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Electrons org-mode
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particles/electrons.org
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160
particles/electrons.org
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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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* Electrons
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:PROPERTIES:
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:header-args: :noweb yes :comments both
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:END:
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Data structure which contains the number of \alpha and \beta electrons.
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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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type t = {
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n_alfa : int ;
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n_beta : int ;
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}
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#+end_src
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#+begin_src ocaml :tangle (eval test-ml) :exports none
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open Common
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open Particles
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open Alcotest
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let test_all () =
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let nuclei =
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"3
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Water
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O 0. 0. 0.
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H -0.756950272703377558 0. -0.585882234512562827
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H 0.756950272703377558 0. -0.585882234512562827
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"
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|> Nuclei.of_xyz_string
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in
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let e = Electrons.of_atoms nuclei in
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#+end_src
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** Creation
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#+begin_src ocaml :tangle (eval mli)
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open Common
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val make : int -> int -> t
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val of_atoms : ?multiplicity:int -> ?charge:int -> Nuclei.t -> t
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(* @param multiplicity default is 1
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@param charge default is 0
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@raise Invalid_argument if the spin multiplicity is not compatible with
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the molecule and the total charge.
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*)
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#+end_src
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| ~make~ | ~make n_alfa n_beta~ |
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| ~of_atoms~ | Creates the data relative to electrons for a molecular system described by ~Nuclei.t~ for a given total charge and spin multiplicity. |
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#+begin_src ocaml :tangle (eval ml) :exports none
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open Common
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let make n_alfa n_beta =
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{ n_alfa ; n_beta }
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let of_atoms ?multiplicity:(multiplicity=1) ?charge:(charge=0) nuclei =
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let positive_charges =
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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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in
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let negative_charges = charge - positive_charges in
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let n_elec = - negative_charges in
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let n_beta = ((n_elec - multiplicity)+1)/2 in
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let n_alfa = n_elec - n_beta in
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let result = { n_alfa ; n_beta } in
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if multiplicity <> (n_alfa - n_beta)+1 then
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invalid_arg (__FILE__^": make");
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result
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#+end_src
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#+begin_src ocaml :tangle (eval test-ml) :exports none
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check int "of_atoms alfa" 5 (Electrons.n_alfa e);
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check int "of_atoms beta" 5 (Electrons.n_beta e);
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#+end_src
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** Access
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#+begin_src ocaml :tangle (eval mli)
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val charge : t -> Charge.t
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val n_elec : t -> int
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val n_alfa : t -> int
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val n_beta : t -> int
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val multiplicity : t -> int
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#+end_src
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| ~charge~ | Sum of the charges of the electrons |
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| ~n_elec~ | Number of electrons |
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| ~n_alfa~ | Number of alpha electrons |
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| ~n_beta~ | Number of beta electrons |
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| ~multiplicity~ | Spin multiplicity: $2S+1$ |
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#+begin_src ocaml :tangle (eval ml) :exports none
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let charge e =
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- (e.n_alfa + e.n_beta)
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|> Charge.of_int
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let n_alfa t = t.n_alfa
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let n_beta t = t.n_beta
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let n_elec t = t.n_alfa + t.n_beta
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let multiplicity t = t.n_alfa - t.n_beta + 1
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#+end_src
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#+begin_src ocaml :tangle (eval test-ml) :exports none
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check int "charge " (-10) (Charge.to_int @@ Electrons.charge e);
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check int "n_elec" 10 (Electrons.n_elec e);
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check int "multiplicity" 1 (Electrons.multiplicity e);
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check int "of_atoms alfa m3" 6 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_alfa));
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check int "of_atoms beta m3" 4 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_beta));
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check int "of_atoms n_elec m3" 10 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_elec));
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check int "of_atoms alfa m2 c1" 5 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_alfa));
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check int "of_atoms beta m2 c1" 4 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_beta));
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check int "of_atoms beta m2 c1" 9 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_elec));
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check int "of_atoms mult m2 c1" 2 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> multiplicity));
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check bool "make" true (Electrons.make 6 4 = Electrons.(of_atoms ~multiplicity:3 nuclei));
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#+end_src
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** Printers
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#+begin_src ocaml :tangle (eval mli)
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val pp : Format.formatter -> t -> unit
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#+end_src
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#+begin_src ocaml :tangle (eval ml) :exports none
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let pp ppf t =
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Format.fprintf ppf "@[n_alfa=%d, n_beta=%d@]" t.n_alfa t.n_beta
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#+end_src
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** Tests
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#+begin_src ocaml :tangle (eval test-ml) :exports none
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()
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let tests = [
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"all", `Quick, test_all
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]
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#+end_src
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@ -1,13 +1,19 @@
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(** Number of {% $\alpha$ %} and {% $\beta$ %} electrons *)
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open Common
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(* [[file:../electrons.org::*Type][Type:2]] *)
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type t = {
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n_alfa : int ;
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n_beta : int ;
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}
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(* Type:2 ends here *)
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(* | ~make~ | ~make n_alfa n_beta~ |
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* | ~of_atoms~ | Creates the data relative to electrons for a molecular system described by ~Nuclei.t~ for a given total charge and spin multiplicity. | *)
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(* [[file:../electrons.org::*Creation][Creation:2]] *)
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open Common
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let make n_alfa n_beta =
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{ n_alfa ; n_beta }
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@ -25,14 +31,32 @@ let of_atoms ?multiplicity:(multiplicity=1) ?charge:(charge=0) nuclei =
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if multiplicity <> (n_alfa - n_beta)+1 then
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invalid_arg (__FILE__^": make");
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result
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(* Creation:2 ends here *)
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(* | ~charge~ | Sum of the charges of the electrons |
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* | ~n_elec~ | Number of electrons |
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* | ~n_alfa~ | Number of alpha electrons |
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* | ~n_beta~ | Number of beta electrons |
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* | ~multiplicity~ | Spin multiplicity: $2S+1$ | *)
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(* [[file:../electrons.org::*Access][Access:2]] *)
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let charge e =
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- (e.n_alfa + e.n_beta)
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|> Charge.of_int
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let n_alfa t = t.n_alfa
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let n_beta t = t.n_beta
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let n_elec t = t.n_alfa + t.n_beta
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let multiplicity t = t.n_alfa - t.n_beta + 1
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(* Access:2 ends here *)
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(* [[file:../electrons.org::*Printers][Printers:2]] *)
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let pp ppf t =
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Format.fprintf ppf "@[n_alfa=%d, n_beta=%d@]" t.n_alfa t.n_beta
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(* Printers:2 ends here *)
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@ -1,33 +1,41 @@
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(** Information related to electrons. *)
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(* Type
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*
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* #+NAME: types *)
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(* [[file:../electrons.org::types][types]] *)
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type t
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(* types ends here *)
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(* Creation *)
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(* [[file:../electrons.org::*Creation][Creation:1]] *)
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open Common
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type t
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val make : int -> int -> t
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(** make [n_alfa] [n_beta] *)
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val of_atoms : ?multiplicity:int -> ?charge:int -> Nuclei.t -> t
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(** Creates the data relative to electrons for a molecular system
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described by {!Nuclei.t} for a given total charge and spin multiplicity.
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@param multiplicity default is 1
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@param charge default is 0
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@raise Invalid_argument if the spin multiplicity is not compatible with
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(* @param multiplicity default is 1
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@param charge default is 0
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@raise Invalid_argument if the spin multiplicity is not compatible with
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the molecule and the total charge.
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*)
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*)
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(* Creation:1 ends here *)
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val charge : t -> Charge.t
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(** Sum of the charges of the electrons. *)
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(* Access *)
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val n_elec : t -> int
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(** Number of electrons *)
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val n_alfa : t -> int
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(** Number of alpha electrons *)
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(* [[file:../electrons.org::*Access][Access:1]] *)
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val charge : t -> Charge.t
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val n_elec : t -> int
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val n_alfa : t -> int
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val n_beta : t -> int
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val multiplicity : t -> int
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(* Access:1 ends here *)
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val n_beta : t -> int
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(** Number of beta electrons *)
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(* Printers *)
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val multiplicity : t -> int
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(** Spin multiplicity: {% $2S+1$ %} *)
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(* [[file:../electrons.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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@ -1,8 +1,8 @@
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(* [[file:../electrons.org::*Type][Type:3]] *)
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open Common
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open Particles
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open Alcotest
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let test_all () =
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let nuclei =
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"3
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@ -14,21 +14,34 @@ H 0.756950272703377558 0. -0.585882234512562827
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|> Nuclei.of_xyz_string
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in
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let e = Electrons.of_atoms nuclei in
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check int "of_atoms alfa" 5 (Electrons.n_alfa e);
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check int "of_atoms beta" 5 (Electrons.n_beta e);
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check int "charge " (-10) (Charge.to_int @@ Electrons.charge e);
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check int "n_elec" 10 (Electrons.n_elec e);
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check int "multiplicity" 1 (Electrons.multiplicity e);
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check int "of_atoms alfa m3" 6 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_alfa));
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check int "of_atoms beta m3" 4 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_beta));
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check int "of_atoms n_elec m3" 10 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_elec));
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check int "of_atoms alfa m2 c1" 5 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_alfa));
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check int "of_atoms beta m2 c1" 4 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_beta));
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check int "of_atoms beta m2 c1" 9 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_elec));
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check int "of_atoms mult m2 c1" 2 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> multiplicity));
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check bool "make" true (Electrons.make 6 4 = Electrons.(of_atoms ~multiplicity:3 nuclei));
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(* Type:3 ends here *)
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(* [[file:../electrons.org::*Creation][Creation:3]] *)
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check int "of_atoms alfa" 5 (Electrons.n_alfa e);
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check int "of_atoms beta" 5 (Electrons.n_beta e);
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(* Creation:3 ends here *)
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(* [[file:../electrons.org::*Access][Access:3]] *)
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check int "charge " (-10) (Charge.to_int @@ Electrons.charge e);
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check int "n_elec" 10 (Electrons.n_elec e);
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check int "multiplicity" 1 (Electrons.multiplicity e);
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check int "of_atoms alfa m3" 6 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_alfa));
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check int "of_atoms beta m3" 4 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_beta));
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check int "of_atoms n_elec m3" 10 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_elec));
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check int "of_atoms alfa m2 c1" 5 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_alfa));
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check int "of_atoms beta m2 c1" 4 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_beta));
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check int "of_atoms beta m2 c1" 9 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_elec));
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check int "of_atoms mult m2 c1" 2 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> multiplicity));
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check bool "make" true (Electrons.make 6 4 = Electrons.(of_atoms ~multiplicity:3 nuclei));
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(* Access:3 ends here *)
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(* Tests *)
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(* [[file:../electrons.org::*Tests][Tests:1]] *)
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()
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let tests = [
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"all", `Quick, test_all
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]
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(* Tests:1 ends here *)
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