Separated wrap option to reduce opy and pasted code. Fixed warnings and added wrapping when inserting a dislocation or loop

src/elements.f90

@@ -41,6 +41,8 @@ module elements
     integer :: basis_type(10,10)
     real(kind=dp) :: lapa(10)
 
+    !Additional module level variables we need 
+    logical :: wrap_flag
     public 
     contains
 
@@ -313,7 +315,7 @@ module elements
         real(kind=dp), dimension(3, max_basisnum*max_esize**3), intent(out) :: r_interp !Interpolated atomic positions
 
         !Internal variables
-        integer :: i, it, is, ir, ibasis, inod, ia, bnum, lat_type_temp
+        integer :: it, is, ir, ibasis, inod, ia, bnum, lat_type_temp
         real(kind=dp), allocatable :: a_shape(:)
         real(kind=dp) :: t, s, r
         
@@ -390,7 +392,7 @@ module elements
         integer, intent(in) :: num
         integer, intent(inout), dimension(num) :: index
 
-        integer :: i, j
+        integer :: i
 
         call heapsort(index)
 
@@ -413,7 +415,7 @@ module elements
         integer, intent(in) :: num
         integer, intent(inout), dimension(num) :: index
 
-        integer :: i, j
+        integer :: i
 
         call heapsort(index)
 
@@ -436,5 +438,15 @@ module elements
             end if            
             ele_num = ele_num - 1
         end do 
+
     end subroutine delete_elements
+
+    subroutine wrap_atoms
+        !This subroutine wraps atoms back into the simulation cell if they have exited for any reason
+        integer :: i
+        do i = 1, atom_num
+            call apply_periodic(r_atom(:,i))
+        end do 
+    end subroutine wrap_atoms
+
 end module elements