Modified for ocaml 4.04

ocaml/Address.ml

@@ -1,4 +1,4 @@
-open Core.Std
+open Core
 
 module Tcp : sig
   type t 

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 Core
 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 =

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 Core;;
 open Qptypes;;
 
-type t = int64 array with sexp
+type t = int64 array [@@deriving sexp]
 
 let to_int64_array (x:t) = (x:int64 array)
 

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

@@ -1,4 +1,4 @@
-open Core.Std
+open Core
 open Qptypes
 
 exception GTO_Read_Failure of string
@@ -11,7 +11,7 @@ type fmt =
 type t =
 { sym  : Symmetry.t ;
   lc   : ((GaussianPrimitive.t * AO_coef.t) list)
-} with sexp
+} [@@deriving sexp]
 
 
 let of_prim_coef_list pc =

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 Core;;
 open Qptypes;;
 
-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

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 Core
 
 (*
 let rec transpose = function

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 Core;;
 
 (* A range is a string of the type:
  * 
@@ -12,7 +12,7 @@ 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
@@ -71,8 +71,8 @@ let to_string l =
 let test_module () =
   let s = "[72-107,36-53,126-131]" in
   let l = of_string s in
-  print_string s ; print_newline () ;
+  print_string s ; Out_channel.newline stdout ;
-  List.iter ~f:(fun x -> Printf.printf "%d, " x) l ; print_newline () ;
+  List.iter ~f:(fun x -> Printf.printf "%d, " x) l ; Out_channel.newline stdout ;
-  to_string l |> print_string ;  print_newline () ;
+  to_string l |> print_string ;  Out_channel.newline stdout
 ;;
 

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 +1,112 @@
+include String
+
+(** Split a string on a given character *)
+let split ?(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 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 
+  
+

ocaml/Symmetry.ml

@@ -1,7 +1,7 @@
 open Qptypes
-open Core.Std
+open Core
 
-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.

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

@@ -1,4 +1,4 @@
-open Core.Std;;
+open Core;;
 open Qptypes;;
 
 let to_md5 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_add_aux_basis.ml

@@ -1,206 +0,0 @@
-open Qputils
-open Qptypes
-open Core.Std
-
-let spec =
-  let open Command.Spec in
-  empty 
-  +> flag "o" (optional string)
-     ~doc:"file Name of the new EZFIO file. Default is suffixed by .RI"
-  +> flag "b" (required string)
-     ~doc:"string Name of basis set."
-  +> anon (" EZFIO file)" %: file )
-
-type element =
-| Element of Element.t
-| Int_elem of (Nucl_number.t * Element.t)
-
-    
-(** Returns the list of available basis sets *)
-let list_basis () =
-  let basis_list = 
-    Qpackage.root ^ "/install/emsl/EMSL_api.py list_basis | grep \"-RI\" " 
-    |> Unix.open_process_in 
-    |> In_channel.input_lines
-    |> List.map ~f:(fun x -> 
-       match String.split x ~on:'\'' with
-       | [] -> ""
-       | a :: [] 
-       | _ :: a :: _ -> String.strip a
-      )
-  in 
-  List.sort basis_list ~cmp:String.ascending
-  |> String.concat ~sep:"\n" 
-
-
-(** Run the program *)
-let run ?o b ezfio_file =
-
-  let new_filename = 
-    match o with
-    | Some filename -> filename
-    | None -> ezfio_file ^ ".RI"
-  in
-  let () =
-    match Sys.is_directory new_filename with
-    | `Yes ->  failwith "Output directory exists"
-    | _ -> ()
-  in
-  let status =
-    Printf.sprintf "cp -r %s %s" ezfio_file new_filename
-    |> Unix.system 
-  in
-  ignore status;
-
-  Ezfio.set_file new_filename;
-
- (**********
-  Basis set
-  **********)
-
-  let basis_table =
-     Hashtbl.Poly.create ()
-  in
-
-  (* Open basis set channels *)
-  let basis_channel element =
-    let key =
-      match element with
-      | Element e -> Element.to_string e
-      | Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i)  (Element.to_string e)
-    in
-    match Hashtbl.find basis_table key with
-    | Some in_channel -> 
-        in_channel
-    | None -> raise Not_found
-  in
-  
-  let temp_filename =
-    Filename.temp_file "qp_create_" ".basis"
-  in
-  let () = 
-    Sys.remove temp_filename
-  in
-
-  let fetch_channel basis =
-    let command =
-      Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename 
-          ^ "." ^ basis ^ "\" \"" ^ basis ^"\""
-    in
-    let long_basis = 
-      Qpackage.root ^ "/data/basis/" ^ basis
-    in
-    match 
-      Sys.is_file basis,
-      Sys.is_file long_basis
-    with
-    | `Yes, _    -> In_channel.create basis
-    | `No , `Yes -> In_channel.create long_basis
-    | _ -> 
-      begin
-        let filename = 
-          Unix.open_process_in command
-          |> In_channel.input_all
-          |> String.strip
-        in
-        let new_channel =
-          In_channel.create filename
-        in
-        Unix.unlink filename;
-        new_channel
-      end
-  in
-
-  let rec build_basis = function
-  | [] -> ()
-  | elem_and_basis_name :: rest -> 
-    begin
-      match (String.lsplit2 ~on:':' elem_and_basis_name) with
-      | None -> (* Principal basis *)
-        begin
-          let basis = 
-            elem_and_basis_name 
-          in
-          let new_channel =
-            fetch_channel basis
-          in
-          List.iter nuclei ~f:(fun elem->
-            let key = 
-              Element.to_string elem.Atom.element
-            in
-            match Hashtbl.add basis_table ~key:key ~data:new_channel with
-            | `Ok -> ()
-            | `Duplicate -> ()
-          )
-        end
-      | Some (key, basis) -> (*Aux basis *)
-        begin
-          let elem  = 
-            try
-              Element (Element.of_string key)
-            with Element.ElementError _ ->
-              let result = 
-                match (String.split ~on:',' key) with
-                | i :: k :: [] -> (Nucl_number.of_int @@ int_of_string i, Element.of_string k)
-                | _ -> failwith "Expected format is int,Element:basis"
-              in Int_elem result
-          and basis =
-            String.lowercase basis
-          in
-          let key = 
-             match elem with
-             | Element e -> Element.to_string e
-             | Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i) (Element.to_string e)
-          in
-          let new_channel =
-            fetch_channel basis
-          in
-          begin
-            match Hashtbl.add basis_table ~key:key ~data:new_channel with
-            | `Ok -> ()
-            | `Duplicate ->
-              let e = 
-                match elem with
-                | Element e -> e
-                | Int_elem (_,e) -> e
-              in
-              failwith ("Duplicate definition of basis for "^(Element.to_long_string e))
-          end
-       end
-    end;
-    build_basis rest
-  in
-  String.split ~on:'|' b
-  |> List.rev_map ~f:String.strip 
-  |> build_basis
-  in
-
-  let basis =
-    Input.AO_basis.read ()
-  in
-  ()
-
-
-let command = 
-    Command.basic 
-    ~summary: "Quantum Package command"
-    ~readme:(fun () -> "
-
-=== Available basis sets ===
-
-" ^ (list_basis ()) ^ "
-
-============================
-
-Extents the basis set to add an auxiliary basis set.
-" )
-    spec
-    (fun o b ezfio_file () -> run ?o b ezfio_file )
-
-
-let () =
-    Command.run command
-
-
-
-

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 +1,4 @@
-open Core.Std;;
+open Core;;
 
 let input_data = "
 * Positive_float : float  
@@ -160,14 +160,14 @@ let input_ezfio = "
 
 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 +182,7 @@ 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 +190,7 @@ end = struct
   | Read
   | Write
   | None
-  with sexp
+  [@@deriving sexp]
 
   let to_string = function
   | Read   -> \"Read\"
@@ -210,12 +210,12 @@ 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
@@ -225,7 +225,7 @@ end
 ;;
 
 let parse_input input=
-  print_string "open Core.Std;;\nlet warning = print_string;;\n" ;
+  print_string "open Core;;\nlet warning = print_string;;\n" ;
   let rec parse result = function
     | [] -> result
     | ( "" , ""   )::tail -> parse result tail
@@ -255,13 +255,13 @@ let parse_input input=
 
 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

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

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