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Fix basis bugs when working on trexio

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This commit is contained in:
Anthony Scemama 2021-12-30 14:43:14 +01:00
parent 7fba7a1209
commit 2a98378fca
2 changed files with 38 additions and 28 deletions
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60
ocaml/qp_create_ezfio.ml
View File

@ -91,7 +91,7 @@ let run ?o b au c d m p cart xyz_file =
| Element e -> Element.to_string e | Element e -> Element.to_string e
| Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i) (Element.to_string e) | Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i) (Element.to_string e)
in in
Hashtbl.find basis_table key Hashtbl.find basis_table key
in in
let temp_filename = 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 Element.to_string elem.Atom.element
in in
Hashtbl.add basis_table key new_channel Hashtbl.add basis_table key new_channel
) nuclei ) nuclei
end end
| Some (key, basis) -> (*Aux basis *) | Some (key, basis) -> (*Aux basis *)
begin begin
@ -277,6 +277,16 @@ let run ?o b au c d m p cart xyz_file =
) nuclei ) nuclei
in 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 molecule =
let n_elec_to_remove = let n_elec_to_remove =
List.fold_left (fun accu x -> List.fold_left (fun accu x ->
@ -293,13 +303,13 @@ let run ?o b au c d m p cart xyz_file =
Molecule.nuclei = Molecule.nuclei =
let charges = let charges =
list_map (fun x -> Positive_int.to_int x.Pseudo.n_elec list_map (fun x -> Positive_int.to_int x.Pseudo.n_elec
|> Float.of_int) pseudo |> Float.of_int) pseudo
|> Array.of_list |> Array.of_list
in in
List.mapi (fun i x -> List.mapi (fun i x ->
{ x with Atom.charge = (Charge.to_float x.Atom.charge) -. charges.(i) { x with Atom.charge = (Charge.to_float x.Atom.charge) -. charges.(i)
|> Charge.of_float } |> Charge.of_float }
) molecule.Molecule.nuclei ) molecule.Molecule.nuclei
} }
in in
let nuclei = let nuclei =
@ -356,11 +366,11 @@ let run ?o b au c d m p cart xyz_file =
in in
if (x > accu) then x if (x > accu) then x
else accu else accu
) 0 x.Pseudo.non_local ) 0 x.Pseudo.non_local
in in
if (x > accu) then x if (x > accu) then x
else accu else accu
) 0 pseudo ) 0 pseudo
in in
let kmax = let kmax =
@ -368,10 +378,10 @@ let run ?o b au c d m p cart xyz_file =
list_map (fun x -> list_map (fun x ->
List.filter (fun (y,_) -> List.filter (fun (y,_) ->
(Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj) = i) (Positive_int.to_int y.Pseudo.GaussianPrimitive_non_local.proj) = i)
x.Pseudo.non_local x.Pseudo.non_local
|> List.length ) pseudo |> List.length ) pseudo
|> List.fold_left (fun accu x -> |> 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 -> |> Array.fold_left (fun accu i ->
if i > accu then i else accu) 0 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 in
tmp_array_dz_k.(i).(j) <- y; tmp_array_dz_k.(i).(j) <- y;
tmp_array_n_k.(i).(j) <- z; tmp_array_n_k.(i).(j) <- z;
) x.Pseudo.local ) x.Pseudo.local
) pseudo ; ) pseudo ;
let concat_2d tmp_array = let concat_2d tmp_array =
let data = let data =
Array.map Array.to_list tmp_array Array.map Array.to_list tmp_array
|> Array.to_list |> Array.to_list
|> List.concat |> List.concat
in 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_dz_kl.(k).(i).(j) <- y;
tmp_array_n_kl.(k).(i).(j) <- z; tmp_array_n_kl.(k).(i).(j) <- z;
last_idx.(k) <- i+1; last_idx.(k) <- i+1;
) x.Pseudo.non_local ) x.Pseudo.non_local
) pseudo ; ) pseudo ;
let concat_3d tmp_array = let concat_3d tmp_array =
let data = let data =
Array.map (fun x -> Array.map (fun x ->
Array.map Array.to_list x Array.map Array.to_list x
|> Array.to_list |> Array.to_list
|> List.concat) tmp_array |> List.concat) tmp_array
|> Array.to_list |> Array.to_list
|> List.concat |> List.concat
in 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_num ao_num;
Ezfio.set_ao_basis_ao_basis b; Ezfio.set_ao_basis_ao_basis b;
Ezfio.set_basis_basis b; Ezfio.set_basis_basis b;
let ao_prim_num = list_map (fun (_,g,_) -> List.length g.Gto.lc) 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_nucl = list_map (fun (_,_,n) -> Nucl_number.to_int n) long_basis
and ao_power= and ao_power=
let l = list_map (fun (x,_,_) -> x) long_basis in 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.x)) l)@
@ -526,7 +536,7 @@ let run ?o b au c d m p cart xyz_file =
else s) 0 ao_prim_num else s) 0 ao_prim_num
in in
let gtos = let gtos =
list_map (fun (_,x,_) -> x) long_basis list_map (fun (_,x,_) -> x) long_basis
in in
let create_expo_coef ec = 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 begin match ec with
| `Coefs -> list_map (fun x-> | `Coefs -> list_map (fun x->
list_map (fun (_,coef) -> 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-> | `Expos -> list_map (fun x->
list_map (fun (prim,_) -> AO_expo.to_float list_map (fun (prim,_) -> AO_expo.to_float
prim.GaussianPrimitive.expo) x.Gto.lc) gtos prim.GaussianPrimitive.expo) x.Gto.lc) gtos
end end
in in
let rec get_n n accu = function 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 list_map ( fun (g,_) -> g.Gto.lc ) basis
in in
let ang_mom = 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 let x, _ = List.hd l in
Angmom.to_l x.GaussianPrimitive.sym |> Qptypes.Positive_int.to_int Angmom.to_l x.GaussianPrimitive.sym |> Qptypes.Positive_int.to_int
) lc ) lc
@ -577,7 +587,7 @@ let run ?o b au c d m p cart xyz_file =
|> List.concat |> List.concat
in in
let coef = let coef =
list_map (fun l -> list_map (fun l ->
list_map (fun (_,x) -> Qptypes.AO_coef.to_float x) l list_map (fun (_,x) -> Qptypes.AO_coef.to_float x) l
) lc ) lc
|> List.concat |> 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) ; ~rank:1 ~dim:[| prim_num |] ~data:shell_idx) ;
Ezfio.set_basis_basis_nucleus_index (Ezfio.ezfio_array_of_list Ezfio.set_basis_basis_nucleus_index (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| shell_num |] ~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 Ezfio.set_basis_nucleus_shell_num(Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| nucl_num |] ~rank:1 ~dim:[| nucl_num |]
~data:( ~data:(
list_map (fun (_,n) -> Nucl_number.to_int n) basis list_map (fun (_,n) -> Nucl_number.to_int n) basis
|> List.fold_left (fun accu i -> |> List.fold_left (fun accu i ->
match accu with match accu with
| [] -> [(1,i)] | [] -> [(1,i)]
| (h,j) :: rest -> if j == i then ((h+1,j)::rest) else ((1,i)::(h,j)::rest) | (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."; anonymous "FILE" Mandatory "Input file in xyz format or z-matrix.";
] ]
|> set_specs |> set_specs
end; 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 | None -> 0
| Some x -> ( if x.[0] = 'm' then | Some x -> ( if x.[0] = 'm' then
~- (int_of_string (String.sub x 1 (String.length x - 1))) ~- (int_of_string (String.sub x 1 (String.length x - 1)))
else else
int_of_string x ) int_of_string x )
in in

6
src/pseudo/EZFIO.cfg
View File

@ -10,7 +10,7 @@ type:integer
interface: ezfio,provider interface: ezfio,provider
[pseudo_n_k] [pseudo_n_k]
doc: Number of gaussians in the local component doc: Powers of r - 2 in the local component
type: integer type: integer
interface: ezfio,provider interface: ezfio,provider
size: (nuclei.nucl_num,pseudo.pseudo_klocmax) size: (nuclei.nucl_num,pseudo.pseudo_klocmax)
@ -38,7 +38,7 @@ type:integer
interface: ezfio,provider interface: ezfio,provider
[pseudo_n_kl] [pseudo_n_kl]
doc: Number of functions in the non-local component doc: Powers of r - 2 in the non-local component
type: integer type: integer
interface: ezfio,provider interface: ezfio,provider
size: (nuclei.nucl_num,pseudo.pseudo_kmax,0:pseudo.pseudo_lmax) size: (nuclei.nucl_num,pseudo.pseudo_kmax,0:pseudo.pseudo_lmax)
@ -69,7 +69,7 @@ default: 1000
[pseudo_grid_rmax] [pseudo_grid_rmax]
type: double precision type: double precision
doc: R_max of the QMC grid doc: R_max of the QMC grid
interface: ezfio,provider,ocaml interface: ezfio,provider,ocaml
default: 10.0 default: 10.0