Working shift command for merge

src/io.f90

@@ -194,6 +194,7 @@ module io
             select case(trim(adjustl(type_ele(i))))
             case('fcc')
                 do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
+                    call apply_periodic(r_interp(:,iatom))
                     write(11, '(2i16, 3f23.15)') atom_num+iatom, type_interp(iatom), r_interp(:,iatom)
                 end do
             end select

src/mode_merge.f90

@@ -8,7 +8,9 @@ module mode_merge
     use elements
 
     character(len=4) :: dim
-    integer :: in_num
+    integer :: in_num, new_starts(2)
+    real(kind=dp) :: shift_vec(3)
+    logical :: wrap, shift_flag
 
     public 
     contains
@@ -18,12 +20,23 @@ module mode_merge
         integer :: i
         real(kind=dp) :: displace(3), temp_box_bd(6)
 
+        wrap = .false.
+        shift_flag = .false.
+
+        shift_vec(:) = 0.0_dp
         !First we parse the merge command
         call parse_command(arg_pos)
 
         !Now loop over all files and stack them 
         do i = 1, in_num
             displace(:) = 0.0_dp
+            
+            !The new starts variable dictate where in the atom and element array each new 
+            !file starts. This is used for additional options that can be applied to solely 
+            !these new atoms/elements that are read in.
+            new_starts(1) = atom_num + 1
+            new_starts(2) = ele_num + 1
+
             if ((i==1).or.(trim(adjustl(dim)) == 'none')) then 
                 call read_in(i, displace, temp_box_bd)
                 call grow_box(temp_box_bd)
@@ -40,6 +53,8 @@ module mode_merge
                 call read_in(i, displace, temp_box_bd)
                 call grow_box(temp_box_bd)
             end if 
+
+            if(shift_flag) call shift(new_starts, i)
         end do
 
         return
@@ -89,7 +104,16 @@ module mode_merge
 
             !Choose what to based on what the option string is 
             select case(trim(textholder))
-
+            case('shift')
+                shift_flag = .true.
+                do i = 1,3 
+                    arg_pos = arg_pos + 1
+                    call get_command_argument(arg_pos, textholder, arglen)
+                    if (arglen==0) stop "Missing vector component for shift command"
+                    read(textholder, *) shift_vec(i)
+                end do
+            case('wrap')
+                wrap = .true.
             case default
                 !If it isn't an available option to mode merge then we just exit
                 exit 
@@ -97,4 +121,52 @@ module mode_merge
         end do
 
     end subroutine parse_command
+
+    subroutine shift(array_start, filenum)
+        !This subroutine applies a shift to newly added atoms and elements. It also wraps the atoms 
+        !if the user provides the wrap flag
+
+        integer, dimension(2), intent(in) :: array_start
+        integer, intent(in) :: filenum
+
+        integer :: i, j, ibasis, inod
+        real(kind=dp), dimension(3) :: current_shift
+
+
+        !Calculate the current shift which is the filenum-1 multiplied by the user specified shift
+        current_shift = (filenum-1)*shift_vec
+
+        !First shift all the atoms
+        do i = array_start(1), atom_num
+            r_atom(:,i) = r_atom(:,i) + current_shift
+        end do 
+
+        !Now shift all the elements
+        do i = array_start(2), ele_num
+            do inod = 1, ng_node(lat_ele(i))
+                do ibasis = 1, basisnum(lat_ele(i))
+                    r_node(:,ibasis, inod, i) = r_node(:,ibasis, inod, i) + current_shift
+                end do
+            end do
+        end do
+
+        !Now we check if we have to wrap the atoms, nodes are not wrapped. For elements the periodic 
+        !boundary conditions are applied in the actual CAC codes
+        if(wrap) then   
+            do i = array_start(1), atom_num 
+                call apply_periodic(r_atom(:,i))
+            end do
+
+        !If we don't include the wrap command then we have to increase the size of the box
+        else
+            do i = 1,3
+                if (current_shift(i) < -lim_zero) then 
+                    box_bd(2*i-1) = box_bd(2*i-1) - current_shift(i)
+                else if (current_shift(i) > lim_zero) then 
+                    box_bd(2*i) = box_bd(2*i) + current_shift(i)
+                end if
+            end do
+        end if
+
+    end subroutine shift
 end module mode_merge

src/subroutines.f90

@@ -249,4 +249,23 @@ module subroutines
       end do      
      
     end subroutine siftdown
+
+
+    subroutine apply_periodic(r)
+        !This function checks if an atom is outside the box and wraps it back in. This is generally used when some 
+        !kind of displacement is applied but the simulation cell is desired to be maintained as the same size.
+
+        real(kind=dp), dimension(3), intent(inout) :: r
+
+        integer :: j 
+
+        do j = 1, 3
+            if (r(j) > box_bd(2*j)) then 
+                r(j) = r(j) - box_bd(2*j)
+            else if (r(j) < box_bd(2*j-1)) then 
+                r(j) = r(j) + box_bd(2*j-1)
+            end if
+        end do
+    end subroutine
+
 end module subroutines