From 2a98378fcab6454c060e3cd4ad543506c16e2103 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Thu, 30 Dec 2021 14:43:14 +0100 Subject: [PATCH] Fix basis bugs when working on trexio --- ocaml/qp_create_ezfio.ml | 60 +++++++++++++++++++++++----------------- src/pseudo/EZFIO.cfg | 6 ++-- 2 files changed, 38 insertions(+), 28 deletions(-) diff --git a/ocaml/qp_create_ezfio.ml b/ocaml/qp_create_ezfio.ml index 8fcaf5fc..be6c305b 100644 --- a/ocaml/qp_create_ezfio.ml +++ b/ocaml/qp_create_ezfio.ml @@ -91,7 +91,7 @@ let run ?o b au c d m p cart xyz_file = | Element e -> Element.to_string e | Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i) (Element.to_string e) in - Hashtbl.find basis_table key + Hashtbl.find basis_table key in let temp_filename = @@ -132,7 +132,7 @@ let run ?o b au c d m p cart xyz_file = Element.to_string elem.Atom.element in Hashtbl.add basis_table key new_channel - ) nuclei + ) nuclei end | Some (key, basis) -> (*Aux basis *) begin @@ -277,6 +277,16 @@ let run ?o b au c d m p cart xyz_file = ) nuclei in + let z_core = + List.map (fun x -> + Positive_int.to_int x.Pseudo.n_elec + |> float_of_int + ) pseudo + in + let nucl_num = (List.length z_core) in + Ezfio.set_pseudo_nucl_charge_remove (Ezfio.ezfio_array_of_list + ~rank:1 ~dim:[| nucl_num |] ~data:z_core); + let molecule = let n_elec_to_remove = List.fold_left (fun accu x -> @@ -293,13 +303,13 @@ let run ?o b au c d m p cart xyz_file = Molecule.nuclei = let charges = list_map (fun x -> Positive_int.to_int x.Pseudo.n_elec - |> Float.of_int) pseudo + |> Float.of_int) pseudo |> Array.of_list in List.mapi (fun i x -> { x with Atom.charge = (Charge.to_float x.Atom.charge) -. charges.(i) |> Charge.of_float } - ) molecule.Molecule.nuclei + ) molecule.Molecule.nuclei } in let nuclei = @@ -356,11 +366,11 @@ let run ?o b au c d m p cart xyz_file = in if (x > accu) then x else accu - ) 0 x.Pseudo.non_local + ) 0 x.Pseudo.non_local in if (x > accu) then x else accu - ) 0 pseudo + ) 0 pseudo in let kmax = @@ -368,10 +378,10 @@ let run ?o b au c d m p cart xyz_file = list_map (fun x -> List.filter (fun (y,_) -> (Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj) = i) - x.Pseudo.non_local - |> List.length ) pseudo + x.Pseudo.non_local + |> List.length ) pseudo |> List.fold_left (fun accu x -> - if accu > x then accu else x) 0 + if accu > x then accu else x) 0 ) |> Array.fold_left (fun accu i -> if i > accu then i else accu) 0 @@ -396,11 +406,11 @@ let run ?o b au c d m p cart xyz_file = in tmp_array_dz_k.(i).(j) <- y; tmp_array_n_k.(i).(j) <- z; - ) x.Pseudo.local + ) x.Pseudo.local ) pseudo ; let concat_2d tmp_array = let data = - Array.map Array.to_list tmp_array + Array.map Array.to_list tmp_array |> Array.to_list |> List.concat in @@ -438,14 +448,14 @@ let run ?o b au c d m p cart xyz_file = tmp_array_dz_kl.(k).(i).(j) <- y; tmp_array_n_kl.(k).(i).(j) <- z; last_idx.(k) <- i+1; - ) x.Pseudo.non_local + ) x.Pseudo.non_local ) pseudo ; let concat_3d tmp_array = let data = Array.map (fun x -> Array.map Array.to_list x |> Array.to_list - |> List.concat) tmp_array + |> List.concat) tmp_array |> Array.to_list |> List.concat in @@ -513,8 +523,8 @@ let run ?o b au c d m p cart xyz_file = 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 + 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)@ @@ -526,7 +536,7 @@ let run ?o b au c d m p cart xyz_file = else s) 0 ao_prim_num in let gtos = - list_map (fun (_,x,_) -> x) long_basis + list_map (fun (_,x,_) -> x) long_basis in let create_expo_coef ec = @@ -534,10 +544,10 @@ let run ?o b au c d m p cart xyz_file = begin match ec with | `Coefs -> list_map (fun x-> list_map (fun (_,coef) -> - AO_coef.to_float coef) x.Gto.lc) gtos + 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 + prim.GaussianPrimitive.expo) x.Gto.lc) gtos end in let rec get_n n accu = function @@ -567,7 +577,7 @@ let run ?o b au c d m p cart xyz_file = list_map ( fun (g,_) -> g.Gto.lc ) basis in let ang_mom = - list_map (fun (l : (GaussianPrimitive.t * Qptypes.AO_coef.t) list) -> + 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 @@ -577,7 +587,7 @@ let run ?o b au c d m p cart xyz_file = |> List.concat in let coef = - list_map (fun l -> + list_map (fun l -> list_map (fun (_,x) -> Qptypes.AO_coef.to_float x) l ) lc |> List.concat @@ -610,14 +620,14 @@ let run ?o b au c d m p cart xyz_file = ~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) + ~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 + |> 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) ) [] @@ -713,7 +723,7 @@ If a file with the same name as the basis set exists, this file will be read. O anonymous "FILE" Mandatory "Input file in xyz format or z-matrix."; ] - |> set_specs + |> set_specs end; @@ -737,7 +747,7 @@ If a file with the same name as the basis set exists, this file will be read. O | None -> 0 | Some x -> ( if x.[0] = 'm' then ~- (int_of_string (String.sub x 1 (String.length x - 1))) - else + else int_of_string x ) in diff --git a/src/pseudo/EZFIO.cfg b/src/pseudo/EZFIO.cfg index 952ebe04..2b76a5c3 100644 --- a/src/pseudo/EZFIO.cfg +++ b/src/pseudo/EZFIO.cfg @@ -10,7 +10,7 @@ type:integer interface: ezfio,provider [pseudo_n_k] -doc: Number of gaussians in the local component +doc: Powers of r - 2 in the local component type: integer interface: ezfio,provider size: (nuclei.nucl_num,pseudo.pseudo_klocmax) @@ -38,7 +38,7 @@ type:integer interface: ezfio,provider [pseudo_n_kl] -doc: Number of functions in the non-local component +doc: Powers of r - 2 in the non-local component type: integer interface: ezfio,provider size: (nuclei.nucl_num,pseudo.pseudo_kmax,0:pseudo.pseudo_lmax) @@ -69,7 +69,7 @@ default: 1000 [pseudo_grid_rmax] type: double precision -doc: R_max of the QMC grid +doc: R_max of the QMC grid interface: ezfio,provider,ocaml default: 10.0