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Cleaned localization
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@ -1,4 +1,4 @@
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(* [[file:~/QCaml/mo/localization.org::*Type][Type:3]] *)
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(** Types *)
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open Linear_algebra
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type localization_kind =
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@ -28,12 +28,10 @@ type t =
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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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@ -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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@ -201,15 +197,11 @@ let kappa_boys in_basis =
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r2 (phi_x_phi%:(i,i)) (phi_y_phi%:(i,i)) (phi_z_phi%:(i,i)))
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|> Vector.sum
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)
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(* Boys:1 ends here *)
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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 +328,10 @@ 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 +365,3 @@ 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 +1,5 @@
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(* Type
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*
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* #+NAME: types *)
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(** Molecular orbital localization *)
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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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@ -12,26 +9,31 @@ 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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(** Returns the kind of localized MOs *)
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val simulation : t -> Simulation.t
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(** Returns the simulation environment in which the MOs are localized *)
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val selected_mos : t -> int list
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(** List of indices of the orbitals involved in the localization *)
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val kappa :
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kind:localization_kind ->
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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
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* the value of the localization function
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*)
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val make :
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kind:localization_kind ->
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@ -40,13 +42,11 @@ 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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val pp : Format.formatter -> t -> unit
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(* Printers:1 ends here *)
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(** Printers *)
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val pp : Format.formatter -> t -> unit
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@ -1,520 +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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* Orbital localization
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:PROPERTIES:
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:header-args: :noweb yes :comments both
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:END:
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Molecular orbital localization function.
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Boys:
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Edmiston-Rudenberg:
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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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open Linear_algebra
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type localization_kind =
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| Edmiston
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| Boys
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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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#+end_src
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#+begin_src ocaml :tangle (eval mli)
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type localization_data
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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 localization_data =
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{
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coefficients : (ao, loc) Matrix.t ;
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kappa : (loc, loc) Matrix.t ;
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scaling : float ;
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loc_value : float ;
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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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mo_basis : Basis.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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#+end_src
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** Edmiston-Rudenberg
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#+begin_src ocaml :tangle (eval ml) :exports none
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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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|> Simulation.ao_basis
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in
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let ee_ints = Ao.Basis.ee_ints ao_basis in
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let n_ao = Ao.Basis.size ao_basis in
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let n_mo = Matrix.dim2 m_C in
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(* Temp arrays for integral transformation *)
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let m_pqr =
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Bigarray.(Array3.create Float64 fortran_layout n_ao n_ao n_ao)
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in
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let m_qr_i = Matrix.create (n_ao*n_ao) n_mo in
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let m_ri_j = Matrix.create (n_ao*n_mo) n_mo in
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let m_ij_k = Matrix.create (n_mo*n_mo) n_mo in
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let m_a12 = Bigarray.(Array2.create Float64 fortran_layout n_mo n_mo) in
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let m_b12 = Bigarray.(Array2.create Float64 fortran_layout n_mo n_mo) in
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Bigarray.Array2.fill m_b12 0.;
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Bigarray.Array2.fill m_a12 0.;
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let v_d =
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Vector.init n_mo (fun _ -> 0.)
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|> Vector.to_bigarray_inplace
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in
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Array.iter (fun s ->
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Array.iter (fun r ->
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Array.iter (fun q ->
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Array.iter (fun p ->
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m_pqr.{p,q,r} <- Four_idx_storage.get_phys ee_ints p q r s
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) (Util.array_range 1 n_ao)
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) (Util.array_range 1 n_ao)
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) (Util.array_range 1 n_ao);
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let m_p_qr =
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Bigarray.reshape (Bigarray.genarray_of_array3 m_pqr) [| n_ao ; n_ao*n_ao |]
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|> Bigarray.array2_of_genarray
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|> Matrix.of_bigarray_inplace
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in
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(* (qr,i) = <i r|q s> = \sum_p <p r | q s> C_{pi} *)
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Matrix.gemm_tn_inplace ~c:m_qr_i m_p_qr m_C;
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let m_q_ri =
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let x = Matrix.to_bigarray_inplace m_qr_i |> Bigarray.genarray_of_array2 in
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Bigarray.reshape_2 x n_ao (n_ao*n_mo) |> Matrix.of_bigarray_inplace
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in
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(* (ri,j) = <i r | j s> = \sum_q <i r | q s> C_{qj} *)
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Matrix.gemm_tn_inplace ~c:m_ri_j m_q_ri m_C;
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let m_r_ij =
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let x = Matrix.to_bigarray_inplace m_ri_j |> Bigarray.genarray_of_array2 in
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Bigarray.reshape_2 x n_ao (n_mo*n_mo) |> Matrix.of_bigarray_inplace
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in
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(* (ij,k) = <i k | j s> = \sum_r <i r | j s> C_{rk} *)
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Matrix.gemm_tn_inplace ~c:m_ij_k m_r_ij m_C;
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let m_ijk =
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let x = Matrix.to_bigarray_inplace m_ij_k |> Bigarray.genarray_of_array2 in
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Bigarray.reshape x [| n_mo ; n_mo ; n_mo |]
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|> Bigarray.array3_of_genarray
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in
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let m_Cx = Matrix.to_bigarray_inplace m_C in
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Array.iter (fun j ->
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Array.iter (fun i ->
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m_b12.{i,j} <- m_b12.{i,j} +. m_Cx.{s,j} *. (m_ijk.{i,i,i} -. m_ijk.{j,i,j});
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m_a12.{i,j} <- m_a12.{i,j} +. m_ijk.{i,i,j} *. m_Cx.{s,j} -.
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0.25 *. ( (m_ijk.{i,i,i} -. m_ijk.{j,i,j}) *. m_Cx.{s,i} +.
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(m_ijk.{j,j,j} -. m_ijk.{i,j,i}) *. m_Cx.{s,j})
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) (Util.array_range 1 n_mo);
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v_d.{j} <- v_d.{j} +. m_ijk.{j,j,j} *. m_Cx.{s,j}
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) (Util.array_range 1 n_mo)
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) (Util.array_range 1 n_ao);
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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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begin
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let x = 1./. sqrt (m_b12.{i,j} *. m_b12.{i,j} +. m_a12.{i,j} *. m_a12.{i,j} ) in
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if asin (m_b12.{i,j} /. x) > 0. then
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0.25 *. acos( -. m_a12.{i,j} *. x)
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else
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-. 0.25 *. acos( -. m_a12.{i,j} *. x )
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end
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in
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(
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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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#+end_src
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** Boys
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#+begin_src ocaml :tangle (eval ml) :exports none
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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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|> Simulation.ao_basis
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in
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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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let x_jj = x%:(j,j) in
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let x_ij = x%:(i,j) in
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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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in
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if (abs_float x > 1.e-15) then x else 0.
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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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let x_jj = x%:(j,j) in
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let x_ij = x%:(i,j) in
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let y = x_ii -. x_jj in
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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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in
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if (abs_float x > 1.e-15) then x else 0.
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)
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in
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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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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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else
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-. 0.25 *. ( pi +. x)
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in
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(
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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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let r2 x y z = x*.x +. y*.y +. z*.z in
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Vector.init n_mo ( fun i ->
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r2 (phi_x_phi%:(i,i)) (phi_y_phi%:(i,i)) (phi_z_phi%:(i,i)))
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|> Vector.sum
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)
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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 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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val kappa :
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kind:localization_kind ->
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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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val make :
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kind:localization_kind ->
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?max_iter:int ->
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?convergence:float ->
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Basis.t ->
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int list ->
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t
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val to_basis : t -> Basis.t
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#+end_src
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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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#+begin_src ocaml :tangle (eval ml) :exports none
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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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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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match Lazy.force x with
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| Some _ -> accu + 1
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| None -> accu
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) 0 t.data
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let last_iteration t =
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Util.of_some @@ Lazy.force t.data.(n_iterations t - 1)
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(*
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let ao_basis t = Simulation.ao_basis (simulation t)
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,*)
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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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in
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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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||||
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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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let kappa, loc_value = kappa_loc x in
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let convergence = abs_float (Matrix.amax kappa) in
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let kappa = Matrix.scale scaling kappa in
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let coefficients = next_coef kappa x in
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{ coefficients ; kappa ; scaling ; convergence ; loc_value ; iteration }
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in
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||||
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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
|
||||
let accept =
|
||||
new_loc_value >= data.loc_value*.0.98
|
||||
in
|
||||
if accept then
|
||||
let coefficients = next_coef new_kappa data.coefficients in
|
||||
let scaling = min 1. (data.scaling *. 1.1) in
|
||||
let kappa = Matrix.scale scaling new_kappa in
|
||||
let convergence = new_convergence in
|
||||
let loc_value = new_loc_value in
|
||||
{ coefficients ; kappa ; scaling ; convergence ; loc_value ; iteration }
|
||||
else
|
||||
let scaling =
|
||||
data.scaling *. 0.5
|
||||
in
|
||||
{ data with scaling ; iteration }
|
||||
in
|
||||
|
||||
let array_data =
|
||||
|
||||
let storage =
|
||||
Array.make max_iter None
|
||||
in
|
||||
|
||||
let rec loop = function
|
||||
| 0 -> Some (iteration data_initial)
|
||||
| n -> begin
|
||||
match storage.(n) with
|
||||
| Some result -> Some result
|
||||
| None -> begin
|
||||
let data = loop (n-1) in
|
||||
match data with
|
||||
| None -> None
|
||||
| Some data -> begin
|
||||
(* Check convergence *)
|
||||
let converged =
|
||||
data.convergence < convergence
|
||||
in
|
||||
if converged then
|
||||
None
|
||||
else
|
||||
begin
|
||||
storage.(n-1) <- Some data ;
|
||||
storage.(n) <- Some (iteration data);
|
||||
storage.(n)
|
||||
end
|
||||
end
|
||||
end
|
||||
end
|
||||
in
|
||||
Array.init max_iter (fun i -> lazy (loop i))
|
||||
in
|
||||
{ kind ; mo_basis ; data = array_data ; selected_mos }
|
||||
|
||||
|
||||
|
||||
let to_basis t =
|
||||
let mo_basis = t.mo_basis in
|
||||
let simulation = Basis.simulation mo_basis in
|
||||
let mo_occupation = Basis.mo_occupation mo_basis in
|
||||
|
||||
let data = last_iteration t in
|
||||
|
||||
let mo_coef_array = Matrix.to_col_vecs (Basis.mo_coef mo_basis) in
|
||||
let new_mos =
|
||||
Matrix.to_col_vecs data.coefficients
|
||||
in
|
||||
selected_mos t
|
||||
|> List.iteri (fun i j -> mo_coef_array.(j-1) <- new_mos.(i)) ;
|
||||
let mo_coef = Matrix.of_col_vecs mo_coef_array in
|
||||
Basis.make ~simulation ~mo_type:(Localized "Boys") ~mo_occupation ~mo_coef ()
|
||||
|
||||
#+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 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@]@]@."
|
||||
"" "#" "Localization " "Convergence" "Scaling";
|
||||
Format.fprintf ppf "@[%4s%s@]@." "" line;
|
||||
Array.iter (fun data ->
|
||||
let data = Lazy.force data in
|
||||
match data with
|
||||
| None -> ()
|
||||
| Some data ->
|
||||
let loc = data.loc_value in
|
||||
let conv = data.convergence in
|
||||
let scaling = data.scaling in
|
||||
let iteration = data.iteration in
|
||||
begin
|
||||
Format.fprintf ppf "@[%4s@[%5d@]@,@[%16.8f@]@,@[%16.4e@]@,@[%11.4f@]@]@." ""
|
||||
iteration loc conv scaling ;
|
||||
end
|
||||
) t.data;
|
||||
Format.fprintf ppf "@[%4s%s@]@." "" line
|
||||
|
||||
|
||||
let pp ppf t =
|
||||
Format.fprintf ppf "@.@[%s@]@." (String.make 70 '=');
|
||||
Format.fprintf ppf "@[%34s %-34s@]@." (match t.kind with
|
||||
| Boys -> "Boys"
|
||||
| Edmiston -> "Edmiston-Ruedenberg"
|
||||
) "MO Localization";
|
||||
Format.fprintf ppf "@[%s@]@.@." (String.make 70 '=');
|
||||
Format.fprintf ppf "@[%a@]@." pp_iterations t;
|
||||
|
||||
#+end_src
|
||||
|
||||
** Tests
|
||||
|
||||
#+begin_src ocaml :tangle (eval test-ml) :exports none
|
||||
|
||||
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);
|
||||
]
|
||||
,*)
|
||||
|
||||
#+end_src
|
||||
@ -1,10 +1,12 @@
|
||||
(* [[file:../simulation.org::*Simulation][Simulation:2]] *)
|
||||
(** Simulation *)
|
||||
|
||||
open Common
|
||||
open Particles
|
||||
open Operators
|
||||
(* Simulation:2 ends here *)
|
||||
|
||||
(* [[file:../simulation.org::*Type][Type:2]] *)
|
||||
|
||||
(** Type *)
|
||||
|
||||
type t = {
|
||||
charge : Charge.t;
|
||||
electrons : Electrons.t;
|
||||
@ -12,36 +14,20 @@ type t = {
|
||||
ao_basis : Ao.Basis.t;
|
||||
operators : Operator.t list;
|
||||
}
|
||||
(* Type:2 ends here *)
|
||||
|
||||
|
||||
(** Access *)
|
||||
|
||||
(* | ~nuclei~ | Nuclear coordinates used in the smiulation |
|
||||
* | ~charge~ | Total charge (electrons + nuclei) |
|
||||
* | ~electrons~ | Electrons used in the simulation |
|
||||
* | ~ao_basis~ | Atomic basis set |
|
||||
* | ~nuclear_repulsion~ | Nuclear repulsion energy |
|
||||
* | ~operators~ | List of extra operators (range-separation, f12, etc) | *)
|
||||
|
||||
|
||||
(* [[file:../simulation.org::*Access][Access:2]] *)
|
||||
let nuclei t = t.nuclei
|
||||
let charge t = t.charge
|
||||
let electrons t = t.electrons
|
||||
let ao_basis t = t.ao_basis
|
||||
let nuclear_repulsion t = Nuclei.repulsion @@ nuclei t
|
||||
let operators t = t.operators
|
||||
(* Access:2 ends here *)
|
||||
|
||||
|
||||
(** Creation *)
|
||||
|
||||
(* Defaults:
|
||||
* - multiplicity : ~1~
|
||||
* - charge : ~0~
|
||||
* - operators : ~[]~ *)
|
||||
|
||||
|
||||
(* [[file:../simulation.org::*Creation][Creation:2]] *)
|
||||
let make
|
||||
?(multiplicity=1)
|
||||
?(charge=0)
|
||||
@ -63,13 +49,14 @@ let make
|
||||
in
|
||||
|
||||
{ charge ; nuclei ; electrons ; ao_basis ; operators}
|
||||
(* Creation:2 ends here *)
|
||||
|
||||
(* [[file:../simulation.org::*Printers][Printers:2]] *)
|
||||
|
||||
(** Printers *)
|
||||
|
||||
let pp ppf t =
|
||||
let formula = Nuclei.formula t.nuclei in
|
||||
let n_aos = Ao.Basis.size t.ao_basis in
|
||||
let n_ops = List.length t.operators in
|
||||
Format.fprintf ppf "@[@[%s@], @[%a@], @[%d AOs@], @[%d operators@]@]"
|
||||
formula Electrons.pp t.electrons n_aos n_ops
|
||||
(* Printers:2 ends here *)
|
||||
|
||||
|
||||
@ -1,50 +1,45 @@
|
||||
(* Simulation
|
||||
* :PROPERTIES:
|
||||
* :header-args: :noweb yes :comments both
|
||||
* :END:
|
||||
*
|
||||
* Contains the state of the simulation.
|
||||
*
|
||||
* #+NAME: open *)
|
||||
(** Contains the state of the simulation. *)
|
||||
|
||||
(* [[file:../simulation.org::open][open]] *)
|
||||
open Common
|
||||
open Particles
|
||||
open Operators
|
||||
(* open ends here *)
|
||||
|
||||
(* Type
|
||||
*
|
||||
* #+NAME: types *)
|
||||
|
||||
(* [[file:../simulation.org::types][types]] *)
|
||||
type t
|
||||
(* types ends here *)
|
||||
|
||||
(* Access *)
|
||||
|
||||
|
||||
(* [[file:../simulation.org::*Access][Access:1]] *)
|
||||
(** Access *)
|
||||
|
||||
val nuclei : t -> Nuclei.t
|
||||
(** Nuclear coordinates used in the smiulation *)
|
||||
|
||||
val charge : t -> Charge.t
|
||||
(** Total charge (electrons + nuclei) *)
|
||||
|
||||
val electrons : t -> Electrons.t
|
||||
(** Electrons used in the simulation *)
|
||||
|
||||
val ao_basis : t -> Ao.Basis.t
|
||||
(** Atomic basis set *)
|
||||
|
||||
val nuclear_repulsion : t -> float
|
||||
(** Nuclear repulsion energy *)
|
||||
|
||||
val operators : t -> Operator.t list
|
||||
(* Access:1 ends here *)
|
||||
|
||||
(* Creation *)
|
||||
(** List of extra operators (range-separation, f12, etc) *)
|
||||
|
||||
|
||||
(* [[file:../simulation.org::*Creation][Creation:1]] *)
|
||||
(** Creation *)
|
||||
|
||||
val make : ?multiplicity:int -> ?charge:int ->
|
||||
?operators:Operator.t list-> nuclei:Nuclei.t ->
|
||||
Ao.Basis.t -> t
|
||||
(* Creation:1 ends here *)
|
||||
|
||||
(* Printers *)
|
||||
(** Defaults:
|
||||
* - multiplicity : ~1~
|
||||
* - charge : ~0~
|
||||
* - operators : ~[]~
|
||||
*)
|
||||
|
||||
|
||||
(* [[file:../simulation.org::*Printers][Printers:1]] *)
|
||||
(** Printers *)
|
||||
|
||||
val pp : Format.formatter -> t -> unit
|
||||
(* Printers:1 ends here *)
|
||||
|
||||
@ -1,131 +0,0 @@
|
||||
#+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
|
||||
|
||||
* Simulation
|
||||
:PROPERTIES:
|
||||
:header-args: :noweb yes :comments both
|
||||
:END:
|
||||
|
||||
Contains the state of the simulation.
|
||||
|
||||
#+NAME: open
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
open Common
|
||||
open Particles
|
||||
open Operators
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
<<open>>
|
||||
#+end_src
|
||||
|
||||
** Type
|
||||
|
||||
#+NAME: types
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
type t
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
type t = {
|
||||
charge : Charge.t;
|
||||
electrons : Electrons.t;
|
||||
nuclei : Nuclei.t;
|
||||
ao_basis : Ao.Basis.t;
|
||||
operators : Operator.t list;
|
||||
}
|
||||
#+end_src
|
||||
|
||||
** Access
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val nuclei : t -> Nuclei.t
|
||||
val charge : t -> Charge.t
|
||||
val electrons : t -> Electrons.t
|
||||
val ao_basis : t -> Ao.Basis.t
|
||||
val nuclear_repulsion : t -> float
|
||||
val operators : t -> Operator.t list
|
||||
#+end_src
|
||||
|
||||
| ~nuclei~ | Nuclear coordinates used in the smiulation |
|
||||
| ~charge~ | Total charge (electrons + nuclei) |
|
||||
| ~electrons~ | Electrons used in the simulation |
|
||||
| ~ao_basis~ | Atomic basis set |
|
||||
| ~nuclear_repulsion~ | Nuclear repulsion energy |
|
||||
| ~operators~ | List of extra operators (range-separation, f12, etc) |
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let nuclei t = t.nuclei
|
||||
let charge t = t.charge
|
||||
let electrons t = t.electrons
|
||||
let ao_basis t = t.ao_basis
|
||||
let nuclear_repulsion t = Nuclei.repulsion @@ nuclei t
|
||||
let operators t = t.operators
|
||||
#+end_src
|
||||
|
||||
** Creation
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val make : ?multiplicity:int -> ?charge:int ->
|
||||
?operators:Operator.t list-> nuclei:Nuclei.t ->
|
||||
Ao.Basis.t -> t
|
||||
#+end_src
|
||||
|
||||
Defaults:
|
||||
- multiplicity : ~1~
|
||||
- charge : ~0~
|
||||
- operators : ~[]~
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let make
|
||||
?(multiplicity=1)
|
||||
?(charge=0)
|
||||
?(operators=[])
|
||||
~nuclei
|
||||
ao_basis
|
||||
=
|
||||
|
||||
(* Tune Garbage Collector *)
|
||||
let gc = Gc.get () in
|
||||
Gc.set { gc with space_overhead = 1000 };
|
||||
|
||||
let electrons =
|
||||
Electrons.of_atoms ~multiplicity ~charge nuclei
|
||||
in
|
||||
|
||||
let charge =
|
||||
Charge.(Nuclei.charge nuclei + Electrons.charge electrons)
|
||||
in
|
||||
|
||||
{ charge ; nuclei ; electrons ; ao_basis ; operators}
|
||||
#+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 =
|
||||
let formula = Nuclei.formula t.nuclei in
|
||||
let n_aos = Ao.Basis.size t.ao_basis in
|
||||
let n_ops = List.length t.operators in
|
||||
Format.fprintf ppf "@[@[%s@], @[%a@], @[%d AOs@], @[%d operators@]@]"
|
||||
formula Electrons.pp t.electrons n_aos n_ops
|
||||
#+end_src
|
||||
|
||||
#+RESULTS:
|
||||
: Line 2, characters 16-30:
|
||||
: 2 | let formula = Nuclei.formula t.nuclei in
|
||||
: ^^^^^^^^^^^^^^
|
||||
: Error: Unbound module Nuclei
|
||||
|
||||
Loading…
Reference in New Issue
Block a user