Merge branch 'master' of github.com:scemama/quantum_package

ocaml/Address.ml

@@ -1,4 +1,3 @@
-open Core.Std
 
 module Tcp : sig
   type t 
@@ -8,7 +7,7 @@ module Tcp : sig
 end = struct
   type t = string
   let of_string x =
-    if not (String.is_prefix ~prefix:"tcp://" x) then
+    if not (String_ext.is_prefix ~prefix:"tcp://" x) then
       invalid_arg "Address Invalid"
     ;
     x
@@ -26,7 +25,7 @@ module Ipc : sig
 end = struct
   type t = string
   let of_string x =
-    assert (String.is_prefix ~prefix:"ipc://" x);
+    assert (String_ext.is_prefix ~prefix:"ipc://" x);
     x
   let create name =
     Printf.sprintf "ipc://%s" name
@@ -41,7 +40,7 @@ module Inproc : sig
 end = struct
   type t = string
   let of_string x =
-    assert (String.is_prefix ~prefix:"inproc://" x);
+    assert (String_ext.is_prefix ~prefix:"inproc://" x);
     x
   let create name =
     Printf.sprintf "inproc://%s" name

ocaml/Atom.ml

@@ -1,4 +1,4 @@
-open Core.Std
+open Core
 
 exception AtomError of string
 
@@ -6,7 +6,7 @@ type t =
 { element : Element.t ;
   charge  : Charge.t ;
   coord   : Point3d.t ;
-} with sexp
+} [@@deriving sexp]
 
 (** Read xyz coordinates of the atom *)
 let of_string ~units s =

ocaml/Basis.ml

@@ -1,7 +1,7 @@
-open Core.Std
+open Sexplib.Std
 open Qptypes
 
-type t = (Gto.t * Nucl_number.t) list with sexp
+type t = (Gto.t * Nucl_number.t) list [@@deriving sexp]
 
 (** Read all the basis functions of an element *)
 let read in_channel at_number =
@@ -16,7 +16,7 @@ let read in_channel at_number =
 
 (** Find an element in the basis set file *)
 let find in_channel element =
-  In_channel.seek in_channel 0L;
+  seek_in in_channel 0;
   let element_read = ref Element.X in
   while !element_read <> element
   do
@@ -56,13 +56,13 @@ let to_string_general ~fmt ~atom_sep ?ele_array b =
     do_work ((Gto.to_string ~fmt g)::accu) n tail
   in
   do_work [new_nucleus 1] 1 b
-  |> String.concat ~sep:"\n"
+  |> String.concat "\n"
 
 let to_string_gamess ?ele_array =
     to_string_general ?ele_array ~fmt:Gto.Gamess ~atom_sep:""
 
 let to_string_gaussian ?ele_array b =
-  String.concat ~sep:"\n"
+  String.concat "\n"
   [ to_string_general ?ele_array ~fmt:Gto.Gaussian ~atom_sep:"****" b ; "****" ]
 
 let to_string ?(fmt=Gto.Gamess) =

ocaml/Bit.ml

@@ -1,4 +1,4 @@
-open Core.Std;;
+open Core;;
 
 (*
 Type for bits 
@@ -11,7 +11,7 @@ Zero | One
 type t      = 
 | One 
 | Zero 
-with sexp
+[@@deriving sexp]
 
 let to_string = function
   | Zero -> "0"

ocaml/Bit.mli

@@ -1,4 +1,4 @@
-type t = One | Zero with sexp
+type t = One | Zero [@@deriving sexp]
 
 (** String conversions for printing *)
 val to_string : t -> string

ocaml/Bitlist.ml

@@ -1,5 +1,5 @@
 open Qptypes
-open Core.Std
+open Core
 
 (*
 Type for bits strings

ocaml/Charge.ml

@@ -1,6 +1,6 @@
-open Core.Std
+open Core
 
-type t = float with sexp
+type t = float [@@deriving sexp]
 
 let of_float x = x
 let of_int   i = Float.of_int i

ocaml/Charge.mli

@@ -1,4 +1,4 @@
-type t = float with sexp
+type t = float [@@deriving sexp]
 
 (** Float conversion functions *)
 val to_float : t -> float

ocaml/Determinant.ml

@@ -1,7 +1,7 @@
-open Core.Std;;
+open Qptypes
-open Qptypes;;
+open Sexplib.Std
 
-type t = int64 array with sexp
+type t = int64 array [@@deriving sexp]
 
 let to_int64_array (x:t) = (x:int64 array)
 
@@ -9,8 +9,8 @@ let to_int64_array (x:t) = (x:int64 array)
 let to_alpha_beta x = 
   let x = to_int64_array x in
   let n_int = (Array.length x)/2 in
-  ( Array.init n_int ~f:(fun i -> x.(i)) ,
+  ( Array.init n_int (fun i -> x.(i)) ,
-    Array.init n_int ~f:(fun i -> x.(i+n_int)) )
+    Array.init n_int (fun i -> x.(i+n_int)) )
 
 
 let to_bitlist_couple x =
@@ -28,12 +28,14 @@ let bitlist_to_string ~mo_tot_num x =
   let len = 
     MO_number.to_int mo_tot_num
   in
-  List.map x ~f:(function
+  let s = 
-      | Bit.Zero -> "-"
+    List.map (function
-      | Bit.One  -> "+" 
+        | Bit.Zero -> "-"
-  )
+        | Bit.One  -> "+" 
-  |> String.concat
+    ) x
-  |> String.sub ~pos:0 ~len 
+    |> String.concat ""
+  in
+  String.sub s 0 len 
 
 
 
@@ -77,6 +79,6 @@ let to_string ~mo_tot_num x =
   let (xa,xb) = to_bitlist_couple x in
   [ "  " ; bitlist_to_string ~mo_tot_num xa ; "\n" ;
     "  " ; bitlist_to_string ~mo_tot_num xb ]
-  |> String.concat 
+  |> String.concat ""
 
 

ocaml/Determinant.mli

@@ -5,7 +5,7 @@
   * where each int64 is a list of 64 MOs. When the bit is set
   * to 1, the MO is occupied.
   *)
-type t = int64 array with sexp
+type t = int64 array [@@deriving sexp]
 
 (** Transform to an int64 array *)
 val to_int64_array : t -> int64 array

ocaml/Element.ml

@@ -1,4 +1,4 @@
-open Core.Std
+open Core
 open Qptypes
 
 exception ElementError of string
@@ -11,7 +11,7 @@ type t =
 |K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
 |Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
                            |Pt          
-with sexp
+[@@deriving sexp]
 
 let of_string x = 
   match (String.capitalize (String.lowercase x)) with

ocaml/Element.mli

@@ -8,7 +8,7 @@ type t =
 |K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
 |Rb|Sr|Y |Zr|Nb|Mo|Tc|Ru|Rh|Pd|Ag|Cd|In|Sn|Sb|Te|I |Xe
                            |Pt
-with sexp
+[@@deriving sexp]
 
 (** String conversion functions *)
 val of_string : string -> t

ocaml/Excitation.ml

@@ -1,14 +1,14 @@
-open Core.Std;;
+open Core
-open Qptypes;;
+open Qptypes
 
 module Hole = struct
-    type t = MO_class.t with sexp
+    type t = MO_class.t [@@deriving sexp]
     let of_mo_class x = x
     let to_mo_class x = x
 end
 
 module Particle = struct
-    type t = MO_class.t with sexp
+    type t = MO_class.t [@@deriving sexp]
     let of_mo_class x = x
     let to_mo_class x = x
 end
@@ -16,7 +16,7 @@ end
 type t =
 | Single of Hole.t*Particle.t
 | Double of Hole.t*Particle.t*Hole.t*Particle.t
-with sexp;;
+[@@deriving sexp]
 
 let create_single ~hole ~particle =
   MO_class.(
@@ -29,7 +29,7 @@ let create_single ~hole ~particle =
   | (          _, Inactive _ ) -> failwith "Particles can not be in virtual MOs"
   | (h, p) -> Single ( (Hole.of_mo_class h), (Particle.of_mo_class p) )
   )
-;;
+
 
 let double_of_singles s1 s2 =
   let (h1,p1) = match s1 with
@@ -40,14 +40,14 @@ let double_of_singles s1 s2 =
   | _ -> assert false
   in
   Double (h1,p1,h2,p2)
-;;
+
 
 let create_double ~hole1 ~particle1 ~hole2 ~particle2 =
   let s1 = create_single ~hole:hole1 ~particle:particle1
   and s2 =  create_single ~hole:hole2 ~particle:particle2
   in
   double_of_singles s1 s2
-;;
+
 
 let to_string = function
   | Single (h,p) ->
@@ -68,5 +68,5 @@ let to_string = function
         (MO_class.to_string (Particle.to_mo_class p2));
         "]"]
       |> String.concat ~sep:" "
-;;
+
 

ocaml/Excitation.mli

@@ -18,7 +18,7 @@ module Particle :
 type t =
   | Single of Hole.t * Particle.t
   | Double of Hole.t * Particle.t * Hole.t * Particle.t
-with sexp
+[@@deriving sexp]
 
 val create_single : hole:MO_class.t -> particle:MO_class.t -> t
 

ocaml/GaussianPrimitive.ml

@@ -1,10 +1,10 @@
 open Qptypes
-open Core.Std
+open Core
 
 type t =
 { sym  : Symmetry.t ;
   expo : AO_expo.t ;
-} with sexp
+} [@@deriving sexp]
 
 let to_string p = 
   let { sym = s ; expo = e } = p in

ocaml/Generic_input_of_rst.ml

@@ -1,4 +1,4 @@
-open Core.Std;;
+open Core;;
 open Qptypes;;
 
 

ocaml/Gto.ml

@@ -1,5 +1,5 @@
-open Core.Std
 open Qptypes
+open Sexplib.Std
 
 exception GTO_Read_Failure of string
 exception End_Of_Basis
@@ -11,11 +11,11 @@ type fmt =
 type t =
 { sym  : Symmetry.t ;
   lc   : ((GaussianPrimitive.t * AO_coef.t) list)
-} with sexp
+} [@@deriving sexp]
 
 
 let of_prim_coef_list pc =
-  let (p,c) = List.hd_exn pc in
+  let (p,c) = List.hd pc in
   let sym = p.GaussianPrimitive.sym in
   let rec check = function
   | [] -> `OK
@@ -37,12 +37,12 @@ let of_prim_coef_list pc =
 let read_one in_channel =
   (* Fetch number of lines to read on first line *)
   let buffer = input_line in_channel in
-  if ( (String.strip buffer) = "" ) then
+  if ( (String_ext.strip buffer) = "" ) then
      raise End_Of_Basis;
   let sym_str = String.sub buffer 0 2 in
   let   n_str = String.sub buffer 2 ((String.length buffer)-2) in
-  let sym = Symmetry.of_string (String.strip sym_str) in
+  let sym = Symmetry.of_string (String_ext.strip sym_str) in
-  let n = Int.of_string (String.strip n_str) in
+  let n = int_of_string (String_ext.strip n_str) in
   (* Read all the primitives *)
   let rec read_lines result = function
   | 0 -> result
@@ -50,18 +50,19 @@ let read_one in_channel =
     begin
       let line_buffer = input_line in_channel in
       let buffer = line_buffer 
-      |> String.split ~on:' ' 
+      |> String_ext.split ~on:' ' 
-      |> List.filter ~f:(fun x -> x <> "")
+      |> List.filter (fun x -> x <> "")
       in
       match buffer with
       | [ j ; expo ; coef ] ->
         begin
-          let coef = String.tr ~target:'D' ~replacement:'e' coef
+          let coef =
+            Str.global_replace (Str.regexp "D") "e" coef
           in
           let p =
             GaussianPrimitive.of_sym_expo sym 
-              (AO_expo.of_float (Float.of_string expo) )
+              (AO_expo.of_float (float_of_string expo) )
-          and c = AO_coef.of_float (Float.of_string coef) in
+          and c = AO_coef.of_float (float_of_string coef) in
           read_lines ( (p,c)::result) (i-1)
         end
       | _ -> raise (GTO_Read_Failure line_buffer)
@@ -89,7 +90,7 @@ let to_string_gamess { sym = sym ; lc = lc } =
     do_work (result::accu) (i+1) tail
   in
   (do_work [result] 1 lc)
-  |> String.concat ~sep:"\n"
+  |> String.concat "\n"
 
 
 (** Write the GTO in Gaussian format *)
@@ -109,7 +110,7 @@ let to_string_gaussian { sym = sym ; lc = lc } =
     do_work (result::accu) (i+1) tail
   in
   (do_work [result] 1 lc)
-  |> String.concat ~sep:"\n"
+  |> String.concat "\n"
 
 
 (** Transform the gto to a string *)

ocaml/Gto.mli

@@ -7,7 +7,7 @@ type fmt =
 type t =
   { sym : Symmetry.t ;
     lc  : (GaussianPrimitive.t * Qptypes.AO_coef.t) list;
-  } with sexp
+  } [@@deriving sexp]
 
 (** Create from a list of GaussianPrimitive.t * Qptypes.AO_coef.t *)
 val of_prim_coef_list :

ocaml/Input.ml

@@ -1,6 +1,6 @@
 open Qputils;;
 open Qptypes;;
-open Core.Std;;
+open Core;;
 
 include Input_ao_basis;;
 include Input_bitmasks;;

ocaml/Input_ao_basis.ml

@@ -1,6 +1,6 @@
 open Qptypes;;
 open Qputils;;
-open Core.Std;;
+open Core;;
 
 module Ao_basis : sig
   type t = 
@@ -13,7 +13,7 @@ module Ao_basis : sig
       ao_coef         : AO_coef.t array;
       ao_expo         : AO_expo.t array;
       ao_cartesian    : bool;
-    } with sexp
+    } [@@deriving sexp]
   ;;
   val read : unit -> t option
   val to_string : t -> string
@@ -32,7 +32,7 @@ end = struct
       ao_coef         : AO_coef.t array;
       ao_expo         : AO_expo.t array;
       ao_cartesian    : bool;
-    } with sexp
+    } [@@deriving sexp]
   ;;
 
   let get_default = Qpackage.get_ezfio_default "ao_basis";;

ocaml/Input_bi_integrals.ml

@@ -1,6 +1,6 @@
 open Qptypes;;
 open Qputils;;
-open Core.Std;;
+open Core;;
 
 module Bielec_integrals : sig
   type t = 
@@ -11,7 +11,7 @@ module Bielec_integrals : sig
       threshold_ao       : Threshold.t;
       threshold_mo       : Threshold.t;
       direct             : bool;
-    } with sexp
+    } [@@deriving sexp]
   ;;
   val read  : unit -> t option
   val write : t -> unit
@@ -27,7 +27,7 @@ end = struct
       threshold_ao       : Threshold.t;
       threshold_mo       : Threshold.t;
       direct             : bool;
-    } with sexp
+    } [@@deriving sexp]
   ;;
 
   let get_default = Qpackage.get_ezfio_default "bielec_integrals";;

ocaml/Input_bitmasks.ml

@@ -1,6 +1,6 @@
 open Qptypes;;
 open Qputils;;
-open Core.Std;;
+open Core;;
 
 module Bitmasks : sig
   type t = 
@@ -10,7 +10,7 @@ module Bitmasks : sig
       generators         : int64 array;
       n_mask_cas         : Bitmask_number.t;
       cas                : int64 array;
-    } with sexp
+    } [@@deriving sexp]
   ;;
   val read : unit -> t option 
   val to_string : t -> string
@@ -22,7 +22,7 @@ end = struct
       generators         : int64 array;
       n_mask_cas         : Bitmask_number.t;
       cas                : int64 array;
-    } with sexp
+    } [@@deriving sexp]
   ;;
 
   let get_default = Qpackage.get_ezfio_default "bitmasks";;

ocaml/Input_determinants_by_hand.ml

@@ -1,6 +1,6 @@
 open Qptypes;;
 open Qputils;;
-open Core.Std;;
+open Core;;
 
 module Determinants_by_hand : sig
   type t = 
@@ -11,7 +11,7 @@ module Determinants_by_hand : sig
       expected_s2            : Positive_float.t;
       psi_coef               : Det_coef.t array;
       psi_det                : Determinant.t array;
-    } with sexp
+    } [@@deriving sexp]
   val read  : unit -> t
   val read_maybe  : unit -> t option
   val write : t -> unit
@@ -30,7 +30,7 @@ end = struct
       expected_s2            : Positive_float.t;
       psi_coef               : Det_coef.t array;
       psi_det                : Determinant.t array;
-    } with sexp
+    } [@@deriving sexp]
   ;;
 
   let get_default = Qpackage.get_ezfio_default "determinants";;

ocaml/Input_electrons.ml

@@ -1,12 +1,12 @@
 open Qptypes;;
 open Qputils;;
-open Core.Std;;
+open Core;;
 
 module Electrons : sig
   type t = 
     { elec_alpha_num     : Elec_alpha_number.t;
       elec_beta_num      : Elec_beta_number.t;
-    } with sexp
+    } [@@deriving sexp]
   ;;
   val read  : unit -> t option
   val write : t -> unit
@@ -18,7 +18,7 @@ end = struct
   type t = 
     { elec_alpha_num     : Elec_alpha_number.t;
       elec_beta_num      : Elec_beta_number.t;
-    } with sexp
+    } [@@deriving sexp]
   ;;
 
   let get_default = Qpackage.get_ezfio_default "electrons";;

ocaml/Input_mo_basis.ml

@@ -1,6 +1,6 @@
 open Qptypes
 open Qputils
-open Core.Std
+open Core
 
 type t_mo = 
     { mo_tot_num      : MO_number.t ;
@@ -9,7 +9,7 @@ type t_mo =
       mo_occ          : MO_occ.t array;
       mo_coef         : (MO_coef.t array) array;
       ao_md5          : MD5.t;
-    } with sexp
+    } [@@deriving sexp]
 
 module Mo_basis : sig
   type t = t_mo

ocaml/Input_nuclei_by_hand.ml

@@ -1,6 +1,6 @@
 open Qptypes;;
 open Qputils;;
-open Core.Std;;
+open Core;;
 
 module Nuclei_by_hand : sig
   type t = 
@@ -8,7 +8,7 @@ module Nuclei_by_hand : sig
       nucl_label      : Element.t array;
       nucl_charge     : Charge.t array;
       nucl_coord      : Point3d.t array;
-    } with sexp
+    } [@@deriving sexp]
   ;;
   val read  : unit -> t option
   val write : t -> unit 
@@ -22,7 +22,7 @@ end = struct
       nucl_label      : Element.t array;
       nucl_charge     : Charge.t array;
       nucl_coord      : Point3d.t array;
-    } with sexp
+    } [@@deriving sexp]
   ;;
 
   let get_default = Qpackage.get_ezfio_default "nuclei";;

ocaml/Io_ext.ml

@@ -0,0 +1,24 @@
+let input_lines filename =
+  let in_channel =
+    open_in filename
+  in
+  let rec aux accu = 
+    try
+      let newline = 
+        input_line in_channel
+      in
+      aux (newline::accu)
+    with End_of_file -> accu
+  in
+  let result = 
+    List.rev (aux [])
+  in
+  close_in in_channel;
+  result
+
+
+
+let read_all filename = 
+  input_lines filename
+  |> String.concat "\n"
+

ocaml/Long_basis.ml

@@ -1,7 +1,7 @@
-open Core.Std;;
+open Qptypes
-open Qptypes;;
+open Sexplib.Std
 
-type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t ) list with sexp
+type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t ) list [@@deriving sexp]
 
 let of_basis b =
   let rec do_work accu = function
@@ -10,14 +10,14 @@ let of_basis b =
         begin
           let new_accu = 
             Symmetry.Xyz.of_symmetry g.Gto.sym 
-            |> List.rev_map ~f:(fun x-> (x,g,n)) 
+            |> List.rev_map (fun x-> (x,g,n)) 
           in
           do_work (new_accu@accu) tail
         end
   in
   do_work [] b
   |> List.rev
-;;
+
 
 let to_basis b =
   let rec do_work accu = function
@@ -25,7 +25,7 @@ let to_basis b =
   | (s,g,n)::tail -> 
     let first_sym = 
       Symmetry.Xyz.of_symmetry g.Gto.sym
-      |> List.hd_exn
+      |> List.hd
     in
     let new_accu = 
       if ( s = first_sym ) then
@@ -36,19 +36,19 @@ let to_basis b =
     do_work new_accu tail
   in
   do_work [] b 
-;;
+
 
 let to_string b =
-  let middle = List.map ~f:(fun (x,y,z) -> 
+  let middle = List.map (fun (x,y,z) -> 
-     "( "^((Int.to_string (Nucl_number.to_int z)))^", "^
+     "( "^((string_of_int (Nucl_number.to_int z)))^", "^
      (Symmetry.Xyz.to_string x)^", "^(Gto.to_string y)
      ^" )"
   ) b
-  |> String.concat ~sep:",\n"
+  |> String.concat ",\n"
   in "("^middle^")"
-;;
 
-include To_md5;;
+
+include To_md5
 let to_md5 = to_md5 sexp_of_t
-;;
+
 

ocaml/Long_basis.mli

@@ -5,7 +5,7 @@ open Qptypes;;
   * all the D orbitals are converted to xx, xy, xz, yy, yx
   * etc
 *)
-type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t) list with sexp
+type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t) list [@@deriving sexp]
 
 (** Transform a basis to a long basis *)
 val of_basis :

ocaml/MO_class.ml

@@ -1,4 +1,4 @@
-open Core.Std
+open Core
 open Qptypes 
 
 type t = 
@@ -7,7 +7,7 @@ type t =
   | Active   of MO_number.t list
   | Virtual  of MO_number.t list
   | Deleted  of MO_number.t list
-with sexp
+[@@deriving sexp]
 
 
 let to_string  x = 

ocaml/MO_class.mli

@@ -4,7 +4,7 @@ type t =
   | Active   of Qptypes.MO_number.t list
   | Virtual  of Qptypes.MO_number.t list
   | Deleted  of Qptypes.MO_number.t list
-with sexp
+[@@deriving sexp]
 
 
 (** Create different excitation classes *)

ocaml/MO_label.ml

@@ -1,4 +1,4 @@
-open Core.Std;;
+open Core;;
 
 type t =
 | Guess
@@ -7,7 +7,7 @@ type t =
 | Localized
 | Orthonormalized
 | None
-with sexp
+[@@deriving sexp]
 ;;
 
 let to_string = function

ocaml/MO_label.mli

@@ -5,7 +5,7 @@ type t =
   | Localized
   | Orthonormalized
   | None
-with sexp
+[@@deriving sexp]
 
 (** String representation *)
 val to_string : t -> string

ocaml/Makefile

@@ -11,8 +11,8 @@ endif
 
 LIBS=
 PKGS=
-OCAMLCFLAGS="-g -warn-error A"
+OCAMLCFLAGS="-g"
-OCAMLBUILD=ocamlbuild -j 0 -syntax camlp4o -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS) 
+OCAMLBUILD=ocamlbuild -j 0 -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS) 
 MLLFILES=$(wildcard *.mll) 
 MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml Input_auto_generated.ml qp_edit.ml 
 MLIFILES=$(wildcard *.mli) git

ocaml/Message.ml

@@ -1,4 +1,4 @@
-open Core.Std
+open Core
 open Qptypes
 
 (** New job : Request to create a new multi-tasked job *)

ocaml/Molecule.ml

@@ -1,14 +1,14 @@
-open Core.Std ;;
+open Qptypes 
-open Qptypes ;;
+open Sexplib.Std
 
-exception MultiplicityError of string;;
+exception MultiplicityError of string
-exception XYZError ;;
+exception XYZError 
 
 type t = {
   nuclei     : Atom.t list ;
   elec_alpha : Elec_alpha_number.t ;
   elec_beta  : Elec_beta_number.t ;
-} with sexp
+} [@@deriving sexp]
 
 let get_charge { nuclei  ; elec_alpha ; elec_beta } =
   let result =
@@ -19,7 +19,7 @@ let get_charge { nuclei  ; elec_alpha ; elec_beta } =
   | a::rest -> (Charge.to_float a.Atom.charge) +. nucl_charge rest
   | [] -> 0.
   in
-  Charge.of_float (nucl_charge nuclei  -. (Float.of_int result))
+  Charge.of_float (nucl_charge nuclei  -. (float_of_int result))
 
 
 let get_multiplicity m = 
@@ -59,9 +59,10 @@ let name m =
   | a::rest ->
       begin
         let e = a.Atom.element in
-        match (List.Assoc.find accu e) with
+        try
-        | None   -> build_list (List.Assoc.add accu e 1) rest
+          let i = List.assoc e accu in
-        | Some i -> build_list (List.Assoc.add accu e (i+1)) rest
+          build_list ( (e,i+1)::(List.remove_assoc e accu) ) rest
+        with Not_found -> build_list ( (e,1)::accu ) rest
       end
   | [] -> accu
   in
@@ -83,7 +84,7 @@ let name m =
   let result =
      build_list [] nuclei |> build_name [c ; ", " ; mult]
   in
-  String.concat (result)
+  String.concat "" result
 
 
 let to_string_general ~f m = 
@@ -95,8 +96,8 @@ let to_string_general ~f m =
   let title =
      name m
   in
-  [ Int.to_string n ; title ] @  (List.map ~f nuclei)
+  [ string_of_int n ; title ] @  (List.map f nuclei)
-  |> String.concat ~sep:"\n"
+  |> String.concat "\n"
 
 let to_string =
   to_string_general ~f:(fun x -> Atom.to_string Units.Angstrom x)
@@ -109,9 +110,9 @@ let of_xyz_string
     ?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1))
     ?(units=Units.Angstrom)
     s =
-  let l = String.split s ~on:'\n'
+  let l = String_ext.split s ~on:'\n'
-       |> List.filter ~f:(fun x -> x <> "")
+       |> List.filter (fun x -> x <> "")
-       |> List.map ~f:(fun x -> Atom.of_string units x)
+       |> List.map (fun x -> Atom.of_string units x)
   in
   let ne = ( get_charge { 
         nuclei=l ;
@@ -145,25 +146,28 @@ let of_xyz_file
     ?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1))
     ?(units=Units.Angstrom)
     filename =
-  let (x,buffer) = In_channel.read_all filename 
+  let lines = 
-  |> String.lsplit2_exn ~on:'\n'
+    match Io_ext.input_lines filename with
+    | natoms :: title :: rest -> 
+        begin
+          try
+            if (int_of_string @@ String_ext.strip natoms) <= 0 then
+              raise XYZError
+          with
+          | _ -> raise XYZError
+        end;
+        String.concat "\n" rest
+    | _ -> failwith ("Problem in xyz file "^filename)
   in
-  let result =
+  of_xyz_string ~charge:charge ~multiplicity:multiplicity 
-    try
+    ~units:units lines
-      (int_of_string @@ String.strip x) > 0
-    with
-    | Failure "int_of_string"  -> false
-  in
-  if not result then raise XYZError;
-  let (_,buffer) = String.lsplit2_exn buffer ~on:'\n' in
-  of_xyz_string ~charge ~multiplicity ~units buffer
 
 
 let of_zmt_file  
     ?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1))
     ?(units=Units.Angstrom)
     filename = 
-  In_channel.read_all filename
+  Io_ext.read_all filename
   |> Zmatrix.of_string
   |> Zmatrix.to_xyz_string
   |> of_xyz_string ~charge ~multiplicity ~units
@@ -182,14 +186,14 @@ let of_file
 let distance_matrix molecule =
   let coord =
     molecule.nuclei
-    |> List.map ~f:(fun x -> x.Atom.coord)
+    |> List.map (fun x -> x.Atom.coord)
     |> Array.of_list
   in
   let n = 
     Array.length coord
   in
   let result =
-    Array.make_matrix ~dimx:n  ~dimy:n 0.
+    Array.make_matrix n n 0.
   in
   for i = 0 to (n-1)
   do
@@ -203,6 +207,7 @@ let distance_matrix molecule =
   
   
 
+open Core ;;
 include To_md5
 let to_md5 = to_md5 sexp_of_t
 

ocaml/Molecule.mli

@@ -4,7 +4,7 @@ type t = {
   nuclei     : Atom.t list;
   elec_alpha : Qptypes.Elec_alpha_number.t;
   elec_beta  : Qptypes.Elec_beta_number.t;
-} with sexp
+} [@@deriving sexp]
 
 (** Returns the charge of the molecule *)
 val get_charge       : t -> Charge.t

ocaml/Multiplicity.ml

@@ -1,7 +1,7 @@
-open Core.Std;;
+open Core;;
 open Qptypes ;;
 
-type t = Strictly_positive_int.t with sexp
+type t = Strictly_positive_int.t [@@deriving sexp]
 
 let of_int = Strictly_positive_int.of_int ;;
 let to_int = Strictly_positive_int.to_int ;;

ocaml/Multiplicity.mli

@@ -1,4 +1,4 @@
-type t = Qptypes.Strictly_positive_int.t with sexp
+type t = Qptypes.Strictly_positive_int.t [@@deriving sexp]
 
 (** Conversion from int *)
 val of_int : int -> t

ocaml/Point3d.ml

@@ -1,11 +1,11 @@
-open Core.Std;;
+open Core;;
 open Qptypes;;
 
 type t = {
   x : float ;
   y : float ;
   z : float ;
-} with sexp
+} [@@deriving sexp]
 
 let of_tuple ~units (x,y,z) =
   let f = match units with 

ocaml/Point3d.mli

@@ -2,7 +2,7 @@ type t =
 { x : float;
   y : float;
   z : float;
-} with sexp
+} [@@deriving sexp]
 
 (** Create from a tuple of floats *)
 val of_tuple  : units:Units.units -> float*float*float -> t

ocaml/Primitive.mli

@@ -1,7 +1,7 @@
 type t =
 { sym : Symmetry.t;
   expo : Qptypes.AO_expo.t;
-} with sexp
+} [@@deriving sexp]
 
 (** Conversion to string for printing *)
 val to_string : t -> string

ocaml/Progress_bar.ml

@@ -1,4 +1,4 @@
-open Core.Std
+open Core
 
 type t =
 { 
@@ -53,13 +53,13 @@ let display_tty bar =
     in
     let stop_time =
       let x = 
-        Time.Span.to_float running_time
+        Time.Span.to_sec running_time
       in
       if (percent > 0.) then
         x *. 100. /. percent -. x
-        |> Time.Span.of_float
+        |> Time.Span.of_sec
       else
-        Time.Span.of_float 0.
+        Time.Span.of_sec 0.
     in
     Printf.eprintf "%s : [%s] %4.1f%%  | %10s, ~%10s left\r%!"
       bar.title
@@ -67,7 +67,7 @@ let display_tty bar =
       percent
       (Time.Span.to_string running_time)
       (stop_time |> Time.Span.to_string );
-    { bar with dirty = false ; next = Time.add now (Time.Span.of_float 0.1) }
+    { bar with dirty = false ; next = Time.add now (Time.Span.of_sec 0.1) }
   
 
 let display_file bar =
@@ -80,19 +80,19 @@ let display_file bar =
     in
     let stop_time =
       let x = 
-        Time.Span.to_float running_time
+        Time.Span.to_sec running_time
       in
       if (percent > 0.) then
         x *. 100. /. percent -. x
-        |> Time.Span.of_float
+        |> Time.Span.of_sec
       else
-        Time.Span.of_float 0.
+        Time.Span.of_sec 0.
     in
     Printf.eprintf "%5.2f %%  in  %20s, ~%20s left\n%!"
       percent
       (Time.Span.to_string running_time)
       (Time.Span.to_string stop_time);
-    { bar with dirty = false ; next = Time.add (Time.now ()) (Time.Span.of_float 2.) }
+    { bar with dirty = false ; next = Time.add (Time.now ()) (Time.Span.of_sec 2.) }
   
 
 

ocaml/Pseudo.ml

@@ -1,4 +1,4 @@
-open Core.Std
+open Core
 open Qptypes
 
 
@@ -7,7 +7,7 @@ module GaussianPrimitive_local : sig
   type t = { 
     expo    : AO_expo.t ;
     r_power : R_power.t ;
-  } with sexp
+  } [@@deriving sexp]
 
   val of_expo_r_power : AO_expo.t -> R_power.t -> t
   val to_string : t -> string
@@ -17,7 +17,7 @@ end = struct
   type t = { 
     expo    : AO_expo.t ;
     r_power : R_power.t ;
-  } with sexp
+  } [@@deriving sexp]
 
   let of_expo_r_power dz n = 
      { expo = dz ; r_power = n }
@@ -35,7 +35,7 @@ module GaussianPrimitive_non_local : sig
     expo    : AO_expo.t ;
     r_power : R_power.t ;
     proj    : Positive_int.t
-  } with sexp
+  } [@@deriving sexp]
 
   val of_proj_expo_r_power : Positive_int.t -> AO_expo.t -> R_power.t -> t
   val to_string : t -> string
@@ -46,7 +46,7 @@ end = struct
     expo    : AO_expo.t ;
     r_power : R_power.t ;
     proj    : Positive_int.t
-  } with sexp
+  } [@@deriving sexp]
 
   let of_proj_expo_r_power p dz n = 
      { expo = dz ; r_power = n ; proj = p }
@@ -66,7 +66,7 @@ type t = {
   n_elec    : Positive_int.t ;
   local     : (GaussianPrimitive_local.t * AO_coef.t ) list ;
   non_local : (GaussianPrimitive_non_local.t * AO_coef.t ) list 
-} with sexp
+} [@@deriving sexp]
 
 let empty e =
   { element   = e;

ocaml/Qpackage.ml

@@ -1,4 +1,4 @@
-open Core.Std;;
+open Core;;
 open Qptypes;;
 open Qputils;;
 

ocaml/Qputils.ml

@@ -1,4 +1,4 @@
-open Core.Std
+open Sexplib
 
 (*
 let rec transpose = function
@@ -14,12 +14,12 @@ let rec transpose = function
 
 let input_to_sexp s =
     let result = 
-      String.split_lines s 
+      String_ext.split ~on:'\n' s 
-      |> List.filter ~f:(fun x->
+      |> List.filter (fun x-> (String_ext.strip x) <> "")
-         (String.strip x) <> "")
+      |> List.map (fun x-> "("^ 
-      |> List.map ~f:(fun x->
+        (Str.global_replace (Str.regexp "=") " " x)
-         "("^(String.tr '=' ' ' x)^")")
+        ^")")
-      |> String.concat 
+      |> String.concat ""
     in
     print_endline ("("^result^")");
     "("^result^")"
@@ -29,10 +29,10 @@ let rmdir dirname =
   let rec remove_one dir =
     Sys.chdir dir;
     Sys.readdir "."
-    |> Array.iter ~f:(fun x ->
+    |> Array.iter (fun x ->
-      match (Sys.is_directory x, Sys.is_file x) with
+      match (Sys.is_directory x, Sys.file_exists x) with
-      | (`Yes, _) -> remove_one x
+      | (true, _) -> remove_one x
-      | (_, `Yes) -> Sys.remove x
+      | (_, true) -> Sys.remove x
       | _ -> failwith ("Unable to remove file "^x^".")
     );
     Sys.chdir "..";

ocaml/README_qp_edit.rst

@@ -19,7 +19,7 @@ of the block.
          r_y    : Y_type.t
         ...
          last_r : bool
-      } with sexp
+      } [@@deriving sexp]
     ;;
     val read  : unit -> t
     val write : t -> unit
@@ -31,7 +31,7 @@ of the block.
          r_y    : Y_type.t
         ...
          last_r : bool
-      } with sexp
+      } [@@deriving sexp]
     ;;
 
     let get_default = Qpackage.get_ezfio_default "new_keyword";;

ocaml/Range.ml

@@ -1,4 +1,4 @@
-open Core.Std;;
+open Sexplib.Std
 
 (* A range is a string of the type:
  * 
@@ -12,14 +12,14 @@ open Core.Std;;
 *)
 
 
-type t = int list with sexp
+type t = int list [@@deriving sexp] 
 
 let expand_range r =
-  match String.lsplit2 ~on:'-' r with
+  match String_ext.lsplit2 ~on:'-' r with
   | Some (s, f) ->
       begin
-        let start = Int.of_string s
+        let start = int_of_string s
-        and finish =  Int.of_string f
+        and finish =  int_of_string f
         in
         assert (start <= finish) ;
         let rec do_work = function
@@ -31,9 +31,9 @@ let expand_range r =
       begin
         match r with
           | "" -> []
-          | _  -> [Int.of_string r] 
+          | _  -> [int_of_string r] 
       end
-;;
+
 
 let of_string s =
   match s.[0] with
@@ -43,36 +43,37 @@ let of_string s =
     assert (s.[0] = '[') ;
     assert (s.[(String.length s)-1] = ']') ;
     let s = String.sub s 1 ((String.length s) - 2) in
-    let l = String.split ~on:',' s in
+    let l = String_ext.split ~on:',' s in
-    let l = List.map ~f:expand_range l in
+    let l = List.map expand_range l in
-  List.concat l |> List.dedup ~compare:Int.compare |> List.sort ~cmp:Int.compare
+  List.concat l
-;;
+  |> List.sort_uniq compare 
+
 
 let to_string l =
   let rec do_work buf symbol = function
     | [] -> buf
     | a::([] as t) -> 
-          do_work (buf^symbol^(Int.to_string a)) "" t
+          do_work (buf^symbol^(string_of_int a)) "" t
     | a::(b::q as t) ->
         if (b-a = 1) then
           do_work buf "-" t
         else
-          do_work (buf^symbol^(Int.to_string a)^","^(Int.to_string b)) "" t
+          do_work (buf^symbol^(string_of_int a)^","^(string_of_int b)) "" t
   in
   let result = 
     match l with
     | [] ->
         "[]"
     | h::t  ->
-        do_work ("["^(Int.to_string h)) "" l in
+        do_work ("["^(string_of_int h)) "" l in
   (String.sub result 0 ((String.length result)))^"]"
-;;
+
 
 let test_module () =
   let s = "[72-107,36-53,126-131]" in
   let l = of_string s in
   print_string s ; print_newline () ;
-  List.iter ~f:(fun x -> Printf.printf "%d, " x) l ; print_newline () ;
+  List.iter (fun x -> Printf.printf "%d, " x) l ; print_newline () ;
-  to_string l |> print_string ;  print_newline () ;
+  to_string l |> print_string ;  print_newline ();
-;;
+
 

ocaml/Range.mli

@@ -1,4 +1,4 @@
-type t = int list with sexp
+type t = int list [@@deriving sexp] 
 
 (** A range is a sorted list of ints in an interval.
     It is created using a string :

ocaml/String_ext.ml

@@ -0,0 +1,142 @@
+include String
+
+(** Split a string on a given character *)
+let split ?(on=' ') str = 
+  split_on_char on str
+(*
+    let rec do_work ?(accu=[]) ?(left="") = function
+    | "" -> List.rev (left::accu)
+    | s  ->
+        let new_s =
+            (length s) - 1
+            |> sub s 1 
+        in
+        if (s.[0] = on) then
+            let new_accu = 
+                left :: accu
+            in
+            do_work ~accu:new_accu new_s
+        else
+            let new_left =
+                concat "" [ left ; make 1 s.[0] ]
+            in
+            do_work ~accu ~left:new_left new_s
+    in
+    do_work str
+*)
+  
+
+(** Strip blanks on the left of a string *)
+let ltrim s =
+    let rec do_work s l =
+        match s.[0] with
+        | '\n'
+        | ' ' -> do_work (sub s 1 (l-1)) (l-1)
+        | _ -> s
+    in
+    let l =
+        length s
+    in
+    if (l > 0) then
+        do_work s l
+    else
+        s
+
+(** Strip blanks on the right of a string *)
+let rtrim s =
+    let rec do_work s l =
+        let newl =
+            l-1
+        in
+        match s.[newl] with
+        | '\n'
+        | ' ' -> do_work (sub s 0 (newl)) (newl)
+        | _ -> s
+    in
+    let l = 
+        length s
+    in
+    if (l > 0) then
+        do_work s l
+    else
+        s
+
+
+(** Strip blanks on the right and left of a string *)
+let strip = String.trim
+
+
+(** Split a string in two pieces when a character is found the 1st time from the left *)
+let lsplit2_exn ?(on=' ') s =
+    let length = 
+        String.length s
+    in
+    let rec do_work i = 
+        if (i = length) then
+           begin
+              raise Not_found
+           end
+        else if (s.[i] = on) then
+           ( String.sub s 0 i, 
+             String.sub s (i+1) (length-i-1) )
+        else
+           do_work (i+1)
+    in
+    do_work 0
+
+
+(** Split a string in two pieces when a character is found the 1st time from the right *)
+let rsplit2_exn ?(on=' ') s =
+    let length = 
+        String.length s
+    in
+    let rec do_work i = 
+        if (i = -1) then
+           begin
+              raise Not_found
+           end
+        else if (s.[i] = on) then
+           ( String.sub s 0 i, 
+             String.sub s (i+1) (length-i-1) )
+        else
+           do_work (i-1)
+    in
+    do_work length
+
+
+let lsplit2 ?(on=' ') s =
+  try
+    Some (lsplit2_exn ~on s) 
+  with
+  | Not_found -> None
+
+
+let rsplit2 ?(on=' ') s =
+  try
+    Some (rsplit2_exn ~on s) 
+  with
+  | Not_found -> None
+
+
+let to_list s =
+  Array.init (String.length s) (fun i -> s.[i])
+  |> Array.to_list
+
+
+let fold ~init ~f s =
+    to_list s
+    |> List.fold_left f init 
+
+  
+let is_prefix ~prefix s =
+  let len =
+    String.length prefix
+  in
+  if len > String.length s then
+    false
+  else
+    prefix = String.sub s 0 len 
+
+
+let of_char c =
+  String.make 1 c

ocaml/Symmetry.ml

@@ -1,7 +1,7 @@
 open Qptypes
-open Core.Std
+open Sexplib.Std
 
-type t = S|P|D|F|G|H|I|J|K|L with sexp
+type t = S|P|D|F|G|H|I|J|K|L [@@deriving sexp]
 
 let to_string = function
   | S -> "S"
@@ -77,7 +77,7 @@ type st = t
 module Xyz = struct
   type t = { x: Positive_int.t ;
              y: Positive_int.t ;
-             z: Positive_int.t } with sexp
+             z: Positive_int.t } [@@deriving sexp]
   type state_type = Null | X | Y | Z
 
   (** Builds an XYZ triplet from a string.
@@ -86,7 +86,7 @@ module Xyz = struct
     let flush state accu number =
       let n = 
         if (number = "") then 1
-        else (Int.of_string number) 
+        else (int_of_string number) 
       in
       match state with
       | X -> { x= Positive_int.(of_int ( (to_int accu.x) +n));
@@ -111,10 +111,9 @@ module Xyz = struct
     | 'Z'::rest | 'z'::rest -> 
         let new_accu = flush state accu number in 
         do_work Z new_accu "" rest
-    | c::rest -> do_work state accu (number^(String.of_char c)) rest
+    | c::rest -> do_work state accu (number^(String_ext.of_char c)) rest
     in
-    String.to_list_rev s 
+    String_ext.to_list s 
-    |> List.rev 
     |> do_work Null 
      { x=Positive_int.of_int 0 ; 
        y=Positive_int.of_int 0 ;

ocaml/Symmetry.mli

@@ -1,4 +1,4 @@
-type t = S | P | D | F | G | H | I | J | K | L with sexp
+type t = S | P | D | F | G | H | I | J | K | L [@@deriving sexp]
 
 (** Creatio from strings *)
 val to_string : t -> string
@@ -16,7 +16,7 @@ module Xyz :
       x : Qptypes.Positive_int.t;
       y : Qptypes.Positive_int.t;
       z : Qptypes.Positive_int.t;
-    } with sexp
+    } [@@deriving sexp]
 
     (** The string format contains the powers of x,y and z in a
         format like "x2z3" *)

ocaml/TaskServer.ml

@@ -1,4 +1,4 @@
-open Core.Std
+open Core
 open Qptypes
 
 
@@ -63,7 +63,7 @@ let bind_socket ~socket_type ~socket ~port =
         ZMQ.Socket.bind socket @@ Printf.sprintf "tcp://*:%d" port;
         loop (-1)
       with
-      | Unix.Unix_error _ -> (Time.pause @@ Time.Span.of_float 1. ; loop (i-1) )
+      | Unix.Unix_error _ -> (Time.pause @@ Time.Span.of_sec 1. ; loop (i-1) )
       | other_exception -> raise other_exception
   in loop 60
 

ocaml/To_md5.ml

@@ -1,5 +1,5 @@
-open Core.Std;;
+open Qptypes
-open Qptypes;;
+open Sexplib
 
 let to_md5 sexp_of_t t =
   sexp_of_t t

ocaml/_tags

@@ -1,3 +1,3 @@
-true: package(core,cryptokit,ZMQ,sexplib.syntax,str)
+true: package(core,cryptokit,ZMQ,str,ppx_sexp_conv,ppx_deriving)
 true: thread
 false: profile

ocaml/qp_basis_clean.ml

@@ -1,4 +1,4 @@
-open Core.Std
+open Core
 
 let filenames =
   let dir_name = Qpackage.root^"/data/basis/"

ocaml/qp_create_ezfio_from_xyz.ml

@@ -1,6 +1,6 @@
 open Qputils
 open Qptypes
-open Core.Std
+open Core
 
 let spec =
   let open Command.Spec in

ocaml/qp_create_guess.ml

@@ -1,6 +1,6 @@
 open Qputils
 open Qptypes
-open Core.Std
+open Core
 
 let run ~multiplicity ezfio_file =
   if (not (Sys.file_exists_exn ezfio_file)) then

ocaml/qp_print.ml

@@ -1,6 +1,6 @@
 open Qputils;;
 open Qptypes;;
-open Core.Std;;
+open Core;;
 
 type input_action =
   | Basis

ocaml/qp_print_basis.ml

@@ -1,4 +1,4 @@
-open Core.Std
+open Core
 open Qptypes
 
 let basis () =

ocaml/qp_run.ml

@@ -1,4 +1,4 @@
-open Core.Std
+open Core
 open Qputils
 
 (* Environment variables :
@@ -132,7 +132,7 @@ let run slave exe ezfio_file =
     Sys.remove qp_run_address_filename;
 
   let duration = Time.diff (Time.now()) time_start 
-  |> Core.Span.to_string in
+  |> Time.Span.to_string in
   Printf.printf "Wall time : %s\n\n" duration;
   if (exit_code <> 0) then
     exit exit_code

ocaml/qp_set_mo_class.ml

@@ -1,6 +1,6 @@
 open Qputils
 open Qptypes
-open Core.Std
+open Core
 
 (*
  * Command-line arguments

ocaml/qptypes_generator.ml

@@ -1,4 +1,10 @@
-open Core.Std;;
+let global_replace x = 
+  x
+  |> Str.global_replace (Str.regexp "Float.to_string") "string_of_float"
+  |> Str.global_replace (Str.regexp "Float.of_string") "float_of_string"
+  |> Str.global_replace (Str.regexp "Int.to_string") "string_of_int"
+  |> Str.global_replace (Str.regexp "Int.of_string") "int_of_string"
+  |> Str.global_replace (Str.regexp "String.\(to\|of\)_string") ""
 
 let input_data = "
 * Positive_float : float  
@@ -118,8 +124,12 @@ let input_data = "
 
 * MD5 : string
   assert ((String.length x) = 32);
-  assert (String.fold x ~init:true ~f:(fun accu x ->
+  assert (
-     accu && (x < 'g')));
+    let a =
+      Array.init (String.length x) (fun i -> x.[i])
+    in
+    Array.fold_left (fun accu x -> accu && (x < 'g')) true a
+    );
 
 * Rst_string : string
 
@@ -127,7 +137,7 @@ let input_data = "
   assert (x <> \"\") ;
 
 "
-;;
+
 
 let input_ezfio = "
 * MO_number : int
@@ -156,18 +166,18 @@ let input_ezfio = "
   More than 10 billion of determinants
 
 "
-;;
+
 
 let untouched = "
 module MO_guess : sig
-  type t with sexp
+  type t [@@deriving sexp]
   val to_string : t -> string
   val of_string : string -> t
 end = struct
   type t = 
   | Huckel
   | HCore
-  with sexp
+  [@@deriving sexp]
 
   let to_string = function
   | Huckel -> \"Huckel\"
@@ -182,7 +192,7 @@ end = struct
 end
 
 module Disk_access : sig
-  type t with sexp
+  type t [@@deriving sexp]
   val to_string : t -> string
   val of_string : string -> t
 end = struct
@@ -190,7 +200,7 @@ end = struct
   | Read
   | Write
   | None
-  with sexp
+  [@@deriving sexp]
 
   let to_string = function
   | Read   -> \"Read\"
@@ -206,62 +216,63 @@ end = struct
 end
 "
 
-;;
+
 
 let template = format_of_string "
 module %s : sig
-  type t with sexp
+  type t [@@deriving sexp]
   val to_%s : t -> %s
   val of_%s : %s %s -> t
   val to_string : t -> string
 end = struct
-  type t = %s with sexp
+  type t = %s [@@deriving sexp]
   let to_%s x = x
   let of_%s %s x = ( %s x )
   let to_string x = %s.to_string x
 end
 
 "
-;;
+
 
 let parse_input input=
-  print_string "open Core.Std;;\nlet warning = print_string;;\n" ;
+  print_string "open Sexplib.Std\nlet warning = print_string\n" ;
   let rec parse result = function
     | [] -> result
     | ( "" , ""   )::tail -> parse result tail
     | ( t  , text )::tail -> 
         let name,typ,params,params_val = 
-          match String.split ~on:':' t with
+          match String_ext.split ~on:':' t with
           | [name;typ] -> (name,typ,"","")
           | name::typ::params::params_val -> (name,typ,params,
-            (String.concat params_val ~sep:":") )
+            (String.concat ":" params_val) )
           | _ -> assert false
         in
-        let typ  = String.strip typ
+        let typ  = String_ext.strip typ
-        and name = String.strip name in
+        and name = String_ext.strip name in
         let typ_cap = String.capitalize typ in
         let newstring = Printf.sprintf template name typ typ typ params_val typ typ 
-          typ typ params ( String.strip text ) typ_cap
+          typ typ params ( String_ext.strip text ) typ_cap
         in
         List.rev (parse (newstring::result) tail )
   in
-     String.split ~on:'*' input
+     String_ext.split ~on:'*' input
-  |> List.map ~f:(String.lsplit2_exn ~on:'\n') 
+  |> List.map (String_ext.lsplit2_exn ~on:'\n') 
   |> parse []
-  |> String.concat 
+  |> String.concat  ""
+  |> global_replace
   |> print_string
-;;
+
 
 
 let ezfio_template = format_of_string "
 module %s : sig
-  type t with sexp
+  type t [@@deriving sexp]
   val to_%s : t -> %s
   val get_max : unit -> %s
   val of_%s : ?min:%s -> ?max:%s -> %s -> t
   val to_string : t -> string
 end = struct
-  type t = %s with sexp
+  type t = %s [@@deriving sexp]
   let to_string x = %s.to_string x
   let get_max () =
     if (Ezfio.has_%s ()) then
@@ -287,24 +298,24 @@ end = struct
     end
 end
 "
-;;
+
 
 let parse_input_ezfio input=
   let parse s = 
     match (
-      String.split s ~on:'\n'
+      String_ext.split s ~on:'\n'
-      |> List.filter ~f:(fun x -> (String.strip x) <> "")
+      |> List.filter (fun x -> (String_ext.strip x) <> "")
     ) with
     | [] -> ""
     | a :: b :: c :: d :: [] ->
       begin
-        let (name,typ) = String.lsplit2_exn ~on:':' a
+        let (name,typ) = String_ext.lsplit2_exn ~on:':' a
         and ezfio_func = b
-        and (min, max) = String.lsplit2_exn ~on:':' c
+        and (min, max) = String_ext.lsplit2_exn ~on:':' c
         and msg = d
         in 
         let (name, typ, ezfio_func, min, max, msg) = 
-        match (List.map [ name ; typ ; ezfio_func ; min ; max ; msg ] ~f:String.strip) with
+        match List.map String_ext.strip [ name ; typ ; ezfio_func ; min ; max ; msg ] with
         | [ name ; typ ; ezfio_func ; min ; max ; msg ] -> (name, typ, ezfio_func, min, max, msg)
         | _ -> assert false
         in
@@ -314,16 +325,17 @@ let parse_input_ezfio input=
       end
     | _ -> failwith "Error in input_ezfio"
   in
-     String.split ~on:'*' input
+     String_ext.split ~on:'*' input
-  |> List.map ~f:parse
+  |> List.map parse
-  |> String.concat 
+  |> String.concat ""
+  |> global_replace
   |> print_string
-;;
+
 
 let () = 
   parse_input input_data ;
   parse_input_ezfio input_ezfio;
-  print_endline untouched;
+  print_endline untouched
 
 
 

ocaml/test_basis.ml

@@ -1,4 +1,4 @@
-open Core.Std;;
+open Core;;
 open Qputils;;
 open Qptypes;;
 

ocaml/test_gto.ml

@@ -1,4 +1,4 @@
-open Core.Std
+open Core
 open Qptypes
 
 let test_prim () = 

ocaml/test_message.ml

@@ -1,4 +1,4 @@
-open Core.Std
+open Core
 
 let () =
   Message.of_string "new_job ao_integrals tcp://127.0.0.1 inproc://ao_ints:12345"

ocaml/test_molecule.ml

@@ -1,4 +1,4 @@
-open Core.Std ;;
+open Core ;;
 open Qptypes ;;
 
 let test_molecule () =

ocaml/test_pseudo.ml

@@ -1,4 +1,4 @@
-open Core.Std
+open Core
 open Qputils
 open Qptypes
 

ocaml/test_queuing_system.ml

@@ -1,4 +1,4 @@
-open Core.Std
+open Core
 
 let () =
 

ocaml/test_symmetry.ml

@@ -1,15 +1,13 @@
-open Core.Std
 open Qputils
 open Qptypes
 open Symmetry
 
 let () =
   "SPDFGHIJKL"
-  |> String.to_list_rev
+  |> String_ext.to_list
-  |> List.rev
+  |> List.map of_char
-  |> List.map ~f:of_char
+  |> List.map Xyz.of_symmetry
-  |> List.map ~f:Xyz.of_symmetry
+  |> List.iter (fun x -> List.iter (fun y -> Xyz.to_string y |> print_endline) x ;
-  |> List.iter ~f:(fun x -> List.iter x ~f:(fun y -> Xyz.to_string y |> print_endline) ;
      print_newline ();)
 
 

ocaml/test_task_server.ml

@@ -1,5 +1,3 @@
-open Core
-
 let () =
   TaskServer.run 12345
 

scripts/ezfio_interface/ezfio_generate_ocaml.py

@@ -170,7 +170,7 @@ class EZFIO_ocaml(object):
             else:
                 l_template += ["    {0:<30} : {1};".format(p, t.ocaml)]
 
-        l_template += ["  } with sexp",
+        l_template += ["  } [@@deriving sexp]",
                        ";;"]
 
         # ~#~#~#~#~#~ #

scripts/ezfio_interface/qp_edit_template

@@ -4,7 +4,7 @@
 
 open Qputils
 open Qptypes
-open Core.Std
+open Core
 
 (** Interactive editing of the input.