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

src/call_option.f90

@@ -15,8 +15,11 @@ subroutine call_option(option, arg_pos)
     case('-ow')
         arg_pos = arg_pos + 1
         continue
-    case default
+    case('-wrap')
-        print *, 'Option ', trim(adjustl(option)), ' is not currently accepted. Skipping to next argument'
         arg_pos = arg_pos + 1
+        continue
+    case default
+        print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.'
+        stop 3 
     end select
 end subroutine call_option

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

src/io.f90

@@ -363,7 +363,7 @@ module io
         !NOTE: This code doesn't work for arbitrary number of basis atoms per node. It assumes that the 
         !each element has only 1 atom type at the node.
         character(len=100), intent(in) :: file
-        integer :: interp_max, i, j, lat_size, inod, ibasis, ip, unique_index(10), unique_num
+        integer :: interp_max, i, j, inod, ibasis, ip, unique_index(10), unique_num
         real(kind=dp) :: box_vec(3)
 
 1  format('time' / i16, f23.15)

src/main.f90

@@ -39,20 +39,27 @@ program main
     call box_init
     call random_seed
     force_overwrite=.false.
+    wrap_flag = .false.
 
     end_mode_arg = 0
     
     ! Command line parsing
     arg_num = command_argument_count()
 
-    !Check to see if overwrite flag is passed
+    !First check to see if certain commands are passed, these commands must be known before code 
+    !is executed.
     do i = 1, arg_num
         call get_command_argument(i,argument)
         select case(trim(adjustl(argument)))
 
+        !This lets us know if we are overwriting all files
         case('-ow')
             force_overwrite = .true.
             print *, "Overwrite flag passed, output files will be overwritten"
+
+        !This lets us know if we need to wrap atomic positions back into the cell
+        case('-wrap')
+            wrap_flag=.true.
         end select 
     end do 
     !Determine if a mode is being used and what it is. The first argument has to be the mode
@@ -86,11 +93,14 @@ program main
             call call_option(argument, arg_pos)
         !Otherwise print that the argument is not accepted and move on
         else
-            print *, trim(adjustl(argument)), " is not accepted. Skipping to next argument"
+            print *, trim(adjustl(argument)), " is not an accepted command."
-            arg_pos = arg_pos + 1
+            stop 3
         end if
     end do
 
+    !If wrap flag was passed then call the wrap atoms command
+    if(wrap_flag) call wrap_atoms
+
     !Check to make sure a file was passed to be written out and then write out 
             ! Before building do a check on the file
     if (outfilenum == 0) then

src/mode_convert.f90

@@ -11,7 +11,7 @@ module mode_convert
     subroutine convert(arg_pos)
         !This subroutine converts a single input file from one format to another
         integer, intent(out) :: arg_pos
-        character(len=100) :: infile, outfile
+        character(len=100) :: infile
         real(kind = dp) :: temp_box_bd(6)
         !First read in the file
         call get_command_argument(2, infile)

src/mode_create.f90

@@ -24,7 +24,6 @@ module mode_create
     subroutine create(arg_pos)
         ! Main subroutine which controls execution
 
-        character(len=100) :: textholder
         integer, intent(out) :: arg_pos
 
         integer :: i, ibasis, inod
@@ -128,7 +127,8 @@ module mode_create
             !Now that it is built multiply by the lattice parameter
             box_bd = box_bd*lattice_parameter
 
-            print *, "Using mode create, ", lat_ele_num, " elements are created and ", lat_atom_num*basisnum(1), " atoms are created."
+            print *, "Using mode create, ", lat_ele_num, " elements are created and ", lat_atom_num*basisnum(1), &
+                     " atoms are created."
 
             !Allocate variables 
             call alloc_ele_arrays(lat_ele_num, lat_atom_num*basisnum(1))
@@ -309,7 +309,6 @@ module mode_create
         integer :: i,  inod, bd_in_lat(6), bd_in_array(6), ix, iy, iz,  numlatpoints, ele(3,8), rzero(3), &
                    vlat(3), temp_lat(3,8), m, n, o
         real(kind=dp) :: v(3), temp_nodes(3,1,8)
-        real(kind=dp), allocatable :: resize_lat_array(:,:)
         logical, allocatable :: lat_points(:,:,:)
         logical :: node_in_bd(8)
 

src/mode_merge.f90

@@ -10,7 +10,7 @@ module mode_merge
     character(len=4) :: dim
     integer :: in_num, new_starts(2)
     real(kind=dp) :: shift_vec(3)
-    logical :: wrap, shift_flag
+    logical :: shift_flag
 
     public 
     contains
@@ -22,7 +22,6 @@ module mode_merge
 
         print *, '-----------------------Mode Merge---------------------------'
         
-        wrap = .false.
         shift_flag = .false.
 
         shift_vec(:) = 0.0_dp
@@ -115,8 +114,6 @@ module mode_merge
                     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 
@@ -126,13 +123,12 @@ module mode_merge
     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 
+        !This subroutine applies a shift to newly added atoms and elements.  
-        !if the user provides the wrap flag
 
         integer, dimension(2), intent(in) :: array_start
         integer, intent(in) :: filenum
 
-        integer :: i, j, ibasis, inod
+        integer :: i, ibasis, inod
         real(kind=dp), dimension(3) :: current_shift
 
 
@@ -155,15 +151,8 @@ module mode_merge
             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
+        if(.not.(wrap_flag)) then 
             do i = 1,3
                 if (current_shift(i) < -lim_zero) then 
                     box_bd(2*i-1) = box_bd(2*i-1) - current_shift(i)

src/opt_disl.f90

@@ -47,8 +47,8 @@ module opt_disl
         integer, intent(inout) :: arg_pos
 
         integer :: i,arglen
-        character(len=8) :: ori_string
         character(len=100) :: textholder
+        character(len=8) :: ori_string
 
         !Parse all of the commands
         arg_pos = arg_pos + 1
@@ -180,6 +180,9 @@ module opt_disl
             end do
         end if
 
+        !Now make sure all atoms are wrapped back into the simulation cell
+        call wrap_atoms
+
     end subroutine dislgen
 
     subroutine parse_disloop(arg_pos)
@@ -187,8 +190,7 @@ module opt_disl
 
         integer, intent(inout) :: arg_pos
 
-        integer :: i,arglen, sbox
+        integer :: i,arglen
-        character(len=8) :: ori_string
         character(len=100) :: textholder
 
         !Parse all of the commands
@@ -392,6 +394,9 @@ module opt_disl
             end do 
         end do
         return
+
+        !Now make sure all atoms are wrapped back into the simulation cell
+        call wrap_atoms
     end subroutine
 
     !********************************************************

src/opt_group.f90

@@ -11,7 +11,7 @@ module opt_group
     integer :: group_ele_num, group_atom_num, remesh_size
     character(len=15) :: type, shape !Type indicates what element type is selected and shape is the group shape
     real(kind=dp) :: block_bd(6), disp_vec(3)
-    logical :: displace, wrap
+    logical :: displace
 
     integer, allocatable :: element_index(:), atom_index(:) 
 
@@ -96,8 +96,6 @@ module opt_group
                     if (arglen==0) stop "Missing vector component for shift command"
                     read(textholder, *) disp_vec(i)
                 end do
-            case('wrap')
-                wrap = .true.
             case('remesh')
                 arg_pos = arg_pos + 1
                 call get_command_argument(arg_pos, textholder, arglen)
@@ -192,16 +190,8 @@ module opt_group
             end do 
         end do
 
-        !Now either apply periodic boundaries if wrap command was passed or adjust box dimensions
-                !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 = 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
+        if (.not.(wrap_flag)) then 
             do i = 1,3
                 if (disp_vec(i) < -lim_zero) then 
                     box_bd(2*i-1) = box_bd(2*i-1) - disp_vec(i)
@@ -235,8 +225,8 @@ module opt_group
                     !Get the interpolated atom positions
                     call interpolate_atoms(type_ele(ie), size_ele(ie), lat_ele(ie), r_node(:,:,:,ie), type_interp, r_interp)
 
-                    !Loop over all interpolated atoms and add them to the system, we apply periodic boundaries here as well to make sure 
+                    !Loop over all interpolated atoms and add them to the system, we apply periodic boundaries 
-                    !they are in the box
+                    !here as well to make sure they are in the box
                     do j = 1, basisnum(lat_ele(ie))*size_ele(ie)**3
                         call apply_periodic(r_interp(:,j))
                         call add_atom(type_interp(j), r_interp(:,j))

src/subroutines.f90

@@ -5,6 +5,7 @@ module subroutines
     implicit none
 
     integer :: allostat, deallostat
+
     public
     contains