bug fix maintenance (#361)

crest-lab · Oct 11, 2024 · a12cb48 · a12cb48
2 parents a71e303 9908b42
commit a12cb48
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Showing 21 changed files with 193 additions and 60 deletions.
diff --git a/src/algos/dynamics.f90 b/src/algos/dynamics.f90
@@ -69,9  69,11 @@ subroutine crest_moleculardynamics(env,tim)
   !>--- check if we have any MD & calculation settings allocated
   if (.not. mddat%requested) then
     write (stdout,*) 'MD requested, but no MD settings present.'
     env%iostatus_meta = status_config
     return
   else if (calc%ncalculations < 0) then
     write (stdout,*) 'MD requested, but no calculation settings present.'
     env%iostatus_meta = status_config
     return
   end if
 
@@ -99,7  101,8 @@ subroutine crest_moleculardynamics(env,tim)
     write (stdout,*) 'MD run completed successfully'
     write (stdout,*) 'Trajectory written to ',trjf
   else
-    write (stdout,*) 'MD run terminated with error'
     write (stdout,*) 'WARNING: MD run terminated ABNORMALLY'
     env%iostatus_meta = status_failed
   end if
 !========================================================================================!
   call tim%stop(14)

diff --git a/src/algos/numhess.f90 b/src/algos/numhess.f90
@@ -162,6  162,8 @@ subroutine crest_numhess(env,tim)
         write (stdout,*) 'At least two calculation level must be'
         write (stdout,*) 'given for the calculation of the effective Hessian.'
         write (stdout,*)
         env%iostatus_meta = status_config
         return
 
       end if
 
@@ -388,7  390,8 @@ subroutine thermo_standalone(env)
     write(stdout,'(1x,a,a)') 'Reading frequencies from:  ',trim(env%thermo%vibfile)
     call rdfreq(env%thermo%vibfile,nat3,freq)
   else
-    error stop 'No Hessian or vibspectrum file allocated for thermo routine!'
     write(stdout,'(1x,a)') 'No Hessian or vibspectrum file allocated for thermo routine!'
     call creststop(status_input)
   endif
   write(stdout,*) 
 

diff --git a/src/algos/optimization.f90 b/src/algos/optimization.f90
@@ -98,6  98,7 @@ subroutine crest_optimization(env,tim)
     close (ich)
   else
     write (stdout,*) 'geometry optimization FAILED!'
     env%iostatus_meta = status_failed
   endif
 
   write (stdout,*)
@@ -169,7  170,8 @@ subroutine crest_ensemble_optimization(env,tim)
   if (ex) then
     ensnam = env%ensemblename
   else
-    write (stdout,*) 'no ensemble file provided.'
     write (stdout,*) '**ERROR** no ensemble file provided.'
     env%iostatus_meta = status_input
     return
   end if
 
@@ -178,7  180,11 @@ subroutine crest_ensemble_optimization(env,tim)
 
 !>---- read the input ensemble
   call rdensembleparam(ensnam,nat,nall)
-  if (nall .lt. 1) return
   if (nall .lt. 1)then
     write (stdout,*) '**ERROR** empty ensemble file.'
     env%iostatus_meta = status_input
     return
   endif
   allocate (xyz(3,nat,nall),at(nat),eread(nall))
   call rdensemble(ensnam,nat,nall,at,xyz,eread)
 !>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<!
@@ -275,7  281,8 @@ subroutine crest_ensemble_screening(env,tim)
   if (ex) then
     ensnam = env%ensemblename
   else
-    write (stdout,*) 'no ensemble file provided.'
     write (stdout,*) '**ERROR** no ensemble file provided.'
     env%iostatus_meta = status_input
     return
   end if
 
@@ -284,8  291,11 @@ subroutine crest_ensemble_screening(env,tim)
 
 !>---- read the input ensemble
   call rdensembleparam(ensnam,nat,nall)
-  if (nall .lt. 1) return
-
   if (nall .lt. 1)then
     write (stdout,*) '**ERROR** empty ensemble file.'
     env%iostatus_meta = status_input
     return
   endif
 !>--- set OMP parallelization
   call new_ompautoset(env,'auto',nall,T,Tn)
 
@@ -305,7  315,8 @@ subroutine crest_ensemble_screening(env,tim)
   call rmrfw('crest_rotamers_')
   call optlev_to_multilev(3.0d0,multilevel)
   call crest_multilevel_oloop(env,ensnam,multilevel)
-
   if(env%iostatus_meta .ne. 0 ) return
 
 !>--- printout
   call catdel('cregen.out.tmp')
   write (stdout,'(/,1x,a,1x,a)') 'Final ensemble on file','<'//trim(ensemblefile)//'>'

diff --git a/src/algos/protonate.f90 b/src/algos/protonate.f90
@@ -149,6  149,7 @@ subroutine crest_new_protonate(env,tim)
     write (stdout,*) 'WARNING: No suitable protonation sites found!'
     write (stdout,*) '         Confirm whether you expect π- or LP-centers for your molecule!'
     write (stdout,*)
     env%iostatus_meta = status_failed
     return
   end if
   deallocate (tmpcalc)
@@ -176,6  177,7 @@ subroutine crest_new_protonate(env,tim)
     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.'
     env%iostatus_meta = status_failed
     return
   end if
 
@@ -368,7  370,7 @@ subroutine protonation_candidates(env,mol,natp,np,protxyz,at,xyz,npnew)
 
   if (natp .ne. mol%nat env%protb%amount) then
     write (stdout,'(a)') 'WARNING: Inconsistent number of atoms in protonation routine'
-    error stop
     call creststop(status_args)
   end if
 
   if (env%protb%swelem) then
@@ -902,7  904,7 @@ subroutine deprotonation_candidates(env,mol,natp,np,at,xyz,npnew)
 
   if (natp .ne. mol%nat-env%protb%amount) then
     write (stdout,'(a)') 'WARNING: Inconsistent number of atoms in deprotonation routine'
-    error stop
     call creststop(status_args)
   end if
 
   if (env%protb%swelem) then
@@ -1114,6  1116,7 @@ subroutine crest_new_tautomerize(env,tim)
     write (stdout,*) 'WARNING: No suitable protonation sites found!'
     write (stdout,*) '         Confirm whether you expect π- or LP-centers for your molecule!'
     write (stdout,*)
     env%iostatus_meta = status_failed
     return
   end if
   deallocate (tmpcalc)
@@ -1340,7  1343,7 @@ subroutine tautomer_candidates(env,mol,natp,npadd,npremove,protxyz,at,xyz,npnew)
 
   if (natp .ne. mol%nat) then
     write (stdout,'(a)') 'WARNING: Inconsistent number of atoms in protonation routine'
-    error stop
     call creststop(status_args)
   end if
 
   ati = 1  !> always refer to Hydrogen for tautomers

diff --git a/src/algos/search_1.f90 b/src/algos/search_1.f90
@@ -96,7  96,8 @@ subroutine crest_search_1(env,tim)
 !>--- read ensemble
   call rdensembleparam(ensnam,nat,nall)
   if (nall .lt. 1) then
-    write(stdout,*) 'empty ensemble file'
     write(stdout,*) '**ERROR** empty ensemble file'
     env%iostatus_meta = status_failed
     return
   endif
   allocate (xyz(3,nat,nall),at(nat),eread(nall))

diff --git a/src/algos/search_conformers.f90 b/src/algos/search_conformers.f90
@@ -90,6  90,7 @@ subroutine crest_search_imtdgc(env,tim)
    call tim%start(1,'Trial metadynamics (MTD)')
    call trialmd(env)  
    call tim%stop(1)
    if(env%iostatus_meta .ne. 0 ) return
   end if
 
 !===========================================================!
@@ -134,6  135,7 @@ subroutine crest_search_imtdgc(env,tim)
     call optlev_to_multilev(env%optlev,multilevel)
     call crest_multilevel_oloop(env,ensnam,multilevel)
     call tim%stop(3)
     if(env%iostatus_meta .ne. 0 ) return
 
 !>--- save the CRE under a backup name
     call checkname_xyz(crefile,atmp,str)
@@ -186,6  188,7 @@ subroutine crest_search_imtdgc(env,tim)
     call tim%start(4,'Molecular dynamics (MD)')
     call crest_rotamermds(env,conformerfile)
     call tim%stop(4)
     if(env%iostatus_meta .ne. 0 ) return
 
 !>--- Reoptimization of trajectories
     call checkname_xyz(crefile,atmp,btmp)
@@ -195,6  198,7 @@ subroutine crest_search_imtdgc(env,tim)
     call tim%start(3,'Geometry optimization')
     call crest_multilevel_wrap(env,trim(atmp),-1)
     call tim%stop(3)
     if(env%iostatus_meta .ne. 0 ) return
 
     call elowcheck(lower,env)
     if (lower) then
@@ -211,6  215,8 @@ subroutine crest_search_imtdgc(env,tim)
       call tim%start(5,'Genetic crossing (GC)')
       call crest_newcross3(env)
       call tim%stop(5)
       if(env%iostatus_meta .ne. 0 ) return
 
       call confg_chk3(env)
       call elowcheck(lower,env)
       if (lower) then
@@ -236,6  242,7 @@ subroutine crest_search_imtdgc(env,tim)
     call checkname_xyz(crefile,atmp,str)
     call crest_multilevel_wrap(env,trim(atmp),0) 
     call tim%stop(3)                 
     if(env%iostatus_meta .ne. 0 ) return
 
 !==========================================================!
 !>--- final ensemble sorting
@@ -357,7  364,8 @@ end subroutine crest_refine
 !>--- read ensemble
   call rdensembleparam(ensnam,nat,nall)
   if (nall .lt. 1) then
-    write(stdout,*) 'empty ensemble file ',trim(ensnam)
     write(stdout,*) '**ERROR** empty ensemble file ',trim(ensnam)
     env%iostatus_meta = status_failed
     return
   endif
   allocate (xyz(3,nat,nall),at(nat),eread(nall))
@@ -389,8  397,9 @@ end subroutine crest_refine
      !>--- check for empty ensemble content
        call rdensembleparam(trim(inpnam),nat,nall)
        if (nall .lt. 1) then
-         write(stdout,*) 'empty ensemble file',trim(inpnam)
-         stop
          write(stdout,*) '**ERROR** empty ensemble file',trim(inpnam)
          env%iostatus_meta = status_failed
          return
        endif
 
        write(stdout,*)
@@ -405,8  414,9 @@ end subroutine crest_refine
      !>--- check for empty ensemble content (again)
        call rdensembleparam(trim(inpnam),nat,nall)
        if (nall .lt. 1) then
-         write(stdout,*) 'empty ensemble file',trim(inpnam)
-         stop
          write(stdout,*) '**ERROR** empty ensemble file',trim(inpnam)
          env%iostatus_meta = status_failed
          return
        endif
      !>--- read new ensemble for next iteration
        allocate (xyz(3,nat,nall),at(nat),eread(nall))
@@ -508,7  518,8 @@ subroutine crest_rotamermds(env,ensnam)
   call env%ref%to(mol)
   call rdensembleparam(ensnam,nat,nall)
   if (nall .lt. 1) then
-    write(stdout,*) 'empty ensemble file',trim(ensnam)
     write(stdout,*) '**ERROR** empty ensemble file',trim(ensnam)
     env%iostatus_meta = status_failed
     return
   endif
 
@@ -615,6  626,7 @@ subroutine crest_newcross3(env)
       multilevel(4) = .true.
     end if
     call crest_multilevel_oloop(env,'confcross.xyz',multilevel)
     if(env%iostatus_meta .ne. 0 ) return
 
 !>-- append optimized crossed structures and original to a single file
     call checkname_xyz(crefile,inpnam,outnam)

diff --git a/src/algos/search_entropy.f90 b/src/algos/search_entropy.f90
@@ -96,6  96,7 @@ subroutine crest_search_entropy(env,tim)
    call tim%start(1,'Trial metadynamics (MTD)')
    call trialmd(env)    
    call tim%stop(1)
    if(env%iostatus_meta .ne. 0) return
   end if
 
 !===========================================================!
@@ -140,6  141,7 @@ subroutine crest_search_entropy(env,tim)
       call optlev_to_multilev(env%optlev,multilevel)
       call crest_multilevel_oloop(env,ensnam,multilevel)
       call tim%stop(3)
       if(env%iostatus_meta .ne. 0 ) return
 
 !>--- save the CRE under a backup name
       call checkname_xyz(crefile,atmp,str)
@@ -210,6  212,7 @@ subroutine crest_search_entropy(env,tim)
           !>-- start from the current crest_conformers.xyz
           call crest_smtd_mds(env,conformerfile)
           call tim%stop(6)
           if(env%iostatus_meta .ne. 0) return
           call emtdcheckempty(env,fail,env%emtd%nbias)
 
           if (fail) then
@@ -226,6  229,7 @@ subroutine crest_search_entropy(env,tim)
             multilevel = (/.true.,.false.,.false.,.false.,.false.,.true./)
             call crest_multilevel_oloop(env,trim(atmp),multilevel)
             call tim%stop(3)
             if(env%iostatus_meta .ne. 0 ) return
 
 !>--- if in the entropy mode a lower structure was found -> cycle (required for extrapolation)
             call elowcheck(lower,env)
@@ -311,7  315,8 @@ subroutine crest_smtd_mds(env,ensnam)
   call env%ref%to(mol)
   call rdensembleparam(ensnam,nat,nall)
   if (nall .lt. 1) then
-    write (stdout,*) 'empty ensemble file',trim(ensnam)
     write (stdout,*) '**ERROR** empty ensemble file',trim(ensnam)
     env%iostatus_meta = status_failed
     return
   end if
 
@@ -449,7  454,10 @@ subroutine crest_init_multimd_smtd(env,mddats,nsim,biasfile)
 
 !>--- load static bias stuctures
   inquire (file=biasfile,exist=ex)
-  if (.not.ex) error stop 'Could not initialize static metadynamics'
   if (.not.ex)then
     write(stdout,'(a,a)') 'Could not initialize static metadynamics: missing ',trim(biasfile)
     call creststop(status_input)
   endif
   call rdensembleparam(biasfile,nat,nall)
   allocate (xyz(3,nat,nall),at(nat),eread(nall))
   call rdensemble(biasfile,nat,nall,at,xyz,eread)

diff --git a/src/algos/search_mecp.f90 b/src/algos/search_mecp.f90
@@ -50,8  50,9 @@ subroutine crest_search_mecp(env,tim)
 !>--- check calculation setup
   ex = env%calc%ncalculations > 1
   if (.not.ex) then
-    write (stdout,*) 'not enough calculation levels specified for MECP search.'
-    error stop
     write (stdout,*) '**ERROR** Not enough calculation levels specified for MECP search.'
     env%iostatus_meta = status_config
     return
   end if
   call print_gapcons(env%calc)
 
@@ -120,6  121,7 @@ end subroutine crest_search_mecp
 
 subroutine print_gapcons(calc)
   use crest_parameters
   use crest_data
   use crest_calculator
   implicit none
 
@@ -152,8  154,8 @@ subroutine print_gapcons(calc)
   end do
 
   if (.not.ex) then
-    write (stdout,*) 'no gap constraint provided'
-    error stop
     write (stdout,*) '**ERROR** no gap constraint provided'
     call creststop(status_config)
   else
     write (stdout,*)
   end if

diff --git a/src/algos/search_newnci.f90 b/src/algos/search_newnci.f90
@@ -87,6  87,7 @@ subroutine crest_search_newnci(env,tim)
     call tim%start(1,'Trial metadynamics (MTD)')
     call trialmd(env)
     call tim%stop(1)
     if(env%iostatus_meta .ne. 0 ) return
   end if
 
 !===========================================================!
@@ -131,6  132,7 @@ subroutine crest_search_newnci(env,tim)
       call optlev_to_multilev(env%optlev,multilevel)
       call crest_multilevel_oloop(env,ensnam,multilevel)
       call tim%stop(3)
       if(env%iostatus_meta .ne. 0 ) return
 
 !>--- save the CRE under a backup name
       call checkname_xyz(crefile,atmp,str)
@@ -192,6  194,7 @@ subroutine crest_search_newnci(env,tim)
   call checkname_xyz(crefile,atmp,str)
   call crest_multilevel_wrap(env,trim(atmp),0)
   call tim%stop(3)
   if(env%iostatus_meta .ne. 0 ) return
 
 !==========================================================!
 !>--- print CREGEN results and clean up Directory a bit