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Fix for #252 #253

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merged 2 commits into from
Jan 21, 2024
Merged

Fix for #252 #253

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c5dbb30
Fix "internal write to self" error for protonation
pprcht Jan 21, 2024
8bcb668
Fix error in tautomerization script
pprcht Jan 21, 2024
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8 changes: 5 additions & 3 deletions src/legacy_algos/protonate.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -204,7 +204,7 @@ subroutine xtblmo(env)
implicit none
type(systemdata) :: env
character(len=80) :: fname
character(len=512) :: jobcall
character(len=:),allocatable :: jobcall
integer :: io
character(len=*),parameter :: pipe = ' > xtb.out 2>/dev/null'

Expand All @@ -218,8 +218,10 @@ subroutine xtblmo(env)
!---- jobcall
write (*,*)
write (*,'('' LMO calculation ... '')',advance='no')
write (jobcall,'(a,1x,a,1x,a,'' --sp --lmo'',1x,a)') &
& trim(env%ProgName),trim(fname),trim(env%gfnver),trim(env%solv)
jobcall = trim(env%ProgName)
jobcall = trim(jobcall)//' '//trim(fname)
jobcall = trim(jobcall)//' '//trim(env%gfnver)
jobcall = trim(jobcall)//' --sp --lmo '//trim(env%solv)
jobcall = trim(jobcall)//trim(pipe)
call command(trim(jobcall),io)
write (*,'(''done.'')')
Expand Down
54 changes: 29 additions & 25 deletions src/legacy_algos/tautomerize.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -414,26 +414,24 @@ subroutine protens(ens,env,prot,tim)
real(wp) :: percent

character(len=*) :: ens
character(len=32) :: dirn
character(len=256) :: thispath,tmppath
character(len=256) :: filename
character(len=128) :: inpnam,outnam
character(len=512) :: jobcall

character(len=:),allocatable :: jobcall
logical :: niceprint

real(wp),allocatable :: xyz(:,:,:),eread(:)
integer,allocatable :: at(:)

character(len=*),parameter :: dirn='PROT'
!call printprotcy

!--- some settings
call getcwd(thispath)
dirn = 'PROT'
niceprint = env%niceprint
refchrg = env%chrg

r = makedir(trim(dirn))
r = makedir(dirn)

!--- read the file
call rdensembleparam(ens,nat,nall)
Expand All @@ -443,11 +441,11 @@ subroutine protens(ens,env,prot,tim)
natp = nat+1

!--- change dir
call chdir(trim(dirn))
call chdir(dirn)
call getcwd(tmppath)
!--- make new dirs
do i = 1,nall
write (filename,'(a,i0)') trim(dirn),i
write (filename,'(a,i0)') dirn,i
r = makedir(trim(filename))
call chdir(trim(filename))
call wrc0('coord',nat,at,xyz(:,:,i))
Expand All @@ -464,8 +462,12 @@ subroutine protens(ens,env,prot,tim)
end if

!--- creating the job
write (jobcall,'(a,1x,a,1x,a,'' --sp --lmo '',a,1x,a,a)') &
& trim(env%ProgName),'coord',trim(env%gfnver),trim(env%solv),' > xtb.out 2>/dev/null'
jobcall = trim(env%ProgName)
jobcall = trim(jobcall)//' '//'coord'
jobcall = trim(jobcall)//' '//trim(env%gfnver)
jobcall = trim(jobcall)//' --sp --lmo '//trim(env%solv)
jobcall = trim(jobcall)//' > xtb.out 2>/dev/null'


!--- calculation loop for LMOs
call tim%start(1,'LMO calc.')
Expand All @@ -475,30 +477,32 @@ subroutine protens(ens,env,prot,tim)
if (niceprint) then
call printprogbar(0.0_wp)
end if
!$omp parallel &
!$omp shared( vz,jobcall,nall,dirn,percent,k,niceprint )
!$omp single

!!$omp parallel &
!!$omp shared( vz,jobcall,nall,percent,k,niceprint ) &
!!$omp private(filename)
!!$omp single
do i = 1,nall
vz = i
!$omp task firstprivate( vz ) private( filename,io )
! !$omp task firstprivate( vz ) private( io )
call initsignal()
write (filename,'(a,i0)') trim(dirn),vz
write (filename,'(a,i0)') dirn,vz
call command('cd '//trim(filename)//' && '//trim(jobcall),io)
!$omp critical
! !$omp critical
k = k+1
if (niceprint) then
percent = float(k)/float(nall)*100.0d0
call printprogbar(percent)
else
write (6,'(1x,i0)',advance='no') k
flush (6)
write (stdout,'(1x,i0)',advance='no') k
flush (stdout)
end if
!$omp end critical
!$omp end task
! !$omp end critical
! !$omp end task
end do
!$omp taskwait
!$omp end single
!$omp end parallel
!!$omp taskwait
!!$omp end single
!!$omp end parallel
!--- this is a test for BASF
if (env%threads > 8) then
call sleep(5)
Expand All @@ -507,7 +511,7 @@ subroutine protens(ens,env,prot,tim)
write (*,'(a)',advance='no') 'Collecting generated protomers ...'
jobcall = trim(tmppath)//'/'//'protomers.xyz'
do i = 1,nall
write (filename,'(a,i0)') trim(dirn),i
write (filename,'(a,i0)') dirn,i
call chdir(trim(filename))
call coord2xyz('coordprot.0','struc_0.xyz')
call appendto('struc_0.xyz',jobcall)
Expand Down Expand Up @@ -565,7 +569,7 @@ subroutine protens(ens,env,prot,tim)

!--- change back to original dir and copy the file with optimized protomers
call chdir(thispath)
write (jobcall,'(a,a,a)') trim(tmppath),'/','protonated.xyz'
jobcall = trim(tmppath)//'/'//'protonared.xyz'
call rename(trim(jobcall),'protonated.xyz')
call rmrf(dirn)
return
Expand Down