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Added nuclei.org
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parent
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@ -1,8 +1,21 @@
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(* [[file:../nuclei.org::*Type][Type:2]] *)
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open Common
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open Xyz_ast
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type t = (Element.t * Coordinate.t) array
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open Xyz_ast
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(* Type:2 ends here *)
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(* | ~of_xyz_string~ | Create from a string, in xyz format |
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* | ~of_xyz_file~ | Create from a file, in xyz format |
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* | ~of_zmt_string~ | Create from a string, in z-matrix format |
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* | ~of_zmt_file~ | Create from a file, in z-matrix format |
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* | ~to_string~ | Transform to a string, for printing |
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* | ~of_filename~ | Detects the type of file (xyz, z-matrix) and reads the file | *)
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(* [[file:../nuclei.org::*Conversion][Conversion:2]] *)
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let of_xyz_lexbuf lexbuf =
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let data =
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Xyz_parser.input Nuclei_lexer.read_all lexbuf
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@ -41,9 +54,9 @@ 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) ->
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(e, Coordinate.(angstrom_to_bohr @@ make_angstrom { x ; y ; z} ))
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)
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(e, Coordinate.(angstrom_to_bohr @@ make_angstrom { x ; y ; z} ))
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)
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let of_zmt_file filename =
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let ic = open_in filename in
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@ -56,11 +69,11 @@ let of_zmt_file filename =
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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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|> of_zmt_string
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let to_string atoms =
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"
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"
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Nuclear Coordinates (Angstrom)
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------------------------------
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@ -69,27 +82,50 @@ let to_string atoms =
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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 open Coordinate in
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let coord =
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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.x coord.y coord.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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(Array.mapi (fun i (e, coord) ->
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let open Coordinate in
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let coord =
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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.x coord.y coord.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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of_xyz_file filename
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let to_xyz_string t =
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[ string_of_int (Array.length t) ; "" ] @
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( Array.map (fun (e, coord) ->
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let open Coordinate in
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let coord =
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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.x coord.y coord.z
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) t
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|> Array.to_list )
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|> String.concat "\n"
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(* Conversion:2 ends here *)
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(* | ~repulsion~ | Nuclear repulsion energy, in atomic units |
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* | ~charge~ | Sum of the charges of the nuclei |
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* | ~small_core~ | Number of core electrons in the small core model |
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* | ~large_core~ | Number of core electrons in the large core model | *)
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(* [[file:../nuclei.org::*Query][Query:2]] *)
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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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@ -100,10 +136,10 @@ let repulsion nuclei =
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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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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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) 0. nuclei
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) 0. nuclei
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let charge nuclei =
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@ -112,36 +148,15 @@ let charge 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.map (fun (e, coord) ->
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let open Coordinate in
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let coord =
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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.x coord.y coord.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.map (fun (e, coord) ->
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let open Coordinate in
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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.x coord.y coord.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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let large_core a =
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Array.fold_left (fun accu (e,_) -> accu + (Element.large_core e)) 0 a
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(* Query:2 ends here *)
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(* [[file:../nuclei.org::*Printers][Printers:2]] *)
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let pp ppf t =
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Format.fprintf ppf "@[%s@]" (to_string t)
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(* Printers:2 ends here *)
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@ -1,39 +1,42 @@
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(** Data structure for the molecular geometry, represented as an array
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of tuples ({!Element.t}, {!Coordinate.t}).
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*)
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(* Type
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*
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* #+NAME: types *)
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(* [[file:../nuclei.org::types][types]] *)
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open Common
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type t = (Element.t * Coordinate.t) array
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(* types ends here *)
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(* Conversion *)
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(* [[file:../nuclei.org::*Conversion][Conversion:1]] *)
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val of_xyz_string : string -> t
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(** Create from a string, in [xyz] format. *)
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val of_xyz_file : string -> t
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(** Create from a file, in [xyz] format. *)
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val to_xyz_string : t -> string
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val of_xyz_file : string -> t
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val of_zmt_string : string -> t
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(** Create from a string, in z-matrix format. *)
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val of_zmt_file : string -> t
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val of_zmt_file : string -> t
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(** Create from a file, in z-matrix format. *)
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val to_string : t -> string
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(** Transform to a string, for printing. *)
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val to_string : t -> string
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val of_filename : string -> t
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(** Detects the type of file ([xyz], z-matrix) and reads the file. *)
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(* Conversion:1 ends here *)
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(* Query *)
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val repulsion : t -> float
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(** Nuclear repulsion energy, in atomic units. *)
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val charge : t -> Charge.t
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(** Sum of the charges of the nuclei. *)
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(* [[file:../nuclei.org::*Query][Query:1]] *)
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val repulsion : t -> float
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val charge : t -> Charge.t
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val small_core : t -> int
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(** Number of core electrons in the small core model. *)
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val large_core : t -> int
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(* Query:1 ends here *)
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val to_xyz_string : t -> string
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val to_t2_string : t -> string
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(* Printers *)
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(* [[file:../nuclei.org::*Printers][Printers:1]] *)
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val pp : Format.formatter -> t -> unit
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(* Printers:1 ends here *)
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@ -1,3 +1,10 @@
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(* Lexer
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*
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* =nuclei_lexer.mll= contains the description of the lexemes used in
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* an xyz file. *)
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(* [[file:../nuclei.org::*Lexer][Lexer:1]] *)
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{
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open Xyz_parser
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}
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@ -6,8 +13,8 @@ let eol = ['\n']
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let white = [' ' '\t']+
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let word = [^' ' '\t' '\n']+
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let letter = ['A'-'Z' 'a'-'z']
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let integer = ['0'-'9']+
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let real = '-'? (integer '.' integer | integer '.' | '.' integer) (['e' 'E'] ('+'|'-')? integer)?
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let integer = ['0'-'9']+
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let real = '-'? (integer '.' integer | integer '.' | '.' integer) (['e' 'E'] ('+'|'-')? integer)?
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rule read_all = parse
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@ -38,3 +45,4 @@ rule read_all = parse
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done;
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*)
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}
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(* Lexer:1 ends here *)
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@ -1,6 +1,10 @@
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(** When an [xyz] file is read by the [Xyz_parser.mly], it is converted into
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an {!xyz_file} data structure. *)
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(* When an xyz file is read by =xyz_parser.mly=, it is converted into
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* an ~xyz_file~ data structure. *)
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(* [[file:../nuclei.org::*Parser][Parser:2]] *)
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open Common
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type nucleus =
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@ -15,4 +19,4 @@ type xyz_file =
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file_title : string ;
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nuclei : nucleus list ;
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}
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(* Parser:2 ends here *)
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@ -1,5 +1,3 @@
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/* Parses nuclear coordinates in xyz format */
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%{
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open Common
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@ -84,5 +82,3 @@ atoms_list:
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| atoms_list SPACE INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT EOL { output_of_int $5 $7 $9 $3 :: $1 }
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| atoms_list SPACE INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { output_of_int $5 $7 $9 $3 :: $1 }
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;
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393
particles/nuclei.org
Normal file
393
particles/nuclei.org
Normal file
@ -0,0 +1,393 @@
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#+begin_src elisp tangle: no :results none :exports none
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(setq pwd (file-name-directory buffer-file-name))
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(setq name (file-name-nondirectory (substring buffer-file-name 0 -4)))
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(setq lib (concat pwd "lib/"))
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(setq testdir (concat pwd "test/"))
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(setq mli (concat lib name ".mli"))
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(setq ml (concat lib name ".ml"))
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(setq test-ml (concat testdir name ".ml"))
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(org-babel-tangle)
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#+end_src
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* Nuclei
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:PROPERTIES:
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:header-args: :noweb yes :comments both
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:END:
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** Type
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#+NAME: types
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#+begin_src ocaml :tangle (eval mli)
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open Common
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type t = (Element.t * Coordinate.t) array
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#+end_src
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#+begin_src ocaml :tangle (eval ml) :exports none
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<<types>>
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open Xyz_ast
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#+end_src
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** xyz file lexer/parser
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*** Lexer
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=nuclei_lexer.mll= contains the description of the lexemes used in
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an xyz file.
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#+begin_src ocaml :tangle lib/nuclei_lexer.mll :export none
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{
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open Xyz_parser
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}
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let eol = ['\n']
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let white = [' ' '\t']+
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let word = [^' ' '\t' '\n']+
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let letter = ['A'-'Z' 'a'-'z']
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let integer = ['0'-'9']+
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let real = '-'? (integer '.' integer | integer '.' | '.' integer) (['e' 'E'] ('+'|'-')? integer)?
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rule read_all = parse
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| eof { EOF }
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| eol { EOL }
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| white as w { SPACE w }
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| integer as i { INTEGER (int_of_string i) }
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| real as f { FLOAT (float_of_string f) }
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| word as w { WORD w }
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{
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(* DEBUG
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let () =
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let ic = open_in "h2o.xyz" in
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let lexbuf = Lexing.from_channel ic in
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while true do
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let s =
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match read_all lexbuf with
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| EOL -> "EOL"
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| SPACE w -> "SPACE("^w^")"
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| INTEGER i -> "INTEGER("^(string_of_int i)^")"
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| FLOAT f -> "FLOAT("^(string_of_float f)^")"
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| WORD w -> "WORD("^w^")"
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| EOF -> "EOF"
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in
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print_endline s
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done;
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*)
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}
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#+end_src
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*** Parser
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=xyz_parser.mly= parses nuclear coordinates in xyz format.
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#+begin_src ocaml :tangle lib/xyz_parser.mly :export none :comments none
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%{
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open Common
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let make_angstrom x y z =
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Coordinate.(make_angstrom {
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x ; y ; z
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})
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let output_of f x y z =
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let a = make_angstrom x y z in
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fun e ->
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{
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Xyz_ast.
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element = f e;
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coord = a ;
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}
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let output_of_string = output_of Element.of_string
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let output_of_int = output_of Element.of_int
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||||
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%}
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%token EOL
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%token <string> SPACE
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%token <string> WORD
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%token <int> INTEGER
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%token <float> FLOAT
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%token EOF
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%start input
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%type <Xyz_ast.xyz_file> input
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%% /* Grammar rules and actions follow */
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input:
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| integer title atoms_xyz {
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{
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number_of_atoms = $1;
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file_title = $2;
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nuclei = $3;
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||||
}
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||||
}
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||||
;
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||||
|
||||
|
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integer:
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||||
| INTEGER EOL { $1 }
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||||
| INTEGER SPACE EOL { $1 }
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||||
| SPACE INTEGER EOL { $2 }
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||||
| SPACE INTEGER SPACE EOL { $2 }
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||||
;
|
||||
|
||||
title:
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||||
| title_list EOL { $1 }
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||||
;
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||||
|
||||
text:
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||||
| WORD { $1 }
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||||
| SPACE { $1 }
|
||||
| FLOAT { (string_of_float $1)}
|
||||
| INTEGER { (string_of_int $1)}
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||||
;
|
||||
|
||||
title_list:
|
||||
| { "" }
|
||||
| title_list text { ($1 ^ $2) }
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||||
;
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||||
|
||||
atoms_xyz:
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||||
| atoms_list EOL { List.rev $1 }
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||||
| atoms_list EOF { List.rev $1 }
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||||
;
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||||
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||||
atoms_list:
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||||
| { [] }
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||||
| atoms_list WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT EOL { output_of_string $4 $6 $8 $2 :: $1 }
|
||||
| atoms_list WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { output_of_string $4 $6 $8 $2 :: $1 }
|
||||
| atoms_list INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT EOL { output_of_int $4 $6 $8 $2 :: $1 }
|
||||
| atoms_list INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { output_of_int $4 $6 $8 $2 :: $1 }
|
||||
| atoms_list SPACE WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT EOL { output_of_string $5 $7 $9 $3 :: $1 }
|
||||
| atoms_list SPACE WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { output_of_string $5 $7 $9 $3 :: $1 }
|
||||
| atoms_list SPACE INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT EOL { output_of_int $5 $7 $9 $3 :: $1 }
|
||||
| atoms_list SPACE INTEGER SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { output_of_int $5 $7 $9 $3 :: $1 }
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||||
;
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||||
#+end_src
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||||
|
||||
When an xyz file is read by =xyz_parser.mly=, it is converted into
|
||||
an ~xyz_file~ data structure.
|
||||
|
||||
#+begin_src ocaml :tangle lib/xyz_ast.mli
|
||||
open Common
|
||||
|
||||
type nucleus =
|
||||
{
|
||||
element: Element.t ;
|
||||
coord : Coordinate.angstrom Coordinate.point;
|
||||
}
|
||||
|
||||
type xyz_file =
|
||||
{
|
||||
number_of_atoms : int ;
|
||||
file_title : string ;
|
||||
nuclei : nucleus list ;
|
||||
}
|
||||
#+end_src
|
||||
|
||||
** Conversion
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val of_xyz_string : string -> t
|
||||
val to_xyz_string : t -> string
|
||||
val of_xyz_file : string -> t
|
||||
|
||||
val of_zmt_string : string -> t
|
||||
val of_zmt_file : string -> t
|
||||
|
||||
val to_string : t -> string
|
||||
|
||||
val of_filename : string -> t
|
||||
#+end_src
|
||||
|
||||
| ~of_xyz_string~ | Create from a string, in xyz format |
|
||||
| ~of_xyz_file~ | Create from a file, in xyz format |
|
||||
| ~of_zmt_string~ | Create from a string, in z-matrix format |
|
||||
| ~of_zmt_file~ | Create from a file, in z-matrix format |
|
||||
| ~to_string~ | Transform to a string, for printing |
|
||||
| ~of_filename~ | Detects the type of file (xyz, z-matrix) and reads the file |
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
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 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"
|
||||
#+end_src
|
||||
|
||||
** Query
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val repulsion : t -> float
|
||||
val charge : t -> Charge.t
|
||||
val small_core : t -> int
|
||||
val large_core : t -> int
|
||||
#+end_src
|
||||
|
||||
| ~repulsion~ | Nuclear repulsion energy, in atomic units |
|
||||
| ~charge~ | Sum of the charges of the nuclei |
|
||||
| ~small_core~ | Number of core electrons in the small core model |
|
||||
| ~large_core~ | Number of core electrons in the large core model |
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
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 small_core a =
|
||||
Array.fold_left (fun accu (e,_) -> accu + (Element.small_core e)) 0 a
|
||||
|
||||
|
||||
let large_core a =
|
||||
Array.fold_left (fun accu (e,_) -> accu + (Element.large_core e)) 0 a
|
||||
#+end_src
|
||||
|
||||
** Printers
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val pp : Format.formatter -> t -> unit
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let pp ppf t =
|
||||
Format.fprintf ppf "@[%s@]" (to_string t)
|
||||
#+end_src
|
||||
|
||||
** Tests
|
||||
|
||||
#+begin_src ocaml :tangle (eval test-ml) :exports none
|
||||
open Common
|
||||
open Particles
|
||||
open Alcotest
|
||||
|
||||
let wd = Common.Qcaml.root ^ Filename.dir_sep ^ "test"
|
||||
|
||||
let test_xyz molecule length repulsion charge core =
|
||||
let xyz = Nuclei.of_xyz_file (wd^Filename.dir_sep^molecule^".xyz") in
|
||||
check int "length" length (Array.length xyz);
|
||||
check (float 1.e-4) "repulsion" repulsion (Nuclei.repulsion xyz);
|
||||
check int "charge" charge (Charge.to_int @@ Nuclei.charge xyz);
|
||||
check int "small_core" core (Nuclei.small_core xyz);
|
||||
()
|
||||
|
||||
let tests = [
|
||||
"caffeine", `Quick, (fun () -> test_xyz "caffeine" 24 917.0684 102 28);
|
||||
"water", `Quick, (fun () -> test_xyz "water" 3 9.19497 10 2);
|
||||
]
|
||||
#+end_src
|
||||
|
||||
@ -1,3 +1,7 @@
|
||||
(* Tests *)
|
||||
|
||||
|
||||
(* [[file:../nuclei.org::*Tests][Tests:1]] *)
|
||||
open Common
|
||||
open Particles
|
||||
open Alcotest
|
||||
@ -16,3 +20,4 @@ let tests = [
|
||||
"caffeine", `Quick, (fun () -> test_xyz "caffeine" 24 917.0684 102 28);
|
||||
"water", `Quick, (fun () -> test_xyz "water" 3 9.19497 10 2);
|
||||
]
|
||||
(* Tests:1 ends here *)
|
||||
|
||||
Loading…
Reference in New Issue
Block a user