From 6f745a6e25927583afcfeae2d66ef527949da37b Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Thu, 23 Oct 2014 14:42:14 +0200
Subject: [PATCH] Corrected bugs in ocaml

---
 ocaml/Basis.ml                    |  4 ++--
 ocaml/Basis.mli                   |  8 ++++----
 ocaml/Gto.ml                      |  2 +-
 ocaml/Long_basis.ml               |  4 ++--
 ocaml/Long_basis.mli              |  6 +++---
 ocaml/Molecule.ml                 | 27 +++++++++++++--------------
 ocaml/Multiplicity.ml             | 10 +++++-----
 ocaml/Primitive.ml                |  4 ++--
 ocaml/qp_create_ezfio_from_xyz.ml | 12 ++++++------
 ocaml/qp_print.ml                 |  4 ++--
 ocaml/qptypes_generator.ml        |  9 +--------
 ocaml/test_basis.ml               |  4 ++--
 ocaml/test_gto.ml                 | 10 +++++-----
 setup_environment.sh              |  1 +
 14 files changed, 49 insertions(+), 56 deletions(-)

diff --git a/ocaml/Basis.ml b/ocaml/Basis.ml
index ba575761..844269ed 100644
--- a/ocaml/Basis.ml
+++ b/ocaml/Basis.ml
@@ -1,7 +1,7 @@
 open Core.Std;;
 open Qptypes;;
 
-type t = (Gto.t * Atom_number.t) list;;
+type t = (Gto.t * Nucl_number.t) list;;
 
 (** Read all the basis functions of an element *)
 let read in_channel at_number =
@@ -37,7 +37,7 @@ let read_element in_channel at_number element =
 
 let to_string b =
   List.map ~f:(fun (g,n) ->
-     let n = Atom_number.to_int n in
+     let n = Nucl_number.to_int n in
      (Int.to_string n)^":"^(Gto.to_string g)) b
   |> String.concat ~sep:"\n"
 ;;
diff --git a/ocaml/Basis.mli b/ocaml/Basis.mli
index b9465d8c..276578f4 100644
--- a/ocaml/Basis.mli
+++ b/ocaml/Basis.mli
@@ -1,17 +1,17 @@
 open Qptypes;;
 
-type t = (Gto.t * Atom_number.t) list
+type t = (Gto.t * Nucl_number.t) list
 
 (** Read all the basis functions of an element and set the number of the
   * atom *)
-val read : in_channel -> Atom_number.t -> (Gto.t * Atom_number.t) list
+val read : in_channel -> Nucl_number.t -> (Gto.t * Nucl_number.t) list
 
 (** Find an element in the basis set file *)
 val find : in_channel -> Element.t -> Element.t
 
 (** Read the basis of an element from the file *)
 val read_element :
-  in_channel -> Atom_number.t -> Element.t -> (Gto.t * Atom_number.t) list
+  in_channel -> Nucl_number.t -> Element.t -> (Gto.t * Nucl_number.t) list
 
 (** Convert the basis to a string *)
-val to_string :  (Gto.t * Atom_number.t) list -> string
+val to_string :  (Gto.t * Nucl_number.t) list -> string
diff --git a/ocaml/Gto.ml b/ocaml/Gto.ml
index 8abc3837..fc1953b2 100644
--- a/ocaml/Gto.ml
+++ b/ocaml/Gto.ml
@@ -53,7 +53,7 @@ let read_one in_channel =
       | [ j ; expo ; coef ] ->
         begin
           let p = { Primitive.sym = sym ;
-                    Primitive.expo = Positive_float.of_float
+                    Primitive.expo = AO_expo.of_float
                         (Float.of_string expo)
                   }
           and c = AO_coef.of_float (Float.of_string coef) in
diff --git a/ocaml/Long_basis.ml b/ocaml/Long_basis.ml
index b5a600f9..c59a628a 100644
--- a/ocaml/Long_basis.ml
+++ b/ocaml/Long_basis.ml
@@ -1,7 +1,7 @@
 open Core.Std;;
 open Qptypes;;
 
-type t = (Symmetry.Xyz.t * Gto.t * Atom_number.t ) list;;
+type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t ) list;;
 
 let of_basis b =
   let rec do_work accu = function
@@ -22,7 +22,7 @@ let of_basis b =
 
 let to_string b =
   List.map ~f:(fun (x,y,z) -> 
-     (Int.to_string (Atom_number.to_int z))^":"^
+     (Int.to_string (Nucl_number.to_int z))^":"^
      (Symmetry.Xyz.to_string x)^" "^(Gto.to_string y)
   ) b
   |> String.concat ~sep:"\n"
diff --git a/ocaml/Long_basis.mli b/ocaml/Long_basis.mli
index 934505eb..6c9c8db3 100644
--- a/ocaml/Long_basis.mli
+++ b/ocaml/Long_basis.mli
@@ -5,12 +5,12 @@ open Qptypes;;
   * all the D orbitals are converted to xx, xy, xz, yy, yx
   * etc
 *)
-type t = (Symmetry.Xyz.t * Gto.t * Atom_number.t) list
+type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t) list
 
 (** Transform a basis to a long basis *)
 val of_basis :
-  (Gto.t * Atom_number.t) list -> (Symmetry.Xyz.t * Gto.t * Atom_number.t) list
+  (Gto.t * Nucl_number.t) list -> (Symmetry.Xyz.t * Gto.t * Nucl_number.t) list
 
 (** Convert the basis into its string representation *)
 val to_string :
-  (Symmetry.Xyz.t * Gto.t * Atom_number.t) list -> string
+  (Symmetry.Xyz.t * Gto.t * Nucl_number.t) list -> string
diff --git a/ocaml/Molecule.ml b/ocaml/Molecule.ml
index 7e467ffb..5454d8db 100644
--- a/ocaml/Molecule.ml
+++ b/ocaml/Molecule.ml
@@ -5,12 +5,13 @@ exception MultiplicityError of string;;
 
 type t = {
   nuclei     : Atom.t list ;
-  elec_alpha : Positive_int.t ;
-  elec_beta  : Positive_int.t ;
+  elec_alpha : Elec_alpha_number.t ;
+  elec_beta  : Elec_beta_number.t ;
 }
 
 let get_charge { nuclei  ; elec_alpha ; elec_beta } =
-  let result = Positive_int.(to_int elec_alpha + to_int elec_beta) in
+  let result = (Elec_alpha_number.to_int elec_alpha) +
+     (Elec_beta_number.to_int elec_beta) in
   let rec nucl_charge = function
   | a::rest -> (Charge.to_float a.Atom.charge) +. nucl_charge rest
   | [] -> 0.
@@ -19,14 +20,12 @@ let get_charge { nuclei  ; elec_alpha ; elec_beta } =
 ;;
 
 let get_multiplicity m = 
-  let elec_alpha = m.elec_alpha
-  |> Positive_int.to_int
-  |> Strictly_positive_int.of_int in
+  let elec_alpha = m.elec_alpha in
   Multiplicity.of_alpha_beta elec_alpha m.elec_beta
 ;;
 
 let get_nucl_num m =
-  Strictly_positive_int.of_int (List.length m.nuclei)
+  Nucl_number.of_int (List.length m.nuclei)
 ;;
 
 let name m = 
@@ -88,22 +87,22 @@ let of_xyz_string
   in
   let ne = ( get_charge { 
         nuclei=l ;
-        elec_alpha=(Positive_int.of_int 0) ;
-        elec_beta=(Positive_int.of_int 0) } 
+        elec_alpha=(Elec_alpha_number.of_int 1) ;
+        elec_beta=(Elec_beta_number.of_int 0) } 
       |> Charge.to_int 
-      ) - charge 
-      |> Positive_int.of_int 
+      ) - 1 - charge 
+      |> Elec_number.of_int 
   in
   let (na,nb) = Multiplicity.to_alpha_beta ne multiplicity in
   let result = 
   { nuclei = l ;
-    elec_alpha = (Positive_int.of_int na) ;
-    elec_beta  = (Positive_int.of_int nb) }
+    elec_alpha = na ;
+    elec_beta  = nb }
   in
   if ((get_multiplicity result) <> multiplicity) then
      let msg = Printf.sprintf
       "With %d electrons multiplicity %d is impossible"
-      (Positive_int.to_int ne)
+      (Elec_number.to_int ne)
       (Multiplicity.to_int multiplicity)
      in
      raise (MultiplicityError msg);
diff --git a/ocaml/Multiplicity.ml b/ocaml/Multiplicity.ml
index a50d38ef..a66233a8 100644
--- a/ocaml/Multiplicity.ml
+++ b/ocaml/Multiplicity.ml
@@ -1,3 +1,4 @@
+open Core.Std;;
 open Qptypes ;;
 
 type t = Strictly_positive_int.t;;
@@ -19,17 +20,16 @@ let to_string m =
 ;;
    
 let of_alpha_beta a b =
-  let a = Strictly_positive_int.to_int a 
-  and b = Positive_int.to_int b
+  let a = Elec_alpha_number.to_int a 
+  and b = Elec_beta_number.to_int b
   in
   assert (a >= b);
   of_int (1 + a - b)
 ;;
 
 let to_alpha_beta ne m = 
-  let ne = Positive_int.to_int ne in
+  let ne = Elec_number.to_int ne in
   let nb = (ne-(to_int m)+1)/2 in
   let na = ne - nb in
-  assert (na >= nb) ;
-  (na,nb)
+  (Elec_alpha_number.of_int na, Elec_beta_number.of_int nb)
 ;;
diff --git a/ocaml/Primitive.ml b/ocaml/Primitive.ml
index 1f52b0d9..82a94fa4 100644
--- a/ocaml/Primitive.ml
+++ b/ocaml/Primitive.ml
@@ -3,13 +3,13 @@ open Core.Std;;
 
 type t =
 { sym  : Symmetry.t ;
-  expo : Positive_float.t ;
+  expo : AO_expo.t ;
 }
 
 let to_string p = 
   let { sym = s ; expo = e } = p in
   Printf.sprintf "(%s, %f)" 
    (Symmetry.to_string s)
-   (Positive_float.to_float e)
+   (AO_expo.to_float e)
 ;;
   
diff --git a/ocaml/qp_create_ezfio_from_xyz.ml b/ocaml/qp_create_ezfio_from_xyz.ml
index c5512354..d35cb42b 100644
--- a/ocaml/qp_create_ezfio_from_xyz.ml
+++ b/ocaml/qp_create_ezfio_from_xyz.ml
@@ -48,9 +48,9 @@ let run ?o b c m xyz_file =
   Ezfio.set_file ezfio_file;
 
   (* Write Electrons *)
-  Ezfio.set_electrons_elec_alpha_num ( Positive_int.to_int
+  Ezfio.set_electrons_elec_alpha_num ( Elec_alpha_number.to_int
     molecule.Molecule.elec_alpha ) ;
-  Ezfio.set_electrons_elec_beta_num  ( Positive_int.to_int
+  Ezfio.set_electrons_elec_beta_num  ( Elec_beta_number.to_int
     molecule.Molecule.elec_beta  ) ;
 
   (* Write Nuclei *)
@@ -74,9 +74,9 @@ let run ?o b c m xyz_file =
 
   (* Write Basis set *)
   let basis =
-    let rec do_work (accu:(Atom.t*Atom_number.t) list) (n:int) = function
+    let rec do_work (accu:(Atom.t*Nucl_number.t) list) (n:int) = function
     | [] -> accu
-    | e::tail -> let new_accu = (e,(Atom_number.of_int n))::accu in
+    | e::tail -> let new_accu = (e,(Nucl_number.of_int n))::accu in
       do_work new_accu (n+1) tail
     in
     do_work [] 1  nuclei
@@ -90,7 +90,7 @@ let run ?o b c m xyz_file =
   Ezfio.set_ao_basis_ao_num ao_num;
   Ezfio.set_ao_basis_ao_basis b;
   let ao_prim_num = List.map long_basis ~f:(fun (_,g,_) -> List.length g.Gto.lc) 
-  and ao_nucl = List.map long_basis ~f:(fun (_,_,n) -> Atom_number.to_int n)
+  and ao_nucl = List.map long_basis ~f:(fun (_,_,n) -> Nucl_number.to_int n)
   and ao_power= 
     let l = List.map long_basis ~f:(fun (x,_,_) -> x) in
     (List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.x)) )@
@@ -109,7 +109,7 @@ let run ?o b c m xyz_file =
         | `Coefs -> List.map gtos ~f:(fun x->
           List.map x.Gto.lc ~f:(fun (_,coef) -> AO_coef.to_float coef) )
         | `Expos -> List.map gtos ~f:(fun x->
-          List.map x.Gto.lc ~f:(fun (prim,_) -> Positive_float.to_float
+          List.map x.Gto.lc ~f:(fun (prim,_) -> AO_expo.to_float
           prim.Primitive.expo) )
         end
       in
diff --git a/ocaml/qp_print.ml b/ocaml/qp_print.ml
index 0053b441..6734b00a 100644
--- a/ocaml/qp_print.ml
+++ b/ocaml/qp_print.ml
@@ -55,9 +55,9 @@ let run_i ~action ezfio_filename =
     let nucl_charge = Ezfio.((get_nuclei_nucl_charge ()).data)
       |> Ezfio.flattened_ezfio_data |> Array.map ~f:(Float.to_int) 
     and n_alpha = input.Input.Electrons.elec_alpha_num
-      |> Strictly_positive_int.to_int
+      |> Elec_alpha_number.to_int
     and n_beta  = input.Input.Electrons.elec_beta_num 
-      |> Positive_int.to_int
+      |> Elec_beta_number.to_int
     in Array.fold ~init:(-n_alpha-n_beta) ~f:(fun x y -> x+y) nucl_charge
   in
 
diff --git a/ocaml/qptypes_generator.ml b/ocaml/qptypes_generator.ml
index 8ab5b5cf..fa3bbdd5 100644
--- a/ocaml/qptypes_generator.ml
+++ b/ocaml/qptypes_generator.ml
@@ -36,13 +36,6 @@ let input_data = "
 * Non_empty_string : string
   assert (x <> \"\") ;
 
-* Atom_number : int  
-  assert (x > 0) ; 
-  if (x > 1000) then
-    warning \"More than 1000 atoms\";
-  if (Ezfio.has_nuclei_nucl_num ()) then
-    assert (x <= (Ezfio.get_nuclei_nucl_num ()));
-
 * MO_number : int  
   assert (x > 0) ; 
   if (x > 1000) then
@@ -60,7 +53,7 @@ let input_data = "
 * Nucl_number : int  
   assert (x > 0) ; 
   if (x > 1000) then
-    warning \"More than 1000 Atoms\";
+    warning \"More than 1000 atoms\";
   if (Ezfio.has_nuclei_nucl_num ()) then
     assert (x <= (Ezfio.get_nuclei_nucl_num ()));
 
diff --git a/ocaml/test_basis.ml b/ocaml/test_basis.ml
index 8fb18ffe..1f029bf6 100644
--- a/ocaml/test_basis.ml
+++ b/ocaml/test_basis.ml
@@ -17,8 +17,8 @@ let test_module () =
     let nuclei = molecule.Molecule.nuclei in
 
     let basis = 
-      (Basis.read_element basis_channel (Atom_number.of_int 1) Element.F) @ 
-      (Basis.read_element basis_channel (Atom_number.of_int 2) Element.F) 
+      (Basis.read_element basis_channel (Nucl_number.of_int 1) Element.F) @ 
+      (Basis.read_element basis_channel (Nucl_number.of_int 2) Element.F) 
     in
 
     Long_basis.of_basis basis 
diff --git a/ocaml/test_gto.ml b/ocaml/test_gto.ml
index a39de97e..3675f501 100644
--- a/ocaml/test_gto.ml
+++ b/ocaml/test_gto.ml
@@ -4,7 +4,7 @@ open Qptypes;;
 let test_prim () = 
   let p = 
    { Primitive.sym  = Symmetry.P ; 
-     Primitive.expo = Positive_float.of_float 0.15} in
+     Primitive.expo = AO_expo.of_float 0.15} in
   Primitive.to_string p
   |> print_string
 ;;
@@ -23,14 +23,14 @@ let test_gto_1 () =
 let test_gto_2 () =
   let in_channel = open_in "/home/scemama/quantum_package/data/basis/cc-pvdz" in
   ignore (input_line in_channel);
-  let basis = Basis.read in_channel (Atom_number.of_int 1) in
-  List.iter basis ~f:(fun (x,n)-> Printf.printf "%d:%s\n" (Atom_number.to_int n) (Gto.to_string x))
+  let basis = Basis.read in_channel (Nucl_number.of_int 1) in
+  List.iter basis ~f:(fun (x,n)-> Printf.printf "%d:%s\n" (Nucl_number.to_int n) (Gto.to_string x))
 ;;
 
 let test_gto () =
   let in_channel = open_in "/home/scemama/quantum_package/data/basis/cc-pvdz" in
-  let basis = Basis.read_element in_channel (Atom_number.of_int 1) Element.C in
-  List.iter basis ~f:(fun (x,n)-> Printf.printf "%d:%s\n" (Atom_number.to_int n) (Gto.to_string x))
+  let basis = Basis.read_element in_channel (Nucl_number.of_int 1) Element.C in
+  List.iter basis ~f:(fun (x,n)-> Printf.printf "%d:%s\n" (Nucl_number.to_int n) (Gto.to_string x))
 ;;
 
 let test_module () =
diff --git a/setup_environment.sh b/setup_environment.sh
index 085cef6a..e462b317 100755
--- a/setup_environment.sh
+++ b/setup_environment.sh
@@ -41,6 +41,7 @@ then
 fi
 
 # Ocaml installation
+# Check if m4 and curl are OK
 make -C ocaml Qptypes.ml
 if [[ $? -ne 0 ]]
 then