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https://github.com/LCPQ/quantum_package
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Merge branch 'master' of github.com:LCPQ/quantum_package
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commit
1deea047f9
@ -131,9 +131,11 @@ end = struct
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|> States_number.of_int
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;;
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let write_n_states_diag n =
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States_number.to_int n
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|> Ezfio.set_determinants_n_states_diag
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let write_n_states_diag ~n_states n =
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let n_states = States_number.to_int n_states
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and n = States_number.to_int n
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in
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Ezfio.set_determinants_n_states_diag (max n_states n)
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;;
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@ -232,20 +234,27 @@ end = struct
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let read_psi_coef () =
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if not (Ezfio.has_determinants_psi_coef ()) then
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Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| 1 |] ~data:[1.]
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begin
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let n_states =
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read_n_states ()
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|> States_number.to_int
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in
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Ezfio.ezfio_array_of_list ~rank:2 ~dim:[| 1 ; n_states |]
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~data:(List.init n_states ~f:(fun i -> if (i=0) then 1. else 0. ))
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|> Ezfio.set_determinants_psi_coef
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;
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end;
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Ezfio.get_determinants_psi_coef ()
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|> Ezfio.flattened_ezfio
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|> Array.map ~f:Det_coef.of_float
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;;
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let write_psi_coef ~n_det c =
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let write_psi_coef ~n_det ~n_states c =
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let n_det = Det_number.to_int n_det
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and c = Array.to_list c
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|> List.map ~f:Det_coef.to_float
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and n_states = States_number.to_int n_states
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in
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Ezfio.ezfio_array_of_list ~rank:1 ~dim:[| n_det |] ~data:c
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Ezfio.ezfio_array_of_list ~rank:2 ~dim:[| n_det ; n_states |] ~data:c
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|> Ezfio.set_determinants_psi_coef
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;;
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@ -339,14 +348,14 @@ end = struct
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write_mo_label mo_label;
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write_n_det n_det;
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write_n_states n_states;
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write_n_states_diag n_states_diag;
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write_n_states_diag ~n_states:n_states n_states_diag;
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write_n_det_max_jacobi n_det_max_jacobi;
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write_threshold_generators threshold_generators;
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write_threshold_selectors threshold_selectors;
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write_read_wf read_wf;
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write_expected_s2 expected_s2;
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write_s2_eig s2_eig;
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write_psi_coef ~n_det:n_det psi_coef;
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write_psi_coef ~n_det:n_det psi_coef ~n_states:n_states;
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write_psi_det ~n_int:n_int ~n_det:n_det psi_det;
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;;
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@ -6,29 +6,85 @@ 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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~doc:"file Name of the created EZFIO file."
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+> flag "b" (required string)
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~doc:"name Basis set."
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~doc:"definition of basis set."
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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 "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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~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1."
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+> anon ("xyz_file" %: string)
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;;
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let run ?o b c m xyz_file =
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(* Open basis set channel *)
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let basis_channel =
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In_channel.create
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(Qpackage.root ^ "/data/basis/" ^ (String.lowercase b))
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in
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(* Read molecule *)
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let molecule =
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(Molecule.of_xyz_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 nuclei = molecule.Molecule.nuclei in
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let basis_table = Hashtbl.Poly.create () in
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(* Open basis set channels *)
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let basis_channel element =
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let key = Element.to_string element 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 ->
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begin
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Printf.printf "%s is not defined in basis %s.\nEnter alternate basis : %!"
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(Element.to_long_string element) b ;
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let bas =
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match In_channel.input_line stdin with
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| Some line -> String.strip line |> String.lowercase
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| None -> failwith "Aborted"
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in
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let new_channel = In_channel.create
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(Qpackage.root ^ "/data/basis/" ^ bas)
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in
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Hashtbl.add_exn basis_table ~key:key ~data:new_channel;
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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 new_channel = In_channel.create
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(Qpackage.root ^ "/data/basis/" ^ elem_and_basis_name)
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in
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List.iter nuclei ~f:(fun x->
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let key = Element.to_string x.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 = Element.of_string key
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and basis = String.lowercase basis
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in
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let new_channel = In_channel.create
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(Qpackage.root ^ "/data/basis/" ^ basis)
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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 -> failwith ("Duplicate definition of basis for "^(Element.to_long_string elem))
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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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(* Build EZFIO File name *)
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let ezfio_file =
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@ -54,7 +110,6 @@ let run ?o b c m xyz_file =
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molecule.Molecule.elec_beta ) ;
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(* Write Nuclei *)
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let nuclei = molecule.Molecule.nuclei in
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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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@ -74,18 +129,32 @@ let run ?o b c m xyz_file =
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(* Write Basis set *)
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let basis =
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let nmax = Nucl_number.get_max () 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 -> let new_accu = (e,(Nucl_number.of_int ~max:nmax n))::accu in
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| e::tail ->
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let new_accu = (e,(Nucl_number.of_int ~max:nmax n))::accu in
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do_work new_accu (n+1) tail
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in
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do_work [] 1 nuclei
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let result = do_work [] 1 nuclei
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|> List.rev
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|> List.map ~f:(fun (x,i) ->
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Basis.read_element basis_channel i x.Atom.element)
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try
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Basis.read_element (basis_channel x.Atom.element) i x.Atom.element
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with
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| End_of_file ->
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begin
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let alt_channel = basis_channel x.Atom.element in
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Basis.read_element alt_channel i x.Atom.element
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end
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| _ -> assert false
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)
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|> List.concat
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in
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(* close all in_channels *)
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result
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in
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let long_basis = Long_basis.of_basis basis in
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let ao_num = List.length long_basis in
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Ezfio.set_ao_basis_ao_num ao_num;
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@ -150,8 +219,14 @@ let run ?o b c m xyz_file =
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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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"Creates an EZFIO directory from a standard xyz file
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~readme:(fun () -> "
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Creates an EZFIO directory from a standard xyz file.
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The basis set is defined as a single string if all the
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atoms are taken from the same basis set, otherwise specific
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elements can be defined as follows:
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-b \"cc-pcvdz H:cc-pvdz C:6-31g\"
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")
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spec
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(fun o b c m xyz_file () ->
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