Working on the basis set in xyz->ezfio

ocaml/Basis.ml

@@ -1,13 +1,14 @@
 open Core.Std;;
+open Qptypes;;
 
-type t = Gto.t list;;
+type t = (Gto.t * Atom_number.t) list;;
 
 (** Read all the basis functions of an element *)
-let read in_channel =
+let read in_channel at_number =
   let rec read result =
     try
       let gto = Gto.read_one in_channel in
-      read (gto::result)
+      read ( (gto,at_number)::result)
     with
     | Gto.End_Of_Basis -> List.rev result
   in read []  
@@ -28,12 +29,15 @@ let find in_channel element =
   !element_read
 ;;
 
-let read_element in_channel element =
+(** Read an element from the file *)
+let read_element in_channel at_number element =
   ignore (find in_channel element) ;
-  read in_channel ;
+  read in_channel at_number ;
 ;;
 
 let to_string b =
-  List.map ~f:Gto.to_string b
+  List.map ~f:(fun (g,n) ->
+     let n = Atom_number.to_int n in
+     (Int.to_string n)^":"^(Gto.to_string g)) b
   |> String.concat ~sep:"\n"
 ;;

ocaml/Basis.mli

@@ -0,0 +1,17 @@
+open Qptypes;;
+
+type t = (Gto.t * Atom_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
+
+(** 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
+
+(** Convert the basis to a string *)
+val to_string :  (Gto.t * Atom_number.t) list -> string

ocaml/Long_basis.ml

@@ -1,15 +1,16 @@
 open Core.Std;;
+open Qptypes;;
 
-type t = (Symmetry.Xyz.t * Gto.t) list;;
+type t = (Symmetry.Xyz.t * Gto.t * Atom_number.t ) list;;
 
 let of_basis b =
   let rec do_work accu = function
     | [] -> accu
-    | g::tail ->
+    | (g,n)::tail ->
         begin
           let new_accu = 
             Symmetry.Xyz.of_symmetry g.Gto.sym 
-            |> List.map ~f:(fun x-> (x,g)) 
+            |> List.map ~f:(fun x-> (x,g,n)) 
           in
           do_work (new_accu@accu) tail
         end
@@ -20,7 +21,8 @@ let of_basis b =
 
 
 let to_string b =
-  List.map ~f:(fun (x,y) -> 
+  List.map ~f:(fun (x,y,z) -> 
+     (Int.to_string (Atom_number.to_int z))^":"^
      (Symmetry.Xyz.to_string x)^" "^(Gto.to_string y)
   ) b
   |> String.concat ~sep:"\n"

ocaml/Long_basis.mli

@@ -0,0 +1,16 @@
+open Qptypes;;
+
+(** A long basis is a basis set where 
+  * all the P orbitals are converted to x, y, z
+  * all the D orbitals are converted to xx, xy, xz, yy, yx
+  * etc
+*)
+type t = (Symmetry.Xyz.t * Gto.t * Atom_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
+
+(** Convert the basis into its string representation *)
+val to_string :
+  (Symmetry.Xyz.t * Gto.t * Atom_number.t) list -> string

ocaml/Makefile

@@ -13,7 +13,7 @@ endif
 LIBS=
 PKGS=
 OCAMLCFLAGS=-g
-OCAMLBUILD=ocamlbuild -cflags $(OCAMLCFLAGS) -lflags -g
+OCAMLBUILD=ocamlbuild -j 0 -cflags $(OCAMLCFLAGS) -lflags -g 
 MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml
 MLIFILES=$(wildcard *.mli) 
 ALL_TESTS=$(patsubst %.ml,%.byte,$(wildcard test_*.ml))
@@ -26,7 +26,8 @@ default: $(ALL_TESTS) $(ALL_EXE)
 executables: $(ALL_EXE)
 
 %.inferred.mli: $(MLFILES)
-	$(OCAMLBUILD) $*.inferred.mli -cflags -i -use-ocamlfind  $(PKGS)
+	$(OCAMLBUILD) $*.inferred.mli -use-ocamlfind  $(PKGS) 
+	mv _build/$*.inferred.mli .
 
 %.byte: $(MLFILES) $(MLIFILES)
 	$(OCAMLBUILD) $*.byte  -use-ocamlfind  $(PKGS)

ocaml/qp_create_ezfio_from_xyz.ml

@@ -81,8 +81,37 @@ File : %s\n" c m b xyz_file;
     ~rank:2 ~dim:[| nucl_num ; 3 |] ~data:coords);
 
   (* Write Basis set *)
-  let basis = 
-  let long_basis = Long_basis
+  let basis =
+    let rec do_work (accu:(Atom.t*Atom_number.t) list) (n:int) = function
+    | [] -> accu
+    | e::tail -> let new_accu = (e,(Atom_number.of_int n))::accu in
+      do_work new_accu (n+1) tail
+    in
+    do_work [] 1  nuclei
+    |> List.rev
+    |> List.map ~f:(fun (x,i) ->
+       Basis.read_element basis_channel i x.Atom.element) 
+    |> List.concat
+  in
+  let long_basis = Long_basis.of_basis basis in
+  let ao_num = List.length long_basis in
+  Ezfio.set_ao_basis_ao_num ao_num;
+  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)
+  in
+  Ezfio.set_ao_basis_ao_prim_num (Ezfio.ezfio_array_of_list
+    ~rank:1 ~dim:[| ao_num |] ~data:ao_prim_num) ;
+  Ezfio.set_ao_basis_ao_nucl(Ezfio.ezfio_array_of_list
+    ~rank:1 ~dim:[| ao_num |] ~data:ao_nucl) ;
+
+(*
+ao_basis
+  ao_power           integer       (ao_basis_ao_num,3)
+  ao_prim_num_max    integer       = maxval(ao_basis_ao_prim_num)
+  ao_coef            double precision (ao_basis_ao_num,ao_basis_ao_prim_num_max)
+  ao_expo            double precision (ao_basis_ao_num,ao_basis_ao_prim_num_max)
+
+*)
 
 ;;
 

ocaml/qptypes_generator.ml

@@ -28,6 +28,13 @@ 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

ocaml/test_basis.ml

@@ -1,5 +1,6 @@
 open Core.Std;;
 open Qputils;;
+open Qptypes;;
 
 let test_module () =
   
@@ -13,12 +14,14 @@ let test_module () =
       Molecule.of_xyz_file xyz_file 
     in
 
+    let nuclei = molecule.Molecule.nuclei in
+
     let basis = 
-      (Basis.read_element basis_channel Element.F) @ 
-      (Basis.read_element basis_channel Element.F) 
+      (Basis.read_element basis_channel (Atom_number.of_int 1) Element.F) @ 
+      (Basis.read_element basis_channel (Atom_number.of_int 2) Element.F) 
     in
 
-    Long_basis.of_basis basis
+    Long_basis.of_basis basis 
     |> Long_basis.to_string 
     |> print_endline
 ;;

ocaml/test_gto.ml

@@ -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 in
-  List.iter basis ~f:(fun x-> Printf.printf "%s\n" (Gto.to_string x))
+  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 test_gto () =
   let in_channel = open_in "/home/scemama/quantum_package/data/basis/cc-pvdz" in
-  let basis = Basis.read_element in_channel Element.C in
-  List.iter basis ~f:(fun x-> Printf.printf "%s\n" (Gto.to_string x))
+  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 test_module () =