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getinp.f90
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!
! Written by Leandro Martínez, 2009-2011.
! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez,
! Ernesto G. Birgin.
!
! Subroutine getinp: subroutine that reads the input file
!
subroutine getinp()
use exit_codes
use sizes
use compute_data, only : ntype, natoms, idfirst, nmols, ityperest, coor, restpars
use input
use usegencan
implicit none
integer :: i, k, ii, iarg, iline, idatom, iatom, in, lixo, irest, itype, itest,&
imark, ioerr, nloop0, iread, idfirstatom
double precision :: clen
character(len=strl) :: record, blank
logical :: inside_structure
! Clearing the blank character arrays
do i = 1, strl
blank(i:i) = ' '
end do
! Getting random seed and optional optimization parameters if set
seed = 1234567
randini = .false.
check = .false.
chkgrad = .false.
iprint1 = 2
iprint2 = 2
discale = 1.1d0
writeout = 10
maxit = 20
nloop = 0
nloop0 = 0
movefrac = 0.05
movebadrandom = .false.
precision = 1.d-2
writebad = .false.
add_amber_ter = .false.
amber_ter_preserve = .false.
add_box_sides = .false.
add_sides_fix = 0.d0
sidemax = 1000.d0
ioerr = 0
avoidoverlap = .true.
packall = .false.
use_short_tol = .false.
crd = .false.
inside_structure = .false.
do i = 1, nlines
if ( keyword(i,1).eq.'structure') inside_structure = .true.
if ( keyword(i,1).eq.'end' .and. &
keyword(i,2).eq.'structure') inside_structure = .false.
if(keyword(i,1).eq.'seed') then
read(keyword(i,2),*,iostat=ioerr) seed
if ( ioerr /= 0 ) exit
if ( seed == -1 ) call seed_from_time(seed)
else if(keyword(i,1).eq.'randominitialpoint') then
randini = .true.
else if(keyword(i,1).eq.'check') then
check = .true.
else if(keyword(i,1).eq.'writebad') then
writebad = .true.
else if(keyword(i,1).eq.'precision') then
read(keyword(i,2),*,iostat=ioerr) precision
if ( ioerr /= 0 ) exit
write(*,*) ' Optional precision set: ', precision
else if(keyword(i,1).eq.'movefrac') then
read(keyword(i,2),*,iostat=ioerr) movefrac
if ( ioerr /= 0 ) exit
write(*,*) ' Optional movefrac set: ', movefrac
else if(keyword(i,1).eq.'movebadrandom') then
movebadrandom = .true.
write(*,*) ' Will move randomly bad molecues (movebadrandom) '
else if(keyword(i,1).eq.'chkgrad') then
chkgrad = .true.
else if(keyword(i,1).eq.'writeout') then
read(keyword(i,2),*,iostat=ioerr) writeout
if ( ioerr /= 0 ) exit
write(*,*) ' Output frequency: ', writeout
else if(keyword(i,1).eq.'maxit') then
read(keyword(i,2),*,iostat=ioerr) maxit
if ( ioerr /= 0 ) exit
write(*,*) ' User defined GENCAN number of iterations: ', maxit
else if(keyword(i,1).eq.'nloop') then
if( .not. inside_structure ) then
read(keyword(i,2),*,iostat=ioerr) nloop
if ( ioerr /= 0 ) exit
end if
else if(keyword(i,1).eq.'nloop0') then
if( .not. inside_structure ) then
read(keyword(i,2),*,iostat=ioerr) nloop0
if ( ioerr /= 0 ) exit
end if
else if(keyword(i,1).eq.'discale') then
read(keyword(i,2),*,iostat=ioerr) discale
if ( ioerr /= 0 ) exit
write(*,*) ' Optional initial tolerance scale: ', discale
else if(keyword(i,1).eq.'sidemax') then
read(keyword(i,2),*,iostat=ioerr) sidemax
if ( ioerr /= 0 ) exit
write(*,*) ' User set maximum system dimensions: ', sidemax
else if(keyword(i,1).eq.'fbins') then
read(keyword(i,2),*,iostat=ioerr) fbins
if ( ioerr /= 0 ) exit
write(*,*) ' User set linked-cell bin parameter: ', fbins
else if(keyword(i,1).eq.'add_amber_ter') then
add_amber_ter = .true.
write(*,*) ' Will add the TER flag between molecules. '
else if(keyword(i,1).eq.'amber_ter_preserve') then
amber_ter_preserve = .true.
write(*,*) ' TER flags for fixed molecules will be kept if found. '
else if(keyword(i,1).eq.'avoid_overlap') then
if ( keyword(i,2).eq.'yes') then
avoidoverlap = .true.
write(*,*) ' Will avoid overlap to fixed molecules at initial point. '
else
avoidoverlap = .false.
write(*,*) ' Will NOT avoid overlap to fixed molecules at initial point. '
end if
else if(keyword(i,1).eq.'packall') then
packall = .true.
write(*,*) ' Will pack all molecule types from the beginning. '
else if(keyword(i,1).eq.'use_short_tol') then
use_short_tol = .true.
write(*,*) ' Will use a short distance penalty for all atoms. '
else if(keyword(i,1).eq.'writecrd') then
crd = .true.
write(*,*) ' Will write output also in CRD format '
read(keyword(i,2),*,iostat=ioerr) crdfile
else if(keyword(i,1).eq.'add_box_sides') then
add_box_sides = .true.
write(*,*) ' Will print BOX SIDE informations. '
read(keyword(i,2),*,iostat=ioerr) add_sides_fix
if ( ioerr /= 0 ) then
ioerr = 0
cycle
end if
write(*,*) ' Will sum ', add_sides_fix,' to each side length on print'
else if(keyword(i,1).eq.'iprint1') then
read(keyword(i,2),*,iostat=ioerr) iprint1
if ( ioerr /= 0 ) exit
write(*,*) ' Optional printvalue 1 set: ', iprint1
else if(keyword(i,1).eq.'iprint2') then
read(keyword(i,2),*,iostat=ioerr) iprint2
if ( ioerr /= 0 ) exit
write(*,*) ' Optional printvalue 2 set: ', iprint2
else if( keyword(i,1) /= 'tolerance' .and. &
keyword(i,1) /= 'short_tol_dist' .and. &
keyword(i,1) /= 'short_tol_scale' .and. &
keyword(i,1) /= 'structure' .and. &
keyword(i,1) /= 'end' .and. &
keyword(i,1) /= 'atoms' .and. &
keyword(i,1) /= 'output' .and. &
keyword(i,1) /= 'filetype' .and. &
keyword(i,1) /= 'number' .and. &
keyword(i,1) /= 'inside' .and. &
keyword(i,1) /= 'outside' .and. &
keyword(i,1) /= 'fixed' .and. &
keyword(i,1) /= 'center' .and. &
keyword(i,1) /= 'centerofmass' .and. &
keyword(i,1) /= 'over' .and. &
keyword(i,1) /= 'above' .and. &
keyword(i,1) /= 'below' .and. &
keyword(i,1) /= 'constrain_rotation' .and. &
keyword(i,1) /= 'radius' .and. &
keyword(i,1) /= 'fscale' .and. &
keyword(i,1) /= 'short_radius' .and. &
keyword(i,1) /= 'short_radius_scale' .and. &
keyword(i,1) /= 'resnumbers' .and. &
keyword(i,1) /= 'connect' .and. &
keyword(i,1) /= 'changechains' .and. &
keyword(i,1) /= 'chain' .and. &
keyword(i,1) /= 'discale' .and. &
keyword(i,1) /= 'maxit' .and. &
keyword(i,1) /= 'movebadrandom' .and. &
keyword(i,1) /= 'maxmove' .and. &
keyword(i,1) /= 'add_amber_ter' .and. &
keyword(i,1) /= 'amber_ter_preserve' .and. &
keyword(i,1) /= 'sidemax' .and. &
keyword(i,1) /= 'seed' .and. &
keyword(i,1) /= 'randominitialpoint' .and. &
keyword(i,1) /= 'restart_from' .and. &
keyword(i,1) /= 'restart_to' .and. &
keyword(i,1) /= 'nloop' .and. &
keyword(i,1) /= 'nloop0' .and. &
keyword(i,1) /= 'writeout' .and. &
keyword(i,1) /= 'writebad' .and. &
keyword(i,1) /= 'check' .and. &
keyword(i,1) /= 'iprint1' .and. &
keyword(i,1) /= 'iprint2' .and. &
keyword(i,1) /= 'writecrd' .and. &
keyword(i,1) /= 'segid' .and. &
keyword(i,1) /= 'chkgrad' ) then
write(*,*) ' ERROR: Keyword not recognized: ', trim(keyword(i,1))
stop exit_code_input_error
end if
end do
if ( ioerr /= 0 ) then
write(*,*) ' ERROR: Some optional keyword was not used correctly: ', trim(keyword(i,1))
stop exit_code_input_error
end if
write(*,*) ' Seed for random number generator: ', seed
call init_random_number(seed)
! Checking for the name of the output file to be created
xyzout = '####'
do iline = 1, nlines
if(keyword(iline,1).eq.'output') then
xyzout = keyword(iline,2)
xyzout = trim(adjustl(xyzout))
end if
end do
if(xyzout(1:4) == '####') then
write(*,*)' ERROR: Output file not (correctly?) specified. '
stop exit_code_input_error
end if
write(*,*)' Output file: ', trim(adjustl(xyzout))
! Reading structure files
itype = 0
do iline = 1, nlines
if(keyword(iline,1).eq.'structure') then
itype = itype + 1
record = keyword(iline,2)
write(*,*) ' Reading coordinate file: ', trim(adjustl(record))
! Reading pdb input files
if(pdb) then
name(itype) = trim(adjustl(record))
record = keyword(iline,2)
pdbfile(itype) = trim(record)
idfirst(itype) = 1
idfirstatom = 0
do ii = itype - 1, 1, -1
idfirst(itype) = idfirst(itype) + natoms(ii)
end do
open(10,file=keyword(iline,2),status='old',iostat=ioerr)
if ( ioerr /= 0 ) call failopen(keyword(iline,2))
! Read coordinates
record(1:6) = '######'
do while(record(1:4).ne.'ATOM'.and.record(1:6).ne.'HETATM')
read(10,str_format) record
end do
idatom = idfirst(itype) - 1
do while(idatom.lt.natoms(itype)+idfirst(itype)-1)
if(record(1:4).eq.'ATOM'.or.record(1:6).eq.'HETATM') then
idatom = idatom + 1
amass(idatom) = 1.d0
maxcon(idatom) = 0
! Read the index of the first atom, to adjust connectivities, if any
if(idfirstatom == 0) read(record(7:11),*,iostat=ioerr) idfirstatom
read(record,"( t31,f8.3,t39,f8.3,t47,f8.3 )",iostat=ioerr) &
(coor(idatom,k),k=1,3)
if( ioerr /= 0 ) then
record = keyword(iline,2)
write(*,*) ' ERROR: Failed to read coordinates from', &
' file: ', trim(adjustl(record))
write(*,*) ' Probably the coordinates are not in', &
' standard PDB file format. '
write(*,*) ' Standard PDB format specifications', &
' can be found at: '
write(*,*) ' www.rcsb.org/pdb '
stop exit_code_input_error
end if
! This only tests if residue numbers can be read, they are used
! only for output
read(record(23:26),*,iostat=ioerr) itest
if( ioerr /= 0 ) then
record = pdbfile(itype)
write(*,*) ' ERROR: Failed reading residue number',&
' from PDB file: ', trim(adjustl(record))
write(*,*) ' Residue numbers are integers that',&
' must be within 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 '
stop exit_code_input_error
end if
end if
read(10,str_format,iostat=ioerr) record
end do
!
! Read connectivity, if there is any specified
!
do while(.true.)
if ( ioerr /= 0 ) exit
if(record(1:6).eq.'CONECT') then
iread = 7
read(record(iread:iread+4),*,iostat=ioerr) iatom
iatom = iatom - idfirstatom + 1
idatom = idfirst(itype) - 1 + iatom
if(ioerr /= 0) then
write(*,*) " ERROR: Could not read atom index from CONECT line: "
write(*,*) trim(adjustl(record))
stop exit_code_input_error
end if
iread = iread + 5
read(record(iread:iread+4),*,iostat=ioerr) nconnect(idatom,1)
if(ioerr /= 0) then
write(*,*) " ERROR: Could not read any connection index from CONECT line: "
write(*,*) trim(adjustl(record))
stop exit_code_input_error
end if
nconnect(idatom,1) = nconnect(idatom,1) - idfirstatom + 1
maxcon(idatom) = 1
do while(.true.)
iread = iread + 5
read(record(iread:iread+4),*,iostat=ioerr) nconnect(idatom,maxcon(idatom)+1)
if(ioerr == 0) then
maxcon(idatom) = maxcon(idatom) + 1
nconnect(idatom,maxcon(idatom)) = nconnect(idatom,maxcon(idatom)) - idfirstatom + 1
else
exit
end if
end do
end if
read(10,str_format,iostat=ioerr) record
end do
close(10)
end if
! Reading tinker input files
if(tinker) then
open(10,file=keyword(iline,2),status='old',iostat=ioerr)
if ( ioerr /= 0 ) call failopen(keyword(iline,2))
idfirst(itype) = 1
do ii = itype - 1, 1, -1
idfirst(itype) = idfirst(itype) + natoms(ii)
end do
record = keyword(iline,2)
call setcon(record(1:64),idfirst(itype))
open(10,file = keyword(iline,2), status = 'old')
record = blank
do while(record.le.blank)
read(10,str_format) record
end do
i = 1
do while(record(i:i).le.' ')
i = i + 1
if ( i > strl ) exit
end do
iarg = i
if ( i < strl ) then
do while(record(i:i).gt.' ')
i = i + 1
if ( i > strl ) exit
end do
end if
read(record(iarg:i-1),*) natoms(itype)
if ( i < strl ) then
do while(record(i:i).le.' ')
i = i + 1
if ( i > strl ) exit
end do
end if
iarg = i
if ( i < strl ) then
do while(record(i:i).gt.' ')
i = i + 1
if ( i > strl ) exit
end do
end if
read(record(iarg:i-1),str_format) name(itype)
record = name(itype)
name(itype) = trim(adjustl(record))
if(name(itype).lt.' ') name(itype) = 'Without_title'
idatom = idfirst(itype) - 1
do iatom = 1, natoms(itype)
idatom = idatom + 1
record = blank
do while(record.le.blank)
read(10,str_format) record
end do
i = 1
do while(record(i:i).le.' ')
i = i + 1
if ( i > strl ) exit
end do
iarg = i
if ( i < strl ) then
do while(record(i:i).gt.' ')
i = i + 1
if ( i > strl ) exit
end do
end if
read(record(iarg:i-1),*) in
if ( i < strl ) then
do while(record(i:i).le.' ')
i = i + 1
if ( i > strl ) exit
end do
end if
iarg = i
if ( i < strl ) then
do while(record(i:i).gt.' ')
i = i + 1
if ( i > strl ) exit
end do
end if
read(record(iarg:i-1),*) ele(idatom)
read(record(i:strl),*) (coor(idatom,k), k = 1, 3),&
(nconnect(idatom, k), k = 1, maxcon(idatom))
amass(idatom) = 1.d0
end do
close(10)
end if
! Reading xyz input files
if(xyz) then
open(10,file=keyword(iline,2),status='old',iostat=ioerr)
if ( ioerr /= 0 ) call failopen(keyword(iline,2))
read(10,*) natoms(itype)
read(10,str_format) name(itype)
if(name(itype).lt.' ') name(itype) = 'Without_title'
idfirst(itype) = 1
do ii = itype - 1, 1, -1
idfirst(itype) = idfirst(itype) + natoms(ii)
end do
idatom = idfirst(itype) - 1
do iatom = 1, natoms(itype)
idatom = idatom + 1
record = blank
read(10,str_format) record
read(record,*) ele(idatom), (coor(idatom,k),k=1,3)
amass(idatom) = 1.d0
end do
close(10)
end if
! Reading moldy input files
if(moldy) then
open(10,file=keyword(iline,2), status ='old',iostat=ioerr)
if ( ioerr /= 0 ) call failopen(keyword(iline,2))
read(10,*) name(itype), nmols(itype)
natoms(itype) = 0
do while(.true.)
read(10,str_format,iostat=ioerr) record
if ( ioerr /= 0 ) exit
if(record.gt.' '.and.record(1:3).ne.'end') &
natoms(itype) = natoms(itype) + 1
end do
close(10)
idfirst(itype) = 1
do ii = itype - 1, 1, -1
idfirst(itype) = idfirst(itype) + natoms(ii)
end do
open(10,file=keyword(iline,2),status='old')
read(10,str_format) record
idatom = idfirst(itype) - 1
do iatom = 1, natoms(itype)
idatom = idatom + 1
read(10,str_format) record
read(record,*) lixo, (coor(idatom,k), k = 1, 3),&
amass(idatom), charge(idatom), ele(idatom)
end do
close(10)
end if
end if
end do
ntype = itype
write(*,*) ' Number of independent structures: ', ntype
write(*,*) ' The structures are: '
do itype = 1, ntype
record = name(itype)
write(*,*) ' Structure ', itype, ':', trim(adjustl(record)),&
'(',natoms(itype),' atoms)'
end do
! Setting the vectors for the number of GENCAN loops
if(nloop.eq.0) then
nloop_all = 200*ntype
nloop = nloop_all
else
nloop_all = nloop
end if
write(*,*) ' Maximum number of GENCAN loops for all molecule packing: ', nloop_all
do itype = 1, ntype
if ( nloop_type(itype) == 0 ) then
nloop_type(itype) = nloop_all
else
write(*,*) ' Maximum number of GENCAN loops for type: ', itype, ': ', nloop_type(itype)
end if
end do
! nloop0 are the number of loops for the initial phase packing
if(nloop0.eq.0) then
nloop0 = 20*ntype
else
write(*,*) ' Maximum number of GENCAN loops-0 for all molecule packing: ', nloop0
end if
do itype = 1, ntype
if ( nloop0_type(itype) == 0 ) then
nloop0_type(itype) = nloop0
else
write(*,*) ' Maximum number of GENCAN loops-0 for type: ', itype, ': ', nloop0_type(itype)
end if
end do
! Reading the restrictions that were set
irest = 0
ioerr = 0
do iline = 1, nlines
if(keyword(iline,1).eq.'fixed') then
irest = irest + 1
irestline(irest) = iline
ityperest(irest) = 1
read(keyword(iline,2),*,iostat=ioerr) restpars(irest,1)
read(keyword(iline,3),*,iostat=ioerr) restpars(irest,2)
read(keyword(iline,4),*,iostat=ioerr) restpars(irest,3)
read(keyword(iline,5),*,iostat=ioerr) restpars(irest,4)
read(keyword(iline,6),*,iostat=ioerr) restpars(irest,5)
read(keyword(iline,7),*,iostat=ioerr) restpars(irest,6)
end if
if(keyword(iline,1).eq.'inside') then
irest = irest + 1
irestline(irest) = iline
if(keyword(iline,2).eq.'cube') then
ityperest(irest) = 2
read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1)
read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2)
read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3)
read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4)
else if(keyword(iline,2).eq.'box') then
ityperest(irest) = 3
read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1)
read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2)
read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3)
read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4)
read(keyword(iline,7),*,iostat=ioerr) restpars(irest,5)
read(keyword(iline,8),*,iostat=ioerr) restpars(irest,6)
else if(keyword(iline,2).eq.'sphere') then
ityperest(irest) = 4
read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1)
read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2)
read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3)
read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4)
else if(keyword(iline,2).eq.'ellipsoid') then
ityperest(irest) = 5
read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1)
read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2)
read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3)
read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4)
read(keyword(iline,7),*,iostat=ioerr) restpars(irest,5)
read(keyword(iline,8),*,iostat=ioerr) restpars(irest,6)
read(keyword(iline,9),*,iostat=ioerr) restpars(irest,7)
else if(keyword(iline,2).eq.'cylinder') then
ityperest(irest) = 12
read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1)
read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2)
read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3)
read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4)
read(keyword(iline,7),*,iostat=ioerr) restpars(irest,5)
read(keyword(iline,8),*,iostat=ioerr) restpars(irest,6)
read(keyword(iline,9),*,iostat=ioerr) restpars(irest,7)
read(keyword(iline,10),*,iostat=ioerr) restpars(irest,9)
restpars(irest,8) = restpars(irest,4)**2 + &
restpars(irest,5)**2 + &
restpars(irest,6)**2
if(restpars(irest,8).lt.1.d-10) then
write(*,*) ' ERROR: The norm of the director vector', &
' of the cylinder constraint cannot be zero.'
ioerr = 1
else
clen = dsqrt(restpars(irest,8))
restpars(irest,4) = restpars(irest,4) / clen
restpars(irest,5) = restpars(irest,5) / clen
restpars(irest,6) = restpars(irest,6) / clen
end if
else
ioerr = 1
end if
end if
if(keyword(iline,1).eq.'outside') then
irest = irest + 1
irestline(irest) = iline
if(keyword(iline,2).eq.'cube') then
ityperest(irest) = 6
read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1)
read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2)
read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3)
read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4)
else if(keyword(iline,2).eq.'box') then
ityperest(irest) = 7
read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1)
read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2)
read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3)
read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4)
read(keyword(iline,7),*,iostat=ioerr) restpars(irest,5)
read(keyword(iline,8),*,iostat=ioerr) restpars(irest,6)
else if(keyword(iline,2).eq.'sphere') then
ityperest(irest) = 8
read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1)
read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2)
read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3)
read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4)
else if(keyword(iline,2).eq.'ellipsoid') then
ityperest(irest) = 9
read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1)
read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2)
read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3)
read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4)
read(keyword(iline,7),*,iostat=ioerr) restpars(irest,5)
read(keyword(iline,8),*,iostat=ioerr) restpars(irest,6)
read(keyword(iline,9),*,iostat=ioerr) restpars(irest,7)
else if(keyword(iline,2).eq.'cylinder') then
ityperest(irest) = 13
read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1)
read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2)
read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3)
read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4)
read(keyword(iline,7),*,iostat=ioerr) restpars(irest,5)
read(keyword(iline,8),*,iostat=ioerr) restpars(irest,6)
read(keyword(iline,9),*,iostat=ioerr) restpars(irest,7)
read(keyword(iline,10),*,iostat=ioerr) restpars(irest,9)
restpars(irest,8) = restpars(irest,4)**2 + &
restpars(irest,5)**2 + &
restpars(irest,6)**2
if(restpars(irest,8).lt.1.d-10) then
write(*,*) ' ERROR: The norm of the director vector',&
' of the cylinder constraint cannot be zero.'
ioerr = 1
else
clen = dsqrt(restpars(irest,8))
restpars(irest,4) = restpars(irest,4) / clen
restpars(irest,5) = restpars(irest,5) / clen
restpars(irest,6) = restpars(irest,6) / clen
end if
else
ioerr = 1
end if
end if
if(keyword(iline,1).eq.'over' .or. keyword(iline,1).eq.'above') then
irest = irest + 1
irestline(irest) = iline
ityperest(irest) = 10
read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1)
read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2)
read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3)
read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4)
if(keyword(iline,2).ne.'plane') ioerr = 1
end if
if(keyword(iline,1).eq.'below') then
irest = irest + 1
irestline(irest) = iline
ityperest(irest) = 11
read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1)
read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2)
read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3)
read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4)
if(keyword(iline,2).ne.'plane') ioerr = 1
end if
if ( ioerr /= 0 ) then
write(*,*) ' ERROR: Some restriction is not set correctly. '
stop exit_code_input_error
end if
end do
nrest = irest
write(*,*) ' Total number of restrictions: ', nrest
! Getting the tolerance
ioerr = 1
dism = -1.d0
do iline = 1, nlines
if(keyword(iline,1).eq.'tolerance') then
read(keyword(iline,2),*,iostat=ioerr) dism
if ( ioerr /= 0 ) then
write(*,*) ' ERROR: Failed reading tolerance. '
stop exit_code_input_error
end if
exit
end if
end do
if ( ioerr /= 0 ) then
write(*,*) ' ERROR: Overall tolerance not set. Use, for example: tolerance 2.0 '
stop exit_code_input_error
end if
write(*,*) ' Distance tolerance: ', dism
! Reading, if defined, the short distance penalty parameters
ioerr = 1
short_tol_dist = dism/2.d0
! Reading short_tol_dist
do iline = 1, nlines
if(keyword(iline,1).eq.'short_tol_dist') then
read(keyword(iline,2),*,iostat=ioerr) short_tol_dist
if ( ioerr /= 0 ) then
write(*,*) ' ERROR: Failed reading short_tol_dist. '
stop exit_code_input_error
end if
if ( short_tol_dist > dism ) then
write(*,*) ' ERROR: The short_tol_dist parameter must be smaller than the tolerance. '
stop exit_code_input_error
end if
write(*,*) ' User defined short tolerance distance: ', short_tol_dist
short_tol_dist = short_tol_dist**2
exit
end if
end do
! Reading short_tol_scale
short_tol_scale = 3.d0
do iline = 1, nlines
if(keyword(iline,1).eq.'short_tol_scale') then
read(keyword(iline,2),*,iostat=ioerr) short_tol_scale
if ( ioerr /= 0 ) then
write(*,*) ' ERROR: Failed reading short_tol_scale. '
stop exit_code_input_error
end if
if ( short_tol_dist <= 0.d0 ) then
write(*,*) ' ERROR: The short_tol_scale parameter must be positive. '
stop exit_code_input_error
end if
write(*,*) ' User defined short tolerance scale: ', short_tol_scale
exit
end if
end do
! Assigning the input lines that correspond to each structure
itype = 0
iline = 0
do while(iline < nlines)
iline = iline + 1
if(keyword(iline,1).eq.'structure') then
itype = itype + 1
linestrut(itype,1) = iline
iline = iline + 1
do while(keyword(iline,1).ne.'end'.or.&
keyword(iline,2).ne.'structure')
if(keyword(iline,1) == 'structure'.or.&
iline == nlines) then
write(*,*) ' ERROR: Structure specification not ending with "end structure"'
stop exit_code_input_error
end if
iline = iline + 1
end do
linestrut(itype,2) = iline
end if
end do
! If pdb files, get the type of residue numbering output for each
! molecule
if(pdb) then
do itype = 1, ntype
connect(itype) = .true.
resnumbers(itype) = -1
changechains(itype) = .false.
chain(itype) = "#"
segid(itype) = ""
maxmove(itype) = nmols(itype)
do iline = 1, nlines
if(iline.gt.linestrut(itype,1).and.&
iline.lt.linestrut(itype,2)) then
if(keyword(iline,1).eq.'changechains') then
changechains(itype) = .true.
end if
if(keyword(iline,1).eq.'maxmove') then
read(keyword(iline,2),*) maxmove(itype)
end if
if(keyword(iline,1).eq.'resnumbers') then
read(keyword(iline,2),*) resnumbers(itype)
end if
if(keyword(iline,1).eq.'connect') then
if(keyword(iline,2) == "no") then
connect(itype) = .false.
end if
end if
if(keyword(iline,1).eq.'chain') then
read(keyword(iline,2),*) chain(itype)
end if
if(keyword(iline,1).eq.'segid') then
read(keyword(iline,2),*) segid(itype)
end if
end if
end do
if (crd) then
if (itype.gt.1 .and. segid(itype)=="") then
if (segid(itype-1) /= "") then
write(*,*) ' Warning: Type of segid not defined for ', itype,'. Keeping it same as previous'
endif
segid(itype) = segid(itype-1)
endif
endif
if ( resnumbers(itype) == -1 ) then
write(*,*) ' Warning: Type of residue numbering not',&
' set for structure ',itype
call setrnum(pdbfile(itype),imark)
if(imark.eq.1) resnumbers(itype) = 0
if(imark.gt.1) resnumbers(itype) = 1
end if
write(*,*) ' Residue numbering set for structure ',itype,':',&
resnumbers(itype)
write(*,*) ' Swap chains of molecules of structure ',&
itype,':', changechains(itype)
if ( chain(itype) /= "#" ) then
write(*,*) ' Specific chain identifier set for structure ',itype,':',chain(itype)
end if
if ( chain(itype) /= "#" .and. changechains(itype) ) then
write(*,*) " ERROR: 'changechains' and 'chain' input parameters are not compatible "
write(*,*) " for a single structure. "
stop exit_code_input_error
end if
end do
end if
! Write the number of molecules of each type
do itype = 1, ntype
write(*,*) ' Number of molecules of type ', itype, ': ', nmols(itype)
if(pdb.and.nmols(itype).gt.9999) then
write(*,*) ' Warning: There will be more than 9999 molecules of type ',itype
if (.not. crd) write(*,*) ' Residue numbering is reset after 9999. '
if (crd) write(*,*) ' Residue numbering is reset after 9999 in pdb but not in crd. '
if ( chain(itype) == "#" ) then
write(*,*) ' Each set be will be assigned a different chain in the PDB output file. '
end if
end if
if(crd.and.nmols(itype).gt.99999999) then
write(*,*) ' Warning: There will be more than 99999999 molecules of type ',itype
write(*,*) ' Residue numbering is reset after 99999999 in crd. '
endif
end do
! Checking if restart files will be used for each structure or for the whole system
restart_from(0) = "none"
restart_to(0) = "none"
do itype = 1, ntype
restart_from(itype) = "none"
restart_to(itype) = "none"
end do
lines: do iline = 1, nlines
if ( keyword(iline,1) == 'restart_from' ) then
do itype = 1, ntype
if(iline.gt.linestrut(itype,1).and.&
iline.lt.linestrut(itype,2)) then
restart_from(itype) = keyword(iline,2)
cycle lines
end if
end do
if( restart_from(0) == 'none' ) then
restart_from(0) = keyword(iline,2)
else
write(*,*) ' ERROR: More than one definition of restart_from file for all system. '
stop exit_code_input_error
end if
end if
if ( keyword(iline,1) == 'restart_to' ) then
do itype = 1, ntype
if(iline.gt.linestrut(itype,1).and.&
iline.lt.linestrut(itype,2)) then
restart_to(itype) = keyword(iline,2)
cycle lines
end if
end do
if( restart_to(0) == 'none' ) then
restart_to(0) = keyword(iline,2)
else
write(*,*) ' ERROR: More than one definition of restart_to file for all system. '
stop exit_code_input_error
end if
end if
end do lines
return
end subroutine getinp
!
! Subroutine that stops if failed to open file
!
subroutine failopen(record)
use exit_codes
use sizes
character(len=strl) :: record
write(*,*)
write(*,*) ' ERROR: Could not open file. '
write(*,*) ' Could not find file: ',trim(record)
write(*,*) ' Please check if all the input and structure '
write(*,*) ' files are in the current directory or if the'
write(*,*) ' correct paths are provided.'
write(*,*)
stop exit_code_open_file
end subroutine failopen
!
! Subroutine that checks if a pdb structure has one or more than
! one residue
!
subroutine setrnum(file,nres)
use sizes
implicit none
integer :: iread, ires, ireslast, nres, ioerr
character(len=strl) :: file
character(len=strl) :: record
open(10,file=file,status='old')
iread = 0
nres = 1
do while(nres.eq.1)
read(10,str_format,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) ires
if ( ioerr /= 0 ) cycle
iread = iread + 1
if(iread.gt.1) then
if(ires.ne.ireslast) then
nres = 2
close(10)
return
end if
end if
ireslast = ires
end if
end do
close(10)
return
end subroutine setrnum
!
! Subroutine that computes de number of connections of each atom
! for tinker xyz files
!
subroutine setcon(xyzfile,idfirst)
use sizes
use input, only : maxcon
implicit none
integer :: idfirst
integer :: natoms, idatom, iatom, ic, i
character(len=64) :: xyzfile
character(len=120) :: record
open(10, file = xyzfile, status='old')
read(10,*) natoms
idatom = idfirst - 1
do iatom = 1, natoms
idatom = idatom + 1
read(10,"( a120 )") record
ic = 0
do i = 1, 119
if(record(i:i).gt.' '.and.record(i+1:i+1).le.' ') ic = ic + 1
end do
maxcon(idatom) = ic - 5
end do
close(10)
return
end subroutine setcon
!
! Subroutine getkeywords: gets keywords and values from the input
! file in a more robust way
!
subroutine getkeywords()