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packmolnew.f
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c
c Written by Leandro Martínez, 2009-2011.
c Copyright (c) 2009-2011, Leandro Martínez, Jose Mario Martinez,
c Ernesto G. Birgin.
c
c This program is free software; you can redistribute it and/or
c modify it under the terms of the GNU General Public License
c as published by the Free Software Foundation; either version 2
c of the License, or (at your option) any later version.
c
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
c
c Packmol: A package for building initial configurations for
c molecular dynamics simulations, to be published, 2008.
c
c http://www.ime.unicamp.br/~martinez/packmol
c
c Usage (see the page above for further information):
c
c ./packmol < inputfile.inp
c
c References:
c
c L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez,
c PACKMOL: A package for building initial configurations for
c molecular dynamics simulations, J. Comp. Chem. 30:2157-2164, 2009.
c
c J. M. Martinez and L. Martinez,
c Packing optimization for the automated generation of complex
c system's initial configurations for molcular dynamics and
c docking. J. Comp. Chem. 24:819-825, 2003.
c
c This version of Packmol uses the optimization method GENCAN which
c is a part of the TANGO (Trustable Algorithms for Nonlinear General
c Optimization) project.
c Reference:
c E. G. Birgin, J. M. Martinez, Comp. Opt. Appl. 23:101-125, 2002.
c http://www.ime.usp.br/~egbirgin/tango
c
c
program packmol
implicit none
include 'sizes.i'
include 'molpa.i'
include 'gencan.i'
integer irestline(maxrest)
integer linestrut(maxtype,2)
integer itype, nrest, irest, idatom, iatom
integer ntemp, ntfix, idtemp, nmtemp, natemp, nlines
integer linesttmp1, linesttmp2, jtype
integer ntmol, n, iftype, icart, imol
integer i, iline, iiatom, iat, iirest, iratcount
integer isem
integer nloop, loop
integer maxcon(maxatom)
integer ntcon(9), nconnect(maxatom,8)
integer ntottemp, ilubar, ilugan
integer resnumbers(maxtype), resntemp
integer charl, writeout
c integer iargc, narg, charl, writeout
double precision v1(3),v2(3),v3(3)
double precision x(nn), xfull(nn), xbest(nn)
double precision disini
double precision cmx, cmy, cmz, beta, gama, teta
double precision xtemp, ytemp, ztemp
double precision fx, bestf, flast, fout
double precision fimp, fimprov, precision
double precision amass(maxatom), charge(maxatom)
double precision discale, movefrac
double precision add_sides_fix
real etime, tarray(2), time0
character*200 keyword(maxlines,maxkeywords)
character*200 record
character*200 name(maxtype)
character*80 pdbfile(maxtype), xyzfile
character*3 ele(maxatom)
character*200 xyzout
logical fix,fixed(maxtype),fixtmp,randini,check,chkgrad
logical pdb,tinker,xyz,moldy,rests,writebad
logical add_amber_ter, add_box_sides
logical movebadprint, hasbad
c Start time computation
time0 = etime(tarray)
c If the user tried to run without redirection, output error
c
c narg = iargc()
c call getarg(1,record)
c if(record.gt." ") then
c if(narg.gt.0) then
c if(record.le."0") then
c record = "inputfile.inp"
c end if
c write(*,*)
c write(*,*) ' Packmol must be run with input file redirection:'
c write(*,*) ' packmol < ',record(1:charl(record))
c write(*,*)
c stop
c end if
c end if
c
c Printing title
1 format( 62('#'), /,/
+ ' PACKMOL - Packing optimization for the automated', /
+ ' generation of starting configurations for', /
+ ' molecular dynamics. ',/
+ ' ',/
+ t42,' Version 1.1.2.272 ',/
+ ,/,62('#'), /,/)
write(*,1)
c Reading input file
call getinp(dism,precision,
+ ntype,nlines,nrest,
+ natoms,idfirst,nconnect,maxcon,nmols,
+ isem,
+ discale,nloop,
+ irestline,ityperest,linestrut,
+ coor,amass,charge,restpars,
+ pdbfile,name,ele,keyword,
+ xyzout,writeout,writebad,
+ tinker,pdb,xyz,moldy,check,chkgrad,
+ randini,resnumbers,movefrac,
+ add_amber_ter,add_box_sides,add_sides_fix)
c Put molecules in their center of mass
call cenmass(coor,amass,
+ ntype,nlines,
+ idfirst,natoms,
+ keyword,linestrut)
c Computing the total number of atoms
ntotat = 0
do itype = 1, ntype
ntotat = ntotat + natoms(itype) * nmols(itype)
end do
write(*,*) ' Total number of atoms: ', ntotat
if(ntotat.gt.maxatom) then
write(*,*)' ERROR: Total number of atoms greater than maxatom.'
write(*,*)' Change the maxatom (sizes.i file) '
stop
end if
c Put fixed molecules in the specified position
do itype = 1, ntype
fixed(itype) = .false.
end do
do irest = 1, nrest
if(ityperest(irest).eq.1) then
do itype = 1, ntype
if(irestline(irest).gt.linestrut(itype,1).and.
+ irestline(irest).lt.linestrut(itype,2)) then
cmx = restpars(irest,1)
cmy = restpars(irest,2)
cmz = restpars(irest,3)
beta = restpars(irest,4)
gama = restpars(irest,5)
teta = restpars(irest,6)
c Compute rotation matrix from euler angles
call eulerfixed(beta,gama,teta,v1,v2,v3)
idatom = idfirst(itype) - 1
do iatom = 1, natoms(itype)
idatom = idatom + 1
xtemp = coor(idatom,1)*v1(1)
+ + coor(idatom,2)*v2(1)
+ + coor(idatom,3)*v3(1)
ytemp = coor(idatom,1)*v1(2)
+ + coor(idatom,2)*v2(2)
+ + coor(idatom,3)*v3(2)
ztemp = coor(idatom,1)*v1(3)
+ + coor(idatom,2)*v2(3)
+ + coor(idatom,3)*v3(3)
coor(idatom, 1) = xtemp + cmx
coor(idatom, 2) = ytemp + cmy
coor(idatom, 3) = ztemp + cmz
end do
record = name(itype)
write(*,*) ' Molecule ',record(1:charl(record)),
+ '(',itype,') will be fixed.'
fixed(itype) = .true.
if(nmols(itype).gt.1) then
write(*,*)' ERROR: You cannot set number > 1',
+ ' for fixed molecules. '
stop
end if
end if
end do
end if
end do
c Reseting parameters for removing the fixed molecules
fix = .false.
ntemp = 0
do itype = 1, ntype
if(fixed(itype)) then
fix = .true.
else
ntemp = ntemp + 1
end if
end do
ntfix = ntype
ntype = ntemp
do i = 1, ntfix - ntype
do itype = 1, ntfix - 1
if(fixed(itype)) then
record = name(itype)
fixtmp = fixed(itype)
idtemp = idfirst(itype)
nmtemp = nmols(itype)
natemp = natoms(itype)
resntemp = resnumbers(itype)
if(pdb) xyzfile = pdbfile(itype)
linesttmp1 = linestrut(itype,1)
linesttmp2 = linestrut(itype,2)
jtype = itype + 1
if(.not.fixed(jtype)) then
name(itype) = name(jtype)
name(jtype) = record(1:10)
idfirst(itype) = idfirst(jtype)
idfirst(jtype) = idtemp
fixed(itype) = fixed(jtype)
fixed(jtype) = fixtmp
nmols(itype) = nmols(jtype)
nmols(jtype) = nmtemp
natoms(itype) = natoms(jtype)
natoms(jtype) = natemp
resnumbers(itype) = resnumbers(jtype)
resnumbers(jtype) = resntemp
if(pdb) then
pdbfile(itype) = pdbfile(jtype)
pdbfile(jtype) = xyzfile
end if
linestrut(itype,1) = linestrut(jtype,1)
linestrut(itype,2) = linestrut(jtype,2)
linestrut(jtype,1) = linesttmp1
linestrut(jtype,2) = linesttmp2
end if
end if
end do
end do
c Computing the number of variables
c
c ntype: 1...ntype (counter for the number of free structures)
c
c ntfix: 1...ntype...ntfix (counter for the total number of structures)
c
ntmol = 0
do itype = 1, ntfix
ntmol = ntmol + nmols(itype)
end do
ntotmol = 0
do itype = 1, ntype
ntotmol = ntotmol + nmols(itype)
end do
n = ntotmol * 6
write(*,*) ' Total number of molecules: ', ntmol
write(*,*) ' Number of fixed molecules: ', ntmol - ntotmol
write(*,*) ' Number of free molecules: ', ntotmol
write(*,*) ' Number of variables: ', n
c Computing the total number of fixed atoms
natfix = 0
if(fix) then
do iftype = ntype + 1, ntfix
natfix = natfix + natoms(iftype)
end do
end if
write(*,*) ' Total number of fixed atoms: ', natfix
c Setting the array that contains the restrictions per atom
icart = natfix
do itype = 1, ntype
rests = .false.
do imol = 1, nmols(itype)
idatom = idfirst(itype) - 1
do iatom = 1, natoms(itype)
icart = icart + 1
idatom = idatom + 1
nratom(icart) = 0
iratcount = 0
do i = 1, mrperatom
iratom(icart,i) = 0
end do
iline = linestrut(itype,1)
do while(iline.lt.linestrut(itype,2))
iline = iline + 1
if(keyword(iline,1).eq.'atoms') then
iiatom = -1
do iat = 2, maxkeywords
read(keyword(iline,iat),*,err=130,end=130) iiatom
if(iatom.eq.iiatom) goto 130
end do
130 continue
do while(keyword(iline,1).ne.'end'.and.
+ keyword(iline,2).ne.'atoms')
iline = iline + 1
if(iatom.eq.iiatom) then
if(keyword(iline,1).eq.'inside'.or.
+ keyword(iline,1).eq.'outside'.or.
+ keyword(iline,1).eq.'over'.or.
+ keyword(iline,1).eq.'below') then
nratom(icart) = nratom(icart) + 1
iratcount = iratcount + 1
do irest = 1, nrest
if(irestline(irest).eq.iline) iirest = irest
end do
iratom(icart,iratcount) = iirest
end if
end if
end do
iline = iline - 1
else if(keyword(iline,1).eq.'inside'.or.
+ keyword(iline,1).eq.'outside'.or.
+ keyword(iline,1).eq.'over'.or.
+ keyword(iline,1).eq.'below') then
nratom(icart) = nratom(icart) + 1
iratcount = iratcount + 1
do irest = 1, nrest
if(irestline(irest).eq.iline) iirest = irest
end do
iratom(icart,iratcount) = iirest
end if
end do
if(nratom(icart).gt.0) rests = .true.
end do
if(.not.rests) then
write(*,*) ' ERROR: Some molecule has no geometrical',
+ ' restriction defined: nothing to do.'
stop
end if
end do
end do
c If there are no variables (only fixed molecules, stop)
if(n.eq.0) then
call output(x,amass,
+ irestline,linestrut,maxcon,ntcon,nconnect,
+ nrest,ntfix,resnumbers,
+ ele,pdbfile,xyzout,name,
+ pdb,tinker,xyz,moldy,fix,
+ add_amber_ter,add_box_sides,add_sides_fix)
write(*,908)
write(*,*) ' There are only fixed molecules, therefore '
write(*,*) ' there is nothing to do. '
write(*,*) ' The output file contains the fixed molecule '
write(*,*) ' in the desired position. '
write(*,908)
stop
end if
c
c (Re)setting parameters and building initial point
c
call initial(isem,randini,x,n,ntfix,fix,moldy,
+ chkgrad,nloop,discale,precision,movefrac,check)
c Computing the energy at the initial point
disini = dism
dism2 = dism * dism
call feasy(x,fx)
write(*,*) ' Objective function at initial point: ', fx
bestf = fx
flast = fx
fout = fx
do i = 1, n
xbest(i) = x(i)
end do
if(check) then
call output(x,amass,
+ irestline,linestrut,maxcon,ntcon,nconnect,
+ nrest,ntfix,resnumbers,
+ ele,pdbfile,xyzout,name,
+ pdb,tinker,xyz,moldy,fix,
+ add_amber_ter,add_box_sides,add_sides_fix)
write(*,*) ' Wrote initial point to output file: ',
+ xyzout(1:charl(xyzout))
stop
end if
c
c Main loop: first pack types of molecules separately, then
c pack all molecules together
c
do i = 1, nn
xfull(i) = x(i)
end do
ntemp = n
ntottemp = ntotmol
if(ntype.eq.1) then
itype = 1
else
itype = 0
end if
do while(itype.le.ntype+1)
itype = itype + 1
c Use slightly larger tolerance than required to improove convergence
dism = discale * disini
dism2 = dism * dism
if(itype.le.ntype) then
if(nmols(itype).eq.1) itype = itype + 1
end if
c Adjusting parameters for packing only this type
if(itype.le.ntype) then
write(*,*)
write(*,908)
write(*,*)
write(*,*) ' Packing molecules of type ', itype
write(*,*)
write(*,908)
908 format(62('#'))
do i = 1, ntype
if(i.eq.itype) then
comptype(i) = .true.
else
comptype(i) = .false.
end if
end do
n = nmols(itype) * 6
ntotmol = nmols(itype)
ilubar = 0
do i = 1, itype - 1
ilubar = ilubar + nmols(i) * 3
end do
ilubar = ilubar + 1
ilugan = ntemp/2 + ilubar
do i = 1, n / 2
x(i) = xfull(ilubar)
x(i+n/2) = xfull(ilugan)
ilubar = ilubar + 1
ilugan = ilugan + 1
end do
end if
c If itype=ntype+1 restore original vectors and pack all molecules
if(itype.eq.ntype+1) then
n = ntemp
ntotmol = ntottemp
do i = 1, n
x(i) = xfull(i)
end do
do itype = 1, ntype
comptype(itype) = .true.
end do
if(ntype.gt.1) then
write(*,*)
write(*,908)
write(*,*)
write(*,*)' Solving the problem for all molecules together.'
write(*,*)
write(*,908)
write(*,*)
end if
end if
loop = -1
do while(loop.le.nloop)
loop = loop + 1
c Reseting the parameters relative to the improvement of the function
if(loop.eq.0) then
fimp = 1.d99
fimprov = fimp
call feasy(x,fx)
bestf = fx
flast = fx
end if
c Moving bad molecules
if(fimp.le.10.d0) then
movebadprint = .true.
call movebad(n,x,fx,movefrac,precision,isem,
+ hasbad,movebadprint)
flast = fx
end if
if(loop.eq.nloop.and.itype.eq.ntype+1) then
write(*,*)' STOP: Maximum number of GENCAN loops achieved.'
call checkpoint(n,xbest,amass,
+ nrest,ntfix,nloop,
+ irestline,linestrut,maxcon,ntcon,nconnect,
+ ele,pdbfile,xyzout,name,
+ pdb,tinker,xyz,moldy,fix,
+ movefrac,precision,isem,resnumbers,
+ add_amber_ter,add_box_sides,add_sides_fix)
stop
end if
write(*,905) loop, dism
905 format( /, 17('-'),' Starting GENCAN loop(',i4,') ',17('-'),/
+ ' Tolerance:',f10.2)
C CALL GENCAN
write(*,700)
700 format(' Packing:|0 ',tr39,' 10|')
call pgencan(n,x,fx)
c Compute the statistics of the last optimization loop
call feasy(x,fx)
if(bestf.gt.0.d0) fimprov = -100.d0 * (fx - bestf) / bestf
if(bestf.eq.0.d0) fimprov = 100.d0
if(flast.gt.0.d0) fimp = -100.d0 * (fx - flast) / flast
if(flast.eq.0.d0) fimp = 100.d0
fimp = dmin1(99.99d0,dmax1(-99.99d0,fimp))
fimprov = dmin1(99.99d0,dmax1(-99.99d0,fimprov))
write(*,907) fx, bestf, fimprov, fimp,
+ dmin1(10.d0,dsqrt(fdist)), frest
907 format( /
* ' Function value from last GENCAN loop: f = ', e10.5, /
* ' Best function value before: f = ', e10.5, /
* ' Improvement from best function value: ', f8.2, ' %',/
* ' Improvement from last loop: ', f8.2, ' %', /
* ' Minimum distance between atoms: ', f10.6, /
* ' Maximum violation of the constraints: ', e10.5, /
* 62('-'),/)
flast = fx
c If the distance between molecules is satisfactory, restore disini
if(dsqrt(fdist).ge.disini) then
dism = disini
dism2 = dism * dism
end if
c Updating best point
if(fx.le.bestf) then
bestf = fx
if(itype.eq.ntype+1) then
do i = 1, n
xbest(i) = x(i)
end do
end if
end if
c Writing output file
if(itype.eq.ntype+1) then
if( ( ( disini-dsqrt(fdist).lt.precision.and.
+ frest.lt.precision ) .or. bestf.lt.precision )
+ .or. ( mod(loop+1,writeout).eq.0 .and.
+ ( writebad .or. bestf.lt.fout ) ) ) then
fout = bestf
if(writebad) then
call output(x,amass,
+ irestline,linestrut,maxcon,ntcon,nconnect,
+ nrest,ntfix,resnumbers,
+ ele,pdbfile,xyzout,name,
+ pdb,tinker,xyz,moldy,fix,
+ add_amber_ter,add_box_sides,add_sides_fix)
write(*,*) ' Current point written to file: ',
+ xyzout(1:charl(xyzout))
else
call output(xbest,amass,
+ irestline,linestrut,maxcon,ntcon,nconnect,
+ nrest,ntfix,resnumbers,
+ ele,pdbfile,xyzout,name,
+ pdb,tinker,xyz,moldy,fix,
+ add_amber_ter,add_box_sides,add_sides_fix)
write(*,*) ' Best solution written to file: ',
+ xyzout(1:charl(xyzout))
end if
end if
end if
c When the solution is found, print success information and stop
if((disini-dsqrt(fdist).lt.precision.and.
+ frest.lt.precision).or.
+ bestf.lt.precision) then
if(itype.le.ntype) then
write(*,908)
write(*,*)' Packing solved for molecules of type', itype
write(*,*)' Objective function value: ', bestf
write(*,*)' Minimum distance between atoms: ',dsqrt(fdist)
write(*,*)' Max. constraint violation: ', frest
write(*,908)
loop = nloop + 1
else
909 format(/, 62('#'),/, /,
+ t27, ' Success! ', /,
+ t10, ' Final objective function value: ', e10.5, /,
+ t10, ' Minimum distance between atoms: ', f10.6, /,
+ t10, ' Maximum violation of the constraints: ', e10.5,/,
+ 62('-'), /,
+ ' Please cite this work if Packmol was useful: ',/,
+ ' L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez, ',/,
+ ' PACKMOL: A package for building initial configurations ',/,
+ ' for molecular dynamics simulations. ',/,
+ ' Journal of Computational Chemistry, 30:2157-2164,2009.',
+ /,/,62('#'),/)
write(*,909) bestf, dsqrt(fdist), frest
write(*,*) ' Running time: ',
+ etime(tarray) - time0,' seconds. '
stop
end if
end if
c End do of loop do:
end do
if(itype.le.ntype) then
ilubar = 0
do i = 1, itype - 1
ilubar = ilubar + nmols(i)*3
end do
ilubar = ilubar + 1
ilugan = ntemp/2 + ilubar
do i = 1, n/2
xfull(ilubar) = x(i)
xfull(ilugan) = x(i+n/2)
ilubar = ilubar + 1
ilugan = ilugan + 1
end do
end if
c End of itype do:
end do
end