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63 lines
1.6 KiB
OCaml
63 lines
1.6 KiB
OCaml
type t = (Element.t * Coordinate.t) array
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let of_xyz_file ~filename =
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let lexbuf =
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let ic = open_in filename in
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Lexing.from_channel ic
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in
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Xyz_parser.input Nuclei_lexer.read_all lexbuf
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let of_zmt_file ~filename =
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let ic = open_in filename in
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let rec aux accu =
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try
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let line = input_line ic in
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aux (line::accu)
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with End_of_file ->
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close_in ic;
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List.rev accu
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|> String.concat "\n"
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in aux []
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|> Zmatrix.of_string
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|> Zmatrix.to_xyz
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|> Array.map (fun (e,x,y,z) -> (e, Coordinate.of_3_floats x y z ))
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let to_string atoms =
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"
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Nuclear Coordinates (Angstrom)
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------------------------------
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-----------------------------------------------------------------------
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Center Atomic Element Coordinates (Angstroms)
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Number X Y Z
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-----------------------------------------------------------------------
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" ^
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(Array.mapi (fun i (e, coord) ->
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let coord =
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Coordinate.to_Angstrom coord
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in
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Printf.sprintf " %5d %5d %5s %12.6f %12.6f %12.6f"
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(i+1) (Element.to_int e) (Element.to_string e)
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(Coordinate.x coord) (Coordinate.y coord) (Coordinate.z coord)
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) atoms
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|> Array.to_list
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|> String.concat "\n" ) ^
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"
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-----------------------------------------------------------------------
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"
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let file : string option ref = ref None
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let set_file f =
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file := Some f
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let nuclei = lazy(
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match !file with
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| None -> failwith "coordinate file not defined"
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| Some filename -> of_xyz_file ~filename
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)
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