mirror of https://gitlab.com/scemama/QCaml.git
Removing org-mode
This commit is contained in:
parent
744f2a0552
commit
d6ef25d55a
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@ -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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@ -32,41 +19,29 @@ 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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| 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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(* 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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@ -1,6 +1,8 @@
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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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| Boys
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@ -18,7 +20,7 @@ type localization_data =
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convergence : float ;
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iteration : int ;
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}
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type t =
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{
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kind : localization_kind ;
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@ -26,14 +28,10 @@ type t =
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data : localization_data option lazy_t array ;
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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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(* [[file:~/QCaml/mo/localization.org::*Edmiston-Rudenberg][Edmiston-Rudenberg:1]] *)
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(** Edmiston-Rudenberg *)
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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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@ -117,7 +115,7 @@ let kappa_edmiston in_basis m_C =
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) (Util.array_range 1 n_ao);
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let f i j =
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let f i j =
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if i=j then
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0.
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else
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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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@ -147,11 +143,11 @@ let kappa_boys in_basis =
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let multipole = Ao.Basis.multipole ao_basis in
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fun m_C ->
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let n_mo = Matrix.dim2 m_C in
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let phi_x_phi = Matrix.xt_o_x ~x:m_C ~o:(multipole "x") in
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let phi_y_phi = Matrix.xt_o_x ~x:m_C ~o:(multipole "y") in
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let phi_z_phi = Matrix.xt_o_x ~x:m_C ~o:(multipole "z") in
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let m_b12 =
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let g x i j =
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let x_ii = x%:(i,i) in
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@ -160,13 +156,13 @@ let kappa_boys in_basis =
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(x_ii -. x_jj) *. x_ij
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in
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Matrix.init_cols n_mo n_mo (fun i j ->
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let x =
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(g phi_x_phi i j) +. (g phi_y_phi i j) +. (g phi_z_phi i j)
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let x =
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(g phi_x_phi i j) +. (g phi_y_phi i j) +. (g phi_z_phi i j)
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in
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if (abs_float x > 1.e-15) then x else 0.
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)
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)
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in
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let m_a12 =
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let g x i j =
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let x_ii = x%:(i,i) in
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@ -176,18 +172,18 @@ let kappa_boys in_basis =
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(x_ij *. x_ij) -. 0.25 *. y *. y
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in
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Matrix.init_cols n_mo n_mo (fun i j ->
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let x =
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(g phi_x_phi i j) +. (g phi_y_phi i j) +. (g phi_z_phi i j)
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let x =
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(g phi_x_phi i j) +. (g phi_y_phi i j) +. (g phi_z_phi i j)
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in
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if (abs_float x > 1.e-15) then x else 0.
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)
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)
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in
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let f i j =
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let f i j =
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let pi = Constants.pi in
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if i=j then
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0.
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else
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else
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let x = atan2 (m_b12%:(i,j)) (m_a12%:(i,j)) in
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if x >= 0. then
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0.25 *. (pi -. x)
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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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@ -218,7 +212,7 @@ let kappa ~kind =
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match kind with
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| Edmiston -> kappa_edmiston
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| Boys -> kappa_boys
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let n_iterations t =
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Array.fold_left (fun accu x ->
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@ -238,20 +232,20 @@ let ao_basis t = Simulation.ao_basis (simulation t)
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let make ~kind ?(max_iter=500) ?(convergence=1.e-6) mo_basis selected_mos =
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let kappa_loc = kappa ~kind mo_basis in
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let mo_array = Matrix.to_col_vecs (Basis.mo_coef mo_basis) in
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let mos_vec_list = List.map (fun i -> mo_array.(i-1)) selected_mos in
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let x: (ao,loc) Matrix.t =
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Matrix.of_col_vecs_list mos_vec_list
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Matrix.of_col_vecs_list mos_vec_list
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in
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let next_coef kappa x =
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let next_coef kappa x =
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let r = Matrix.exponential_antisymmetric kappa in
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let m_C = Matrix.gemm_nt x r in
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m_C
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in
|
||||
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||||
let data_initial =
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||||
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||||
let data_initial =
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let iteration = 0
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and scaling = 0.1
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in
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||||
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|
@ -262,7 +256,7 @@ let make ~kind ?(max_iter=500) ?(convergence=1.e-6) mo_basis selected_mos =
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{ coefficients ; kappa ; scaling ; convergence ; loc_value ; iteration }
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in
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let iteration data =
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let iteration data =
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let iteration = data.iteration+1 in
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let new_kappa, new_loc_value = kappa_loc data.coefficients in
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let new_convergence = abs_float (Matrix.amax new_kappa) in
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@ -318,33 +312,34 @@ let make ~kind ?(max_iter=500) ?(convergence=1.e-6) mo_basis selected_mos =
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Array.init max_iter (fun i -> lazy (loop i))
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in
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{ kind ; mo_basis ; data = array_data ; selected_mos }
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|
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let to_basis t =
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let to_basis t =
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let mo_basis = t.mo_basis in
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let simulation = Basis.simulation mo_basis in
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let mo_occupation = Basis.mo_occupation mo_basis in
|
||||
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let data = last_iteration t in
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|
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let mo_coef_array = Matrix.to_col_vecs (Basis.mo_coef mo_basis) in
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let new_mos =
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Matrix.to_col_vecs data.coefficients
|
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Matrix.to_col_vecs data.coefficients
|
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in
|
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selected_mos 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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||||
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(* [[file:~/QCaml/mo/localization.org::*Printers][Printers:2]] *)
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(** Printers *)
|
||||
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||||
let linewidth = 60
|
||||
|
||||
let pp_iterations ppf t =
|
||||
let line = (String.make linewidth '-') in
|
||||
Format.fprintf ppf "@[%4s%s@]@." "" line;
|
||||
Format.fprintf ppf "@[%4s@[%5s@]@,@[%16s@]@,@[%16s@]@,@[%11s@]@]@."
|
||||
Format.fprintf ppf "@[%4s@[%5s@]@,@[%16s@]@,@[%16s@]@,@[%11s@]@]@."
|
||||
"" "#" "Localization " "Convergence" "Scaling";
|
||||
Format.fprintf ppf "@[%4s%s@]@." "" line;
|
||||
Array.iter (fun data ->
|
||||
|
|
@ -372,4 +367,3 @@ let pp ppf t =
|
|||
) "MO Localization";
|
||||
Format.fprintf ppf "@[%s@]@.@." (String.make 70 '=');
|
||||
Format.fprintf ppf "@[%a@]@." pp_iterations t;
|
||||
(* Printers:2 ends here *)
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
(* Type
|
||||
*
|
||||
* #+NAME: types *)
|
||||
(** Orbital localization *)
|
||||
|
||||
|
||||
(** Types *)
|
||||
|
||||
(* [[file:~/QCaml/mo/localization.org::types][types]] *)
|
||||
open Linear_algebra
|
||||
|
||||
|
||||
type localization_kind =
|
||||
| Edmiston
|
||||
| Boys
|
||||
|
|
@ -12,17 +12,13 @@ type localization_kind =
|
|||
type mo = Mo_dim.t
|
||||
type ao = Ao.Ao_dim.t
|
||||
type loc
|
||||
(* types ends here *)
|
||||
|
||||
(* [[file:~/QCaml/mo/localization.org::*Type][Type:2]] *)
|
||||
type localization_data
|
||||
type localization_data
|
||||
type t
|
||||
(* Type:2 ends here *)
|
||||
|
||||
(* Access *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/mo/localization.org::*Access][Access:1]] *)
|
||||
(** Access *)
|
||||
|
||||
val kind : t -> localization_kind
|
||||
val simulation : t -> Simulation.t
|
||||
val selected_mos : t -> int list
|
||||
|
|
@ -32,21 +28,20 @@ val kappa :
|
|||
Basis.t ->
|
||||
( ao,loc) Matrix.t ->
|
||||
(loc,loc) Matrix.t * float
|
||||
(** Returns the $\kappa$ antisymmetric matrix used for the rotation matrix and the value of the localization function *)
|
||||
|
||||
val make :
|
||||
kind:localization_kind ->
|
||||
?max_iter:int ->
|
||||
?convergence:float ->
|
||||
?max_iter:int ->
|
||||
?convergence:float ->
|
||||
Basis.t ->
|
||||
int list ->
|
||||
t
|
||||
(** Performs the orbital localization *)
|
||||
|
||||
val to_basis : t -> Basis.t
|
||||
(* Access:1 ends here *)
|
||||
|
||||
(* Printers *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/mo/localization.org::*Printers][Printers:1]] *)
|
||||
(** Printers *)
|
||||
|
||||
val pp : Format.formatter -> t -> unit
|
||||
(* Printers:1 ends here *)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,72 @@
|
|||
(* Tests *)
|
||||
|
||||
let test_localization =
|
||||
|
||||
let nuclei =
|
||||
Particles.Nuclei.of_xyz_string
|
||||
" 10
|
||||
Hydrogen chain, d=1.8 Angstrom
|
||||
H -4.286335 0.000000 0.000000
|
||||
H -3.333816 0.000000 0.000000
|
||||
H -2.381297 0.000000 0.000000
|
||||
H -1.428778 0.000000 0.000000
|
||||
H -0.476259 0.000000 0.000000
|
||||
H 0.476259 0.000000 0.000000
|
||||
H 1.428778 0.000000 0.000000
|
||||
H 2.381297 0.000000 0.000000
|
||||
H 3.333816 0.000000 0.000000
|
||||
H 4.286335 0.000000 0.000000
|
||||
" in
|
||||
|
||||
let basis_file = "/home/scemama/qp2/data/basis/sto-6g" in
|
||||
|
||||
let ao_basis =
|
||||
Ao.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
|
||||
in
|
||||
|
||||
|
||||
let charge = 0 in
|
||||
|
||||
let multiplicity = 1 in
|
||||
|
||||
let simulation =
|
||||
Simulation.make ~charge ~multiplicity ~nuclei ao_basis
|
||||
in
|
||||
|
||||
let hf =
|
||||
Mo.Hartree_fock.make ~guess:`Hcore simulation
|
||||
in
|
||||
|
||||
let mo_basis =
|
||||
Mo.Basis.of_hartree_fock hf
|
||||
in
|
||||
|
||||
let localized_mo_basis =
|
||||
Mo.Localization.make
|
||||
~kind:Mo.Localization.Boys
|
||||
mo_basis
|
||||
[4;5;6;7;8]
|
||||
|> Mo.Localization.to_basis
|
||||
in
|
||||
|
||||
Format.printf "%a" (Mo.Basis.pp ~start:1 ~finish:10) localized_mo_basis
|
||||
|
||||
|
||||
(*
|
||||
open Common
|
||||
open Alcotest
|
||||
let wd = Qcaml.root ^ Filename.dir_sep ^ "test" in
|
||||
|
||||
let test_xyz molecule length repulsion charge core =
|
||||
let xyz = Nuclei.of_xyz_file (wd^Filename.dir_sep^molecule^".xyz") in
|
||||
check int "length" length (Array.length xyz);
|
||||
check (float 1.e-4) "repulsion" repulsion (Nuclei.repulsion xyz);
|
||||
check int "charge" charge (Charge.to_int @@ Nuclei.charge xyz);
|
||||
check int "small_core" core (Nuclei.small_core xyz);
|
||||
()
|
||||
|
||||
let tests = [
|
||||
"caffeine", `Quick, (fun () -> test_xyz "caffeine" 24 917.0684 102 28);
|
||||
"water", `Quick, (fun () -> test_xyz "water" 3 9.19497 10 2);
|
||||
]
|
||||
*)
|
||||
|
|
@ -1,13 +1,6 @@
|
|||
(* [[file:~/QCaml/top/install_printers.org::*Intall printers][Intall printers:3]] *)
|
||||
(** Intall printers printers:3]] *)
|
||||
let printers =
|
||||
[
|
||||
"Common.Powers.pp" ;
|
||||
"Common.Range.pp" ;
|
||||
"Common.Spin.pp" ;
|
||||
"Common.Zkey.pp" ;
|
||||
"Gaussian.Atomic_shell.pp" ;
|
||||
"Gaussian.Atomic_shell_pair.pp" ;
|
||||
"Gaussian.Atomic_shell_pair_couple.pp" ;
|
||||
"Mo.Frozen_core.pp" ;
|
||||
"Mo.Localization.pp" ;
|
||||
"Particles.Electrons.pp" ;
|
||||
|
|
@ -16,7 +9,7 @@ let printers =
|
|||
"Particles.Zmatrix.pp" ;
|
||||
"Perturbation.Mp2.pp" ;
|
||||
"Simulation.pp" ;
|
||||
|
||||
|
||||
]
|
||||
|
||||
let eval_exn str =
|
||||
|
|
@ -34,4 +27,3 @@ let rec install_printers = function
|
|||
let () =
|
||||
if not (install_printers printers) then
|
||||
Format.eprintf "Problem installing QCaml-printers@."
|
||||
(* Intall printers:3 ends here *)
|
||||
|
|
|
|||
Loading…
Reference in New Issue