Added Input_nuclei.ml

ocaml/Input.ml

@@ -13,5 +13,6 @@ include Input_electrons;;
 include Input_full_ci;;
 include Input_hartree_fock;;
 include Input_mo_basis;;
+include Input_nuclei;;
 
 

ocaml/Input_nuclei.ml

@@ -0,0 +1,85 @@
+open Qptypes;;
+open Qputils;;
+open Core.Std;;
+
+module Nuclei : sig
+  type t = 
+    { nucl_num        : Nucl_number.t ;
+      nucl_label      : Element.t array;
+      nucl_charge     : Charge.t array;
+      nucl_coord      : Point3d.t array;
+    }
+  ;;
+  val read : unit -> t
+  val to_string : t -> string
+end = struct
+  type t = 
+    { nucl_num        : Nucl_number.t ;
+      nucl_label      : Element.t array;
+      nucl_charge     : Charge.t array;
+      nucl_coord      : Point3d.t array;
+    }
+  ;;
+
+  let get_default = Qpackage.get_ezfio_default "nuclei";;
+
+  let read_nucl_num () = 
+    Ezfio.get_nuclei_nucl_num ()
+    |> Nucl_number.of_int
+  ;;
+
+  let read_nucl_label () =
+    (Ezfio.get_nuclei_nucl_label ()).Ezfio.data
+    |> Ezfio.flattened_ezfio_data
+    |> Array.map ~f:Element.of_string 
+  ;;
+
+  let read_nucl_charge () =
+    (Ezfio.get_nuclei_nucl_charge () ).Ezfio.data
+    |> Ezfio.flattened_ezfio_data
+    |> Array.map ~f:Charge.of_float
+  ;;
+
+  let read_nucl_coord () =
+    let nucl_num = Nucl_number.to_int (read_nucl_num ()) in
+    let raw_data = 
+    (Ezfio.get_nuclei_nucl_coord() ).Ezfio.data
+    |> Ezfio.flattened_ezfio_data
+    in
+    let zero = Point3d.of_string Units.Bohr "0. 0. 0." in
+    let result = Array.create nucl_num zero in
+    for i=0 to (nucl_num-1)
+    do
+      result.(i) <- Point3d.({ x=raw_data.(i);
+                              y=raw_data.(nucl_num+i);
+                              z=raw_data.(2*nucl_num+i); });
+    done;
+    result
+  ;;
+
+  let read () =
+    { nucl_num        = read_nucl_num ();
+      nucl_label      = read_nucl_label () ;
+      nucl_charge     = read_nucl_charge ();
+      nucl_coord      = read_nucl_coord ();
+    }
+  ;;
+
+  let to_string b =
+    Printf.sprintf "
+nucl_num         = %s
+nucl_label       = %s
+nucl_charge      = %s
+nucl_coord       = %s
+"
+    (Nucl_number.to_string b.nucl_num)
+    (b.nucl_label |> Array.to_list |> List.map
+      ~f:(Element.to_string) |> String.concat ~sep:", " )
+    (b.nucl_charge |> Array.to_list |> List.map
+      ~f:(Charge.to_string) |> String.concat ~sep:", " )
+    (b.nucl_coord  |> Array.to_list |> List.map
+      ~f:(Point3d.to_string Units.Bohr) |> String.concat ~sep:"\n" )
+
+end
+
+

ocaml/test_input.ml

@@ -68,6 +68,13 @@ let test_mo () =
   print_endline (Input.Mo_basis.to_string b);
 ;;
 
+let test_nucl () =
+  Ezfio.set_file "F2.ezfio" ;
+  let b = Input.Nuclei.read ()
+  in
+  print_endline (Input.Nuclei.to_string b);
+;;
+
 (*
 test_hf ();;
 test_ao ();;
@@ -76,5 +83,6 @@ test_bitmasks ();
 test_cis ();
 test_dets ();
 test_cisd_sc2 ();
-*)
 test_mo ();;
+*)
+test_nucl ();