Added sbox_ori option for when reading in restart files

README.md

@@ -277,6 +277,14 @@ Delete requires the usage of additional keywords to specify which delete action
 
 This command will delete all overlapping atoms within a specific cutoff radius `rc_off`. This currently does not affect elements. 
 
+### Option sbox_ori
+
+```
+-sbox_ori sbox [hkl] [hkl] [hkl]
+```
+
+This option is primarily used when reading data from non .mb formats. This code simply sets the orientation variable for the specified sub box `sbox`.
+
 ****
 
 ## Position Specification

src/call_option.f90

@@ -29,6 +29,8 @@ subroutine call_option(option, arg_pos)
         call get_command_argument(arg_pos, box_bc)
         arg_pos=arg_pos+1
         bound_called = .true.
+    case('-sbox_ori')
+        call sbox_ori(arg_pos)
     case('-delete')
         call run_delete(arg_pos)
     case default

src/opt_orient.f90

@@ -133,4 +133,29 @@ module opt_orient
         box_bd = orig_box_bd
     end subroutine unorient
 
+    subroutine sbox_ori(arg_pos)
+        integer, intent(inout) :: arg_pos
+
+        integer :: i, sbox_in, arg_len
+        real(kind = dp) :: new_orient(3,3)
+        character(len=100) :: textholder 
+        character(len=8) :: ori_string
+
+        arg_pos = arg_pos + 1
+        call get_command_argument(arg_pos, textholder,arg_len)
+        if (arg_len== 0) stop 'Missing sbox in sbox_ori command'
+        read(textholder,*) sbox_in
+
+        do i = 1, 3
+            arg_pos = arg_pos + 1
+            call get_command_argument(arg_pos, ori_string, arg_len)
+            if (arg_len == 0) print *, "Missing orientation vector in -orient option"
+            call parse_ori_vec(ori_string, new_orient(i,:))
+            new_orient(i,:) = new_orient(i,:) / norm2(new_orient(i,:))
+        end do
+
+        sub_box_ori(:,:,sbox_in) = new_orient
+        arg_pos = arg_pos + 1
+
+    end subroutine sbox_ori
 end module opt_orient