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131 lines
3.3 KiB
OCaml
131 lines
3.3 KiB
OCaml
open Util
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open Xyz_ast
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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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let data =
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Xyz_parser.input Nuclei_lexer.read_all lexbuf
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in
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let len = List.length data.nuclei in
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if len <> data.number_of_atoms then
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Printf.sprintf "Error: expected %d atoms but %d read"
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data.number_of_atoms len
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|> failwith;
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List.map (fun nucleus ->
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nucleus.element, Coordinate.angstrom_to_bohr nucleus.coord
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) data.nuclei
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|> Array.of_list
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let of_zmt_string buffer =
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Zmatrix.of_string buffer
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|> Zmatrix.to_xyz
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|> Array.map (fun (e,x,y,z) -> (e, Coordinate.angstrom_to_bohr (Angstrom.make {Point.x ; y ; z} )))
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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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|> of_zmt_string
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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.bohr_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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coord.Angstrom.x coord.Angstrom.y coord.Angstrom.z
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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 of_filename filename =
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of_xyz_file filename
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let repulsion nuclei =
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let get_charge e =
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Element.to_charge e
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|> Charge.to_float
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in
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Array.fold_left ( fun accu (e1, coord1) ->
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accu +.
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Array.fold_left (fun accu (e2, coord2) ->
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let r = Coordinate.(norm (coord1 |- coord2)) in
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if r > 0. then
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accu +. 0.5 *. (get_charge e2) *. (get_charge e1) /. r
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else accu
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) 0. nuclei
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) 0. nuclei
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let charge nuclei =
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Array.fold_left (fun accu (e, _) -> accu + Charge.to_int (Element.to_charge e) )
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0 nuclei
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|> Charge.of_int
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let to_xyz_string t =
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[ string_of_int (Array.length t) ; "" ] @
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( Array.mapi (fun i (e, coord) ->
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let coord =
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Coordinate.bohr_to_angstrom coord
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in
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Printf.sprintf " %5s %12.6f %12.6f %12.6f"
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(Element.to_string e) coord.Angstrom.x coord.Angstrom.y coord.Angstrom.z
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) t
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|> Array.to_list )
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|> String.concat "\n"
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let to_t2_string t =
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[ "# nAt nEl nCore nRyd" ;
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Printf.sprintf " %d %d %d 0" (Array.length t)
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(Array.fold_left (+) 0 (Array.map (fun (e,_) -> Element.to_int e) t) )
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(2 * Array.length t);
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"# Znuc x y z" ]
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@ (Array.mapi (fun i (e, coord) ->
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Printf.sprintf " %5f %12.6f %12.6f %12.6f"
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(Element.to_int e |> float_of_int) coord.Bohr.x coord.Bohr.y coord.Bohr.z
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) t
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|> Array.to_list )
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|> String.concat "\n"
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let small_core a =
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Array.fold_left (fun accu (e,_) -> accu + (Element.small_core e)) 0 a
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