Fix basis bugs when working on trexio
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7fba7a1209
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@ -91,7 +91,7 @@ let run ?o b au c d m p cart xyz_file =
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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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Hashtbl.find basis_table key
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in
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let temp_filename =
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@ -132,7 +132,7 @@ let run ?o b au c d m p cart xyz_file =
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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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) nuclei
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end
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| Some (key, basis) -> (*Aux basis *)
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begin
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@ -277,6 +277,16 @@ let run ?o b au c d m p cart xyz_file =
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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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@ -293,13 +303,13 @@ let run ?o b au c d m p cart xyz_file =
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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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|> 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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) molecule.Molecule.nuclei
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}
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in
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let nuclei =
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@ -356,11 +366,11 @@ let run ?o b au c d m p cart xyz_file =
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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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) 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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) 0 pseudo
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in
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let kmax =
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@ -368,10 +378,10 @@ let run ?o b au c d m p cart xyz_file =
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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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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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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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@ -396,11 +406,11 @@ let run ?o b au c d m p cart xyz_file =
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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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) 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.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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@ -438,14 +448,14 @@ let run ?o b au c d m p cart xyz_file =
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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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) 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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|> 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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@ -513,8 +523,8 @@ let run ?o b au c d m p cart xyz_file =
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Ezfio.set_ao_basis_ao_num ao_num;
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Ezfio.set_ao_basis_ao_basis b;
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Ezfio.set_basis_basis b;
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let ao_prim_num = list_map (fun (_,g,_) -> List.length g.Gto.lc) long_basis
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and ao_nucl = list_map (fun (_,_,n) -> Nucl_number.to_int n) long_basis
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let ao_prim_num = list_map (fun (_,g,_) -> List.length g.Gto.lc) long_basis
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and ao_nucl = list_map (fun (_,_,n) -> Nucl_number.to_int n) long_basis
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and ao_power=
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let l = list_map (fun (x,_,_) -> x) long_basis in
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(list_map (fun t -> Positive_int.to_int Angmom.Xyz.(t.x)) l)@
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@ -526,7 +536,7 @@ let run ?o b au c d m p cart xyz_file =
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else s) 0 ao_prim_num
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in
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let gtos =
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list_map (fun (_,x,_) -> x) long_basis
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list_map (fun (_,x,_) -> x) long_basis
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in
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let create_expo_coef ec =
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@ -534,10 +544,10 @@ let run ?o b au c d m p cart xyz_file =
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begin match ec with
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| `Coefs -> list_map (fun x->
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list_map (fun (_,coef) ->
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AO_coef.to_float coef) x.Gto.lc) gtos
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AO_coef.to_float coef) x.Gto.lc) gtos
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| `Expos -> list_map (fun x->
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list_map (fun (prim,_) -> AO_expo.to_float
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prim.GaussianPrimitive.expo) x.Gto.lc) gtos
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prim.GaussianPrimitive.expo) x.Gto.lc) gtos
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end
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in
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let rec get_n n accu = function
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@ -567,7 +577,7 @@ let run ?o b au c d m p cart xyz_file =
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list_map ( fun (g,_) -> g.Gto.lc ) basis
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in
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let ang_mom =
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list_map (fun (l : (GaussianPrimitive.t * Qptypes.AO_coef.t) list) ->
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list_map (fun (l : (GaussianPrimitive.t * Qptypes.AO_coef.t) list) ->
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let x, _ = List.hd l in
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Angmom.to_l x.GaussianPrimitive.sym |> Qptypes.Positive_int.to_int
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) lc
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@ -577,7 +587,7 @@ let run ?o b au c d m p cart xyz_file =
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|> List.concat
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in
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let coef =
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list_map (fun l ->
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list_map (fun l ->
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list_map (fun (_,x) -> Qptypes.AO_coef.to_float x) l
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) lc
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|> List.concat
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@ -610,14 +620,14 @@ let run ?o b au c d m p cart xyz_file =
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~rank:1 ~dim:[| prim_num |] ~data:shell_idx) ;
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Ezfio.set_basis_basis_nucleus_index (Ezfio.ezfio_array_of_list
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~rank:1 ~dim:[| shell_num |]
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~data:( list_map (fun (_,n) -> Nucl_number.to_int n) basis)
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~data:( list_map (fun (_,n) -> Nucl_number.to_int n) basis)
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) ;
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Ezfio.set_basis_nucleus_shell_num(Ezfio.ezfio_array_of_list
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~rank:1 ~dim:[| nucl_num |]
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~data:(
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list_map (fun (_,n) -> Nucl_number.to_int n) basis
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|> List.fold_left (fun accu i ->
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match accu with
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|> List.fold_left (fun accu i ->
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match accu with
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| [] -> [(1,i)]
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| (h,j) :: rest -> if j == i then ((h+1,j)::rest) else ((1,i)::(h,j)::rest)
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) []
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@ -713,7 +723,7 @@ If a file with the same name as the basis set exists, this file will be read. O
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anonymous "FILE" Mandatory "Input file in xyz format or z-matrix.";
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]
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|> set_specs
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|> set_specs
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end;
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@ -737,7 +747,7 @@ If a file with the same name as the basis set exists, this file will be read. O
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| None -> 0
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| Some x -> ( if x.[0] = 'm' then
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~- (int_of_string (String.sub x 1 (String.length x - 1)))
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else
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else
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int_of_string x )
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in
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@ -10,7 +10,7 @@ type:integer
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interface: ezfio,provider
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[pseudo_n_k]
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doc: Number of gaussians in the local component
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doc: Powers of r - 2 in the local component
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type: integer
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interface: ezfio,provider
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size: (nuclei.nucl_num,pseudo.pseudo_klocmax)
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@ -38,7 +38,7 @@ type:integer
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interface: ezfio,provider
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[pseudo_n_kl]
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doc: Number of functions in the non-local component
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doc: Powers of r - 2 in the non-local component
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type: integer
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interface: ezfio,provider
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size: (nuclei.nucl_num,pseudo.pseudo_kmax,0:pseudo.pseudo_lmax)
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@ -69,7 +69,7 @@ default: 1000
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[pseudo_grid_rmax]
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type: double precision
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doc: R_max of the QMC grid
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doc: R_max of the QMC grid
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interface: ezfio,provider,ocaml
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default: 10.0
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