mirror of
https://github.com/LCPQ/quantum_package
synced 2024-11-14 01:53:55 +01:00
123 lines
3.2 KiB
OCaml
123 lines
3.2 KiB
OCaml
open Core.Std ;;
|
|
open Qptypes ;;
|
|
|
|
exception MultiplicityError of string;;
|
|
|
|
type t = {
|
|
nuclei : Atom.t list ;
|
|
elec_alpha : Positive_int.t ;
|
|
elec_beta : Positive_int.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 -> (Charge.to_float a.Atom.charge) +. nucl_charge rest
|
|
| [] -> 0.
|
|
in
|
|
Charge.of_float (nucl_charge nuclei -. (Float.of_int result))
|
|
;;
|
|
|
|
let get_multiplicity m =
|
|
let elec_alpha = m.elec_alpha
|
|
|> Positive_int.to_int
|
|
|> Strictly_positive_int.of_int in
|
|
Multiplicity.of_alpha_beta elec_alpha m.elec_beta
|
|
;;
|
|
|
|
let get_nucl_num m =
|
|
Strictly_positive_int.of_int (List.length m.nuclei)
|
|
;;
|
|
|
|
let name m =
|
|
let cm = Charge.to_int (get_charge m) in
|
|
let c =
|
|
match cm with
|
|
| 0 -> ""
|
|
| 1 -> " (+)"
|
|
| (-1) -> " (-)"
|
|
| i when i>1 -> Printf.sprintf " (%d+)" i
|
|
| i -> Printf.sprintf " (%d-)" (-i)
|
|
in
|
|
let mult = Multiplicity.to_string (get_multiplicity m) in
|
|
let { nuclei ; elec_alpha ; elec_beta } = m in
|
|
let rec build_list accu = function
|
|
| a::rest ->
|
|
begin
|
|
let e = a.Atom.element in
|
|
match (List.Assoc.find accu e) with
|
|
| None -> build_list (List.Assoc.add accu e 1) rest
|
|
| Some i -> build_list (List.Assoc.add accu e (i+1)) rest
|
|
end
|
|
| [] -> accu
|
|
in
|
|
let rec build_name accu = function
|
|
| (a, n)::rest ->
|
|
let a = Element.to_string a in
|
|
begin
|
|
match n with
|
|
| 1 -> build_name (a::accu) rest
|
|
| i when i>1 ->
|
|
let tmp = Printf.sprintf "%s%d" a i
|
|
in build_name (tmp::accu) rest
|
|
| _ -> assert false
|
|
end
|
|
| [] -> accu
|
|
in
|
|
let result = build_list [] nuclei |> build_name [c ; ", " ; mult]
|
|
in
|
|
String.concat (result)
|
|
;;
|
|
|
|
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:(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=Units.Angstrom)
|
|
s =
|
|
let l = String.split s ~on:'\n'
|
|
|> List.filter ~f:(fun x -> x <> "")
|
|
|> List.map ~f:(fun x -> Atom.of_string units x)
|
|
in
|
|
let ne = ( get_charge {
|
|
nuclei=l ;
|
|
elec_alpha=(Positive_int.of_int 0) ;
|
|
elec_beta=(Positive_int.of_int 0) }
|
|
|> Charge.to_int
|
|
) - charge
|
|
|> Positive_int.of_int
|
|
in
|
|
let (na,nb) = Multiplicity.to_alpha_beta ne multiplicity in
|
|
let result =
|
|
{ nuclei = l ;
|
|
elec_alpha = (Positive_int.of_int na) ;
|
|
elec_beta = (Positive_int.of_int nb) }
|
|
in
|
|
if ((get_multiplicity result) <> multiplicity) then
|
|
let msg = Printf.sprintf
|
|
"With %d electrons multiplicity %d is impossible"
|
|
(Positive_int.to_int ne)
|
|
(Multiplicity.to_int multiplicity)
|
|
in
|
|
raise (MultiplicityError msg);
|
|
else () ;
|
|
result
|
|
;;
|
|
|
|
|
|
let of_xyz_file
|
|
?(charge=0) ?(multiplicity=(Multiplicity.of_int 1))
|
|
filename =
|
|
let (_,buffer) = In_channel.read_all filename
|
|
|> String.lsplit2_exn ~on:'\n' in
|
|
let (_,buffer) = String.lsplit2_exn buffer ~on:'\n' in
|
|
of_xyz_string ~charge:charge ~multiplicity:multiplicity buffer
|
|
;;
|