Allow setting neighbors to 0 via detailed input

src/approxrab.f90

@@ -46,7 +46,7 @@ module xtb_approxrab
       2.75372921, 2.62540906, 2.55860939, 3.32492356, 2.65140898,& ! 80
       1.52014458, 2.54984804, 1.72021963, 2.69303422, 1.81031095,&
       2.34224386,&
-      2.52387890,& !@thomas TODO
+      2.52387890,&
       2.30204667, 1.60119300, 2.00000000, 2.00000000, 2.00000000,& ! 92
       2.00000000, 2.00000000, 2.00000000, 2.00000000, 2.00000000,&
       2.00000000, 2.00000000, 2.00000000, 2.00000000, 2.00000000,& ! 102
@@ -71,7 +71,7 @@ module xtb_approxrab
       2.33473532, 2.19498900, 2.12678348, 2.34895048, 2.33422774,&
       2.86560827, 2.62488837, 2.88376127, 2.75174124, 2.83054552,&
       2.63264944,&
-      4.24537037,& !@thomas TODO
+      4.24537037,&
       3.66542289, 4.20000000, 4.20000000, 4.20000000, 4.20000000,& ! 92
       4.20000000, 4.20000000, 4.20000000, 4.20000000, 4.20000000,&
       4.20000000, 4.20000000, 4.20000000, 4.20000000, 4.20000000,& ! 102
@@ -96,7 +96,7 @@ module xtb_approxrab
       0.04671159, 0.06758819, 0.09488437, 0.07556405, 0.13384502,& ! 90
       0.03203572, 0.04235009, 0.03153769,-0.00152488, 0.02714675,&
       0.04800662,&
-      0.04582912,& !@thomas TODO
+      0.04582912,&
       0.10557321, 0.02167468, 0.05463616, 0.05370913, 0.05985441,& ! 92
       0.02793994, 0.02922983, 0.02220438, 0.03340460,-0.04110969,&
      -0.01987240, 0.07260201, 0.07700000, 0.07700000, 0.07700000,& ! 102

src/gfnff/gfnff_ini.f90

@@ -2452,10 +2452,10 @@ subroutine gfnff_topo_changes(env, neigh)
    ! check if hardcoded size of ffnb is still up to date
    if (size(set%ffnb, dim=1).ne.neigh%numnb) call env%error('The array set%ffnb has not been adjusted to changes in neigh%numnb.', source)
    ! only do something if there are changes stored in set%ffnb
-   if(set%ffnb(1,1).ne.0) then
+   if(set%ffnb(1,1).ne.-1) then
       d2=size(set%ffnb, dim=2)
       do i=1, d2
-         if (set%ffnb(1,i).eq.0) exit
+         if (set%ffnb(1,i).eq.-1) exit
          idx=set%ffnb(1,i)
          int_tmp = set%ffnb(2:41,i)
          neigh%nb(1:40,idx,1) = int_tmp

src/set_module.f90

@@ -1508,16 +1508,18 @@ subroutine set_ffnb(env,key,val)
    character(len=*),intent(in) :: val
    integer :: i,j,k,l
    integer :: i_start,i_end,i_ffnb
+   logical :: nonb
 
    k=1 ! start at 1 since first entry of ffnb is the atom index that the following NBs belong to
    i_start=1
    i_end=1
    i_ffnb=0
+   nonb = .false. ! expect that the atom should have neighbors
    do i=1, len(val)
       ! get next empty row in ffnb and read atom index into first entry
       if (val(i:i).eq.":") then
          do j=1,size(set%ffnb, dim=2)
-           if (set%ffnb(1,j).eq.0 .and. i_ffnb.eq.0) then
+           if (set%ffnb(1,j).eq.-1 .and. i_ffnb.eq.0) then
               i_ffnb = j ! index of next empty row
               l=i-1
               ! we take care of ":" and "," and trust read() to handle whitespaces
@@ -1531,17 +1533,30 @@ subroutine set_ffnb(env,key,val)
       if (val(i:i).eq.",") then
          k = k + 1
          i_end=i-1
-             read(val(i_start:i_end), *) set%ffnb(k,i_ffnb)
-             i_start=i+1
+         read(val(i_start:i_end), *) set%ffnb(k,i_ffnb)
+         ! if the first neighbor index (k=2) is zero the atom (k=1) has no neighbors
+         if (set%ffnb(k,i_ffnb) == 0 .and. k == 2) then
+           nonb = .true.
+         endif
+         i_start=i+1
       endif
       ! read the last neighbor into ffnb
       if (i.eq.len(val)) then
          k = k + 1
          read(val(i_start:), *) set%ffnb(k,i_ffnb)
+         ! if the first neighbor index (k=2) is zero the atom (k=1) has no neighbors
+         if (set%ffnb(k,i_ffnb) == 0 .and. k == 2) then
+           nonb = .true.
+         endif
+         ! set rest of ffnb to 0
+         set%ffnb(k+1:41, i_ffnb) = 0
       endif
    enddo
-   set%ffnb(42,i_ffnb) = k - 1 ! number of neighbors of atom set%ffnb(1,i_ffnb) 
-
+   if (nonb) then
+     set%ffnb(2:,i_ffnb) = 0
+   else
+     set%ffnb(42,i_ffnb) = k - 1 ! number of neighbors of atom set%ffnb(1,i_ffnb) 
+   endif
 
 end subroutine set_ffnb
 

src/setparam.f90

@@ -519,7 +519,7 @@ module xtb_setparam
    !> GFN-FF manual setup of nb list via xcontrol
    !  allows a maximum of 164 atoms neighbors to be changed
    !  ffnb(42,i) stores the number of neighbors of atom i
-   integer :: ffnb(42,164) = 0
+   integer :: ffnb(42,164) = -1
    end type TSet
 
    type(TSet) :: set