Working commit for dislocation generation branch

src/main.f90

@@ -17,7 +17,7 @@ program main
     use io
     
 
-    integer ::  i, end_mode_arg, arg_num
+    integer ::  i, end_mode_arg, arg_num, arg_pos
     character(len=100) ::  argument
 
     !Call initialization functions
@@ -37,12 +37,25 @@ program main
     end if
 
     !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)
+    arg_pos = end_mode_arg
+    do while(.true.)
+        !Exit the loop if we are done reading
+        if(arg_pos > arg_num) exit
+
+        call get_command_argument(arg_pos, argument)
 
         !Check to see if a filename was passed
         if(scan(argument,'.',.true.) > 0) then 
             call get_out_file(argument)
+            arg_pos = arg_pos + 1
+
+        !Check to see if an option has been passed
+        else if(argument(1:1) == '-') then 
+            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
         end if
     end do