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Input_nuclei is written by qp_edit

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This commit is contained in:
Anthony Scemama 2014-11-03 22:24:40 +01:00
parent 1ffc72cc79
commit f9fe342c58
4 changed files with 137 additions and 65 deletions
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7
ocaml/Gto.ml
View File

@ -67,13 +67,6 @@ let read_one in_channel =
(** Transform the gto to a string *)
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)
(String.concat (List.map ~f:f lc) ~sep:", ")
;;
let to_string { sym = sym ; lc = lc } =
let result =
Printf.sprintf "%s %3d" (Symmetry.to_string sym) (List.length lc)

33
ocaml/Input_ao_basis.ml
View File

@ -145,16 +145,12 @@ end = struct
let print_sym =
let l = List.init (Array.length b.ao_power) ~f:(
fun i -> ( (i+1),b.ao_nucl.(i),b.ao_power.(i) ) ) in
let rec do_work count = function
let rec do_work = function
| [] -> []
| (i,n,x)::tail ->
if (count < 2) then
(Printf.sprintf " (%4d) %d:%-8s" i (Nucl_number.to_int n) (Symmetry.Xyz.to_string x))::
(do_work (count+1) tail)
else
(Printf.sprintf " (%4d) %d:%-8s\n" i (Nucl_number.to_int n) (Symmetry.Xyz.to_string x))::
(do_work 0 tail)
in do_work 0 l
(Printf.sprintf " %5d %6d %-8s\n" i (Nucl_number.to_int n) (Symmetry.Xyz.to_string x))::
(do_work tail)
in do_work l
|> String.concat
in
@ -168,9 +164,12 @@ Basis set ::
%s
Symmetries ::
======= ========= ===========
Basis Nucleus Symmetries
======= ========= ===========
%s
======= ========= ===========
" b.ao_basis
(Basis.to_string short_basis
@ -181,6 +180,22 @@ Symmetries ::
|> Rst_string.of_string
;;
let read_rst s =
let s = Rst_string.to_string s
|> String.split ~on:'\n'
in
let rec extract_basis = function
| [] -> failwith "Error in basis set"
| line :: tail ->
let line = String.strip line in
if line = "Basis set ::" then
String.concat tail ~sep:"\n"
else
extract_basis tail
in
extract_basis s
;;
let to_md5 b =
let short_basis = to_basis b in
Basis.to_md5 short_basis

158
ocaml/Input_nuclei.ml
View File

@ -10,7 +10,8 @@ module Nuclei : sig
nucl_coord : Point3d.t array;
} with sexp
;;
val read : unit -> t
val read : unit -> t
val write : t -> unit
val to_string : t -> string
val to_rst : t -> Rst_string.t
val of_rst : Rst_string.t -> t
@ -30,18 +31,52 @@ end = struct
Nucl_number.of_int ~max:nmax nmax
;;
let write_nucl_num n =
Nucl_number.to_int n
|> Ezfio.set_nuclei_nucl_num
;;
let read_nucl_label () =
Ezfio.get_nuclei_nucl_label ()
|> Ezfio.flattened_ezfio
|> Array.map ~f:Element.of_string
;;
let write_nucl_label ~nucl_num labels =
let nucl_num =
Nucl_number.to_int nucl_num
in
let labels =
Array.to_list labels
|> List.map ~f:Element.to_string
in
Ezfio.ezfio_array_of_list ~rank:1
~dim:[| nucl_num |] ~data:labels
|> Ezfio.set_nuclei_nucl_label
;;
let read_nucl_charge () =
Ezfio.get_nuclei_nucl_charge ()
|> Ezfio.flattened_ezfio
|> Array.map ~f:Charge.of_float
;;
let write_nucl_charge ~nucl_num charges =
let nucl_num =
Nucl_number.to_int nucl_num
in
let charges =
Array.to_list charges
|> List.map ~f:Charge.to_float
in
Ezfio.ezfio_array_of_list ~rank:1
~dim:[| nucl_num |] ~data:charges
|> Ezfio.set_nuclei_nucl_charge
;;
let read_nucl_coord () =
let nucl_num = Nucl_number.to_int (read_nucl_num ()) in
let raw_data =
@ -59,6 +94,81 @@ end = struct
result
;;
let write_nucl_coord ~nucl_num coord =
let nucl_num =
Nucl_number.to_int nucl_num
in
let coord = Array.to_list coord in
let coord =
(List.map ~f:(fun x-> x.Point3d.x) coord) @
(List.map ~f:(fun x-> x.Point3d.y) coord) @
(List.map ~f:(fun x-> x.Point3d.z) coord)
in
Ezfio.ezfio_array_of_list ~rank:2
~dim:[| nucl_num ; 3 |] ~data:coord
|> Ezfio.set_nuclei_nucl_coord
;;
let read () =
{ nucl_num = read_nucl_num ();
nucl_label = read_nucl_label () ;
nucl_charge = read_nucl_charge ();
nucl_coord = read_nucl_coord ();
}
;;
let write { nucl_num ;
nucl_label ;
nucl_charge ;
nucl_coord ;
} =
write_nucl_num nucl_num ;
write_nucl_label ~nucl_num:nucl_num nucl_label;
write_nucl_charge ~nucl_num:nucl_num nucl_charge;
write_nucl_coord ~nucl_num:nucl_num 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" )
;;
let to_rst b =
let nucl_num = Nucl_number.to_int b.nucl_num in
let text =
( Printf.sprintf " %d\n "
nucl_num
) :: (
List.init nucl_num ~f:(fun i->
Printf.sprintf " %-3s %d %s"
(b.nucl_label.(i) |> Element.to_string)
(b.nucl_charge.(i) |> Charge.to_int )
(b.nucl_coord.(i) |> Point3d.to_string Units.Angstrom) )
) |> String.concat ~sep:"\n"
in
Printf.sprintf "
Nuclear coordinates in xyz format (Angstroms) ::
%s
" text
|> Rst_string.of_string
;;
let of_rst s =
let l = Rst_string.to_string s
|> String.split ~on:'\n'
@ -104,52 +214,6 @@ end = struct
}
;;
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" )
;;
let to_rst b =
let nucl_num = Nucl_number.to_int b.nucl_num in
let text =
( Printf.sprintf " %d\n "
nucl_num
) :: (
List.init nucl_num ~f:(fun i->
Printf.sprintf " %-3s %d %s"
(b.nucl_label.(i) |> Element.to_string)
(b.nucl_charge.(i) |> Charge.to_int )
(b.nucl_coord.(i) |> Point3d.to_string Units.Angstrom) )
) |> String.concat ~sep:"\n"
in
Printf.sprintf "
Nuclear coordinates in xyz format (Angstroms) ::
%s
" text
|> Rst_string.of_string
;;
end

4
ocaml/qp_edit.ml
View File

@ -91,8 +91,8 @@ let set str s =
| Cisd_sc2 ->
*)
| Nuclei ->
let b = Input.Nuclei.of_rst str in
print_string (Input.Nuclei.to_string b);
Input.Nuclei.of_rst str
|> Input.Nuclei.write;
| Bielec_integrals ->
let b = Input.Bielec_integrals.of_rst str in
print_string (Input.Bielec_integrals.to_string b);