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Added zmatrix
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@ -1,3 +1,3 @@
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(** Atomic mass. *)
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(* [[file:../mass.org::*Atomic mass][Atomic mass:2]] *)
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include Common.Non_negative_float
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(* Atomic mass:2 ends here *)
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@ -1,3 +1,12 @@
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(** Atomic mass. *)
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(* Atomic mass
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* :PROPERTIES:
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* :header-args: :noweb yes :comments both
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* :END:
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*
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* Atomic mass, a non-negative float.
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*
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* #+NAME: types *)
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(* [[file:../mass.org::types][types]] *)
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include module type of Common.Non_negative_float
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(* types ends here *)
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@ -1,3 +1,4 @@
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(* [[file:../zmatrix.org::*Type][Type:2]] *)
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module StringMap = Map.Make(String)
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type atom_id = int
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@ -5,7 +6,25 @@ type angle = Label of string | Value of float
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type distance = Label of string | Value of float
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type dihedral = Label of string | Value of float
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let pi = acos (-1.)
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type line =
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| First of Element.t
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| Second of (Element.t * distance)
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| Third of (Element.t * atom_id * distance * atom_id * angle)
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| Other of (Element.t * atom_id * distance * atom_id * angle * atom_id * dihedral )
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| Coord of (string * float)
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type t = (line array * float StringMap.t)
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(* Type:2 ends here *)
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(* | ~of_string~ | Reads a z-matrix from a string |
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* | ~to_xyz~ | Converts to xyz format, as in the ~Nuclei~ module |
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* | ~to_xyz_string~ | Converts to xyz format, as a string | *)
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(* [[file:../zmatrix.org::*Conversion][Conversion:2]] *)
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let pi = Common.Constants.pi
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let to_radian = pi /. 180.
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let rec in_range (xmin, xmax) x =
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@ -50,7 +69,6 @@ let dihedral_of_string : string -> dihedral =
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dihedral_of_float @@ float_of_string s
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with _ -> Label s
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let int_of_atom_id : atom_id -> int = fun x -> x
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let float_of_distance : float StringMap.t -> distance -> float =
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@ -69,25 +87,17 @@ let float_of_dihedral : float StringMap.t -> dihedral -> float =
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| Label s -> StringMap.find s map
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type line =
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| First of Element.t
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| Second of (Element.t * distance)
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| Third of (Element.t * atom_id * distance * atom_id * angle)
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| Other of (Element.t * atom_id * distance * atom_id * angle * atom_id * dihedral )
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| Coord of (string * float)
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let string_of_line map =
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let f_r = float_of_distance map
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and f_a = float_of_angle map
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and f_d = float_of_dihedral map
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and i_i = int_of_atom_id
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in function
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| First e -> Printf.sprintf "%-3s" (Element.to_string e)
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| Second (e, r) -> Printf.sprintf "%-3s %5d %f" (Element.to_string e) 1 (f_r r)
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| Third (e, i, r, j, a) -> Printf.sprintf "%-3s %5d %f %5d %f" (Element.to_string e) (i_i i) (f_r r) (i_i j) (f_a a)
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| Other (e, i, r, j, a, k, d) -> Printf.sprintf "%-3s %5d %f %5d %f %5d %f" (Element.to_string e) (i_i i) (f_r r) (i_i j) (f_a a) (i_i k) (f_d d)
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| Coord (c, f) -> Printf.sprintf "%s %f" c f
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| First e -> Printf.sprintf "%-3s" (Element.to_string e)
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| Second (e, r) -> Printf.sprintf "%-3s %5d %f" (Element.to_string e) 1 (f_r r)
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| Third (e, i, r, j, a) -> Printf.sprintf "%-3s %5d %f %5d %f" (Element.to_string e) (i_i i) (f_r r) (i_i j) (f_a a)
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| Other (e, i, r, j, a, k, d) -> Printf.sprintf "%-3s %5d %f %5d %f %5d %f" (Element.to_string e) (i_i i) (f_r r) (i_i j) (f_a a) (i_i k) (f_d d)
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| Coord (c, f) -> Printf.sprintf "%s %f" c f
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let line_of_string l =
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@ -118,8 +128,6 @@ let line_of_string l =
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| _ -> failwith ("Syntax error: "^l)
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type t = (line array * float StringMap.t)
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let of_string t =
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let l =
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Str.split (Str.regexp "\n") t
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@ -196,10 +204,10 @@ let rotation_matrix axis angle =
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a *. a +. d *. d -. b *. b -. c *. c)]
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let apply_rotation_matrix rot u =
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(dot rot.(0) u, dot rot.(1) u, dot rot.(2) u)
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let to_xyz (z,map) =
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let result =
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Array.make (Array.length z) None
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@ -296,6 +304,14 @@ let to_xyz_string (l,map) =
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Printf.sprintf "%s %f %f %f\n" (Element.to_string e) x y z)
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|> Array.to_list
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)
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(* Conversion:2 ends here *)
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(* [[file:../zmatrix.org::*Printers][Printers:2]] *)
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let pp ppf (a, map) =
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let f = string_of_line map in
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Format.fprintf ppf "@[";
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Array.iter (fun line ->
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Format.fprintf ppf "%s@." (f line)
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) a;
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Format.fprintf ppf "@]"
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(* Printers:2 ends here *)
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23
particles/lib/zmatrix.mli
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23
particles/lib/zmatrix.mli
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@ -0,0 +1,23 @@
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(* Type
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*
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* #+NAME: types *)
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(* [[file:../zmatrix.org::types][types]] *)
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type t
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(* types ends here *)
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(* Conversion *)
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(* [[file:../zmatrix.org::*Conversion][Conversion:1]] *)
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val of_string : string -> t
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val to_xyz : t -> (Element.t * float * float * float) array
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val to_xyz_string : t -> string
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(* Conversion:1 ends here *)
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(* Printers *)
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(* [[file:../zmatrix.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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27
particles/mass.org
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27
particles/mass.org
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@ -0,0 +1,27 @@
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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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* Atomic mass
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:PROPERTIES:
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:header-args: :noweb yes :comments both
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:END:
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Atomic mass, a non-negative float.
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#+NAME: types
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#+begin_src ocaml :tangle (eval mli)
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include module type of Common.Non_negative_float
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#+end_src
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#+begin_src ocaml :tangle (eval ml) :exports none
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include Common.Non_negative_float
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#+end_src
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354
particles/zmatrix.org
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354
particles/zmatrix.org
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@ -0,0 +1,354 @@
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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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* Z-matrix
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:PROPERTIES:
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:header-args: :noweb yes :comments both
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:END:
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Z-matrix representation of nuclear coordinates.
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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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type t
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#+end_src
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#+begin_src ocaml :tangle (eval ml) :exports none
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module StringMap = Map.Make(String)
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type atom_id = int
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type angle = Label of string | Value of float
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type distance = Label of string | Value of float
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type dihedral = Label of string | Value of float
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type line =
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| First of Element.t
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| Second of (Element.t * distance)
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| Third of (Element.t * atom_id * distance * atom_id * angle)
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| Other of (Element.t * atom_id * distance * atom_id * angle * atom_id * dihedral )
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| Coord of (string * float)
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type t = (line array * float StringMap.t)
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#+end_src
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** Conversion
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#+begin_src ocaml :tangle (eval mli)
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val of_string : string -> t
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val to_xyz : t -> (Element.t * float * float * float) array
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val to_xyz_string : t -> string
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#+end_src
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| ~of_string~ | Reads a z-matrix from a string |
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| ~to_xyz~ | Converts to xyz format, as in the ~Nuclei~ module |
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| ~to_xyz_string~ | Converts to xyz format, as a string |
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#+begin_src ocaml :tangle (eval ml) :exports none
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let pi = Common.Constants.pi
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let to_radian = pi /. 180.
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let rec in_range (xmin, xmax) x =
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if (x <= xmin) then
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in_range (xmin, xmax) (x -. xmin +. xmax )
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else if (x > xmax) then
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in_range (xmin, xmax) (x -. xmax +. xmin )
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else
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x
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let atom_id_of_int : int -> atom_id =
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fun x -> ( assert (x>0) ; x)
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let distance_of_float : float -> distance =
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fun x -> ( assert (x>=0.) ; Value x)
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let angle_of_float : float -> angle =
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fun x -> Value (in_range (-180., 180.) x)
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let dihedral_of_float : float -> dihedral =
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fun x -> Value (in_range (-360., 360.) x)
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let atom_id_of_string : string -> atom_id =
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fun i -> atom_id_of_int @@ int_of_string i
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let distance_of_string : string -> distance =
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fun s ->
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try
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distance_of_float @@ float_of_string s
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with _ -> Label s
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let angle_of_string : string -> angle =
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fun s ->
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try
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angle_of_float @@ float_of_string s
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with _ -> Label s
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let dihedral_of_string : string -> dihedral =
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fun s ->
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try
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dihedral_of_float @@ float_of_string s
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with _ -> Label s
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let int_of_atom_id : atom_id -> int = fun x -> x
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let float_of_distance : float StringMap.t -> distance -> float =
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fun map -> function
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| Value x -> x
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| Label s -> StringMap.find s map
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let float_of_angle : float StringMap.t -> angle -> float =
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fun map -> function
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| Value x -> x
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| Label s -> StringMap.find s map
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let float_of_dihedral : float StringMap.t -> dihedral -> float =
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fun map -> function
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| Value x -> x
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| Label s -> StringMap.find s map
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let string_of_line map =
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let f_r = float_of_distance map
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and f_a = float_of_angle map
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and f_d = float_of_dihedral map
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and i_i = int_of_atom_id
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in function
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| First e -> Printf.sprintf "%-3s" (Element.to_string e)
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| Second (e, r) -> Printf.sprintf "%-3s %5d %f" (Element.to_string e) 1 (f_r r)
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| Third (e, i, r, j, a) -> Printf.sprintf "%-3s %5d %f %5d %f" (Element.to_string e) (i_i i) (f_r r) (i_i j) (f_a a)
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| Other (e, i, r, j, a, k, d) -> Printf.sprintf "%-3s %5d %f %5d %f %5d %f" (Element.to_string e) (i_i i) (f_r r) (i_i j) (f_a a) (i_i k) (f_d d)
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| Coord (c, f) -> Printf.sprintf "%s %f" c f
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let line_of_string l =
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let line_clean =
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Str.split (Str.regexp " ") l
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|> List.filter (fun x -> x <> "")
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in
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match line_clean with
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| e :: [] -> First (Element.of_string e)
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| e :: _ :: r :: [] -> Second
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(Element.of_string e,
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distance_of_string r)
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| e :: i :: r :: j :: a :: [] -> Third
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(Element.of_string e,
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atom_id_of_string i,
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distance_of_string r,
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atom_id_of_string j,
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angle_of_string a)
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| e :: i :: r :: j :: a :: k :: d :: [] -> Other
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(Element.of_string e,
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atom_id_of_string i,
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distance_of_string r,
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atom_id_of_string j,
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angle_of_string a,
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atom_id_of_string k,
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dihedral_of_string d)
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| c :: f :: [] -> Coord (c, float_of_string f)
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| _ -> failwith ("Syntax error: "^l)
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let of_string t =
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let l =
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Str.split (Str.regexp "\n") t
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|> List.map String.trim
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|> List.filter (fun x -> x <> "")
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|> List.map line_of_string
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in
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let l =
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match l with
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| First _ :: Second _ :: Third _ :: _
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| First _ :: Second _ :: Coord _ :: []
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| First _ :: Second _ :: []
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| First _ :: [] -> l
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| _ -> failwith "Syntax error"
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in
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let (l, m) =
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let rec work lst map = function
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| (First _ as x) :: rest
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| (Second _ as x) :: rest
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| (Third _ as x) :: rest
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| (Other _ as x) :: rest -> work (x::lst) map rest
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| (Coord (c,f)) :: rest -> work lst (StringMap.add c f map) rest
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| [] -> (List.rev lst, map)
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in
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work [] (StringMap.empty) l
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in
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(Array.of_list l, m)
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(** Linear algebra *)
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let (|-) (x,y,z) (x',y',z') =
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( x-.x', y-.y', z-.z' )
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let (|+) (x,y,z) (x',y',z') =
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( x+.x', y+.y', z+.z' )
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let (|.) s (x,y,z) =
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( s*.x, s*.y, s*.z )
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let dot (x,y,z) (x',y',z') =
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x*.x' +. y*.y' +. z*.z'
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let norm u =
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sqrt @@ dot u u
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let normalized u =
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1. /. (norm u) |. u
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let cross (x,y,z) (x',y',z') =
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((y *. z' -. z *. y'), -. (x *. z' -. z *. x'), (x *. y' -. y *. x'))
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let rotation_matrix axis angle =
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(* Euler-Rodrigues formula for rotation matrix, taken from
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https://github.com/jevandezande/zmatrix/blob/master/converter.py
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,*)
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let a =
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(cos (angle *. to_radian *. 0.5))
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in
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let (b, c, d) =
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(-. sin (angle *. to_radian *. 0.5)) |. (normalized axis)
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in
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Array.of_list @@
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[(a *. a +. b *. b -. c *. c -. d *. d,
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2. *. (b *. c -. a *. d),
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2. *. (b *. d +. a *. c));
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(2. *. (b *. c +. a *. d),
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a *. a +. c *. c -.b *. b -. d *. d,
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2. *. (c *. d -. a *. b));
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(2. *. (b *. d -. a *. c),
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2. *. (c *. d +. a *. b),
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a *. a +. d *. d -. b *. b -. c *. c)]
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let apply_rotation_matrix rot u =
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(dot rot.(0) u, dot rot.(1) u, dot rot.(2) u)
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let to_xyz (z,map) =
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let result =
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Array.make (Array.length z) None
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in
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let get_cartesian_coord i =
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match result.(i-1) with
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| None -> failwith @@ Printf.sprintf "Atom %d is defined in the future" i
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| Some (_, x, y, z) -> (x, y, z)
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in
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let append_line i' =
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match z.(i') with
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| First e ->
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result.(i') <- Some (e, 0., 0., 0.)
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| Second (e, r) ->
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let r =
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float_of_distance map r
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in
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result.(i') <- Some (e, 0., 0., r)
|
||||
| Third (e, i, r, j, a) ->
|
||||
begin
|
||||
let i, r, j, a =
|
||||
int_of_atom_id i,
|
||||
float_of_distance map r,
|
||||
int_of_atom_id j,
|
||||
float_of_angle map a
|
||||
in
|
||||
let ui, uj =
|
||||
get_cartesian_coord i,
|
||||
get_cartesian_coord j
|
||||
in
|
||||
let u_ij =
|
||||
(uj |- ui)
|
||||
in
|
||||
let rot =
|
||||
rotation_matrix (0., 1., 0.) a
|
||||
in
|
||||
let new_vec =
|
||||
apply_rotation_matrix rot ( r |. (normalized u_ij))
|
||||
in
|
||||
let (x, y, z) =
|
||||
new_vec |+ ui
|
||||
in
|
||||
result.(i') <- Some (e, x, y, z)
|
||||
end
|
||||
| Other (e, i, r, j, a, k, d) ->
|
||||
begin
|
||||
let i, r, j, a, k, d =
|
||||
int_of_atom_id i,
|
||||
float_of_distance map r,
|
||||
int_of_atom_id j,
|
||||
float_of_angle map a,
|
||||
int_of_atom_id k,
|
||||
float_of_dihedral map d
|
||||
in
|
||||
let ui, uj, uk =
|
||||
get_cartesian_coord i,
|
||||
get_cartesian_coord j,
|
||||
get_cartesian_coord k
|
||||
in
|
||||
let u_ij, u_kj =
|
||||
(uj |- ui) , (uj |- uk)
|
||||
in
|
||||
let normal =
|
||||
cross u_ij u_kj
|
||||
in
|
||||
let new_vec =
|
||||
r |. (normalized u_ij)
|
||||
|> apply_rotation_matrix (rotation_matrix normal a)
|
||||
|> apply_rotation_matrix (rotation_matrix u_ij d)
|
||||
in
|
||||
let (x, y, z) =
|
||||
new_vec |+ ui
|
||||
in
|
||||
result.(i') <- Some (e, x, y, z)
|
||||
end
|
||||
| Coord _ -> ()
|
||||
in
|
||||
Array.iteri (fun i _ -> append_line i) z;
|
||||
let result =
|
||||
Array.map (function
|
||||
| Some x -> x
|
||||
| None -> failwith "Some atoms were not defined" ) result
|
||||
in
|
||||
result
|
||||
|
||||
|
||||
let to_xyz_string (l,map) =
|
||||
String.concat "\n"
|
||||
( to_xyz (l,map)
|
||||
|> Array.map (fun (e,x,y,z) ->
|
||||
Printf.sprintf "%s %f %f %f\n" (Element.to_string e) x y z)
|
||||
|> Array.to_list
|
||||
)
|
||||
#+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 (a, map) =
|
||||
let f = string_of_line map in
|
||||
Format.fprintf ppf "@[";
|
||||
Array.iter (fun line ->
|
||||
Format.fprintf ppf "%s@." (f line)
|
||||
) a;
|
||||
Format.fprintf ppf "@]"
|
||||
#+end_src
|
||||
|
||||
@ -46,13 +46,12 @@ let eval_exn str =
|
||||
|
||||
|
||||
let rec install_printers = function
|
||||
| [] -> true
|
||||
| [] -> eval_exn "#require \"lacaml.top\";;"
|
||||
| printer :: printers ->
|
||||
let cmd = Printf.sprintf "#install_printer %s;;" printer in
|
||||
eval_exn cmd && install_printers printers
|
||||
|
||||
let () =
|
||||
eval_exn "#require \"lacaml.top\";;";
|
||||
if not (install_printers printers) then
|
||||
Format.eprintf "Problem installing QCaml-printers@."
|
||||
|
||||
|
||||
@ -11,6 +11,7 @@ let printers =
|
||||
"Common.Zkey.pp" ;
|
||||
"Particles.Electrons.pp" ;
|
||||
"Particles.Element.pp" ;
|
||||
"Particles.Zmatrix.pp" ;
|
||||
|
||||
]
|
||||
|
||||
@ -21,13 +22,12 @@ let eval_exn str =
|
||||
|
||||
|
||||
let rec install_printers = function
|
||||
| [] -> true
|
||||
| [] -> eval_exn "#require \"lacaml.top\";;"
|
||||
| printer :: printers ->
|
||||
let cmd = Printf.sprintf "#install_printer %s;;" printer in
|
||||
eval_exn cmd && install_printers printers
|
||||
|
||||
let () =
|
||||
eval_exn "#require \"lacaml.top\";;";
|
||||
if not (install_printers printers) then
|
||||
Format.eprintf "Problem installing QCaml-printers@."
|
||||
(* Intall printers:2 ends here *)
|
||||
|
||||
Loading…
Reference in New Issue
Block a user