Merge branch 'grimme-lab:main' into aISS_update

.github/workflows/fortran-build.yml

@@ -23,10 +23,10 @@ jobs:
 
     steps:
     - name: Checkout code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Setup Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: 3.x
 
@@ -109,10 +109,10 @@ jobs:
 
     steps:
     - name: Checkout code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Setup Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: 3.x
 
@@ -149,7 +149,7 @@ jobs:
 
     steps:
     - name: Checkout code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Setup Python
       uses: actions/setup-python@v4

CMakeLists.txt

@@ -19,7 +19,7 @@ option(WITH_OBJECT "To build using object library" TRUE)
 option(INSTALL_MODULES "Install Fortran module files to include directory." FALSE)
 
 # Buggy CMake versions
-if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.27.0)
+if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.27.0 AND CMAKE_VERSION VERSION_LESS 3.28.0)
    set(WITH_OBJECT FALSE)
 endif()
 
@@ -45,11 +45,13 @@ if(NOT TARGET "mctc-lib::mctc-lib")
 endif()
 
 if(NOT TARGET "tblite::tblite" AND WITH_TBLITE)
-  find_package("tblite" REQUIRED)
+   find_package("tblite" REQUIRED)
+   add_compile_definitions(-DWITH_TBLITE)
 endif()
 
 if(NOT TARGET "cpcmx::cpcmx" AND WITH_CPCMX)
-  find_package("cpcmx" REQUIRED)
+   find_package("cpcmx" REQUIRED)
+   add_compile_definitions(-DWITH_CPCMX)
 endif()
 
 if(NOT TARGET "test-drive::test-drive")
@@ -147,11 +149,10 @@ target_link_libraries(
    "$<$<BOOL:${WITH_OpenMP}>:OpenMP::OpenMP_Fortran>"
    "mctc-lib::mctc-lib"
    "$<$<BOOL:${WITH_CPCMX}>:cpcmx::cpcmx>"
-   "$<$<BOOL:${WITH_TBLITE}>:tblite::tblite>"
+   $<$<BOOL:${WITH_TBLITE}>:tblite::tblite>
 )
 
-
- set_target_properties(
+set_target_properties(
    "lib-${PROJECT_NAME}-static"
    PROPERTIES
    Fortran_MODULE_DIRECTORY "${PROJECT_BINARY_DIR}/include"
@@ -224,6 +225,7 @@ target_link_libraries(
    PRIVATE
    "lib-${PROJECT_NAME}-static"
 )
+
 set_target_properties(
   ${PROJECT_NAME}-exe
   PROPERTIES

man/xtb.1.adoc

@@ -268,7 +268,7 @@ GENERAL
      clutter the screen less (not supported in every unit)
 
 *--ceasefiles*::
-     reduce the amount of output and files written
+     reduce the amount of output and files written (e.g. xtbtopo.mol)
 
 *--strict*::
      turns all warnings into hard errors
@@ -345,6 +345,9 @@ OUTPUT
 *hessian*::
    contains the (not mass weighted) cartesian Hessian, *--namespace* compatible.
 
+*xtbtopo.mol*::
+   topology information written in molfile format.
+
 *xtbopt.xyz*, *xtbopt.coord*::
    optimized geometry in the same format as the input geometry.
 

meson.build

@@ -137,6 +137,10 @@ xtb_exe = executable(
   dependencies: xtb_dep_static,
   link_language: 'fortran',
   install: install,
+  fortran_args: [
+    '-DWITH_TBLITE=@0@'.format(tblite_dep.found() ? 1 : 0),
+    '-DWITH_CPCMX=@0@'.format(cpx_dep.found() ? 1 : 0),
+  ],
 )
 
 xtb_header = files('include/xtb.h')

src/constrain_param.f90

@@ -452,12 +452,19 @@ subroutine set_constr(env,key,val,nat,at,idMap,xyz)
       potset%pos%n = size(list)
    case('atoms')
       call atl%new(val)
-      if (atl%get_error()) then
-         call env%warning('something is wrong in the fixing list',source)
-         return
+      if (val.eq."all") then
+         allocate(list(nat))
+         do i=1,nat
+            list(i)=i
+         enddo 
+      else
+         if (atl%get_error()) then
+            call env%warning('something is wrong in the fixing list',source)
+            return
+         endif
+         if (potset%pos%n > 0) call atl%add(potset%pos%atoms(:potset%pos%n))
+         call atl%to_list(list)
       endif
-      if (potset%pos%n > 0) call atl%add(potset%pos%atoms(:potset%pos%n))
-      call atl%to_list(list)
       potset%pos%atoms = list
       potset%pos%n = size(list)
 

src/geoopt_driver.f90

@@ -18,66 +18,81 @@
 module xtb_geoopt
 contains
 
+!> wrapper for relaxation engines
+!> more info: https://xtb-docs.readthedocs.io/en/latest/optimization.html 
 subroutine geometry_optimization &
       &   (env,mol,wfn,calc,egap,et,maxiter,maxcycle_in,etot,g,sigma, &
       &    tight,pr,initial_sp,fail)
+
    use xtb_mctc_accuracy, only : wp
    use xtb_mctc_io, only : stdout
-
    use xtb_type_molecule
    use xtb_type_restart
    use xtb_type_calculator
    use xtb_type_data
-
    use xtb_optimizer
    use xtb_relaxation_engine
    use xtb_single
-
    use xtb_setparam
 
-   ! Declaration section
    implicit none
 
    character(len=*), parameter :: source = 'xtb_geoopt'
 
-   !> Dummy-argument list
+   !> instace of polymorphic calculatior
    class(TCalculator), intent(inout) :: calc
-      !! instance of calculatior
+
+   !> calculation environment
    type(TEnvironment), intent(inout) :: env
-      !! calculation environment
+
+   !> molecular data information
    type(TMolecule), intent(inout) :: mol
-      !! molecular information
+
+   !> wavefunction
    type(TRestart),intent(inout) :: wfn
-      !! wavefunction
+
+   !> optimization level
    integer, intent(in)    :: tight
-      !! optimization level
+
+   !> max number of SCC cycles
    integer, intent(in)    :: maxiter
-      !! max number of SCC cycles
+
+   !> max number of optimization cycles
    integer, intent(in)    :: maxcycle_in
-      !! max number of optimization cycles
+
+   !> total energy
    real(wp),intent(inout) :: etot
-      !! total energy
+
+   !> electronic temperature 
    real(wp),intent(in)    :: et
-      !! electronic temprature 
+
+   !> HOMO-LUMO gap
    real(wp),intent(inout) :: egap
-      !! HOMO-LUMO gap
+
+   !> gradients
    real(wp),intent(inout) :: g(3,mol%n)
-      !! gradients
+
+   !> strain derivatives
    real(wp),intent(inout) :: sigma(3,3)
-      !! strain derivatives
+
+   !> internal printlevel 
    logical, intent(in)    :: pr
-      !! printlevel 
+
+   !> optimization convergence
    logical, intent(out)   :: fail
-      !! true->  optimization not converged
+
+   !> perform initial single point 
    logical, intent(in)    :: initial_sp
-      !! true->  perform initial single point 
 
-   !> Local variables
    type(scc_results) :: res
    logical :: final_sp, exitRun
    integer :: printlevel
    integer :: ilog
 
+!----------------!
+! Initialization !
+!----------------!
+
    final_sp = pr
 
    if (pr) then
@@ -88,10 +103,9 @@ subroutine geometry_optimization &
       printlevel = 0
    endif
 
-   !> create optimization log file
+   ! create/open optimization log !
    if (.not.allocated(set%opt_logfile)) then
       call open_file(ilog,'xtbopt.log','w')
-      !! default
    else
       if (set%opt_logfile == '-') then
          ilog = stdout
@@ -102,36 +116,46 @@ subroutine geometry_optimization &
       endif
    endif
 
+   ! create ONIOM optimization logs for low & high methods ! 
    if (set%oniom_settings%logs) then
       call open_file(set%oniom_settings%ilog1,"low.inner_region.log",'w')
       call open_file(set%oniom_settings%ilog2,"high.inner_region.log",'w')
    endif
 
-   call mol%update
-      !! update interatomic and minimum image(periodic) distances 
+   call mol%update ! update interatomic and minimum image (periodic) distances 
+
+!-------------!
+! Calculation !
+!-------------!
 
    if (initial_sp)  call singlepoint &
          &(env,mol,wfn,calc, &
          & egap,et,maxiter,printlevel-1,.false.,.false.,1.0_wp,etot,g,sigma,res)
 
-   !> actual calculation
    select case(set%opt_engine)
-   case(p_engine_rf)
+   case(p_engine_rf) ! ANCopt !
       call ancopt &
          &(env,ilog,mol,wfn,calc, &
          & egap,et,maxiter,maxcycle_in,etot,g,sigma,tight,pr,fail)
-      final_sp = .true.
-         !! required since ANCopt might perform an untracked displacement
+      final_sp = .true. ! required since ANCopt might perform an untracked displacement 
+
    case(p_engine_lbfgs)
-      call l_ancopt &
+      call l_ancopt & ! L-ANCopt !
          &(env,ilog,mol,wfn,calc, &
          & tight,maxcycle_in,etot,egap,g,sigma,printlevel,fail)
+
    case(p_engine_inertial)
-      call fire &
+      call fire & ! FIRE !
          &(env,ilog,mol,wfn,calc, &
          & tight,maxcycle_in,etot,egap,g,sigma,printlevel,fail)
+
    end select
-
+
+!-----------------!
+! Post-processing !
+!-----------------!
+
+   ! check convergence !
    if (pr) then
       if (fail) then
          call touch_file('NOT_CONVERGED')
@@ -141,14 +165,14 @@ subroutine geometry_optimization &
       endif
    end if
 
-   call env%check(exitRun)
-      !! check if any errors occur
+   call env%check(exitRun) ! error check 
 
    if (exitRun) then
       call env%rescue("Trying to recover from failed geometry optimization", source)
       fail = .true.
    end if
 
+   ! print fine details of optimized geometry !
    if (pr.and.set%pr_finalstruct) then
       write(env%unit,'(''================'')')
       write(env%unit,*) 'final structure:'
@@ -157,17 +181,18 @@ subroutine geometry_optimization &
    endif
    if (pr.and.set%pr_geosum) call geosum(mol%n,mol%at,mol%xyz)
 
-   !> usually final SP is performed for all three engines
+   ! final SP (usually for all engines) !
    if (final_sp) then
       if (pr) call generic_header(env%unit,'Final Singlepoint',49,10)
       call singlepoint &
          &(env,mol,wfn,calc, &
          & egap,et,maxiter,printlevel,.false.,.false.,1.0_wp,etot,g,sigma,res)
    endif
 
-   if (ilog .ne.stdout) call close_file(ilog)
-      !! close log file if it is not printed out on stdout
+   ! close log file !
+   if (ilog.ne.stdout) call close_file(ilog)
 
+   ! close ONIOM optlogs !
    if (set%oniom_settings%logs) then
       call close_file(set%oniom_settings%ilog1)
       call close_file(set%oniom_settings%ilog2)

src/optimizer.f90

@@ -202,7 +202,9 @@ subroutine ancopt(env,ilog,mol,chk,calc, &
    character(len=*),parameter :: chrfmt = &
       '(10x,":",3x,a,a18,      10x,":")'
 
-
+   ! Print ANCopt header !
+   call ancopt_header(env%unit,set%veryverbose)
+
    if(mol%n.eq.1) return
       !! do not optimize for 1 molecule
    if (profile) call timer%new(8,.false.)