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output.f90
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!
! Written by Leandro Martínez, 2009-2011.
! Copyright (c) 2009-2011, Leandro Martínez, Jose Mario Martinez,
! Ernesto G. Birgin.
!
! Subroutine output: Subroutine that writes the output file
!
subroutine output(n,x,stat)
use sizes
use compute_data
use input
implicit none
integer, intent(out) :: stat
integer :: n, k, i, ilugan, ilubar, itype, imol, idatom,&
irest, iimol, ichain, iatom, irec, ilres, ifres,&
iires, strlength, irescount,&
icart, i_ref_atom, ioerr
integer :: nr, nres, imark
integer :: i_fixed, i_not_fixed
double precision :: x(n)
double precision :: tens(4,4), v(4,4), dv(4)
double precision :: v1(3), v2(3), v3(3)
double precision :: xbar, ybar, zbar, beta, gama, teta, xcm, ycm, zcm
double precision :: xlength, ylength, zlength
double precision :: xxyx, xxyy, xxyz, xyyz, xyyy, xzyx,&
xzyy, xzyz, xyyx, xq, yq, zq, q0, q1, q2, q3
double precision :: xtemp, ytemp, ztemp
double precision :: sxmin, symin, szmin, sxmax, symax, szmax
character :: write_chain, even_chain, odd_chain
character(len=64) :: title
character(len=80) :: pdb_atom_line, pdb_hetatm_line, tinker_atom_line
character(len=200) :: record
! Job title
title = '# Built with Packmol '
!
! Write restart files, if required
!
! Restart file for all system
if ( restart_to(0) /= 'none' ) then
record = restart_to(0)
open(10,file=restart_to(0),iostat=ioerr)
if ( ioerr /= 0 ) then
write(*,*) ' ERROR: Could not open restart_to file: ', trim(adjustl(record))
stat = 2
return
end if
ilubar = 0
ilugan = ntotmol*3
do i = 1, ntotmol
write(10,"(6(tr1,es23.16))") x(ilubar+1), x(ilubar+2), x(ilubar+3), &
x(ilugan+1), x(ilugan+2), x(ilugan+3)
ilubar = ilubar + 3
ilugan = ilugan + 3
end do
close(10)
write(*,*) ' Wrote restart file for all system: ', trim(adjustl(record))
end if
! Restart files for specific molecule types
ilubar = 0
ilugan = ntotmol*3
do itype = 1, ntype
if ( restart_to(itype) /= 'none' ) then
record = restart_to(itype)
open(10,file=record,iostat=ioerr)
if ( ioerr /= 0 ) then
write(*,*) ' ERROR: Could not open restart_to file: ', trim(adjustl(record))
stat = 2
return
end if
do i = 1, nmols(itype)
write(10,"(6(tr1,es23.16))") x(ilubar+1), x(ilubar+2), x(ilubar+3), &
x(ilugan+1), x(ilugan+2), x(ilugan+3)
ilubar = ilubar + 3
ilugan = ilugan + 3
end do
close(10)
write(*,*) ' Wrote restart file: ', trim(adjustl(record))
else
ilubar = ilubar + nmols(itype)*3
ilugan = ilugan + nmols(itype)*3
end if
end do
! Write the output (xyz file)
if(xyz) then
open(30,file=xyzout,status='unknown')
write(30,*) ntotat
write(30,*) title
ilubar = 0
ilugan = ntotmol*3
icart = natfix
i_not_fixed = 0
i_fixed = ntype
do itype = 1, ntfix
if ( .not. fixedoninput(itype) ) then
i_not_fixed = i_not_fixed + 1
do imol = 1, nmols(i_not_fixed)
xbar = x(ilubar+1)
ybar = x(ilubar+2)
zbar = x(ilubar+3)
beta = x(ilugan+1)
gama = x(ilugan+2)
teta = x(ilugan+3)
call eulerrmat(beta,gama,teta,v1,v2,v3)
idatom = idfirst(i_not_fixed) - 1
do iatom = 1, natoms(i_not_fixed)
icart = icart + 1
idatom = idatom + 1
call compcart(icart,xbar,ybar,zbar,&
coor(idatom,1),coor(idatom,2),&
coor(idatom,3),&
v1,v2,v3)
write(30,"( tr2,a,tr2,3(tr2,f14.6) )") trim(ele(idatom)), (xcart(icart, k), k = 1, 3)
end do
ilugan = ilugan + 3
ilubar = ilubar + 3
end do
else
i_fixed = i_fixed + 1
idatom = idfirst(i_fixed) - 1
do iatom = 1, natoms(i_fixed)
idatom = idatom + 1
write(30,"( tr2,a,tr2,3(tr2,f14.6) )") trim(ele(idatom)), (coor(idatom,k),k=1,3)
end do
end if
end do
close(30)
end if
! write the output as a MOLDY file
if(moldy) then
open(30,file=xyzout,status='unknown')
! For square moldy boxes, this must be the side dimensions of the box
sxmin = 1.d30
symin = 1.d30
szmin = 1.d30
sxmax = -1.d30
symax = -1.d30
szmax = -1.d30
do irest = 1, nrest
if(ityperest(irest).eq.2) then
sxmin = dmin1(restpars(irest,1),sxmin)
symin = dmin1(restpars(irest,2),symin)
szmin = dmin1(restpars(irest,3),szmin)
sxmax = dmax1(restpars(irest,4)+restpars(irest,1),sxmax)
symax = dmax1(restpars(irest,4)+restpars(irest,2),symax)
szmax = dmax1(restpars(irest,4)+restpars(irest,3),szmax)
else if(ityperest(irest).eq.3) then
sxmin = dmin1(restpars(irest,1),sxmin)
symin = dmin1(restpars(irest,2),symin)
szmin = dmin1(restpars(irest,3),szmin)
sxmax = dmax1(restpars(irest,4),sxmax)
symax = dmax1(restpars(irest,5),symax)
szmax = dmax1(restpars(irest,6),szmax)
else
write(*,*) ' WARNING: The first line of the moldy output'
write(*,*) ' file contains the size of the sides of the'
write(*,*) ' paralelogram that defines the system. '
write(*,*) ' The numbers printed may not be correct in '
write(*,*) ' this case because regions other than cubes '
write(*,*) ' or boxes were used. '
sxmin = dmin1(sxmin,sizemin(1))
symin = dmin1(symin,sizemin(2))
szmin = dmin1(szmin,sizemin(3))
sxmax = dmax1(sxmax,sizemax(1))
symax = dmax1(symax,sizemax(2))
szmax = dmax1(szmax,sizemax(3))
end if
end do
xlength = sxmax - sxmin
ylength = symax - symin
zlength = szmax - szmin
write(30,"( 3(tr1,f12.6),' 90 90 90 1 1 1 ' )") xlength, ylength, zlength
ilubar = 0
ilugan = ntotmol*3
i_not_fixed = 0
i_fixed = ntype
do itype = 1, ntfix
if ( .not. fixedoninput(itype) ) then
i_not_fixed = i_not_fixed + 1
record = name(i_not_fixed)
do imol = 1, nmols(i_not_fixed)
xbar = (x(ilubar+1) - sxmin) / xlength
ybar = (x(ilubar+2) - symin) / ylength
zbar = (x(ilubar+3) - szmin) / zlength
beta = x(ilugan+1)
gama = x(ilugan+2)
teta = x(ilugan+3)
call eulerrmat(beta,gama,teta,v1,v2,v3)
! Computing cartesian coordinates and quaternions
xxyx = 0.d0
xxyy = 0.d0
xxyz = 0.d0
xyyx = 0.d0
xyyy = 0.d0
xyyz = 0.d0
xzyx = 0.d0
xzyy = 0.d0
xzyz = 0.d0
idatom = idfirst(i_not_fixed) - 1
do iatom = 1, natoms(i_not_fixed)
idatom = idatom + 1
xq = coor(idatom, 1)*v1(1) &
+ coor(idatom, 2)*v2(1) &
+ coor(idatom, 3)*v3(1)
yq = coor(idatom, 1)*v1(2) &
+ coor(idatom, 2)*v2(2) &
+ coor(idatom, 3)*v3(2)
zq = coor(idatom, 1)*v1(3) &
+ coor(idatom, 2)*v2(3) &
+ coor(idatom, 3)*v3(3)
! Recovering quaternions for molecule imol
xxyx = xxyx + xq * coor(idatom,1) * amass(idatom)
xxyy = xxyy + xq * coor(idatom,2) * amass(idatom)
xxyz = xxyz + xq * coor(idatom,3) * amass(idatom)
xyyx = xyyx + yq * coor(idatom,1) * amass(idatom)
xyyy = xyyy + yq * coor(idatom,2) * amass(idatom)
xyyz = xyyz + yq * coor(idatom,3) * amass(idatom)
xzyx = xzyx + zq * coor(idatom,1) * amass(idatom)
xzyy = xzyy + zq * coor(idatom,2) * amass(idatom)
xzyz = xzyz + zq * coor(idatom,3) * amass(idatom)
end do
tens(1,1) = xxyx + xyyy + xzyz
tens(1,2) = xzyy - xyyz
tens(2,2) = xxyx - xyyy - xzyz
tens(1,3) = xxyz - xzyx
tens(2,3) = xxyy + xyyx
tens(3,3) = xyyy - xzyz - xxyx
tens(1,4) = xyyx - xxyy
tens(2,4) = xzyx + xxyz
tens(3,4) = xyyz + xzyy
tens(4,4) = xzyz - xxyx - xyyy
nr = 16
call jacobi (tens, 4, 4, dv, v, nr)
q0 = v(1,4)
q1 = v(2,4)
q2 = v(3,4)
q3 = v(4,4)
record = name(i_not_fixed)
xbar = dmin1(0.999999d0,xbar)
ybar = dmin1(0.999999d0,ybar)
zbar = dmin1(0.999999d0,zbar)
write(30,"( a10,tr1,7(f12.6) )") record(1:strlength(record)), xbar, ybar, zbar, &
q0, q1, q2, q3
ilugan = ilugan + 3
ilubar = ilubar + 3
end do
else
i_fixed = i_fixed + 1
idatom = idfirst(i_fixed) - 1
! Getting the specified position of the molecule
do irest = 1, nrest
if(irestline(irest).gt.linestrut(i_fixed,1).and.&
irestline(irest).lt.linestrut(i_fixed,2)) then
xcm = restpars(irest,1) - sxmin
ycm = restpars(irest,2) - symin
zcm = restpars(irest,3) - szmin
beta = -restpars(irest,4)
gama = -restpars(irest,5)
teta = -restpars(irest,6)
end if
end do
call eulerrmat(beta,gama,teta,v1,v2,v3)
! Computing cartesian coordinates and quaternions
xxyx = 0.d0
xxyy = 0.d0
xxyz = 0.d0
xyyx = 0.d0
xyyy = 0.d0
xyyz = 0.d0
xzyx = 0.d0
xzyy = 0.d0
xzyz = 0.d0
idatom = idfirst(i_fixed) - 1
do iatom = 1, natoms(i_fixed)
idatom = idatom + 1
xtemp = coor(idatom,1) - xcm
ytemp = coor(idatom,2) - ycm
ztemp = coor(idatom,3) - zcm
xq = xtemp*v1(1) + ytemp*v2(1) + ztemp*v3(1)
yq = xtemp*v1(2) + ytemp*v2(2) + ztemp*v3(2)
zq = xtemp*v1(3) + ytemp*v2(3) + ztemp*v3(3)
xxyx = xxyx + xtemp * xq * amass(idatom)
xxyy = xxyy + xtemp * yq * amass(idatom)
xxyz = xxyz + xtemp * zq * amass(idatom)
xyyx = xyyx + ytemp * xq * amass(idatom)
xyyy = xyyy + ytemp * yq * amass(idatom)
xyyz = xyyz + ytemp * zq * amass(idatom)
xzyx = xzyx + ztemp * xq * amass(idatom)
xzyy = xzyy + ztemp * yq * amass(idatom)
xzyz = xzyz + ztemp * zq * amass(idatom)
end do
tens(1,1) = xxyx + xyyy + xzyz
tens(1,2) = xzyy - xyyz
tens(2,2) = xxyx - xyyy - xzyz
tens(1,3) = xxyz - xzyx
tens(2,3) = xxyy + xyyx
tens(3,3) = xyyy - xzyz - xxyx
tens(1,4) = xyyx - xxyy
tens(2,4) = xzyx + xxyz
tens(3,4) = xyyz + xzyy
tens(4,4) = xzyz - xxyx - xyyy
nr = 16
call jacobi (tens, 4, 4, dv, v, nr)
q0 = v(1,4)
q1 = v(2,4)
q2 = v(3,4)
q3 = v(4,4)
xcm = xcm / xlength
ycm = ycm / ylength
zcm = zcm / zlength
record = name(itype)
xcm = dmin1(0.999999d0,xcm)
ycm = dmin1(0.999999d0,ycm)
zcm = dmin1(0.999999d0,zcm)
write(30,"( a10,tr1,7(f12.6) )") record(1:strlength(record)),&
xcm, ycm, zcm, q0, q1, q2, q3
end if
end do
close(30)
end if
! write the output as pdb file
if(pdb) then
pdb_atom_line = "( t1,a5,t7,i5,t12,a10,t22,a1,t23,&
&i4,t27,a1,t31,f8.3,t39,f8.3,t47,&
&f8.3,t55,a26 )"
pdb_hetatm_line = "( t1,a6,t7,i5,t12,a10,t22,a1,&
&t23,i4,t27,a1,t31,f8.3,t39,&
&f8.3,t47,f8.3,t55,a26 )"
open(30,file=xyzout,status='unknown')
write(30,"( &
&'HEADER ',/&
&'TITLE ', a64,/&
&'REMARK Packmol generated pdb file ',/&
&'REMARK Home-Page: ',&
&'http://www.ime.unicamp.br/~martinez/packmol',/,&
&'REMARK' )" ) title
if(add_box_sides) then
write(30,"( 'CRYST1',t7,f9.2,t16,f9.2,t25,f9.2,&
&t34,f7.2,t41,f7.2,t48,f7.2,&
&t56,'P 1 1' )") &
sizemax(1)-sizemin(1) + add_sides_fix,&
sizemax(2)-sizemin(2) + add_sides_fix,&
sizemax(3)-sizemin(3) + add_sides_fix,&
90., 90., 90.
end if
ilubar = 0
ilugan = ntotmol*3
icart = natfix
i_ref_atom = 0
iimol = 0
ichain = 0
i_not_fixed = 0
i_fixed = ntype
irescount = 1
do itype = 1, ntfix
if ( .not. fixedoninput(itype) ) then
i_not_fixed = i_not_fixed + 1
! Counting the number of residues of this molecule
open(15,file=pdbfile(i_not_fixed),status='old')
ifres = 0
do
read(15,"( a80 )",iostat=ioerr) record
if ( ioerr /= 0 ) exit
if ( record(1:4).eq.'ATOM'.or.record(1:6).eq.'HETATM' ) then
read(record(23:26),*,iostat=ioerr) imark
if ( ioerr /= 0 ) then
record = pdbfile(i_not_fixed)
write(*,*) ' ERROR: Failed reading residue number ',&
' from PDB file: ', record(1:strlength(record))
write(*,*) ' Residue numbers are integers that must',&
' be between columns 23 and 26. '
write(*,*) ' Other characters within these columns',&
' will cause input/output errors. '
write(*,*) ' Standard PDB format specifications can',&
' be found at: '
write(*,*) ' www.rcsb.org/pdb '
stat = 2
return
end if
if ( ifres .eq. 0 ) ifres = imark
ilres = imark
end if
end do
nres = ilres - ifres + 1
do irec = 1, 80
record(irec:irec) = ' '
end do
mol: do imol = 1, nmols(i_not_fixed)
iimol = iimol + 1
rewind(15)
read(15,"( a80 )",iostat=ioerr) record
do while(record(1:4).ne.'ATOM'.and.record(1:6).ne.'HETATM')
read(15,"( a80 )",iostat=ioerr) record
end do
if( chain(i_not_fixed) == "#" ) then
if(imol.eq.1.or.mod(imol,9999).eq.1) then
ichain = ichain + 1
if( changechains(i_not_fixed) ) then
call chainc(ichain,odd_chain)
ichain = ichain + 1
call chainc(ichain,even_chain)
else
call chainc(ichain,even_chain)
odd_chain = even_chain
end if
end if
if ( mod(imol,2) == 0 ) write_chain = even_chain
if ( mod(imol,2) /= 0 ) write_chain = odd_chain
else
write_chain = chain(i_not_fixed)
end if
xbar = x(ilubar+1)
ybar = x(ilubar+2)
zbar = x(ilubar+3)
beta = x(ilugan+1)
gama = x(ilugan+2)
teta = x(ilugan+3)
call eulerrmat(beta,gama,teta,v1,v2,v3)
idatom = idfirst(i_not_fixed) - 1
iatom = 0
do while(iatom.lt.natoms(i_not_fixed))
iatom = iatom + 1
icart = icart + 1
idatom = idatom + 1
i_ref_atom = i_ref_atom + 1
call compcart(icart,xbar,ybar,zbar,&
coor(idatom,1),coor(idatom,2),&
coor(idatom,3),v1,v2,v3)
if(iatom.gt.1) then
read(15,"( a80 )",iostat=ioerr) record
if ( ioerr /= 0 ) exit mol
end if
if(record(1:4).ne.'ATOM'.and.record(1:6).ne.'HETATM') then
iatom = iatom - 1
icart = icart - 1
idatom = idatom - 1
i_ref_atom = i_ref_atom - 1
cycle
end if
! Setting residue numbers for this molecule
imark = 0
read(record(23:26),*,iostat=ioerr) imark
if ( ioerr /= 0 ) imark = 1
if(resnumbers(i_not_fixed).eq.0) then
iires = mod(imol,9999)
else if(resnumbers(i_not_fixed).eq.1) then
iires = imark
else if(resnumbers(i_not_fixed).eq.2) then
iires = mod(imark-ifres+irescount,9999)
else if(resnumbers(i_not_fixed).eq.3) then
iires = mod(iimol,9999)
end if
if(iires.eq.0) iires = 9999
! Writing output line
if(record(1:4).eq.'ATOM') then
write(30, pdb_atom_line) record(1:5), i_ref_atom,&
record(12:21), write_chain, iires,&
record(27:27),&
(xcart(icart,k), k = 1, 3),&
record(55:80)
end if
if(record(1:6).eq.'HETATM') then
write(30,pdb_hetatm_line) record(1:6), i_ref_atom,&
record(12:21), write_chain, iires,&
record(27:27),&
(xcart(icart,k), k = 1, 3),&
record(55:80)
end if
end do
irescount = irescount + nres
ilugan = ilugan + 3
ilubar = ilubar + 3
if(add_amber_ter) write(30,"('TER')")
end do mol
close(15)
else
i_fixed = i_fixed + 1
! Counting the number of residues of this molecule
open(15,file=pdbfile(i_fixed),status='old')
ifres = 0
do
read(15,"( a80 )",iostat=ioerr) record
if ( ioerr /= 0 ) exit
if ( record(1:4).eq.'ATOM'.or.record(1:6).eq.'HETATM' ) then
read(record(23:26),*,iostat=ioerr) imark
if ( ioerr /= 0 ) then
record = pdbfile(i_not_fixed)
write(*,*) ' ERROR: Failed reading residue number ',&
' from PDB file: ', record(1:strlength(record))
write(*,*) ' Residue numbers are integers that must',&
' be between columns 23 and 26. '
write(*,*) ' Other characters within these columns',&
' will cause input/output errors. '
write(*,*) ' Standard PDB format specifications can',&
' be found at: '
write(*,*) ' www.rcsb.org/pdb '
stat = 2
return
end if
if ( ifres .eq. 0 ) ifres = imark
ilres = imark
end if
end do
nres = ilres - ifres + 1
iimol = iimol + 1
idatom = idfirst(i_fixed) - 1
rewind(15)
read(15,"( a80 )",iostat=ioerr) record
do while(record(1:4).ne.'ATOM'.and.record(1:6).ne.'HETATM')
read(15,"( a80 )",iostat=ioerr) record
end do
iatom = 0
do while(iatom.lt.natoms(i_fixed))
iatom = iatom + 1
idatom = idatom + 1
i_ref_atom = i_ref_atom + 1
if(iatom.gt.1) then
read(15,"( a80 )",iostat=ioerr) record
if ( ioerr /= 0 ) exit
end if
if(record(1:4).ne.'ATOM'.and.record(1:6).ne.'HETATM') then
write(30,"( a80 )") record(1:80)
iatom = iatom - 1
icart = icart - 1
idatom = idatom - 1
i_ref_atom = i_ref_atom - 1
cycle
end if
read(record(23:26),*) imark
if(resnumbers(i_fixed).eq.0) then
iires = 1
else if(resnumbers(i_fixed).eq.1) then
iires = imark
else if(resnumbers(i_fixed).eq.2) then
iires = mod(imark-ifres+irescount,9999)
else if(resnumbers(i_fixed).eq.3) then
iires = mod(iimol,9999)
end if
if ( chain(i_fixed) == "#" ) then
write_chain = record(22:22)
else
write_chain = chain(i_fixed)
end if
if(record(1:4).eq.'ATOM') then
write(30,pdb_atom_line) record(1:5), i_ref_atom,&
record(12:21), write_chain, iires,&
record(27:27),&
(coor(idatom,k), k = 1, 3),&
record(55:80)
end if
if(record(1:6).eq.'HETATM') then
write(30,pdb_hetatm_line) record(1:6), i_ref_atom,&
record(12:21), write_chain, iires,&
record(27:27),&
(coor(idatom,k), k = 1, 3),&
record(55:80)
end if
end do
irescount = irescount + nres
close(15)
if(add_amber_ter) write(30,"('TER')")
end if
end do
write(30,"('END')")
close(30)
end if
! Write the output (tinker xyz file)
if(tinker) then
tinker_atom_line = "( i7,tr2,a,3(tr2,f10.6),9(tr2,i7) )"
open(30, file = xyzout,status='unknown')
write(30,"( i6,tr2,a64 )") ntotat, title
ilubar = 0
ilugan = ntotmol*3
icart = natfix
i_ref_atom = 0
i_not_fixed = 0
i_fixed = ntype
do itype = 1, ntfix
if ( .not. fixedoninput(itype) ) then
i_not_fixed = i_not_fixed + 1
do imol = 1, nmols(i_not_fixed)
xbar = x(ilubar+1)
ybar = x(ilubar+2)
zbar = x(ilubar+3)
beta = x(ilugan+1)
gama = x(ilugan+2)
teta = x(ilugan+3)
call eulerrmat(beta,gama,teta,v1,v2,v3)
idatom = idfirst(i_not_fixed) - 1
do iatom = 1, natoms(i_not_fixed)
icart = icart + 1
idatom = idatom + 1
call compcart(icart,xbar,ybar,zbar,&
coor(idatom,1),coor(idatom,2),&
coor(idatom,3),&
v1,v2,v3)
ntcon(1) = nconnect(idatom,1)
do k = 2, maxcon(idatom)
ntcon(k) = nconnect(idatom,k) + i_ref_atom
end do
write(30,tinker_atom_line) i_ref_atom+iatom,&
trim(ele(idatom)), (xcart(icart, k), k = 1, 3),&
(ntcon(k), k = 1, maxcon(idatom))
end do
i_ref_atom = i_ref_atom + natoms(i_not_fixed)
ilugan = ilugan + 3
ilubar = ilubar + 3
end do
else
i_fixed = i_fixed + 1
idatom = idfirst(i_fixed) - 1
do iatom = 1, natoms(i_fixed)
idatom = idatom + 1
ntcon(1) = nconnect(idatom,1)
do k = 2, maxcon(idatom)
ntcon(k) = nconnect(idatom,k) + i_ref_atom
end do
write(30,tinker_atom_line) i_ref_atom+iatom, trim(ele(idatom)),&
(coor(idatom,k), k = 1, 3),&
(ntcon(k), k = 1, maxcon(idatom))
end do
i_ref_atom = i_ref_atom + natoms(i_fixed)
end if
end do
close(30)
end if
stat = 0
return
end subroutine output