 format (2x,a1,1x,2f6.2,a60)
310 format (2x,a1,1x,a60)
320 format (3f10.4)
400 format (i4,1x,a2,3x,3(d21.14,1x),1x,a5,1x,i5)
410 format (i4,f12.6)
412 format(A6,I5,1x,A2,3x,A3,2x,i4,4x,3f8.3,f6.2,f6.2,4x,2x,A6)
500 format (1x,'Lattice parameters:',/(3f15.8))
550 format (3f15.8)
600 format (i4,1x,'Atom coordinates (Angstrom):',/
$(3d24.15,1x,a5))
700 format (1x,'Atom velocities (Angstrom/s):',/(3d24.15))
800 format (1x,'Atom accelerations (Angstrom/s**2):',/(3d24.15))
900 format (1x,'Previous atom accelerations:',/(3d24.15))
1000 format (1x,'MD-temperature (K):',/(1d24.15))
1050 format (1x,'Connections, bond orders and lone pairs:')
1100 format (8i3,8f8.4)
1200 format (i4)
1300 format (a40,i6,f12.4,6f7.2)
1400 format (a2,3f10.5,3f15.5,i6)
1401 format (a2,3f10.5,i6)
1500 format ('BIOGRF',i4)
1600 format ('XTLGRF',i4)
1700 format ('DESCRP ',a60)
1800 format ('REMARK ',a60)
1900 format ('FFIELD ',a40)
2000 format ('RUTYPE ',a40)
2100 format ('CRYSTX ',6f11.5)
2200 format ('CELLS ',6i5)
2300 format ('# At1 At2 R12 Force1 Force2 ',
$'dR12/dIteration(MD only)')
2400 format ('BOND RESTRAINT ',2i4,f8.4,f8.2,f8.5,f10.7)
2500 format ('# At1 At2 At3 Angle Force1 Force2',
$' dAngle/dIteration (MD only)')
2600 format ('ANGLE RESTRAINT ',3i4,2f8.2,f8.4,f9.6)
2700 format ('# At1 At2 At3 At3 Angle Force1 ',
$'Force2 dAngle/dIteration (MD only)')
2800 format ('TORSION RESTRAINT ',4i4,2f8.2,f8.4,f9.6)
2900 format ('FORMAT ATOM (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,',
$'3f10.5,1x,a5,i3,i2,1x,f8.5)')
3000 format ('HETATM',1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,
$a5,i3,i2,1x,f8.5)
3100 format ('FORMAT CONECT (a6,12i6)')
3200 format ('CONECT',12i6)
3300 format ('UNIT ENERGY kcal')
3400 format ('ENERGY',5x,f14.6)
3500 format ('END')
end
************************************************************************
************************************************************************
subroutine readc
************************************************************************
#include "cbka.blk"
#include "cbkc.blk"
#include "cbkcha.blk"
#include "cbkconst.blk"
#include "cbkdistan.blk"
#include "cbkinit.blk"
#include "cbktregime.blk"
#include "control.blk"
#include "opt.blk"
#include "small.blk"
character*6 qident
character*20 qhulp
* dimension qident(100)
************************************************************************
* *
* Read control file *
* *
************************************************************************
c$$$c if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$c write (65,*) 'In readc'
c$$$c call timer(65)
c$$$c close (65)
c$$$c end if
if (mdstep.gt.0.or.nit.gt.0) nmmsav=nmm
************************************************************************
* *
* Set default values *
* *
************************************************************************
nreac=0
axis1=200.0d0
axis2=200.0d0
axis3=200.0d0
cutof2=0.001d0
cutof3=0.300d0
tsetor=298.0d0
tset2=298.0d0
pset=0.0d0
tincr=0.0d0
tstep=0.5d0
* swa=0.0 !Moved to force field
* swb=12.5 !Moved to force field
taut=2.5d0
taut2=2.5d0
ndtau=50000
taup=500.0d0
vqnd=100.0d0
errnh=1.0d0
range=2.5d0
maxstp=1000
nequi=0
nmethod=3
ncha=3
ncha2=1
nchaud=1
nvlist=25
nrep1=5
nsav=50
icheck=0
ivels=0
itfix=0
ncontrol=25
noutpt=0
napp=0
nsurp=0
ncons=2
nrand=0
nmm=0
endpo=1.0d0
endpo2=1.0d0
nfc=50
nsav2=50
nmmax=50
i5758=0
parc1=1.0d0
parc2=0.001d0
icell=0
ingeo=1
ccpar=1.0005d0
icelo2=0
nrdd=0
nrddf=200000
nbiolab=0
c ngeofor=0
nincrop=0
accerr=2.50d0
vrange=2.50d0
vlbora=5.00d0
nsav3=1000
nhop2=25
nprevrun=0
ndebug=0
volcha=10.00d0
ixmolo=0
inpt=0
iconne=0
imolde=0
ianaly=0
icentr=0
itrans=0
itrout=0
tpnrad=300.0d0
ityrad=3
iexx=1
iexy=1
iexz=1
syscha=0.00d0
inmov1=0
inmov2=0
vfield=0.00d0
itstep=0
ifreq=0
isymm=1
icpres=0
delvib=0.0001d0
c shock variables
shock_vel = 2.d0 ! impact velocity for shock simulations (nm/ps)
shock_z_sep = 10.0d0 ! separation z value to apply initial velocities in shocks
ishock_type = 0.0d0 ! shock type. 0: simple impact; 1: compressing c axis
c Hugoniostat variables
Hug_E0 = 0.d0 ! Reference energy
Hug_P0 = 0.d0 ! Reference pressure
Hug_V0 = 0.d0 ! Reference volume
c Shear flow simulations for viscosity
xImpVcm = 1.d0 ! velocity applied in shear simulations (in nm/ps), left half mover at -xImpVcm and right at +xImpVcm
c$$$************************************************************************
c$$$* *
c$$$* Read control-file *
c$$$* *
c$$$************************************************************************
c$$$ open (10,file='control',status='old')
c$$$ 10 read (10,'(a20)',end=20,err=30)qhulp
c$$$ if (qhulp(1:1).eq.'#') goto 10
c$$$ read (qhulp,*,err=30)vhulp
c$$$ read (qhulp,'(8x,a6)',err=30)qident
c$$$ if (qident.eq.'Hug_V0') Hug_P0=vhulp
c$$$ if (qident.eq.'Hug_P0') Hug_V0=vhulp
c$$$ if (qident.eq.'Hug_E0') Hug_E0=vhulp
c$$$ if (qident.eq.'shea_v') xImpVcm=vhulp
c$$$ if (qident.eq.'shok_t') ishock_type=int(vhulp)
c$$$ if (qident.eq.'shok_z') shock_z_sep=vhulp
c$$$ if (qident.eq.'shok_v') shock_vel=vhulp
c$$$ if (qident.eq.'nreac') nreac=int(vhulp)
c$$$ if (qident.eq.'axis1') axis1=vhulp
c$$$ if (qident.eq.'axis2') axis2=vhulp
c$$$ if (qident.eq.'axis3') axis3=vhulp
c$$$ if (qident.eq.'cutof2') cutof2=vhulp
c$$$ if (qident.eq.'cutof3') cutof3=vhulp
c$$$ if (qident.eq.'mdtemp') tsetor=vhulp
c$$$ if (qident.eq.'mdtem2') tset2=vhulp
c$$$ if (qident.eq.'mdpres') pset=vhulp*0.001
c$$$ if (qident.eq.'tincr') tincr=vhulp
c$$$ if (qident.eq.'tstep') tstep=vhulp
c$$$* if (qident.eq.'lowtap') swa=vhulp !Moved to force field
c$$$* if (qident.eq.'uptap') swb=vhulp !Moved to force field
c$$$ if (qident.eq.'tdamp1') taut=vhulp
c$$$ if (qident.eq.'tdamp2') taut2=vhulp
c$$$ if (qident.eq.'ntdamp') ndtau=int(vhulp)
c$$$ if (qident.eq.'pdamp1') taup=vhulp
c$$$ if (qident.eq.'tdhoov') vqnd=vhulp
c$$$ if (qident.eq.'achoov') errnh=vhulp/100.0
c$$$ if (qident.eq.'range') range=vhulp
c$$$ if (qident.eq.'nmdit') maxstp=int(vhulp)
c$$$ if (qident.eq.'nmdeqi') nequi=int(vhulp)
c$$$ if (qident.eq.'imdmet') nmethod=int(vhulp)
c$$$ if (qident.eq.'icharg') ncha=int(vhulp)
nchaold=ncha
c$$$ if (qident.eq.'ichaen') ncha2=int(vhulp)
c$$$ if (qident.eq.'ichupd') nchaud=int(vhulp)
c$$$ if (qident.eq.'iout1') nrep1=int(vhulp)
c$$$ if (qident.eq.'iout2') nsav=int(vhulp)
c$$$ if (qident.eq.'icheck') ntest=int(vhulp)
c$$$ if (qident.eq.'ivels') nvel=int(vhulp)
c$$$ if (qident.eq.'itfix') ntscale=int(vhulp)
c$$$ if (qident.eq.'irecon') ncontrol=int(vhulp)
c$$$ if (qident.eq.'iout3') noutpt=int(vhulp)
c$$$ if (qident.eq.'iappen') napp=int(vhulp)
c$$$ if (qident.eq.'isurpr') nsurp=int(vhulp)
c$$$ if (qident.eq.'itdmet') ncons=int(vhulp)
c$$$ if (qident.eq.'iravel') nrand=int(vhulp)
c$$$ if (qident.eq.'imetho') nmm=int(vhulp)
c$$$ if (qident.eq.'endmm') endpo=vhulp
endpoold=endpo
c$$$ if (qident.eq.'endmd') endpo2=vhulp
c$$$ if (qident.eq.'imaxmo') nfc=int(vhulp)
nfcold=nfc
c$$$ if (qident.eq.'iout4') nsav2=int(vhulp)
c$$$ if (qident.eq.'imaxit') nmmax=int(vhulp)
nmmaxold=nmmax
c$$$ if (qident.eq.'iout5') i5758=int(vhulp)
c$$$ if (qident.eq.'parsca') parc1=vhulp
c$$$ if (qident.eq.'parext') parc2=vhulp
c$$$ if (qident.eq.'icelop') icell=int(vhulp)
icellold=icell
c$$$ if (qident.eq.'igeopt') ingeo=int(vhulp)
c$$$ if (qident.eq.'celopt') ccpar=vhulp
c$$$ if (qident.eq.'icelo2') icelo2=int(vhulp)
icelo2old=icelo2
c$$$ if (qident.eq.'ideve1') nrdd=int(vhulp)
c$$$ if (qident.eq.'ideve2') nrddf=int(vhulp)
c$$$ if (qident.eq.'ibiola') nbiolab=int(vhulp)
c$$$c if (qident.eq.'igeofo') ngeofor=int(vhulp)
c$$$ if (qident.eq.'iincop') nincrop=int(vhulp)
c$$$ if (qident.eq.'accerr') accincr=vhulp
c$$$ if (qident.eq.'iout6') nsav3=int(vhulp)
c$$$ if (qident.eq.'irten') nhop2=int(vhulp)
c$$$ if (qident.eq.'npreit') nprevrun=int(vhulp)
c$$$ if (qident.eq.'idebug') ndebug=int(vhulp)
c$$$ if (qident.eq.'volcha') volcha=vhulp
c$$$ if (qident.eq.'ixmolo') ixmolo=int(vhulp)
c$$$ if (qident.eq.'inpt') inpt=int(vhulp)
c$$$ if (qident.eq.'iconne') iconne=int(vhulp)
c$$$ if (qident.eq.'imolde') imolde=int(vhulp)
c$$$ if (qident.eq.'ianaly') ianaly=int(vhulp)
c$$$ if (qident.eq.'icentr') icentr=int(vhulp)
c$$$ if (qident.eq.'itrans') itrans=int(vhulp)
c$$$ if (qident.eq.'itrout') itrout=int(vhulp)
c$$$ if (qident.eq.'nvlist') nvlist=int(vhulp)
c$$$ if (qident.eq.'vrange') vrange=vhulp
c$$$ if (qident.eq.'vlbora') vlbora=vhulp
c$$$ if (qident.eq.'tpnrad') tpnrad=vhulp
c$$$ if (qident.eq.'ityrad') ityrad=int(vhulp)
c$$$ if (qident.eq.'iexx') iexx=int(vhulp)
c$$$ if (qident.eq.'iexy') iexy=int(vhulp)
c$$$ if (qident.eq.'iexz') iexz=int(vhulp)
c$$$ if (qident.eq.'syscha') syscha=vhulp
c$$$ if (qident.eq.'inmov1') inmov1=int(vhulp)
c$$$ if (qident.eq.'inmov2') inmov2=int(vhulp)
c$$$ if (qident.eq.'itstep') itstep=int(vhulp)
c$$$ if (qident.eq.'ifreq') ifreq=int(vhulp)
c$$$ if (qident.eq.'isymm') isymm=int(vhulp)
c$$$ if (qident.eq.'icpres') icpres=int(vhulp)
c$$$ if (qident.eq.'delvib') delvib=vhulp
c$$$ goto 10
c$$$ 20 continue
close (10)
axis(1)=axis1
axis(2)=axis2
axis(3)=axis3
if (axiss(1).gt.zero) then
axis(1)=axiss(1)
axis(2)=axiss(2)
axis(3)=axiss(3)
end if
if (tincr.lt.0.0001.and.tincr.gt.-0.0001) tset=tsetor
iequi=1
if (nequi.gt.0) iequi=0
if (iopt.eq.1.and.napp.eq.1) then
stop 'No fort.7 and fort.8 append with iopt=1 !'
end if
if (mdstep.gt.0.or.nit.gt.0) nmm=nmmsav
if (mdstep.gt.0.and.itstep.eq.1) then
tstepmax=tstep
tstep=tstep*(tsetor/tempmd)
if (tstep.gt.tstepmax) tstep=tstepmax
end if
tstep=1.0d-15*tstep
taus=taut
taut=1.0d-15*taut
taut2=1.0d-15*taut2
taup=1.0d-15*taup
ts2=tstep/2.0
ts22=tstep*ts2
return
30 continue
write (*,*)'Error reading control-file'
stop 'Error reading control-file'
************************************************************************
* *
* Format part *
* *
************************************************************************
1050 format (f7.3)
1055 format (f7.4)
1056 format (f9.4)
1060 format (i8)
1070 format (f7.5)
end
************************************************************************
************************************************************************
subroutine staint
************************************************************************
#include "cbka.blk"
#include "cbkdcell.blk"
#include "cbkqa.blk"
#include "control.blk"
#include "small.blk"
#include "cbkc.blk"
#include "cbkconst.blk"
dimension bvt(nat,4)
************************************************************************
* *
* Generate cartesian coordinates from internal coordinate input *
* *
************************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In staint'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
k=0
10 read (3,1200,end=20,err=20)(ijk(k+1,k1),k1=1,3),k2,qa(k+1),
$bvt(k+1,3),bvt(k+1,2),bvt(k+1,1)
qlabel(k+1)=qa(k+1)
qresi1(k+1)=' '
qresi2(k+1)=' '
qresi3(k+1)=' '
qffty(k+1)=' '
if (k2.ne.k+1) then
write (*,*)'Wrong order in internal coordinates at atom:',k2
goto 20
* stop 'Wrong order in internal coordinates'
end if
k=k+1
if (k.gt.nat) then
write (*,*)na,nat
stop 'Maximum number of atoms exceeded'
end if
goto 10
20 continue
na=k
************************************************************************
* *
* CALCULATION OF CARTESIAN COORDINATES FROM INTERNAL COORDINAATES *
* *
************************************************************************
12 C(1,1)=ZERO
C(1,2)=ZERO
C(1,3)=ZERO
C(2,1)=BVT(2,1)
C(2,2)=ZERO
C(2,3)=ZERO
HR=(BVT(3,2)-90.0D0)*DGRRDN
C(3,1)=C(2,1)+BVT(3,1)*SIN(HR)
C(3,2)=BVT(3,1)*COS(HR)
C(3,3)=ZERO
DO 32 K1=4,NA
J=IJK(K1,2)
KB=K1-1
XH=C(J,1)
YH=C(J,2)
ZH=C(J,3)
DO 13 K2=1,KB
C(K2,1)=C(K2,1)-XH
C(K2,2)=C(K2,2)-YH
C(K2,3)=C(K2,3)-ZH
DO 13 K3=1,3
13 IF (ABS(C(K2,K3)).LT.1.0D-15) C(K2,K3)=1.0D-15
K=IJK(K1,3)
P2=C(K,2)*C(K,2)+C(K,3)*C(K,3)
IF (P2.NE.ZERO) THEN
P=SQRT(P2)
Q=SQRT(C(K,1)*C(K,1)+P2)
SA=C(K,2)/P
CA=C(K,3)/P
SB=-C(K,1)/Q
CB=P/Q
ELSE
SA=ZERO
CA=ONE
SB=ONE
CB=ZERO
ENDIF
DO 16 K2=1,KB
AZ=C(K2,1)
BZ=C(K2,2)
C(K2,1)=AZ*CB+BZ*SB*SA+C(K2,3)*SB*CA
C(K2,2)=BZ*CA-C(K2,3)*SA
16 C(K2,3)=-AZ*SB+BZ*CB*SA+C(K2,3)*CB*CA
IF (C(K,3).LE.ZERO) THEN
DO 17 K2=1,KB
17 C(K2,3)=-C(K2,3)
ENDIF
I=IJK(K1,1)
IF (1.0D5*ABS(C(I,1)).LE.ABS(C(I,2))) THEN
T1=HALF*PI
ELSE
YX=ABS(C(I,2)/C(I,1))
T1=ATAN(YX)
ENDIF
IF (C(I,1).GE.ZERO.AND.C(I,2).LT.ZERO) T1=TWO*PI-T1
IF (C(I,1).LT.ZERO.AND.C(I,2).GE.ZERO) T1=PI-T1
IF (C(I,1).LT.ZERO.AND.C(I,2).LT.ZERO) T1=T1+PI
DO 31 K2=1,KB
IF (C(K2,1).EQ.ZERO.AND.C(K2,2).EQ.ZERO) GOTO 31
IF (1.0D5*ABS(C(K2,1)).LT.ABS(C(K2,2))) THEN
T2=HALF*PI
ELSE
YX=ABS(C(K2,2)/C(K2,1))
T2=ATAN(YX)
ENDIF
IF (C(K2,1).GE.ZERO.AND.C(K2,2).LT.ZERO) T2=TWO*PI-T2
IF (C(K2,1).LT.ZERO.AND.C(K2,2).GE.ZERO) T2=PI-T2
IF (C(K2,1).LT.ZERO.AND.C(K2,2).LT.ZERO) T2=T2+PI
T3=T2-T1
IF (T3.LT.ZERO)T3=T3+TWO*PI
RZ=SQRT(C(K2,1)*C(K2,1)+C(K2,2)*C(K2,2))
C(K2,1)=RZ*COS(T3)
C(K2,2)=RZ*SIN(T3)
31 CONTINUE
HR=(BVT(K1,2)-90.0D0)*DGRRDN
HT=BVT(K1,3)*DGRRDN
CHR=COS(HR)
C(K1,1)=BVT(K1,1)*CHR*COS(HT)
C(K1,2)=BVT(K1,1)*CHR*SIN(HT)
32 C(K1,3)=C(IJK(K1,3),3)+BVT(K1,1)*SIN(HR)
return
1200 FORMAT(4I3,1X,A2,3F10.5,4X,I1,F10.5)
end
************************************************************************
************************************************************************
subroutine outint
************************************************************************
#include "cbka.blk"
#include "cbkabo.blk"
#include "cbkbo.blk"
#include "cbkconst.blk"
#include "cbkia.blk"
#include "cbkinit.blk"
#include "cbknubon2.blk"
#include "cbkqa.blk"
#include "cbktregime.blk"
#include "control.blk"
#include "small.blk"
#include "cbksrtbon1.blk"
************************************************************************
* *
* Output internal coordinates *
* *
************************************************************************
dimension dvdc(3,3),dargdc(3,3)
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In outint'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
write (91,50)qmol
open (82,file='output.MOP',status='unknown')
write (82,*)
write (82,'(a40)')qmol
write (82,*)
close (82)
* IF (NMOLO.GT.1) THEN
* WRITE(6,*)' OUTPUT INTERNAL COORDINATES NOT POSSIBLE FOR ',
* $'CALCULATION ON MORE THAN ONE MOLECULE'
* RETURN
* END IF
************************************************************************
* *
* Output of internal coordinates. *
* First 3 atoms of other input file. *
* *
************************************************************************
N1=1
N2=2
N3=3
C open (82,file='output.MOP',status='unknown',access='append')
write(91,100)N1,qa(n1)
write(82,'(2x,a2,f12.6,i3,f12.6,i3,f12.6,i3,1x,3i4)')qa(n1),
$zero,nzero,zero,nzero,zero,nzero,nzero,nzero,nzero
call dista2(n1,n2,rr,dx,dy,dz)
write(91,200)N1,N2,qa(n2),RR
write(82,'(2x,a2,f12.6,i3,f12.6,i3,f12.6,i3,1x,3i4)')qa(n2),
$rr,none,zero,nzero,zero,nzero,n1,nzero,nzero
close (82)
call dista2(n2,n3,rr,dx,dy,dz)
hv=zero
call calvalres(n1,n2,n3,arg,hv,dvdc,dargdc)
WRITE(91,300)N1,N2,N3,qa(n3),rdndgr*HV,RR
C open (82,file='output.MOP',status='unknown',access='append')
write(82,'(2x,a2,f12.6,i3,f12.6,i3,f12.6,i3,1x,3i4)')qa(n3),
$rr,none,rdndgr*hv,none,zero,nzero,n2,n1,nzero
close (82)
naih=3
do i1=naih+1,na
bomax=zero
j1=0
do i2=1,ia(i1,2)
iob=ia(i1,2+i2)
ncubo=nubon2(i1,i2)
if (bo(ncubo).gt.bomax.and.iob.lt.i1) then
bomax=bo(ncubo)
j1=iob
end if
end do
if (j1.eq.0) j1=i1-1
call dista2(j1,i1,rr,dx,dy,dz)
bomax=zero
j2=0
do i2=1,ia(j1,2)
iob=ia(j2,2+i2)
ncubo=nubon2(j1,i2)
if (bo(ncubo).gt.bomax.and.iob.lt.i1.and.
$abo(iob).gt.bo(ncubo)+0.2) then
bomax=bo(ncubo)
j2=iob
end if
end do
if (j2.eq.0) j2=i1-2
if (j2.eq.j1) j2=j2+1
call calvalres(j2,j1,i1,arg,hh,dvdc,dargdc)
bomax=zero
j3=0
do i2=1,ia(j2,2)
iob=ia(j2,2+i2)
ncubo=nubon2(j2,i2)
if (bo(ncubo).gt.bomax.and.iob.lt.i1.and.iob.ne.j1) then
bomax=bo(ncubo)
j3=iob
end if
end do
if (j3.eq.0) j3=i1-3
if (j3.eq.j2.and.j3.ne.j1-1) j3=j3+1
if (j3.eq.j2.and.j3.ne.j1-2) j3=j3+2
if (j3.eq.j1.and.j3.ne.j2-1) j3=j3+1
if (j3.eq.j1.and.j3.ne.j2-2) j3=j3+2
call caltor(j3,j2,j1,i1,ht)
write(91,400)j3,j2,j1,i1,qa(i1),ht,rdndgr*hh,rr
C open (82,file='output.MOP',status='unknown',access='append')
write(82,'(2x,a2,f12.6,i3,f12.6,i3,f12.6,i3,1x,3i4)')qa(i1),
$rr,none,rdndgr*hh,none,ht,none,j1,j2,j3
close (82)
end do
close(82)
return
50 format (' I',2x,a60)
100 FORMAT(9X,I3,1x,a2)
200 FORMAT(6X,2I3,1x,a2,20X,F10.5)
300 FORMAT(3X,3I3,1x,a2,10X,2F10.5)
400 FORMAT(4I3,1x,a2,3F10.5)
end
************************************************************************
************************************************************************
subroutine outres
************************************************************************
#include "cbka.blk"
#include "cbkbo.blk"
#include "cbkch.blk"
#include "cbkd.blk"
#include "cbkenergies.blk"
#include "cbkh.blk"
#include "cbkimove.blk"
#include "cbkrbo.blk"
#include "cbktorang.blk"
#include "cbktorsion.blk"
#include "cbktregime.blk"
#include "cbkvalence.blk"
#include "control.blk"
#include "opt.blk"
#include "small.blk"
#include "cbkinit.blk"
************************************************************************
* *
* Output molecular data *
* *
************************************************************************
dimension isort(100),iad1(100),iad2(100),iad3(100),iad4(100)
character*60 qm2
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In outres'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
read (9,100,end=50)idata,qm2
* if (qm2.ne.qmol) then
* write (*,*)'Wrong molecule in outres-file'
* write (*,*)qmol
* write (*,*)qm2
* return
* end if
do 25 i1=1,idata
read (9,200)isort(i1),iad1(i1),iad2(i1),iad3(i1),iad4(i1)
ndata2=ndata2+1
if (isort(i1).eq.1) then
* do i2=1,nbon
* if (ib(i2,2).eq.iad1(i1).and.ib(i2,3).eq.iad2(i1)) then
* if (iopt.ne.1) write (81,*)iad1(i1),iad2(i1),rbo(i2)
* caldat(ndata2)=rbo(i2)
* end if
* end do
call dista2(iad1(i1),iad2(i1),dish,dx,dy,dz)
write (81,*)iad1(i1),iad2(i1),dish
caldat(ndata2)=dish
end if
if (isort(i1).eq.2) then
do i2=1,nval
if (iv(i2,2).eq.iad1(i1).and.iv(i2,3).eq.iad2(i1).and.
$iv(i2,4).eq.iad3(i1)) then
if (iopt.ne.1) write (81,*)iad1(i1),iad2(i1),
$iad3(i1),h(i2)*rdndgr
caldat(ndata2)=h(i2)*rdndgr
end if
end do
end if
if (isort(i1).eq.3) then
do i2=1,ntor
if (it(i2,2).eq.iad1(i1).and.it(i2,3).eq.iad2(i1).and.
$it(i2,4).eq.iad3(i1).and.it(i2,5).eq.iad4(i1)) then
if (iopt.ne.1) write (81,*)iad1(i1),iad2(i1),iad3(i1),iad4(i1),
$abs(thg(i2))
caldat(ndata2)=abs(thg(i2))
end if
end do
end if
if (isort(i1).eq.4) then
if (iopt.ne.1) write (81,*)estrmin
caldat(ndata2)=estrmin
end if
if (isort(i1).eq.5) then
if (iopt.ne.1) write (81,*)estrmin
caldat(ndata2)=estrmin
end if
if (isort(i1).eq.6) then
if (iopt.ne.1) write (81,*)iad1(i1),axiss(iad1(i1))
caldat(ndata2)=axiss(iad1(i1))
end if
if (isort(i1).eq.7) then
if (iopt.ne.1) write (81,*)eco
caldat(ndata2)=eco
end if
if (isort(i1).eq.8) then
do i2=1,nbon
if (ib(i2,2).eq.iad1(i1).and.ib(i2,3).eq.iad2(i1)) then
if (iopt.ne.1) write (81,*)iad1(i1),iad2(i1),bo(i2)
caldat(ndata2)=bo(i2)
end if
end do
end if
if (isort(i1).eq.9) then
if (iopt.ne.1) write (81,*)ch(iad1(i1))
caldat(ndata2)=ch(iad1(i1))
end if
if (isort(i1).eq.10) then
rmsg=0.0
nmovh=0
do i2=1,na
do i3=1,3
rmsg=rmsg+imove(i2)*d(i3,i2)*d(i3,i2)
nmovh=nmovh+imove(i2)
end do
end do
rmsg=sqrt(rmsg/float(nmovh*3))
if (iopt.ne.1) write (81,*)rmsg
caldat(ndata2)=rmsg
end if
if (isort(i1).eq.11) then
if (iopt.ne.1) write (81,*)1000.0*pressu
caldat(ndata2)=1000.0*pressu
end if
25 continue
50 return
************************************************************************
* *
* Format part *
* *
************************************************************************
100 format (i3,a60)
200 format (5i3)
end
************************************************************************
************************************************************************
subroutine readgeo
************************************************************************
#include "cbka.blk"
#include "cbkc.blk"
#include "cbkconst.blk"
#include "cbkdistan.blk"
#include "cbkinit.blk"
#include "cbkqa.blk"
#include "cbksrtbon1.blk"
#include "cbktregime.blk"
#include "cellcoord.blk"
#include "control.blk"
#include "small.blk"
character*80 qromb
character*25 qfileh
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In readgeo'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
if (ngeofor.eq.-1) return
**********************************************************************
* *
* Read in system geometry *
* *
**********************************************************************
if (ngeofor.eq.0) then
call readdelphi (qfileh,iend,naold)
namov=na
end if
if (ngeofor.eq.1) then
call readbgf(iend,naold)
end if
if (ngeofor.eq.2) then
**********************************************************************
* *
* Read in free format (xmol) geometry *
* *
**********************************************************************
qr='1'
read (3,'(i6)')na
namov=na
read (3,'(a60)')qmol
do i1=1,na
read (3,'(a80)')qromb
ifirstchar=80
do i2=1,80
if (qromb(i2:i2).ne.' '.and.i2.lt.ifirstchar) ifirstchar=i2
end do
read (qromb(ifirstchar:80),'(a2)')qa(i1)
read (qromb(ifirstchar+2:80),*)c(i1,1),c(i1,2),c(i1,3)
qlabel(i1)=qa(i1)
qresi1(i1)=' '
qresi2(i1)=' '
qresi3(i1)=' '
qffty(i1)=' '
end do
ibity=1
axiss(1)=-1.0
end if
if (ngeofor.eq.3) then
**********************************************************************
* *
* Read in ChemDraw CC1-file *
* *
**********************************************************************
qr='1'
read (3,*)na
namov=na
read (3,'(a60)')qmol
do i1=1,na
read (3,'(2x,a2,5x,3f12.6)')qa(i1),c(i1,1),c(i1,2),c(i1,3)
end do
end if
if (ngeofor.eq.4) then
**********************************************************************
* *
* Read in .pdb-format *
* *
**********************************************************************
qr='C'
call readpdb(iendf)
namov=na
ibity=1
axiss(1)=-1.0
qfile(nprob)=qmol
if (iendf.eq.1) stop 'End-of-file while reading in .pdb'
end if
**********************************************************************
* *
* Set up periodic system *
* *
**********************************************************************
axis(1)=axiss(1)
axis(2)=axiss(2)
axis(3)=axiss(3)
angle(1)=angles(1)
angle(2)=angles(2)
angle(3)=angles(3)
if (axiss(1).lt.zero) then
axis(1)=axis1
axis(2)=axis2
axis(3)=axis3
angle(1)=90.0
angle(2)=90.0
angle(3)=90.0
end if
halfa=angle(1)*dgrrdn
hbeta=angle(2)*dgrrdn
hgamma=angle(3)*dgrrdn
sinalf=sin(halfa)
cosalf=cos(halfa)
sinbet=sin(hbeta)
cosbet=cos(hbeta)
cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
if (cosphi.gt.1.0) cosphi=1.0
sinphi=sqrt(one-cosphi*cosphi)
tm11=axis(1)*sinbet*sinphi
tm21=axis(1)*sinbet*cosphi
tm31=axis(1)*cosbet
tm22=axis(2)*sinalf
tm32=axis(2)*cosalf
tm33=axis(3)
return
end
************************************************************************
************************************************************************
subroutine readdelphi (qfileh,iend,naold)
************************************************************************
#include "cbka.blk"
#include "cbkc.blk"
#include "cbkconst.blk"
#include "cbkd.blk"
#include "cbkdcell.blk"
#include "cbkdistan.blk"
#include "cbkff.blk"
#include "cbkh.blk"
#include "cbkinit.blk"
#include "cbkqa.blk"
#include "cbkrestr.blk"
#include "cbksrtbon1.blk"
#include "cbktregime.blk"
#include "cellcoord.blk"
#include "control.blk"
#include "opt.blk"
#include "small.blk"
character*25 qfileh
**********************************************************************
* *
* Read in geometries in Delphi-format (xyz) *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In readdelphi'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
if (imodfile.eq.1) then
open (3,file=qfileh,status='old')
end if
nmmax=nmmaxold
nfc=nfcold
ibity=1
iredo=1
endpo=endpoold
icell=icellold
icelo2=icelo2old
iend=0
read (3,1000,end=900)qr,qmol
**********************************************************************
* *
* Read in restraint information (optional) *
* *
**********************************************************************
if (qr.eq.'R'.or.qr.eq.'P'.or.qr.eq.'X') then
qmol=qmol(7:60)
qmolset(nuge)=qmol
read (18,1070,end=4,err=4) nrestra
do i1=1,nrestra
read (18,1090)irstra(i1,1),irstra(i1,2),rrstra(i1),vkrstr(i1),
$vkrst2(i1),rrcha(i1)
end do
4 continue
end if
**********************************************************************
* *
* Read in torsion restraint information (optional) *
* *
**********************************************************************
if (qr.eq.'T'.or.qr.eq.'X') then
if (qr.eq.'T') then
qmol=qmol(7:60)
qmolset(nuge)=qmol
end if
read (28,1070,end=6,err=6) nrestrat
do i1=1,nrestrat
read (28,1091)irstrat(i1,1),irstrat(i1,2),irstrat(i1,3),
$irstrat(i1,4),trstra(i1),vkrt(i1),vkr2t(i1),rtcha(i1)
end do
6 continue
end if
**********************************************************************
* *
* Read in valency angle restraint information (optional) *
* *
**********************************************************************
if (qr.eq.'V') then
qmol=qmol(7:60)
qmolset(nuge)=qmol
read (38,1070,end=7,err=7) nrestrav
do i1=1,nrestrav
read (38,1092)irstrav(i1,1),irstrav(i1,2),irstrav(i1,3),
$vrstra(i1),vkrv(i1),vkr2v(i1)
end do
7 continue
end if
**********************************************************************
* *
* Read in geometry *
* *
**********************************************************************
ibh2=0
iequi=1
iexco=0
if (nequi.gt.0) iequi=0
axiss(1)=-1.0
if (qr.eq.'O'.or.qr.eq.'L') stop 'Not xyz-format'
if (qr.eq.'I') then !Delphi internal coordinates
if (nsurp.ge.2) stop 'Int.coordinates only with 1 gemetry'
call staint
goto 20
end if
if (qr.eq.'B') then !Previous geometry with volume reduction
read (3,*)
vred=(1.0-0.01*volcha)**(0.33333)
iexco=1
na=naold
do i1=1,3
qmol=qmol
axiss(i1)=vred*axis(i1)
angles(i1)=angle(i1)
do i2=1,na
c(i2,i1)=vred*c(i2,i1)
end do
end do
halfa=angles(1)*dgrrdn
hbeta=angles(2)*dgrrdn
hgamma=angles(3)*dgrrdn
sinalf=sin(halfa)
cosalf=cos(halfa)
sinbet=sin(hbeta)
cosbet=cos(hbeta)
cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
if (cosphi.gt.1.0) cosphi=1.0
sinphi=sqrt(one-cosphi*cosphi)
tm11=axiss(1)*sinbet*sinphi
tm21=axiss(1)*sinbet*cosphi
tm31=axiss(1)*cosbet
tm22=axiss(2)*sinalf
tm32=axiss(2)*cosalf
tm33=axiss(3)
kx=int(2.0*swb/tm11)
ky=int(2.0*swb/tm22)
kz=int(2.0*swb/tm33)
ibity=2
goto 20
end if
if (qr.eq.'S') then !Previous geometry with volume expansion
read (3,*)
vexp=(1.0+0.01*volcha)**(0.33333)
na=naold
iexco=1
do i1=1,3
qmol=qmol
axiss(i1)=vexp*axis(i1)
angles(i1)=angle(i1)
do i2=1,na
c(i2,i1)=vexp*c(i2,i1)
end do
end do
halfa=angles(1)*dgrrdn
hbeta=angles(2)*dgrrdn
hgamma=angles(3)*dgrrdn
sinalf=sin(halfa)
cosalf=cos(halfa)
sinbet=sin(hbeta)
cosbet=cos(hbeta)
cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
if (cosphi.gt.1.0) cosphi=1.0
sinphi=sqrt(one-cosphi*cosphi)
tm11=axiss(1)*sinbet*sinphi
tm21=axiss(1)*sinbet*cosphi
tm31=axiss(1)*cosbet
tm22=axiss(2)*sinalf
tm32=axiss(2)*cosalf
tm33=axiss(3)
kx=int(2.0*swb/tm11)
ky=int(2.0*swb/tm22)
kz=int(2.0*swb/tm33)
ibity=2
goto 20
end if
if (qr.eq.'F'.or.qr.eq.'Y'.or.qr.eq.'3'.or.qr.eq.'5'.
$or.qr.eq.'P') then
kx=0
ky=0
kz=0
ibity=2
read(3,1005)axiss(1),axiss(2),axiss(3)
read(3,1005)angles(1),angles(2),angles(3)
halfa=angles(1)*dgrrdn
hbeta=angles(2)*dgrrdn
hgamma=angles(3)*dgrrdn
sinalf=sin(halfa)
cosalf=cos(halfa)
sinbet=sin(hbeta)
cosbet=cos(hbeta)
cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
if (cosphi.gt.1.0) cosphi=1.0
sinphi=sqrt(one-cosphi*cosphi)
tm11=axiss(1)*sinbet*sinphi
tm21=axiss(1)*sinbet*cosphi
tm31=axiss(1)*cosbet
tm22=axiss(2)*sinalf
tm32=axiss(2)*cosalf
tm33=axiss(3)
kx=int(2.0*swb/tm11)
ky=int(2.0*swb/tm22)
kz=int(2.0*swb/tm33)
end if
if (qr.eq.'M'.or.qr.eq.'A') then
nmmsav=nmm
nmm=2
end if
if (qr.eq.'A') nmm=1
if (qr.eq.'D') then
endpo=endpo/25
nmmax=nmmax*5
qruid='HIGH PRECISION'
end if
if (qr.eq.'H') then
nmmax=nmmax/10
qruid='LOW PRECISION'
end if
if (qr.eq.'1'.or.qr.eq.'5') then
nmm=1
nmmax=1
qruid='SINGLE POINT'
end if
if (qr.eq.'Y') then
icell=0
qruid='NO CELL OPT'
end if
10 read (3,1100,end=20,err=20)ir,qa(na+1),(c(na+1,i2),i2=1,3)
qlabel(na+1)=qa(na+1)
qresi1(na+1)=' '
qresi2(na+1)=' '
qresi3(na+1)=' '
qffty(na+1)=' '
if (ir.eq.0) goto 20
na=na+1
if (na.gt.nat) then
write (*,*)'Maximum number of atom exceeded ',na,nat
stop 'Maximum number of atoms exceeded'
end if
goto 10
20 continue
if (imodfile.eq.1) close (3)
return
900 iend=1
return
1000 format (2x,a1,1x,a60)
1005 format (3f10.4)
1070 format (i3)
1090 format (2i4,2f8.4,f8.6,f10.8)
1091 format (4i4,2f8.4,3f8.6)
1092 format (3i4,2f8.4,2f8.6)
1100 format (i4,1x,a2,3x,3d22.15,1x,a5,1x,i5)
end
************************************************************************
************************************************************************
subroutine readbgf(iendf,naold)
************************************************************************
#include "cbka.blk"
#include "cbkc.blk"
#include "cbkcha.blk"
#include "cbkcharmol.blk"
#include "cbkconst.blk"
#include "cbkd.blk"
#include "cbkdcell.blk"
#include "cbkdistan.blk"
#include "cbkenergies.blk"
#include "cbkff.blk"
#include "cbkh.blk"
#include "cbkimove.blk"
#include "cbkinit.blk"
#include "cbkqa.blk"
#include "cbkrestr.blk"
#include "cbksrtbon1.blk"
#include "cbktregime.blk"
#include "cellcoord.blk"
#include "control.blk"
#include "opt.blk"
#include "small.blk"
character*80 qromb
character*2 qrom
character*5 quen
character*5 qlabhulp
character*25 qfileh
character*200 qhulp
**********************************************************************
* *
* Read in BIOGRAF-geometry *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In readbgf'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
iendf=0
ienread=0
iredo=0
qremark(1)=' '
enmol=zero
formol=zero
c$$$ if (imodfile.eq.1) then
c$$$ open (3,file=qfileh,status='old')
c$$$ end if
open (3,file='fort.3',status='old')
read (3,'(a40)',end=900)qromb
ibity=0
if (qromb(1:6).eq.'BIOGRF') ibity=1
if (qromb(1:6).eq.'XTLGRF') ibity=2
if (ibity.eq.0) then
write (*,*)qromb(1:6)
stop 'Unknown Biograf-file'
end if
read (qromb,'(6x,i4)')ibgfversion
if (ibity.eq.1) qr='C'
if (ibity.eq.2) qr='F'
iremark=0
iformat=0
iline=0
iexco=0
iruid=1
vvol=1.0
nmcharge=0
nmmax=nmmaxold
nfc=nfcold
ncha=nchaold
endpo=endpoold
icell=icellold
icelo2=icelo2old
axiss(1)=-1.0
30 read (3,'(a200)',end=46,err=40)qhulp
qstrana1(1:200)=qhulp
iline=iline+1
irecog=0
if (qhulp(1:6).eq.'DESCRP') then
read (qhulp,'(7x,a40)',end=46,err=46)qmol
irecog=1
end if
if (qhulp(1:6).eq.'REMARK') then
if (iremark.lt.20) iremark=iremark+1
read (qhulp,'(7x,a40)',end=46,err=46)qremark(iremark)
irecog=1
end if
if (qhulp(1:6).eq.'FORMAT') then
if (iformat.lt.20) iformat=iformat+1
read(qhulp,'(7x,a40)',end=46,err=46)qformat(iformat)
irecog=1
end if
if (qhulp(1:7).eq.'VCHANGE') then
read (qhulp(8:60),*)vvol
vred=(1.0+(vvol-1.0))**(0.33333333)
iexco=1
na=naold
qmol=qmol
do i1=1,3
axiss(i1)=vred*axis(i1)
angles(i1)=angle(i1)
do i2=1,na
cglobal(i2,i1)=vred*cglobal(i2,i1)
end do
end do
halfa=angles(1)*dgrrdn
hbeta=angles(2)*dgrrdn
hgamma=angles(3)*dgrrdn
sinalf=sin(halfa)
cosalf=cos(halfa)
sinbet=sin(hbeta)
cosbet=cos(hbeta)
cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
if (cosphi.gt.1.0) cosphi=1.0
sinphi=sqrt(one-cosphi*cosphi)
tm11=axiss(1)*sinbet*sinphi
tm21=axiss(1)*sinbet*cosphi
tm31=axiss(1)*cosbet
tm22=axiss(2)*sinalf
tm32=axiss(2)*cosalf
tm33=axiss(3)
kx=int(2.0*swb/tm11)
ky=int(2.0*swb/tm22)
kz=int(2.0*swb/tm33)
ibity=2
irecog=1
end if
if (qhulp(1:7).eq.'VCHANGX') then
read (qhulp(8:60),*)vvol
vred=vvol
iexco=1
na=naold
qmol=qmol
do i1=1,3
axiss(i1)=axis(i1)
angles(i1)=angle(i1)
do i2=1,na
cglobal(i2,i1)=cglobal(i2,i1)
end do
end do
axiss(1)=vred*axiss(1)
do i2=1,na
cglobal(i2,1)=vred*cglobal(i2,1)
end do
halfa=angles(1)*dgrrdn
hbeta=angles(2)*dgrrdn
hgamma=angles(3)*dgrrdn
sinalf=sin(halfa)
cosalf=cos(halfa)
sinbet=sin(hbeta)
cosbet=cos(hbeta)
cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
if (cosphi.gt.1.0) cosphi=1.0
sinphi=sqrt(one-cosphi*cosphi)
tm11=axiss(1)*sinbet*sinphi
tm21=axiss(1)*sinbet*cosphi
tm31=axiss(1)*cosbet
tm22=axiss(2)*sinalf
tm32=axiss(2)*cosalf
tm33=axiss(3)
kx=int(2.0*swb/tm11)
ky=int(2.0*swb/tm22)
kz=int(2.0*swb/tm33)
ibity=2
irecog=1
end if
if (qhulp(1:7).eq.'VCHANGY') then
read (qhulp(8:60),*)vvol
vred=vvol
iexco=1
na=naold
qmol=qmol
do i1=1,3
axiss(i1)=axis(i1)
angles(i1)=angle(i1)
do i2=1,na
cglobal(i2,i1)=cglobal(i2,i1)
end do
end do
axiss(2)=vred*axiss(2)
do i2=1,na
cglobal(i2,2)=vred*cglobal(i2,2)
end do
halfa=angles(1)*dgrrdn
hbeta=angles(2)*dgrrdn
hgamma=angles(3)*dgrrdn
sinalf=sin(halfa)
cosalf=cos(halfa)
sinbet=sin(hbeta)
cosbet=cos(hbeta)
cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
if (cosphi.gt.1.0) cosphi=1.0
sinphi=sqrt(one-cosphi*cosphi)
tm11=axiss(1)*sinbet*sinphi
tm21=axiss(1)*sinbet*cosphi
tm31=axiss(1)*cosbet
tm22=axiss(2)*sinalf
tm32=axiss(2)*cosalf
tm33=axiss(3)
kx=int(2.0*swb/tm11)
ky=int(2.0*swb/tm22)
kz=int(2.0*swb/tm33)
ibity=2
irecog=1
end if
if (qhulp(1:7).eq.'VCHANGZ') then
read (qhulp(8:60),*)vvol
vred=vvol
iexco=1
na=naold
qmol=qmol
do i1=1,3
axiss(i1)=axis(i1)
angles(i1)=angle(i1)
do i2=1,na
cglobal(i2,i1)=cglobal(i2,i1)
end do
end do
axiss(3)=vred*axiss(3)
do i2=1,na
cglobal(i2,3)=vred*cglobal(i2,3)
end do
halfa=angles(1)*dgrrdn
hbeta=angles(2)*dgrrdn
hgamma=angles(3)*dgrrdn
sinalf=sin(halfa)
cosalf=cos(halfa)
sinbet=sin(hbeta)
cosbet=cos(hbeta)
cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
if (cosphi.gt.1.0) cosphi=1.0
sinphi=sqrt(one-cosphi*cosphi)
tm11=axiss(1)*sinbet*sinphi
tm21=axiss(1)*sinbet*cosphi
tm31=axiss(1)*cosbet
tm22=axiss(2)*sinalf
tm32=axiss(2)*cosalf
tm33=axiss(3)
kx=int(2.0*swb/tm11)
ky=int(2.0*swb/tm22)
kz=int(2.0*swb/tm33)
ibity=2
irecog=1
end if
if (qhulp(1:6).eq.'CRYSTX') then
read (qhulp,'(8x,6f11.5)',end=46,err=46)axiss(1),
$axiss(2),axiss(3),angles(1),angles(2),angles(3)
kx=0
ky=0
kz=0
halfa=angles(1)*dgrrdn
hbeta=angles(2)*dgrrdn
hgamma=angles(3)*dgrrdn
sinalf=sin(halfa)
cosalf=cos(halfa)
sinbet=sin(hbeta)
cosbet=cos(hbeta)
cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
if (cosphi.gt.1.0) cosphi=1.0
sinphi=sqrt(one-cosphi*cosphi)
tm11=axiss(1)*sinbet*sinphi
tm21=axiss(1)*sinbet*cosphi
tm31=axiss(1)*cosbet
tm22=axiss(2)*sinalf
tm32=axiss(2)*cosalf
tm33=axiss(3)
kx=int(2.0*swb/tm11)
ky=int(2.0*swb/tm22)
kz=int(2.0*swb/tm33)
qr='F'
if (nmmax.eq.1.and.nmmaxold.gt.1) qr='5'
if (icell.eq.0.and.icellold.gt.0) qr='Y'
ibity=2
irecog=1
end if
if (qhulp(1:6).eq.'PERIOD') then
read (qhulp,'(7x,i3)',end=46,err=46)iperiod
irecog=1
end if
if (qhulp(1:4).eq.'AXES') then
read (qhulp,'(7x,a3)',end=46,err=46)qbgfaxes
irecog=1
end if
if (qhulp(1:6).eq.'SGNAME') then
read (qhulp,'(7x,a3)',end=46,err=46)qbgfsgn
irecog=1
end if
* if (qhulp(1:5).eq.'CELLS') then
* read (qhulp,'(7x,*)',end=40,err=40)kx,ky,kz
* irecog=1
* end if
if (qhulp(1:6).eq.'HETATM') then
if (ibgfversion.lt.400) then
read (qhulp,
$'(7x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5)'
$,end=40,err=40)
$ir,qlabel(na+1),qresi1(na+1),qresi2(na+1),qresi3(na+1),
$cglobal(na+1,1),cglobal(na+1,2),
$cglobal(na+1,3),qffty(na+1),ibgr1(na+1),ibgr2(na+1),
$chgglobal(na+1)
else
stop 'Unsupported Biograf-version'
end if
qlabhulp=qlabel(na+1)
if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:5)
if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:4)
if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:3)
if (qlabhulp(1:1).eq.'C ') qa(na+1)='C '
if (qlabhulp(1:2).eq.'Ca') qa(na+1)='Ca'
if (qlabhulp(1:2).eq.'Cl') qa(na+1)='Cl'
if (qlabhulp(1:2).eq.'Cu') qa(na+1)='Cu'
if (qlabhulp(1:2).eq.'Co') qa(na+1)='Co'
if (qlabhulp(1:1).eq.'H ') qa(na+1)='H '
if (qlabhulp(1:2).eq.'He') qa(na+1)='He'
if (qlabhulp(1:1).eq.'N ') qa(na+1)='N '
if (qlabhulp(1:2).eq.'Ni') qa(na+1)='Ni'
if (qlabhulp(1:1).eq.'O ') qa(na+1)='O '
if (qlabhulp(1:1).eq.'B ') qa(na+1)='B '
if (qlabhulp(1:1).eq.'F ') qa(na+1)='F '
if (qlabhulp(1:2).eq.'Fe') qa(na+1)='Fe'
if (qlabhulp(1:1).eq.'P ') qa(na+1)='P '
if (qlabhulp(1:1).eq.'S ') qa(na+1)='S '
if (qlabhulp(1:1).eq.'Y ') qa(na+1)='Y '
if (qlabhulp(1:2).eq.'Al ') qa(na+1)='Al'
if (qlabhulp(1:2).eq.'Au ') qa(na+1)='Au'
if (qlabhulp(1:2).eq.'Si') qa(na+1)='Si'
if (qlabhulp(1:2).eq.'Pt') qa(na+1)='Pt'
if (qlabhulp(1:2).eq.'Mo') qa(na+1)='Mo'
if (qlabhulp(1:2).eq.'Mg') qa(na+1)='Mg'
if (qlabhulp(1:2).eq.'Ar') qa(na+1)='Ar'
if (qlabhulp(1:2).eq.'Zr') qa(na+1)='Zr'
if (qlabhulp(1:2).eq.'Ti') qa(na+1)='Ti'
if (qlabhulp(1:2).eq.'Ru') qa(na+1)='Ru'
if (qlabhulp(1:2).eq.'Ba') qa(na+1)='Ba'
if (qlabhulp(1:2).eq.'Bi') qa(na+1)='Bi'
if (qlabhulp(1:2).eq.'Li') qa(na+1)='Li'
if (qlabhulp(1:2).eq.'V ') qa(na+1)='V '
if (qlabhulp(1:2).eq.'X ') qa(na+1)='X '
na=na+1
if (na.gt.nattot) then
write (*,*)'Number of atoms:read ',na
write (*,*)'Maximum number of atoms: ',nattot
stop
$'Maximum number of atoms exceeded; increase nattot in cbka.blk'
end if
irecog=1
end if
if (qhulp(1:6).eq.'RUTYPE') then !run-type identifiers
irecrun=0
read (qhulp,'(7x,a40)',end=46,err=46)qruid
if (qruid(1:10).eq.'NORMAL RUN') then
iruid=0
irecrun=1
end if
if (qruid(1:14).eq.'HIGH PRECISION') then
endpo=endpo/25
nmmax=nmmax*5
qr='D'
iruid=1
irecrun=1
end if
if (qruid(1:13).eq.'LOW PRECISION') then
nmmax=nmmax/10
qr='H'
iruid=1
irecrun=1
end if
if (qruid(1:12).eq.'SINGLE POINT') then
iruid=1
nmmax=1
qr='1'
if (ibity.eq.2) qr='5'
irecrun=1
end if
if (qruid(1:11).eq.'NO CELL OPT') then
iruid=1
icell=0
if (ibity.eq.2) qr='Y'
irecrun=1
end if
if (qruid(1:8).eq.'CELL OPT') then
iruid=1
icell=1
iexco=0 !Override from VCHANGE
read (qruid,'(8x,i6)',end=46,err=46)ncellopt
if (ncellopt.eq.2) icell=2 !cell optimisation during energy minimisation
if (ncellopt.eq.3) icelo2=4 !c/a optimisation
if (ncellopt.eq.4) icelo2=1 !only a optimisation
if (ncellopt.eq.5) icelo2=2 !only b optimisation
if (ncellopt.eq.6) icelo2=3 !only c optimisation
if (ncellopt.eq.7) then
icelo2=4 !c/a optimisation
icell=2 !cell optimisation during energy minimisation
end if
if (ibity.eq.2) qr='F'
irecrun=1
end if
if (qruid(1:6).eq.'MAXMOV') then
iruid=1
read (qruid,'(6x,i6)',end=46,err=46)nfc
irecrun=1
end if
if (qruid(1:4).eq.'REDO') then
iruid=1
read (qruid,'(4x,i6)',end=46,err=46)iredo
irecrun=1
end if
if (qruid(1:5).eq.'MAXIT') then
iruid=1
read (qruid,'(6x,i6)',end=46,err=46)nmmax
if (qruid(14:18).eq.'ENDPO') then
read (qruid,'(18x,f6.3)',end=46,err=46)endpo
end if
irecrun=1
end if
if (qruid(1:5).eq.'ENDPO') then
iruid=1
read (qruid,'(6x,f6.3)',end=46,err=46)endpo
irecrun=1
end if
if (qruid(1:9).eq.'CHARGEMET') then
iruid=1
read (qruid,'(9x,i6)',end=46,err=46)ncha
irecrun=1
end if
if (irecrun.eq.0) then
write (*,*)'Warning: ignored RUTYPE identifier ',qruid(1:12)
end if
irecog=1
end if
if (qhulp(1:14).eq.'BOND RESTRAINT') then
nrestra=nrestra+1
istart=15
call stranal(istart,iend,vout,iout,1)
irstra(nrestra,1)=iout
istart=iend
call stranal(istart,iend,vout,iout,1)
irstra(nrestra,2)=iout
istart=iend
call stranal(istart,iend,vout,iout,1)
rrstra(nrestra)=vout
istart=iend
call stranal(istart,iend,vout,iout,1)
vkrstr(nrestra)=vout
istart=iend
call stranal(istart,iend,vout,iout,1)
vkrst2(nrestra)=vout
istart=iend
call stranal(istart,iend,vout,iout,1)
rrcha(nrestra)=vout
istart=iend
call stranal(istart,iend,vout,iout,1)
itstart(nrestra)=iout
istart=iend
call stranal(istart,iend,vout,iout,1)
itend(nrestra)=iout
istart=iend
* read (qhulp,'(15x,2i4,f8.4,f8.2,f8.5,f10.7)',end=46,err=46)
* $irstra(nrestra,1),irstra(nrestra,2),rrstra(nrestra),
* $vkrstr(nrestra),vkrst2(nrestra),rrcha(nrestra)
qr='R'
irecog=1
end if
if (qhulp(1:15).eq.'ANGLE RESTRAINT') then
nrestrav=nrestrav+1
read (qhulp,'(16x,3i4,2f8.2,f8.4,f9.6)',end=46,err=46)
$irstrav(nrestrav,1),irstrav(nrestrav,2),irstrav(nrestrav,3),
$vrstra(nrestrav),vkrv(nrestrav),vkr2v(nrestrav),
$rvcha(nrestrav)
qr='V'
irecog=1
end if
if (qhulp(1:17).eq.'TORSION RESTRAINT') then
nrestrat=nrestrat+1
read (qhulp,'(18x,4i4,2f8.2,f8.4,f9.6)',end=46,err=46)
$irstrat(nrestrat,1),irstrat(nrestrat,2),irstrat(nrestrat,3),
$irstrat(nrestrat,4),trstra(nrestrat),vkrt(nrestrat),
$vkr2t(nrestrat),rtcha(nrestrat)
qr='T'
irecog=1
end if
if (qhulp(1:16).eq.'MASCEN RESTRAINT') then
nrestram=nrestram+1
istart=17
call stranal(istart,iend,vout,iout,1)
istart=iend
irstram(nrestram,1)=0
if (qstrana2.eq.'x') irstram(nrestram,1)=1
if (qstrana2.eq.'y') irstram(nrestram,1)=2
if (qstrana2.eq.'z') irstram(nrestram,1)=3
if (qstrana2.eq.'p') irstram(nrestram,1)=4 !fixed center of mass
if (irstram(nrestram,1).eq.0)
$stop 'Error in mass centre restraint'
call stranal(istart,iend,vout,iout,1)
istart=iend
irstram(nrestram,2)=iout
call stranal(istart,iend,vout,iout,1)
istart=iend
irstram(nrestram,3)=iout
call stranal(istart,iend,vout,iout,1)
istart=iend
rmstra1(nrestram)=vout
call stranal(istart,iend,vout,iout,1)
istart=iend
if (irstram(nrestram,1).le.3) irstram(nrestram,4)=iout
if (irstram(nrestram,1).eq.4) rmstra2(nrestram)=vout
call stranal(istart,iend,vout,iout,1)
istart=iend
if (irstram(nrestram,1).le.3) irstram(nrestram,5)=iout
if (irstram(nrestram,1).eq.4) rmstra3(nrestram)=vout
call stranal(istart,iend,vout,iout,1)
istart=iend
if (irstram(nrestram,1).le.3) rmstra2(nrestram)=vout
call stranal(istart,iend,vout,iout,1)
istart=iend
if (irstram(nrestram,1).le.3) rmstra3(nrestram)=vout
call stranal(istart,iend,vout,iout,1)
istart=iend
if (irstram(nrestram,1).le.3) rmcha(nrestram)=vout
irecog=1
end if
if (qhulp(1:9).eq.'MOLCHARGE') then
nmcharge=nmcharge+1
istart=10
call stranal(istart,iend,vout,iout,1)
istart=iend
iat1mc(nmcharge)=iout
call stranal(istart,iend,vout,iout,1)
istart=iend
iat2mc(nmcharge)=iout
call stranal(istart,iend,vout,iout,1)
istart=iend
vmcha(nmcharge)=vout
irecog=1
end if
if (qhulp(1:8).eq.'FIXATOMS') then
istart=9
call stranal(istart,iend,vout,iout,1)
if1=iout
istart=iend
call stranal(istart,iend,vout,iout,1)
if2=iout
do i12=if1,if2
imove(i12)=0
end do
irecog=1
end if
if (qhulp(1:11).eq.'UNIT ENERGY') then
eenconv=zero
read (qhulp,'(14x,a5)',end=46,err=46)quen
if (quen.eq.'eV') eenconv=23.0408
if (quen.eq.'EV') eenconv=23.0408
if (quen.eq.'ev') eenconv=23.0408
if (quen.eq.'h') eenconv=627.5
if (quen.eq.'H') eenconv=627.5
if (quen.eq.'kcal') eenconv=1.0
if (quen.eq.'kCal') eenconv=1.0
if (quen.eq.'KCAL') eenconv=1.0
if (eenconv.eq.zero) then
write (*,*)quen,': unknown energy unit; assuming kcal/mol'
eenconv=1.0
end if
irecog=1
end if
if (qhulp(1:6).eq.'ENERGY') then
read (qhulp(7:80),*,end=46,err=46)enmol
ienread=1
irecog=1
end if
if (qhulp(1:6).eq.'GEOUPD') then
icgeopt(nprob)=0
icgeo=0
irecog=1
end if
if (qhulp(1:9).eq.'NO GEOUPD') then
icgeopt(nprob)=1
icgeo=1
irecog=1
end if
if (qhulp(1:9).eq.'FREQUENCY') then
ifreqset(nprob)=1
ifreq=1
irecog=1
end if
* if (qhulp(1:5).eq.'FORCE') then
* read (qhulp(6:80),*,end=46,err=46)formol
* ienread=1
* irecog=1
* end if
if (qhulp(1:6).eq.'FFIELD') goto 30
if (qhulp(1:6).eq.'CONECT') goto 30
if (qhulp(1:5).eq.'ORDER') goto 30
if (qhulp(1:1).eq.'#') goto 30
if (qhulp(1:3).eq.'END') goto 45
if (irecog.eq.0) then
write (*,*)'Warning: ignored line starting with: ',qhulp(1:10)
end if
goto 30
40 write (*,*)'Error on line ',iline+1,' of Biograf-input'
stop
45 read (3,*,err=46,end=46)
46 continue
if (ienread.eq.1) then
if (eenconv.eq.zero) then
write (*,*)'No energy unit given; assuming kcal/mol'
eenconv=1.0
end if
enmol=enmol*eenconv !Convert energies to kcal/mol
end if
namov=0 !calculate number of moving atoms
do i1=1,na
if (imove(i1).eq.1) namov=namov+1
end do
if (imodfile.eq.1) close (3)
return
900 iendf=1
return
end
************************************************************************
************************************************************************
subroutine readpdb (iendf)
************************************************************************
#include "cbka.blk"
#include "cbkc.blk"
#include "cbkqa.blk"
#include "control.blk"
#include "opt.blk"
#include "small.blk"
#include "cbksrtbon1.blk"
character*200 qhulp
**********************************************************************
* *
* Read in .pdb-geometry *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In readpdb'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
iendf=1
qmol='pdb_in'
5 read (3,'(a200)',end=10,err=900) qhulp
qstrana1(1:200)=qhulp
istart=1
call stranal(istart,iend,vout,iout,1)
istart=iend
if (qstrana2(1:6).eq.'HEADER') then
call stranal(istart,iend,vout,iout,1)
istart=iend
qmol=qstrana2(1:20)
end if
if (qstrana2(1:6).eq.'HETATM'.or.qstrana2(1:4).eq.'ATOM') then
call stranal(istart,iend,vout,iout,1)
istart=iend
call stranal(istart,iend,vout,iout,1)
istart=iend
qa(na+1)=qstrana2(1:2)
call stranal(istart,iend,vout,iout,1)
istart=iend
call stranal(istart,iend,vout,iout,1)
istart=iend
call stranal(istart,iend,vout,iout,1)
istart=iend
c(na+1,1)=vout
call stranal(istart,iend,vout,iout,1)
istart=iend
c(na+1,2)=vout
call stranal(istart,iend,vout,iout,1)
istart=iend
c(na+1,3)=vout
na=na+1
end if
if (qstrana2(1:3).eq.'END'.or.qstrana2(2:4).eq.'END') then
iendf=0
goto 10
end if
goto 5
10 continue
return
900 write (*,*)'Error reading in .pdb-format'
stop 'Error reading in .pdb-format'
end
************************************************************************
************************************************************************
subroutine readtreg
************************************************************************
#include "cbka.blk"
#include "cbktregime.blk"
#include "control.blk"
#include "small.blk"
dimension isumattreg(mtreg)
character*200 qrom
**********************************************************************
* *
* Read in temperature regime *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In readtreg'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
ntrc=0
open (19,file='tregime.in',status='old',err=60)
10 read (19,'(a200)',end=50,err=900)qrom
qstrana1(1:200)=qrom
if (qrom(1:1).eq.'#') goto 10
istart=1
ntrc=ntrc+1
if (ntrc.gt.mtreg) then
write (*,*)'Too many temperature regimes in tregime.in;',
$' inrease mtreg in cbka.blk'
stop 'Too many temperature regimes in tregime.in'
end if
call stranal(istart,iend,vout,iout,1)
nittc(ntrc)=iout
istart=iend
if (ntrc.gt.1) then
if (nittc(ntrc).lt.nittc(ntrc-1)) then
ntrc=ntrc-1
write (*,*)'Warning: wrong order or empty line in tregime.in'
write (*,*)'Ignored lines below iteration:',nittc(ntrc)
goto 50
end if
end if
call stranal(istart,iend,vout,iout,1)
nntreg(ntrc)=iout
if (nntreg(ntrc).gt.mtzone) then
write (*,*)'Too many temperature zones in tregime.in;',
$' inrease mtzone in cbka.blk'
stop 'Too many temperature zones in tregime.in'
end if
istart=iend
isumattreg(ntrc)=0
do i1=1,nntreg(ntrc)
call stranal(istart,iend,vout,iout,1)
ia1treg(ntrc,i1)=iout
istart=iend
call stranal(istart,iend,vout,iout,1)
ia2treg(ntrc,i1)=iout
istart=iend
isumattreg(ntrc)=isumattreg(ntrc)+1+ia2treg(ntrc,i1)-
$ia1treg(ntrc,i1)
call stranal(istart,iend,vout,iout,1)
tsettreg(ntrc,i1)=vout
istart=iend
call stranal(istart,iend,vout,iout,1)
tdamptreg(ntrc,i1)=vout
istart=iend
call stranal(istart,iend,vout,iout,1)
dttreg(ntrc,i1)=vout
istart=iend
end do
goto 10
50 continue
close (19)
60 continue
**********************************************************************
* *
* Check consistency temperature programs in tregime.in *
* *
**********************************************************************
if (ntrc.gt.0) then
do i1=1,ntrc
if (isumattreg(i1).ne.na) then
write (*,*)'Inconsistency in temperature regime nr.',i1
write (*,*)'Number of atoms defined in tregime.in:',
$isumattreg(i1)
write (*,*)'Number of atoms in system:',na
stop 'Inconsistency in tregime.in'
end if
end do
end if
return
900 stop 'Error reading tregime.in'
end
************************************************************************
************************************************************************
subroutine readvreg
************************************************************************
#include "cbka.blk"
#include "cbkc.blk"
#include "cbkvregime.blk"
#include "control.blk"
character*200 qrom
**********************************************************************
* *
* Read in volume regime *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In readvreg'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
nvrc=0
open (19,file='vregime.in',status='old',err=60)
10 read (19,'(a200)',end=50,err=900)qrom
qstrana1(1:200)=qrom
if (qrom(1:1).eq.'#') goto 10
istart=1
nvrc=nvrc+1
if (nvrc.gt.mvreg) then
write (*,*)'Too many volume regimes in vregime.in;',
$' inrease mvreg in cbka.blk'
stop 'Too many volume regimes in vregime.in'
end if
call stranal(istart,iend,vout,iout,1)
nitvc(nvrc)=iout
istart=iend
if (nvrc.gt.1) then
if (nitvc(nvrc).lt.nitvc(nvrc-1)) then
nvrc=nvrc-1
write (*,*)'Warning: wrong order or empty line in vregime.in'
write (*,*)'Ignored lines below iteration:',nitvc(nvrc)
goto 50
end if
end if
call stranal(istart,iend,vout,iout,1)
nnvreg(nvrc)=iout
if (nnvreg(nvrc).gt.mvzone) then
write (*,*)'Too many volume regimes in vregime.in;',
$' inrease mvzone in cbka.blk'
stop 'Too many volume zones in vregime.in'
end if
istart=iend
do i1=1,nnvreg(nvrc)
call stranal(istart,iend,vout,iout,1)
if (qstrana2(1:1).ne.'a'.and.qstrana2(1:1).ne.'b'.and.
$qstrana2(1:1).ne.'c'.and.qstrana2(1:4).ne.'alfa'.and.
$qstrana2(1:4).ne.'beta'.and.qstrana2(1:5).ne.'gamma') then
write (*,*)qstrana2
write (*,*)'Invalid cell parameter type in vregime.in ;',
$' use a,b,c,alfa,beta or gamma'
stop 'Invalid cell parameter type in vregime.in'
end if
qvtype(nvrc,i1)=qstrana2
istart=iend
call stranal(istart,iend,vout,iout,1)
dvvreg(nvrc,i1)=vout
istart=iend
call stranal(istart,iend,vout,iout,1)
ivsca(nvrc,i1)=1
if (qstrana2(1:1).eq.'n') ivsca(nvrc,i1)=0
istart=iend
end do
goto 10
50 continue
close (19)
60 continue
return
900 stop 'Error reading vregime.in'
end
************************************************************************
************************************************************************
subroutine readereg
************************************************************************
#include "cbka.blk"
#include "cbkeregime.blk"
#include "control.blk"
character*200 qrom
**********************************************************************
* *
* Read in electric field regime *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In readereg'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
nerc=0
open (19,file='eregime.in',status='old',err=60)
10 read (19,'(a200)',end=50,err=900)qrom
qstrana1(1:200)=qrom
if (qrom(1:1).eq.'#') goto 10
istart=1
nerc=nerc+1
if (nerc.gt.mereg) then
write (*,*)'Too many electric field regimes in eregime.in;',
$' inrease mereg in cbka.blk'
stop 'Too many electric field regimes in eregime.in'
end if
call stranal(istart,iend,vout,iout,1)
nitec(nerc)=iout
if (nerc.gt.1) then
if (nitec(nerc).lt.nitec(nerc-1)) then
nerc=nerc-1
write (*,*)'Warning: wrong order or empty line in eregime.in'
write (*,*)'Ignored lines below iteration:',nitec(nerc)
goto 50
end if
end if
istart=iend
call stranal(istart,iend,vout,iout,1)
nnereg(nerc)=iout
if (nnereg(nerc).gt.mezone) then
write (*,*)'Too many electric field zones in eregime.in;',
$' inrease mezone in cbka.blk'
stop 'Too many electric field zones in vregime.in'
end if
istart=iend
do i1=1,nnereg(nerc)
call stranal(istart,iend,vout,iout,1)
if (qstrana2(1:1).ne.'x'.and.qstrana2(1:1).ne.'y'.and.
$qstrana2(1:1).ne.'z') then
write (*,*)qstrana2
write (*,*)'Invalid field direction in eregime.in ;',
$' use x,y or z'
stop 'Invalid field direction in eregime.in'
end if
qetype(nerc,i1)=qstrana2
istart=iend
call stranal(istart,iend,vout,iout,1)
ereg(nerc,i1)=vout
istart=iend
end do
goto 10
50 continue
close (19)
60 continue
return
900 stop 'Error reading vregime.in'
end
************************************************************************
************************************************************************
subroutine readaddmol
************************************************************************
#include "cbka.blk"
#include "cbkatomcoord.blk"
#include "cbkc.blk"
#include "cbkff.blk"
#include "cbkh.blk"
#include "control.blk"
character*80 qromb
character*200 qhulp
character*5 qlabhulp
**********************************************************************
* *
* Read in molecule coordinates. This molecule will be added to *
* the system at regular intervals *
* Accepts only .bgf-format *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In readaddmol'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
**********************************************************************
* *
* Set default values *
* *
**********************************************************************
iaddfreq=-1 !frequency of molecule addition; <0: no addition
xadd=-9000.0 !x-coordinate for added molecule; <-5000.0: random
yadd=-9000.0 !y-coordinate for added molecule; <-5000.0: random
zadd=-9000.0 !z-coordinate for added molecule; <-5000.0: random
iveladd=1 !1: random initial velocities; 2: read in velocities
!from addmol.vel
addist=-1.00 !Minimum distance between added molecule and rest
!of system. < 0.0: do not check
nadattempt=10 !Number of attempts at adding the molecule
taddmol=-1.0 !Temperature added molecule. <0.0: system temperature
open (19,file='addmol.bgf',status='old',err=60)
read (19,'(a40)',end=900,err=900)qromb
if (qromb(1:6).ne.'BIOGRF') then
write (*,*)'addmol.bgf should start with BIOGRF'
stop 'addmol.bgf should start with BIOGRF'
end if
naa=0
iline=0
30 read (19,'(a200)',end=900,err=900)qhulp
irecog=0
iline=iline+1
if (qhulp(1:6).eq.'DESCRP') then
irecog=1
end if
if (qhulp(1:6).eq.'FORMAT') then
irecog=1
end if
if (qhulp(1:6).eq.'REMARK') then
irecog=1
end if
if (qhulp(1:6).eq.'HETATM') then
irecog=1
read (qhulp,'(7x,i5,1x,a5,1x,3x,1x,1x,1x,5x,3f10.5)'
$,end=900,err=900)
$ir,qlabhulp,cadd(naa+1,1),cadd(naa+1,2),cadd(naa+1,3)
if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:5)
if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:4)
if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:3)
if (qlabhulp(1:1).eq.'C ') qadd(naa+1)='C '
if (qlabhulp(1:2).eq.'Ca') qadd(naa+1)='Ca'
if (qlabhulp(1:2).eq.'Cl') qadd(naa+1)='Cl'
if (qlabhulp(1:2).eq.'Cu') qadd(naa+1)='Cu'
if (qlabhulp(1:2).eq.'Co') qadd(naa+1)='Co'
if (qlabhulp(1:1).eq.'H ') qadd(naa+1)='H '
if (qlabhulp(1:2).eq.'He') qadd(naa+1)='He'
if (qlabhulp(1:1).eq.'N ') qadd(naa+1)='N '
if (qlabhulp(1:2).eq.'Ni') qadd(naa+1)='Ni'
if (qlabhulp(1:1).eq.'O ') qadd(naa+1)='O '
if (qlabhulp(1:1).eq.'B ') qadd(naa+1)='B '
if (qlabhulp(1:1).eq.'F ') qadd(naa+1)='F '
if (qlabhulp(1:2).eq.'Fe') qadd(naa+1)='Fe'
if (qlabhulp(1:1).eq.'P ') qadd(naa+1)='P '
if (qlabhulp(1:1).eq.'S ') qadd(naa+1)='S '
if (qlabhulp(1:1).eq.'Y ') qadd(naa+1)='Y '
if (qlabhulp(1:2).eq.'Al') qadd(naa+1)='Al'
if (qlabhulp(1:2).eq.'Au') qadd(naa+1)='Au'
if (qlabhulp(1:2).eq.'Si') qadd(naa+1)='Si'
if (qlabhulp(1:2).eq.'Pt') qadd(naa+1)='Pt'
if (qlabhulp(1:2).eq.'Mo') qadd(naa+1)='Mo'
if (qlabhulp(1:2).eq.'Mg') qadd(naa+1)='Mg'
if (qlabhulp(1:2).eq.'Ar') qadd(naa+1)='Ar'
if (qlabhulp(1:2).eq.'Zr') qadd(naa+1)='Zr'
if (qlabhulp(1:2).eq.'Ba') qadd(naa+1)='Ba'
if (qlabhulp(1:2).eq.'X ') qadd(naa+1)='X '
ityadd(naa+1)=0
do i1=1,nso !Find force field type
if (qadd(naa+1).eq.qas(i1)) ityadd(naa+1)=i1
end do
if (ityadd(naa+1).eq.0) then
write (*,*) 'Unknown atom type:',qadd(naa+1)
stop 'Unknown atom type'
end if
naa=naa+1
end if
if (qhulp(1:7).eq.'FREQADD') then
irecog=1
read (qhulp,'(8x,i6)',end=900,err=900) iaddfreq
end if
if (qhulp(1:6).eq.'VELADD') then
irecog=1
read (qhulp,'(8x,i6)',end=900,err=900) iveladd
end if
if (qhulp(1:6).eq.'STARTX') then
irecog=1
read (qhulp,'(7x,f8.2)',end=900,err=900) xadd
end if
if (qhulp(1:6).eq.'STARTY') then
irecog=1
read (qhulp,'(7x,f8.2)',end=900,err=900) yadd
end if
if (qhulp(1:6).eq.'STARTZ') then
irecog=1
read (qhulp,'(7x,f8.2)',end=900,err=900) zadd
end if
if (qhulp(1:6).eq.'ADDIST') then
irecog=1
read (qhulp,'(7x,f8.2)',end=900,err=900) addist
end if
if (qhulp(1:8).eq.'NATTEMPT') then
irecog=1
read (qhulp,'(9x,i6)',end=900,err=900) nadattempt
end if
if (qhulp(1:7).eq.'TADDMOL') then
irecog=1
read (qhulp,'(8x,f8.2)',end=900,err=900) taddmol
end if
if (qhulp(1:6).eq.'FFIELD') goto 30
if (qhulp(1:6).eq.'CONECT') goto 30
if (qhulp(1:5).eq.'ORDER') goto 30
if (qhulp(1:1).eq.'#') goto 30
if (qhulp(1:3).eq.'END') goto 45
if (irecog.eq.0) then
write (*,*)'Warning: ignored line starting with: ',qhulp(1:10)
end if
goto 30
45 continue
close (19)
if (iveladd.eq.2) then
open (19,file='addmol.vel',status='old',err=800)
read (19,*)
read (19,'(3d24.15)',err=850,end=850)
$((veladd(j,i),j=1,3),i=1,naa)
close (19)
end if
************************************************************************
* *
* Place molecule at origin *
* *
************************************************************************
ccx=0.0
ccy=0.0
ccz=0.0
do i1=1,naa
ccx=ccx+cadd(i1,1)/float(naa)
ccy=ccy+cadd(i1,2)/float(naa)
ccz=ccz+cadd(i1,3)/float(naa)
end do
do i1=1,naa
cadd(i1,1)=cadd(i1,1)-ccx
cadd(i1,2)=cadd(i1,2)-ccy
cadd(i1,3)=cadd(i1,3)-ccz
end do
60 continue
return
800 stop 'Error opening addmol.vel'
850 stop 'Error or end of file reading addmol.vel'
900 write (*,*)'Error or end-of-file reading addmol.bgf on line:',
$iline
return
end
************************************************************************
**********************************************************************
subroutine writegeo(nunit1)
**********************************************************************
#include "cbka.blk"
#include "cbkc.blk"
#include "cbkconst.blk"
#include "cbkqa.blk"
#include "cbkrestr.blk"
#include "cbktregime.blk"
#include "cellcoord.blk"
#include "control.blk"
#include "opt.blk"
#include "small.blk"
#include "cbksrtbon1.blk"
#include "cbkinit.blk"
**********************************************************************
* *
* Copy new geometries to unit nunit1 *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In writegeo'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
if (axiss(1).lt.zero) then
if (nrestra.eq.0.and.nrestrat.eq.0.and.
$nrestrav.eq.0)
$write (nunit1,300)qr,qmol
if (nrestra.gt.0) write (nunit1,301)qr,
$rrstra(1),qmol
if (nrestrav.gt.0) write (nunit1,301)qr,
$vrstra(1),qmol
if (nrestrat.gt.0) write (nunit1,301)qr,
$trstra(1),qmol
else
write (nunit1,310)qr,qmol
write (nunit1,320)axiss(1),axiss(2),axiss(3)
write (nunit1,320)angles(1),angles(2),angles(3)
end if
do i1=1,na
if (nbiolab.ne.1) write (nunit1,400)i1,qa(i1),(c(i1,i2),i2=1,3)
if (nbiolab.eq.1) write (nunit1,401)i1,qa(i1),(c(i1,i2),i2=1,3) !Delphi-format
end do
if (nbiolab.ne.1) write (nunit1,*)
return
300 format (2x,a1,1x,a60)
301 format (2x,a1,1x,f6.2,a60)
310 format (2x,a1,1x,a60)
320 format (3f10.4)
400 format (i4,1x,a2,3x,3(d21.14,1x),1x,a5,1x,i5)
401 format (i3,2x,a2,3x,3(d21.14,1x),1x,a5,1x,i5)
end
**********************************************************************
**********************************************************************
subroutine writebgf(nunit1)
**********************************************************************
#include "cbka.blk"
#include "cbkc.blk"
#include "cbkcha.blk"
#include "cbkcharmol.blk"
#include "cbkconst.blk"
#include "cbkenergies.blk"
#include "cbkia.blk"
#include "cbkimove.blk"
#include "cbkinit.blk"
#include "cbkqa.blk"
#include "cbkrestr.blk"
#include "cbktregime.blk"
#include "cellcoord.blk"
#include "control.blk"
#include "opt.blk"
#include "cbksrtbon1.blk"
#include "small.blk"
dimension qdir(3)
character*2 qt
character*1 qdir
**********************************************************************
* *
* Copy new Biograf-geometries to unit nunit1 *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In newbgf'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
irom=1
qdir(1)='x'
qdir(2)='y'
qdir(3)='z'
ibgfversion=200
if (ibity.eq.1) write (nunit1,1500)ibgfversion
if (ibity.eq.2) write (nunit1,1600)ibgfversion
* if (qr.ne.'F'.and.qr.ne.'5'.and.qr.ne.'Y')
* $write (nunit1,1500)ibgfversion
* if (qr.eq.'F'.or.qr.eq.'5'.or.qr.eq.'Y')
* $write (nunit1,1600)ibgfversion
write (nunit1,1700)qmol
* write (nunit1,1700)qkeyw(nprob)
do i1=1,iremark
write (nunit1,1800)qremark(i1)
end do
qruid='NORMAL RUN'
if (iruid.eq.0) then
write (nunit1,2000)
else
if (abs(endpo-endpoold).gt.1e-5) write (nunit1,2010)endpo
if (nmmax.ne.nmmaxold) write (nunit1,2020)nmmax
if (nfc.ne.nfcold) write (nunit1,2030)nfc
if (ncha.ne.nchaold) write (nunit1,2036)ncha
if (iredo.gt.1) write (nunit1,2035)iredo
if (icell.ne.icellold) then
if (icell.eq.0) write (nunit1,2033)
if (icell.gt.0) write (nunit1,2034)ncellopt
end if
end if
if (iexco.ne.0.and.nsurp.gt.0) then
write (nunit1,2040)vvol
write (nunit1,3500)
write (nunit1,*)
return
end if
if (nmcharge.gt.0) then
do i3=1,nmcharge
write (nunit1,2050)iat1mc(i3),iat2mc(i3),vmcha(i3)
end do
end if
ims=0
do i1=1,na
if (ims.eq.0.and.imove(i1).eq.0) then
if1=i1
ims=1
end if
if (ims.eq.1.and.imove(i1).eq.1) then
write (nunit1,2060)if1,i1-1
ims=0
end if
end do
if (ims.eq.1) then
write (nunit1,2060)if1,na
end if
* if (qr.eq.'F'.or.qr.eq.'5'.or.qr.eq.'Y')
if (ibity.eq.2)
$write (nunit1,2100)axiss(1),axiss(2),axiss(3),angles(1),
$angles(2),angles(3)
if (nrestra.gt.0) write (nunit1,2300)
do i2=1,nrestra
write (nunit1,2400)
$irstra(i2,1),irstra(i2,2),rrstra(i2),
$vkrstr(i2),vkrst2(i2),rrcha(i2),itstart(i2),itend(i2)
end do
if (nrestrav.gt.0) write (nunit1,2500)
do i2=1,nrestrav
write (nunit1,2600)
$irstrav(i2,1),irstrav(i2,2),irstrav(i2,3),
$vrstra(i2),vkrv(i2),vkr2v(i2),zero
end do
if (nrestrat.gt.0) write (nunit1,2700)
do i2=1,nrestrat
write (nunit1,2800)
$irstrat(i2,1),irstrat(i2,2),irstrat(i2,3),
$irstrat(i2,4),trstra(i2),vkrt(i2),
$vkr2t(i2),zero
end do
if (nrestram.gt.0) write (nunit1,2810)
do i2=1,nrestram
write (nunit1,2820)
$qdir(irstram(i2,1)),irstram(i2,2),irstram(i2,3),
$rmstra1(i2),irstram(i2,4),irstram(i2,5),rmstra2(i2),
$rmstra3(i2),rmcha(i2)
end do
if (icgeo.eq.0.and.ingeo.eq.0) write (nunit1,2830)
if (icgeo.eq.1.and.ingeo.eq.1) write (nunit1,2840)
if (ifreq.eq.1) write (nunit1,2850)
write (nunit1,2900)
do i2=1,na
write (nunit1,3000)i2,qa(i2),c(i2,1),c(i2,2),c(i2,3),
$qa(i2),irom,irom,chgbgf(i2)
end do
write (nunit1,3100)
if (nsurp.lt.2) then
do i1=1,na
write (nunit1,3200)i1,(iag(i1,2+i2),i2=1,iag(i1,2))
end do
write (nunit1,3300)
write (nunit1,3400)estrc
end if
write (nunit1,3500)
write (nunit1,*)
return
1500 format ('BIOGRF',i4)
1600 format ('XTLGRF',i4)
1700 format ('DESCRP ',a60)
1800 format ('REMARK ',a60)
1900 format ('FFIELD ',a40)
2000 format ('RUTYPE NORMAL RUN')
2010 format ('RUTYPE ENDPO',f6.3)
2020 format ('RUTYPE MAXIT',i6)
2030 format ('RUTYPE MAXMOV',i6)
2033 format ('RUTYPE NO CELL OPT')
2034 format ('RUTYPE CELL OPT',i6)
2035 format ('RUTYPE REDO',i6)
2036 format ('RUTYPE CHARGEMET',i6)
2040 format ('VCHANGE',f8.4)
2050 format ('MOLCHARGE',2i4,f6.2)
2060 format ('FIXATOMS',2i6)
2100 format ('CRYSTX ',6f11.5)
2200 format ('CELLS ',6i5)
2300 format ('# At1 At2 R12 Force1 Force2 ',
$'dR12/dIter(MD) Start (MD) End (MD)')
2400 format ('BOND RESTRAINT ',2i4,f8.4,f8.2,f8.4,1x,f10.7,2i8)
2500 format ('# At1 At2 At3 Angle Force1 Force2',
$' dAngle/dIteration (MD only)')
2600 format ('ANGLE RESTRAINT ',3i4,2f8.2,f8.4,f9.6)
2700 format ('# At1 At2 At3 At3 Angle Force1 ',
$'Force2 dAngle/dIteration (MD only)')
2800 format ('TORSION RESTRAINT ',4i4,2f8.2,f8.4,f9.6)
2810 format ('# x/y/z At1 At2 R At3 At4 Force1',
$' Force2 dR/dIteration (MD only)')
2820 format ('MASCEN RESTRAINT ',a1,1x,2i4,f8.2,2i4,2f8.2,f9.6)
2830 format ('GEOUPD')
2840 format ('NO GEOUPD')
2850 format ('FREQUENCY')
2900 format ('FORMAT ATOM (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,',
$'3f10.5,1x,a5,i3,i2,1x,f8.5)')
3000 format ('HETATM',1x,i5,1x,a2,3x,1x,3x,1x,1x,1x,5x,3f10.5,1x,
$a5,i3,i2,1x,f8.5)
3100 format ('FORMAT CONECT (a6,12i6)')
3200 format ('CONECT',12i6)
3300 format ('UNIT ENERGY kcal')
3400 format ('ENERGY',5x,f14.6)
3500 format ('END')
end
**********************************************************************
**********************************************************************
subroutine writeen(tottime,sum1,sdev,sdeva,sum12,sumt,sump,
$sumtt,tmax,eaver,eav2,eav3,etot2,ediff)
**********************************************************************
#include "cbka.blk"
#include "cbkcha.blk"
#include "cbkenergies.blk"
#include "cbkrestr.blk"
#include "cbktorang.blk"
#include "cbktorsion.blk"
#include "cbktregime.blk"
#include "control.blk"
#include "small.blk"
dimension disres(mrestra)
**********************************************************************
* *
* Write out MD statistics to units 71,73 and 76 *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In writeen'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
if (nrep1.gt.1)
$sdev=sqrt((sum12-sum1*sum1/float(nrep1))/float(nrep1-1))
eavn=eaver/float(mdstep)
if (mdstep.gt.1)
$sdeva=sqrt((eav3-eav2*eav2/float(mdstep))/float(mdstep-1))
C open (71,file='fort.71',status='unknown',access='append')
C open (73,file='fort.73',status='unknown',access='append')
write (71,'(i8,2i4,1x,19(f10.2,1x))')mdstep+nprevrun,nmolo,
$nmolo5,estrc,ekin,estrc+ekin,tempmd,sum1/float(nrep1),eavn,
$sumt/float(nrep1),tmax,sump/float(nrep1),sdev,sdeva,tset,
$tstep*1d+15,rmsg,tottime
write (73,'(i8,1x,14(f10.2,1x))')mdstep+nprevrun,eb,ea,elp,
$emol,ev,ecoa,ehb,et,eco,ew,ep,ech,efi
close (71)
close (73)
if ((sumt/float(nrep1)).gt.tset) then
if (invt.eq.0) write (*,*)'Switched to NVT in iteration',mdstep
invt=1
end if
C if (nrestra.gt.0.or.nrestrat.gt.0)
C $open (76,file='fort.76',status='unknown',access='append')
if (nrestra.gt.0) then
do i2=1,nrestra
call dista2(irstra(i2,1),irstra(i2,2),disres(i2),dx,dy,dz)
end do
C open (76,file='fort.76',status='unknown',access='append')
write (76,'(i8,1x,40f12.4)')mdstep,eres,estrc,
$(rrstra(i2),disres(i2),i2=1,nrestra)
end if
if (nrestrat.gt.0) then
C open (76,file='fort.76',status='unknown',access='append')
do i2=1,nrestrat
do i3=1,ntor
ih1=irstrat(i2,1)
ih2=irstrat(i2,2)
ih3=irstrat(i2,3)
ih4=irstrat(i2,4)
if (ih1.eq.it(i3,2).and.ih2.eq.it(i3,3).and.ih3.eq.it(i3,4)
$.and.ih4.eq.it(i3,5)) ittr=i3
end do
write (76,'(i8,1x,40f12.4)')mdstep,eres,
$trstra(i2),thg(ittr)
end do
end if
if (nrestra.gt.0.or.nrestrat.gt.0) close(76)
if (nrestram.gt.0) then
C open (76,file='fort.76',status='unknown',access='append')
do i2=1,nrestram
write (76,'(2i8,1x,20f12.4)')mdstep,i2,eres,rmstra1(i2),
$dismacen(i2)
end do
close (76)
end if
return
end
**********************************************************************
************************************************************************
subroutine molanal
************************************************************************
#include "cbka.blk"
#include "cbkbo.blk"
#include "cbkconst.blk"
#include "cbkdcell.blk"
#include "cbkff.blk"
#include "cbkia.blk"
#include "cbkrbo.blk"
#include "control.blk"
#include "opt.blk"
#include "small.blk"
#include "cbksrtbon1.blk"
dimension iam(nat,mbond+3),nmolata(nmolmax,nat)
dimension molfra(nmolmax,nsort),ndup(nmolmax)
character*40 qmolan1
character*100 qmolan
logical found
************************************************************************
* *
* Analyse and output molecular fragments *
* *
************************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In molanal'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
do i1=1,nmolmax
do i2=1,nsort
molfra(i1,i2)=0
end do
ndup(i1)=1
end do
do i1=1,na
do i2=1,mbond+3
iam(i1,i2)=0
end do
end do
************************************************************************
* *
* Create connection table based on corrected bond orders *
* *
************************************************************************
do i1=1,nbon
if (bo(i1).gt.cutof3) then
j1=ib(i1,2)
j2=ib(i1,3)
iam(j1,2)=iam(j1,2)+1
iam(j1,2+iam(j1,2))=j2
iam(j2,2)=iam(j2,2)+1
iam(j2,2+iam(j2,2))=j1
end if
end do
**********************************************************************
* *
* Find molecules *
* *
**********************************************************************
nmolo6=0
found=.FALSE.
DO 61 k1=1,na
IF (iam(K1,3+mbond).EQ.0) found=.TRUE.
61 IF (iam(K1,3+mbond).GT.nmolo6) nmolo6=iam(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
nmolo6=nmolo6+1
if (nmolo6.gt.nmolmax) stop 'Too many molecules in system'
iam(N2,3+mbond)=nmolo6
67 FOUND=.FALSE.
DO 66 N1=N2+1,na
IF (iam(N1,3+mbond).NE.0) GOTO 66
DO 65 L=1,mbond
IF (iam(N1,l+2).EQ.0) GOTO 66
IF (iam(iam(N1,l+2),3+mbond).EQ.nmolo6) THEN
FOUND=.TRUE.
iam(N1,3+mbond)=nmolo6
GOTO 66
ENDIF
65 CONTINUE
66 CONTINUE
IF (FOUND) GOTO 67
DO 63 N3=N2+1,NA
63 if (iam(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 (iam(N1,L+2).EQ.0) GOTO 72
IF (iam(iam(N1,L+2),3+mbond).NE.iam(N1,3+mbond)) THEN
FOUND=.TRUE.
ENDIF
71 CONTINUE
72 CONTINUE
IF (FOUND) THEN
write (7,'(i4,a40)')na,qmol
do i1=1,na
write (7,'(40i4)')i1,iam(i1,1),(iam(i1,2+i2),i2=1,nsbmax),
$iam(i1,3+mbond)
end do
STOP' Mol.nrs. not consistent; maybe wrong cell parameters'
ENDIF
do i1=1,nmolo6
natmol=0
do i2=1,na
if (iam(i2,3+mbond).eq.i1) then
natmol=natmol+1
nmolata(i1,natmol+1)=i2
end if
end do
nmolata(i1,1)=natmol
end do
************************************************************************
* *
* Analyze molecules *
* *
************************************************************************
do i1=1,nmolo6
do i2=1,nmolata(i1,1)
i3=nmolata(i1,1+i2)
ityp=ia(i3,1)
molfra(i1,ityp)=molfra(i1,ityp)+1
end do
end do
do i1=1,nmolo6
isee=0
do i2=1,nmolo6
isee2=1
do i3=1,nso
if (molfra(i1,i3).ne.molfra(i2,i3)) isee2=0
end do
if (isee2.eq.1.and.i1.gt.i2.and.isee.eq.0) then !molecule type already exists
ndup(i2)=ndup(i2)+1
ndup(i1)=0
isee=1
end if
end do
end do
C open (45,file='molfra.out',status='unknown',access='append')
if (mdstep.eq.0) write (45,100)cutof3
write (45,110)
ntotmol=0
ntotat=0
vtotmass=zero
do i1=1,nmolo6
if (ndup(i1).gt.0) then
* write (45,110)i1,(molfra(i1,i2),i2=1,nso),ndup(i1)
ntotmol=ntotmol+ndup(i1)
qmolan=' '
qmolan1=' '
istart=-4
ihulp=0
vmass=zero
do i2=1,nso
vmass=vmass+molfra(i1,i2)*amas(i2)
ntotat=ntotat+molfra(i1,i2)*ndup(i1)
if (molfra(i1,i2).gt.0) then
istart=istart+6
iend=istart+5
if (molfra(i1,i2).gt.1) then
write (qmolan(istart:iend),'(a2,i3)')qas(i2),molfra(i1,i2)
else
write (qmolan(istart:iend-2),'(a2)')qas(i2)
end if
end if
end do
ihulp=1
do i2=1,iend
if (qmolan(i2:i2).ne.' ') then
qmolan1(ihulp:ihulp)=qmolan(i2:i2)
ihulp=ihulp+1
end if
end do
* write (45,120)ndup(i1),qmolan(1:iend),vmass
write (45,120)mdstep,ndup(i1),qmolan1,vmass
vtotmass=vtotmass+ndup(i1)*vmass
end if
end do
write (45,*)'Total number of molecules:',ntotmol
write (45,*)'Total number of atoms:',ntotat
write (45,*)'Total system mass:',vtotmass
close (45)
return
100 format('Bond order cutoff:',f6.4)
110 format('Iteration Freq. Molecular formula',15x,'Molecular mass')
120 format(i8,i4,' x ',a35,f10.4)
end
************************************************************************
************************************************************************
subroutine stranal(istart,iend,vout,iout,icheck)
************************************************************************
#include "cbka.blk"
#include "cbkconst.blk"
#include "opt.blk"
character*1 qchar
dimension qchar(5)
**********************************************************************
* *
* Analyze string for special characters; find words in string *
* *
**********************************************************************
qchar(1)=' '
qchar(2)='/'
ifound1=0
do i1=istart,200
ifound2=0
do i2=1,icheck
if (qstrana1(i1:i1).eq.qchar(i2)) then
ifound2=1
if (ifound1.eq.1) then !End of word
iend=i1
goto 10
end if
end if
end do
if (ifound2.eq.0.and.ifound1.eq.0) then !Start of word
istart2=i1
ifound1=1
end if
end do
10 continue
qstrana2=' '
vout=zero
iout=0
if (ifound1.eq.1) then
qstrana2=qstrana1(istart2:iend-1)
istart=istart2
vout=zero
read (qstrana2,*,end=20,err=20) vout
20 iout=int(vout)
end if
return
end
************************************************************************
**********************************************************************
subroutine dipmom(naold,dpmm,xdip,ydip,zdip,xdir,ydir,zdir)
**********************************************************************
#include "cbka.blk"
#include "cbkc.blk"
#include "cbkch.blk"
#include "cbkconst.blk"
#include "control.blk"
#include "small.blk"
**********************************************************************
* *
* Calculate and output dipole moment *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In dipmom'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
************************************************************************
* *
* CONVERSION FACTOR TO DEBYE UNITS IS CALCULATED *
* THE CALCULATION IS INITIALIZED *
* *
************************************************************************
ELCHG=1.60217733D-19 ! [C] = [As]
CLIGHT=2.99792458D8 ! [m/s]
DBCONV=ONE/(CLIGHT*ELCHG*1.0D11)
CHCPX=ZERO
CHCPY=ZERO
CHCPZ=ZERO
CHCMX=ZERO
CHCMY=ZERO
CHCMZ=ZERO
XDIP=ZERO
YDIP=ZERO
ZDIP=ZERO
XGRD=ZERO
YGRD=ZERO
ZGRD=ZERO
************************************************************************
* *
* CALCULATION OF MAGNITUDE AND CENTRES OF POSITIVE AND NEGATIVE *
* CHARGES *
* *
************************************************************************
if (na.eq.0) na=naold
CHRG=ZERO
DO 4 K1=1,NA
CHK1=CH(K1)
IF (CHK1.EQ.ZERO) GOTO 4
IF (CHK1.LT.ZERO) GOTO 3
CHRG=CHRG+CHK1
CHCPX=CHCPX+CHK1*C(K1,1)
CHCPY=CHCPY+CHK1*C(K1,2)
CHCPZ=CHCPZ+CHK1*C(K1,3)
GOTO 4
3 CHCMX=CHCMX-CHK1*C(K1,1)
CHCMY=CHCMY-CHK1*C(K1,2)
CHCMZ=CHCMZ-CHK1*C(K1,3)
4 CONTINUE
************************************************************************
* *
* CALCULATION OF DISTANCE BETWEEN CENTRES AND OF DIPOLE MOMENT *
* IN DEBIJE UNITS *
* *
************************************************************************
CHDSTX=CHCPX-CHCMX
CHDSTY=CHCPY-CHCMY
CHDSTZ=CHCPZ-CHCMZ
DPMM=SQRT(CHDSTX*CHDSTX+CHDSTY*CHDSTY+CHDSTZ*CHDSTZ)/DBCONV
IF(DPMM.LT.1.0D-4)RETURN
XDIP=HALF*(CHCPX+CHCMX)/CHRG
YDIP=HALF*(CHCPY+CHCMY)/CHRG
ZDIP=HALF*(CHCPZ+CHCMZ)/CHRG
GRTST=MAX(CHDSTX,CHDSTY,CHDSTZ)
XDIR=-CHDSTX/GRTST
YDIR=-CHDSTY/GRTST
ZDIR=-CHDSTZ/GRTST
open (64,file='dipole.out',status='unknown')
write (64,100)dpmm,xdip,ydip,zdip,xdir,ydir,zdir
close (64)
100 format ('Dipole moment (Debye):',f12.4,' Location:',3f12.4,
$' Direction (-side):',3f12.4)
return
end
************************************************************************
**********************************************************************
subroutine readtraj(ivels)
**********************************************************************
#include "cbka.blk"
#include "cbkatomcoord.blk"
#include "cbkc.blk"
#include "cbkconst.blk"
#include "cbkdistan.blk"
#include "cbktregime.blk"
#include "cellcoord.blk"
#include "control.blk"
#include "small.blk"
#include "cbkinit.blk"
**********************************************************************
* *
* Read in trajectory file *
* *
**********************************************************************
c$$$ if (ndebug.eq.1) then
c$$$C open (65,file='fort.65',status='unknown',access='append')
c$$$ write (65,*) 'In readtraj'
c$$$ call timer(65)
c$$$ close (65)
c$$$ end if
open(unit=66,file='moldyn.vel',status='old',err=10)
ivels=1
read (66,*)
read (66,100)aaxis,baxis,caxis
read (66,100)angles(1),angles(2),angles(3)
if (qr.eq.'F'.or.qr.eq.'P'.or.ngeofor.eq.1) then
axis(1)=aaxis
axis(2)=baxis
axis(3)=caxis
axiss(1)=axis(1)
axiss(2)=axis(2)
axiss(3)=axis(3)
angle(1)=angles(1)
angle(2)=angles(2)
angle(3)=angles(3)
halfa=angle(1)*dgrrdn
hbeta=angle(2)*dgrrdn
hgamma=angle(3)*dgrrdn
sinalf=sin(halfa)
cosalf=cos(halfa)
sinbet=sin(hbeta)
cosbet=cos(hbeta)
cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
if (cosphi.gt.1.0) cosphi=1.0
sinphi=sqrt(one-cosphi*cosphi)
tm11=axis(1)*sinbet*sinphi
tm21=axis(1)*sinbet*cosphi
tm31=axis(1)*cosbet
tm22=axis(2)*sinalf
tm32=axis(2)*cosalf
tm33=axis(3)
end if
if (aaxis.ne.axis(1).or.baxis.ne.axis(2).or.caxis.ne.axis(3))
$stop 'Wrong cell parameters in moldyn.vel'
read (66,200)nan
if (nan.ne.na) stop 'Wrong number of atoms in moldyn.vel-file'
if (nbiolab.eq.1) write (*,*)'Warning: using labels in vels-file'
read (66,250)((c(i,j),j=1,3),qlabel(i),i=1,na)
read (66,*)
read (66,300)((vel(j,i),j=1,3),i=1,na)
read (66,*)
read (66,300)((accel(j,i),j=1,3),i=1,na)
read (66,*)
read (66,300,end=10,err=10)((aold(j,i),j=1,3),i=1,na)
read (66,*)
read (66,300,end=10,err=10)tempmd
read (66,*)
read (66,350,end=10,err=10)nsbma2
10 continue
**********************************************************************
* *
* Format part *
* *
**********************************************************************
100 format(3d15.8)
200 format(i4)
250 format(3d24.15,1x,a5)
300 format(3d24.15)
350 format(i3)
400 format (8i3,8f8.4)
return
end
**********************************************************************
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