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Working on aux basis
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206
ocaml/qp_add_aux_basis.ml
Normal file
206
ocaml/qp_add_aux_basis.ml
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@ -0,0 +1,206 @@
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open Qputils
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open Qptypes
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open Core.Std
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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 new EZFIO file. Default is suffixed by .RI"
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+> flag "b" (required string)
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~doc:"string Name of basis set."
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+> anon (" EZFIO 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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(** 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 | grep \"-RI\" "
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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 ezfio_file =
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let new_filename =
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match o with
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| Some filename -> filename
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| None -> ezfio_file ^ ".RI"
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in
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let () =
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match Sys.is_directory new_filename with
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| `Yes -> failwith "Output directory exists"
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| _ -> ()
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in
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let status =
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Printf.sprintf "cp -r %s %s" ezfio_file new_filename
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|> Unix.system
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in
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ignore status;
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Ezfio.set_file new_filename;
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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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in
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let basis =
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Input.AO_basis.read ()
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in
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()
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let command =
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Command.basic
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~summary: "Quantum Package command"
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~readme:(fun () -> "
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=== Available basis sets ===
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" ^ (list_basis ()) ^ "
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============================
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Extents the basis set to add an auxiliary basis set.
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" )
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spec
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(fun o b ezfio_file () -> run ?o b ezfio_file )
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let () =
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Command.run command
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