128 lines
3.3 KiB
OCaml
128 lines
3.3 KiB
OCaml
open Core.Std ;;
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open Qptypes ;;
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exception MultiplicityError of string;;
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type t = {
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nuclei : Atom.t list ;
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elec_alpha : Elec_alpha_number.t ;
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elec_beta : Elec_beta_number.t ;
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} with sexp
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let get_charge { nuclei ; elec_alpha ; elec_beta } =
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let result = (Elec_alpha_number.to_int elec_alpha) +
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(Elec_beta_number.to_int elec_beta) in
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let rec nucl_charge = function
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| a::rest -> (Charge.to_float a.Atom.charge) +. nucl_charge rest
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| [] -> 0.
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in
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Charge.of_float (nucl_charge nuclei -. (Float.of_int result))
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;;
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let get_multiplicity m =
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let elec_alpha = m.elec_alpha in
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Multiplicity.of_alpha_beta elec_alpha m.elec_beta
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;;
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let get_nucl_num m =
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Nucl_number.of_int (List.length m.nuclei)
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;;
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let name m =
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let cm = Charge.to_int (get_charge m) in
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let c =
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match cm with
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| 0 -> ""
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| 1 -> " (+)"
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| (-1) -> " (-)"
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| i when i>1 -> Printf.sprintf " (%d+)" i
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| i -> Printf.sprintf " (%d-)" (-i)
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in
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let mult = Multiplicity.to_string (get_multiplicity m) in
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let { nuclei ; elec_alpha ; elec_beta } = m in
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let rec build_list accu = function
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| a::rest ->
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begin
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let e = a.Atom.element in
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match (List.Assoc.find accu e) with
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| None -> build_list (List.Assoc.add accu e 1) rest
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| Some i -> build_list (List.Assoc.add accu e (i+1)) rest
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end
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| [] -> accu
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in
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let rec build_name accu = function
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| (a, n)::rest ->
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let a = Element.to_string a in
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begin
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match n with
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| 1 -> build_name (a::accu) rest
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| i when i>1 ->
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let tmp = Printf.sprintf "%s%d" a i
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in build_name (tmp::accu) rest
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| _ -> assert false
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end
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| [] -> accu
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in
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let result = build_list [] nuclei |> build_name [c ; ", " ; mult]
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in
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String.concat (result)
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;;
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let to_string m =
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let { nuclei ; elec_alpha ; elec_beta } = m in
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let n = List.length nuclei in
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let title = name m in
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[ Int.to_string n ; title ] @ (List.map ~f:(fun x -> Atom.to_string
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Units.Angstrom x) nuclei)
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|> String.concat ~sep:"\n"
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;;
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let of_xyz_string
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?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1))
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?(units=Units.Angstrom)
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s =
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let l = String.split s ~on:'\n'
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|> List.filter ~f:(fun x -> x <> "")
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|> List.map ~f:(fun x -> Atom.of_string units x)
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in
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let ne = ( get_charge {
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nuclei=l ;
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elec_alpha=(Elec_alpha_number.of_int 1) ;
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elec_beta=(Elec_beta_number.of_int 0) }
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|> Charge.to_int
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) + 1 - (Charge.to_int charge)
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|> Elec_number.of_int
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in
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let (na,nb) = Multiplicity.to_alpha_beta ne multiplicity in
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let result =
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{ nuclei = l ;
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elec_alpha = na ;
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elec_beta = nb }
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in
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if ((get_multiplicity result) <> multiplicity) then
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let msg = Printf.sprintf
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"With %d electrons multiplicity %d is impossible"
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(Elec_number.to_int ne)
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(Multiplicity.to_int multiplicity)
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in
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raise (MultiplicityError msg);
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else () ;
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result
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;;
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let of_xyz_file
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?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1))
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?(units=Units.Angstrom)
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filename =
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let (_,buffer) = In_channel.read_all filename
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|> String.lsplit2_exn ~on:'\n' in
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let (_,buffer) = String.lsplit2_exn buffer ~on:'\n' in
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of_xyz_string ~charge:charge ~multiplicity:multiplicity
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~units:units buffer
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;;
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include To_md5;;
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let to_md5 = to_md5 sexp_of_t
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;;
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