701 lines
21 KiB
OCaml
701 lines
21 KiB
OCaml
open Qputils
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open Qptypes
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open Core
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let spec =
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let open Command.Spec in
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empty
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+> flag "o" (optional string)
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~doc:"file Name of the created EZFIO file."
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+> flag "b" (required string)
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~doc:"string Name of basis set."
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+> flag "au" no_arg
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~doc:"Input geometry is in atomic units."
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+> flag "c" (optional_with_default 0 int)
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~doc:"int Total charge of the molecule. Default is 0."
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+> flag "d" (optional_with_default 0. float)
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~doc:"float Add dummy atoms. x * (covalent radii of the atoms)"
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+> flag "m" (optional_with_default 1 int)
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~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1."
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+> flag "p" (optional string)
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~doc:"string Name of the pseudopotential"
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+> flag "cart" no_arg
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~doc:" Compute AOs in the Cartesian basis set (6d, 10f, ...)"
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+> anon ("(xyz_file|zmt_file)" %: file )
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type element =
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| Element of Element.t
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| Int_elem of (Nucl_number.t * Element.t)
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(** Handle dummy atoms placed on bonds *)
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let dummy_centers ~threshold ~molecule ~nuclei =
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let d =
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Molecule.distance_matrix molecule
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in
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let n =
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Array.length d
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in
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let nuclei =
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Array.of_list nuclei
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in
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let rec aux accu = function
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| (-1,_) -> accu
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| (i,-1) -> aux accu (i-1,i-1)
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| (i,j) when (i>j) ->
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let new_accu =
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let x,y =
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Element.covalent_radius (nuclei.(i)).Atom.element |> Positive_float.to_float,
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Element.covalent_radius (nuclei.(j)).Atom.element |> Positive_float.to_float
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in
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let r =
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( x +. y ) *. threshold
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in
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if d.(i).(j) < r then
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(i,x,j,y,d.(i).(j)) :: accu
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else
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accu
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in aux new_accu (i,j-1)
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| (i,j) when (i=j) -> aux accu (i,j-1)
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| _ -> assert false
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in
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aux [] (n-1,n-1)
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|> List.map ~f:(fun (i,x,j,y,r) ->
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let f =
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x /. (x +. y)
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in
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let u =
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Point3d.of_tuple ~units:Units.Bohr
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( nuclei.(i).Atom.coord.Point3d.x +.
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(nuclei.(j).Atom.coord.Point3d.x -. nuclei.(i).Atom.coord.Point3d.x) *. f,
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nuclei.(i).Atom.coord.Point3d.y +.
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(nuclei.(j).Atom.coord.Point3d.y -. nuclei.(i).Atom.coord.Point3d.y) *. f,
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nuclei.(i).Atom.coord.Point3d.z +.
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(nuclei.(j).Atom.coord.Point3d.z -. nuclei.(i).Atom.coord.Point3d.z) *. f)
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in
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Atom.{ element = Element.X ; charge = Charge.of_int 0 ; coord = u }
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)
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(** Returns the list of available basis sets *)
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let list_basis () =
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let basis_list =
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Qpackage.root ^ "/install/emsl/EMSL_api.py list_basis"
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|> Unix.open_process_in
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|> In_channel.input_lines
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|> List.map ~f:(fun x ->
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match String.split x ~on:'\'' with
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| [] -> ""
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| a :: []
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| _ :: a :: _ -> String.strip a
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)
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in
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List.sort basis_list ~cmp:String.ascending
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|> String.concat ~sep:"\n"
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(** Run the program *)
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let run ?o b au c d m p cart xyz_file =
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(* Read molecule *)
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let molecule =
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if au then
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(Molecule.of_file xyz_file ~charge:(Charge.of_int c)
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~multiplicity:(Multiplicity.of_int m) ~units:Units.Bohr)
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else
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(Molecule.of_file xyz_file ~charge:(Charge.of_int c)
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~multiplicity:(Multiplicity.of_int m) )
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in
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let dummy =
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dummy_centers ~threshold:d ~molecule ~nuclei:molecule.Molecule.nuclei
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in
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let nuclei =
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molecule.Molecule.nuclei @ dummy
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in
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(**********
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Basis set
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**********)
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let basis_table =
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Hashtbl.Poly.create ()
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in
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(* Open basis set channels *)
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let basis_channel element =
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let key =
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match element with
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| Element e -> Element.to_string e
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| Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i) (Element.to_string e)
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in
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match Hashtbl.find basis_table key with
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| Some in_channel ->
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in_channel
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| None -> raise Not_found
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in
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let temp_filename =
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Filename.temp_file "qp_create_" ".basis"
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in
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let () =
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Sys.remove temp_filename
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in
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let fetch_channel basis =
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let command =
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Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename
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^ "." ^ basis ^ "\" \"" ^ basis ^"\""
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in
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let long_basis =
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Qpackage.root ^ "/data/basis/" ^ basis
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in
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match
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Sys.is_file basis,
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Sys.is_file long_basis
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with
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| `Yes, _ -> In_channel.create basis
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| `No , `Yes -> In_channel.create long_basis
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| _ ->
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begin
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let filename =
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Unix.open_process_in command
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|> In_channel.input_all
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|> String.strip
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in
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let new_channel =
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In_channel.create filename
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in
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Unix.unlink filename;
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new_channel
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end
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in
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let rec build_basis = function
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| [] -> ()
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| elem_and_basis_name :: rest ->
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begin
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match (String.lsplit2 ~on:':' elem_and_basis_name) with
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| None -> (* Principal basis *)
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begin
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let basis =
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elem_and_basis_name
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in
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let new_channel =
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fetch_channel basis
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in
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List.iter nuclei ~f:(fun elem->
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let key =
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Element.to_string elem.Atom.element
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in
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match Hashtbl.add basis_table ~key:key ~data:new_channel with
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| `Ok -> ()
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| `Duplicate -> ()
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)
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end
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| Some (key, basis) -> (*Aux basis *)
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begin
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let elem =
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try
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Element (Element.of_string key)
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with Element.ElementError _ ->
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let result =
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match (String.split ~on:',' key) with
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| i :: k :: [] -> (Nucl_number.of_int @@ int_of_string i, Element.of_string k)
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| _ -> failwith "Expected format is int,Element:basis"
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in Int_elem result
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and basis =
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String.lowercase basis
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in
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let key =
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match elem with
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| Element e -> Element.to_string e
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| Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i) (Element.to_string e)
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in
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let new_channel =
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fetch_channel basis
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in
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begin
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match Hashtbl.add basis_table ~key:key ~data:new_channel with
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| `Ok -> ()
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| `Duplicate ->
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let e =
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match elem with
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| Element e -> e
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| Int_elem (_,e) -> e
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in
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failwith ("Duplicate definition of basis for "^(Element.to_long_string e))
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end
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end
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end;
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build_basis rest
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in
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String.split ~on:'|' b
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|> List.rev_map ~f:String.strip
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|> build_basis;
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(***************
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Pseudopotential
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***************)
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let pseudo_table =
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Hashtbl.Poly.create ()
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in
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(* Open pseudo channels *)
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let pseudo_channel element =
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let key =
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Element.to_string element
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in
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Hashtbl.find pseudo_table key
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in
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let temp_filename =
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Filename.temp_file "qp_create_" ".pseudo"
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in
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let () =
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Sys.remove temp_filename
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in
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let fetch_channel pseudo =
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let long_pseudo =
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Qpackage.root ^ "/data/pseudo/" ^ pseudo
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in
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match
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Sys.is_file pseudo,
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Sys.is_file long_pseudo
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with
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| `Yes, _ -> In_channel.create pseudo
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| `No , `Yes -> In_channel.create long_pseudo
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| _ -> failwith ("Pseudo file "^pseudo^" not found.")
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in
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let rec build_pseudo = function
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| [] -> ()
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| elem_and_pseudo_name :: rest ->
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begin
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match (String.lsplit2 ~on:':' elem_and_pseudo_name) with
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| None -> (* Principal pseudo *)
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begin
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let pseudo =
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elem_and_pseudo_name
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in
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let new_channel =
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fetch_channel pseudo
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in
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List.iter nuclei ~f:(fun elem->
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let key =
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Element.to_string elem.Atom.element
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in
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match Hashtbl.add pseudo_table ~key:key ~data:new_channel with
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| `Ok -> ()
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| `Duplicate -> ()
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)
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end
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| Some (key, pseudo) -> (*Aux pseudo *)
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begin
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let elem =
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Element.of_string key
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and pseudo =
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String.lowercase pseudo
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in
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let key =
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Element.to_string elem
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in
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let new_channel =
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fetch_channel pseudo
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in
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begin
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match Hashtbl.add pseudo_table ~key:key ~data:new_channel with
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| `Ok -> ()
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| `Duplicate -> failwith ("Duplicate definition of pseudo for "^(Element.to_long_string elem))
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end
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end
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end;
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build_pseudo rest
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in
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let () =
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match p with
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| None -> ()
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| Some p ->
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String.split ~on:'|' p
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|> List.rev_map ~f:String.strip
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|> build_pseudo
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in
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(* Build EZFIO File name *)
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let ezfio_file =
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match o with
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| Some x -> x
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| None ->
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begin
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match String.rsplit2 ~on:'.' xyz_file with
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| Some (x,"xyz")
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| Some (x,"zmt") -> x^".ezfio"
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| _ -> xyz_file^".ezfio"
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end
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in
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if Sys.file_exists_exn ezfio_file then
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failwith (ezfio_file^" already exists");
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let write_file () =
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(* Create EZFIO *)
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Ezfio.set_file ezfio_file;
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(* Write Pseudo *)
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let pseudo =
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List.map nuclei ~f:(fun x ->
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match pseudo_channel x.Atom.element with
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| Some channel -> Pseudo.read_element channel x.Atom.element
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| None -> Pseudo.empty x.Atom.element
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)
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in
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let molecule =
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let n_elec_to_remove =
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List.fold pseudo ~init:0 ~f:(fun accu x ->
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accu + (Positive_int.to_int x.Pseudo.n_elec))
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in
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{ Molecule.elec_alpha =
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(Elec_alpha_number.to_int molecule.Molecule.elec_alpha)
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- n_elec_to_remove/2
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|> Elec_alpha_number.of_int;
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Molecule.elec_beta =
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(Elec_beta_number.to_int molecule.Molecule.elec_beta)
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- (n_elec_to_remove - n_elec_to_remove/2)
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|> Elec_beta_number.of_int;
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Molecule.nuclei =
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let charges =
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List.map pseudo ~f:(fun x -> Positive_int.to_int x.Pseudo.n_elec
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|> Float.of_int)
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|> Array.of_list
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in
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List.mapi molecule.Molecule.nuclei ~f:(fun i x ->
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{ x with Atom.charge = (Charge.to_float x.Atom.charge) -. charges.(i)
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|> Charge.of_float }
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)
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}
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in
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let nuclei =
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molecule.Molecule.nuclei @ dummy
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in
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(* Write Electrons *)
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Ezfio.set_electrons_elec_alpha_num ( Elec_alpha_number.to_int
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molecule.Molecule.elec_alpha ) ;
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Ezfio.set_electrons_elec_beta_num ( Elec_beta_number.to_int
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molecule.Molecule.elec_beta ) ;
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(* Write Nuclei *)
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let labels =
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List.map ~f:(fun x->Element.to_string x.Atom.element) nuclei
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and charges =
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List.map ~f:(fun x-> Atom.(Charge.to_float x.charge)) nuclei
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and coords =
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(List.map ~f:(fun x-> x.Atom.coord.Point3d.x) nuclei) @
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(List.map ~f:(fun x-> x.Atom.coord.Point3d.y) nuclei) @
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(List.map ~f:(fun x-> x.Atom.coord.Point3d.z) nuclei) in
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let nucl_num = (List.length labels) in
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Ezfio.set_nuclei_nucl_num nucl_num ;
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Ezfio.set_nuclei_nucl_label (Ezfio.ezfio_array_of_list
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~rank:1 ~dim:[| nucl_num |] ~data:labels);
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Ezfio.set_nuclei_nucl_charge (Ezfio.ezfio_array_of_list
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~rank:1 ~dim:[| nucl_num |] ~data:charges);
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Ezfio.set_nuclei_nucl_coord (Ezfio.ezfio_array_of_list
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~rank:2 ~dim:[| nucl_num ; 3 |] ~data:coords);
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(* Write pseudopotential *)
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let () =
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match p with
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| None -> Ezfio.set_pseudo_do_pseudo false
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| _ -> Ezfio.set_pseudo_do_pseudo true
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in
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let klocmax =
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List.fold pseudo ~init:0 ~f:(fun accu x ->
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let x =
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List.length x.Pseudo.local
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in
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if (x > accu) then x
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else accu
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)
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and lmax =
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List.fold pseudo ~init:0 ~f:(fun accu x ->
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let x =
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List.fold x.Pseudo.non_local ~init:0 ~f:(fun accu (x,_) ->
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let x =
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Positive_int.to_int x.Pseudo.GaussianPrimitive_non_local.proj
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in
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if (x > accu) then x
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else accu
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)
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in
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if (x > accu) then x
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else accu
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)
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in
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let kmax =
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Array.init (lmax+1) ~f:(fun i->
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List.map pseudo ~f:(fun x ->
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List.filter x.Pseudo.non_local ~f:(fun (y,_) ->
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(Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj) = i)
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|> List.length )
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|> List.fold ~init:0 ~f:(fun accu x ->
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if accu > x then accu else x)
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)
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|> Array.fold ~init:0 ~f:(fun accu i ->
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if i > accu then i else accu)
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in
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let () =
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Ezfio.set_pseudo_pseudo_klocmax klocmax;
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Ezfio.set_pseudo_pseudo_kmax kmax;
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Ezfio.set_pseudo_pseudo_lmax lmax;
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let tmp_array_v_k, tmp_array_dz_k, tmp_array_n_k =
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Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0. ,
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Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0. ,
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Array.make_matrix ~dimx:klocmax ~dimy:nucl_num 0
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in
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List.iteri pseudo ~f:(fun j x ->
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List.iteri x.Pseudo.local ~f:(fun i (y,c) ->
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tmp_array_v_k.(i).(j) <- AO_coef.to_float c;
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let y, z =
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AO_expo.to_float y.Pseudo.GaussianPrimitive_local.expo,
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R_power.to_int y.Pseudo.GaussianPrimitive_local.r_power
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in
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tmp_array_dz_k.(i).(j) <- y;
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tmp_array_n_k.(i).(j) <- z;
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)
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);
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let concat_2d tmp_array =
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let data =
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Array.map tmp_array ~f:Array.to_list
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|> Array.to_list
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|> List.concat
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in
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Ezfio.ezfio_array_of_list ~rank:2 ~dim:[|nucl_num ; klocmax|] ~data
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in
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concat_2d tmp_array_v_k
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|> Ezfio.set_pseudo_pseudo_v_k ;
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concat_2d tmp_array_dz_k
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|> Ezfio.set_pseudo_pseudo_dz_k;
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concat_2d tmp_array_n_k
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|> Ezfio.set_pseudo_pseudo_n_k;
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let tmp_array_v_kl, tmp_array_dz_kl, tmp_array_n_kl =
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Array.init (lmax+1) ~f:(fun _ ->
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(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0. )),
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Array.init (lmax+1) ~f:(fun _ ->
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(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0. )),
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Array.init (lmax+1) ~f:(fun _ ->
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(Array.make_matrix ~dimx:kmax ~dimy:nucl_num 0 ))
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in
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List.iteri pseudo ~f:(fun j x ->
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let last_idx =
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Array.create ~len:(lmax+1) 0
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in
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List.iter x.Pseudo.non_local ~f:(fun (y,c) ->
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let k, y, z =
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Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj,
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AO_expo.to_float y.Pseudo.GaussianPrimitive_non_local.expo,
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R_power.to_int y.Pseudo.GaussianPrimitive_non_local.r_power
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in
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let i =
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last_idx.(k)
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|
in
|
|
tmp_array_v_kl.(k).(i).(j) <- AO_coef.to_float c;
|
|
tmp_array_dz_kl.(k).(i).(j) <- y;
|
|
tmp_array_n_kl.(k).(i).(j) <- z;
|
|
last_idx.(k) <- i+1;
|
|
)
|
|
);
|
|
let concat_3d tmp_array =
|
|
let data =
|
|
Array.map tmp_array ~f:(fun x ->
|
|
Array.map x ~f:Array.to_list
|
|
|> Array.to_list
|
|
|> List.concat)
|
|
|> Array.to_list
|
|
|> List.concat
|
|
in
|
|
Ezfio.ezfio_array_of_list ~rank:3 ~dim:[|nucl_num ; kmax ; lmax+1|] ~data
|
|
in
|
|
concat_3d tmp_array_v_kl
|
|
|> Ezfio.set_pseudo_pseudo_v_kl ;
|
|
concat_3d tmp_array_dz_kl
|
|
|> Ezfio.set_pseudo_pseudo_dz_kl ;
|
|
concat_3d tmp_array_n_kl
|
|
|> Ezfio.set_pseudo_pseudo_n_kl ;
|
|
in
|
|
|
|
|
|
|
|
|
|
(* Write Basis set *)
|
|
let basis =
|
|
|
|
let nmax =
|
|
Nucl_number.get_max ()
|
|
in
|
|
let rec do_work (accu:(Atom.t*Nucl_number.t) list) (n:int) = function
|
|
| [] -> accu
|
|
| e::tail ->
|
|
let new_accu =
|
|
(e,(Nucl_number.of_int ~max:nmax n))::accu
|
|
in
|
|
do_work new_accu (n+1) tail
|
|
in
|
|
let result = do_work [] 1 nuclei
|
|
|> List.rev
|
|
|> List.map ~f:(fun (x,i) ->
|
|
try
|
|
let e =
|
|
match x.Atom.element with
|
|
| Element.X -> Element.H
|
|
| e -> e
|
|
in
|
|
let key =
|
|
Int_elem (i,x.Atom.element)
|
|
in
|
|
try
|
|
Basis.read_element (basis_channel key) i e
|
|
with Not_found ->
|
|
let key =
|
|
Element x.Atom.element
|
|
in
|
|
try
|
|
Basis.read_element (basis_channel key) i e
|
|
with Not_found ->
|
|
failwith (Printf.sprintf "Basis not found for atom %d (%s)" (Nucl_number.to_int i)
|
|
(Element.to_string x.Atom.element) )
|
|
with
|
|
| End_of_file -> failwith
|
|
("Element "^(Element.to_string x.Atom.element)^" not found in basis set.")
|
|
)
|
|
|> List.concat
|
|
in
|
|
(* close all in_channels *)
|
|
result
|
|
in
|
|
let long_basis = Long_basis.of_basis basis in
|
|
let ao_num = List.length long_basis in
|
|
Ezfio.set_ao_basis_ao_num ao_num;
|
|
Ezfio.set_ao_basis_ao_basis b;
|
|
let ao_prim_num = List.map long_basis ~f:(fun (_,g,_) -> List.length g.Gto.lc)
|
|
and ao_nucl = List.map long_basis ~f:(fun (_,_,n) -> Nucl_number.to_int n)
|
|
and ao_power=
|
|
let l = List.map long_basis ~f:(fun (x,_,_) -> x) in
|
|
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.x)) )@
|
|
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.y)) )@
|
|
(List.map l ~f:(fun t -> Positive_int.to_int Symmetry.Xyz.(t.z)) )
|
|
in
|
|
let ao_prim_num_max = List.fold ~init:0 ~f:(fun s x ->
|
|
if x > s then x
|
|
else s) ao_prim_num
|
|
in
|
|
let gtos =
|
|
List.map long_basis ~f:(fun (_,x,_) -> x)
|
|
in
|
|
|
|
let create_expo_coef ec =
|
|
let coefs =
|
|
begin match ec with
|
|
| `Coefs -> List.map gtos ~f:(fun x->
|
|
List.map x.Gto.lc ~f:(fun (_,coef) -> AO_coef.to_float coef) )
|
|
| `Expos -> List.map gtos ~f:(fun x->
|
|
List.map x.Gto.lc ~f:(fun (prim,_) -> AO_expo.to_float
|
|
prim.GaussianPrimitive.expo) )
|
|
end
|
|
in
|
|
let rec get_n n accu = function
|
|
| [] -> List.rev accu
|
|
| h::tail ->
|
|
let y =
|
|
begin match List.nth h n with
|
|
| Some x -> x
|
|
| None -> 0.
|
|
end
|
|
in
|
|
get_n n (y::accu) tail
|
|
in
|
|
let rec build accu = function
|
|
| n when n=ao_prim_num_max -> accu
|
|
| n -> build ( accu @ (get_n n [] coefs) ) (n+1)
|
|
in
|
|
build [] 0
|
|
in
|
|
|
|
let ao_coef = create_expo_coef `Coefs
|
|
and ao_expo = create_expo_coef `Expos
|
|
in
|
|
let () =
|
|
Ezfio.set_ao_basis_ao_prim_num (Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| ao_num |] ~data:ao_prim_num) ;
|
|
Ezfio.set_ao_basis_ao_nucl(Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| ao_num |] ~data:ao_nucl) ;
|
|
Ezfio.set_ao_basis_ao_power(Ezfio.ezfio_array_of_list
|
|
~rank:2 ~dim:[| ao_num ; 3 |] ~data:ao_power) ;
|
|
Ezfio.set_ao_basis_ao_coef(Ezfio.ezfio_array_of_list
|
|
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_coef) ;
|
|
Ezfio.set_ao_basis_ao_expo(Ezfio.ezfio_array_of_list
|
|
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_expo) ;
|
|
Ezfio.set_ao_basis_ao_cartesian(cart);
|
|
in
|
|
match Input.Ao_basis.read () with
|
|
| None -> failwith "Error in basis"
|
|
| Some x -> Input.Ao_basis.write x
|
|
in
|
|
let () =
|
|
try write_file () with
|
|
| ex ->
|
|
begin
|
|
begin
|
|
match Sys.is_directory ezfio_file with
|
|
| `Yes -> rmdir ezfio_file
|
|
| _ -> ()
|
|
end;
|
|
raise ex;
|
|
end
|
|
in ()
|
|
|
|
|
|
|
|
let command =
|
|
Command.basic_spec
|
|
~summary: "Quantum Package command"
|
|
~readme:(fun () -> "
|
|
|
|
=== Available basis sets ===
|
|
|
|
" ^ (list_basis ()) ^ "
|
|
|
|
============================
|
|
|
|
Creates an EZFIO directory from a standard xyz file or from a z-matrix file
|
|
in Gaussian format. The basis set is defined as a single string if all the
|
|
atoms are taken from the same basis set, otherwise specific elements can be
|
|
defined as follows:
|
|
|
|
-b \"cc-pcvdz | H:cc-pvdz | C:6-31g\"
|
|
-b \"cc-pvtz | 1,H:sto-3g | 3,H:6-31g\"
|
|
|
|
If a file with the same name as the basis set exists, this file will be read.
|
|
Otherwise, the basis set is obtained from the database.
|
|
|
|
" )
|
|
spec
|
|
(fun o b au c d m p cart xyz_file () ->
|
|
run ?o b au c d m p cart xyz_file )
|
|
|
|
|
|
let () =
|
|
Command.run command
|
|
|
|
|
|
|
|
|