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https://github.com/LCPQ/quantum_package
synced 2024-08-25 05:51:46 +02:00
Input_nuclei is written by qp_edit
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@ -67,13 +67,6 @@ let read_one in_channel =
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(** Transform the gto to a string *)
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let to_string { sym = sym ; lc = lc } =
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let f (p,c) = Printf.sprintf "( %s, %f )" (Primitive.to_string p) (AO_coef.to_float c)
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in
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Printf.sprintf "( %s, %s )" (Symmetry.to_string sym)
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(String.concat (List.map ~f:f lc) ~sep:", ")
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;;
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let to_string { sym = sym ; lc = lc } =
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let result =
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Printf.sprintf "%s %3d" (Symmetry.to_string sym) (List.length lc)
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@ -145,16 +145,12 @@ end = struct
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let print_sym =
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let l = List.init (Array.length b.ao_power) ~f:(
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fun i -> ( (i+1),b.ao_nucl.(i),b.ao_power.(i) ) ) in
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let rec do_work count = function
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let rec do_work = function
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| [] -> []
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| (i,n,x)::tail ->
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if (count < 2) then
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(Printf.sprintf " (%4d) %d:%-8s" i (Nucl_number.to_int n) (Symmetry.Xyz.to_string x))::
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(do_work (count+1) tail)
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else
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(Printf.sprintf " (%4d) %d:%-8s\n" i (Nucl_number.to_int n) (Symmetry.Xyz.to_string x))::
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(do_work 0 tail)
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in do_work 0 l
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(Printf.sprintf " %5d %6d %-8s\n" i (Nucl_number.to_int n) (Symmetry.Xyz.to_string x))::
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(do_work tail)
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in do_work l
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|> String.concat
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in
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@ -168,9 +164,12 @@ Basis set ::
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%s
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Symmetries ::
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======= ========= ===========
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Basis Nucleus Symmetries
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======= ========= ===========
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%s
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======= ========= ===========
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" b.ao_basis
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(Basis.to_string short_basis
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@ -181,6 +180,22 @@ Symmetries ::
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|> Rst_string.of_string
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;;
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let read_rst s =
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let s = Rst_string.to_string s
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|> String.split ~on:'\n'
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in
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let rec extract_basis = function
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| [] -> failwith "Error in basis set"
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| line :: tail ->
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let line = String.strip line in
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if line = "Basis set ::" then
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String.concat tail ~sep:"\n"
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else
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extract_basis tail
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in
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extract_basis s
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;;
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let to_md5 b =
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let short_basis = to_basis b in
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Basis.to_md5 short_basis
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@ -11,6 +11,7 @@ module Nuclei : sig
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} with sexp
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;;
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val read : unit -> t
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val write : t -> unit
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val to_string : t -> string
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val to_rst : t -> Rst_string.t
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val of_rst : Rst_string.t -> t
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@ -30,18 +31,52 @@ end = struct
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Nucl_number.of_int ~max:nmax nmax
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;;
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let write_nucl_num n =
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Nucl_number.to_int n
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|> Ezfio.set_nuclei_nucl_num
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;;
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let read_nucl_label () =
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Ezfio.get_nuclei_nucl_label ()
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|> Ezfio.flattened_ezfio
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|> Array.map ~f:Element.of_string
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;;
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let write_nucl_label ~nucl_num labels =
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let nucl_num =
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Nucl_number.to_int nucl_num
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in
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let labels =
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Array.to_list labels
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|> List.map ~f:Element.to_string
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in
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Ezfio.ezfio_array_of_list ~rank:1
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~dim:[| nucl_num |] ~data:labels
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|> Ezfio.set_nuclei_nucl_label
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;;
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let read_nucl_charge () =
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Ezfio.get_nuclei_nucl_charge ()
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|> Ezfio.flattened_ezfio
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|> Array.map ~f:Charge.of_float
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;;
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let write_nucl_charge ~nucl_num charges =
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let nucl_num =
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Nucl_number.to_int nucl_num
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in
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let charges =
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Array.to_list charges
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|> List.map ~f:Charge.to_float
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in
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Ezfio.ezfio_array_of_list ~rank:1
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~dim:[| nucl_num |] ~data:charges
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|> Ezfio.set_nuclei_nucl_charge
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;;
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let read_nucl_coord () =
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let nucl_num = Nucl_number.to_int (read_nucl_num ()) in
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let raw_data =
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@ -59,6 +94,81 @@ end = struct
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result
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;;
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let write_nucl_coord ~nucl_num coord =
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let nucl_num =
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Nucl_number.to_int nucl_num
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in
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let coord = Array.to_list coord in
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let coord =
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(List.map ~f:(fun x-> x.Point3d.x) coord) @
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(List.map ~f:(fun x-> x.Point3d.y) coord) @
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(List.map ~f:(fun x-> x.Point3d.z) coord)
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in
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Ezfio.ezfio_array_of_list ~rank:2
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~dim:[| nucl_num ; 3 |] ~data:coord
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|> Ezfio.set_nuclei_nucl_coord
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;;
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let read () =
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{ nucl_num = read_nucl_num ();
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nucl_label = read_nucl_label () ;
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nucl_charge = read_nucl_charge ();
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nucl_coord = read_nucl_coord ();
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}
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;;
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let write { nucl_num ;
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nucl_label ;
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nucl_charge ;
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nucl_coord ;
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} =
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write_nucl_num nucl_num ;
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write_nucl_label ~nucl_num:nucl_num nucl_label;
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write_nucl_charge ~nucl_num:nucl_num nucl_charge;
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write_nucl_coord ~nucl_num:nucl_num nucl_coord;
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;;
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let to_string b =
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Printf.sprintf "
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nucl_num = %s
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nucl_label = %s
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nucl_charge = %s
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nucl_coord = %s
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"
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(Nucl_number.to_string b.nucl_num)
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(b.nucl_label |> Array.to_list |> List.map
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~f:(Element.to_string) |> String.concat ~sep:", " )
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(b.nucl_charge |> Array.to_list |> List.map
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~f:(Charge.to_string) |> String.concat ~sep:", " )
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(b.nucl_coord |> Array.to_list |> List.map
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~f:(Point3d.to_string Units.Bohr) |> String.concat ~sep:"\n" )
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;;
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let to_rst b =
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let nucl_num = Nucl_number.to_int b.nucl_num in
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let text =
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( Printf.sprintf " %d\n "
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nucl_num
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) :: (
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List.init nucl_num ~f:(fun i->
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Printf.sprintf " %-3s %d %s"
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(b.nucl_label.(i) |> Element.to_string)
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(b.nucl_charge.(i) |> Charge.to_int )
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(b.nucl_coord.(i) |> Point3d.to_string Units.Angstrom) )
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) |> String.concat ~sep:"\n"
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in
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Printf.sprintf "
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Nuclear coordinates in xyz format (Angstroms) ::
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%s
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" text
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|> Rst_string.of_string
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;;
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let of_rst s =
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let l = Rst_string.to_string s
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|> String.split ~on:'\n'
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@ -104,52 +214,6 @@ end = struct
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}
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;;
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let read () =
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{ nucl_num = read_nucl_num ();
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nucl_label = read_nucl_label () ;
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nucl_charge = read_nucl_charge ();
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nucl_coord = read_nucl_coord ();
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}
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;;
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let to_string b =
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Printf.sprintf "
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nucl_num = %s
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nucl_label = %s
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nucl_charge = %s
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nucl_coord = %s
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"
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(Nucl_number.to_string b.nucl_num)
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(b.nucl_label |> Array.to_list |> List.map
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~f:(Element.to_string) |> String.concat ~sep:", " )
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(b.nucl_charge |> Array.to_list |> List.map
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~f:(Charge.to_string) |> String.concat ~sep:", " )
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(b.nucl_coord |> Array.to_list |> List.map
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~f:(Point3d.to_string Units.Bohr) |> String.concat ~sep:"\n" )
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;;
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let to_rst b =
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let nucl_num = Nucl_number.to_int b.nucl_num in
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let text =
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( Printf.sprintf " %d\n "
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nucl_num
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) :: (
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List.init nucl_num ~f:(fun i->
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Printf.sprintf " %-3s %d %s"
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(b.nucl_label.(i) |> Element.to_string)
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(b.nucl_charge.(i) |> Charge.to_int )
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(b.nucl_coord.(i) |> Point3d.to_string Units.Angstrom) )
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) |> String.concat ~sep:"\n"
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in
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Printf.sprintf "
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Nuclear coordinates in xyz format (Angstroms) ::
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%s
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" text
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|> Rst_string.of_string
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;;
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end
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@ -91,8 +91,8 @@ let set str s =
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| Cisd_sc2 ->
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*)
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| Nuclei ->
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let b = Input.Nuclei.of_rst str in
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print_string (Input.Nuclei.to_string b);
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Input.Nuclei.of_rst str
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|> Input.Nuclei.write;
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| Bielec_integrals ->
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let b = Input.Bielec_integrals.of_rst str in
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print_string (Input.Bielec_integrals.to_string b);
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