From 61d54ffbfc6d8fc498e66c4a3c7485e052aa26df Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Wed, 17 Sep 2014 14:57:12 +0200
Subject: [PATCH] Added Long_basis in ocaml

---
 ocaml/Basis.ml                     |  5 +++++
 ocaml/Long_basis.ml                | 27 +++++++++++++++++++++++++++
 ocaml/{symmetry.ml => Symmetry.ml} | 10 +++++++++-
 ocaml/qp_create_ezfio_from_xyz.ml  |  1 +
 ocaml/test_basis.ml                | 26 ++++++++++++++++++++++++++
 5 files changed, 68 insertions(+), 1 deletion(-)
 create mode 100644 ocaml/Long_basis.ml
 rename ocaml/{symmetry.ml => Symmetry.ml} (92%)
 create mode 100644 ocaml/test_basis.ml

diff --git a/ocaml/Basis.ml b/ocaml/Basis.ml
index cfce7a52..7fb4736d 100644
--- a/ocaml/Basis.ml
+++ b/ocaml/Basis.ml
@@ -15,6 +15,7 @@ let read in_channel =
 
 (** Find an element in the basis set file *)
 let find in_channel element =
+  In_channel.seek in_channel 0L;
   let element_read = ref Element.X in
   while !element_read <> element
   do
@@ -32,3 +33,7 @@ let read_element in_channel element =
   read in_channel ;
 ;;
 
+let to_string b =
+  List.map ~f:Gto.to_string b
+  |> String.concat ~sep:"\n"
+;;
diff --git a/ocaml/Long_basis.ml b/ocaml/Long_basis.ml
new file mode 100644
index 00000000..b602a630
--- /dev/null
+++ b/ocaml/Long_basis.ml
@@ -0,0 +1,27 @@
+open Core.Std;;
+
+type t = (Symmetry.Xyz.t * Gto.t) list;;
+
+let of_basis b =
+  let rec do_work accu = function
+    | [] -> accu
+    | g::tail ->
+        begin
+          let new_accu = 
+            Symmetry.Xyz.of_symmetry g.Gto.sym 
+            |> List.map ~f:(fun x-> (x,g)) 
+          in
+          do_work (new_accu@accu) tail
+        end
+  in
+  do_work [] b
+  |> List.rev
+;;
+
+
+let to_string b =
+  List.map ~f:(fun (x,y) -> 
+     (Symmetry.Xyz.to_string x)^" "^(Gto.to_string y)
+  ) b
+  |> String.concat ~sep:"\n"
+;;
diff --git a/ocaml/symmetry.ml b/ocaml/Symmetry.ml
similarity index 92%
rename from ocaml/symmetry.ml
rename to ocaml/Symmetry.ml
index bf9b09b2..aac3ed18 100644
--- a/ocaml/symmetry.ml
+++ b/ocaml/Symmetry.ml
@@ -54,19 +54,24 @@ let to_l = function
   | K -> Positive_int.of_int 8
   | L -> Positive_int.of_int 9
 
+type st = t
+;;
+
 module Xyz : sig
   type t
   val  of_string : string -> t
   val  to_string : t -> string 
   val  get_l     : t -> Positive_int.t
+  val  of_symmetry : st -> t list
 end = struct
   type t = { x: Positive_int.t ;
              y: Positive_int.t ;
              z: Positive_int.t }
 
   type state_type = Null | X | Y | Z
-  (* Input string is like "x2z3" *)
 
+  (** Builds an XYZ triplet from a string.
+    * The input string is like "x2z3" *)
   let of_string s =
     let flush state accu number =
       let n = 
@@ -106,6 +111,7 @@ end = struct
        z=Positive_int.of_int 0 } "" 
   ;;
 
+  (** Transforms an XYZ triplet to a string *)
   let to_string t = 
     let x = match (Positive_int.to_int t.x) with
     | 0 -> ""
@@ -123,6 +129,7 @@ end = struct
     x^y^z
   ;;
 
+ (** Returns the l quantum number from a XYZ powers triplet *)
   let get_l t =
    let x = Positive_int.to_int t.x
    and y = Positive_int.to_int t.y
@@ -130,6 +137,7 @@ end = struct
    in Positive_int.of_int (x+y+z)
  ;;
 
+ (** Returns a list of XYZ powers for a given symmetry *)
  let of_symmetry sym =
    let l = Positive_int.to_int (to_l sym) in
    let create_z xyz = 
diff --git a/ocaml/qp_create_ezfio_from_xyz.ml b/ocaml/qp_create_ezfio_from_xyz.ml
index 4a8bca24..8a40155b 100644
--- a/ocaml/qp_create_ezfio_from_xyz.ml
+++ b/ocaml/qp_create_ezfio_from_xyz.ml
@@ -81,6 +81,7 @@ File : %s\n" c m b xyz_file;
     ~rank:2 ~dim:[| nucl_num ; 3 |] ~data:coords);
 
   (* Write Basis set *)
+
 ;;
 
 let command = 
diff --git a/ocaml/test_basis.ml b/ocaml/test_basis.ml
new file mode 100644
index 00000000..278821f4
--- /dev/null
+++ b/ocaml/test_basis.ml
@@ -0,0 +1,26 @@
+open Core.Std;;
+open Qputils;;
+
+let test_module () =
+  
+    let basis_channel =
+      let b = "cc-pvdz" in
+      In_channel.create (Qpackage.root / "data/basis" / (String.lowercase b))
+    in
+
+    let molecule =
+      let xyz_file = "F2.xyz" in
+      Molecule.of_xyz_file xyz_file 
+    in
+
+    let basis = 
+      (Basis.read_element basis_channel Element.F) @ 
+      (Basis.read_element basis_channel Element.F) 
+    in
+
+    Long_basis.of_basis basis
+    |> Long_basis.to_string 
+    |> print_endline
+;;
+
+test_module ();