mirror of
https://gitlab.com/scemama/QCaml.git
synced 2024-12-23 04:43:32 +01:00
131 lines
3.3 KiB
OCaml
131 lines
3.3 KiB
OCaml
open Util
|
|
open Xyz_ast
|
|
|
|
type t = (Element.t * Coordinate.t) array
|
|
|
|
let of_xyz_file filename =
|
|
let lexbuf =
|
|
let ic = open_in filename in
|
|
Lexing.from_channel ic
|
|
in
|
|
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_zmt_string buffer =
|
|
Zmatrix.of_string buffer
|
|
|> Zmatrix.to_xyz
|
|
|> Array.map (fun (e,x,y,z) -> (e, Coordinate.angstrom_to_bohr (Angstrom.make {Point.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 coord =
|
|
Coordinate.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.Angstrom.x coord.Angstrom.y coord.Angstrom.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.mapi (fun i (e, coord) ->
|
|
let coord =
|
|
Coordinate.bohr_to_angstrom coord
|
|
in
|
|
Printf.sprintf " %5s %12.6f %12.6f %12.6f"
|
|
(Element.to_string e) coord.Angstrom.x coord.Angstrom.y coord.Angstrom.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.mapi (fun i (e, coord) ->
|
|
Printf.sprintf " %5f %12.6f %12.6f %12.6f"
|
|
(Element.to_int e |> float_of_int) coord.Bohr.x coord.Bohr.y coord.Bohr.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
|
|
|
|
|