Added lots of mli files for better error messages

ocaml/Atom.ml

@@ -23,7 +23,7 @@ let of_string u s =
   | [ name; x; y; z ] ->
     let e = Element.of_string name in
     { element = e ;
-      charge  = Charge.of_int (Element.to_charge e);
+      charge  = Element.to_charge e;
       coord   = Point3d.of_string u (String.concat [x; y; z] ~sep:" ")
     }
   | _ -> raise (AtomError s)

ocaml/Atom.mli

@@ -0,0 +1,9 @@
+exception AtomError of string
+
+type t = { element : Element.t; charge : Charge.t; coord : Point3d.t; } 
+
+val t_of_sexp : Sexplib.Sexp.t -> t
+val sexp_of_t : t -> Sexplib.Sexp.t
+
+val of_string : Units.units -> string -> t
+val to_string : Units.units -> t -> string

ocaml/Basis.ml

@@ -56,10 +56,8 @@ let to_string b =
   do_work [new_nucleus 1] 1 b
   |> String.concat ~sep:"\n"
 ;;
-(*
+
-  List.map ~f:(fun (g,n) ->
+include To_md5;;
-     let n = Nucl_number.to_int n in
+let to_md5 = to_md5 sexp_of_t
-     (Int.to_string n)^":"^(Gto.to_string g)) b
+;;
-;;
-*)
 

ocaml/Basis.mli

@@ -15,3 +15,6 @@ val read_element :
 
 (** Convert the basis to a string *)
 val to_string :  (Gto.t * Nucl_number.t) list -> string
+
+(** Convert the basis to an MD5 hash *)
+val to_md5 :  (Gto.t * Nucl_number.t) list -> MD5.t

ocaml/Bit.ml

@@ -8,9 +8,9 @@ Zero | One
 
 *)
 
-type bit      = 
+type t      = 
-   | One 
+| One 
-   | Zero 
+| Zero 
 with sexp
 
 let to_string = function

ocaml/Bit.mli

@@ -0,0 +1,10 @@
+type t = One | Zero with sexp
+
+(** String conversions for printing *)
+val to_string : t -> string
+
+(** Logical operations *)
+val and_operator : t -> t -> t
+val or_operator  : t -> t -> t
+val xor_operator : t -> t -> t
+val not_operator : t -> t

ocaml/Bitlist.ml

@@ -7,7 +7,7 @@ Type for bits strings
 list of Bits
 *)
 
-type bit_list = Bit.bit list
+type t = Bit.t list
 
 (* String representation *)
 let to_string b = 

ocaml/Bitlist.mli

@@ -0,0 +1,32 @@
+type t = Bit.t list
+
+(** The zero bit list *)
+val zero : Qptypes.N_int_number.t -> t
+
+(** Convert to a string for printing *)
+val to_string : t -> string
+
+(** int64 conversion functions *)
+
+val of_int64 : int64 -> t
+val to_int64 : t -> int64
+
+val of_int64_list : int64 list -> t
+val to_int64_list : t -> int64 list
+
+(** Get the number of needed int64 elements to encode the bit list *)
+val n_int_of_mo_tot_num : int -> Qptypes.N_int_number.t
+
+(** Conversion to MO numbers *)
+val to_mo_number_list : t -> Qptypes.MO_number.t list
+val of_mo_number_list :
+  Qptypes.N_int_number.t -> Qptypes.MO_number.t list -> t
+
+(** Logical operators *)
+val and_operator : t -> t -> t
+val xor_operator : t -> t -> t
+val or_operator  : t -> t -> t
+val not_operator : t -> t
+
+(** Count the number of bits set to one *)
+val popcnt : t -> int

ocaml/Charge.mli

@@ -1,8 +1,13 @@
 type t = float with sexp
 
+(** Float conversion functions *)
 val to_float : t -> float
-val to_int   : t -> int
-val to_string: t -> string 
 val of_float : float -> t
+
+(** Int conversion functions *)
+val to_int   : t -> int
 val of_int   : int -> t
+
+(** String conversion functions *)
+val to_string: t -> string 
 val of_string: string -> t

ocaml/Element.ml

@@ -132,47 +132,49 @@ let to_long_string = function
 | Kr  -> "Krypton"
 ;;
 
-let to_charge = function
+let to_charge c = 
-| X   -> 0
+  let result = match c with
-| H   -> 1
+  | X   -> 0
-| He  -> 2
+  | H   -> 1
-| Li  -> 3
+  | He  -> 2
-| Be  -> 4
+  | Li  -> 3
-| B   -> 5
+  | Be  -> 4
-| C   -> 6
+  | B   -> 5
-| N   -> 7
+  | C   -> 6
-| O   -> 8
+  | N   -> 7
-| F   -> 9
+  | O   -> 8
-| Ne  -> 10
+  | F   -> 9
-| Na  -> 11
+  | Ne  -> 10
-| Mg  -> 12
+  | Na  -> 11
-| Al  -> 13
+  | Mg  -> 12
-| Si  -> 14
+  | Al  -> 13
-| P   -> 15
+  | Si  -> 14
-| S   -> 16
+  | P   -> 15
-| Cl  -> 17
+  | S   -> 16
-| Ar  -> 18
+  | Cl  -> 17
-| K   -> 19
+  | Ar  -> 18
-| Ca  -> 20
+  | K   -> 19
-| Sc  -> 21
+  | Ca  -> 20
-| Ti  -> 22
+  | Sc  -> 21
-| V   -> 23
+  | Ti  -> 22
-| Cr  -> 24
+  | V   -> 23
-| Mn  -> 25
+  | Cr  -> 24
-| Fe  -> 26
+  | Mn  -> 25
-| Co  -> 27
+  | Fe  -> 26
-| Ni  -> 28
+  | Co  -> 27
-| Cu  -> 29
+  | Ni  -> 28
-| Zn  -> 30
+  | Cu  -> 29
-| Ga  -> 31
+  | Zn  -> 30
-| Ge  -> 32
+  | Ga  -> 31
-| As  -> 33
+  | Ge  -> 32
-| Se  -> 34
+  | As  -> 33
-| Br  -> 35
+  | Se  -> 34
-| Kr  -> 36
+  | Br  -> 35
+  | Kr  -> 36
+  in Charge.of_int result
 ;;
 
-let of_charge = function
+let of_charge c = match (Charge.to_int c) with
 |  0   ->  X   
 |  1   ->  H   
 |  2   ->  He  

ocaml/Element.mli

@@ -0,0 +1,18 @@
+exception ElementError of string
+
+type t =
+|X
+|H                                                 |He
+|Li|Be                              |B |C |N |O |F |Ne
+|Na|Mg                              |Al|Si|P |S |Cl|Ar
+|K |Ca|Sc|Ti|V |Cr|Mn|Fe|Co|Ni|Cu|Zn|Ga|Ge|As|Se|Br|Kr
+with sexp
+
+(** String conversion functions *)
+val of_string : string -> t
+val to_string : t -> string
+val to_long_string : t -> string
+
+(** get the positive charge *)
+val to_charge : t -> Charge.t
+val of_charge : Charge.t -> t

ocaml/Excitation.ml

@@ -1,21 +1,13 @@
 open Core.Std;;
 open Qptypes;;
 
-module Hole : sig
+module Hole = struct
-    type t with sexp
-    val to_mo_class  : t -> MO_class.t
-    val of_mo_class  : MO_class.t -> t
-end = struct
     type t = MO_class.t with sexp
     let of_mo_class x = x
     let to_mo_class x = x
 end
 
-module Particle : sig
+module Particle = struct
-    type t with sexp
-    val to_mo_class  : t -> MO_class.t
-    val of_mo_class  : MO_class.t -> t
-end = struct
     type t = MO_class.t with sexp
     let of_mo_class x = x
     let to_mo_class x = x
@@ -26,9 +18,6 @@ type t =
 | Double of Hole.t*Particle.t*Hole.t*Particle.t
 with sexp;;
 
-let failwith s = raise (Failure s)
-;;
-
 let create_single ~hole ~particle =
   MO_class.(
   match (hole,particle) with

ocaml/Excitation.mli

@@ -0,0 +1,30 @@
+module Hole :
+  sig
+    type t
+    val to_mo_class : t -> MO_class.t
+    val of_mo_class : MO_class.t -> t
+    val t_of_sexp : Sexplib.Sexp.t -> t
+    val sexp_of_t : t -> Sexplib.Sexp.t
+  end
+module Particle :
+  sig
+    type t
+    val to_mo_class : t -> MO_class.t
+    val of_mo_class : MO_class.t -> t
+    val t_of_sexp : Sexplib.Sexp.t -> t
+    val sexp_of_t : t -> Sexplib.Sexp.t
+  end
+
+type t =
+  | Single of Hole.t * Particle.t
+  | Double of Hole.t * Particle.t * Hole.t * Particle.t
+with sexp
+
+val create_single : hole:MO_class.t -> particle:MO_class.t -> t
+
+val double_of_singles : t -> t -> t
+
+val create_double : hole1:MO_class.t -> particle1:MO_class.t ->
+                    hole2:MO_class.t -> particle2:MO_class.t -> t
+
+val to_string : t -> string

ocaml/Gto.mli

@@ -0,0 +1,16 @@
+exception GTO_Read_Failure of string
+exception End_Of_Basis
+type t =
+  { sym : Symmetry.t ;
+    lc  : (Primitive.t * Qptypes.AO_coef.t) list;
+  } with sexp
+
+(** Create from a list of Primitive.t * Qptypes.AO_coef.t *)
+val of_prim_coef_list :
+  (Primitive.t * Qptypes.AO_coef.t) list -> t
+
+(** Read from a file *)
+val read_one : in_channel -> t
+
+(** Convert to string for printing *)
+val to_string : t -> string

ocaml/Input_ao_basis.ml

@@ -16,6 +16,7 @@ module Ao_basis : sig
   ;;
   val read : unit -> t
   val to_string : t -> string
+  val to_md5 : t -> MD5.t
   val debug : t -> string
 end = struct
   type t = 
@@ -103,8 +104,8 @@ end = struct
       ao_expo         = read_ao_expo () ;
     }
   ;;
-
+    
-  let to_string b =
+  let to_long_basis b =
     let ao_num = AO_number.to_int b.ao_num in
     let gto_array = Array.init (AO_number.to_int b.ao_num)
       ~f:(fun i ->
@@ -121,27 +122,35 @@ end = struct
         Gto.of_prim_coef_list prims
       )
     in
-    let long_basis = 
+    let rec do_work accu sym gto nucl =
-      let rec do_work accu sym gto nucl =
+      match (sym, gto, nucl) with
-        match (sym, gto, nucl) with
+        | (s::srest, g::grest, n::nrest) -> 
-          | (s::srest, g::grest, n::nrest) -> 
+          do_work ((s,g,n)::accu) srest grest nrest
-            do_work ((s,g,n)::accu) srest grest nrest
+        | ([],[],[]) -> List.rev accu
-          | ([],[],[]) -> List.rev accu
+        | _ -> assert false
-          | _ -> assert false
-      in
-      do_work [] 
-        (Array.to_list b.ao_power)
-        (Array.to_list gto_array)
-        (Array.to_list b.ao_nucl)
-    in
-    let short_basis =
-      Long_basis.to_basis long_basis
     in
+    do_work [] 
+      (Array.to_list b.ao_power)
+      (Array.to_list gto_array)
+      (Array.to_list b.ao_nucl)
+  ;;
+
+  let to_basis b =
+    to_long_basis b
+    |> Long_basis.to_basis
+  ;;
+      
+  let to_string b =
+    let short_basis = to_basis b in
     Printf.sprintf "Basis name : %s\n\n%s" b.ao_basis
     (Basis.to_string short_basis)
   ;;
+
+  let to_md5 b =
+    let short_basis = to_basis b in
+    Basis.to_md5 short_basis
+  ;;
     
-      
   let debug b =
     Printf.sprintf "
 ao_basis        = %s
@@ -152,6 +161,7 @@ ao_nucl         = %s
 ao_power        = %s
 ao_coef         = %s
 ao_expo         = %s
+md5             = %s
 "
     b.ao_basis
     (AO_number.to_string b.ao_num)
@@ -166,6 +176,7 @@ ao_expo         = %s
       |> String.concat ~sep:", ")
     (b.ao_expo  |> Array.to_list |> List.map ~f:AO_expo.to_string
       |> String.concat ~sep:", ")
+    (to_md5 b |> MD5.to_string )
 
   ;;
 end

ocaml/Long_basis.ml

@@ -47,3 +47,8 @@ let to_string b =
   |> String.concat ~sep:",\n"
   in "("^middle^")"
 ;;
+
+include To_md5;;
+let to_md5 = to_md5 sexp_of_t
+;;
+

ocaml/MO_class.mli

@@ -0,0 +1,21 @@
+type t =
+  | Core     of Qptypes.MO_number.t list
+  | Inactive of Qptypes.MO_number.t list
+  | Active   of Qptypes.MO_number.t list
+  | Virtual  of Qptypes.MO_number.t list
+  | Deleted  of Qptypes.MO_number.t list
+with sexp
+
+
+(** Create different excitation classes *)
+val create_core     : string -> t
+val create_inactive : string -> t
+val create_active   : string -> t
+val create_virtual  : string -> t
+val create_deleted  : string -> t
+
+(** Convert to a Bitlist.t *)
+val to_bitlist      : Qptypes.N_int_number.t -> t -> Bitlist.t
+
+(** Convert to string for printing *)
+val to_string : t -> string

ocaml/Molecule.ml

@@ -78,7 +78,7 @@ let to_string m =
 ;;
 
 let of_xyz_string
-    ?(charge=0) ?(multiplicity=(Multiplicity.of_int 1))
+    ?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1))
     ?(units=Units.Angstrom)
     s =
   let l = String.split s ~on:'\n'
@@ -90,7 +90,7 @@ let of_xyz_string
         elec_alpha=(Elec_alpha_number.of_int 1) ;
         elec_beta=(Elec_beta_number.of_int 0) } 
       |> Charge.to_int 
-      ) + 1 - charge 
+      ) + 1 - (Charge.to_int charge)
       |> Elec_number.of_int 
   in
   let (na,nb) = Multiplicity.to_alpha_beta ne multiplicity in
@@ -112,10 +112,16 @@ let of_xyz_string
 
 
 let of_xyz_file
-    ?(charge=0) ?(multiplicity=(Multiplicity.of_int 1))
+    ?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1))
+    ?(units=Units.Angstrom)
     filename =
   let (_,buffer) = In_channel.read_all filename 
   |> String.lsplit2_exn ~on:'\n' in
   let (_,buffer) = String.lsplit2_exn buffer ~on:'\n' in
-  of_xyz_string ~charge:charge ~multiplicity:multiplicity buffer
+  of_xyz_string ~charge:charge ~multiplicity:multiplicity 
+    ~units:units buffer
+;;
+
+include To_md5;;
+let to_md5 = to_md5 sexp_of_t
 ;;

ocaml/Molecule.mli

@@ -0,0 +1,38 @@
+exception MultiplicityError of string
+
+type t = {
+  nuclei     : Atom.t list;
+  elec_alpha : Qptypes.Elec_alpha_number.t;
+  elec_beta  : Qptypes.Elec_beta_number.t;
+} with sexp
+
+(** Returns the charge of the molecule *)
+val get_charge       : t -> Charge.t
+
+(** Returns the multiplicity of the molecule *)
+val get_multiplicity : t -> Multiplicity.t
+
+(** Returns the number of nuclei *)
+val get_nucl_num : t -> Qptypes.Nucl_number.t
+
+(** The name of the molecule *)
+val name : t -> string
+
+(** Conversion for printing *)
+val to_string : t -> string
+
+
+(** Creates a molecule from an xyz file *)
+val of_xyz_file :
+  ?charge:Charge.t -> 
+  ?multiplicity:Multiplicity.t ->
+  ?units:Units.units -> string -> t
+
+(** Creates a molecule from an xyz file in a string *)
+val of_xyz_string :
+  ?charge:Charge.t ->
+  ?multiplicity:Multiplicity.t ->
+  ?units:Units.units -> string -> t
+
+(** Computes the MD5 hash *)
+val to_md5 : t -> Qptypes.MD5.t

ocaml/Multiplicity.mli

@@ -0,0 +1,19 @@
+type t = Qptypes.Strictly_positive_int.t with sexp
+
+(** Conversion from int *)
+val of_int : int -> t
+val to_int : t -> int
+
+(** Computation from the number of alpha and beta electrons *)
+val of_alpha_beta :
+  Qptypes.Elec_alpha_number.t ->
+  Qptypes.Elec_beta_number.t -> t
+
+(** Generation of the number of alpha and beta electrons *)
+val to_alpha_beta :
+  Qptypes.Elec_number.t ->  t ->
+  Qptypes.Elec_alpha_number.t * Qptypes.Elec_beta_number.t
+
+(** Conversion to string for printing *)
+val to_string : t-> string
+

ocaml/Point3d.mli

@@ -0,0 +1,17 @@
+type t =
+{ x : float;
+  y : float;
+  z : float;
+} with sexp
+
+(** Create from an xyz string *)
+val of_string : Units.units -> string -> t
+
+(** Convert to a string for printing *)
+val to_string : Units.units -> t -> string
+
+(** Computes the squared distance between 2 points *)
+val distance2 : t -> t -> Qptypes.Positive_float.t
+
+(** Computes the distance between 2 points *)
+val distance : t -> t -> float

ocaml/_tags

@@ -1,3 +1,3 @@
-true: package(core,sexplib.syntax)
+true: package(core,sexplib.syntax,cryptokit)
 true: thread
 

ocaml/qp_create_ezfio_from_xyz.ml

@@ -26,8 +26,8 @@ let run ?o b c m xyz_file =
 
   (* Read molecule *)
   let molecule =
-    Molecule.of_xyz_file xyz_file ~charge:c
+    (Molecule.of_xyz_file xyz_file ~charge:(Charge.of_int c)
-      ~multiplicity:(Multiplicity.of_int m)
+      ~multiplicity:(Multiplicity.of_int m) )
   in
 
   (* Build EZFIO File name *)

ocaml/qp_print.ml

@@ -59,6 +59,7 @@ let run_i ~action ezfio_filename =
     and n_beta  = input.Input.Electrons.elec_beta_num 
       |> Elec_beta_number.to_int
     in Array.fold ~init:(-n_alpha-n_beta) ~f:(fun x y -> x+y) nucl_charge
+    |> Charge.of_int
   in
 
   let compute_multiplicity () =
@@ -80,7 +81,7 @@ let run_i ~action ezfio_filename =
        Ezfio.((get_nuclei_nucl_label ()).data) |> Ezfio.flattened_ezfio_data
       else
         Array.map ~f:(fun x-> x
-          |> Float.to_int
+          |> Charge.of_float
           |> Element.of_charge 
           |> Element.to_string ) nucl_charge
     in

ocaml/qptypes_generator.ml

@@ -121,6 +121,8 @@ let input_data = "
 * Elec_number : int
   assert (x > 0) ;
 
+* MD5 : string
+  assert ((String.length x) = 32);
 "
 ;;
 

ocaml/test_basis.ml

@@ -35,6 +35,7 @@ let test_module () =
     ;
     print_string "Short basis\n===========\n";
     print_endline (Basis.to_string basis);
+    print_endline ("MD5: "^(Basis.to_md5 basis |> MD5.to_string));
 ;;
 
 test_module ();

ocaml/test_elements.ml

@@ -1,6 +1,6 @@
 let test_module () = 
   let atom = Element.of_string "Cobalt" in
-  Printf.printf "%s %d\n" (Element.to_string atom) (Element.to_charge atom)
+  Printf.printf "%s %d\n" (Element.to_string atom) (Charge.to_int (Element.to_charge atom))
 ;;
 
 test_module ();;

ocaml/test_input.ml

@@ -95,5 +95,5 @@ test_hf ();;
 test_mo ();;
 test_nucl ();
 *)
-test_bielec_intergals ();;
+test_ao ();;
 

ocaml/test_molecule.ml

@@ -21,7 +21,7 @@ H           1.0       0.54386314      0.00000000     -0.92559535
   print_string "---\n";
   let m = Molecule.of_xyz_string xyz 
   in print_endline (Molecule.name m) ;
-  let m = Molecule.of_xyz_string xyz ~charge:1 ~multiplicity:(Multiplicity.of_int 2)
+  let m = Molecule.of_xyz_string xyz ~charge:(Charge.of_int 1) ~multiplicity:(Multiplicity.of_int 2)
   in print_endline (Molecule.name m) ;
 
   let xyz =
@@ -31,7 +31,7 @@ O        1.65102147      0.00000000     -2.35602344
 H        0.54386314      0.00000000     -0.92559535
 "
   in
-  let m = Molecule.of_xyz_string xyz ~charge:(-2) 
+  let m = Molecule.of_xyz_string xyz ~charge:(Charge.of_int (-2))
   in print_endline (Molecule.name m) ;
   print_endline (Molecule.to_string m);
   print_string "---------\n";

scripts/install_ocaml.sh

@@ -4,6 +4,7 @@
 # Thu Oct 23 21:58:40 CEST 2014
 
 QPACKAGE_ROOT=${PWD}
+PACKAGES="core cryptokit"
 
 make -C ocaml Qptypes.ml &> /dev/null
 if [[ $? -ne 0 ]]
@@ -13,7 +14,7 @@ then
   cat < ocamlbrew-install.sh | env OCAMLBREW_FLAGS="-r" bash | tee ocamlbrew_install.log
   grep "source " ocamlbrew_install.log | grep "etc/ocamlbrew.bashrc"  >> quantum_package.rc
   source quantum_package.rc
-  echo Y | opam install core 
+  echo Y | opam install ${PACKAGES}
 fi
 make -C ocaml Qptypes.ml