Added qp_print.ml

ocaml/Atom.ml

@@ -2,24 +2,6 @@ open Core.Std;;
 
 exception AtomError of string
 
-module Charge : sig
-  type t 
-  val to_float : t -> float
-  val to_int   : t -> int
-  val to_string: t -> string 
-  val of_float : float -> t
-  val of_int   : int -> t
-  val of_string: string -> t
-end = struct
-  type t = float
-  let to_float x = x
-  let to_int   x = Float.to_int x
-  let to_string x = Float.to_string (to_float x)
-  let of_float x = x
-  let of_int   i = Float.of_int i
-  let of_string s = Float.of_string s
-end
-
 type t =
 { element : Element.t ;
   charge  : Charge.t ;
@@ -41,16 +23,16 @@ let of_string u s =
   | [ name; x; y; z ] ->
     let e = Element.of_string name in
     { element = e ;
-      charge  = Charge.of_int (Element.charge e);
+      charge  = Charge.of_int (Element.to_charge e);
       coord   = Point3d.of_string u (String.concat [x; y; z] ~sep:" ")
     }
   | _ -> raise (AtomError s)
 ;;
   
-let to_string a =
+let to_string u a =
   [ Element.to_string a.element ;
     Charge.to_string  a.charge ;
-    Point3d.to_string a.coord ]
+    Point3d.to_string u a.coord ]
   |> String.concat ?sep:(Some "   ")
 ;;
 

ocaml/Charge.ml

@@ -0,0 +1,17 @@
+open Core.Std;;
+
+type t = float
+
+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 = 
+  if x >= 0. then
+    Printf.sprintf "+%f" x
+  else
+    Printf.sprintf "%f" x
+;;
+

ocaml/Charge.mli

@@ -0,0 +1,8 @@
+type t = float
+
+val to_float : t -> float
+val to_int   : t -> int
+val to_string: t -> string 
+val of_float : float -> t
+val of_int   : int -> t
+val of_string: string -> t

ocaml/Element.ml

@@ -46,7 +46,7 @@ let of_string = function
 | "Se" | "Selenium" -> Se
 | "Br" | "Bromine" -> Br
 | "Kr" | "Krypton" -> Kr
-| x -> raise (ElementError ("Atom "^x^" unknown"))
+| x -> raise (ElementError ("Element "^x^" unknown"))
 ;;
 
 let to_string = function
@@ -129,7 +129,7 @@ let to_long_string = function
 | Kr  -> "Krypton"
 ;;
 
-let charge = function
+let to_charge = function
 | X   -> 0
 | H   -> 1
 | He  -> 2
@@ -169,3 +169,44 @@ let charge = function
 | Kr  -> 36
 ;;
 
+let of_charge = function
+|  0   ->  X   
+|  1   ->  H   
+|  2   ->  He  
+|  3   ->  Li  
+|  4   ->  Be  
+|  5   ->  B   
+|  6   ->  C   
+|  7   ->  N   
+|  8   ->  O   
+|  9   ->  F   
+|  10  ->  Ne  
+|  11  ->  Na  
+|  12  ->  Mg  
+|  13  ->  Al  
+|  14  ->  Si  
+|  15  ->  P   
+|  16  ->  S   
+|  17  ->  Cl  
+|  18  ->  Ar  
+|  19  ->  K   
+|  20  ->  Ca  
+|  21  ->  Sc  
+|  22  ->  Ti  
+|  23  ->  V   
+|  24  ->  Cr  
+|  25  ->  Mn  
+|  26  ->  Fe  
+|  27  ->  Co  
+|  28  ->  Ni  
+|  29  ->  Cu  
+|  30  ->  Zn  
+|  31  ->  Ga  
+|  32  ->  Ge  
+|  33  ->  As  
+|  34  ->  Se  
+|  35  ->  Br  
+|  36  ->  Kr  
+| x -> raise (ElementError ("Element of charge "^(string_of_int x)^" unknown"))
+;;
+

ocaml/Makefile

@@ -32,7 +32,7 @@ executables: $(ALL_EXE)
 %.byte: $(MLFILES) $(MLIFILES)
 	rm -f -- $*
 	$(OCAMLBUILD) $*.byte  -use-ocamlfind  $(PKGS)
-	ln -s $*.native $*
+	ln -s $*.byte $*
 
 %.native: $(MLFILES) $(MLIFILES)
 	rm -f -- $*

ocaml/Molecule.ml

@@ -12,10 +12,10 @@ type t = {
 let get_charge { nuclei  ; elec_alpha ; elec_beta } =
   let result = Positive_int.(to_int elec_alpha + to_int elec_beta) in
   let rec nucl_charge = function
-  | a::rest -> Atom.(Charge.to_float a.charge) +. nucl_charge rest
+  | a::rest -> (Charge.to_float a.Atom.charge) +. nucl_charge rest
   | [] -> 0.
   in
-  nucl_charge nuclei  -. (Float.of_int result)
+  Charge.of_float (nucl_charge nuclei  -. (Float.of_int result))
 ;;
 
 let get_multiplicity m = 
@@ -27,7 +27,7 @@ let get_nucl_num m =
 ;;
 
 let name m = 
-  let cm = Float.to_int (get_charge m) in
+  let cm = Charge.to_int (get_charge m) in
   let c = 
      match cm with
      | 0 -> ""
@@ -70,13 +70,14 @@ let to_string m =
   let { nuclei  ; elec_alpha ; elec_beta } = m in
   let n = List.length nuclei in
   let title = name m in
-  [ Int.to_string n ; title ] @ (List.map ~f:Atom.to_string nuclei)
+  [ Int.to_string n ; title ] @ (List.map ~f:(fun x -> Atom.to_string
+  Units.Angstrom x) nuclei)
   |> String.concat ~sep:"\n"
 ;;
 
 let of_xyz_string
     ?(charge=0) ?(multiplicity=(Multiplicity.of_int 1))
-    ?(units=Point3d.Angstrom)
+    ?(units=Units.Angstrom)
     s =
   let l = String.split s ~on:'\n'
        |> List.filter ~f:(fun x -> x <> "")
@@ -86,8 +87,8 @@ let of_xyz_string
         nuclei=l ;
         elec_alpha=(Positive_int.of_int 0) ;
         elec_beta=(Positive_int.of_int 0) } 
-      |> Float.to_int 
-      )- charge 
+      |> Charge.to_int 
+      ) - charge 
       |> Positive_int.of_int 
   in
   let (na,nb) = Multiplicity.to_alpha_beta ne multiplicity in

ocaml/Point3d.ml

@@ -1,10 +1,5 @@
 open Core.Std;;
 
-type units = 
-| Bohr
-| Angstrom
-;;
-
 type t = {
   x : float ;
   y : float ;
@@ -13,11 +8,9 @@ type t = {
 
 (** Read x y z coordinates in string s with units u *)
 let of_string u s =
-  let f = 
-    begin match u with
-    | Bohr -> 1.
-    | Angstrom -> 1. /. 0.52917721092
-    end
+  let f = match u with 
+    | Units.Bohr     -> 1.
+    | Units.Angstrom -> Units.angstrom_to_bohr 
   in
   let l = s
   |> String.split ~on:' '
@@ -40,8 +33,12 @@ let distance2 p1 p2 =
 let distance p1 p2 = sqrt (distance2 p1 p2)
 ;;
 
-let to_string p =
+let to_string u p =
+  let f = match u with 
+    | Units.Bohr     -> 1.
+    | Units.Angstrom -> Units.bohr_to_angstrom
+  in
   let { x=x ; y=y ; z=z } = p in
-  Printf.sprintf "%f  %f  %f" x y z
+  Printf.sprintf "%f  %f  %f" (x*.f) (y*.f) (z*.f)
 ;;
   

ocaml/Units.ml

@@ -0,0 +1,11 @@
+
+type units = 
+| Bohr
+| Angstrom
+;;
+
+let angstrom_to_bohr = 1. /. 0.52917721092
+let bohr_to_angstrom = 0.52917721092
+;;
+
+

ocaml/qp_create_ezfio_from_xyz.ml

@@ -18,14 +18,6 @@ let spec =
 
 let run ?o b c m xyz_file =
 
-(*
-  (* DEBUG *)
-  Printf.printf "Charge : %d
-Multiplicity : %d
-Basis : %s
-File : %s\n" c m b xyz_file;
-*)
-
   (* Open basis set channel *)
   let basis_channel =
     In_channel.create

ocaml/qp_print.ml

@@ -0,0 +1,168 @@
+open Qputils;;
+open Qptypes;;
+open Core.Std;;
+
+type input_action =
+  | Basis
+  | Nuclei
+  | Charge
+  | Multiplicity
+  | Electrons
+;;
+
+let create_i_action = function
+  | "basis" -> Basis
+  | "nucl" -> Nuclei
+  | "charge" -> Charge
+  | "mult" -> Multiplicity
+  | "elec" -> Electrons
+  | _ -> raise (Failure "Action should be:
+  * basis
+  * nucl
+  * charge
+  * mult
+  * elec
+")
+
+;;
+
+let spec =
+  let open Command.Spec in
+  empty 
+  +> flag "i"  (optional string)
+     ~doc:"Prints input data"
+  +> flag "o" (optional string)
+     ~doc:"Prints output data"
+  +> anon ("ezfio_file" %: string)
+;;
+
+let run_i ~action ezfio_filename =
+
+  let action = create_i_action action in
+
+  if (not (Sys.file_exists_exn ezfio_filename)) then
+    failwith (ezfio_filename^" does not exists");
+
+  Ezfio.set_file ezfio_filename;
+
+  let print_basis () =
+    Printf.printf "%s\n" (Ezfio.get_ao_basis_ao_basis ())
+  in
+
+
+  let compute_charge () =
+    let nucl_charge = Ezfio.((get_nuclei_nucl_charge ()).data)
+      |> Ezfio.flattened_ezfio_data |> Array.map ~f:(Float.to_int) 
+    and n_alpha = Ezfio.get_electrons_elec_alpha_num ()
+    and n_beta  = Ezfio.get_electrons_elec_beta_num ()
+    in Array.fold ~init:(-n_alpha-n_beta) ~f:(fun x y -> x+y) nucl_charge
+  in
+
+  let compute_multiplicity () =
+    let n_alpha = Positive_int.of_int (Ezfio.get_electrons_elec_alpha_num ())
+    and n_beta  = Positive_int.of_int (Ezfio.get_electrons_elec_beta_num ())
+    in Multiplicity.of_alpha_beta n_alpha n_beta
+  in
+
+  let create_molecule () =
+    let nucl_num = Ezfio.get_nuclei_nucl_num () 
+    and nucl_charge = Ezfio.((get_nuclei_nucl_charge ()).data)
+       |> Ezfio.flattened_ezfio_data
+    and nucl_coord = Ezfio.((get_nuclei_nucl_coord ()).data )
+       |> Ezfio.flattened_ezfio_data
+    in
+    let nucl_label =
+      if (Ezfio.has_nuclei_nucl_label ()) then
+       Ezfio.((get_nuclei_nucl_label ()).data) |> Ezfio.flattened_ezfio_data
+      else
+        Array.map ~f:(fun x-> x
+          |> Float.to_int
+          |> Element.of_charge 
+          |> Element.to_string ) nucl_charge
+    in
+    let buffer = ref "" in
+    for i=0 to (nucl_num-1) do
+      buffer := !buffer ^ (Printf.sprintf "%s %f %f %f %f\n"
+        nucl_label.(i)
+        nucl_charge.(i)
+        nucl_coord.(i)
+        nucl_coord.(i+nucl_num)
+        nucl_coord.(i+nucl_num+nucl_num)
+      )
+    done ;
+    let charge = compute_charge () in
+    let mult = compute_multiplicity () in
+    Molecule.of_xyz_string ~charge:charge ~multiplicity:mult !buffer
+  in
+
+  let print_nuclei () =
+    let molecule = create_molecule () in
+    print_endline (Molecule.to_string molecule)
+
+  and print_charge () = 
+    let molecule = create_molecule () in
+    Printf.printf "%s" (Charge.to_string (Molecule.get_charge molecule))
+
+  and print_multiplicity () = 
+    let molecule = create_molecule () in
+    Printf.printf "%s" (Multiplicity.to_string (Molecule.get_multiplicity
+    molecule))
+
+  and print_electrons () = ()
+
+  in
+  match action with
+  | Basis        -> print_basis ()
+  | Nuclei       -> print_nuclei ()
+  | Charge       -> print_charge ()
+  | Multiplicity -> print_multiplicity ()
+  | Electrons    -> print_electrons ()
+;;
+
+let run_o ~action ezfio_filename =
+
+  if (not (Sys.file_exists_exn ezfio_filename)) then
+    failwith (ezfio_filename^" does not exists");
+
+  (* Open EZFIO *)
+  Ezfio.set_file ezfio_filename;
+
+;;
+
+let command = 
+    Command.basic 
+    ~summary: "Quantum Package command"
+    ~readme:(fun () ->
+      "
+Prints data contained into the EZFIO file.
+
+Input data :
+
+  * basis
+  * nuclei
+  * charge
+  * multiplicity
+  * electrons
+
+Output data :
+
+  * 
+      ")
+    spec
+    (fun i o ezfio_file () ->
+      match (i,o) with
+      | (Some i, None) -> run_i ~action:i ezfio_file
+      | (None, Some o) -> run_o ~action:o ezfio_file
+      | (Some _, Some _) -> 
+          raise (Failure "Error : please specify -i or -o but not both.")
+      | (None, None) -> 
+          raise (Failure "Error : please specify -i or -o.")
+    )
+;;
+
+let () =
+    Command.run command
+;;
+
+
+

ocaml/test_atom.ml

@@ -1,5 +1,5 @@
 let test_atom = 
   let line = "C  6.0  1.  2. 3." in
-  let atom = Atom.of_string Point3d.Bohr line in
-  print_string (Atom.to_string atom)
+  let atom = Atom.of_string Units.Bohr line in
+  print_string (Atom.to_string Units.Angstrom atom)
 ;;

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.charge atom)
+  Printf.printf "%s %d\n" (Element.to_string atom) (Element.to_charge atom)
 ;;
 
 test_module ();;

ocaml/test_point3d.ml

@@ -1,15 +1,19 @@
 let test_point3d_1 () =
   let input = "7.4950000 -0.1499810    0.5085570" in
-  let p3d = Point3d.of_string Point3d.Angstrom input in
-  print_endline(Point3d.to_string p3d);
-  let p3d = Point3d.of_string Point3d.Bohr input in
-  print_endline (Point3d.to_string p3d)
+  let p3d = Point3d.of_string Units.Angstrom input in
+  print_endline(Point3d.to_string Units.Angstrom p3d);
+  let p3d = Point3d.of_string Units.Bohr input in
+  print_endline (Point3d.to_string Units.Bohr p3d)
 ;;
 
 let test_point3d () =
-  let p1 = Point3d.of_string Point3d.Bohr "1. 2. 3." 
-  and p2 = Point3d.of_string Point3d.Bohr "-2. 1. 1.5" in
+  let p1 = Point3d.of_string Units.Bohr "1. 2. 3." 
+  and p2 = Point3d.of_string Units.Bohr "-2. 1. 1.5" in
+  Printf.printf "%f\n" (Point3d.distance p1 p2);
+  let p1 = Point3d.of_string Units.Angstrom "1. 2. 3." 
+  and p2 = Point3d.of_string Units.Angstrom "-2. 1. 1.5" in
   Printf.printf "%f\n" (Point3d.distance p1 p2)
 ;;
 
 test_point3d_1 ();
+test_point3d ();

src/AOs/aos.ezfio_config

@@ -1,4 +1,5 @@
 ao_basis
+  ao_basis           character*(256)
   ao_num             integer
   ao_prim_num        integer       (ao_basis_ao_num)
   ao_nucl            integer       (ao_basis_ao_num)