Safer toml input parsing (#325)

src/algos/parallel.f90

@@ -225,16 +225,18 @@ end subroutine crest_sploop
 !========================================================================================!
 !========================================================================================!
 subroutine crest_oloop(env,nat,nall,at,xyz,eread,dump,customcalc)
-!***************************************************************
+!*******************************************************************************
 !* subroutine crest_oloop
 !* This subroutine performs concurrent geometry optimizations
 !* for the given ensemble. Inputs xyz and eread are overwritten
 !* env        - contains parallelization and other program settings
 !* dump       - decides on whether to dump an ensemble file
+!*              WARNING: the ensemble file will NOT be in the same order
+!*              as the input xyz array. However, the overwritten xyz will be! 
 !* customcalc - customized (optional) calculation level data
 !*
 !* IMPORTANT: xyz should be in Bohr(!) for this routine
-!***************************************************************
+!******************************************************************************
   use crest_parameters,only:wp,stdout,sep
   use crest_calculator
   use omp_lib
@@ -369,6 +371,11 @@ subroutine crest_oloop(env,nat,nall,at,xyz,eread,dump,customcalc)
       end if
       eread(zcopy) = energy
       xyz(:,:,zcopy) = molsnew(job)%xyz(:,:)
+    else if(io==calculations(job)%maxcycle .and. calculations(job)%anopt) then
+      !>--- allow partial optimization?
+      c = c+1
+      eread(zcopy) = energy
+      xyz(:,:,zcopy) = molsnew(job)%xyz(:,:)
     else
       eread(zcopy) = 1.0_wp
     end if

src/algos/protonate.f90

@@ -37,6 +37,7 @@ subroutine crest_new_protonate(env,tim)
   use optimize_module
   use parallel_interface
   use cregen_interface
+  use iomod
   implicit none
   type(systemdata),intent(inout) :: env
   type(timer),intent(inout)      :: tim
@@ -51,12 +52,14 @@ subroutine crest_new_protonate(env,tim)
   real(wp) :: energy,dip
   real(wp),allocatable :: grad(:,:)
   type(calcdata),allocatable :: tmpcalc
+  type(calcdata),allocatable :: tmpcalc_ff
+  type(calculation_settings) :: tmpset
   real(wp),allocatable :: protxyz(:,:)
-  integer :: natp
+  integer :: natp,pstep,npnew
   integer,allocatable :: atp(:)
-  real(wp),allocatable :: xyzp(:,:,:) 
+  real(wp),allocatable :: xyzp(:,:,:)
   real(wp),allocatable :: ep(:)
-  character(len=*),parameter :: partial = '∂E/∂'
+  logical,allocatable :: atlist(:)
 !========================================================================================!
   write (stdout,*)
   !call system('figlet singlepoint')
@@ -68,10 +71,11 @@ subroutine crest_new_protonate(env,tim)
   write (stdout,*) "|_|                                            "
   write (stdout,*) "-----------------------------------------------"
   write (stdout,*) "  automated protonation site screening script  "
+  write (stdout,*) "       revised version (c) P.Pracht 2024       "
   write (stdout,*) 'Cite as:'
-  write (stdout,*) 'P.Pracht, C.A.Bauer, S.Grimme'
-  write (stdout,*) 'JCC, 2017, 38, 2618–2631.'
-  write (stdout,*)
+  write (stdout,*) '  P.Pracht, C.A.Bauer, S.Grimme'
+  write (stdout,*) '  JCC, 2017, 38, 2618–2631.'
+  write (stdout,*) 
 
 !========================================================================================!
   call new_ompautoset(env,'max',0,T,Tn)
@@ -84,18 +88,22 @@ subroutine crest_new_protonate(env,tim)
   write (stdout,*)
 !========================================================================================!
 !>--- The first step is to perfom a LMO calculation to identify suitable protonation sites
+!>--- in this version of the program this step is always done with GFN0-xTB.
+
   call tim%start(14,'LMO center calculation')
   write (stdout,'(a)') repeat('-',80)
   write (stdout,'(a)')
   write (stdout,'(a)',advance='no') '> Setting up GFN0-xTB for LMO center calculation ... '
   flush (stdout)
 
   allocate (grad(3,mol%nat),source=0.0_wp)
+!>--- GFN0 job adapted from global settings
   allocate (tmpcalc)
   call env2calc(env,tmpcalc,mol)
   tmpcalc%calcs(1)%id = jobtype%gfn0
   tmpcalc%calcs(1)%rdwbo = .true.
   tmpcalc%calcs(1)%getlmocent = .true.
+  tmpcalc%calcs(1)%chrg = env%chrg
   tmpcalc%ncalculations = 1
   write (stdout,'(a)') 'done.'
 !>--- and then start it
@@ -119,15 +127,25 @@ subroutine crest_new_protonate(env,tim)
 !>--- check LMO center
   np = tmpcalc%calcs(1)%nprot
   if (np > 0) then
-    write (stdout,'(a,i0,a)') '> ',np,' π- or LP-centers identified as protonation candidates'
+    write (stdout,'(a,i0,a)') '> ',np,' π- or LP-centers identified as protonation candidates:'
     call move_alloc(tmpcalc%calcs(1)%protxyz,protxyz)
-    !do i=1,np
-    !  write(stdout,*) protxyz(1:3,i)
-    !enddo
+    write (stdout,'(1x,a5,1x,a,5x,a)') 'LMO','type','center(xyz/Ang)'
+    do i = 1,np
+      select case (nint(protxyz(4,i)))
+      case (1)
+        write (stdout,'(1x,i5,1x,a,3F12.5)') i,'LP   ',protxyz(1:3,i)*autoaa
+      case (2)
+        write (stdout,'(1x,i5,1x,a,3F12.5)') i,'π    ',protxyz(1:3,i)*autoaa
+      case (3)
+        write (stdout,'(1x,i5,1x,a,3F12.5)') i,'del.π',protxyz(1:3,i)*autoaa
+      case default
+        write (stdout,'(1x,i5,1x,a,3F12.5)') i,'???  ',protxyz(1:3,i)*autoaa  
+      end select
+    end do
   else
     write (stdout,*)
     write (stdout,*) 'WARNING: No suitable protonation sites found!'
-    write (stdout,*) '         Check if you expect π- or LP-centers for your molecule!'
+    write (stdout,*) '         Confirm whether you expect π- or LP-centers for your molecule!'
     write (stdout,*)
     return
   end if
@@ -136,47 +154,164 @@ subroutine crest_new_protonate(env,tim)
 
 !========================================================================================!
 !>--- If we reached this point, we have candidate positions for our protonation!
-  write(stdout,'(a)',advance='yes') '> Generating candidate structures ... '
-  flush(stdout)
+  pstep = 0
+  write (stdout,'(a)',advance='yes') '> Generating candidate structures ... '
+  flush (stdout)
   natp = mol%nat+1
-  allocate(atp(natp), source=0)
-  allocate(xyzp(3,natp,np),ep(np),source=0.0_wp)
-  call protonation_candidates(env,mol,natp,np,protxyz,atp,xyzp)
-  write(stdout,'(a)') '> Write protonate_0.xyz with candidates ... '
-  call wrensemble('protonate_0.xyz',natp,np,atp,xyzp*autoaa,ep)
-  write(stdout,'(a)') '> done.'    
-  write(stdout,*)    
+  allocate (atp(natp),source=0)
+  allocate (xyzp(3,natp,np),ep(np),source=0.0_wp)
 
-!>--- Enforce further constraints, conditions, etc.
-!     (TODO)
+  call protonation_candidates(env,mol,natp,np,protxyz,atp,xyzp,npnew)
+!>--- NOTE: after this the global charge (env%chrg) and all charges saved in the calc levels have been increased
+
+  if (npnew < 1) then
+    write (stdout,*)
+    write (stdout,'(a)') '> WARNING: No remaining protonation sites after applying user defined conditions!'
+    write (stdout,'(a)') '>          Modify the search criteria and check your input structure for sanity.'
+    return
+  end if
+
+  write (atmp,'(a,i0,a)') 'protonate_',pstep,'.xyz'
+  write (stdout,'(a,a,a,i0,a)') '> Write ',trim(atmp),' with ',npnew,' candidates ... '
 
-!>--- Optimize candidates
-  call smallhead('Protomer Ensemble Optimization')
-  call tim%start(15,'Ensemble optimization')
-  call print_opt_data(env%calc,stdout) 
-  call crest_oloop(env,natp,np,atp,xyzp,ep,.true.)
-  call tim%stop(15)
-  write(stdout,'(a)') '> Write protonate_1.xyz with optimized structures ... '
-  call rename(ensemblefile,'protonate_1.xyz')
+  call wrensemble('protonate_0.xyz',natp,npnew,atp,xyzp(:,:,1:npnew)*autoaa,ep(1:npnew))
 
+  write (stdout,'(a)') '> done.'
+  write (stdout,*)
 
+!========================================================================================!
+!>--- Optimize candidates, optional FF pre-step
+  if (env%protb%ffopt) then
+    call smallhead('Protomer Ensemble FF Pre-Optimization')
+    !>--- set up a temporary calculation object
+    write (stdout,'(a)') '> LMO centers can be very close to atoms, leading to initial'
+    write (stdout,'(a)') '  extremely high-energy candidates which may undergo unwanted'
+    write (stdout,'(a)') '  chemical changes in optimizations. Classical force-fields'
+    write (stdout,'(a)') '  with defined bond-topology can help circumvent this issue.'
+    write (stdout,'(a)') '> Setting up force-field structure pre-optimization ...'
+    allocate (tmpcalc_ff)
+    tmpcalc_ff%optnewinit = .true.
+    env%calc%optnewinit = .true.
+    tmpcalc_ff%optnewinit=.true.
+    call tmpset%create('gfnff')
+    tmpset%chrg = env%chrg
+    call tmpcalc_ff%add(tmpset)
+    tmpcalc_ff%maxcycle = 10000
+    call tmpcalc_ff%info(stdout)    
 
+    !>--- Run optimizations
+    call tim%start(15,'Ensemble optimization (FF)')
+    call print_opt_data(tmpcalc_ff,stdout)
+    write (stdout,'(a,i0,a)') '> ',npnew,' structures to optimize ...'
+    call crest_oloop(env,natp,npnew,atp,xyzp(:,:,1:npnew),ep(1:npnew),.false.,tmpcalc_ff)
+    call tim%stop(15)
 
+    deallocate (tmpcalc_ff)
 
-!>--- sorting
-  write(stdout,'(a)') '> Sorting structures by energy ...'
-  call newcregen(env,6,'protonate_1.xyz')
-  write(stdout,'(a)') '> sorted file was renamed to protonated.xyz'
-  call rename('protonate_1.xyz.sorted','protonated.xyz')
+    pstep = pstep+1
+    write (atmp,'(a,i0,a)') 'protonate_',pstep,'.xyz'
+    write (stdout,'(a,a,a)') '> Write ',trim(atmp),' with optimized structures ... '
+    call wrensemble(trim(atmp),natp,npnew,atp,xyzp(:,:,1:npnew)*autoaa,ep(1:npnew))
+
+    !>--- sorting
+    write (stdout,'(a)') '> Sorting structures by energy to remove failed opts. ...'
+    env%ewin = 5000.0_wp
+    call newcregen(env,7,trim(atmp))
+    call rename(trim(atmp)//'.sorted',trim(atmp))
+    write (stdout,'(a)') '> WARNING: These are force-field energies which are '
+    write (stdout,'(a)') '           NOT(!) accurate for bond formation and breaking!'
+    write (stdout,*)
+
+    !>--- re-read sorted ensemble
+    deallocate (xyzp,atp) !> clear this space to re-use it
+    call rdensemble(trim(atmp),natp,npnew,atp,xyzp)
+    xyzp = xyzp*aatoau !> don't forget to restore BOHR
+  end if
 
+!========================================================================================!
+!>--- H-position-only optimization (only makes sense after FF preoptimization)
+  if (env%protb%hnewopt.and.env%protb%ffopt) then
+    call smallhead('Protomer Ensemble Frozen-Atom Optimization')
+    !>--- create temporary calculation from our intended level of theory
+    write (stdout,'(a)') '> Setting up frozen structure optimization ...'
+    allocate (tmpcalc)
+    call env2calc(env,tmpcalc,mol)
+    !>--- freeze all atoms, EXCEPT the new one
+    allocate (atlist(natp),source=.true.)
+    atlist(natp) = .false. !> the new one is always last
+    do i = 1,natp
+      if (atp(i) == 1) then
+        atlist(i) = .false. !> additionally un-freeze all H's (this seems to be beneficial)
+      end if
+    end do
+    tmpcalc%nfreeze = count(atlist)
+    write (stdout,'(a,i0,a)') '> ',tmpcalc%nfreeze,' frozen atoms. All H non-frozen.'
+    call move_alloc(atlist,tmpcalc%freezelist)
+    call tmpcalc%info(stdout)
+
+    !>--- run opt
+    call tim%start(16,'Ensemble optimization (frozen)')
+    write (stdout,'(a,i0,a)') '> ',npnew,' structures to optimize ...'
+    call crest_oloop(env,natp,npnew,atp,xyzp(:,:,1:npnew),ep(1:npnew),.false.,tmpcalc)
+    call tim%stop(16)
+
+    pstep = pstep+1
+    write (atmp,'(a,i0,a)') 'protonate_',pstep,'.xyz'
+    write (stdout,'(a,a,a)') '> Write ',trim(atmp),' with optimized structures ... '
+    call wrensemble(trim(atmp),natp,npnew,atp,xyzp(:,:,1:npnew)*autoaa,ep(1:npnew))
+
+    !>--- sorting
+    write (stdout,'(a)') '> Sorting structures by energy to remove failed opts. ...'
+    env%ewin = env%protb%ewin*10.0_wp  !> large energy threshold
+    call newcregen(env,7,trim(atmp))
+    call rename(trim(atmp)//'.sorted',trim(atmp))
+    write (stdout,*)
+
+    !>--- re-read sorted ensemble
+    deallocate (xyzp,atp) !> clear this space to re-use it
+    call rdensemble(trim(atmp),natp,npnew,atp,xyzp)
+    xyzp = xyzp*aatoau !> don't forget to restore BOHR
+
+    deallocate (tmpcalc)
+  end if
+
+!========================================================================================!
+!>--- Optimize with global settings
+  if (env%protb%finalopt.and.env%protb%ffopt) then
+    call smallhead('Final Protomer Ensemble Optimization')
+    allocate(tmpcalc)
+    call env2calc(env,tmpcalc,mol)
+    call tmpcalc%info(stdout)
+    !tmpcalc%maxcycle=5
+    !tmpcalc%anopt=.true.
+    call tim%start(20,'Ensemble optimization')
+    call print_opt_data(env%calc,stdout)
+    write (stdout,'(a,i0,a)') '> ',npnew,' structures to optimize ...'
+    call crest_oloop(env,natp,npnew,atp,xyzp(:,:,1:npnew),ep,.false.,tmpcalc)
+    call tim%stop(20)
+
+    pstep = pstep+1
+    write (atmp,'(a,i0,a)') 'protonate_',pstep,'.xyz'
+    write (stdout,'(a,a,a)') '> Write ',trim(atmp),' with optimized structures ... '
+    call wrensemble(trim(atmp),natp,npnew,atp,xyzp(:,:,1:npnew)*autoaa,ep(1:npnew))
+
+!>--- sorting
+    write (stdout,'(a)') '> Sorting structures by energy ...'
+    env%ewin = env%protb%ewin
+    call newcregen(env,7,trim(atmp))
+    call rename(trim(atmp)//'.sorted','protonated.xyz')
+  else
+    call rename(trim(atmp),'protonated.xyz')
+  end if
+  write (stdout,'(a)') '> sorted file was renamed to protonated.xyz'
 !========================================================================================!
   return
 end subroutine crest_new_protonate
 
 !========================================================================================!
 !========================================================================================!
 
-subroutine protonation_candidates(env,mol,natp,np,protxyz,at,xyz)
+subroutine protonation_candidates(env,mol,natp,np,protxyz,at,xyz,npnew)
 !********************************************************
 !* generate protonation/ionization candidate structures
 !* The outputs are at and xyz, the latter being in Bohr
@@ -190,30 +325,60 @@ subroutine protonation_candidates(env,mol,natp,np,protxyz,at,xyz)
   type(coord),intent(in) :: mol
   integer,intent(in) :: natp
   integer,intent(in) :: np
-  real(wp),intent(in) :: protxyz(3,np)
+  real(wp),intent(in) :: protxyz(4,np)
   !> OUTPUT
   integer,intent(out)  :: at(natp)
   real(wp),intent(out) :: xyz(3,natp,np)
+  integer,intent(out) :: npnew
   !> LOCAL
-  integer :: i,j,k,l
+  integer :: i,j,k,l,ii
+  integer :: ati,ichrg,ctype
 
   if (natp .ne. mol%nat+1) then
     write (stdout,'(a)') 'WARNING: Inconsistent number of atoms in protonation routine'
     error stop
   end if
 
-  write(stdout,'(a)') '> Increasing the molecular charge by 1'
-  call env%calc%increase_charge()
+  if (env%protb%swelem) then
+!>--- User-defined monoatomic ion
+    ichrg = env%protb%swchrg
+    ati = env%protb%swat
+  else
+!>--- DEFAULT: H⁺
+    ichrg = 1
+    ati = 1
+  endif
+  write (stdout,'(a,i0)') '> Increasing the molecular charge by ',ichrg
+  call env%calc%increase_charge(ichrg)
+  env%chrg = env%chrg + ichrg
+
+!>--- Check if we have some other conditions
+   if(any(.not.env%protb%active_lmo(:)))then
+     write(stdout,'(a)',advance='no') '> User-defined: IGNORING '
+     if(.not.env%protb%active_lmo(1)) write(stdout,'(a)',advance='no') 'π '
+     if(.not.env%protb%active_lmo(2)) write(stdout,'(a)',advance='no') 'LP '  
+     if(.not.env%protb%active_lmo(3)) write(stdout,'(a)',advance='no') 'deloc.π '
+     write(stdout,'(a)') 'LMOs ...'
+   endif   
 
 !>--- Populate
+  npnew = 0
+  ii = 0
   do i = 1,np
+!>--- Enforce further constraints, conditions, etc.
+    ctype = nint(protxyz(4,i))
+    if(.not.env%protb%active_lmo(ctype)) cycle !> skip unselected LMO types
+
+    ii= ii + 1 !> counter of actually created structures
     do j = 1,mol%nat
-      xyz(1:3,j,i) = mol%xyz(1:3,j)
+      xyz(1:3,j,ii) = mol%xyz(1:3,j)
       at(j) = mol%at(j)
     end do
-    xyz(1:3,natp,i) = protxyz(1:3,i)
-    at(natp) = 1
+    xyz(1:3,natp,ii) = protxyz(1:3,i)
+    at(natp) = ati
   end do
+  npnew = ii
+
 end subroutine protonation_candidates
 
 !========================================================================================!