Restructure the command parsing loops so the mode commands only parse the mode options

src/main.f90

@@ -17,8 +17,8 @@ program main
     use io
     
 
-    integer ::  arg_num
-    character(len=100) ::  mode
+    integer ::  i, end_mode_arg, arg_num
+    character(len=100) ::  argument
 
     !Call initialization functions
     call lattice_init
@@ -29,13 +29,29 @@ program main
 
     !Determine if a mode is being used and what it is. The first argument has to be the mode
     !if a mode is being used
-    call get_command_argument(1, mode)
+    call get_command_argument(1, argument)
 
-    mode = trim(adjustl(mode))
-    if (mode(1:2) == '--') then 
-        call call_mode(arg_num, mode)
+    argument = trim(adjustl(argument))
+    if (argument(1:2) == '--') then 
+        call call_mode(end_mode_arg, argument)
     end if
 
-    !Finish by writing the files
+    !Now we loop through all of the arguments and check for passed options or for a filename to be written out
+    do i = end_mode_arg-1, arg_num
+        call get_command_argument(i, argument)
+
+        !Check to see if a filename was passed
+        if(scan(argument,'.',.true.) > 0) then 
+            call get_out_file(argument)
+        end if
+    end do
+
+    !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
+        argument = 'none'
+        call get_out_file(argument)
+    end if
     call write_out
+
 end program main