open Common open Xyz_ast type t = (Element.t * Coordinate.t) array let of_xyz_lexbuf lexbuf = let data = Xyz_parser.input Nuclei_lexer.read_all lexbuf in let len = List.length data.nuclei in if len <> data.number_of_atoms then Printf.sprintf "Error: expected %d atoms but %d read" data.number_of_atoms len |> failwith; List.map (fun nucleus -> nucleus.element, Coordinate.angstrom_to_bohr nucleus.coord ) data.nuclei |> Array.of_list let of_xyz_string input_string = Lexing.from_string input_string |> of_xyz_lexbuf let of_xyz_file filename = let ic = open_in filename in let lexbuf = Lexing.from_channel ic in let result = of_xyz_lexbuf lexbuf in close_in ic; result let of_zmt_string buffer = Zmatrix.of_string buffer |> Zmatrix.to_xyz |> Array.map (fun (e,x,y,z) -> (e, Coordinate.(angstrom_to_bohr @@ make_angstrom { x ; y ; z} )) ) let of_zmt_file filename = let ic = open_in filename in let rec aux accu = try let line = input_line ic in aux (line::accu) with End_of_file -> close_in ic; List.rev accu |> String.concat "\n" in aux [] |> of_zmt_string let to_string atoms = " Nuclear Coordinates (Angstrom) ------------------------------ ----------------------------------------------------------------------- Center Atomic Element Coordinates (Angstroms) Number X Y Z ----------------------------------------------------------------------- " ^ (Array.mapi (fun i (e, coord) -> let open Coordinate in let coord = bohr_to_angstrom coord in Printf.sprintf " %5d %5d %5s %12.6f %12.6f %12.6f" (i+1) (Element.to_int e) (Element.to_string e) coord.x coord.y coord.z ) atoms |> Array.to_list |> String.concat "\n" ) ^ " ----------------------------------------------------------------------- " let of_filename filename = of_xyz_file filename let repulsion nuclei = let get_charge e = Element.to_charge e |> Charge.to_float in Array.fold_left ( fun accu (e1, coord1) -> accu +. Array.fold_left (fun accu (e2, coord2) -> let r = Coordinate.(norm (coord1 |- coord2)) in if r > 0. then accu +. 0.5 *. (get_charge e2) *. (get_charge e1) /. r else accu ) 0. nuclei ) 0. nuclei let charge nuclei = Array.fold_left (fun accu (e, _) -> accu + Charge.to_int (Element.to_charge e) ) 0 nuclei |> Charge.of_int let to_xyz_string t = [ string_of_int (Array.length t) ; "" ] @ ( Array.map (fun (e, coord) -> let open Coordinate in let coord = bohr_to_angstrom coord in Printf.sprintf " %5s %12.6f %12.6f %12.6f" (Element.to_string e) coord.x coord.y coord.z ) t |> Array.to_list ) |> String.concat "\n" let to_t2_string t = [ "# nAt nEl nCore nRyd" ; Printf.sprintf " %d %d %d 0" (Array.length t) (Array.fold_left (+) 0 (Array.map (fun (e,_) -> Element.to_int e) t) ) (2 * Array.length t); "# Znuc x y z" ] @ (Array.map (fun (e, coord) -> let open Coordinate in Printf.sprintf " %5f %12.6f %12.6f %12.6f" (Element.to_int e |> float_of_int) coord.x coord.y coord.z ) t |> Array.to_list ) |> String.concat "\n" let small_core a = Array.fold_left (fun accu (e,_) -> accu + (Element.small_core e)) 0 a