Added s-expressions (sexplib)

ocaml/Atom.ml

@@ -6,7 +6,7 @@ type t =
 { element : Element.t ;
   charge  : Charge.t ;
   coord   : Point3d.t ;
-}
+} with sexp
 
 (** Read xyz coordinates of the atom with unit u *)
 let of_string u s =

ocaml/Basis.ml

@@ -1,7 +1,7 @@
 open Core.Std;;
 open Qptypes;;
 
-type t = (Gto.t * Nucl_number.t) list;;
+type t = (Gto.t * Nucl_number.t) list with sexp;;
 
 (** Read all the basis functions of an element *)
 let read in_channel at_number =

ocaml/Bit.ml

@@ -1,3 +1,4 @@
+open Core.Std;;
 
 (*
 Type for bits 
@@ -10,6 +11,7 @@ Zero | One
 type bit      = 
    | One 
    | Zero 
+with sexp
 
 let to_string = function
   | Zero -> "0"

ocaml/Charge.ml

@@ -1,11 +1,12 @@
 open Core.Std;;
 
-type t = float
+type t = float with sexp;;
 
 let of_float x = x
 let of_int   i = Float.of_int i
 let of_string s = Float.of_string s
 
+
 let to_float x = x
 let to_int   x = Float.to_int x
 let to_string x = 

ocaml/Charge.mli

@@ -1,4 +1,4 @@
-type t = float
+type t = float with sexp
 
 val to_float : t -> float
 val to_int   : t -> int

ocaml/Element.ml

@@ -8,7 +8,7 @@ type t =
 |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;;
 
 let of_string x = 
   match (String.capitalize (String.lowercase x)) with

ocaml/Excitation.ml

@@ -2,21 +2,21 @@ open Core.Std;;
 open Qptypes;;
 
 module Hole : sig
-    type t
+    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
+    type t = MO_class.t with sexp
     let of_mo_class x = x
     let to_mo_class x = x
 end
 
 module Particle : sig
-    type t
+    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
+    type t = MO_class.t with sexp
     let of_mo_class x = x
     let to_mo_class x = x
 end
@@ -24,7 +24,7 @@ end
 type t =
 | Single of Hole.t*Particle.t
 | Double of Hole.t*Particle.t*Hole.t*Particle.t
-;;
+with sexp;;
 
 let failwith s = raise (Failure s)
 ;;

ocaml/Gto.ml

@@ -7,7 +7,7 @@ exception End_Of_Basis
 type t =
 { sym  : Symmetry.t ;
   lc   : ((Primitive.t * AO_coef.t) list)
-}
+} with sexp
 ;;
 
 let of_prim_coef_list pc =
@@ -62,6 +62,7 @@ let read_one in_channel =
       | _ -> raise (GTO_Read_Failure line_buffer)
     end
   in read_lines [] n
+  |> List.rev
   |> of_prim_coef_list
 ;;
 
@@ -70,6 +71,6 @@ let read_one in_channel =
 let to_string { sym = sym ; lc = lc } =
   let f (p,c) = Printf.sprintf "( %s, %f )" (Primitive.to_string p) (AO_coef.to_float c)
   in
-  Printf.sprintf "[ %s : %s ]" (Symmetry.to_string sym)
+  Printf.sprintf "( %s, %s )" (Symmetry.to_string sym)
     (String.concat (List.map ~f:f lc) ~sep:", ")
 ;;

ocaml/Input_ao_basis.ml

@@ -12,10 +12,11 @@ module Ao_basis : sig
       ao_power        : Symmetry.Xyz.t array;
       ao_coef         : AO_coef.t array;
       ao_expo         : AO_expo.t array;
-    }
+    } with sexp
   ;;
   val read : unit -> t
   val to_string : t -> string
+  val debug : t -> string
 end = struct
   type t = 
     { ao_basis        : string ;
@@ -26,7 +27,7 @@ end = struct
       ao_power        : Symmetry.Xyz.t array;
       ao_coef         : AO_coef.t array;
       ao_expo         : AO_expo.t array;
-    }
+    } with sexp
   ;;
 
   let get_default = Qpackage.get_ezfio_default "ao_basis";;
@@ -104,16 +105,56 @@ end = struct
   ;;
 
   let to_string 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 ->
+        let s = Symmetry.Xyz.to_symmetry b.ao_power.(i) in
+        let ao_prim_num = AO_prim_number.to_int b.ao_prim_num.(i) in
+        let prims = List.init ao_prim_num ~f:(fun j ->
+          let prim = { Primitive.sym  = s ;
+                       Primitive.expo = b.ao_expo.(ao_num*j+i)
+                     }
+          in
+          let coef = b.ao_coef.(ao_num*j+i) in
+          (prim,coef)
+        ) in
+        Gto.of_prim_coef_list prims
+      )
+    in
+    let long_basis = 
+      let rec do_work accu sym gto nucl =
+        match (sym, gto, nucl) with
+          | (s::srest, g::grest, n::nrest) -> 
+            do_work ((s,g,n)::accu) srest grest nrest
+          | ([],[],[]) -> List.rev accu
+          | _ -> assert false
+      in
+      do_work [] 
+        (Array.to_list b.ao_power)
+        (Array.to_list gto_array)
+        (Array.to_list b.ao_nucl)
+    in
     Printf.sprintf "
-ao_basis        = \"%s\"
+# AO Basis
-ao_num          = %s
+# ========
-ao_prim_num     = %s
+%s" (Long_basis.to_string long_basis)
-ao_prim_num_max = %s
+  ;;
-ao_nucl         = %s
+    
-ao_power        = %s
+      
-ao_coef         = %s
+  let debug b =
-ao_expo         = %s
+    Printf.sprintf "
-"
+# AO Basis
+# ========
+#
+# ao_basis        = %s
+# ao_num          = %s
+# ao_prim_num     = %s
+# ao_prim_num_max = %s
+# ao_nucl         = %s
+# ao_power        = %s
+# ao_coef         = %s
+# ao_expo         = %s
+#"
     b.ao_basis
     (AO_number.to_string b.ao_num)
     (b.ao_prim_num |> Array.to_list |> List.map
@@ -128,6 +169,6 @@ ao_expo         = %s
     (b.ao_expo  |> Array.to_list |> List.map ~f:AO_expo.to_string
       |> String.concat ~sep:", ")
 
+  ;;
 end
 
-

ocaml/Input_bi_integrals.ml

@@ -11,7 +11,7 @@ module Bielec_integrals : sig
       threshold_ao       : Threshold.t;
       threshold_mo       : Threshold.t;
       direct             : bool;
-    }
+    } with sexp
   ;;
   val read : unit -> t
   val to_string : t -> string
@@ -24,7 +24,7 @@ end = struct
       threshold_ao       : Threshold.t;
       threshold_mo       : Threshold.t;
       direct             : bool;
-    }
+    } with sexp
   ;;
 
   let get_default = Qpackage.get_ezfio_default "bielec_integrals";;

ocaml/Input_bitmasks.ml

@@ -8,7 +8,7 @@ module Bitmasks : sig
       bit_kind           : Bit_kind.t;
       n_mask_gen         : Bitmask_number.t;
       generators         : int64 array;
-    }
+    } with sexp
   ;;
   val read : unit -> t
   val to_string : t -> string
@@ -18,7 +18,7 @@ end = struct
       bit_kind           : Bit_kind.t;
       n_mask_gen         : Bitmask_number.t;
       generators         : int64 array;
-    }
+    } with sexp
   ;;
 
   let get_default = Qpackage.get_ezfio_default "bitmasks";;

ocaml/Input_cis.ml

@@ -10,7 +10,7 @@ module Cis_dressed : sig
       mp2_dressing       : bool;
       standard_doubles   : bool;
       en_2_2             : bool;
-    }
+    } with sexp
   ;;
   val read : unit -> t
   val to_string : t -> string
@@ -22,7 +22,7 @@ end = struct
       mp2_dressing       : bool;
       standard_doubles   : bool;
       en_2_2             : bool;
-    }
+    } with sexp
   ;;
 
   let get_default = Qpackage.get_ezfio_default "cis_dressed";;

ocaml/Input_cisd_sc2.ml

@@ -7,7 +7,7 @@ module Cisd_sc2 : sig
     { n_det_max_cisd_sc2 : Det_number.t;
       pt2_max            : PT2_energy.t;
       do_pt2_end         : bool;
-    }
+    } with sexp
   ;;
   val read : unit -> t
   val to_string : t -> string
@@ -16,7 +16,7 @@ end = struct
     { n_det_max_cisd_sc2 : Det_number.t;
       pt2_max            : PT2_energy.t;
       do_pt2_end         : bool;
-    }
+    } with sexp
   ;;
 
   let get_default = Qpackage.get_ezfio_default "cisd_sc2_selected";;

ocaml/Input_determinants.ml

@@ -18,7 +18,7 @@ module Determinants : sig
       s2_eig                 : bool;
       psi_coef               : Det_coef.t array;
       psi_det                : Determinant.t array;
-    }
+    } with sexp
   ;;
   val read : unit -> t
   val to_string : t -> string
@@ -38,7 +38,7 @@ end = struct
       s2_eig                 : bool;
       psi_coef               : Det_coef.t array;
       psi_det                : Determinant.t array;
-    }
+    } with sexp
   ;;
 
   let get_default = Qpackage.get_ezfio_default "determinants";;

ocaml/Input_electrons.ml

@@ -7,7 +7,7 @@ module Electrons : sig
     { elec_alpha_num     : Elec_alpha_number.t;
       elec_beta_num      : Elec_beta_number.t;
       elec_num           : Elec_number.t;
-    }
+    } with sexp
   ;;
   val read : unit -> t
   val to_string : t -> string
@@ -16,7 +16,7 @@ end = struct
     { elec_alpha_num     : Elec_alpha_number.t;
       elec_beta_num      : Elec_beta_number.t;
       elec_num           : Elec_number.t;
-    }
+    } with sexp
   ;;
 
   let get_default = Qpackage.get_ezfio_default "electrons";;

ocaml/Input_full_ci.ml

@@ -7,7 +7,7 @@ module Full_ci : sig
     { n_det_max_fci      : Det_number.t;
       pt2_max            : PT2_energy.t;
       do_pt2_end         : bool;
-    }
+    } with sexp
   ;;
   val read : unit -> t
   val to_string : t -> string
@@ -16,7 +16,7 @@ end = struct
     { n_det_max_fci      : Det_number.t;
       pt2_max            : PT2_energy.t;
       do_pt2_end         : bool;
-    }
+    } with sexp
   ;;
 
   let get_default = Qpackage.get_ezfio_default "full_ci";;

ocaml/Input_hartree_fock.ml

@@ -6,7 +6,7 @@ module Hartree_fock : sig
   type t = 
     { n_it_scf_max       : Strictly_positive_int.t;
       thresh_scf         : Threshold.t;
-    }
+    } with sexp
   ;;
   val read : unit -> t
   val to_string : t -> string
@@ -14,7 +14,7 @@ end = struct
   type t = 
     { n_it_scf_max       : Strictly_positive_int.t;
       thresh_scf         : Threshold.t;
-    }
+    } with sexp
   ;;
 
   let get_default = Qpackage.get_ezfio_default "hartree_fock";;

ocaml/Input_mo_basis.ml

@@ -8,7 +8,7 @@ module Mo_basis : sig
       mo_label        : Non_empty_string.t;
       mo_occ          : Positive_float.t array;
       mo_coef         : MO_coef.t array;
-    }
+    } with sexp
   ;;
   val read : unit -> t
   val to_string : t -> string
@@ -18,7 +18,7 @@ end = struct
       mo_label        : Non_empty_string.t;
       mo_occ          : Positive_float.t array;
       mo_coef         : MO_coef.t array;
-    }
+    } with sexp
   ;;
 
   let get_default = Qpackage.get_ezfio_default "mo_basis";;

ocaml/Input_nuclei.ml

@@ -8,7 +8,7 @@ module Nuclei : sig
       nucl_label      : Element.t array;
       nucl_charge     : Charge.t array;
       nucl_coord      : Point3d.t array;
-    }
+    } with sexp
   ;;
   val read : unit -> t
   val to_string : t -> string
@@ -18,7 +18,7 @@ end = struct
       nucl_label      : Element.t array;
       nucl_charge     : Charge.t array;
       nucl_coord      : Point3d.t array;
-    }
+    } with sexp
   ;;
 
   let get_default = Qpackage.get_ezfio_default "nuclei";;

ocaml/Long_basis.ml

@@ -1,7 +1,7 @@
 open Core.Std;;
 open Qptypes;;
 
-type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t ) list;;
+type t = (Symmetry.Xyz.t * Gto.t * Nucl_number.t ) list with sexp
 
 let of_basis b =
   let rec do_work accu = function
@@ -21,9 +21,15 @@ let of_basis b =
 
 
 let to_string b =
-  List.map ~f:(fun (x,y,z) -> 
+  Sexp.to_string (sexp_of_t b)
-     (Int.to_string (Nucl_number.to_int z))^":"^
-     (Symmetry.Xyz.to_string x)^" "^(Gto.to_string y)
-  ) b
-  |> String.concat ~sep:"\n"
 ;;
+(*
+  let middle = List.map ~f:(fun (x,y,z) -> 
+     "( "^((Int.to_string (Nucl_number.to_int z)))^", "^
+     (Symmetry.Xyz.to_string x)^", "^(Gto.to_string y)
+     ^" )"
+  ) b
+  |> String.concat ~sep:",\n"
+  in "("^middle^")"
+;;
+*)

ocaml/MO_class.ml

@@ -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
 
 
 let to_string  x = 

ocaml/Makefile

@@ -13,7 +13,7 @@ endif
 LIBS=
 PKGS=
 OCAMLCFLAGS=-g 
-OCAMLBUILD=ocamlbuild -j 0 -cflags $(OCAMLCFLAGS) -lflags -g 
+OCAMLBUILD=ocamlbuild -j 0 -syntax camlp4o -cflags $(OCAMLCFLAGS) -lflags -g  
 MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml
 MLIFILES=$(wildcard *.mli) 
 ALL_TESTS=$(patsubst %.ml,%.byte,$(wildcard test_*.ml))

ocaml/Molecule.ml

@@ -7,7 +7,7 @@ type t = {
   nuclei     : Atom.t list ;
   elec_alpha : Elec_alpha_number.t ;
   elec_beta  : Elec_beta_number.t ;
-}
+} with sexp
 
 let get_charge { nuclei  ; elec_alpha ; elec_beta } =
   let result = (Elec_alpha_number.to_int elec_alpha) +

ocaml/Multiplicity.ml

@@ -1,7 +1,8 @@
 open Core.Std;;
 open Qptypes ;;
 
-type t = Strictly_positive_int.t;;
+type t = Strictly_positive_int.t with sexp
+
 let of_int = Strictly_positive_int.of_int ;;
 let to_int = Strictly_positive_int.to_int ;;
 

ocaml/Point3d.ml

@@ -4,7 +4,7 @@ type t = {
   x : float ;
   y : float ;
   z : float ;
-}
+} with sexp
 
 (** Read x y z coordinates in string s with units u *)
 let of_string u s =

ocaml/Primitive.ml

@@ -4,7 +4,7 @@ open Core.Std;;
 type t =
 { sym  : Symmetry.t ;
   expo : AO_expo.t ;
-}
+} with sexp
 
 let to_string p = 
   let { sym = s ; expo = e } = p in

ocaml/Range.ml

@@ -12,7 +12,7 @@ open Core.Std;;
 *)
 
 
-type t = int list ;;
+type t = int list with sexp
 
 let expand_range r =
   match String.lsplit2 ~on:'-' r with

ocaml/Symmetry.ml

@@ -1,7 +1,7 @@
 open Qptypes;;
 open Core.Std;;
 
-type t = S|P|D|F|G|H|I|J|K|L
+type t = S|P|D|F|G|H|I|J|K|L with sexp
 
 let to_string = function
   | S -> "S"
@@ -53,6 +53,23 @@ let to_l = function
   | J -> Positive_int.of_int 7
   | K -> Positive_int.of_int 8
   | L -> Positive_int.of_int 9
+;;
+
+let of_l i = 
+  let i = Positive_int.to_int i in
+  match i with
+  | 0 -> S
+  | 1 -> P
+  | 2 -> D
+  | 3 -> F
+  | 4 -> G
+  | 5 -> H
+  | 6 -> I
+  | 7 -> J
+  | 8 -> K
+  | 9 -> L
+  | x -> raise (Failure ("Symmetry should be S|P|D|F|G|H|I|J|K|L"))
+;;
 
 type st = t
 ;;
@@ -60,15 +77,16 @@ type st = t
 module Xyz : sig
   type t = { x: Positive_int.t ;
              y: Positive_int.t ;
-             z: Positive_int.t }
+             z: Positive_int.t } with sexp
   val  of_string : string -> t
   val  to_string : t -> string 
   val  get_l     : t -> Positive_int.t
   val  of_symmetry : st -> t list
+  val  to_symmetry : t -> st
 end = struct
   type t = { x: Positive_int.t ;
              y: Positive_int.t ;
-             z: Positive_int.t }
+             z: Positive_int.t } with sexp
   type state_type = Null | X | Y | Z
 
   (** Builds an XYZ triplet from a string.
@@ -127,7 +145,9 @@ end = struct
     | 1 -> "z"
     | i -> Printf.sprintf "z%d" i
     in
-    x^y^z
+    let result = (x^y^z) in
+    if (result = "") then "s"
+    else result
   ;;
 
  (** Returns the l quantum number from a XYZ powers triplet *)
@@ -169,5 +189,7 @@ end = struct
      z=Positive_int.of_int 0 }
    ;;
 
+   let to_symmetry sym = of_l (get_l sym)
+   ;;
 end
 

ocaml/_tags

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

ocaml/qptypes_generator.ml

@@ -126,12 +126,12 @@ let input_data = "
 
 let untouched = "
 module Determinant : sig
-  type t
+  type t with sexp
   val to_int64_array : t -> int64 array
   val of_int64_array : int64 array -> t
   val to_string : t -> string
 end = struct
-  type t = int64 array
+  type t = int64 array with sexp
   let to_int64_array x = x
   let of_int64_array x = 
     if (Ezfio.has_determinants_n_int ()) then
@@ -149,12 +149,12 @@ end
 
 let template = format_of_string "
 module %s : sig
-  type t
+  type t with sexp
   val to_%s : t -> %s
   val of_%s : %s -> t
   val to_string : t -> string
 end = struct
-  type t = %s
+  type t = %s with sexp
   let to_%s x = x
   let of_%s x = ( %s x )
   let to_string x = %s.to_string x

ocaml/test_input.ml

@@ -2,6 +2,7 @@ let test_ao () =
   Ezfio.set_file "F2.ezfio" ;
   let b = Input.Ao_basis.read ()
   in
+  print_endline (Input.Ao_basis.debug b);
   print_endline (Input.Ao_basis.to_string b);
 ;;
 
@@ -84,5 +85,7 @@ test_cis ();
 test_dets ();
 test_cisd_sc2 ();
 test_mo ();;
-*)
 test_nucl ();
+*)
+test_ao ();;
+