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eginer 2022-09-30 16:22:18 +02:00
parent 7c1c761ea8
commit d09e3e7308
4 changed files with 51 additions and 121 deletions
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88
ocaml/qp_create_ezfio.ml
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@ -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
@ -585,12 +595,16 @@ let run ?o b au c d m p cart xyz_file =
let shell_prim_num = let shell_prim_num =
list_map List.length lc list_map List.length lc
in in
let shell_prim_idx = let shell_idx =
let rec make_list n accu = function
| 0 -> accu
| i -> make_list n (n :: accu) (i-1)
in
let rec aux count accu = function let rec aux count accu = function
| [] -> List.rev accu | [] -> List.rev accu
| l::rest -> | l::rest ->
let newcount = count+(List.length l) in let new_l = make_list count accu (List.length l) in
aux newcount (count::accu) rest aux (count+1) new_l rest
in in
aux 1 [] lc aux 1 [] lc
in in
@ -602,26 +616,18 @@ let run ?o b au c d m p cart xyz_file =
~rank:1 ~dim:[| shell_num |] ~data:shell_prim_num); ~rank:1 ~dim:[| shell_num |] ~data:shell_prim_num);
Ezfio.set_basis_shell_ang_mom (Ezfio.ezfio_array_of_list Ezfio.set_basis_shell_ang_mom (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| shell_num |] ~data:ang_mom ) ; ~rank:1 ~dim:[| shell_num |] ~data:ang_mom ) ;
Ezfio.set_basis_shell_prim_index (Ezfio.ezfio_array_of_list Ezfio.set_basis_shell_index (Ezfio.ezfio_array_of_list
~rank:1 ~dim:[| shell_num |] ~data:shell_prim_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:[| nucl_num |] ~rank:1 ~dim:[| shell_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 ->
match accu with
| [] -> []
| (h,j) :: rest -> if j == i then ((h+1,j)::rest) else ((h+1,i)::(h+1,j)::rest)
) [(0,0)]
|> List.rev
|> List.map fst
)) ;
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)
) [] ) []
@ -675,10 +681,8 @@ let () =
let open Command_line in let open Command_line in
begin begin
"Creates an EZFIO directory from a standard xyz file or from a z-matrix file in Gaussian format. The basis set is defined as a single string if all the atoms are taken from the same basis set, otherwise specific elements can be defined as follows: "Creates an EZFIO directory from a standard xyz file or from a z-matrix file in Gaussian format. The basis set is defined as a single string if all the atoms are taken from the same basis set, otherwise specific elements can be defined as follows:
-b \"cc-pcvdz | H:cc-pvdz | C:6-31g\" -b \"cc-pcvdz | H:cc-pvdz | C:6-31g\"
-b \"cc-pvtz | 1,H:sto-3g | 3,H:6-31g\" -b \"cc-pvtz | 1,H:sto-3g | 3,H:6-31g\"
If a file with the same name as the basis set exists, this file will be read. Otherwise, the basis set is obtained from the database. If a file with the same name as the basis set exists, this file will be read. Otherwise, the basis set is obtained from the database.
" |> set_description_doc ; " |> set_description_doc ;
set_header_doc (Sys.argv.(0) ^ " - Quantum Package command"); set_header_doc (Sys.argv.(0) ^ " - Quantum Package command");
@ -717,7 +721,7 @@ 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;
@ -741,7 +745,7 @@ 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

10
src/basis/EZFIO.cfg
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@ -37,16 +37,16 @@ doc: Number of primitives in a shell
size: (basis.shell_num) size: (basis.shell_num)
interface: ezfio, provider interface: ezfio, provider
[shell_prim_index] [shell_index]
type: integer type: integer
doc: Max number of primitives in a shell doc: Index of the shell for each primitive
size: (basis.shell_num) size: (basis.prim_num)
interface: ezfio, provider interface: ezfio, provider
[basis_nucleus_index] [basis_nucleus_index]
type: integer type: integer
doc: Index of the nucleus on which the shell is centered doc: Nucleus on which the shell is centered
size: (nuclei.nucl_num) size: (basis.shell_num)
interface: ezfio, provider interface: ezfio, provider
[prim_normalization_factor] [prim_normalization_factor]

6
src/davidson/EZFIO.cfg
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@ -16,9 +16,3 @@ doc: If |true|, don't use denominator
default: False default: False
interface: ezfio,provider,ocaml interface: ezfio,provider,ocaml
[threshold_nonsym_davidson]
type: Threshold
doc: Thresholds of non-symetric Davidson's algorithm
interface: ezfio,provider,ocaml
default: 1.e-12

68
src/determinants/determinants.irp.f
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@ -652,74 +652,6 @@ subroutine save_wavefunction_general_unormalized(ndet,nstates,psidet,dim_psicoef
end end
subroutine save_wavefunction_general_unormalized(ndet,nstates,psidet,dim_psicoef,psicoef)
implicit none
BEGIN_DOC
! Save the wave function into the |EZFIO| file
END_DOC
use bitmasks
include 'constants.include.F'
integer, intent(in) :: ndet,nstates,dim_psicoef
integer(bit_kind), intent(in) :: psidet(N_int,2,ndet)
double precision, intent(in) :: psicoef(dim_psicoef,nstates)
integer*8, allocatable :: psi_det_save(:,:,:)
double precision, allocatable :: psi_coef_save(:,:)
double precision :: accu_norm
integer :: i,j,k, ndet_qp_edit
if (mpi_master) then
ndet_qp_edit = min(ndet,N_det_qp_edit)
call ezfio_set_determinants_N_int(N_int)
call ezfio_set_determinants_bit_kind(bit_kind)
call ezfio_set_determinants_N_det(ndet)
call ezfio_set_determinants_N_det_qp_edit(ndet_qp_edit)
call ezfio_set_determinants_n_states(nstates)
call ezfio_set_determinants_mo_label(mo_label)
allocate (psi_det_save(N_int,2,ndet))
do i=1,ndet
do j=1,2
do k=1,N_int
psi_det_save(k,j,i) = transfer(psidet(k,j,i),1_8)
enddo
enddo
enddo
call ezfio_set_determinants_psi_det(psi_det_save)
call ezfio_set_determinants_psi_det_qp_edit(psi_det_save)
deallocate (psi_det_save)
allocate (psi_coef_save(ndet,nstates))
do k=1,nstates
do i=1,ndet
psi_coef_save(i,k) = psicoef(i,k)
enddo
enddo
call ezfio_set_determinants_psi_coef(psi_coef_save)
deallocate (psi_coef_save)
allocate (psi_coef_save(ndet_qp_edit,nstates))
do k=1,nstates
do i=1,ndet_qp_edit
psi_coef_save(i,k) = psicoef(i,k)
enddo
enddo
call ezfio_set_determinants_psi_coef_qp_edit(psi_coef_save)
deallocate (psi_coef_save)
call write_int(6,ndet,'Saved determinants')
endif
end
subroutine save_wavefunction_specified(ndet,nstates,psidet,psicoef,ndetsave,index_det_save) subroutine save_wavefunction_specified(ndet,nstates,psidet,psicoef,ndetsave,index_det_save)
implicit none implicit none
BEGIN_DOC BEGIN_DOC