mirror of
https://gitlab.com/scemama/QCaml.git
synced 2024-08-15 17:28:29 +02:00
Removing org-mode
This commit is contained in:
parent
744f2a0552
commit
d6ef25d55a
@ -1,118 +0,0 @@
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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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* Frozen core
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:PROPERTIES:
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:header-args: :noweb yes :comments both
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:END:
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Defines how the core electrons are frozen, for each atom.
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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 kind =
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| All_electron
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| Small
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| Large
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#+end_src
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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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<<types>>
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type t = int array
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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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val make : kind -> Particles.Nuclei.t -> t
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val of_int_list : int list -> t
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val of_int_array : int array -> t
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#+end_src
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| ~make~ | Creates a ~Frozen_core.t~ with the same kind for all atoms |
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| ~of_int_array~ | Creates a ~Frozen_core.t~ giving the number of frozen electrons per atom |
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| ~of_int_list~ | Creates a ~Frozen_core.t~ giving the number of frozen electrons per atom |
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#+begin_example
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let f = Frozen_core.(make Small nuclei) ;;
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val f : Frozen_core.t = [|0; 2; 2; 0|]
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let f = Frozen_core.(of_int_list [0; 2; 2; 0])
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val f : Frozen_core.t = [|0; 2; 2; 0|]
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#+end_example
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#+begin_src ocaml :tangle (eval ml) :exports none
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let make_ae nuclei =
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Array.map (fun _ -> 0) nuclei
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let make_small nuclei =
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Array.map (fun (e,_) -> Particles.Element.small_core e) nuclei
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let make_large nuclei =
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Array.map (fun (e,_) -> Particles.Element.large_core e) nuclei
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let make = function
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| All_electron -> make_ae
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| Small -> make_small
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| Large -> make_large
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external of_int_array : int array -> t = "%identity"
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let of_int_list = Array.of_list
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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 num_elec : t -> int
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val num_mos : t -> int
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#+end_src
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| ~num_elec~ | Number of frozen electrons |
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| ~num_mos~ | Number of frozen molecular orbitals |
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#+begin_example
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Frozen_core.num_elec f ;;
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- : int = 4
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Frozen_core.num_mos f ;;
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- : int = 2
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#+end_example
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#+begin_src ocaml :tangle (eval ml) :exports none
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let num_elec t =
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Array.fold_left ( + ) 0 t
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let num_mos t =
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(num_elec t) / 2
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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 "@[[|";
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Array.iter (fun x -> Format.fprintf ppf "@,@[%d@]" x) t;
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Format.fprintf ppf "|]@]";
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#+end_src
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@ -1,27 +1,14 @@
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(* [[file:~/QCaml/mo/frozen_core.org::*Type][Type:3]] *)
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(** Type *)
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type kind =
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| All_electron
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| Small
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| Large
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type t = int array
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(* Type:3 ends here *)
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(** Creation *)
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(* | ~make~ | Creates a ~Frozen_core.t~ with the same kind for all atoms |
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* | ~of_int_array~ | Creates a ~Frozen_core.t~ giving the number of frozen electrons per atom |
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* | ~of_int_list~ | Creates a ~Frozen_core.t~ giving the number of frozen electrons per atom |
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*
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* #+begin_example
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* let f = Frozen_core.(make Small nuclei) ;;
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* val f : Frozen_core.t = [|0; 2; 2; 0|]
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*
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* let f = Frozen_core.(of_int_list [0; 2; 2; 0])
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* val f : Frozen_core.t = [|0; 2; 2; 0|]
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* #+end_example *)
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(* [[file:~/QCaml/mo/frozen_core.org::*Creation][Creation:2]] *)
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let make_ae nuclei =
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Array.map (fun _ -> 0) nuclei
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@ -40,33 +27,21 @@ let make = function
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external of_int_array : int array -> t = "%identity"
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let of_int_list = Array.of_list
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(* Creation:2 ends here *)
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(** Access *)
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(* | ~num_elec~ | Number of frozen electrons |
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* | ~num_mos~ | Number of frozen molecular orbitals |
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*
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* #+begin_example
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* Frozen_core.num_elec f ;;
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* - : int = 4
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*
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* Frozen_core.num_mos f ;;
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* - : int = 2
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* #+end_example *)
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(* [[file:~/QCaml/mo/frozen_core.org::*Access][Access:2]] *)
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let num_elec t =
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Array.fold_left ( + ) 0 t
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let num_mos t =
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(num_elec t) / 2
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(* Access:2 ends here *)
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(* [[file:~/QCaml/mo/frozen_core.org::*Printers][Printers:2]] *)
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(** Printers *)
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let pp ppf t =
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Format.fprintf ppf "@[[|";
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Array.iter (fun x -> Format.fprintf ppf "@,@[%d@]" x) t;
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Format.fprintf ppf "|]@]";
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(* Printers:2 ends here *)
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@ -1,39 +1,55 @@
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(* Type
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*
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* #+NAME: types *)
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(** Type *)
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(** Defines how the core electrons are frozen, for each atom. *)
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(* [[file:~/QCaml/mo/frozen_core.org::types][types]] *)
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type kind =
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| All_electron
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| Small
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| Large
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(* types ends here *)
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(* [[file:~/QCaml/mo/frozen_core.org::*Type][Type:2]] *)
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type t
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(* Type:2 ends here *)
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(* Creation *)
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(* [[file:~/QCaml/mo/frozen_core.org::*Creation][Creation:1]] *)
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(** Creation *)
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(** Example
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*
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* let f = Frozen_core.(make Small nuclei) ;;
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* val f : Frozen_core.t = [|0; 2; 2; 0|]
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*
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* let f = Frozen_core.(of_int_list [0; 2; 2; 0])
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* val f : Frozen_core.t = [|0; 2; 2; 0|]
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*
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*)
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val make : kind -> Particles.Nuclei.t -> t
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(** Creates a ~Frozen_core.t~ with the same kind for all atoms *)
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val of_int_list : int list -> t
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(** Creates a ~Frozen_core.t~ giving the number of frozen electrons per atom *)
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val of_int_array : int array -> t
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(* Creation:1 ends here *)
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(* Access *)
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(** Creates a ~Frozen_core.t~ giving the number of frozen electrons per atom *)
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(* [[file:~/QCaml/mo/frozen_core.org::*Access][Access:1]] *)
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(** Access *)
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(** Example
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*
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* Frozen_core.num_elec f ;;
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* - : int = 4
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*
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* Frozen_core.num_mos f ;;
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*
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*)
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val num_elec : t -> int
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(** Number of frozen electrons *)
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val num_mos : t -> int
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(* Access:1 ends here *)
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(** Number of frozen molecular orbitals *)
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(* Printers *)
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(** Printers *)
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(* [[file:~/QCaml/mo/frozen_core.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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@ -1,5 +1,7 @@
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(* [[file:~/QCaml/mo/localization.org::*Type][Type:3]] *)
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open Linear_algebra
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open Common
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(** Types *)
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type localization_kind =
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| Edmiston
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@ -27,13 +29,9 @@ type t =
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selected_mos : int list ;
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}
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open Common
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(* Type:3 ends here *)
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(* Edmiston-Rudenberg *)
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(** Edmiston-Rudenberg *)
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(* [[file:~/QCaml/mo/localization.org::*Edmiston-Rudenberg][Edmiston-Rudenberg:1]] *)
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let kappa_edmiston in_basis m_C =
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let ao_basis =
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Basis.simulation in_basis
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@ -133,12 +131,10 @@ let kappa_edmiston in_basis m_C =
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Matrix.init_cols n_mo n_mo ( fun i j -> if i<=j then f i j else -. (f j i) ),
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Vector.sum (Vector.of_bigarray_inplace v_d)
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)
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(* Edmiston-Rudenberg:1 ends here *)
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(* Boys *)
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(* [[file:~/QCaml/mo/localization.org::*Boys][Boys:1]] *)
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(** Boys *)
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let kappa_boys in_basis =
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let ao_basis =
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Basis.simulation in_basis
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@ -205,11 +201,9 @@ let kappa_boys in_basis =
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(* | ~kappa~ | Returns the $\kappa$ antisymmetric matrix used for the rotation matrix and the value of the localization function |
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* | ~make~ | Performs the orbital localization | *)
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(** Access *)
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(* [[file:~/QCaml/mo/localization.org::*Access][Access:2]] *)
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let kind t = t.kind
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let simulation t = Basis.simulation t.mo_basis
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let selected_mos t = t.selected_mos
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@ -336,9 +330,10 @@ let to_basis t =
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|> List.iteri (fun i j -> mo_coef_array.(j-1) <- new_mos.(i)) ;
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let mo_coef = Matrix.of_col_vecs mo_coef_array in
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Basis.make ~simulation ~mo_type:(Localized "Boys") ~mo_occupation ~mo_coef ()
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(* Access:2 ends here *)
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(* [[file:~/QCaml/mo/localization.org::*Printers][Printers:2]] *)
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(** Printers *)
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let linewidth = 60
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let pp_iterations ppf t =
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@ -372,4 +367,3 @@ let pp ppf t =
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) "MO Localization";
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Format.fprintf ppf "@[%s@]@.@." (String.make 70 '=');
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Format.fprintf ppf "@[%a@]@." pp_iterations t;
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(* Printers:2 ends here *)
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@ -1,8 +1,8 @@
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(* Type
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*
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* #+NAME: types *)
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(** Orbital localization *)
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(** Types *)
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(* [[file:~/QCaml/mo/localization.org::types][types]] *)
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open Linear_algebra
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type localization_kind =
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@ -12,17 +12,13 @@ type localization_kind =
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type mo = Mo_dim.t
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type ao = Ao.Ao_dim.t
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type loc
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(* types ends here *)
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(* [[file:~/QCaml/mo/localization.org::*Type][Type:2]] *)
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type localization_data
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type t
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(* Type:2 ends here *)
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(* Access *)
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(* [[file:~/QCaml/mo/localization.org::*Access][Access:1]] *)
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(** Access *)
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val kind : t -> localization_kind
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val simulation : t -> Simulation.t
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val selected_mos : t -> int list
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@ -32,6 +28,7 @@ val kappa :
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Basis.t ->
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( ao,loc) Matrix.t ->
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(loc,loc) Matrix.t * float
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(** Returns the $\kappa$ antisymmetric matrix used for the rotation matrix and the value of the localization function *)
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val make :
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kind:localization_kind ->
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@ -40,13 +37,11 @@ val make :
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Basis.t ->
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int list ->
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t
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(** Performs the orbital localization *)
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val to_basis : t -> Basis.t
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(* Access:1 ends here *)
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(* Printers *)
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(* [[file:~/QCaml/mo/localization.org::*Printers][Printers:1]] *)
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(** Printers *)
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val pp : Format.formatter -> t -> unit
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(* Printers:1 ends here *)
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72
mo/test/localization.ml
Normal file
72
mo/test/localization.ml
Normal file
@ -0,0 +1,72 @@
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(* Tests *)
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let test_localization =
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let nuclei =
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Particles.Nuclei.of_xyz_string
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" 10
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Hydrogen chain, d=1.8 Angstrom
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H -4.286335 0.000000 0.000000
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H -3.333816 0.000000 0.000000
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H -2.381297 0.000000 0.000000
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H -1.428778 0.000000 0.000000
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H -0.476259 0.000000 0.000000
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H 0.476259 0.000000 0.000000
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H 1.428778 0.000000 0.000000
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H 2.381297 0.000000 0.000000
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H 3.333816 0.000000 0.000000
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H 4.286335 0.000000 0.000000
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" in
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let basis_file = "/home/scemama/qp2/data/basis/sto-6g" in
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let ao_basis =
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Ao.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
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in
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let charge = 0 in
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let multiplicity = 1 in
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let simulation =
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Simulation.make ~charge ~multiplicity ~nuclei ao_basis
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in
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let hf =
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Mo.Hartree_fock.make ~guess:`Hcore simulation
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in
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let mo_basis =
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Mo.Basis.of_hartree_fock hf
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in
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let localized_mo_basis =
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Mo.Localization.make
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~kind:Mo.Localization.Boys
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mo_basis
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[4;5;6;7;8]
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|> Mo.Localization.to_basis
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in
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Format.printf "%a" (Mo.Basis.pp ~start:1 ~finish:10) localized_mo_basis
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(*
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open Common
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open Alcotest
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let wd = Qcaml.root ^ Filename.dir_sep ^ "test" in
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let test_xyz molecule length repulsion charge core =
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let xyz = Nuclei.of_xyz_file (wd^Filename.dir_sep^molecule^".xyz") in
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check int "length" length (Array.length xyz);
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check (float 1.e-4) "repulsion" repulsion (Nuclei.repulsion xyz);
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check int "charge" charge (Charge.to_int @@ Nuclei.charge xyz);
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check int "small_core" core (Nuclei.small_core xyz);
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()
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let tests = [
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"caffeine", `Quick, (fun () -> test_xyz "caffeine" 24 917.0684 102 28);
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"water", `Quick, (fun () -> test_xyz "water" 3 9.19497 10 2);
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]
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*)
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@ -1,13 +1,6 @@
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(* [[file:~/QCaml/top/install_printers.org::*Intall printers][Intall printers:3]] *)
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(** Intall printers printers:3]] *)
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let printers =
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[
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"Common.Powers.pp" ;
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"Common.Range.pp" ;
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"Common.Spin.pp" ;
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"Common.Zkey.pp" ;
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"Gaussian.Atomic_shell.pp" ;
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"Gaussian.Atomic_shell_pair.pp" ;
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"Gaussian.Atomic_shell_pair_couple.pp" ;
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"Mo.Frozen_core.pp" ;
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"Mo.Localization.pp" ;
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"Particles.Electrons.pp" ;
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@ -34,4 +27,3 @@ let rec install_printers = function
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let () =
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if not (install_printers printers) then
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Format.eprintf "Problem installing QCaml-printers@."
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(* Intall printers:3 ends here *)
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Reference in New Issue
Block a user