mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-12-23 04:43:45 +01:00
2cffbdcc9d
instead of real/imag parts read separately, use ezfio to read/write complex arrays with extra dimension of size 2 converter needs to be tested (might need to transpose some axes in arrays) converter has extra garbage that needs to be removed after testing
325 lines
9.4 KiB
OCaml
325 lines
9.4 KiB
OCaml
open Qptypes
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open Qputils
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open Sexplib.Std
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module Mo_basis : sig
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type t =
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{ mo_num : MO_number.t ;
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mo_label : MO_label.t;
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mo_class : MO_class.t array;
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mo_occ : MO_occ.t array;
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mo_coef : (MO_coef.t array) array;
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ao_md5 : MD5.t;
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} [@@deriving sexp]
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val read : unit -> t option
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val write : t -> unit
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val reorder : t -> int array -> t
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val to_string : t -> string
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val to_rst : t -> Rst_string.t
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end = struct
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type t =
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{ mo_num : MO_number.t ;
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mo_label : MO_label.t;
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mo_class : MO_class.t array;
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mo_occ : MO_occ.t array;
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mo_coef : (MO_coef.t array) array;
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ao_md5 : MD5.t;
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} [@@deriving sexp]
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let get_default = Qpackage.get_ezfio_default "mo_basis"
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let is_complex = lazy (Ezfio.get_nuclei_is_complex () )
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let read_mo_label () =
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if not (Ezfio.has_mo_basis_mo_label ()) then
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Ezfio.set_mo_basis_mo_label "None"
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;
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Ezfio.get_mo_basis_mo_label ()
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|> MO_label.of_string
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let reorder b ordering =
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{ b with
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mo_coef = Array.map (fun mo ->
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Array.init (Array.length mo)
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(fun i -> mo.(ordering.(i)))
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) b.mo_coef
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}
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let read_ao_md5 () =
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let ao_md5 =
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match (Input_ao_basis.Ao_basis.read ()) with
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| None -> failwith "Unable to read AO basis"
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| Some result -> Input_ao_basis.Ao_basis.to_md5 result
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in
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let result =
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if not (Ezfio.has_mo_basis_ao_md5 ()) then
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begin
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MD5.to_string ao_md5
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|> Ezfio.set_mo_basis_ao_md5
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end;
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Ezfio.get_mo_basis_ao_md5 ()
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|> MD5.of_string
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in
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if (ao_md5 <> result) then
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begin
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Printf.eprintf ":%s:\n:%s:\n%!" (MD5.to_string ao_md5) (MD5.to_string result);
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failwith "The current MOs don't correspond to the current AOs."
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end;
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result
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let read_mo_num () =
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let elec_alpha_num =
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Ezfio.get_electrons_elec_alpha_num ()
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in
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let result =
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Ezfio.get_mo_basis_mo_num ()
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in
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if result < elec_alpha_num then
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failwith "More alpha electrons than MOs";
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MO_number.of_int result
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let read_mo_class () =
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if not (Ezfio.has_mo_basis_mo_class ()) then
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begin
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let mo_num = MO_number.to_int (read_mo_num ()) in
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let data =
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Array.init mo_num (fun _ -> MO_class.(to_string (Active [])))
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|> Array.to_list
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in
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Ezfio.ezfio_array_of_list ~rank:1
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~dim:[| mo_num |] ~data:data
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|> Ezfio.set_mo_basis_mo_class
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end;
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Ezfio.flattened_ezfio (Ezfio.get_mo_basis_mo_class () )
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|> Array.map MO_class.of_string
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let read_mo_occ () =
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if not (Ezfio.has_mo_basis_mo_label ()) then
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begin
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let elec_alpha_num = Ezfio.get_electrons_elec_alpha_num ()
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and elec_beta_num = Ezfio.get_electrons_elec_beta_num ()
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and mo_num = MO_number.to_int (read_mo_num ()) in
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let data = Array.init mo_num (fun i ->
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if (i<elec_beta_num) then 2.
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else if (i < elec_alpha_num) then 1.
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else 0.) |> Array.to_list in
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Ezfio.ezfio_array_of_list ~rank:1
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~dim:[| mo_num |] ~data:data
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|> Ezfio.set_mo_basis_mo_occ
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end;
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Ezfio.flattened_ezfio (Ezfio.get_mo_basis_mo_occ () )
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|> Array.map MO_occ.of_float
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let read_mo_coef () =
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let a =
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(
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if Lazy.force is_complex then
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Ezfio.get_mo_basis_mo_coef_complex ()
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else
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Ezfio.get_mo_basis_mo_coef ()
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)
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|> Ezfio.flattened_ezfio
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|> Array.map MO_coef.of_float
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in
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let mo_num = read_mo_num () |> MO_number.to_int in
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let ao_num = (Array.length a)/mo_num in
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Array.init mo_num (fun j ->
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Array.sub a (j*ao_num) (ao_num)
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)
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let read () =
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if (Ezfio.has_mo_basis_mo_num ()) then
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Some
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{ mo_num = read_mo_num ();
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mo_label = read_mo_label () ;
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mo_class = read_mo_class ();
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mo_occ = read_mo_occ ();
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mo_coef = read_mo_coef ();
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ao_md5 = read_ao_md5 ();
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}
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else
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None
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let mo_coef_to_string mo_coef =
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let ao_num = Array.length mo_coef.(0)
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and mo_num = Array.length mo_coef in
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let rec print_five imin imax =
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match (imax-imin+1) with
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| 1 ->
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let header = [ Printf.sprintf " #%15d" (imin+1) ; ] in
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let new_lines =
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List.init ao_num (fun i ->
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Printf.sprintf " %3d %15.10f " (i+1)
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(MO_coef.to_float mo_coef.(imin ).(i)) )
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in header @ new_lines
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| 2 ->
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let header = [ Printf.sprintf " #%15d %15d" (imin+1) (imin+2) ; ] in
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let new_lines =
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List.init ao_num (fun i ->
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Printf.sprintf " %3d %15.10f %15.10f" (i+1)
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(MO_coef.to_float mo_coef.(imin ).(i))
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(MO_coef.to_float mo_coef.(imin+1).(i)) )
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in header @ new_lines
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| 3 ->
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let header = [ Printf.sprintf " #%15d %15d %15d"
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(imin+1) (imin+2) (imin+3); ] in
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let new_lines =
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List.init ao_num (fun i ->
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Printf.sprintf " %3d %15.10f %15.10f %15.10f" (i+1)
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(MO_coef.to_float mo_coef.(imin ).(i))
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(MO_coef.to_float mo_coef.(imin+1).(i))
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(MO_coef.to_float mo_coef.(imin+2).(i)) )
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in header @ new_lines
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| 4 ->
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let header = [ Printf.sprintf " #%15d %15d %15d %15d"
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(imin+1) (imin+2) (imin+3) (imin+4) ; ] in
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let new_lines =
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List.init ao_num (fun i ->
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Printf.sprintf " %3d %15.10f %15.10f %15.10f %15.10f" (i+1)
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(MO_coef.to_float mo_coef.(imin ).(i))
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(MO_coef.to_float mo_coef.(imin+1).(i))
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(MO_coef.to_float mo_coef.(imin+2).(i))
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(MO_coef.to_float mo_coef.(imin+3).(i)) )
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in header @ new_lines
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| 5 ->
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let header = [ Printf.sprintf " #%15d %15d %15d %15d %15d"
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(imin+1) (imin+2) (imin+3) (imin+4) (imin+5) ; ] in
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let new_lines =
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List.init ao_num (fun i ->
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Printf.sprintf " %3d %15.10f %15.10f %15.10f %15.10f %15.10f" (i+1)
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(MO_coef.to_float mo_coef.(imin ).(i))
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(MO_coef.to_float mo_coef.(imin+1).(i))
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(MO_coef.to_float mo_coef.(imin+2).(i))
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(MO_coef.to_float mo_coef.(imin+3).(i))
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(MO_coef.to_float mo_coef.(imin+4).(i)) )
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in header @ new_lines
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| _ -> assert false
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in
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let rec create_list accu i =
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if (i+4 < mo_num) then
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create_list ( (print_five i (i+3) |> String.concat "\n")::accu ) (i+4)
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else
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(print_five i (mo_num-1) |> String.concat "\n")::accu |> List.rev
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in
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create_list [] 0 |> String.concat "\n\n"
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let to_rst b =
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Printf.sprintf "
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Label of the molecular orbitals ::
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mo_label = %s
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Total number of MOs ::
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mo_num = %s
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MO coefficients ::
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%s
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"
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(MO_label.to_string b.mo_label)
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(MO_number.to_string b.mo_num)
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(mo_coef_to_string b.mo_coef)
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|> Rst_string.of_string
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let to_string b =
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Printf.sprintf "
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mo_label = \"%s\"
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mo_num = %s
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mo_clas = %s
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mo_occ = %s
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mo_coef = %s
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"
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(MO_label.to_string b.mo_label)
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(MO_number.to_string b.mo_num)
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(b.mo_class |> Array.to_list |> List.map
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(MO_class.to_string) |> String.concat ", " )
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(b.mo_occ |> Array.to_list |> List.map
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(MO_occ.to_string) |> String.concat ", " )
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(b.mo_coef |> Array.map
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(fun x-> Array.map MO_coef.to_string x |>
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Array.to_list |> String.concat "," ) |>
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Array.to_list |> String.concat "\n" )
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let write_mo_num n =
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MO_number.to_int n
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|> Ezfio.set_mo_basis_mo_num
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let write_mo_label a =
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MO_label.to_string a
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|> Ezfio.set_mo_basis_mo_label
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let write_mo_class a =
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let mo_num = Array.length a in
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let data = Array.map MO_class.to_string a
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|> Array.to_list
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in Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| mo_num |] ~data
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|> Ezfio.set_mo_basis_mo_class
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let write_mo_occ a =
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let mo_num = Array.length a in
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let data = Array.map MO_occ.to_float a
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|> Array.to_list
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in Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| mo_num |] ~data
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|> Ezfio.set_mo_basis_mo_occ
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let write_md5 a =
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MD5.to_string a
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|> Ezfio.set_mo_basis_ao_md5
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let write_mo_coef a =
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let mo_num = Array.length a in
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let ao_num =
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let x = Array.length a.(0) in
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if Lazy.force is_complex then x/2 else x
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in
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let data =
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Array.map (fun mo -> Array.map MO_coef.to_float mo
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|> Array.to_list) a
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|> Array.to_list
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|> List.concat
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in
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if Lazy.force is_complex then
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(Ezfio.ezfio_array_of_list ~rank:3 ~dim:[| 2 ; ao_num ; mo_num |] ~data
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|> Ezfio.set_mo_basis_mo_coef_complex )
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else
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(Ezfio.ezfio_array_of_list ~rank:2 ~dim:[| ao_num ; mo_num |] ~data
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|> Ezfio.set_mo_basis_mo_coef )
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let write
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{ mo_num : MO_number.t ;
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mo_label : MO_label.t;
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mo_class : MO_class.t array;
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mo_occ : MO_occ.t array;
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mo_coef : (MO_coef.t array) array;
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ao_md5 : MD5.t;
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} =
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write_mo_num mo_num;
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write_mo_label mo_label;
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write_mo_class mo_class;
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write_mo_occ mo_occ;
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write_mo_coef mo_coef;
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write_md5 ao_md5
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end
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