From c6b48bed35384aaaca4aeb93c6bc70d9987e1926 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Sun, 27 Dec 2020 17:23:47 +0100
Subject: [PATCH] Coordinate org

---
 common/coordinate.org     | 273 ++++++++++++++++++++++++++++++++++++++
 common/lib/coordinate.ml  | 171 ++++++++++++++++--------
 common/lib/coordinate.mli | 136 +++++++++++--------
 3 files changed, 467 insertions(+), 113 deletions(-)
 create mode 100644 common/coordinate.org

diff --git a/common/coordinate.org b/common/coordinate.org
new file mode 100644
index 0000000..ea53cb5
--- /dev/null
+++ b/common/coordinate.org
@@ -0,0 +1,273 @@
+#+begin_src elisp tangle: no :results 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 
+
+* Coordinate
+  :PROPERTIES:
+  :header-args: :noweb yes :comments both
+  :END:
+
+  Coordinates in 3D space.
+  
+  All operations on points are done in atomic units. Therefore, 
+  all coordinates are given in bohr and manipulated with this
+  module.
+
+** Type
+
+   #+NAME: types
+   #+begin_src ocaml :tangle (eval mli)
+type bohr 
+type angstrom 
+
+type xyz = {
+  x : float ;
+  y : float ;
+  z : float ;
+}
+
+type 'a point = xyz
+
+type t = bohr point
+
+type axis = X | Y | Z
+   #+end_src
+
+   #+begin_src ocaml :tangle (eval ml) :exports none
+<<types>>
+   #+end_src
+
+** Creation / conversion
+
+*** ~make~
+
+    Creates a point in atomic units.
+
+    #+begin_src ocaml :tangle (eval mli)
+val make : 'a point -> t
+    #+end_src
+
+    #+begin_src ocaml :tangle (eval ml) :exports none
+external make : 'a point -> t = "%identity"
+    #+end_src
+
+*** ~make_angstrom~
+
+    Creates a point in angstrom.
+
+    #+begin_src ocaml :tangle (eval mli)
+val make_angstrom : 'a point -> angstrom point
+    #+end_src
+
+    #+begin_src ocaml :tangle (eval ml) :exports none
+external make_angstrom : 'a point -> angstrom point = "%identity"
+    #+end_src
+
+*** ~bohr_to_angstrom~
+
+    Converts a point in bohr to angstrom. 
+
+    #+begin_src ocaml :tangle (eval mli)
+val bohr_to_angstrom : bohr point -> angstrom point
+    #+end_src
+
+    #+begin_src ocaml :tangle (eval ml) :exports none
+let b_to_a b = Constants.a0     *. b
+
+let bohr_to_angstrom { x ; y ; z } =
+  make { x = b_to_a x ;
+         y = b_to_a y ;
+         z = b_to_a z ; }
+    #+end_src
+
+*** ~angstrom_to_bohr~
+
+    Converts a point in angstrom to bohr. 
+
+    #+begin_src ocaml :tangle (eval mli)
+val angstrom_to_bohr : angstrom point -> bohr point
+    #+end_src
+
+    #+begin_src ocaml :tangle (eval ml) :exports none
+let a_to_b a = Constants.a0_inv *. a
+
+let angstrom_to_bohr { x ; y ; z } =  
+  make { x = a_to_b x ;
+         y = a_to_b y ;
+         z = a_to_b z ; }
+    #+end_src
+
+*** ~zero~
+
+    ~zero~ = (0., 0., 0.)
+
+    #+begin_src ocaml :tangle (eval mli)
+val zero : bohr point
+    #+end_src
+
+    #+begin_src ocaml :tangle (eval ml) :exports none
+let zero =
+  make { x = 0. ; y = 0. ; z = 0. } 
+    #+end_src
+
+*** ~get~
+
+    Extracts the projection of the coordinate on an axis.
+
+    #+begin_example
+Coordinate.(get Y { x=1. ; y=2. ; z=3. }) ;;
+- : float = 2.
+    #+end_example
+
+    #+begin_src ocaml :tangle (eval mli)
+val get : axis -> bohr point -> float
+    #+end_src
+
+    #+begin_src ocaml :tangle (eval ml) :exports none
+let get axis { x ; y ; z } = 
+  match axis with
+  | X -> x 
+  | Y -> y 
+  | Z -> z  
+    #+end_src
+
+** Vector operations
+
+*** Scale
+    
+    #+begin_src ocaml :tangle (eval mli)
+val ( |. ) : float -> t -> t
+    #+end_src
+
+    #+begin_example
+Coordinate.(
+  2. |. { x=1. ; y=2. ; z=3. }
+) ;;
+- : Coordinate.t = {Qcaml.Common.Coordinate.x = 2.; y = 4.; z = 6.}
+    #+end_example
+
+    #+begin_src ocaml :tangle (eval ml) :exports none
+let ( |. )  s { x ; y ; z } =
+  make { x = s *. x ;
+         y = s *. y ;
+         z = s *. z ; }
+    #+end_src
+
+*** Add
+
+    #+begin_src ocaml :tangle (eval mli)
+val ( |+ ) : t -> t -> t
+    #+end_src
+
+    #+begin_example
+Coordinate.(
+  { x=1. ; y=2. ; z=3. } |+ { x=2. ; y=3. ; z=1. } 
+);;
+- : Coordinate.t = {Qcaml.Common.Coordinate.x = 3.; y = 5.; z = 4.}
+    #+end_example
+
+    #+begin_src ocaml :tangle (eval ml) :exports none
+let ( |+ )
+    { x = x1 ; y = y1 ; z = z1 }
+    { x = x2 ; y = y2 ; z = z2 } =
+  make { x = x1 +. x2 ;
+         y = y1 +. y2 ;
+         z = z1 +. z2 ; }
+    #+end_src
+
+*** Subtract
+
+    #+begin_src ocaml :tangle (eval mli)
+val ( |- ) : t -> t -> t
+    #+end_src
+
+    #+begin_example
+Coordinate.(
+  { x=1. ; y=2. ; z=3. } |- { x=2. ; y=3. ; z=1. } 
+);;
+- : Coordinate.t = {Qcaml.Common.Coordinate.x = -1.; y = -1.; z = 2.}
+    #+end_example
+
+    #+begin_src ocaml :tangle (eval ml) :exports none
+let ( |- )
+    { x = x1 ; y = y1 ; z = z1 }
+    { x = x2 ; y = y2 ; z = z2 } =
+  make { x = x1 -. x2 ;
+         y = y1 -. y2 ;
+         z = z1 -. z2 ; }
+    #+end_src
+    
+*** Negative
+
+    #+begin_src ocaml :tangle (eval mli)
+val neg : t -> t
+    #+end_src
+
+    #+begin_example
+Coordinate.neg { x=1. ; y=2. ; z=3. } ;;
+- : Coordinate.t = {Qcaml.Common.Coordinate.x = -1.; y = -2.; z = -3.}
+    #+end_example
+
+    #+begin_src ocaml :tangle (eval ml) :exports none
+let neg a = -1. |. a
+    #+end_src
+
+*** Dot product
+
+    #+begin_src ocaml :tangle (eval mli)
+val dot : t -> t -> float
+    #+end_src
+
+    #+begin_src ocaml :tangle (eval ml) :exports none
+let dot
+    { x = x1 ; y = y1 ; z = z1 }
+    { x = x2 ; y = y2 ; z = z2 } =
+  x1 *. x2 +.
+  y1 *. y2 +.
+  z1 *. z2
+    #+end_src
+
+*** Norm
+
+    #+begin_src ocaml :tangle (eval mli)
+val norm : t -> float
+    #+end_src
+
+    $\ell{^2}$ norm of the vector. 
+
+    #+begin_src ocaml :tangle (eval ml) :exports none
+let norm u =
+  sqrt ( dot u u )
+    #+end_src
+
+
+** Printers
+
+   Coordinates can be printed in bohr or angstrom.
+
+   #+begin_src ocaml :tangle (eval mli)
+val pp : Format.formatter -> t -> unit
+val pp_bohr: Format.formatter -> t -> unit
+val pp_angstrom : Format.formatter -> t -> unit
+   #+end_src
+
+   #+begin_src ocaml :tangle (eval ml) :exports none
+open Format
+let pp ppf c = 
+  fprintf ppf "@[@[%8.4f@] @[%8.4f@] @[%8.4f@]@]" c.x c.y c.z
+
+let pp_bohr ppf c = 
+  fprintf ppf "@[(@[%10f@], @[%10f@], @[%10f@] Bohr)@]" c.x c.y c.z
+
+let pp_angstrom ppf c = 
+  let c = bohr_to_angstrom c in
+  fprintf ppf "@[(@[%10f@], @[%10f@], @[%10f@] Angs)@]" c.x c.y c.z
+   #+end_src
+
diff --git a/common/lib/coordinate.ml b/common/lib/coordinate.ml
index 3109d8e..fed9d11 100644
--- a/common/lib/coordinate.ml
+++ b/common/lib/coordinate.ml
@@ -1,3 +1,4 @@
+(* [[file:../coordinate.org::*Type][Type:2]] *)
 type bohr 
 type angstrom 
 
@@ -11,79 +12,135 @@ 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
+(* Type:2 ends here *)
 
+(* [[file:../coordinate.org::*~make~][~make~:2]] *)
+external make : 'a point -> t = "%identity"
+(* ~make~:2 ends here *)
 
-let a_to_b a = Constants.a0_inv *. a
+(* [[file:../coordinate.org::*~make_angstrom~][~make_angstrom~:2]] *)
+external make_angstrom : 'a point -> angstrom point = "%identity"
+(* ~make_angstrom~:2 ends here *)
+
+(* [[file:../coordinate.org::*~bohr_to_angstrom~][~bohr_to_angstrom~:2]] *)
 let b_to_a b = Constants.a0     *. b
 
 let bohr_to_angstrom { x ; y ; z } =
-  make 
-  {
-    x = b_to_a x ;
-    y = b_to_a y ;
-    z = b_to_a z ;
-  }
+  make { x = b_to_a x ;
+         y = b_to_a y ;
+         z = b_to_a z ; }
+(* ~bohr_to_angstrom~:2 ends here *)
+
+(* [[file:../coordinate.org::*~angstrom_to_bohr~][~angstrom_to_bohr~:2]] *)
+let a_to_b a = Constants.a0_inv *. a
 
 let angstrom_to_bohr { x ; y ; z } =  
-  make 
-  {
-    x = a_to_b x ;
-    y = a_to_b y ;
-    z = a_to_b z ;
-  }
-
+  make { x = a_to_b x ;
+         y = a_to_b y ;
+         z = a_to_b z ; }
+(* ~angstrom_to_bohr~:2 ends here *)
 
+(* [[file:../coordinate.org::*~zero~][~zero~:2]] *)
 let zero =
-  make { x = 0. ; y = 0. ; z = 0. } 
-
-
-(** Linear algebra *)
-let ( |. )  s { x ; y ; z } =
-    make {
-      x = s *. x ;
-      y = s *. y ;
-      z = s *. z ;
-    }
-
-let ( |+ ) { x = x1 ; y = y1 ; z = z1 } { x = x2 ; y = y2 ; z = z2 } =
-  make {
-    x = x1 +. x2 ;
-    y = y1 +. y2 ;
-    z = z1 +. z2 ;
-  }
-
-
-let ( |- ) { x = x1 ; y = y1 ; z = z1 } { x = x2 ; y = y2 ; z = z2 } =
-  make {
-    x = x1 -. x2 ;
-    y = y1 -. y2 ;
-    z = z1 -. z2 ;
-  }
-
-
-let neg a = -1. |. a
-
-
-let dot { x = x1 ; y = y1 ; z = z1 } { x = x2 ; y = y2 ; z = z2 } =
-  x1 *. x2 +. y1 *. y2 +. z1 *. z2
-
-
-let norm u =
-  sqrt ( dot u u )
-
+  make { x = 0. ; y = 0. ; z = 0. }
+(* ~zero~:2 ends here *)
 
+(* [[file:../coordinate.org::*~get~][~get~:2]] *)
 let get axis { x ; y ; z } = 
   match axis with
   | X -> x 
   | Y -> y 
-  | Z -> z  
+  | Z -> z
+(* ~get~:2 ends here *)
 
 
+
+(*     #+begin_example
+ * Coordinate.(
+ *   2. |. { x=1. ; y=2. ; z=3. }
+ * ) ;;
+ * - : Coordinate.t = {Qcaml.Common.Coordinate.x = 2.; y = 4.; z = 6.}
+ *     #+end_example *)
+
+
+(* [[file:../coordinate.org::*Scale][Scale:2]] *)
+let ( |. )  s { x ; y ; z } =
+  make { x = s *. x ;
+         y = s *. y ;
+         z = s *. z ; }
+(* Scale:2 ends here *)
+
+
+
+(*     #+begin_example
+ * Coordinate.(
+ *   { x=1. ; y=2. ; z=3. } |+ { x=2. ; y=3. ; z=1. } 
+ * );;
+ * - : Coordinate.t = {Qcaml.Common.Coordinate.x = 3.; y = 5.; z = 4.}
+ *     #+end_example *)
+
+
+(* [[file:../coordinate.org::*Add][Add:2]] *)
+let ( |+ )
+    { x = x1 ; y = y1 ; z = z1 }
+    { x = x2 ; y = y2 ; z = z2 } =
+  make { x = x1 +. x2 ;
+         y = y1 +. y2 ;
+         z = z1 +. z2 ; }
+(* Add:2 ends here *)
+
+
+
+(*     #+begin_example
+ * Coordinate.(
+ *   { x=1. ; y=2. ; z=3. } |- { x=2. ; y=3. ; z=1. } 
+ * );;
+ * - : Coordinate.t = {Qcaml.Common.Coordinate.x = -1.; y = -1.; z = 2.}
+ *     #+end_example *)
+
+
+(* [[file:../coordinate.org::*Subtract][Subtract:2]] *)
+let ( |- )
+    { x = x1 ; y = y1 ; z = z1 }
+    { x = x2 ; y = y2 ; z = z2 } =
+  make { x = x1 -. x2 ;
+         y = y1 -. y2 ;
+         z = z1 -. z2 ; }
+(* Subtract:2 ends here *)
+
+
+
+(*     #+begin_example
+ * Coordinate.neg { x=1. ; y=2. ; z=3. } ;;
+ * - : Coordinate.t = {Qcaml.Common.Coordinate.x = -1.; y = -2.; z = -3.}
+ *     #+end_example *)
+
+
+(* [[file:../coordinate.org::*Negative][Negative:2]] *)
+let neg a = -1. |. a
+(* Negative:2 ends here *)
+
+(* [[file:../coordinate.org::*Dot product][Dot product:2]] *)
+let dot
+    { x = x1 ; y = y1 ; z = z1 }
+    { x = x2 ; y = y2 ; z = z2 } =
+  x1 *. x2 +.
+  y1 *. y2 +.
+  z1 *. z2
+(* Dot product:2 ends here *)
+
+
+
+(* $\ell{^2}$ norm of the vector.  *)
+
+
+(* [[file:../coordinate.org::*Norm][Norm:2]] *)
+let norm u =
+  sqrt ( dot u u )
+(* Norm:2 ends here *)
+
+(* [[file:../coordinate.org::*Printers][Printers:2]] *)
 open Format
 let pp ppf c = 
   fprintf ppf "@[@[%8.4f@] @[%8.4f@] @[%8.4f@]@]" c.x c.y c.z
@@ -94,4 +151,4 @@ let pp_bohr ppf c =
 let pp_angstrom ppf c = 
   let c = bohr_to_angstrom c in
   fprintf ppf "@[(@[%10f@], @[%10f@], @[%10f@] Angs)@]" c.x c.y c.z
-
+(* Printers:2 ends here *)
diff --git a/common/lib/coordinate.mli b/common/lib/coordinate.mli
index 0521de1..5c73384 100644
--- a/common/lib/coordinate.mli
+++ b/common/lib/coordinate.mli
@@ -1,10 +1,8 @@
-(** Type for coordinates in 3D space.
-
-  All operations on points are done in atomic units. Therefore, 
-  all coordinates are given in bohr and manipulated with this
-  module.
- *)
+(* Type
+ * 
+ *    #+NAME: types *)
 
+(* [[file:../coordinate.org::types][types]] *)
 type bohr 
 type angstrom 
 
@@ -18,91 +16,117 @@ 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
+(* types ends here *)
 
+(* ~make~
+ * 
+ *     Creates a point in atomic units. *)
+
+
+(* [[file:../coordinate.org::*~make~][~make~:1]] *)
+val make : 'a point -> t
+(* ~make~:1 ends here *)
+
+(* ~make_angstrom~
+ * 
+ *     Creates a point in angstrom. *)
+
+
+(* [[file:../coordinate.org::*~make_angstrom~][~make_angstrom~:1]] *)
+val make_angstrom : 'a point -> angstrom point
+(* ~make_angstrom~:1 ends here *)
+
+(* ~bohr_to_angstrom~
+ * 
+ *     Converts a point in bohr to angstrom.  *)
+
+
+(* [[file:../coordinate.org::*~bohr_to_angstrom~][~bohr_to_angstrom~:1]] *)
 val bohr_to_angstrom : bohr point -> angstrom point
-(** Converts a point in bohr to angstrom. *)
+(* ~bohr_to_angstrom~:1 ends here *)
+
+(* ~angstrom_to_bohr~
+ * 
+ *     Converts a point in angstrom to bohr.  *)
 
 
+(* [[file:../coordinate.org::*~angstrom_to_bohr~][~angstrom_to_bohr~:1]] *)
 val angstrom_to_bohr : angstrom point -> bohr point
-(** Converts a point in Angstrom to bohr. *)
+(* ~angstrom_to_bohr~:1 ends here *)
+
+(* ~zero~
+ * 
+ *     ~zero~ = (0., 0., 0.) *)
 
 
+(* [[file:../coordinate.org::*~zero~][~zero~:1]] *)
 val zero : bohr point
-(** [zero = { x = 0. ; y=0. ; z=0. }] *)
+(* ~zero~:1 ends here *)
+
+(* ~get~
+ * 
+ *     Extracts the projection of the coordinate on an axis.
+ * 
+ *     #+begin_example
+ * Coordinate.(get Y { x=1. ; y=2. ; z=3. })
+ * - float: 2.
+ *     #+end_example *)
 
 
+(* [[file:../coordinate.org::*~get~][~get~:1]] *)
 val get : axis -> bohr point -> float
-(** Extracts the projection of the coordinate on an axis.
-
-  Example:
-  
-  [Coordinate.(get Y) { x=1. ; y=2. ; z=3. } -> 2.]
-
-*)
-
-(** {1 Vector operations} *)
+(* ~get~:1 ends here *)
 
+(* Scale *)
+    
 
+(* [[file:../coordinate.org::*Scale][Scale:1]] *)
 val ( |. ) : float -> t -> t
-(** Scale by a float.
+(* Scale:1 ends here *)
 
-  Example:
-
-  [ 2. |. { x=1. ; y=2. ; z=3. } -> { x=2. ; y=4. ; z=6. } ]
-
- *)
+(* Add *)
 
 
+(* [[file:../coordinate.org::*Add][Add:1]] *)
 val ( |+ ) : t -> t -> t
-(** Add two vectors.
+(* Add:1 ends here *)
 
-  Example:
-
-  {[{ x=1. ; y=2. ; z=3. } |+ { x=2. ; y=3. ; z=1. } ->
-    { x=3. ; y=5. ; z=4. }]}
-
- *)
+(* Subtract *)
 
 
+(* [[file:../coordinate.org::*Subtract][Subtract:1]] *)
 val ( |- ) : t -> t -> t
-(** Subtract two vectors.
+(* Subtract:1 ends here *)
 
-  Example:
-
-  {[{ x=1. ; y=2. ; z=3. } |- { x=2. ; y=3. ; z=1. } ->
-    { x=-1. ; y=-1. ; z=2. }]}
-
- *)
+(* Negative *)
 
 
+(* [[file:../coordinate.org::*Negative][Negative:1]] *)
 val neg : t -> t
-(** Example:
+(* Negative:1 ends here *)
 
-{[Coordinate.neg { x=1. ; y=2. ; z=-3. } ->
-    { x=-1. ; y=-2. ; z=3. }]}
+(* Dot product *)
 
- *)
 
+(* [[file:../coordinate.org::*Dot product][Dot product:1]] *)
 val dot : t -> t -> float
-(** Dot product. *)
+(* Dot product:1 ends here *)
+
+(* Norm *)
 
 
+(* [[file:../coordinate.org::*Norm][Norm:1]] *)
 val norm : t -> float
-(** L{^2} norm of the vector. *)
+(* Norm:1 ends here *)
+
+(* Printers
+ * 
+ *    Coordinates can be printed in bohr or angstrom. *)
 
 
-(** {2 Printers} *)
-
-val pp: Format.formatter -> t -> unit
-
+(* [[file:../coordinate.org::*Printers][Printers:1]] *)
+val pp : Format.formatter -> t -> unit
 val pp_bohr: Format.formatter -> t -> unit
-
 val pp_angstrom : Format.formatter -> t -> unit
-
+(* Printers:1 ends here *)