let basis_file : string option ref = ref None
let coord_file : string option ref = ref None


let speclist = [
( "-b" , Arg.String (fun x -> basis_file := Some x) ,
  "File containing the atomic basis set.") ;
( "-c" , Arg.String (fun x -> coord_file := Some x) ,
  "File containing the nuclear coordinates.") ;
]

let run ~coord ~basis =
  let coord_file = 
    match coord with 
    | None -> raise (Invalid_argument "Coordinate file should be specified")
    | Some x -> x
  and basis_file = 
    match basis with 
    | None -> raise (Invalid_argument "Basis set file should be specified")
    | Some x -> x
  in
  let nuclei = 
    Nuclei.of_xyz_file ~filename:coord_file
  and general_basis =
    Gamess_reader.read ~filename:basis_file
  in
  let basis =
    Basis.of_nuclei_and_general_basis nuclei general_basis
  in
  Array.map Basis.to_string basis
  |> Array.iter print_endline 


let () =
  let usage_msg = "Quantum Chemistry Package. Options available:" in
  Arg.parse speclist (fun _ -> ()) usage_msg;
  run ~coord:!coord_file ~basis:!basis_file