mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-11-03 12:43:48 +01:00
788 lines
23 KiB
OCaml
788 lines
23 KiB
OCaml
open Qputils
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open Qptypes
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open Sexplib.Std
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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 (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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(** 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.create 63
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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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Hashtbl.find basis_table key
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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 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.file_exists basis,
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Sys.file_exists long_basis
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with
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| true , _ -> open_in basis
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| false, true -> open_in long_basis
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| _ -> failwith ("Basis "^basis^" not found")
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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_ext.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 (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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Hashtbl.add basis_table key new_channel
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) nuclei
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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_ext.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_ascii 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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Hashtbl.add basis_table key new_channel
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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_ext.split ~on:'|' b
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|> List.rev_map String.trim
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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.create 63
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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_opt 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.file_exists pseudo,
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Sys.file_exists long_pseudo
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with
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| true , _ -> open_in pseudo
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| false, true-> open_in 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_ext.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 (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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Hashtbl.add pseudo_table key new_channel
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) nuclei
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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_ascii 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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Hashtbl.add pseudo_table key new_channel
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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_ext.split ~on:'|' p
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|> List.rev_map String.trim
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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_ext.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 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 (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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) nuclei
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in
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let z_core =
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List.map (fun x ->
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Positive_int.to_int x.Pseudo.n_elec
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|> float_of_int
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) pseudo
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in
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let nucl_num = (List.length z_core) in
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Ezfio.set_pseudo_nucl_charge_remove (Ezfio.ezfio_array_of_list
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~rank:1 ~dim:[| nucl_num |] ~data:z_core);
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let molecule =
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let n_elec_to_remove =
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List.fold_left (fun accu x ->
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accu + (Positive_int.to_int x.Pseudo.n_elec)) 0 pseudo
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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 (fun x -> Positive_int.to_int x.Pseudo.n_elec
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|> Float.of_int) pseudo
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|> Array.of_list
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in
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List.mapi (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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) molecule.Molecule.nuclei
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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 (fun x->Element.to_string x.Atom.element) nuclei
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and charges =
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list_map (fun x-> Atom.(Charge.to_float x.charge)) nuclei
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and coords =
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(list_map (fun x-> x.Atom.coord.Point3d.x) nuclei) @
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(list_map (fun x-> x.Atom.coord.Point3d.y) nuclei) @
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(list_map (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_left (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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) 0 pseudo
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and lmax =
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List.fold_left (fun accu x ->
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let x =
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List.fold_left (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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) 0 x.Pseudo.non_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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) 0 pseudo
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in
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let kmax =
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Array.init (lmax+1) (fun i->
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list_map (fun x ->
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List.filter (fun (y,_) ->
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(Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj) = i)
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x.Pseudo.non_local
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|> List.length ) pseudo
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|> List.fold_left (fun accu x ->
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if accu > x then accu else x) 0
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)
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|> Array.fold_left (fun accu i ->
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if i > accu then i else accu) 0
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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 klocmax nucl_num 0. ,
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Array.make_matrix klocmax nucl_num 0. ,
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Array.make_matrix klocmax nucl_num 0
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in
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List.iteri (fun j x ->
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List.iteri (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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) x.Pseudo.local
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) pseudo ;
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let concat_2d tmp_array =
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let data =
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Array.map Array.to_list tmp_array
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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) (fun _ ->
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(Array.make_matrix kmax nucl_num 0. )),
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Array.init (lmax+1) (fun _ ->
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(Array.make_matrix kmax nucl_num 0. )),
|
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Array.init (lmax+1) (fun _ ->
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(Array.make_matrix kmax nucl_num 0 ))
|
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in
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List.iteri (fun j x ->
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let last_idx =
|
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Array.make (lmax+1) 0
|
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in
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List.iter (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
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tmp_array_v_kl.(k).(i).(j) <- AO_coef.to_float c;
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tmp_array_dz_kl.(k).(i).(j) <- y;
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tmp_array_n_kl.(k).(i).(j) <- z;
|
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last_idx.(k) <- i+1;
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) x.Pseudo.non_local
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) pseudo ;
|
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let concat_3d tmp_array =
|
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let data =
|
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Array.map (fun x ->
|
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Array.map Array.to_list x
|
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|> Array.to_list
|
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|> List.concat) tmp_array
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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:3 ~dim:[|nucl_num ; kmax ; lmax+1|] ~data
|
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in
|
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concat_3d tmp_array_v_kl
|
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|> Ezfio.set_pseudo_pseudo_v_kl ;
|
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concat_3d tmp_array_dz_kl
|
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|> Ezfio.set_pseudo_pseudo_dz_kl ;
|
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concat_3d tmp_array_n_kl
|
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|> Ezfio.set_pseudo_pseudo_n_kl ;
|
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in
|
|
|
|
|
|
|
|
|
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(* Write Basis set *)
|
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let basis =
|
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|
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let nmax =
|
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Nucl_number.get_max ()
|
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in
|
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let rec do_work (accu:(Atom.t*Nucl_number.t) list) (n:int) = function
|
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| [] -> accu
|
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| e::tail ->
|
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let new_accu =
|
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(e,(Nucl_number.of_int ~max:nmax n))::accu
|
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in
|
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do_work new_accu (n+1) tail
|
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in
|
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let result = do_work [] 1 nuclei
|
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|> List.rev
|
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|> list_map (fun (x,i) ->
|
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try
|
|
let e =
|
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match x.Atom.element with
|
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| Element.X -> Element.H
|
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| e -> e
|
|
in
|
|
let key =
|
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Int_elem (i,x.Atom.element)
|
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in
|
|
try
|
|
Basis.read_element (basis_channel key) i e
|
|
with Not_found ->
|
|
let key =
|
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Element x.Atom.element
|
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in
|
|
try
|
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Basis.read_element (basis_channel key) i e
|
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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;
|
|
Ezfio.set_basis_basis b;
|
|
let ao_prim_num = list_map (fun (_,g,_) -> List.length g.Gto.lc) long_basis
|
|
and ao_nucl = list_map (fun (_,_,n) -> Nucl_number.to_int n) long_basis
|
|
and ao_power=
|
|
let l = list_map (fun (x,_,_) -> x) long_basis in
|
|
(list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.x)) l)@
|
|
(list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.y)) l)@
|
|
(list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.z)) l)
|
|
in
|
|
let ao_prim_num_max = List.fold_left (fun s x ->
|
|
if x > s then x
|
|
else s) 0 ao_prim_num
|
|
in
|
|
let gtos =
|
|
list_map (fun (_,x,_) -> x) long_basis
|
|
in
|
|
|
|
let create_expo_coef ec =
|
|
let coefs =
|
|
begin match ec with
|
|
| `Coefs -> list_map (fun x->
|
|
list_map (fun (_,coef) ->
|
|
AO_coef.to_float coef) x.Gto.lc) gtos
|
|
| `Expos -> list_map (fun x->
|
|
list_map (fun (prim,_) -> AO_expo.to_float
|
|
prim.GaussianPrimitive.expo) x.Gto.lc) gtos
|
|
end
|
|
in
|
|
let rec get_n n accu = function
|
|
| [] -> List.rev accu
|
|
| h::tail ->
|
|
let y =
|
|
begin match List.nth_opt 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 () =
|
|
let shell_num = List.length basis in
|
|
let lc : (GaussianPrimitive.t * Qptypes.AO_coef.t) list list =
|
|
list_map ( fun (g,_) -> g.Gto.lc ) basis
|
|
in
|
|
let ang_mom =
|
|
list_map (fun (l : (GaussianPrimitive.t * Qptypes.AO_coef.t) list) ->
|
|
let x, _ = List.hd l in
|
|
Angmom.to_l x.GaussianPrimitive.sym |> Qptypes.Positive_int.to_int
|
|
) lc
|
|
in
|
|
let expo =
|
|
list_map (fun l -> list_map (fun (x,_) -> Qptypes.AO_expo.to_float x.GaussianPrimitive.expo) l ) lc
|
|
|> List.concat
|
|
in
|
|
let coef =
|
|
list_map (fun l ->
|
|
list_map (fun (_,x) -> Qptypes.AO_coef.to_float x) l
|
|
) lc
|
|
|> List.concat
|
|
in
|
|
let shell_prim_num =
|
|
list_map List.length lc
|
|
in
|
|
let shell_idx =
|
|
let rec make_list n accu = function
|
|
| 0 -> accu
|
|
| i -> make_list n (n :: accu) (i-1)
|
|
in
|
|
let rec aux count accu = function
|
|
| [] -> List.rev accu
|
|
| l::rest ->
|
|
let new_l = make_list count accu (List.length l) in
|
|
aux (count+1) new_l rest
|
|
in
|
|
aux 1 [] lc
|
|
in
|
|
let prim_num = List.length coef in
|
|
Ezfio.set_basis_typ "Gaussian";
|
|
Ezfio.set_basis_shell_num shell_num;
|
|
Ezfio.set_basis_prim_num prim_num ;
|
|
Ezfio.set_basis_shell_prim_num (Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| shell_num |] ~data:shell_prim_num);
|
|
Ezfio.set_basis_shell_ang_mom (Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| shell_num |] ~data:ang_mom ) ;
|
|
Ezfio.set_basis_shell_index (Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| prim_num |] ~data:shell_idx) ;
|
|
Ezfio.set_basis_basis_nucleus_index (Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| shell_num |]
|
|
~data:( list_map (fun (_,n) -> Nucl_number.to_int n) basis)
|
|
) ;
|
|
Ezfio.set_basis_nucleus_shell_num(Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| nucl_num |]
|
|
~data:(
|
|
list_map (fun (_,n) -> Nucl_number.to_int n) basis
|
|
|> List.fold_left (fun accu i ->
|
|
match accu with
|
|
| [] -> [(1,i)]
|
|
| (h,j) :: rest -> if j == i then ((h+1,j)::rest) else ((1,i)::(h,j)::rest)
|
|
) []
|
|
|> List.rev
|
|
|> List.map fst
|
|
)) ;
|
|
Ezfio.set_basis_prim_coef (Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| prim_num |] ~data:coef) ;
|
|
Ezfio.set_basis_prim_expo (Ezfio.ezfio_array_of_list
|
|
~rank:1 ~dim:[| prim_num |] ~data:expo) ;
|
|
|
|
|
|
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
|
|
try
|
|
if Sys.is_directory ezfio_file then
|
|
rmdir ezfio_file
|
|
with _ -> ()
|
|
end;
|
|
raise ex;
|
|
end
|
|
in
|
|
ignore @@ Sys.command ("qp_edit -c "^ezfio_file);
|
|
print_endline ezfio_file
|
|
|
|
|
|
|
|
|
|
let () =
|
|
|
|
try (
|
|
|
|
let open Command_line in
|
|
begin
|
|
"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.
|
|
" |> set_description_doc ;
|
|
set_header_doc (Sys.argv.(0) ^ " - Quantum Package command");
|
|
|
|
[ { opt=Optional ; short='o'; long="output";
|
|
arg=With_arg "EZFIO_DIR";
|
|
doc="Name of the created EZFIO directory."} ;
|
|
|
|
{ opt=Mandatory; short='b'; long="basis";
|
|
arg=With_arg "<string>";
|
|
doc="Name of basis set file. Searched in ${QP_ROOT}/data/basis if not found."} ;
|
|
|
|
{ opt=Optional ; short='a'; long="au";
|
|
arg=Without_arg;
|
|
doc="Input geometry is in atomic units."} ;
|
|
|
|
{ opt=Optional ; short='c'; long="charge";
|
|
arg=With_arg "<int>";
|
|
doc="Total charge of the molecule. Default is 0. For negative values, use m instead of -, for ex m1"} ;
|
|
|
|
{ opt=Optional ; short='d'; long="dummy";
|
|
arg=With_arg "<float>";
|
|
doc="Add dummy atoms. x * (covalent radii of the atoms)."} ;
|
|
|
|
{ opt=Optional ; short='m'; long="multiplicity";
|
|
arg=With_arg "<int>";
|
|
doc="Spin multiplicity (2S+1) of the molecule. Default is 1."} ;
|
|
|
|
{ opt=Optional ; short='p'; long="pseudo";
|
|
arg=With_arg "<string>";
|
|
doc="Name of the pseudopotential."} ;
|
|
|
|
{ opt=Optional ; short='x'; long="cartesian";
|
|
arg=Without_arg;
|
|
doc="Compute AOs in the Cartesian basis set (6d, 10f, ...)."} ;
|
|
|
|
anonymous "FILE" Mandatory "Input file in xyz format or z-matrix.";
|
|
]
|
|
|> set_specs
|
|
end;
|
|
|
|
|
|
(* Handle options *)
|
|
let output =
|
|
Command_line.get "output"
|
|
in
|
|
|
|
let basis =
|
|
match Command_line.get "basis" with
|
|
| None -> ""
|
|
| Some x -> x
|
|
in
|
|
|
|
let au =
|
|
Command_line.get_bool "au"
|
|
in
|
|
|
|
let charge =
|
|
match Command_line.get "charge" with
|
|
| None -> 0
|
|
| Some x -> ( if x.[0] = 'm' then
|
|
~- (int_of_string (String.sub x 1 (String.length x - 1)))
|
|
else
|
|
int_of_string x )
|
|
in
|
|
|
|
let dummy =
|
|
match Command_line.get "dummy" with
|
|
| None -> 0.
|
|
| Some x -> float_of_string x
|
|
in
|
|
|
|
let multiplicity =
|
|
match Command_line.get "multiplicity" with
|
|
| None -> 1
|
|
| Some n -> int_of_string n
|
|
in
|
|
|
|
let pseudo =
|
|
Command_line.get "pseudo"
|
|
in
|
|
|
|
let cart =
|
|
Command_line.get_bool "cartesian"
|
|
in
|
|
|
|
let xyz_filename =
|
|
match Command_line.anon_args () with
|
|
| [] -> failwith "input file is missing"
|
|
| x::_ -> x
|
|
in
|
|
|
|
run ?o:output basis au charge dummy multiplicity pseudo cart xyz_filename
|
|
)
|
|
with
|
|
| Failure txt -> Printf.eprintf "Fatal error: %s\n%!" txt
|
|
| Command_line.Error txt -> Printf.eprintf "Command line error: %s\n%!" txt
|
|
|
|
|