mirror of https://gitlab.com/scemama/QCaml.git
Electrons org-mode
This commit is contained in:
parent
65d04a76f2
commit
79f1b581f9
|
|
@ -0,0 +1,160 @@
|
|||
#+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
|
||||
|
||||
* Electrons
|
||||
:PROPERTIES:
|
||||
:header-args: :noweb yes :comments both
|
||||
:END:
|
||||
|
||||
Data structure which contains the number of \alpha and \beta electrons.
|
||||
|
||||
** Type
|
||||
|
||||
#+NAME: types
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
type t
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
type t = {
|
||||
n_alfa : int ;
|
||||
n_beta : int ;
|
||||
}
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval test-ml) :exports none
|
||||
open Common
|
||||
open Particles
|
||||
open Alcotest
|
||||
|
||||
let test_all () =
|
||||
let nuclei =
|
||||
"3
|
||||
Water
|
||||
O 0. 0. 0.
|
||||
H -0.756950272703377558 0. -0.585882234512562827
|
||||
H 0.756950272703377558 0. -0.585882234512562827
|
||||
"
|
||||
|> Nuclei.of_xyz_string
|
||||
in
|
||||
let e = Electrons.of_atoms nuclei in
|
||||
#+end_src
|
||||
|
||||
** Creation
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
open Common
|
||||
|
||||
val make : int -> int -> t
|
||||
|
||||
val of_atoms : ?multiplicity:int -> ?charge:int -> Nuclei.t -> t
|
||||
(* @param multiplicity default is 1
|
||||
@param charge default is 0
|
||||
@raise Invalid_argument if the spin multiplicity is not compatible with
|
||||
the molecule and the total charge.
|
||||
*)
|
||||
#+end_src
|
||||
|
||||
| ~make~ | ~make n_alfa n_beta~ |
|
||||
| ~of_atoms~ | Creates the data relative to electrons for a molecular system described by ~Nuclei.t~ for a given total charge and spin multiplicity. |
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
open Common
|
||||
|
||||
let make n_alfa n_beta =
|
||||
{ n_alfa ; n_beta }
|
||||
|
||||
|
||||
let of_atoms ?multiplicity:(multiplicity=1) ?charge:(charge=0) nuclei =
|
||||
let positive_charges =
|
||||
Array.fold_left (fun accu (e, _) -> accu + Charge.to_int (Element.to_charge e) )
|
||||
0 nuclei
|
||||
in
|
||||
let negative_charges = charge - positive_charges in
|
||||
let n_elec = - negative_charges in
|
||||
let n_beta = ((n_elec - multiplicity)+1)/2 in
|
||||
let n_alfa = n_elec - n_beta in
|
||||
let result = { n_alfa ; n_beta } in
|
||||
if multiplicity <> (n_alfa - n_beta)+1 then
|
||||
invalid_arg (__FILE__^": make");
|
||||
result
|
||||
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval test-ml) :exports none
|
||||
check int "of_atoms alfa" 5 (Electrons.n_alfa e);
|
||||
check int "of_atoms beta" 5 (Electrons.n_beta e);
|
||||
#+end_src
|
||||
|
||||
** Access
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val charge : t -> Charge.t
|
||||
val n_elec : t -> int
|
||||
val n_alfa : t -> int
|
||||
val n_beta : t -> int
|
||||
val multiplicity : t -> int
|
||||
#+end_src
|
||||
|
||||
| ~charge~ | Sum of the charges of the electrons |
|
||||
| ~n_elec~ | Number of electrons |
|
||||
| ~n_alfa~ | Number of alpha electrons |
|
||||
| ~n_beta~ | Number of beta electrons |
|
||||
| ~multiplicity~ | Spin multiplicity: $2S+1$ |
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let charge e =
|
||||
- (e.n_alfa + e.n_beta)
|
||||
|> Charge.of_int
|
||||
|
||||
let n_alfa t = t.n_alfa
|
||||
|
||||
let n_beta t = t.n_beta
|
||||
|
||||
let n_elec t = t.n_alfa + t.n_beta
|
||||
|
||||
let multiplicity t = t.n_alfa - t.n_beta + 1
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval test-ml) :exports none
|
||||
check int "charge " (-10) (Charge.to_int @@ Electrons.charge e);
|
||||
check int "n_elec" 10 (Electrons.n_elec e);
|
||||
check int "multiplicity" 1 (Electrons.multiplicity e);
|
||||
check int "of_atoms alfa m3" 6 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_alfa));
|
||||
check int "of_atoms beta m3" 4 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_beta));
|
||||
check int "of_atoms n_elec m3" 10 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_elec));
|
||||
check int "of_atoms alfa m2 c1" 5 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_alfa));
|
||||
check int "of_atoms beta m2 c1" 4 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_beta));
|
||||
check int "of_atoms beta m2 c1" 9 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_elec));
|
||||
check int "of_atoms mult m2 c1" 2 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> multiplicity));
|
||||
check bool "make" true (Electrons.make 6 4 = Electrons.(of_atoms ~multiplicity:3 nuclei));
|
||||
#+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 "@[n_alfa=%d, n_beta=%d@]" t.n_alfa t.n_beta
|
||||
#+end_src
|
||||
|
||||
** Tests
|
||||
|
||||
#+begin_src ocaml :tangle (eval test-ml) :exports none
|
||||
()
|
||||
|
||||
let tests = [
|
||||
"all", `Quick, test_all
|
||||
]
|
||||
#+end_src
|
||||
|
|
@ -1,13 +1,19 @@
|
|||
(** Number of {% $\alpha$ %} and {% $\beta$ %} electrons *)
|
||||
|
||||
open Common
|
||||
|
||||
(* [[file:../electrons.org::*Type][Type:2]] *)
|
||||
type t = {
|
||||
n_alfa : int ;
|
||||
n_beta : int ;
|
||||
}
|
||||
(* Type:2 ends here *)
|
||||
|
||||
|
||||
|
||||
(* | ~make~ | ~make n_alfa n_beta~ |
|
||||
* | ~of_atoms~ | Creates the data relative to electrons for a molecular system described by ~Nuclei.t~ for a given total charge and spin multiplicity. | *)
|
||||
|
||||
|
||||
(* [[file:../electrons.org::*Creation][Creation:2]] *)
|
||||
open Common
|
||||
|
||||
let make n_alfa n_beta =
|
||||
{ n_alfa ; n_beta }
|
||||
|
||||
|
|
@ -25,14 +31,32 @@ let of_atoms ?multiplicity:(multiplicity=1) ?charge:(charge=0) nuclei =
|
|||
if multiplicity <> (n_alfa - n_beta)+1 then
|
||||
invalid_arg (__FILE__^": make");
|
||||
result
|
||||
(* Creation:2 ends here *)
|
||||
|
||||
|
||||
|
||||
(* | ~charge~ | Sum of the charges of the electrons |
|
||||
* | ~n_elec~ | Number of electrons |
|
||||
* | ~n_alfa~ | Number of alpha electrons |
|
||||
* | ~n_beta~ | Number of beta electrons |
|
||||
* | ~multiplicity~ | Spin multiplicity: $2S+1$ | *)
|
||||
|
||||
|
||||
(* [[file:../electrons.org::*Access][Access:2]] *)
|
||||
let charge e =
|
||||
- (e.n_alfa + e.n_beta)
|
||||
|> Charge.of_int
|
||||
|
||||
|
||||
let n_alfa t = t.n_alfa
|
||||
|
||||
let n_beta t = t.n_beta
|
||||
|
||||
let n_elec t = t.n_alfa + t.n_beta
|
||||
|
||||
let multiplicity t = t.n_alfa - t.n_beta + 1
|
||||
(* Access:2 ends here *)
|
||||
|
||||
(* [[file:../electrons.org::*Printers][Printers:2]] *)
|
||||
let pp ppf t =
|
||||
Format.fprintf ppf "@[n_alfa=%d, n_beta=%d@]" t.n_alfa t.n_beta
|
||||
(* Printers:2 ends here *)
|
||||
|
|
|
|||
|
|
@ -1,33 +1,41 @@
|
|||
(** Information related to electrons. *)
|
||||
(* Type
|
||||
*
|
||||
* #+NAME: types *)
|
||||
|
||||
(* [[file:../electrons.org::types][types]] *)
|
||||
type t
|
||||
(* types ends here *)
|
||||
|
||||
(* Creation *)
|
||||
|
||||
|
||||
(* [[file:../electrons.org::*Creation][Creation:1]] *)
|
||||
open Common
|
||||
|
||||
type t
|
||||
|
||||
val make : int -> int -> t
|
||||
(** make [n_alfa] [n_beta] *)
|
||||
|
||||
val of_atoms : ?multiplicity:int -> ?charge:int -> Nuclei.t -> t
|
||||
(** Creates the data relative to electrons for a molecular system
|
||||
described by {!Nuclei.t} for a given total charge and spin multiplicity.
|
||||
@param multiplicity default is 1
|
||||
@param charge default is 0
|
||||
@raise Invalid_argument if the spin multiplicity is not compatible with
|
||||
(* @param multiplicity default is 1
|
||||
@param charge default is 0
|
||||
@raise Invalid_argument if the spin multiplicity is not compatible with
|
||||
the molecule and the total charge.
|
||||
*)
|
||||
*)
|
||||
(* Creation:1 ends here *)
|
||||
|
||||
val charge : t -> Charge.t
|
||||
(** Sum of the charges of the electrons. *)
|
||||
(* Access *)
|
||||
|
||||
val n_elec : t -> int
|
||||
(** Number of electrons *)
|
||||
|
||||
val n_alfa : t -> int
|
||||
(** Number of alpha electrons *)
|
||||
(* [[file:../electrons.org::*Access][Access:1]] *)
|
||||
val charge : t -> Charge.t
|
||||
val n_elec : t -> int
|
||||
val n_alfa : t -> int
|
||||
val n_beta : t -> int
|
||||
val multiplicity : t -> int
|
||||
(* Access:1 ends here *)
|
||||
|
||||
val n_beta : t -> int
|
||||
(** Number of beta electrons *)
|
||||
(* Printers *)
|
||||
|
||||
val multiplicity : t -> int
|
||||
(** Spin multiplicity: {% $2S+1$ %} *)
|
||||
|
||||
(* [[file:../electrons.org::*Printers][Printers:1]] *)
|
||||
val pp : Format.formatter -> t -> unit
|
||||
(* Printers:1 ends here *)
|
||||
|
|
|
|||
|
|
@ -1,8 +1,8 @@
|
|||
(* [[file:../electrons.org::*Type][Type:3]] *)
|
||||
open Common
|
||||
open Particles
|
||||
open Alcotest
|
||||
|
||||
|
||||
let test_all () =
|
||||
let nuclei =
|
||||
"3
|
||||
|
|
@ -14,21 +14,34 @@ H 0.756950272703377558 0. -0.585882234512562827
|
|||
|> Nuclei.of_xyz_string
|
||||
in
|
||||
let e = Electrons.of_atoms nuclei in
|
||||
check int "of_atoms alfa" 5 (Electrons.n_alfa e);
|
||||
check int "of_atoms beta" 5 (Electrons.n_beta e);
|
||||
check int "charge " (-10) (Charge.to_int @@ Electrons.charge e);
|
||||
check int "n_elec" 10 (Electrons.n_elec e);
|
||||
check int "multiplicity" 1 (Electrons.multiplicity e);
|
||||
check int "of_atoms alfa m3" 6 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_alfa));
|
||||
check int "of_atoms beta m3" 4 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_beta));
|
||||
check int "of_atoms n_elec m3" 10 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_elec));
|
||||
check int "of_atoms alfa m2 c1" 5 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_alfa));
|
||||
check int "of_atoms beta m2 c1" 4 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_beta));
|
||||
check int "of_atoms beta m2 c1" 9 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_elec));
|
||||
check int "of_atoms mult m2 c1" 2 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> multiplicity));
|
||||
check bool "make" true (Electrons.make 6 4 = Electrons.(of_atoms ~multiplicity:3 nuclei));
|
||||
(* Type:3 ends here *)
|
||||
|
||||
(* [[file:../electrons.org::*Creation][Creation:3]] *)
|
||||
check int "of_atoms alfa" 5 (Electrons.n_alfa e);
|
||||
check int "of_atoms beta" 5 (Electrons.n_beta e);
|
||||
(* Creation:3 ends here *)
|
||||
|
||||
(* [[file:../electrons.org::*Access][Access:3]] *)
|
||||
check int "charge " (-10) (Charge.to_int @@ Electrons.charge e);
|
||||
check int "n_elec" 10 (Electrons.n_elec e);
|
||||
check int "multiplicity" 1 (Electrons.multiplicity e);
|
||||
check int "of_atoms alfa m3" 6 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_alfa));
|
||||
check int "of_atoms beta m3" 4 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_beta));
|
||||
check int "of_atoms n_elec m3" 10 (Electrons.(of_atoms ~multiplicity:3 nuclei |> n_elec));
|
||||
check int "of_atoms alfa m2 c1" 5 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_alfa));
|
||||
check int "of_atoms beta m2 c1" 4 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_beta));
|
||||
check int "of_atoms beta m2 c1" 9 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> n_elec));
|
||||
check int "of_atoms mult m2 c1" 2 (Electrons.(of_atoms ~multiplicity:2 ~charge:1 nuclei |> multiplicity));
|
||||
check bool "make" true (Electrons.make 6 4 = Electrons.(of_atoms ~multiplicity:3 nuclei));
|
||||
(* Access:3 ends here *)
|
||||
|
||||
(* Tests *)
|
||||
|
||||
|
||||
(* [[file:../electrons.org::*Tests][Tests:1]] *)
|
||||
()
|
||||
|
||||
let tests = [
|
||||
"all", `Quick, test_all
|
||||
]
|
||||
(* Tests:1 ends here *)
|
||||
|
|
|
|||
Loading…
Reference in New Issue