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Removing org-mode source

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Anthony Scemama 2023-06-27 10:15:50 +02:00
parent 0f0bceb6c3
commit ca727440db
23 changed files with 394 additions and 2359 deletions
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5
Makefile
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@ -11,16 +11,11 @@ DOCS=$(patsubst %, docs/%.html, $(DIRS)) docs/index.html
default: doc build
docs/index.html: docs/index.org
- ./bin/build_doc.sh docs
docs/%.html: %/*.org %/lib/*.ml %/lib/*.mli %/test/*.ml
- ./bin/tangle.sh $*
- ./bin/build_doc.sh $*
docs/top.html: */*.org */lib/*.ml */lib/*.mli
- ./bin/tangle.sh top
- ./bin/build_doc.sh top
doc: $(DOCS)

304
ao/basis.org
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@ -1,304 +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
* Basis
:PROPERTIES:
:header-args: :noweb yes :comments both
:END:
Data structure for Atomic Orbitals.
** Dimensions :noexport:
#+begin_src ocaml :tangle lib/ao_dim.mli :exports none
type t
#+end_src
** Polymorphic types
<<<~Basis.t~>>>
#+NAME: types
#+begin_src ocaml :tangle lib/basis_poly.mli
type t =
| Unknown
| Gaussian of Basis_gaussian.t
#+end_src
#+begin_src ocaml :tangle lib/basis_poly.ml :exports none
<<types>>
#+end_src
** Types
<<<~Basis.t~>>>
#+begin_src ocaml :tangle (eval mli)
type t
type ao = Ao_dim.t
open Common
open Particles
open Operators
open Linear_algebra
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
type t =
{ ao_basis : Basis_poly.t ;
cartesian : bool
}
type ao = Ao_dim.t
open Linear_algebra
open Common
#+end_src
** Conversions
#+begin_src ocaml :tangle (eval mli)
val of_nuclei_and_basis_filename :
?kind:[> `Gaussian ] ->
?operators:Operator.t list ->
?cartesian:bool ->
nuclei:Nuclei.t ->
string ->
t
#+end_src
|--------------------------------+------------------------------------------------------------------------------------------------------------------------|
| ~of_nuclei_and_basis_filename~ | Creates the data structure for the atomic orbitals basis from a molecule ~Nuclei.t~ and the name of the basis-set file |
|--------------------------------+------------------------------------------------------------------------------------------------------------------------|
Defaults:
- ~kind~ : ~`Gaussian~
- ~operators~ : ~[]~
- ~cartesian~ : ~false~
Example:
#+begin_example
let b = Ao.Basis.of_nuclei_and_basis_filename ~nuclei filename;;
val b : Ao.Basis.t = Gaussian Basis, spherical, 15 AOs
#+end_example
#+begin_src ocaml :tangle (eval ml) :exports none
let not_implemented () =
Util.not_implemented "Only Gaussian is implemented"
let of_nuclei_and_basis_filename ?(kind=`Gaussian) ?operators ?(cartesian=false)
~nuclei filename =
match kind with
| `Gaussian ->
let basis =
Gaussian.Basis.of_nuclei_and_basis_filename ~nuclei filename
in
let ao_basis =
Basis_poly.Gaussian (Basis_gaussian.make ~basis ?operators ~cartesian nuclei )
in
{ ao_basis ; cartesian }
| _ -> not_implemented ()
#+end_src
** Access
#+begin_src ocaml :tangle (eval mli)
val size : t -> int
val ao_basis : t -> Basis_poly.t
val overlap : t -> (ao,ao) Matrix.t
val multipole : t -> string -> (ao,ao) Matrix.t
val ortho : t -> (ao,'a) Matrix.t
val eN_ints : t -> (ao,ao) Matrix.t
val kin_ints : t -> (ao,ao) Matrix.t
val ee_ints : t -> ao Four_idx_storage.t
val ee_lr_ints : t -> ao Four_idx_storage.t
val f12_ints : t -> ao Four_idx_storage.t
val f12_over_r12_ints : t -> ao Four_idx_storage.t
val cartesian : t -> bool
val values : t -> Coordinate.t -> ao Vector.t
#+end_src
|---------------------+--------------------------------------------------|
| ~size~ | Number of atomic orbitals in the AO basis set |
| ~ao_basis~ | One-electron basis set |
| ~overlap~ | Overlap matrix |
| ~multipole~ | Multipole matrices |
| ~ortho~ | Orthonormalization matrix of the overlap |
| ~eN_ints~ | Electron-nucleus potential integrals |
| ~kin_ints~ | Kinetic energy integrals |
| ~ee_ints~ | Electron-electron potential integrals |
| ~ee_lr_ints~ | Electron-electron long-range potential integrals |
| ~f12_ints~ | Electron-electron potential integrals |
| ~f12_over_r12_ints~ | Electron-electron potential integrals |
| ~cartesian~ | If true, use cartesian Gaussians (6d, 10f, ...) |
| ~values~ | Values of the AOs evaluated at a given point |
|---------------------+--------------------------------------------------|
#+begin_src ocaml :tangle (eval ml) :exports none
let ao_basis t = t.ao_basis
let size t =
match t.ao_basis with
| Basis_poly.Gaussian b -> Basis_gaussian.size b
| _ -> not_implemented ()
let overlap t =
begin
match t.ao_basis with
| Basis_poly.Gaussian b -> Basis_gaussian.overlap b
| _ -> not_implemented ()
end
|> Matrix.relabel
let multipole t =
begin
match t.ao_basis with
| Basis_poly.Gaussian b ->
let m = Basis_gaussian.multipole b in
fun s ->
Gaussian_integrals.Multipole.matrix m s
|> Matrix.relabel
| _ -> not_implemented ()
end
let ortho t =
begin
match t.ao_basis with
| Basis_poly.Gaussian b -> Basis_gaussian.ortho b
| _ -> not_implemented ()
end
|> Matrix.relabel
let eN_ints t =
begin
match t.ao_basis with
| Basis_poly.Gaussian b -> Basis_gaussian.eN_ints b
| _ -> not_implemented ()
end
|> Matrix.relabel
let kin_ints t =
begin
match t.ao_basis with
| Basis_poly.Gaussian b -> Basis_gaussian.kin_ints b
| _ -> not_implemented ()
end
|> Matrix.relabel
let ee_ints t =
begin
match t.ao_basis with
| Basis_poly.Gaussian b -> Basis_gaussian.ee_ints b
| _ -> not_implemented ()
end
|> Four_idx_storage.relabel
let ee_lr_ints t =
begin
match t.ao_basis with
| Basis_poly.Gaussian b -> Basis_gaussian.ee_lr_ints b
| _ -> not_implemented ()
end
|> Four_idx_storage.relabel
let f12_ints t =
begin
match t.ao_basis with
| Basis_poly.Gaussian b -> Basis_gaussian.f12_ints b
| _ -> not_implemented ()
end
|> Four_idx_storage.relabel
let f12_over_r12_ints t =
begin
match t.ao_basis with
| Basis_poly.Gaussian b -> Basis_gaussian.f12_over_r12_ints b
| _ -> not_implemented ()
end
|> Four_idx_storage.relabel
let cartesian t = t.cartesian
let values t point =
begin
match t.ao_basis with
| Basis_poly.Gaussian b -> Basis_gaussian.values b point
| _ -> not_implemented ()
end
|> Vector.relabel
#+end_src
** TREXIO
*** Read
#+begin_src ocaml :tangle (eval mli)
(*
val of_trexio : Trexio.trexio_file -> t
*)
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
(*
let of_trexio f =
match Trexio.read_basis_type f with
| "G"
| "Gaussian"
| "gaussian" ->
let basis =
Gaussian.Basis.of_trexio f
in
let ao_basis =
Basis_poly.Gaussian (Basis_gaussian.make ~basis ?operators ~cartesian nuclei )
in
{ ao_basis ; cartesian }
| _ -> not_implemented ()
*)
#+end_src
*** Write
#+begin_src ocaml :tangle (eval mli)
(*
val to_trexio : Trexio.trexio_file -> t -> unit
*)
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
(*
let to_trexio f t =
match t.ao_basis with
| Basis_poly.Gaussian b -> Gaussian.Basis.to_trexio f (Basis_gaussian.basis b))
| _ -> not_implemented ()
*)
#+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 =
begin
match t.ao_basis with
| Basis_poly.Gaussian b -> Basis_gaussian.pp ppf b
| _ -> not_implemented ()
end
#+end_src

232
ao/basis_gaussian.org
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@ -1,232 +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
* Gaussian basis
:PROPERTIES:
:header-args: :noweb yes :comments both
:END:
Data structure for Gaussian Atomic Orbitals:
\[
\chi_i(\mathbf{r}) = P_i(\mathbf{r}) \sum_k c_k \exp\left( -\alpha_k (\mathbf{r-R_A})^2 \right)
\]
where the polynomial $P_i$ and the Gaussian part are both centered on
nucleus $A$.
** Type
<<<~Gaussian_basis.t~>>>
#+NAME: types
#+begin_src ocaml :tangle (eval mli)
open Common
open Particles
open Linear_algebra
open Gaussian_integrals
open Operators
type t
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
open Linear_algebra
open Gaussian
open Gaussian_integrals
open Operators
module Basis = Gaussian.Basis
type t =
{
basis : Basis.t ;
overlap : Overlap.t lazy_t;
multipole : Multipole.t lazy_t;
ortho : Orthonormalization.t lazy_t;
eN_ints : Electron_nucleus.t lazy_t;
kin_ints : Kinetic.t lazy_t;
ee_ints : Eri.t lazy_t;
ee_lr_ints : Eri_long_range.t lazy_t;
f12_ints : F12.t lazy_t;
f12_over_r12_ints : Screened_eri.t lazy_t;
cartesian : bool ;
}
#+end_src
** Access
#+begin_src ocaml :tangle (eval mli)
val basis : t -> Gaussian.Basis.t
val cartesian : t -> bool
val ee_ints : t -> Eri.t
val ee_lr_ints : t -> Eri_long_range.t
val eN_ints : t -> Electron_nucleus.t
val f12_ints : t -> F12.t
val f12_over_r12_ints : t -> Screened_eri.t
val kin_ints : t -> Kinetic.t
val multipole : t -> Multipole.t
val ortho : t -> Orthonormalization.t
val overlap : t -> Overlap.t
val size : t -> int
#+end_src
|---------------------+--------------------------------------------------|
| ~basis~ | One-electron basis set |
| ~cartesian~ | If true, use cartesian Gaussians (6d, 10f, ...) |
| ~ee_ints~ | Electron-electron potential integrals |
| ~ee_lr_ints~ | Electron-electron long-range potential integrals |
| ~eN_ints~ | Electron-nucleus potential integrals |
| ~f12_ints~ | Electron-electron potential integrals |
| ~f12_over_r12_ints~ | Electron-electron potential integrals |
| ~kin_ints~ | Kinetic energy integrals |
| ~multipole~ | Multipole matrices |
| ~ortho~ | Orthonormalization matrix of the overlap |
| ~overlap~ | Overlap matrix |
| ~size~ | Number of atomic orbitals |
|---------------------+--------------------------------------------------|
#+begin_src ocaml :tangle (eval ml) :exports none
let basis t = t.basis
let cartesian t = t.cartesian
let ee_ints t = Lazy.force t.ee_ints
let ee_lr_ints t = Lazy.force t.ee_lr_ints
let eN_ints t = Lazy.force t.eN_ints
let f12_ints t = Lazy.force t.f12_ints
let f12_over_r12_ints t = Lazy.force t.f12_over_r12_ints
let kin_ints t = Lazy.force t.kin_ints
let multipole t = Lazy.force t.multipole
let ortho t = Lazy.force t.ortho
let overlap t = Lazy.force t.overlap
let size t = Matrix.dim1 (Lazy.force t.overlap)
#+end_src
** Computation
#+begin_src ocaml :tangle (eval mli)
val values : t ->
Coordinate.t ->
Gaussian.Basis.t Vector.t
#+end_src
|----------+--------------------------------------------------------------|
| ~values~ | Returns the values of all the AOs evaluated at a given point |
|----------+--------------------------------------------------------------|
#+begin_src ocaml :tangle (eval ml) :exports none
module Cs = Contracted_shell
let values t point =
let result = Vector.create (Basis.size t.basis) in
let resultx = Vector.to_bigarray_inplace result in
Array.iter (fun shell ->
Cs.values shell point
|> Array.iteri
(fun i_c value ->
let i = Cs.index shell + i_c + 1 in
resultx.{i} <- value)
) (Basis.contracted_shells t.basis);
result
#+end_src
** Creation
#+begin_src ocaml :tangle (eval mli)
val make : basis:Gaussian.Basis.t ->
?operators:Operator.t list ->
?cartesian:bool ->
Nuclei.t ->
t
#+end_src
Creates the data structure for atomic orbitals from a Gaussian basis and the
molecular geometry ~Nuclei.t~.
Defaults:
- ~operators~ : ~[]~
- ~cartesian~ : ~false~
Example:
#+begin_example
let b = Ao.Basis_gaussian.make ~basis nuclei ;;
val b : Ao.Basis_gaussian.t = Gaussian Basis, spherical, 15 AOs
#+end_example
#+begin_src ocaml :tangle (eval ml) :exports none
let make ~basis ?(operators=[]) ?(cartesian=false) nuclei =
let overlap = lazy (
Overlap.of_basis basis
) in
let ortho = lazy (
Lazy.force overlap
|> Orthonormalization.make ~cartesian ~basis
) in
let eN_ints = lazy (
Electron_nucleus.of_basis_nuclei ~basis nuclei
) in
let kin_ints = lazy (
Kinetic.of_basis basis
) in
let ee_ints = lazy (
Eri.of_basis basis
) in
let rec get_f12 = function
| (Operator.F12 _ as f) :: _ -> f
| [] -> failwith "Missing F12 operator"
| _ :: rest -> get_f12 rest
in
let rec get_rs = function
| (Operator.Range_sep _ as r) :: _ -> r
| [] -> failwith "Missing range-separation operator"
| _ :: rest -> get_rs rest
in
let ee_lr_ints = lazy (
Eri_long_range.of_basis basis~operator:(get_rs operators)
) in
let f12_ints = lazy (
F12.of_basis basis ~operator:(get_f12 operators)
) in
let f12_over_r12_ints = lazy (
Screened_eri.of_basis basis ~operator:(get_f12 operators)
) in
let multipole = lazy (
Multipole.of_basis basis
) in
{ basis ; overlap ; multipole ; ortho ; eN_ints ; kin_ints ; ee_ints ;
ee_lr_ints ; f12_ints ; f12_over_r12_ints ; cartesian }
#+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 cart = if t.cartesian then "cartesian" else "spherical" in
let nao = size t in
Format.fprintf ppf "@[@[Gaussian Basis@], @[%s@], @[%d AOs@]@]"
cart nao
#+end_src

52
ao/lib/basis.ml
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@ -1,4 +1,3 @@
(* [[file:~/QCaml/ao/basis.org::*Types][Types:2]] *)
type t =
{ ao_basis : Basis_poly.t ;
cartesian : bool
@ -8,30 +7,13 @@ type ao = Ao_dim.t
open Linear_algebra
open Common
(* Types:2 ends here *)
(* |--------------------------------+------------------------------------------------------------------------------------------------------------------------|
* | ~of_nuclei_and_basis_filename~ | Creates the data structure for the atomic orbitals basis from a molecule ~Nuclei.t~ and the name of the basis-set file |
* |--------------------------------+------------------------------------------------------------------------------------------------------------------------|
*
* Defaults:
* - ~kind~ : ~`Gaussian~
* - ~operators~ : ~[]~
* - ~cartesian~ : ~false~
*
* Example:
* #+begin_example
* let b = Ao.Basis.of_nuclei_and_basis_filename ~nuclei filename;;
* val b : Ao.Basis.t = Gaussian Basis, spherical, 15 AOs
* #+end_example *)
(* [[file:~/QCaml/ao/basis.org::*Conversions][Conversions:2]] *)
let not_implemented () =
Util.not_implemented "Only Gaussian is implemented"
let of_nuclei_and_basis_filename ?(kind=`Gaussian) ?operators ?(cartesian=false)
~nuclei filename =
match kind with
@ -44,29 +26,10 @@ let of_nuclei_and_basis_filename ?(kind=`Gaussian) ?operators ?(cartesian=false)
in
{ ao_basis ; cartesian }
| _ -> not_implemented ()
(* Conversions:2 ends here *)
(* |---------------------+--------------------------------------------------|
* | ~size~ | Number of atomic orbitals in the AO basis set |
* | ~ao_basis~ | One-electron basis set |
* | ~overlap~ | Overlap matrix |
* | ~multipole~ | Multipole matrices |
* | ~ortho~ | Orthonormalization matrix of the overlap |
* | ~eN_ints~ | Electron-nucleus potential integrals |
* | ~kin_ints~ | Kinetic energy integrals |
* | ~ee_ints~ | Electron-electron potential integrals |
* | ~ee_lr_ints~ | Electron-electron long-range potential integrals |
* | ~f12_ints~ | Electron-electron potential integrals |
* | ~f12_over_r12_ints~ | Electron-electron potential integrals |
* | ~cartesian~ | If true, use cartesian Gaussians (6d, 10f, ...) |
* | ~values~ | Values of the AOs evaluated at a given point |
* |---------------------+--------------------------------------------------| *)
(* [[file:~/QCaml/ao/basis.org::*Access][Access:2]] *)
let ao_basis t = t.ao_basis
let size t =
@ -159,9 +122,8 @@ let values t point =
| _ -> not_implemented ()
end
|> Vector.relabel
(* Access:2 ends here *)
(* [[file:~/QCaml/ao/basis.org::*Read][Read:2]] *)
(*
let of_trexio f =
@ -178,11 +140,8 @@ let of_trexio f =
{ ao_basis ; cartesian }
| _ -> not_implemented ()
*)
(* Read:2 ends here *)
(* [[file:~/QCaml/ao/basis.org::*Write][Write:2]] *)
(*
let to_trexio f t =
match t.ao_basis with
@ -190,13 +149,12 @@ let to_trexio f t =
| _ -> not_implemented ()
*)
(* Write:2 ends here *)
(* [[file:~/QCaml/ao/basis.org::*Printers][Printers:2]] *)
let pp ppf t =
begin
match t.ao_basis with
| Basis_poly.Gaussian b -> Basis_gaussian.pp ppf b
| _ -> not_implemented ()
end
(* Printers:2 ends here *)

99
ao/lib/basis.mli
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@ -1,8 +1,5 @@
(* Types
*
* <<<~Basis.t~>>> *)
(** Data structure for Atomic Orbitals. *)
(* [[file:~/QCaml/ao/basis.org::*Types][Types:1]] *)
type t
type ao = Ao_dim.t
@ -10,61 +7,85 @@ open Common
open Particles
open Operators
open Linear_algebra
(* Types:1 ends here *)
(* Conversions *)
(** Conversions *)
(* [[file:~/QCaml/ao/basis.org::*Conversions][Conversions:1]] *)
val of_nuclei_and_basis_filename :
?kind:[> `Gaussian ] ->
?operators:Operator.t list ->
?cartesian:bool ->
nuclei:Nuclei.t ->
string ->
t
(* Conversions:1 ends here *)
string -> t
(** Creates the data structure for the atomic orbitals basis from a
molecule ~Nuclei.t~ and the name of the basis-set file.
(* Access *)
Defaults:
- ~kind~ : ~`Gaussian~
- ~operators~ : ~[]~
- ~cartesian~ : ~false~
Example:
#+begin_example
let b = Ao.Basis.of_nuclei_and_basis_filename ~nuclei filename;;
val b : Ao.Basis.t = Gaussian Basis, spherical, 15 AOs
#+end_example
*)
(* [[file:~/QCaml/ao/basis.org::*Access][Access:1]] *)
val size : t -> int
val ao_basis : t -> Basis_poly.t
val overlap : t -> (ao,ao) Matrix.t
val multipole : t -> string -> (ao,ao) Matrix.t
val ortho : t -> (ao,'a) Matrix.t
val eN_ints : t -> (ao,ao) Matrix.t
val kin_ints : t -> (ao,ao) Matrix.t
val ee_ints : t -> ao Four_idx_storage.t
val ee_lr_ints : t -> ao Four_idx_storage.t
val f12_ints : t -> ao Four_idx_storage.t
(** Access *)
val size : t -> int
(** Number of atomic orbitals in the AO basis set *)
val ao_basis : t -> Basis_poly.t
(** One-electron basis set *)
val overlap : t -> (ao,ao) Matrix.t
(** Overlap matrix *)
val multipole : t -> string -> (ao,ao) Matrix.t
(** Multipole matrices *)
val ortho : t -> (ao,'a) Matrix.t
(** Orthonormalization matrix of the overlap *)
val eN_ints : t -> (ao,ao) Matrix.t
(** Electron-nucleus potential integrals *)
val kin_ints : t -> (ao,ao) Matrix.t
(** Kinetic energy integrals *)
val ee_ints : t -> ao Four_idx_storage.t
(** Electron-electron potential integrals *)
val ee_lr_ints : t -> ao Four_idx_storage.t
(** Electron-electron long-range potential integrals *)
val f12_ints : t -> ao Four_idx_storage.t
(** Electron-electron potential integrals *)
val f12_over_r12_ints : t -> ao Four_idx_storage.t
val cartesian : t -> bool
val values : t -> Coordinate.t -> ao Vector.t
(* Access:1 ends here *)
(** ectron-electron potential integrals *)
(* Read *)
val cartesian : t -> bool
(** If true, use cartesian Gaussians (6d, 10f, ...) *)
val values : t -> Coordinate.t -> ao Vector.t
(** Values of the AOs evaluated at a given point *)
(* [[file:~/QCaml/ao/basis.org::*Read][Read:1]] *)
(** TREXIO *)
(*
val of_trexio : Trexio.trexio_file -> t
*)
(* Read:1 ends here *)
(** Reads the basis set from a TREXIO file *)
(* Write *)
(* [[file:~/QCaml/ao/basis.org::*Write][Write:1]] *)
(*
val to_trexio : Trexio.trexio_file -> t -> unit
(** Writes the basis set to a TREXIO file *)
*)
(* Write:1 ends here *)
(* Printers *)
(* [[file:~/QCaml/ao/basis.org::*Printers][Printers:1]] *)
val pp : Format.formatter -> t -> unit
(* Printers:1 ends here *)

43
ao/lib/basis_gaussian.ml
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@ -1,4 +1,3 @@
(* [[file:~/QCaml/ao/basis_gaussian.org::*Type][Type:2]] *)
open Linear_algebra
open Gaussian
open Gaussian_integrals
@ -20,27 +19,7 @@ type t =
f12_over_r12_ints : Screened_eri.t lazy_t;
cartesian : bool ;
}
(* Type:2 ends here *)
(* |---------------------+--------------------------------------------------|
* | ~basis~ | One-electron basis set |
* | ~cartesian~ | If true, use cartesian Gaussians (6d, 10f, ...) |
* | ~ee_ints~ | Electron-electron potential integrals |
* | ~ee_lr_ints~ | Electron-electron long-range potential integrals |
* | ~eN_ints~ | Electron-nucleus potential integrals |
* | ~f12_ints~ | Electron-electron potential integrals |
* | ~f12_over_r12_ints~ | Electron-electron potential integrals |
* | ~kin_ints~ | Kinetic energy integrals |
* | ~multipole~ | Multipole matrices |
* | ~ortho~ | Orthonormalization matrix of the overlap |
* | ~overlap~ | Overlap matrix |
* | ~size~ | Number of atomic orbitals |
* |---------------------+--------------------------------------------------| *)
(* [[file:~/QCaml/ao/basis_gaussian.org::*Access][Access:2]] *)
let basis t = t.basis
let cartesian t = t.cartesian
let ee_ints t = Lazy.force t.ee_ints
@ -53,7 +32,6 @@ let multipole t = Lazy.force t.multipole
let ortho t = Lazy.force t.ortho
let overlap t = Lazy.force t.overlap
let size t = Matrix.dim1 (Lazy.force t.overlap)
(* Access:2 ends here *)
@ -62,7 +40,6 @@ let size t = Matrix.dim1 (Lazy.force t.overlap)
* |----------+--------------------------------------------------------------| *)
(* [[file:~/QCaml/ao/basis_gaussian.org::*Computation][Computation:2]] *)
module Cs = Contracted_shell
let values t point =
@ -76,25 +53,10 @@ let values t point =
resultx.{i} <- value)
) (Basis.contracted_shells t.basis);
result
(* Computation:2 ends here *)
(* Creates the data structure for atomic orbitals from a Gaussian basis and the
* molecular geometry ~Nuclei.t~.
*
* Defaults:
* - ~operators~ : ~[]~
* - ~cartesian~ : ~false~
*
* Example:
* #+begin_example
* let b = Ao.Basis_gaussian.make ~basis nuclei ;;
* val b : Ao.Basis_gaussian.t = Gaussian Basis, spherical, 15 AOs
* #+end_example *)
(* [[file:~/QCaml/ao/basis_gaussian.org::*Creation][Creation:2]] *)
let make ~basis ?(operators=[]) ?(cartesian=false) nuclei =
let overlap = lazy (
@ -148,12 +110,11 @@ let make ~basis ?(operators=[]) ?(cartesian=false) nuclei =
{ basis ; overlap ; multipole ; ortho ; eN_ints ; kin_ints ; ee_ints ;
ee_lr_ints ; f12_ints ; f12_over_r12_ints ; cartesian }
(* Creation:2 ends here *)
(* [[file:~/QCaml/ao/basis_gaussian.org::*Printers][Printers:2]] *)
let pp ppf t =
let cart = if t.cartesian then "cartesian" else "spherical" in
let nao = size t in
Format.fprintf ppf "@[@[Gaussian Basis@], @[%s@], @[%d AOs@]@]"
cart nao
(* Printers:2 ends here *)

98
ao/lib/basis_gaussian.mli
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@ -1,9 +1,16 @@
(* Type
*
* <<<~Gaussian_basis.t~>>>
* #+NAME: types *)
(** Gaussian basis
Data structure for Gaussian Atomic Orbitals:
\[
\chi_i(\mathbf{r}) = P_i(\mathbf{r}) \sum_k c_k \exp\left( -\alpha_k (\mathbf{r-R_A})^2 \r$
\]
where the polynomial $P_i$ and the Gaussian part are both centered on
nucleus $A$.
*)
(* [[file:~/QCaml/ao/basis_gaussian.org::types][types]] *)
open Common
open Particles
open Linear_algebra
@ -11,49 +18,74 @@ open Gaussian_integrals
open Operators
type t
(* types ends here *)
(* Access *)
(** Access *)
val basis : t -> Gaussian.Basis.t
(** One-electron basis set *)
val cartesian : t -> bool
(** If true, use cartesian Gaussians (6d, 10f, ...) *)
val ee_ints : t -> Eri.t
(* Electron-electron potential integrals *)
val ee_lr_ints : t -> Eri_long_range.t
(** Electron-electron long-range potential integrals *)
val eN_ints : t -> Electron_nucleus.t
(** Electron-nucleus potential integrals *)
val f12_ints : t -> F12.t
(** Electron-electron potential integrals *)
(* [[file:~/QCaml/ao/basis_gaussian.org::*Access][Access:1]] *)
val basis : t -> Gaussian.Basis.t
val cartesian : t -> bool
val ee_ints : t -> Eri.t
val ee_lr_ints : t -> Eri_long_range.t
val eN_ints : t -> Electron_nucleus.t
val f12_ints : t -> F12.t
val f12_over_r12_ints : t -> Screened_eri.t
val kin_ints : t -> Kinetic.t
val multipole : t -> Multipole.t
val ortho : t -> Orthonormalization.t
(**lectron-electron potential integrals *)
val kin_ints : t -> Kinetic.t
(** Kinetic energy integrals *)
val multipole : t -> Multipole.t
(** Multipole matrices *)
val ortho : t -> Orthonormalization.t
(** Orthonormalization matrix of the overlap *)
val overlap : t -> Overlap.t
val size : t -> int
(* Access:1 ends here *)
(** Overlap matrix *)
(* Computation *)
val size : t -> int
(** Number of atomic orbitals *)
(* [[file:~/QCaml/ao/basis_gaussian.org::*Computation][Computation:1]] *)
val values : t ->
Coordinate.t ->
Gaussian.Basis.t Vector.t
(* Computation:1 ends here *)
(** Computation *)
(* Creation *)
val values : t -> Coordinate.t -> Gaussian.Basis.t Vector.t
(** Returns the values of all the AOs evaluated at a given point *)
(* [[file:~/QCaml/ao/basis_gaussian.org::*Creation][Creation:1]] *)
(** Creation *)
val make : basis:Gaussian.Basis.t ->
?operators:Operator.t list ->
?cartesian:bool ->
Nuclei.t ->
t
(* Creation:1 ends here *)
Nuclei.t -> t
(* Printers *)
(** Creates the data structure for atomic orbitals from a Gaussian basis and the
molecular geometry ~Nuclei.t~.
Defaults:
- ~operators~ : ~[]~
- ~cartesian~ : ~false~
Example:
#+begin_example
let b = Ao.Basis_gaussian.make ~basis nuclei ;;
val b : Ao.Basis_gaussian.t = Gaussian Basis, spherical, 15 AOs
#+end_example
*)
(* [[file:~/QCaml/ao/basis_gaussian.org::*Printers][Printers:1]] *)
(** Printers *)
val pp : Format.formatter -> t -> unit
(* Printers:1 ends here *)

34
bin/build_doc.sh
View File

@ -1,34 +0,0 @@
#!/bin/bash
# Usage: $0 [DIR]
if [[ -z $1 ]] ; then
echo "Usage: $0 [DIR]"
exit -1
fi
if [[ $(basename $PWD) != "QCaml" ]] ; then
echo "This script needs to be run in the QCaml directory"
exit -1
fi
DIR=${1%/}
CONFIG="--load docs/htmlize.el --load docs/config.el"
if [[ ${DIR} == "docs" ]] ; then
emacs --debug-init --batch $CONFIG docs/index.org -f org-html-export-to-html
else
rm -f docs/${DIR}.org
for i in ${DIR}/README.org ${DIR}/[a-z]*.org
do
cat $i >> docs/${DIR}.org
done
emacs --debug-init --batch $CONFIG docs/${DIR}.org -f org-html-export-to-html \
&& rm docs/${DIR}.org
fi

288
common/angular_momentum.org
View File

@ -1,288 +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
* Angular Momentum
:PROPERTIES:
:header-args: :noweb yes :comments both
:END:
Azimuthal quantum number, repsesented as \( s,p,d,\dots \) .
** Type
<<<~Angular_momentum.t~>>>
#+NAME: types
#+begin_src ocaml :tangle (eval mli)
type t =
| S | P | D | F | G | H | I | J | K | L | M | N | O
| Int of int
exception Angular_momentum_error of string
type kind =
Singlet of t
| Doublet of (t * t)
| Triplet of (t * t * t)
| Quartet of (t * t * t * t)
#+end_src
An exception is raised when the ~Angular_momentum.t~ element can't
be created.
The ~kind~ is used to build shells, shell doublets, triplets or
quartets, use in the two-electron operators.
#+begin_src ocaml :tangle (eval ml) :exports none
<<types>>
open Powers
#+end_src
** Conversions
#+begin_src ocaml :tangle (eval mli)
val of_char : char -> t
val to_char : t -> char
val to_int : t -> int
val of_int : int -> t
val to_string : t -> string
#+end_src
| ~of_char~ | Returns an ~Angular_momentum.t~ when a shell is given as a character (case insensitive) |
| ~to_char~ | Converts the angular momentum into a char |
| ~of_int~ | Returns a shell given an $l$ value. |
| ~to_int~ | Returns the $l_{max}$ value of the shell |
| ~to_string~ | Converts the angular momentum into a string |
Example:
#+begin_example
Angular_momentum.of_char 'p';;
- : Angular_momentum.t = P
Angular_momentum.(to_char P);;
- : char = 'P'
Angular_momentum.of_int 2;;
- : Angular_momentum.t = D
Angular_momentum.(to_int D);;
- : int = 2
Angular_momentum.(to_string D);;
- : string = "D"
#+end_example
#+begin_src ocaml :tangle (eval ml) :exports none
let of_char = function
| 's' | 'S' -> S | 'p' | 'P' -> P
| 'd' | 'D' -> D | 'f' | 'F' -> F
| 'g' | 'G' -> G | 'h' | 'H' -> H
| 'i' | 'I' -> I | 'j' | 'J' -> J
| 'k' | 'K' -> K | 'l' | 'L' -> L
| 'm' | 'M' -> M | 'n' | 'N' -> N
| 'o' | 'O' -> O
| c -> raise (Angular_momentum_error (String.make 1 c))
let to_string = function
| S -> "S" | P -> "P"
| D -> "D" | F -> "F"
| G -> "G" | H -> "H"
| I -> "I" | J -> "J"
| K -> "K" | L -> "L"
| M -> "M" | N -> "N"
| O -> "O" | Int i -> string_of_int i
let to_char = function
| S -> 'S' | P -> 'P'
| D -> 'D' | F -> 'F'
| G -> 'G' | H -> 'H'
| I -> 'I' | J -> 'J'
| K -> 'K' | L -> 'L'
| M -> 'M' | N -> 'N'
| O -> 'O' | Int _ -> '_'
let to_int = function
| S -> 0 | P -> 1
| D -> 2 | F -> 3
| G -> 4 | H -> 5
| I -> 6 | J -> 7
| K -> 8 | L -> 9
| M -> 10 | N -> 11
| O -> 12 | Int i -> i
let of_int = function
| 0 -> S | 1 -> P
| 2 -> D | 3 -> F
| 4 -> G | 5 -> H
| 6 -> I | 7 -> J
| 8 -> K | 9 -> L
| 10 -> M | 11 -> N
| 12 -> O | i -> Int i
#+end_src
** Shell functions
#+begin_src ocaml :tangle (eval mli)
val n_functions : t -> int
val zkey_array : kind -> Zkey.t array
#+end_src
| ~n_functions~ | Returns the number of cartesian functions in a shell. |
| ~zkey_array~ | Array of ~Zkey.t~, where each element is a a key associated with the the powers of $x,y,z$. |
Example:
#+begin_example
Angular_momentum.(n_functions D) ;;
- : int = 6
Angular_momentum.( zkey_array (Doublet (P,S)) );;
- : Zkey.t array =
[|< 01125899906842624 | 1, 0, 0, 0, 0, 0 >;
< 01099511627776 | 0, 1, 0, 0, 0, 0 >;
< 01073741824 | 0, 0, 1, 0, 0, 0 >|]
#+end_example
#+begin_src ocaml :tangle (eval ml) :exports none
let n_functions a =
let a =
to_int a
in
(a*a + 3*a + 2)/2
let zkey_array_memo : (kind, Zkey.t array) Hashtbl.t =
Hashtbl.create 13
let zkey_array a =
let keys_1d l =
let create_z { x ; y ; _ } =
Powers.of_int_tuple (x,y,l-(x+y))
in
let rec create_y accu xyz =
let { x ; y ; z ;_ } = xyz in
match y with
| 0 -> (create_z xyz)::accu
| _ -> let ynew = y-1 in
(create_y [@tailcall]) ( (create_z xyz)::accu) (Powers.of_int_tuple (x,ynew,z))
in
let rec create_x accu xyz =
let { x ; z ;_ } = xyz in
match x with
| 0 -> (create_y [] xyz)@accu
| _ -> let xnew = x-1 in
let ynew = l-xnew in
(create_x [@tailcall]) ((create_y [] xyz)@accu) (Powers.of_int_tuple (xnew, ynew, z))
in
create_x [] (Powers.of_int_tuple (l,0,0))
|> List.rev
in
try
Hashtbl.find zkey_array_memo a
with Not_found ->
let result =
begin
match a with
| Singlet l1 ->
List.rev_map (fun x -> Zkey.of_powers_three x) (keys_1d @@ to_int l1)
| Doublet (l1, l2) ->
List.rev_map (fun a ->
List.rev_map (fun b -> Zkey.of_powers_six a b) (keys_1d @@ to_int l2)
) (keys_1d @@ to_int l1)
|> List.concat
| Triplet (l1, l2, l3) ->
List.rev_map (fun a ->
List.rev_map (fun b ->
List.rev_map (fun c ->
Zkey.of_powers_nine a b c) (keys_1d @@ to_int l3)
) (keys_1d @@ to_int l2)
|> List.concat
) (keys_1d @@ to_int l1)
|> List.concat
| Quartet (l1, l2, l3, l4) ->
List.rev_map (fun a ->
List.rev_map (fun b ->
List.rev_map (fun c ->
List.rev_map (fun d ->
Zkey.of_powers_twelve a b c d) (keys_1d @@ to_int l4)
) (keys_1d @@ to_int l3)
|> List.concat
) (keys_1d @@ to_int l2)
|> List.concat
) (keys_1d @@ to_int l1)
|> List.concat
end
|> List.rev
|> Array.of_list
in
Hashtbl.add zkey_array_memo a result;
result
#+end_src
** Arithmetic
#+begin_src ocaml :tangle (eval mli)
val ( + ) : t -> t -> t
val ( - ) : t -> t -> t
#+end_src
Example:
#+begin_example
Angular_momentum.(D + P);;
- : Angular_momentum.t = F
Angular_momentum.(F - P);;
- : Angular_momentum.t = D
#+end_example
#+begin_src ocaml :tangle (eval ml) :exports none
let ( + ) a b =
of_int ( (to_int a) + (to_int b) )
let ( - ) a b =
of_int ( (to_int a) - (to_int b) )
#+end_src
** Printers
Printers can print as a string (default) or as an integer.
#+begin_src ocaml :tangle (eval mli)
val pp : Format.formatter -> t -> unit
val pp_string : Format.formatter -> t -> unit
val pp_int : Format.formatter -> t -> unit
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
let pp_string ppf x =
Format.fprintf ppf "@[%s@]" (to_string x)
let pp_int ppf x =
Format.fprintf ppf "@[%d@]" (to_int x)
let pp = pp_string
#+end_src
** TODO Tests

460
common/bitstring.org
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@ -1,460 +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
* Bit string
:PROPERTIES:
:header-args: :noweb yes :comments both
:END:
We define here a data type to handle bit strings efficiently. When
the bit string contains less than 64 bits, it is stored internally
in a 63-bit integer and uses bitwise instructions. When more than
63 bits are required, the =zarith= library is used to consider the
bit string as a multi-precision integer.
** Single-integer implementation :noexport:
#+begin_src ocaml :tangle (eval ml) :exports none
module One = struct
let of_int x =
assert (x > 0); x
let numbits _ = 63
let zero = 0
let is_zero x = x = 0
let shift_left x i = x lsl i
let shift_right x i = x lsr i
let shift_left_one i = 1 lsl i
let testbit x i = ( (x lsr i) land 1 ) = 1
let logor a b = a lor b
let neg a = - a
let logxor a b = a lxor b
let logand a b = a land b
let lognot a = lnot a
let minus_one a = a - 1
let plus_one a = a + 1
let popcount = function
| 0 -> 0
| r -> Util.popcnt (Int64.of_int r)
let trailing_zeros r =
Util.trailz (Int64.of_int r)
let hamdist a b =
a lxor b
|> popcount
let pp ppf s =
Format.fprintf ppf "@[@[%a@]@]" (Util.pp_bitstring 64)
(Z.of_int s)
end
#+end_src
** Zarith implementation :noexport:
#+begin_src ocaml :tangle (eval ml) :exports none
module Many = struct
let of_z x = x
let zero = Z.zero
let is_zero x = x = Z.zero
let shift_left = Z.shift_left
let shift_right = Z.shift_right
let shift_left_one i = Z.shift_left Z.one i
let testbit = Z.testbit
let logor = Z.logor
let logxor = Z.logxor
let logand = Z.logand
let lognot = Z.lognot
let neg = Z.neg
let minus_one = Z.pred
let plus_one = Z.succ
let trailing_zeros = Z.trailing_zeros
let hamdist = Z.hamdist
let numbits i = max (Z.numbits i) 64
let popcount z =
if z = Z.zero then 0 else Z.popcount z
let pp ppf s =
Format.fprintf ppf "@[@[%a@]@]" (Util.pp_bitstring (Z.numbits s)) s
end
#+end_src
** Type
<<<~Bitstring.t~>>>
#+begin_src ocaml :tangle (eval mli)
type t
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
type t =
| One of int
| Many of Z.t
#+end_src
** Tests header :noexport:
#+begin_src ocaml :tangle (eval test-ml)
open Common.Bitstring
let check_bool = Alcotest.(check bool)
let check msg x = check_bool msg true x
let test_all () =
let x = 8745687 in
let one_x = of_int x in
let z = Z.shift_left (Z.of_int x) 64 in
let many_x = of_z z in
#+end_src
** General implementation
#+begin_src ocaml :tangle (eval mli)
val of_int : int -> t
val of_z : Z.t -> t
val zero : int -> t
val is_zero : t -> bool
val numbits : t -> int
val testbit : t -> int -> bool
val neg : t -> t
val shift_left : t -> int -> t
val shift_right : t -> int -> t
val shift_left_one : int -> int -> t
val logor : t -> t -> t
val logxor : t -> t -> t
val logand : t -> t -> t
val lognot : t -> t
val plus_one : t -> t
val minus_one : t -> t
val hamdist : t -> t -> int
val trailing_zeros : t -> int
val popcount : t -> int
val to_list : ?accu:(int list) -> t -> int list
val permutations : int -> int -> t list
#+end_src
| ~of_int~ | Creates a bit string from an ~int~ |
| ~of_z~ | Creates a bit string from an ~Z.t~ multi-precision integer |
| ~zero~ | ~zero n~ creates a zero bit string with ~n~ bits |
| ~is_zero~ | True if all the bits of the bit string are zero. |
| ~numbits~ | Returns the number of bits used to represent the bit string |
| ~testbit~ | ~testbit t n~ is true if the ~n~-th bit of the bit string ~t~ is set to ~1~ |
| ~neg~ | Returns the negative of the integer interpretation of the bit string |
| ~shift_left~ | ~shift_left t n~ returns a new bit strings with all the bits shifted ~n~ positions to the left |
| ~shift_right~ | ~shift_right t n~ returns a new bit strings with all the bits shifted ~n~ positions to the right |
| ~shift_left_one~ | ~shift_left_one size n~ returns a new bit strings with the ~n~-th bit set to one. It is equivalent as shifting ~1~ by ~n~ bits to the left, ~size~ is the total number of bits of the bit string |
| ~logor~ | Bitwise logical or |
| ~logxor~ | Bitwise logical exclusive or |
| ~logand~ | Bitwise logical and |
| ~lognot~ | Bitwise logical negation |
| ~plus_one~ | Takes the integer representation of the bit string and adds one |
| ~minus_one~ | Takes the integer representation of the bit string and removes one |
| ~hamdist~ | Returns the Hamming distance, i.e. the number of bits differing between two bit strings |
| ~trailing_zeros~ | Returns the number of trailing zeros in the bit string |
| ~permutations~ | ~permutations m n~ generates the list of all possible ~n~-bit strings with ~m~ bits set to ~1~. Algorithm adapted from [[https://graphics.stanford.edu/~seander/bithacks.html#NextBitPermutation][Bit twiddling hacks]] |
| ~popcount~ | Returns the number of bits set to one in the bit string |
| ~to_list~ | Converts a bit string into a list of integers indicating the positions where the bits are set to ~1~. The first value for the position is not ~0~ but ~1~ |
#+begin_src ocaml :tangle (eval ml) :exports none
let of_int x =
One (One.of_int x)
let of_z x =
if Z.numbits x < 64 then One (Z.to_int x) else Many (Many.of_z x)
#+end_src
#+begin_src ocaml :tangle (eval test-ml) :exports none
check_bool "of_x" true (one_x = (of_int x));
check_bool "of_z" true (one_x = (of_z (Z.of_int x)));
#+end_src
Example:
#+begin_example
Bitstring.of_int 15;;
- : Bitstring.t =
++++------------------------------------------------------------
#+end_example
#+begin_src ocaml :tangle (eval ml) :exports none
let zero = function
| n when n < 64 -> One (One.zero)
| _ -> Many (Many.zero)
let numbits = function
| One x -> One.numbits x
| Many x -> Many.numbits x
let is_zero = function
| One x -> One.is_zero x
| Many x -> Many.is_zero x
let neg = function
| One x -> One (One.neg x)
| Many x -> Many (Many.neg x)
let shift_left x i = match x with
| One x -> One (One.shift_left x i)
| Many x -> Many (Many.shift_left x i)
let shift_right x i = match x with
| One x -> One (One.shift_right x i)
| Many x -> Many (Many.shift_right x i)
let shift_left_one = function
| n when n < 64 -> fun i -> One (One.shift_left_one i)
| _ -> fun i -> Many (Many.shift_left_one i)
let testbit = function
| One x -> One.testbit x
| Many x -> Many.testbit x
#+end_src
Example:
#+begin_example
Bitstring.(shift_left (of_int 15) 2);;
- : Bitstring.t =
--++++----------------------------------------------------------
Bitstring.(shift_right (of_int 15) 2);;
- : Bitstring.t =
++--------------------------------------------------------------
Bitstring.shift_left_one 32 4;;
- : Bitstring.t =
----+-----------------------------------------------------------
Bitstring.(testbit (of_int 15) 3);;
- : bool = true
Bitstring.(testbit (of_int 15) 4);;
- : bool = false
#+end_example
#+begin_src ocaml :tangle (eval test-ml) :exports none
check_bool "shift_left1" true (of_int (x lsl 3) = shift_left one_x 3);
check_bool "shift_left2" true (of_z (Z.shift_left z 3) = shift_left many_x 3);
check_bool "shift_left3" true (of_z (Z.shift_left z 100) = shift_left many_x 100);
check_bool "shift_right1" true (of_int (x lsr 3) = shift_right one_x 3);
check_bool "shift_right2" true (of_z (Z.shift_right z 3) = shift_right many_x 3);
check_bool "shift_left_one1" true (of_int (1 lsl 3) = shift_left_one 4 3);
check_bool "shift_left_one2" true (of_z (Z.shift_left Z.one 200) = shift_left_one 300 200);
check_bool "testbit1" true (testbit (of_int 8) 3);
check_bool "testbit2" false (testbit (of_int 8) 2);
check_bool "testbit3" false (testbit (of_int 8) 4);
check_bool "testbit4" true (testbit (of_z (Z.of_int 8)) 3);
check_bool "testbit5" false (testbit (of_z (Z.of_int 8)) 2);
check_bool "testbit6" false (testbit (of_z (Z.of_int 8)) 4);
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
let logor a b =
match a,b with
| One a, One b -> One (One.logor a b)
| Many a, Many b -> Many (Many.logor a b)
| _ -> invalid_arg "Bitstring.logor"
let logxor a b =
match a,b with
| One a, One b -> One (One.logxor a b)
| Many a, Many b -> Many (Many.logxor a b)
| _ -> invalid_arg "Bitstring.logxor"
let logand a b =
match a,b with
| One a, One b -> One (One.logand a b)
| Many a, Many b -> Many (Many.logand a b)
| _ -> invalid_arg "Bitstring.logand"
let lognot = function
| One x -> One (One.lognot x)
| Many x -> Many (Many.lognot x)
#+end_src
Example:
#+begin_example
Bitstring.(logor (of_int 15) (of_int 73));;
- : Bitstring.t =
++++--+---------------------------------------------------------
Bitstring.(logand (of_int 15) (of_int 10));;
- : Bitstring.t =
-+-+------------------------------------------------------------
Bitstring.(logxor (of_int 15) (of_int 73));;
- : Bitstring.t =
-++---+---------------------------------------------------------
#+end_example
#+begin_src ocaml :tangle (eval test-ml) :exports none
check_bool "logor1" true (of_int (1 lor 2) = logor (of_int 1) (of_int 2));
check_bool "logor2" true (of_z (Z.of_int (1 lor 2)) = logor (of_z Z.one) (of_z (Z.of_int 2)));
check_bool "logxor1" true (of_int (1 lxor 2) = logxor (of_int 1) (of_int 2));
check_bool "logxor2" true (of_z (Z.of_int (1 lxor 2)) = logxor (of_z Z.one) (of_z (Z.of_int 2)));
check_bool "logand1" true (of_int (1 land 3) = logand (of_int 1) (of_int 3));
check_bool "logand2" true (of_z (Z.of_int (1 land 3)) = logand (of_z Z.one) (of_z (Z.of_int 3)));
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
let minus_one = function
| One x -> One (One.minus_one x)
| Many x -> Many (Many.minus_one x)
let plus_one = function
| One x -> One (One.plus_one x)
| Many x -> Many (Many.plus_one x)
#+end_src
Example:
#+begin_example
Bitstring.(plus_one (of_int 15));;
- : Bitstring.t =
----+-----------------------------------------------------------
Bitstring.(minus_one (of_int 15));;
- : Bitstring.t =
-+++------------------------------------------------------------
#+end_example
#+begin_src ocaml :tangle (eval ml) :exports none
let trailing_zeros = function
| One x -> One.trailing_zeros x
| Many x -> Many.trailing_zeros x
let hamdist a b = match a, b with
| One a, One b -> One.hamdist a b
| Many a, Many b -> Many.hamdist a b
| _ -> invalid_arg "Bitstring.hamdist"
let popcount = function
| One x -> One.popcount x
| Many x -> Many.popcount x
#+end_src
Example:
#+begin_example
Bitstring.(trailing_zeros (of_int 12));;
- : int = 2
Bitstring.(hamdist (of_int 15) (of_int 73));;
- : int = 3
Bitstring.(popcount (of_int 15));;
- : int = 4
#+end_example
#+begin_src ocaml :tangle (eval ml) :exports none
let rec to_list ?(accu=[]) = function
| t when (is_zero t) -> List.rev accu
| t -> let newlist =
(trailing_zeros t + 1)::accu
in
let b = logand t @@ minus_one t in
(to_list [@tailcall]) ~accu:newlist b
#+end_src
#+begin_src ocaml :tangle (eval test-ml) :exports none
check_bool "to_list" true ([ 1 ; 3 ; 4 ; 6 ] = (to_list (of_int 45)));
#+end_src
Example:
#+begin_example
Bitstring.(to_list (of_int 45));;
- : int list = [1; 3; 4; 6]
#+end_example
#+begin_src ocaml :tangle (eval ml) :exports none
let permutations m n =
let rec aux k u rest =
if k=1 then
List.rev (u :: rest)
else
let t = logor u @@ minus_one u in
let t' = plus_one t in
let not_t = lognot t in
let neg_not_t = neg not_t in
let t'' = shift_right (minus_one @@ logand not_t neg_not_t) (trailing_zeros u + 1) in
(*
let t'' = shift_right (minus_one (logand (lognot t) t')) (trailing_zeros u + 1) in
,*)
(aux [@tailcall]) (k-1) (logor t' t'') (u :: rest)
in
aux (Util.binom n m) (minus_one (shift_left_one n m)) []
#+end_src
Example:
#+begin_example
Bitstring.permutations 2 4;;
- : Bitstring.t list =
[++--------------------------------------------------------------;
+-+-------------------------------------------------------------;
-++-------------------------------------------------------------;
+--+------------------------------------------------------------;
-+-+------------------------------------------------------------;
--++------------------------------------------------------------]
#+end_example
#+begin_src ocaml :tangle (eval test-ml) :exports none
check "permutations"
(permutations 2 4 = List.map of_int
[ 3 ; 5 ; 6 ; 9 ; 10 ; 12 ]);
#+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 = function
| One x -> One.pp ppf x
| Many x -> Many.pp ppf x
#+end_src
** Tests :noexport:
#+begin_src ocaml :tangle (eval test-ml) :exports none
()
let tests = [
"all", `Quick, test_all;
]
#+end_src

152
common/lib/angular_momentum.ml
View File

@ -1,13 +1,3 @@
(* An exception is raised when the ~Angular_momentum.t~ element can't
* be created.
*
* The ~kind~ is used to build shells, shell doublets, triplets or
* quartets, use in the two-electron operators. *)
(* [[file:~/QCaml/common/angular_momentum.org::*Type][Type:2]] *)
type t =
| S | P | D | F | G | H | I | J | K | L | M | N | O
| Int of int
@ -15,42 +5,14 @@ type t =
exception Angular_momentum_error of string
type kind =
Singlet of t
| Singlet of t
| Doublet of (t * t)
| Triplet of (t * t * t)
| Quartet of (t * t * t * t)
open Powers
(* Type:2 ends here *)
(* | ~of_char~ | Returns an ~Angular_momentum.t~ when a shell is given as a character (case insensitive) |
* | ~to_char~ | Converts the angular momentum into a char |
* | ~of_int~ | Returns a shell given an $l$ value. |
* | ~to_int~ | Returns the $l_{max}$ value of the shell |
* | ~to_string~ | Converts the angular momentum into a string |
*
* Example:
* #+begin_example
* Angular_momentum.of_char 'p';;
* - : Angular_momentum.t = P
*
* Angular_momentum.(to_char P);;
* - : char = 'P'
*
* Angular_momentum.of_int 2;;
* - : Angular_momentum.t = D
*
* Angular_momentum.(to_int D);;
* - : int = 2
*
* Angular_momentum.(to_string D);;
* - : string = "D"
* #+end_example *)
(* [[file:~/QCaml/common/angular_momentum.org::*Conversions][Conversions:2]] *)
let of_char = function
| 's' | 'S' -> S | 'p' | 'P' -> P
| 'd' | 'D' -> D | 'f' | 'F' -> F
@ -99,39 +61,22 @@ let of_int = function
| 8 -> K | 9 -> L
| 10 -> M | 11 -> N
| 12 -> O | i -> Int i
(* Conversions:2 ends here *)
(* | ~n_functions~ | Returns the number of cartesian functions in a shell. |
* | ~zkey_array~ | Array of ~Zkey.t~, where each element is a a key associated with the the powers of $x,y,z$. |
*
* Example:
* #+begin_example
* Angular_momentum.(n_functions D) ;;
* - : int = 6
*
* Angular_momentum.( zkey_array (Doublet (P,S)) );;
* - : Zkey.t array =
* [|< 01125899906842624 | 1, 0, 0, 0, 0, 0 >;
* < 01099511627776 | 0, 1, 0, 0, 0, 0 >;
* < 01073741824 | 0, 0, 1, 0, 0, 0 >|]
* #+end_example *)
(* [[file:~/QCaml/common/angular_momentum.org::*Shell functions][Shell functions:2]] *)
let n_functions a =
let a =
to_int a
in
let a = to_int a in
(a*a + 3*a + 2)/2
let zkey_array_memo : (kind, Zkey.t array) Hashtbl.t =
Hashtbl.create 13
(** Keeps data for function ~zkey_array~ *)
let zkey_array_memo : (kind, Zkey.t array) Hashtbl.t = Hashtbl.create 13
let zkey_array a =
let keys_1d l =
let create_z { x ; y ; _ } =
Powers.of_int_tuple (x,y,l-(x+y))
@ -141,15 +86,17 @@ let zkey_array a =
match y with
| 0 -> (create_z xyz)::accu
| _ -> let ynew = y-1 in
(create_y [@tailcall]) ( (create_z xyz)::accu) (Powers.of_int_tuple (x,ynew,z))
(create_y [@tailcall]) ((create_z xyz)::accu)
(Powers.of_int_tuple (x,ynew,z))
in
let rec create_x accu xyz =
let { x ; z ;_ } = xyz in
match x with
| 0 -> (create_y [] xyz)@accu
| _ -> let xnew = x-1 in
let ynew = l-xnew in
(create_x [@tailcall]) ((create_y [] xyz)@accu) (Powers.of_int_tuple (xnew, ynew, z))
let ynew = l-xnew in
(create_x [@tailcall]) ((create_y [] xyz)@accu)
(Powers.of_int_tuple (xnew, ynew, z))
in
create_x [] (Powers.of_int_tuple (l,0,0))
|> List.rev
@ -164,72 +111,59 @@ let zkey_array a =
begin
match a with
| Singlet l1 ->
List.rev_map (fun x -> Zkey.of_powers_three x) (keys_1d @@ to_int l1)
List.rev_map (fun x -> Zkey.of_powers_three x) (keys_1d @@ to_int l1)
| Doublet (l1, l2) ->
List.rev_map (fun a ->
List.rev_map (fun b -> Zkey.of_powers_six a b) (keys_1d @@ to_int l2)
) (keys_1d @@ to_int l1)
|> List.concat
List.rev_map (fun a ->
List.rev_map (fun b -> Zkey.of_powers_six a b) (keys_1d @@ to_int l2)
) (keys_1d @@ to_int l1)
|> List.concat
| Triplet (l1, l2, l3) ->
List.rev_map (fun a ->
List.rev_map (fun b ->
List.rev_map (fun c ->
Zkey.of_powers_nine a b c) (keys_1d @@ to_int l3)
) (keys_1d @@ to_int l2)
|> List.concat
) (keys_1d @@ to_int l1)
|> List.concat
List.rev_map (fun a ->
List.rev_map (fun b ->
List.rev_map (fun c ->
Zkey.of_powers_nine a b c) (keys_1d @@ to_int l3)
) (keys_1d @@ to_int l2)
|> List.concat
) (keys_1d @@ to_int l1)
|> List.concat
| Quartet (l1, l2, l3, l4) ->
List.rev_map (fun a ->
List.rev_map (fun b ->
List.rev_map (fun c ->
List.rev_map (fun d ->
Zkey.of_powers_twelve a b c d) (keys_1d @@ to_int l4)
) (keys_1d @@ to_int l3)
|> List.concat
) (keys_1d @@ to_int l2)
|> List.concat
) (keys_1d @@ to_int l1)
|> List.concat
List.rev_map (fun a ->
List.rev_map (fun b ->
List.rev_map (fun c ->
List.rev_map (fun d ->
Zkey.of_powers_twelve a b c d) (keys_1d @@ to_int l4)
) (keys_1d @@ to_int l3)
|> List.concat
) (keys_1d @@ to_int l2)
|> List.concat
) (keys_1d @@ to_int l1)
|> List.concat
end
|> List.rev
|> Array.of_list
in
Hashtbl.add zkey_array_memo a result;
result
(* Shell functions:2 ends here *)
(* Example:
* #+begin_example
* Angular_momentum.(D + P);;
* - : Angular_momentum.t = F
*
* Angular_momentum.(F - P);;
* - : Angular_momentum.t = D
* #+end_example *)
(* [[file:~/QCaml/common/angular_momentum.org::*Arithmetic][Arithmetic:2]] *)
let ( + ) a b =
of_int ( (to_int a) + (to_int b) )
let ( - ) a b =
of_int ( (to_int a) - (to_int b) )
(* Arithmetic:2 ends here *)
(* [[file:~/QCaml/common/angular_momentum.org::*Printers][Printers:2]] *)
let pp_string ppf x =
Format.fprintf ppf "@[%s@]" (to_string x)
let pp_int ppf x =
Format.fprintf ppf "@[%d@]" (to_int x)
let pp = pp_string
(* Printers:2 ends here *)

79
common/lib/angular_momentum.mli
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@ -1,58 +1,89 @@
(* Type
*
* <<<~Angular_momentum.t~>>>
* #+NAME: types *)
(** Azimuthal quantum number, repsesented as \( s,p,d,\dots \) *)
(* [[file:~/QCaml/common/angular_momentum.org::types][types]] *)
type t =
| S | P | D | F | G | H | I | J | K | L | M | N | O
| Int of int
exception Angular_momentum_error of string
(** An exception is raised when the ~Angular_momentum.t~ element can't
be created. *)
type kind =
Singlet of t
| Singlet of t
| Doublet of (t * t)
| Triplet of (t * t * t)
| Quartet of (t * t * t * t)
(* types ends here *)
(* Conversions *)
(** Type ~kind~ is used to build shells, shell doublets, triplets or
quartets, use in the two-electron operators. *)
(* [[file:~/QCaml/common/angular_momentum.org::*Conversions][Conversions:1]] *)
(** Conversions *)
val of_char : char -> t
(** Returns an ~Angular_momentum.t~ when a shell is given as a character
(case insensitive)
Angular_momentum.of_char 'p';;
- : Angular_momentum.t = P
*)
val to_char : t -> char
(** Converts the angular momentum into a char
Angular_momentum.(to_char P);;
- : char = 'P'
*)
val to_int : t -> int
(** Returns the $l_{max}$ value of the shell
Angular_momentum.(to_int D);;
- : int = 2
*)
val of_int : int -> t
(** Returns a shell given an $l$ value
Angular_momentum.of_int 2;;
- : Angular_momentum.t = D
*)
val to_string : t -> string
(* Conversions:1 ends here *)
(** Converts the angular momentum into a string
(* Shell functions *)
Angular_momentum.(to_string D);;
- : string = "D"
*)
(* [[file:~/QCaml/common/angular_momentum.org::*Shell functions][Shell functions:1]] *)
(** Shell functions *)
val n_functions : t -> int
(** Returns the number of cartesian functions in a shell. *)
val zkey_array : kind -> Zkey.t array
(* Shell functions:1 ends here *)
(* Arithmetic *)
(** Array of ~Zkey.t~, where each element is a a key associated with the
the powers of $x,y,z$. *)
(* [[file:~/QCaml/common/angular_momentum.org::*Arithmetic][Arithmetic:1]] *)
(** Arithmetic *)
val ( + ) : t -> t -> t
(**
Angular_momentum.(D + P);;
- : Angular_momentum.t = F
*)
val ( - ) : t -> t -> t
(* Arithmetic:1 ends here *)
(* Printers
*
* Printers can print as a string (default) or as an integer. *)
(**
Angular_momentum.(F - P);;
- : Angular_momentum.t = D
*)
(* [[file:~/QCaml/common/angular_momentum.org::*Printers][Printers:1]] *)
(** Printers *)
val pp : Format.formatter -> t -> unit
val pp_string : Format.formatter -> t -> unit
val pp_int : Format.formatter -> t -> unit
(* Printers:1 ends here *)

94
common/lib/bitstring.ml
View File

@ -1,12 +1,8 @@
(* Single-integer implementation :noexport: *)
(** Single-integer implementation *)
(* [[file:~/QCaml/common/bitstring.org::*Single-integer implementation][Single-integer implementation:1]] *)
module One = struct
let of_int x =
assert (x > 0); x
let of_int x = assert (x > 0); x
let numbits _ = 63
let zero = 0
let is_zero x = x = 0
@ -38,12 +34,9 @@ module One = struct
(Z.of_int s)
end
(* Single-integer implementation:1 ends here *)
(* Zarith implementation :noexport: *)
(* [[file:~/QCaml/common/bitstring.org::*Zarith implementation][Zarith implementation:1]] *)
(** Zarith implementation *)
module Many = struct
let of_z x = x
@ -71,58 +64,21 @@ module Many = struct
Format.fprintf ppf "@[@[%a@]@]" (Util.pp_bitstring (Z.numbits s)) s
end
(* Zarith implementation:1 ends here *)
(* [[file:~/QCaml/common/bitstring.org::*Type][Type:2]] *)
type t =
| One of int
| Many of Z.t
(* Type:2 ends here *)
(* | ~of_int~ | Creates a bit string from an ~int~ |
* | ~of_z~ | Creates a bit string from an ~Z.t~ multi-precision integer |
* | ~zero~ | ~zero n~ creates a zero bit string with ~n~ bits |
* | ~is_zero~ | True if all the bits of the bit string are zero. |
* | ~numbits~ | Returns the number of bits used to represent the bit string |
* | ~testbit~ | ~testbit t n~ is true if the ~n~-th bit of the bit string ~t~ is set to ~1~ |
* | ~neg~ | Returns the negative of the integer interpretation of the bit string |
* | ~shift_left~ | ~shift_left t n~ returns a new bit strings with all the bits shifted ~n~ positions to the left |
* | ~shift_right~ | ~shift_right t n~ returns a new bit strings with all the bits shifted ~n~ positions to the right |
* | ~shift_left_one~ | ~shift_left_one size n~ returns a new bit strings with the ~n~-th bit set to one. It is equivalent as shifting ~1~ by ~n~ bits to the left, ~size~ is the total number of bits of the bit string |
* | ~logor~ | Bitwise logical or |
* | ~logxor~ | Bitwise logical exclusive or |
* | ~logand~ | Bitwise logical and |
* | ~lognot~ | Bitwise logical negation |
* | ~plus_one~ | Takes the integer representation of the bit string and adds one |
* | ~minus_one~ | Takes the integer representation of the bit string and removes one |
* | ~hamdist~ | Returns the Hamming distance, i.e. the number of bits differing between two bit strings |
* | ~trailing_zeros~ | Returns the number of trailing zeros in the bit string |
* | ~permutations~ | ~permutations m n~ generates the list of all possible ~n~-bit strings with ~m~ bits set to ~1~. Algorithm adapted from [[https://graphics.stanford.edu/~seander/bithacks.html#NextBitPermutation][Bit twiddling hacks]] |
* | ~popcount~ | Returns the number of bits set to one in the bit string |
* | ~to_list~ | Converts a bit string into a list of integers indicating the positions where the bits are set to ~1~. The first value for the position is not ~0~ but ~1~ | *)
(* [[file:~/QCaml/common/bitstring.org::*General implementation][General implementation:2]] *)
let of_int x =
One (One.of_int x)
let of_z x =
if Z.numbits x < 64 then One (Z.to_int x) else Many (Many.of_z x)
(* General implementation:2 ends here *)
(* Example:
* #+begin_example
* Bitstring.of_int 15;;
* - : Bitstring.t =
* ++++------------------------------------------------------------
* #+end_example *)
(* [[file:~/QCaml/common/bitstring.org::*General implementation][General implementation:4]] *)
let zero = function
| n when n < 64 -> One (One.zero)
| _ -> Many (Many.zero)
@ -159,9 +115,9 @@ let shift_left_one = function
let testbit = function
| One x -> One.testbit x
| Many x -> Many.testbit x
(* General implementation:4 ends here *)
(* [[file:~/QCaml/common/bitstring.org::*General implementation][General implementation:6]] *)
(** General implementation *)
let logor a b =
match a,b with
| One a, One b -> One (One.logor a b)
@ -186,9 +142,8 @@ let logand a b =
let lognot = function
| One x -> One (One.lognot x)
| Many x -> Many (Many.lognot x)
(* General implementation:6 ends here *)
(* [[file:~/QCaml/common/bitstring.org::*General implementation][General implementation:8]] *)
let minus_one = function
| One x -> One (One.minus_one x)
| Many x -> Many (Many.minus_one x)
@ -197,25 +152,8 @@ let minus_one = function
let plus_one = function
| One x -> One (One.plus_one x)
| Many x -> Many (Many.plus_one x)
(* General implementation:8 ends here *)
(* Example:
* #+begin_example
* Bitstring.(plus_one (of_int 15));;
* - : Bitstring.t =
* ----+-----------------------------------------------------------
*
* Bitstring.(minus_one (of_int 15));;
* - : Bitstring.t =
* -+++------------------------------------------------------------
* #+end_example *)
(* [[file:~/QCaml/common/bitstring.org::*General implementation][General implementation:9]] *)
let trailing_zeros = function
| One x -> One.trailing_zeros x
| Many x -> Many.trailing_zeros x
@ -230,24 +168,10 @@ let hamdist a b = match a, b with
let popcount = function
| One x -> One.popcount x
| Many x -> Many.popcount x
(* General implementation:9 ends here *)
(* Example:
* #+begin_example
* Bitstring.(trailing_zeros (of_int 12));;
* - : int = 2
*
* Bitstring.(hamdist (of_int 15) (of_int 73));;
* - : int = 3
*
* Bitstring.(popcount (of_int 15));;
* - : int = 4
* #+end_example *)
(* [[file:~/QCaml/common/bitstring.org::*General implementation][General implementation:10]] *)
let rec to_list ?(accu=[]) = function
| t when (is_zero t) -> List.rev accu
@ -267,7 +191,6 @@ let rec to_list ?(accu=[]) = function
* #+end_example *)
(* [[file:~/QCaml/common/bitstring.org::*General implementation][General implementation:12]] *)
let permutations m n =
let rec aux k u rest =
@ -285,10 +208,9 @@ let permutations m n =
(aux [@tailcall]) (k-1) (logor t' t'') (u :: rest)
in
aux (Util.binom n m) (minus_one (shift_left_one n m)) []
(* General implementation:12 ends here *)
(* [[file:~/QCaml/common/bitstring.org::*Printers][Printers:2]] *)
let pp ppf = function
| One x -> One.pp ppf x
| Many x -> Many.pp ppf x
(* Printers:2 ends here *)

145
common/lib/bitstring.mli
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@ -1,47 +1,166 @@
(* Type
*
* <<<~Bitstring.t~>>> *)
(** Bitstring
We define here a data type to handle bit strings efficiently. When
the bit string contains less than 64 bits, it is stored internally
in a 63-bit integer and uses bitwise instructions. When more than
63 bits are required, the =zarith= library is used to consider the
bit string as a multi-precision integer.
*)
(* [[file:~/QCaml/common/bitstring.org::*Type][Type:1]] *)
type t
(* Type:1 ends here *)
(* General implementation *)
(* [[file:~/QCaml/common/bitstring.org::*General implementation][General implementation:1]] *)
val of_int : int -> t
(** Creates a bit string from an ~int~
Bitstring.of_int 15;;
- : Bitstring.t =
++++------------------------------------------------------------
*)
val of_z : Z.t -> t
(** Creates a bit string from an ~Z.t~ multi-precision integer *)
val zero : int -> t
(** ~zero n~ creates a zero bit string with ~n~ bits *)
val is_zero : t -> bool
(** True if all the bits of the bit string are zero. *)
val numbits : t -> int
(** Returns the number of bits used to represent the bit string *)
val testbit : t -> int -> bool
(** ~testbit t n~ is true if the ~n~-th bit of the bit string ~t~ is set to ~1~
Bitstring.(testbit (of_int 15) 3);;
- : bool = true
Bitstring.(testbit (of_int 15) 4);;
- : bool = false
*)
val neg : t -> t
(** Returns the negative of the integer interpretation of the bit string *)
val shift_left : t -> int -> t
(** ~shift_left t n~ returns a new bit strings with all the bits shifted ~n~
positions to the left
Bitstring.(shift_left (of_int 15) 2);;
- : Bitstring.t =
--++++----------------------------------------------------------
*)
val shift_right : t -> int -> t
(** ~shift_right t n~ returns a new bit strings with all the bits shifted ~n~
positions to the right
Bitstring.(shift_right (of_int 15) 2);;
- : Bitstring.t =
++--------------------------------------------------------------
*)
val shift_left_one : int -> int -> t
(** shift_left_one size n~ returns a new bit strings with the ~n~-th bit set to
one. It is equivalent as shifting ~1~ by ~n~ bits to the left, ~size~ is the
total number of bits of the bit string
Bitstring.shift_left_one 32 4;;
- : Bitstring.t =
----+-----------------------------------------------------------
*)
val logor : t -> t -> t
(** Bitwise logical or
Bitstring.(logor (of_int 15) (of_int 73));;
- : Bitstring.t =
++++--+---------------------------------------------------------
*)
val logxor : t -> t -> t
(** Bitwise logical exclusive or
Bitstring.(logxor (of_int 15) (of_int 73));;
- : Bitstring.t =
-++---+---------------------------------------------------------
*)
val logand : t -> t -> t
(** Bitwise logical and
Bitstring.(logand (of_int 15) (of_int 10));;
- : Bitstring.t =
-+-+------------------------------------------------------------
*)
val lognot : t -> t
(** Bitwise logical negation *)
val plus_one : t -> t
(** Takes the integer representation of the bit string and adds one
Bitstring.(plus_one (of_int 15));;
- : Bitstring.t =
----+-----------------------------------------------------------
*)
val minus_one : t -> t
(** Takes the integer representation of the bit string and removes one
Bitstring.(minus_one (of_int 15));;
- : Bitstring.t =
-+++------------------------------------------------------------
*)
val hamdist : t -> t -> int
(** Returns the Hamming distance, i.e. the number of bits differing between two
bit strings
Bitstring.(hamdist (of_int 15) (of_int 73));;
- : int = 3
*)
val trailing_zeros : t -> int
(** Returns the number of trailing zeros in the bit string
Bitstring.(trailing_zeros (of_int 12));;
- : int = 2
*)
val popcount : t -> int
(** Returns the number of bits set to one in the bit string
Bitstring.(popcount (of_int 15));;
- : int = 4
*)
val to_list : ?accu:(int list) -> t -> int list
(** Converts a bit string into a list of integers indicating the positions where
the bits are set to ~1~. The first value for the position is not ~0~ but ~1~
Bitstring.(to_list (of_int 45));;
- : int list = [1; 3; 4; 6]
*)
val permutations : int -> int -> t list
(* General implementation:1 ends here *)
(** ~permutations m n~ generates the list of all possible ~n~-bit strings with
~m~ bits set to ~1~. Algorithm adapted from
[[https://graphics.stanford.edu/~seander/bithacks.html#NextBitPermutation][Bit twiddling hacks]]
(* Printers *)
Bitstring.permutations 2 4;;
- : Bitstring.t list =
[++--------------------------------------------------------------;
+-+-------------------------------------------------------------;
-++-------------------------------------------------------------;
+--+------------------------------------------------------------;
-+-+------------------------------------------------------------;
--++------------------------------------------------------------]
*)
(* [[file:~/QCaml/common/bitstring.org::*Printers][Printers:1]] *)
(** Printers *)
val pp : Format.formatter -> t -> unit
(* Printers:1 ends here *)

10
common/lib/non_negative_float.ml
View File

@ -1,14 +1,5 @@
(* [[file:~/QCaml/common/non_negative_float.org::*Type][Type:2]] *)
type t = float
(* Type:2 ends here *)
(* The ~of_float~ function checks that the float is non-negative.
* The unsafe variant doesn't do this check. *)
(* [[file:~/QCaml/common/non_negative_float.org::*Conversions][Conversions:2]] *)
let of_float x =
if x < 0. then invalid_arg (__FILE__^": of_float");
x
@ -21,4 +12,3 @@ let to_string x =
let of_string x =
let f = float_of_string x in of_float f
(* Conversions:2 ends here *)

19
common/lib/non_negative_float.mli
View File

@ -1,19 +1,14 @@
(* Type
*
* <<<~Non_negative_float.t~>> *)
(* [[file:~/QCaml/common/non_negative_float.org::*Type][Type:1]] *)
(** $x \ge 0$ *)
type t = private float
(* Type:1 ends here *)
(* Conversions *)
(** Conversions *)
(* [[file:~/QCaml/common/non_negative_float.org::*Conversions][Conversions:1]] *)
val of_float : float -> t
val unsafe_of_float : float -> t
val to_float : t -> float
(** Checks that the float is non-negative. *)
val unsafe_of_float : float -> t
(** Fast conversion without checking that the float is non-negative. *)
val to_float : t -> float
val of_string : string -> t
val to_string : t -> string
(* Conversions:1 ends here *)

9
common/lib/qcaml.ml
View File

@ -1,11 +1,3 @@
(* | ~root~ | Path to the QCaml source directory |
* | ~name~ | ~"QCaml"~ |
* | ~num_domains~ | Number of threads in parallel computations | *)
(* [[file:~/QCaml/common/qcaml.org::*QCaml][QCaml:2]] *)
let name = "QCaml"
let root =
@ -29,4 +21,3 @@ let num_domains =
with Not_found -> 1
in
result - 1
(* QCaml:2 ends here *)

16
common/lib/qcaml.mli
View File

@ -1,13 +1,11 @@
(* QCaml
* :PROPERTIES:
* :header-args: :noweb yes :comments both
* :END:
*
* QCaml-specific parameters *)
(** QCaml-specific parameters *)
(* [[file:~/QCaml/common/qcaml.org::*QCaml][QCaml:1]] *)
val root : string
(** Path to the QCaml source directory *)
val name : string
(** "QCaml" *)
val num_domains : int
(* QCaml:1 ends here *)
(** Number of threads in parallel computations. Obtained from the environment variable
~OMP_NUM_THREADS~. *)

55
common/non_negative_float.org
View File

@ -1,55 +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
* Non-negative float
:PROPERTIES:
:header-args: :noweb yes :comments both
:END:
** Type
<<<~Non_negative_float.t~>>
#+begin_src ocaml :tangle (eval mli)
type t = private float
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
type t = float
#+end_src
** Conversions
#+begin_src ocaml :tangle (eval mli)
val of_float : float -> t
val unsafe_of_float : float -> t
val to_float : t -> float
val of_string : string -> t
val to_string : t -> string
#+end_src
The ~of_float~ function checks that the float is non-negative.
The unsafe variant doesn't do this check.
#+begin_src ocaml :tangle (eval ml) :exports none
let of_float x =
if x < 0. then invalid_arg (__FILE__^": of_float");
x
external to_float : t -> float = "%identity"
external unsafe_of_float : float -> t = "%identity"
let to_string x =
let f = to_float x in string_of_float f
let of_string x =
let f = float_of_string x in of_float f
#+end_src

55
common/qcaml.org
View File

@ -1,55 +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
* QCaml
:PROPERTIES:
:header-args: :noweb yes :comments both
:END:
QCaml-specific parameters
#+begin_src ocaml :tangle (eval mli)
val root : string
val name : string
val num_domains : int
#+end_src
| ~root~ | Path to the QCaml source directory |
| ~name~ | ~"QCaml"~ |
| ~num_domains~ | Number of threads in parallel computations |
#+begin_src ocaml :tangle (eval ml) :exports none
let name = "QCaml"
let root =
let rec chop = function
| [] -> []
| x :: _ as l when x = name -> l
| _ :: rest -> chop rest
in
String.split_on_char Filename.dir_sep.[0] (Sys.getcwd ())
|> List.rev
|> chop
|> List.rev
|> String.concat Filename.dir_sep
let num_domains =
let result =
try
Unix.getenv "OMP_NUM_THREADS"
|> int_of_string
with Not_found -> 1
in
result - 1
#+end_src

490
docs/ao.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-04-24 Mon 18:06 -->
<!-- 2023-06-27 Tue 09:39 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Atomic Orbitals</title>
@ -238,28 +238,6 @@ org_html_manager.setup(); // activate after the parameters are set
/*]]>*///-->
// @license-end
</script>
<script type="text/x-mathjax-config">
MathJax.Hub.Config({
displayAlign: "center",
displayIndent: "0em",
"HTML-CSS": { scale: 100,
linebreaks: { automatic: "false" },
webFont: "TeX"
},
SVG: {scale: 100,
linebreaks: { automatic: "false" },
font: "TeX"},
NativeMML: {scale: 100},
TeX: { equationNumbers: {autoNumber: "AMS"},
MultLineWidth: "85%",
TagSide: "right",
TagIndent: ".8em"
}
});
</script>
<script type="text/javascript"
src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS_HTML"></script>
</head>
<body>
<div id="org-div-home-and-up">
@ -272,37 +250,13 @@ org_html_manager.setup(); // activate after the parameters are set
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org87cd388">1. Summary</a></li>
<li><a href="#org5e9a951">2. Gaussian basis</a>
<ul>
<li><a href="#orgf171259">2.1. Type</a></li>
<li><a href="#orgb673ed0">2.2. Access</a></li>
<li><a href="#org11cfca9">2.3. Computation</a></li>
<li><a href="#org2fa1d61">2.4. Creation</a></li>
<li><a href="#org4e9005b">2.5. Printers</a></li>
</ul>
</li>
<li><a href="#org4261d95">3. Basis</a>
<ul>
<li><a href="#org5c0d97e">3.1. Polymorphic types</a></li>
<li><a href="#orga5c49f9">3.2. Types</a></li>
<li><a href="#org08915ff">3.3. Conversions</a></li>
<li><a href="#org2d64081">3.4. Access</a></li>
<li><a href="#org71c045d">3.5. TREXIO</a>
<ul>
<li><a href="#orgaa1a673">3.5.1. Read</a></li>
<li><a href="#org96c21ab">3.5.2. Write</a></li>
</ul>
</li>
<li><a href="#org95b5bdd">3.6. Printers</a></li>
</ul>
</li>
<li><a href="#orgf5a43e5">1. Summary</a></li>
</ul>
</div>
</div>
<div id="outline-container-org87cd388" class="outline-2">
<h2 id="org87cd388"><span class="section-number-2">1</span> Summary</h2>
<div id="outline-container-orgf5a43e5" class="outline-2">
<h2 id="orgf5a43e5"><span class="section-number-2">1</span> Summary</h2>
<div class="outline-text-2" id="text-1">
<p>
This modules contains the data structures used to characterize the
@ -310,444 +264,10 @@ atomic basis set.
</p>
</div>
</div>
<div id="outline-container-org5e9a951" class="outline-2">
<h2 id="org5e9a951"><span class="section-number-2">2</span> Gaussian basis</h2>
<div class="outline-text-2" id="text-2">
<p>
Data structure for Gaussian Atomic Orbitals:
</p>
<p>
\[
\chi_i(\mathbf{r}) = P_i(\mathbf{r}) \sum_k c_k \exp\left( -\alpha_k (\mathbf{r-R_A})^2 \right)
\]
</p>
<p>
where the polynomial \(P_i\) and the Gaussian part are both centered on
nucleus \(A\).
</p>
</div>
<div id="outline-container-orgf171259" class="outline-3">
<h3 id="orgf171259"><span class="section-number-3">2.1</span> Type</h3>
<div class="outline-text-3" id="text-2-1">
<p>
<a id="org1e8ec27"><code>Gaussian_basis.t</code></a>
</p>
<div class="org-src-container">
<pre class="src src-ocaml" id="org74d75c2"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Particles</span>
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Linear_algebra</span>
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Gaussian_integrals</span>
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Operators</span>
<span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-orgb673ed0" class="outline-3">
<h3 id="orgb673ed0"><span class="section-number-3">2.2</span> Access</h3>
<div class="outline-text-3" id="text-2-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">basis</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Gaussian.Basis.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">cartesian</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> bool
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">ee_ints</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Eri.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">ee_lr_ints</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Eri_long_range.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">eN_ints</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Electron_nucleus.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">f12_ints</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">F12.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">f12_over_r12_ints</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Screened_eri.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">kin_ints</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Kinetic.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">multipole</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Multipole.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">ortho</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Orthonormalization.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">overlap</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Overlap.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">size</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> int
</pre>
</div>
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="org-left" />
<col class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left"><code>basis</code></td>
<td class="org-left">One-electron basis set</td>
</tr>
<tr>
<td class="org-left"><code>cartesian</code></td>
<td class="org-left">If true, use cartesian Gaussians (6d, 10f, &#x2026;)</td>
</tr>
<tr>
<td class="org-left"><code>ee_ints</code></td>
<td class="org-left">Electron-electron potential integrals</td>
</tr>
<tr>
<td class="org-left"><code>ee_lr_ints</code></td>
<td class="org-left">Electron-electron long-range potential integrals</td>
</tr>
<tr>
<td class="org-left"><code>eN_ints</code></td>
<td class="org-left">Electron-nucleus potential integrals</td>
</tr>
<tr>
<td class="org-left"><code>f12_ints</code></td>
<td class="org-left">Electron-electron potential integrals</td>
</tr>
<tr>
<td class="org-left"><code>f12_over_r12_ints</code></td>
<td class="org-left">Electron-electron potential integrals</td>
</tr>
<tr>
<td class="org-left"><code>kin_ints</code></td>
<td class="org-left">Kinetic energy integrals</td>
</tr>
<tr>
<td class="org-left"><code>multipole</code></td>
<td class="org-left">Multipole matrices</td>
</tr>
<tr>
<td class="org-left"><code>ortho</code></td>
<td class="org-left">Orthonormalization matrix of the overlap</td>
</tr>
<tr>
<td class="org-left"><code>overlap</code></td>
<td class="org-left">Overlap matrix</td>
</tr>
<tr>
<td class="org-left"><code>size</code></td>
<td class="org-left">Number of atomic orbitals</td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="outline-container-org11cfca9" class="outline-3">
<h3 id="org11cfca9"><span class="section-number-3">2.3</span> Computation</h3>
<div class="outline-text-3" id="text-2-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">values</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span>
<span class="org-tuareg-font-lock-module">Coordinate.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span>
<span class="org-tuareg-font-lock-module">Gaussian.Basis.</span>t <span class="org-tuareg-font-lock-module">Vector.</span>t
</pre>
</div>
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="org-left" />
<col class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left"><code>values</code></td>
<td class="org-left">Returns the values of all the AOs evaluated at a given point</td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="outline-container-org2fa1d61" class="outline-3">
<h3 id="org2fa1d61"><span class="section-number-3">2.4</span> Creation</h3>
<div class="outline-text-3" id="text-2-4">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">make</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-label">basis</span><span class="org-tuareg-font-lock-operator">:</span><span class="org-tuareg-font-lock-module">Gaussian.Basis.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span>
<span class="org-tuareg-font-lock-label">?operators</span><span class="org-tuareg-font-lock-operator">:</span><span class="org-tuareg-font-lock-module">Operator.</span>t list <span class="org-tuareg-font-lock-operator">-&gt;</span>
<span class="org-tuareg-font-lock-label">?cartesian</span><span class="org-tuareg-font-lock-operator">:</span>bool <span class="org-tuareg-font-lock-operator">-&gt;</span>
<span class="org-tuareg-font-lock-module">Nuclei.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span>
t
</pre>
</div>
<p>
Creates the data structure for atomic orbitals from a Gaussian basis and the
molecular geometry <code>Nuclei.t</code>.
</p>
<p>
Defaults:
</p>
<ul class="org-ul">
<li><code>operators</code> : <code>[]</code></li>
<li><code>cartesian</code> : <code>false</code></li>
</ul>
<p>
Example:
</p>
<pre class="example" id="org6d35d9a">
let b = Ao.Basis_gaussian.make ~basis nuclei ;;
val b : Ao.Basis_gaussian.t = Gaussian Basis, spherical, 15 AOs
</pre>
</div>
</div>
<div id="outline-container-org4e9005b" class="outline-3">
<h3 id="org4e9005b"><span class="section-number-3">2.5</span> Printers</h3>
<div class="outline-text-3" id="text-2-5">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-org4261d95" class="outline-2">
<h2 id="org4261d95"><span class="section-number-2">3</span> Basis</h2>
<div class="outline-text-2" id="text-3">
<p>
Data structure for Atomic Orbitals.
</p>
</div>
<div id="outline-container-org5c0d97e" class="outline-3">
<h3 id="org5c0d97e"><span class="section-number-3">3.1</span> Polymorphic types</h3>
<div class="outline-text-3" id="text-3-1">
<p>
<a id="org4d89fcd"><code>Basis.t</code></a>
</p>
<div class="org-src-container">
<pre class="src src-ocaml" id="org628afe5"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span> <span class="org-tuareg-font-lock-operator">=</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">Unknown</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">Gaussian</span> <span class="org-keyword">of</span> <span class="org-tuareg-font-lock-module">Basis_gaussian.</span>t
</pre>
</div>
</div>
</div>
<div id="outline-container-orga5c49f9" class="outline-3">
<h3 id="orga5c49f9"><span class="section-number-3">3.2</span> Types</h3>
<div class="outline-text-3" id="text-3-2">
<p>
<a id="org473035a"><code>Basis.t</code></a>
</p>
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
<span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">ao</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-tuareg-font-lock-module">Ao_dim.</span>t
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Particles</span>
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Operators</span>
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Linear_algebra</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-org08915ff" class="outline-3">
<h3 id="org08915ff"><span class="section-number-3">3.3</span> Conversions</h3>
<div class="outline-text-3" id="text-3-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_nuclei_and_basis_filename</span> <span class="org-tuareg-font-lock-operator">:</span>
<span class="org-tuareg-font-lock-label">?kind</span><span class="org-tuareg-font-lock-operator">:[&gt;</span> <span class="org-tuareg-font-lock-constructor">`Gaussian</span> <span class="org-tuareg-font-lock-operator">]</span> <span class="org-tuareg-font-lock-operator">-&gt;</span>
<span class="org-tuareg-font-lock-label">?operators</span><span class="org-tuareg-font-lock-operator">:</span><span class="org-tuareg-font-lock-module">Operator.</span>t list <span class="org-tuareg-font-lock-operator">-&gt;</span>
<span class="org-tuareg-font-lock-label">?cartesian</span><span class="org-tuareg-font-lock-operator">:</span>bool <span class="org-tuareg-font-lock-operator">-&gt;</span>
<span class="org-tuareg-font-lock-label">nuclei</span><span class="org-tuareg-font-lock-operator">:</span><span class="org-tuareg-font-lock-module">Nuclei.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span>
string <span class="org-tuareg-font-lock-operator">-&gt;</span>
t
</pre>
</div>
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="org-left" />
<col class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left"><code>of_nuclei_and_basis_filename</code></td>
<td class="org-left">Creates the data structure for the atomic orbitals basis from a molecule <code>Nuclei.t</code> and the name of the basis-set file</td>
</tr>
</tbody>
</table>
<p>
Defaults:
</p>
<ul class="org-ul">
<li><code>kind</code> : <code>`Gaussian</code></li>
<li><code>operators</code> : <code>[]</code></li>
<li><code>cartesian</code> : <code>false</code></li>
</ul>
<p>
Example:
</p>
<pre class="example" id="org101d41d">
let b = Ao.Basis.of_nuclei_and_basis_filename ~nuclei filename;;
val b : Ao.Basis.t = Gaussian Basis, spherical, 15 AOs
</pre>
</div>
</div>
<div id="outline-container-org2d64081" class="outline-3">
<h3 id="org2d64081"><span class="section-number-3">3.4</span> Access</h3>
<div class="outline-text-3" id="text-3-4">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">size</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> int
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">ao_basis</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Basis_poly.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">overlap</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-operator">(</span>ao<span class="org-tuareg-font-lock-operator">,</span>ao<span class="org-tuareg-font-lock-operator">)</span> <span class="org-tuareg-font-lock-module">Matrix.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">multipole</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> string <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-operator">(</span>ao<span class="org-tuareg-font-lock-operator">,</span>ao<span class="org-tuareg-font-lock-operator">)</span> <span class="org-tuareg-font-lock-module">Matrix.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">ortho</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-operator">(</span>ao<span class="org-tuareg-font-lock-operator">,</span>'a<span class="org-tuareg-font-lock-operator">)</span> <span class="org-tuareg-font-lock-module">Matrix.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">eN_ints</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-operator">(</span>ao<span class="org-tuareg-font-lock-operator">,</span>ao<span class="org-tuareg-font-lock-operator">)</span> <span class="org-tuareg-font-lock-module">Matrix.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">kin_ints</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-operator">(</span>ao<span class="org-tuareg-font-lock-operator">,</span>ao<span class="org-tuareg-font-lock-operator">)</span> <span class="org-tuareg-font-lock-module">Matrix.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">ee_ints</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> ao <span class="org-tuareg-font-lock-module">Four_idx_storage.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">ee_lr_ints</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> ao <span class="org-tuareg-font-lock-module">Four_idx_storage.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">f12_ints</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> ao <span class="org-tuareg-font-lock-module">Four_idx_storage.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">f12_over_r12_ints</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> ao <span class="org-tuareg-font-lock-module">Four_idx_storage.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">cartesian</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> bool
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">values</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Coordinate.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> ao <span class="org-tuareg-font-lock-module">Vector.</span>t
</pre>
</div>
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="org-left" />
<col class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left"><code>size</code></td>
<td class="org-left">Number of atomic orbitals in the AO basis set</td>
</tr>
<tr>
<td class="org-left"><code>ao_basis</code></td>
<td class="org-left">One-electron basis set</td>
</tr>
<tr>
<td class="org-left"><code>overlap</code></td>
<td class="org-left">Overlap matrix</td>
</tr>
<tr>
<td class="org-left"><code>multipole</code></td>
<td class="org-left">Multipole matrices</td>
</tr>
<tr>
<td class="org-left"><code>ortho</code></td>
<td class="org-left">Orthonormalization matrix of the overlap</td>
</tr>
<tr>
<td class="org-left"><code>eN_ints</code></td>
<td class="org-left">Electron-nucleus potential integrals</td>
</tr>
<tr>
<td class="org-left"><code>kin_ints</code></td>
<td class="org-left">Kinetic energy integrals</td>
</tr>
<tr>
<td class="org-left"><code>ee_ints</code></td>
<td class="org-left">Electron-electron potential integrals</td>
</tr>
<tr>
<td class="org-left"><code>ee_lr_ints</code></td>
<td class="org-left">Electron-electron long-range potential integrals</td>
</tr>
<tr>
<td class="org-left"><code>f12_ints</code></td>
<td class="org-left">Electron-electron potential integrals</td>
</tr>
<tr>
<td class="org-left"><code>f12_over_r12_ints</code></td>
<td class="org-left">Electron-electron potential integrals</td>
</tr>
<tr>
<td class="org-left"><code>cartesian</code></td>
<td class="org-left">If true, use cartesian Gaussians (6d, 10f, &#x2026;)</td>
</tr>
<tr>
<td class="org-left"><code>values</code></td>
<td class="org-left">Values of the AOs evaluated at a given point</td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="outline-container-org71c045d" class="outline-3">
<h3 id="org71c045d"><span class="section-number-3">3.5</span> TREXIO</h3>
<div class="outline-text-3" id="text-3-5">
</div>
<div id="outline-container-orgaa1a673" class="outline-4">
<h4 id="orgaa1a673"><span class="section-number-4">3.5.1</span> Read</h4>
<div class="outline-text-4" id="text-3-5-1">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-comment-delimiter">(*</span>
<span class="org-comment">val of_trexio : Trexio.trexio_file -&gt; t</span>
<span class="org-comment-delimiter">*)</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-org96c21ab" class="outline-4">
<h4 id="org96c21ab"><span class="section-number-4">3.5.2</span> Write</h4>
<div class="outline-text-4" id="text-3-5-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-comment-delimiter">(*</span>
<span class="org-comment">val to_trexio : Trexio.trexio_file -&gt; t -&gt; unit</span>
<span class="org-comment-delimiter">*)</span>
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-org95b5bdd" class="outline-3">
<h3 id="org95b5bdd"><span class="section-number-3">3.6</span> Printers</h3>
<div class="outline-text-3" id="text-3-6">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
</pre>
</div>
</div>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2023-04-24 Mon 18:06</p>
<p class="date">Created: 2023-06-27 Tue 09:39</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

10
docs/top.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-06-26 Mon 15:36 -->
<!-- 2023-06-27 Tue 09:39 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Top-level</title>
@ -250,18 +250,18 @@ org_html_manager.setup(); // activate after the parameters are set
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org88f23a2">1. Summary</a></li>
<li><a href="#orgbaf6a72">1. Summary</a></li>
</ul>
</div>
</div>
<div id="outline-container-org88f23a2" class="outline-2">
<h2 id="org88f23a2"><span class="section-number-2">1</span> Summary</h2>
<div id="outline-container-orgbaf6a72" class="outline-2">
<h2 id="orgbaf6a72"><span class="section-number-2">1</span> Summary</h2>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2023-06-26 Mon 15:36</p>
<p class="date">Created: 2023-06-27 Tue 09:39</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
top/lib/install_printers.ml
View File

@ -1,10 +1,6 @@
(* [[file:~/QCaml/top/install_printers.org::*Intall printers][Intall printers:3]] *)
let printers =
[
"Ao.Basis.pp" ;
"Ao.Basis_gaussian.pp" ;
"Common.Angular_momentum.pp" ;
"Common.Bitstring.pp" ;
"Common.Charge.pp" ;
"Common.Coordinate.pp" ;
"Common.Powers.pp" ;