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Update QCG input file processing #243

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Dec 7, 2023
Merged

Update QCG input file processing #243

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6 changes: 1 addition & 5 deletions src/classes.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -349,7 +349,7 @@ module crest_data
character(len=512) :: homedir !> original directory from which calculation was started
character(len=512) :: scratchdir !> path to the scratch directory
character(len=:),allocatable :: cmd
character(len=:),allocatable :: inputcoords,inputcoords_solv,inputcoords_solu
character(len=:),allocatable :: inputcoords
character(len=:),allocatable :: wbofile
character(len=:),allocatable :: atlist
character(len=:),allocatable :: chargesfilename
Expand Down Expand Up @@ -385,8 +385,6 @@ module crest_data

!>--- property data objects
type(protobj) :: ptb
type(protobj) :: ptb_solvent
type(protobj) :: ptb_solute

!>--- saved constraints
type(constra) :: cts
Expand All @@ -408,8 +406,6 @@ module crest_data

!>--- reference structure data (the input structure)
type(refdata) :: ref
type(refdata) :: qcg_solvent
type(refdata) :: qcg_solute

!>--- QCG data
integer :: qcg_runtype = 0 !> Default is grow, 1= ensemble & opt, 2= e_solv, 3= g_solv
Expand Down
171 changes: 7 additions & 164 deletions src/confparse.f90
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Expand Up @@ -491,6 +491,12 @@ subroutine parseflags(env,arg,nra)

case ('-solvtool','-qcg')
! env%mddumpxyz = 1000
! Set solute file if present
if(i == 2) env%solu_file = trim(arg(i-1))
! Set solvent file if prensent
! If it is another argument, it doesent matter as solvent file is checke in solvtool
if (nra >= i+1) env%solv_file = trim(arg(i+1))
! Set QCG defaults
env%preopt = .false.
env%crestver = crest_solv
env%QCG = .true.
Expand All @@ -501,9 +507,6 @@ subroutine parseflags(env,arg,nra)
env%ewin = 3.0d0
env%doOHflip = .false. !Switch off OH-flip
if (env%iterativeV2) env%iterativeV2 = .false.
if (nra >= i+1) then
env%solv_file = trim(arg(i+1))
end if
exit

case ('-compress')
Expand Down Expand Up @@ -2369,8 +2372,7 @@ subroutine inputcoords(env,arg)

!>--- Redirect for QCG input reading
if (env%QCG) then
arg2 = env%solv_file
call inputcoords_qcg(env,arg,arg2)
!Input coordinates are processed in solvtool.f90 file during solvtool subroutine
return
end if
!>---
Expand Down Expand Up @@ -2444,162 +2446,3 @@ subroutine inputcoords(env,arg)

return
end subroutine inputcoords

!========================================================================================!
!> Convert given QCG coordinate files into (TM format)
!> If the input is in SDF format, document the info to convert the
!> final ensemble back into this format
!========================================================================================!
subroutine inputcoords_qcg(env,arg1,arg2)
use iso_fortran_env,only:wp => real64
use crest_data
use strucrd
use zdata
use iomod
implicit none

type(systemdata) :: env
character(len=*) :: arg1,arg2

logical :: ex11,ex12,ex21,ex22,solu,solv
character(len=:),allocatable :: inputfile
type(coord) :: mol
type(zmolecule) :: zmol,zmol1
integer :: i

!--------------------Checking for input-------------!

inquire (file='solute',exist=solu)
inquire (file=arg1,exist=ex11)
inquire (file='coord',exist=ex12)

inquire (file='solvent',exist=solv)
inquire (file=arg2,exist=ex21)
if (len_trim(arg2) .eq. 0) then !Check if the second argument is just empty
ex21 = .false.
end if
inquire (file='coord',exist=ex22)

if (.not.ex11.and..not.ex12.and..not.solu) then
error stop 'No (valid) solute file! exit.'
else if (.not.ex21.and..not.ex22.and..not.solv) then
error stop 'No (valid) solvent file! exit.'
end if

!---------------Handling solute---------------------!

if (ex11.and.arg1(1:1) .ne. '-') then
call mol%open(arg1)
call mol%write('solute')
call mol%write('solute.xyz')
call mol%deallocate()
inputfile = trim(arg1)
write (*,*) 'Solute-file: ',arg1
env%solu_file = arg1
else if (solu.and..not.ex11) then
call copy('solute','solute.old')
inputfile = 'solute'
write (*,'(/,1x,a)') 'Solute-file: solute'
env%solu_file = 'solute'
else if (ex12.and..not.ex11) then !-- save coord as reference
call copy('coord','coord.old')
call copy('coord','solute')
write (*,'(/,1x,a)') 'Solute-file: coord'
inputfile = 'coord'
env%solu_file = 'coord'
else
write (*,*) 'An error occured processing the solute-input file'
end if

!--- if the input was a SDF file, special handling
env%sdfformat = .false.
call checkcoordtype(inputfile,i)
if (i == 31.or.i == 32) then
! call inpsdf(env,inputfile)
write (*,*) 'QCG currently does not support SDF-files.'
end if

!---------------Handling solvent---------------------!

if (ex21.and.arg2(1:1) .ne. '-'.and.arg2(1:1) .ne. ' ') then
call mol%open(arg2)
call mol%write('solvent')
call mol%write('solvent.xyz')
call mol%deallocate()
inputfile = trim(arg2)
write (*,*) 'Solvent-file: ',arg2
env%solv_file = arg2
else if (solv.and..not.ex21) then
call copy('solvent','solvent.old')
inputfile = 'solvent'
write (*,'(/,1x,a)') 'Solvent-file: solvent'
env%solv_file = 'solvent'
else if (ex22.and..not.ex21) then !-- save coord as reference
call copy('coord','coord.old')
call copy('coord','solvent')
inputfile = 'coord'
write (*,'(/,1x,a)') 'Solvent-file: coord'
env%solv_file = 'coord'
else
write (*,*) 'An error occured during solvent-file processing'
end if

!--- if the input was a SDF file, special handling
env%sdfformat = .false.
call checkcoordtype(inputfile,i)
if (i == 31.or.i == 32) then
!call inpsdf(env,inputfile)
write (*,*) 'QCG currently does not support SDF-files.'
end if

!-------------Checking both files and saving them---------------------------!

!--- after this point there should always be a solvent and solute file present
if (.not.allocated(env%inputcoords_solu)) env%inputcoords_solu = 'solute'
if (.not.allocated(env%inputcoords_solv)) env%inputcoords_solv = 'solvent'

call mol%open('solute')

env%nat = mol%nat
!--- solute geo
env%qcg_solute%nat = mol%nat
env%qcg_solute%at = mol%at
env%qcg_solute%xyz = mol%xyz
if (any((/crest_mfmdgc,crest_imtd,crest_imtd2/) == env%crestver)) then
if (.not.env%autozsort) then
env%qcg_solute%ntopo = mol%nat*(mol%nat+1)/2
allocate (env%qcg_solute%topo(env%qcg_solute%ntopo))
call quicktopo(mol%nat,mol%at,mol%xyz,env%qcg_solute%ntopo,env%qcg_solute%topo)
end if
end if
call mol%deallocate()

call mol%open('solvent')

env%nat = mol%nat
env%rednat = env%nat !get the number of atoms and the reduced number of atoms if some of them are excluded from the RMSD calc in V2
!--- solvent geo
env%qcg_solvent%nat = mol%nat
env%qcg_solvent%at = mol%at
env%qcg_solvent%xyz = mol%xyz
if (any((/crest_mfmdgc,crest_imtd,crest_imtd2/) == env%crestver)) then
if (.not.env%autozsort) then
env%qcg_solvent%ntopo = mol%nat*(mol%nat+1)/2
allocate (env%qcg_solvent%topo(env%qcg_solvent%ntopo))
call quicktopo(mol%nat,mol%at,mol%xyz,env%qcg_solvent%ntopo,env%qcg_solvent%topo)
end if
end if
call mol%deallocate()

!--- for protonation/deprotonation applications get ref. number of fragments
!--- also get some other structure based info
call simpletopo_file('solute',zmol,.false.,.false.,'')
env%ptb_solute%nfrag = zmol%nfrag
call zmol%deallocate()

call simpletopo_file('solvent',zmol1,.false.,.false.,'')
env%ptb_solvent%nfrag = zmol1%nfrag
call zmol1%deallocate()

return
end subroutine inputcoords_qcg
10 changes: 1 addition & 9 deletions src/crest_main.f90
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Expand Up @@ -88,15 +88,7 @@ program CREST
!> SOME I/O STUFF
!=========================================================================================!
!>--- check for the coord file in the working directory
if (env%crestver .eq. crest_solv) then
inquire (file='solute',exist=ex1)
inquire (file='solvent',exist=ex2)
if (.not.ex1) then
error stop 'No solute file found. Exit.'
else if (.not.ex2) then
error stop 'No solvent file found. Exit.'
end if
else
if (env%crestver /= crest_solv) then
inquire (file='coord',exist=ex)
if (.not.ex) then
error stop 'No coord file found. Exit.'
Expand Down
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