Merge branch 'main' of https://github.com/Thomas3R/xtb into main

CMakeLists.txt

@@ -16,6 +16,7 @@
 
 cmake_minimum_required(VERSION 3.17)
 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)
@@ -249,6 +250,15 @@ install(
    "${CMAKE_INSTALL_INCLUDEDIR}"
 )
 
+if (INSTALL_MODULES)
+   install(
+      DIRECTORY
+      "${PROJECT_BINARY_DIR}/include/"
+      DESTINATION
+      "${CMAKE_INSTALL_INCLUDEDIR}"
+   )
+endif()
+
 # xtb-parameters 
 install(
    FILES

man/xcontrol.7.adoc

@@ -439,7 +439,7 @@ NOTE: the scan parser will always terminate in error if the instruction could
 
 $scc
 ~~~~
-*temp*='real'::
+*temp, etemp*='real'::
     electronic temperature for the Fermi smearing
 
 *broydamp*='real'::
@@ -448,7 +448,7 @@ $scc
 *guess*=gasteiger|goedecker|sad::
     different possible guess charges for GFN2-xTB SCC calculation
 
-*maxiteration*='int'::
+*iterations, maxiterations*='int'::
     adjusts the number of SCC iterations in the first/last SCC calculation
 
 $split

man/xtb.1.adoc

@@ -91,8 +91,8 @@ OPTIONS
     The inner region is given as comma-separated indices directly in the commandline
     or in a file with each index on a separate line.
 
-*--etemp* 'REAL'::
-    electronic temperature (default = 300K)
+*--etemp, --temp* 'REAL'::
+    electronic temperature for SCC (default = 300K)
 
 *--esp* ::
     calculate electrostatic potential on VdW-grid
@@ -103,6 +103,9 @@ OPTIONS
 *-a, --acc* 'REAL'::
     accuracy for SCC calculation, lower is better (default = 1.0)
 
+*--iterations, --maxiterations* 'INT'::
+    maximum number of SCC iterations per single point calculation (default = 250)
+
 *--vparam* 'FILE'::
     Parameter file for xTB calculation
 

src/docking/search_nci.f90

@@ -53,6 +53,8 @@ module xtb_docking_search_nci
    use xtb_eeq, only: goedecker_chrgeq
    use xtb_basis, only: newBasisset
    use xtb_gfnff_neighbor, only: TNeigh
+   use xtb_io_writer, only : writeMolecule
+   use xtb_mctc_filetypes, only : generateFileName
    implicit none
 
    private
@@ -174,6 +176,8 @@ END SUBROUTINE Quicksort
       real(wp) :: tmp_e
       !> Minimumposition
       integer :: minpos
+      !> For outprint
+      character(len=:),allocatable :: extension, fin_name
 
       !> Parameter
       real(wp), parameter :: pi2 = 2*3.14159265358979_wp
@@ -949,14 +953,29 @@ END SUBROUTINE Quicksort
 
       call remove_file(iopt)
 
-      call open_file(ifinal, 'best.xyz', 'w')
-      write (ifinal, '(i0)') comb%n
-      write (ifinal, '(f20.14)') final_e(1)
-      do j = 1, comb%n
-         write (ifinal, '(a4,2x,3f20.14)') comb%sym(j), xyz_opt(1, j, 1)*autoang, &
-         &                                 xyz_opt(2, j, 1)*autoang, xyz_opt(3, j, 1)*autoang
-      end do
+      ! Write best structure in format of the largest input molecule
+      comb%xyz(:,:) = xyz_opt(:,:,1)
+      if(molA%n >= molB%n) then
+         comb%ftype=molA%ftype
+      else
+         comb%ftype=molB%ftype
+      end if
+      call generateFileName(fin_name, 'best', '', comb%ftype)
+      call open_file(ifinal, fin_name, 'w')
+      call writeMolecule(comb, ifinal, energy=final_e(1))
+      !If not xyz then best.xyz is written to not have api break
+      if(comb%ftype /= 1)then
+         call open_file(ifinal, 'best.xyz', 'w')
+         write (ifinal, '(i0)') comb%n
+         write (ifinal, '(f20.14)') final_e(1)
+         do j = 1, comb%n
+            write (ifinal, '(a4,2x,3f20.14)') comb%sym(j), xyz_opt(1, j, 1)*autoang, &
+            &                                 xyz_opt(2, j, 1)*autoang, xyz_opt(3, j, 1)*autoang
+         end do
+      end if
       call close_file(ifinal)
+
+
       call delete_file(set%opt_logfile)
 
       !> Printout Interaction Energy

src/prog/main.F90

@@ -1553,7 +1553,7 @@ subroutine parseArguments(env, args, inputFile, paramFile, lgrad, &
       case('--cut')
          call set_cut
 
-      case('--etemp')
+      case('--etemp', '--temp')
          call args%nextArg(sec)
          if (allocated(sec)) then
             call set_scc(env,'temp',sec)
@@ -1635,7 +1635,7 @@ subroutine parseArguments(env, args, inputFile, paramFile, lgrad, &
          call set_write(env,'fod','true')
          call set_scc(env,'temp','5000.0')
 
-      case('--iterations')
+      case('--iterations', '--maxiterations')
          call args%nextArg(sec)
          if (allocated(sec)) then
             call set_scc(env,'maxiterations',sec)

src/set_module.f90

@@ -1520,7 +1520,7 @@ subroutine set_scc(env,key,val)
    select case(key)
    case default ! do nothing
       call env%warning("the key '"//key//"' is not recognized by scc",source)
-   case('temp')
+   case('etemp','temp')
       if (getValue(env,val,ddum).and.set1) set%eTemp = ddum
       set1 = .false.
    case('broydamp')
@@ -1538,7 +1538,7 @@ subroutine set_scc(env,key,val)
          set%guess_charges = p_guess_multieq
       endif
       set3 = .false.
-   case('maxiterations')
+   case('iterations','maxiterations')
       if (getValue(env,val,idum).and.set4) then
          if (idum.le.0) then
             call env%warning('negative SCC-Iterations make no sense',source)