Cleaning

ocaml/Gto.ml

@@ -52,10 +52,9 @@ let read_one in_channel =
       match buffer with
       | [ j ; expo ; coef ] ->
         begin
-          let p = { Primitive.sym = sym ;
-                    Primitive.expo = AO_expo.of_float
-                        (Float.of_string expo)
-                  }
+          let p =
+            Primitive.of_sym_expo sym 
+              (AO_expo.of_float (Float.of_string expo) )
           and c = AO_coef.of_float (Float.of_string coef) in
           read_lines ( (p,c)::result) (i-1)
         end

ocaml/Makefile

@@ -1,5 +1,3 @@
-#TODO : Opam auto-installer in makefile
-
 # Check if QPACKAGE_ROOT is defined
 
 ifndef QPACKAGE_ROOT
@@ -12,8 +10,8 @@ endif
 
 LIBS=
 PKGS=
-OCAMLCFLAGS=-g 
-OCAMLBUILD=ocamlbuild -j 0 -syntax camlp4o -cflags $(OCAMLCFLAGS) -lflags -g  
+OCAMLCFLAGS=-g
+OCAMLBUILD=ocamlbuild -j 0 -syntax camlp4o -cflags $(OCAMLCFLAGS) -lflags -g 
 MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml
 MLIFILES=$(wildcard *.mli) 
 ALL_TESTS=$(patsubst %.ml,%.byte,$(wildcard test_*.ml))
@@ -26,6 +24,9 @@ default: $(ALL_TESTS) $(ALL_EXE)
 executables: 
 	$(MAKE) -C $(QPACKAGE_ROOT)/data executables
 
+%.odoc: $(MLFILES)
+	$(OCAMLBUILD) $*.odoc -use-ocamlfind  $(PKGS) 
+
 %.inferred.mli: $(MLFILES)
 	$(OCAMLBUILD) $*.inferred.mli -use-ocamlfind  $(PKGS) 
 	mv _build/$*.inferred.mli .

ocaml/Point3d.ml

@@ -1,4 +1,5 @@
 open Core.Std;;
+open Qptypes;;
 
 type t = {
   x : float ;
@@ -28,9 +29,10 @@ let distance2 p1 p2 =
   let { x=x1 ; y=y1 ; z=z1 } = p1
   and { x=x2 ; y=y2 ; z=z2 } = p2 in
   (x2-.x1)*.(x2-.x1) +. (y2-.y1)*.(y2-.y1) +. (z2-.z1)*.(z2-.z1) 
+  |> Positive_float.of_float
 ;;
 
-let distance p1 p2 = sqrt (distance2 p1 p2)
+let distance p1 p2 = sqrt (Positive_float.to_float (distance2 p1 p2))
 ;;
 
 let to_string u p =

ocaml/Primitive.ml

@@ -13,3 +13,6 @@ let to_string p =
    (AO_expo.to_float e)
 ;;
   
+let of_sym_expo s e = 
+  { sym=s ; expo=e}
+;;

ocaml/Primitive.mli

@@ -0,0 +1,11 @@
+type t =
+{ sym : Symmetry.t;
+  expo : Qptypes.AO_expo.t;
+} with sexp
+
+(** Conversion to string for printing *)
+val to_string : t -> string
+
+(** Creation *)
+val of_sym_expo : Symmetry.t -> Qptypes.AO_expo.t -> t
+

ocaml/Range.mli

@@ -0,0 +1,10 @@
+type t = int list with sexp
+
+(** A range is a sorted list of ints in an interval.
+    It is created using a string :
+    "[a-b]" : range between a and b (included)
+    "[a]"   : the list with only one integer a
+    "a"     : equivalent to "[a]"
+ *)
+val of_string : string -> t
+val to_string : t -> string

ocaml/Symmetry.ml

@@ -74,16 +74,7 @@ let of_l i =
 type st = t
 ;;
 
-module Xyz : sig
-  type t = { x: Positive_int.t ;
-             y: Positive_int.t ;
-             z: Positive_int.t } with sexp
-  val  of_string : string -> t
-  val  to_string : t -> string 
-  val  get_l     : t -> Positive_int.t
-  val  of_symmetry : st -> t list
-  val  to_symmetry : t -> st
-end = struct
+module Xyz = struct
   type t = { x: Positive_int.t ;
              y: Positive_int.t ;
              z: Positive_int.t } with sexp
@@ -187,9 +178,10 @@ end = struct
    in
    create_x [] { x=(to_l sym) ; y=Positive_int.of_int 0 ;
      z=Positive_int.of_int 0 }
-   ;;
+ ;;
 
-   let to_symmetry sym = of_l (get_l sym)
-   ;;
+ (** Returns the symmetry corresponding to the XYZ triplet *)
+ let to_symmetry sym = of_l (get_l sym)
+ ;;
 end
 

ocaml/Symmetry.mli

@@ -0,0 +1,36 @@
+type t = S | P | D | F | G | H | I | J | K | L with sexp
+
+(** Creatio from strings *)
+val to_string : t -> string
+val of_string : string -> t
+val of_char : char -> t
+
+(** Connexion with l quantum number *)
+val to_l : t -> Qptypes.Positive_int.t
+val of_l : Qptypes.Positive_int.t -> t
+
+type st = t
+module Xyz :
+  sig
+    type t = {
+      x : Qptypes.Positive_int.t;
+      y : Qptypes.Positive_int.t;
+      z : Qptypes.Positive_int.t;
+    } with sexp
+
+    (** The string format contains the powers of x,y and z in a
+        format like "x2z3" *)
+
+    val of_string : string -> t
+    val to_string : t -> string
+
+    (** Returns the quantum number l *)
+    val get_l : t -> Qptypes.Positive_int.t
+
+    (** Returns a list of XYZ powers for a given symmetry *)
+    val of_symmetry : st -> t list
+
+    (** Returns the symmetry corresponding to the XYZ powers *)
+    val to_symmetry : t -> st
+
+  end

ocaml/Units.mli

@@ -0,0 +1,7 @@
+type units = Bohr | Angstrom
+
+(** Conversion functions *)
+val angstrom_to_bohr : float
+val bohr_to_angstrom : float
+
+