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Introduced phantom types for Bohr/Angstrom

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This commit is contained in:
Anthony Scemama 2019-06-18 14:29:57 +02:00
parent c517a6d6a5
commit 91a2ec1288
11 changed files with 90 additions and 93 deletions
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6
Basis/TwoElectronRRVectorized.ml
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@ -756,14 +756,14 @@ let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
in
let empty = Array.make (maxm+1) 0. in
let center_qc_tmp = Array.init nq (fun cd ->
Bohr.make { Point.
Coordinate.make { Coordinate.
x = (center_qc Co.X).(cd) ;
y = (center_qc Co.Y).(cd) ;
z = (center_qc Co.Z).(cd) ;
})
in
Array.iteri (fun ab shell_ab ->
let center_pa = Bohr.make { Point.
let center_pa = Coordinate.make { Coordinate.
x = (center_pa Co.X).(ab) ;
y = (center_pa Co.Y).(ab) ;
z = (center_pa Co.Z).(ab) ;
@ -789,7 +789,7 @@ let contracted_class_shell_pairs ~zero_m ?schwartz_p ?schwartz_q shell_p shell_q
in
zero_m Zp.{
maxm ; expo_p_inv ; expo_q_inv ; norm_pq_sq ;
center_pq = Bohr.make Point.{x ; y ; z} ;
center_pq = Coordinate.make Coordinate.{x ; y ; z} ;
center_pa ; center_qc = center_qc_tmp.(cd) ;
normalization ;
}

17
Nuclei/Nuclei.ml
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@ -28,7 +28,9 @@ let of_xyz_file filename =
let of_zmt_string buffer =
Zmatrix.of_string buffer
|> Zmatrix.to_xyz
|> Array.map (fun (e,x,y,z) -> (e, Coordinate.angstrom_to_bohr (Angstrom.make {Point.x ; y ; z} )))
|> Array.map (fun (e,x,y,z) ->
(e, Coordinate.(angstrom_to_bohr @@ make_angstrom { x ; y ; z} ))
)
let of_zmt_file filename =
@ -56,12 +58,13 @@ let to_string atoms =
-----------------------------------------------------------------------
" ^
(Array.mapi (fun i (e, coord) ->
let open Coordinate in
let coord =
Coordinate.bohr_to_angstrom coord
bohr_to_angstrom coord
in
Printf.sprintf " %5d %5d %5s %12.6f %12.6f %12.6f"
(i+1) (Element.to_int e) (Element.to_string e)
coord.Angstrom.x coord.Angstrom.y coord.Angstrom.z
coord.x coord.y coord.z
) atoms
|> Array.to_list
|> String.concat "\n" ) ^
@ -100,11 +103,12 @@ let charge nuclei =
let to_xyz_string t =
[ string_of_int (Array.length t) ; "" ] @
( Array.mapi (fun i (e, coord) ->
let open Coordinate in
let coord =
Coordinate.bohr_to_angstrom coord
bohr_to_angstrom coord
in
Printf.sprintf " %5s %12.6f %12.6f %12.6f"
(Element.to_string e) coord.Angstrom.x coord.Angstrom.y coord.Angstrom.z
(Element.to_string e) coord.x coord.y coord.z
) t
|> Array.to_list )
|> String.concat "\n"
@ -117,8 +121,9 @@ let to_t2_string t =
(2 * Array.length t);
"# Znuc x y z" ]
@ (Array.mapi (fun i (e, coord) ->
let open Coordinate in
Printf.sprintf " %5f %12.6f %12.6f %12.6f"
(Element.to_int e |> float_of_int) coord.Bohr.x coord.Bohr.y coord.Bohr.z
(Element.to_int e |> float_of_int) coord.x coord.y coord.z
) t
|> Array.to_list )
|> String.concat "\n"

2
Nuclei/Nuclei.mli
View File

@ -2,7 +2,7 @@
of tuples ({!Element.t}, {!Coordinate.t}).
*)
type t = (Element.t * Bohr.t) array
type t = (Element.t * Coordinate.t) array
val of_xyz_file : string -> t

2
Nuclei/Xyz_ast.mli
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@ -4,7 +4,7 @@
type nucleus =
{
element: Element.t ;
coord : Angstrom.t;
coord : Coordinate.angstrom Coordinate.point;
}
type xyz_file =

5
Nuclei/Xyz_parser.mly
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@ -3,10 +3,9 @@
%{
exception InputError of string
let make_angstrom x y z =
Angstrom.make {
Point.
Coordinate.(make_angstrom {
x ; y ; z
}
})
let output_of f x y z =
let a = make_angstrom x y z in

1
Utils/Angstrom.ml
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@ -1 +0,0 @@
include Bohr

4
Utils/Angstrom.mli
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@ -1,4 +0,0 @@
(** 3D point in cartesian coordinates, where units are Angstroms. *)
include module type of Bohr

11
Utils/Bohr.ml
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@ -1,11 +0,0 @@
type t = {
x : float ;
y : float ;
z : float ;
}
external make : Point.t -> t = "%identity"

12
Utils/Bohr.mli
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@ -1,12 +0,0 @@
(** 3D point in cartesian coordinates, where units are atomic units (Bohr). *)
type t = private {
x : float ;
y : float ;
z : float ;
}
val make : Point.t -> t

53
Utils/Coordinate.ml
View File

@ -1,7 +1,19 @@
type bohr = Bohr.t
type angstrom = Angstrom.t
type bohr
type angstrom
type t = bohr
type xyz = {
x : float ;
y : float ;
z : float ;
}
type 'a point = xyz
type t = bohr point
external make : 'a point -> t = "%identity"
external make_angstrom : 'a point -> angstrom point = "%identity"
type axis = X | Y | Z
@ -9,19 +21,17 @@ type axis = X | Y | Z
let a_to_b a = Constants.a0_inv *. a
let b_to_a b = Constants.a0 *. b
let bohr_to_angstrom { Bohr.x ; y ; z } =
Angstrom.make
let bohr_to_angstrom { x ; y ; z } =
make
{
Point.
x = b_to_a x ;
y = b_to_a y ;
z = b_to_a z ;
}
let angstrom_to_bohr { Angstrom.x ; y ; z } =
Bohr.make
let angstrom_to_bohr { x ; y ; z } =
make
{
Point.
x = a_to_b x ;
y = a_to_b y ;
z = a_to_b z ;
@ -29,30 +39,27 @@ let angstrom_to_bohr { Angstrom.x ; y ; z } =
let zero =
Bohr.make { Point.x = 0. ; y = 0. ; z = 0. }
make { x = 0. ; y = 0. ; z = 0. }
(** Linear algebra *)
let ( |. ) s { Bohr.x ; y ; z } =
Bohr.make {
Point.
let ( |. ) s { x ; y ; z } =
make {
x = s *. x ;
y = s *. y ;
z = s *. z ;
}
let ( |+ ) { Bohr.x = x1 ; y = y1 ; z = z1 } { Bohr.x = x2 ; y = y2 ; z = z2 } =
Bohr.make {
Point.
let ( |+ ) { x = x1 ; y = y1 ; z = z1 } { x = x2 ; y = y2 ; z = z2 } =
make {
x = x1 +. x2 ;
y = y1 +. y2 ;
z = z1 +. z2 ;
}
let ( |- ) { Bohr.x = x1 ; y = y1 ; z = z1 } { Bohr.x = x2 ; y = y2 ; z = z2 } =
Bohr.make {
Point.
let ( |- ) { x = x1 ; y = y1 ; z = z1 } { x = x2 ; y = y2 ; z = z2 } =
make {
x = x1 -. x2 ;
y = y1 -. y2 ;
z = z1 -. z2 ;
@ -62,7 +69,7 @@ let ( |- ) { Bohr.x = x1 ; y = y1 ; z = z1 } { Bohr.x = x2 ; y = y2 ; z = z2 } =
let neg a = -1. |. a
let dot { Bohr.x = x1 ; y = y1 ; z = z1 } { Bohr.x = x2 ; y = y2 ; z = z2 } =
let dot { x = x1 ; y = y1 ; z = z1 } { x = x2 ; y = y2 ; z = z2 } =
x1 *. x2 +. y1 *. y2 +. z1 *. z2
@ -70,7 +77,7 @@ let norm u =
sqrt ( dot u u )
let get axis { Bohr.x ; y ; z } =
let get axis { x ; y ; z } =
match axis with
| X -> x
| Y -> y
@ -79,14 +86,12 @@ let get axis { Bohr.x ; y ; z } =
open Format
let pp ppf c =
let open Bohr in
fprintf ppf "@[@[%8.4f@] @[%8.4f@] @[%8.4f@]@]" c.x c.y c.z
let pp_bohr ppf c =
let open Bohr in
fprintf ppf "@[(@[%10f@], @[%10f@], @[%10f@] Bohr)@]" c.x c.y c.z
let pp_angstrom ppf c =
let c = bohr_to_angstrom c in
let open Angstrom in
fprintf ppf "@[(@[%10f@], @[%10f@], @[%10f@] Angs)@]" c.x c.y c.z

70
Utils/Coordinate.mli
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@ -1,92 +1,108 @@
(** Type for coordinates in 3D space.
All operations on points are done in atomic units. Therefore,
all coordinates are given in {!Bohr.t} and manipulated with this
all coordinates are given in bohr and manipulated with this
module.
*)
type t = Bohr.t
type bohr
type angstrom
type xyz = {
x : float ;
y : float ;
z : float ;
}
type 'a point = xyz
type t = bohr point
val make : 'a point -> t
(** Creates a point in atomic units *)
val make_angstrom : 'a point -> angstrom point
(** Creates a point in Angstrom *)
type axis = X | Y | Z
val bohr_to_angstrom : Bohr.t -> Angstrom.t
(** Converts a point in Bohr to Angstrom. *)
val bohr_to_angstrom : bohr point -> angstrom point
(** Converts a point in bohr to angstrom. *)
val angstrom_to_bohr : Angstrom.t -> Bohr.t
(** Converts a point in Angstrom to Bohr. *)
val angstrom_to_bohr : angstrom point -> bohr point
(** Converts a point in Angstrom to bohr. *)
val zero : Bohr.t
(** [zero = { Bohr.x = 0. ; y=0. ; z=0. }] *)
val zero : bohr point
(** [zero = { x = 0. ; y=0. ; z=0. }] *)
val get : axis -> Bohr.t -> float
val get : axis -> bohr point -> float
(** Extracts the projection of the coordinate on an axis.
Example:
[Coordinate.(get Y) { Bohr.x=1. ; y=2. ; z=3. } -> 2.]
[Coordinate.(get Y) { x=1. ; y=2. ; z=3. } -> 2.]
*)
(** {1 Vector operations} *)
val ( |. ) : float -> Bohr.t -> Bohr.t
val ( |. ) : float -> t -> t
(** Scale by a float.
Example:
[ 2. |. { Bohr.x=1. ; y=2. ; z=3. } -> { Bohr.x=2. ; y=4. ; z=6. } ]
[ 2. |. { x=1. ; y=2. ; z=3. } -> { x=2. ; y=4. ; z=6. } ]
*)
val ( |+ ) : Bohr.t -> Bohr.t -> Bohr.t
val ( |+ ) : t -> t -> t
(** Add two vectors.
Example:
{[{ Bohr.x=1. ; y=2. ; z=3. } |+ { Bohr.x=2. ; y=3. ; z=1. } ->
{ Bohr.x=3. ; y=5. ; z=4. }]}
{[{ x=1. ; y=2. ; z=3. } |+ { x=2. ; y=3. ; z=1. } ->
{ x=3. ; y=5. ; z=4. }]}
*)
val ( |- ) : Bohr.t -> Bohr.t -> Bohr.t
val ( |- ) : t -> t -> t
(** Subtract two vectors.
Example:
{[{ Bohr.x=1. ; y=2. ; z=3. } |- { Bohr.x=2. ; y=3. ; z=1. } ->
{ Bohr.x=-1. ; y=-1. ; z=2. }]}
{[{ x=1. ; y=2. ; z=3. } |- { x=2. ; y=3. ; z=1. } ->
{ x=-1. ; y=-1. ; z=2. }]}
*)
val neg : Bohr.t -> Bohr.t
val neg : t -> t
(** Example:
{[Coordinate.neg { Bohr.x=1. ; y=2. ; z=-3. } ->
{ Bohr.x=-1. ; y=-2. ; z=3. }]}
{[Coordinate.neg { x=1. ; y=2. ; z=-3. } ->
{ x=-1. ; y=-2. ; z=3. }]}
*)
val dot : Bohr.t -> Bohr.t -> float
val dot : t -> t -> float
(** Dot product. *)
val norm : Bohr.t -> float
val norm : t -> float
(** L{^2} norm of the vector. *)
(** {2 Printers} *)
val pp: Format.formatter -> Bohr.t -> unit
val pp: Format.formatter -> t -> unit
val pp_bohr: Format.formatter -> Bohr.t -> unit
val pp_bohr: Format.formatter -> t -> unit
val pp_angstrom : Format.formatter -> Bohr.t -> unit
val pp_angstrom : Format.formatter -> t -> unit