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

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"
-            arg_pos = arg_pos + 1
+            print *, trim(adjustl(argument)), " is not an accepted command."
+            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