Merge branch 'development' into 'main'

Development

See merge request hepplestone/artemis!11

Author: nedttaylor

src/interfaces.f90

@@ -43,7 +43,7 @@ subroutine gen_terminations(lat,bas,miller_plane,axis,directory,&
        thickness,udef_layer_sep)
     implicit none
     integer :: unit
-    integer :: itmp1,j,iterm,term_start,term_end,iterm_step
+    integer :: itmp1,iterm,term_start,term_end,iterm_step
     integer :: old_natom,ncells,thickness_val,ntrans
     double precision :: height
     character(len=1024) :: dirname,filename,pwd
@@ -264,9 +264,9 @@ end subroutine gen_interfaces_restart
 !!!#############################################################################
   subroutine gen_interfaces(tolerance,inlw_lat,inup_lat,inlw_bas,inup_bas)
     implicit none
-    integer :: i,j,iterm,jterm,ntrans,ifit,iunique,old_natom,itmp1,old_intf
+    integer :: j,iterm,jterm,ntrans,ifit,iunique,old_natom,itmp1,old_intf
     integer :: iterm_step,jterm_step
-    integer :: lw_ncells,up_ncells,istep
+    integer :: lw_ncells,up_ncells
     integer :: lw_layered_axis,up_layered_axis
     integer :: intf_start,intf_end
     integer :: lw_term_start,lw_term_end,up_term_start,up_term_end
@@ -872,7 +872,7 @@ subroutine gen_shifts_and_swaps(lat,bas,axis,intf_loc,bond,&
 !!!-----------------------------------------------------------------------------
 !!! Generates sets of shifts based on shift version
 !!!-----------------------------------------------------------------------------
-    if(ishift.eq.0) allocate(output_shifts(nshift,3))
+    if(ishift.eq.0.or.ishift.eq.1) allocate(output_shifts(nshift,3))
     select case(ishift)
     case(1)
        output_shifts(1,:3)=0.D0
@@ -1469,7 +1469,7 @@ subroutine prepare_slab(lat, bas, map, term, iterm, thickness, ncells, &
           end if
        end do ortho_check
     end if
-    call normalise_basis(bas,dtmp=0.9999D0,lfloor=.true.)
+    call normalise_basis(bas,dtmp=0.9999D0,lfloor=.true.,zero_round=0.D0)
 
 
   end subroutine prepare_slab

src/lib/mod_edit_geom.f90

@@ -180,6 +180,11 @@ function get_min_bulk_bond(lat,bas) result(min_bond)
 
 
     min_bond=huge(0.D0)
+    if(bas%natom.eq.1)then
+       min_bond = min(modu(lat(1,:3)),modu(lat(2,:3)),modu(lat(3,:3)))
+       return
+    end if
+
     do is=1,bas%nspec
        do ia=1,bas%spec(is)%num
 
@@ -199,7 +204,6 @@ function get_min_bulk_bond(lat,bas) result(min_bond)
        end do
     end do
 
-
   end function get_min_bulk_bond
 !!!#############################################################################
 
@@ -891,12 +895,11 @@ end subroutine region_rot
 !!!#############################################################################
 !!! convert basis coordinates to be within +val -> val-1
 !!!#############################################################################
-!!! MAKE AN OPTIONAL SETTING TO MOVE CLOSES ATOM TO ZERO TO ACTUAL ZERO
-  subroutine normalise_basis(bas,dtmp,lfloor,lround)
+  subroutine normalise_basis(bas,dtmp,lfloor,lround,zero_round)
     implicit none
     integer :: is,ia,j
     double precision :: ceil,flr,dround
-    double precision, optional :: dtmp
+    double precision, optional :: dtmp, zero_round
     type(bas_type) :: bas
     logical :: lfloor1,lround1
     logical, optional :: lfloor,lround
@@ -926,6 +929,10 @@ subroutine normalise_basis(bas,dtmp,lfloor,lround)
                      abs(bas%spec(is)%atom(ia,j)).lt.dround) &
                      bas%spec(is)%atom(ia,j)=flr
              end if
+             if(present(zero_round))then
+                if(abs(bas%spec(is)%atom(ia,j)).lt.dround) &
+                     bas%spec(is)%atom(ia,j)=zero_round
+             end if
           end do
        end do
     end do

src/mod_shifting.f90

@@ -745,11 +745,11 @@ function get_shifts_DON(lat,bas,axis,intf_loc,nstore,c_scale,offset,&
     use edit_geom, only: get_bulk,wyck_spec_type,get_wyckoff
     use interface_identifier, only: gen_single_DON,nstep_default,den_of_neigh_type
     implicit none
-    integer :: i,j,k,l,is,ia,ja,jb,jc,count1,itmp1,itmp2
+    integer :: i,j,k,l,is,ia,ja,jb,jc,count1,itmp1
     integer :: ntrans,iatom,nneigh,ncheck
     real :: stepsize,max_sep,dist_max
     real :: rtmp1,rtmp2,rtmp3
-    double precision :: bond,depth,cur_vac,c_shift,val,dtmp1,dtmp2
+    double precision :: val,dtmp1,dtmp2
     logical :: lbulk, lpresent
     type(confine_type) :: confine
     integer, dimension(2) :: plane_loc