QCaml/particles/nuclei.org

#+begin_src elisp tangle: no :results none :exports none
(setq pwd (file-name-directory buffer-file-name))
(setq name (file-name-nondirectory (substring buffer-file-name 0 -4)))
(setq lib (concat pwd "lib/"))
(setq testdir (concat pwd "test/"))
(setq mli (concat lib name ".mli"))
(setq ml  (concat lib name ".ml"))
(setq test-ml  (concat testdir name ".ml"))
(org-babel-tangle)
#+end_src

* Nuclei
  :PROPERTIES:
  :header-args: :noweb yes :comments both
  :END:

** Type
   <<<~Nuclei.t~>>>

   #+NAME: types
   #+begin_src ocaml :tangle (eval mli)
open Common

type t = (Element.t * Coordinate.t) array
   #+end_src

   #+begin_src ocaml :tangle (eval ml) :exports none
open Common

type t = (Element.t * Coordinate.t) array
open Xyz_ast
   #+end_src

** xyz file lexer/parser

*** Lexer

 =nuclei_lexer.mll= contains the description of the lexemes used in
    an xyz file.

    #+begin_src ocaml :tangle lib/nuclei_lexer.mll :export none
{
open Xyz_parser
}

let eol = ['\n']
let white = [' ' '\t']+
let word = [^' ' '\t' '\n']+
let letter = ['A'-'Z' 'a'-'z']
let integer = ['0'-'9']+
let real = '-'? (integer '.' integer | integer '.' | '.' integer) (['e' 'E'] ('+'|'-')? integer)?


rule read_all = parse
  | eof            { EOF }
  | eol            { EOL }
  | white   as w   { SPACE w }
  | integer as i   { INTEGER (int_of_string i) }
  | real    as f   { FLOAT (float_of_string f) }
  | word    as w   { WORD w }


{
(* DEBUG
 let () =
   let ic = open_in "h2o.xyz" in
   let lexbuf = Lexing.from_channel ic in
   while true do
     let s =
      match read_all lexbuf with
      | EOL -> "EOL"
      | SPACE w -> "SPACE("^w^")"
      | INTEGER i -> "INTEGER("^(string_of_int i)^")"
      | FLOAT f -> "FLOAT("^(string_of_float f)^")"
      | WORD w -> "WORD("^w^")"
      | EOF -> "EOF"
     in
     print_endline s
   done;
*)
}
    #+end_src

*** Parser

 =xyz_parser.mly= parses nuclear coordinates in xyz format.
    #+begin_src ocaml :tangle lib/xyz_parser.mly :export none  :comments none
%{
open Common

let make_angstrom x y z =
  Coordinate.(make_angstrom {
    x ; y ; z
  })

let output_of f x y z =
  let a = make_angstrom x y z in
  fun e ->
  {
    Xyz_ast.
    element = f e;
    coord = a ;
  }

let output_of_string = output_of Element.of_string
let output_of_int    = output_of Element.of_int

%}

%token EOL
%token <string> SPACE
%token <string> WORD
%token <int> INTEGER
%token <float> FLOAT
%token EOF

%start input
%type <Xyz_ast.xyz_file> input

%% /* Grammar rules and actions follow */

input:
  | integer title atoms_xyz {
      {
        number_of_atoms = $1;
        file_title = $2;
        nuclei = $3;
      }
    }
;


integer:
  | INTEGER EOL { $1 }
  | INTEGER SPACE EOL { $1 }
  | SPACE INTEGER EOL { $2 }
  | SPACE INTEGER SPACE EOL { $2 }
;

title:
  | title_list EOL { $1 }
;

text:
  | WORD    { $1 }
  | SPACE   { $1 }
  | FLOAT   { (string_of_float $1)}
  | INTEGER { (string_of_int $1)}
;

title_list:
  | { "" }
  | title_list text { ($1 ^ $2) }
;

atoms_xyz:
  | atoms_list EOL { List.rev $1 }
  | atoms_list EOF { List.rev $1 }
;

atoms_list:
  | { [] }
  | 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 }
;
    #+end_src

    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 formula    : t -> string
val repulsion  : t -> float
val charge     : t -> Charge.t
val small_core : t -> int
val large_core : t -> int
   #+end_src

   | ~formula~    | Returns the chemical formula                     |
   | ~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 formula t =
  let dict = Hashtbl.create 67 in
  Array.iter (fun (e,_) ->
    let e = Element.to_string e in
    let value =
      try (Hashtbl.find dict e) + 1
      with Not_found -> 1
    in
    Hashtbl.replace dict e value
  ) t;
  Hashtbl.to_seq_keys dict
  |> List.of_seq
  |> List.sort String.compare
  |> List.fold_left (fun accu key ->
    let x = Hashtbl.find dict key in
    accu ^ key ^ "_{" ^ (string_of_int x) ^ "}") ""



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

** TREXIO

*** Read

    #+begin_src ocaml :tangle (eval mli)
val of_trexio : Trexio.trexio_file -> t
    #+end_src

    #+begin_src ocaml :tangle (eval ml) :exports none
let of_trexio f =
  let num    = Trexio.read_nucleus_num    f in
  let charge = Trexio.read_nucleus_charge f
               |> Array.map Charge.of_float in
  let coord  = Trexio.read_nucleus_coord  f in
  Array.init num (fun i ->
      let coord = Coordinate.{ x = coord.(3*i)   ;
                               y = coord.(3*i+1) ;
                               z = coord.(3*i+2) } in
      (Element.of_charge charge.(i), Coordinate.make coord)
    )
    #+end_src

*** Write

    #+begin_src ocaml :tangle (eval mli)
val to_trexio : Trexio.trexio_file -> t -> unit
    #+end_src

    #+begin_src ocaml :tangle (eval ml) :exports none
let to_trexio f t =
  let num = Array.length t in
  Trexio.write_nucleus_num f num;

  Array.map (fun (e, _) -> Element.to_charge e |> Charge.to_float) t
  |> Trexio.write_nucleus_charge f;

  Array.map (fun (e, _) -> Element.to_string e) t
  |> Trexio.write_nucleus_label f;

  let coord = Array.init (num*3) (fun _ -> 0.) in
  Array.iteri (fun i (_, xyz) ->
      coord.(3*i)   <- Coordinate.(get X xyz) ;
      coord.(3*i+1) <- Coordinate.(get Y xyz) ;
      coord.(3*i+2) <- Coordinate.(get Z xyz) ) t;
  Trexio.write_nucleus_coord f coord;

  repulsion t
  |> Trexio.write_nucleus_repulsion f

    #+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