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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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) nuclei
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in
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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 molecule =
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let n_elec_to_remove =
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let n_elec_to_remove =
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List.fold_left (fun accu x ->
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List.fold_left (fun accu x ->
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@ -585,12 +595,16 @@ let run ?o b au c d m p cart xyz_file =
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let shell_prim_num =
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let shell_prim_num =
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list_map List.length lc
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list_map List.length lc
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in
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in
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let shell_prim_idx =
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let shell_idx =
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let rec make_list n accu = function
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| 0 -> accu
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| i -> make_list n (n :: accu) (i-1)
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in
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let rec aux count accu = function
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let rec aux count accu = function
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| [] -> List.rev accu
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| [] -> List.rev accu
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| l::rest ->
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| l::rest ->
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let newcount = count+(List.length l) in
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let new_l = make_list count accu (List.length l) in
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aux newcount (count::accu) rest
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aux (count+1) new_l rest
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in
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in
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aux 1 [] lc
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aux 1 [] lc
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in
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in
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@ -602,20 +616,12 @@ let run ?o b au c d m p cart xyz_file =
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~rank:1 ~dim:[| shell_num |] ~data:shell_prim_num);
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~rank:1 ~dim:[| shell_num |] ~data:shell_prim_num);
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Ezfio.set_basis_shell_ang_mom (Ezfio.ezfio_array_of_list
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Ezfio.set_basis_shell_ang_mom (Ezfio.ezfio_array_of_list
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~rank:1 ~dim:[| shell_num |] ~data:ang_mom ) ;
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~rank:1 ~dim:[| shell_num |] ~data:ang_mom ) ;
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Ezfio.set_basis_shell_prim_index (Ezfio.ezfio_array_of_list
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Ezfio.set_basis_shell_index (Ezfio.ezfio_array_of_list
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~rank:1 ~dim:[| shell_num |] ~data:shell_prim_idx) ;
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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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Ezfio.set_basis_basis_nucleus_index (Ezfio.ezfio_array_of_list
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~rank:1 ~dim:[| nucl_num |]
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~rank:1 ~dim:[| shell_num |]
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~data:(
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~data:( list_map (fun (_,n) -> Nucl_number.to_int n) basis)
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list_map (fun (_,n) -> Nucl_number.to_int n) basis
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) ;
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|> List.fold_left (fun accu i ->
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match accu with
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| [] -> []
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| (h,j) :: rest -> if j == i then ((h+1,j)::rest) else ((h+1,i)::(h+1,j)::rest)
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) [(0,0)]
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|> List.rev
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|> List.map fst
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)) ;
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Ezfio.set_basis_nucleus_shell_num(Ezfio.ezfio_array_of_list
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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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~rank:1 ~dim:[| nucl_num |]
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~data:(
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~data:(
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@ -675,10 +681,8 @@ let () =
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let open Command_line in
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let open Command_line in
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begin
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begin
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"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:
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"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:
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-b \"cc-pcvdz | H:cc-pvdz | C:6-31g\"
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-b \"cc-pcvdz | H:cc-pvdz | C:6-31g\"
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-b \"cc-pvtz | 1,H:sto-3g | 3,H:6-31g\"
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-b \"cc-pvtz | 1,H:sto-3g | 3,H:6-31g\"
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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.
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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.
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" |> set_description_doc ;
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" |> set_description_doc ;
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set_header_doc (Sys.argv.(0) ^ " - Quantum Package command");
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set_header_doc (Sys.argv.(0) ^ " - Quantum Package command");
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@ -37,16 +37,16 @@ doc: Number of primitives in a shell
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size: (basis.shell_num)
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size: (basis.shell_num)
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interface: ezfio, provider
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interface: ezfio, provider
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[shell_prim_index]
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[shell_index]
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type: integer
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type: integer
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doc: Max number of primitives in a shell
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doc: Index of the shell for each primitive
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size: (basis.shell_num)
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size: (basis.prim_num)
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interface: ezfio, provider
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interface: ezfio, provider
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[basis_nucleus_index]
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[basis_nucleus_index]
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type: integer
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type: integer
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doc: Index of the nucleus on which the shell is centered
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doc: Nucleus on which the shell is centered
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size: (nuclei.nucl_num)
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size: (basis.shell_num)
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interface: ezfio, provider
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interface: ezfio, provider
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[prim_normalization_factor]
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[prim_normalization_factor]
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@ -16,9 +16,3 @@ doc: If |true|, don't use denominator
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default: False
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default: False
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interface: ezfio,provider,ocaml
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interface: ezfio,provider,ocaml
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[threshold_nonsym_davidson]
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type: Threshold
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doc: Thresholds of non-symetric Davidson's algorithm
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interface: ezfio,provider,ocaml
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default: 1.e-12
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@ -652,74 +652,6 @@ subroutine save_wavefunction_general_unormalized(ndet,nstates,psidet,dim_psicoef
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end
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end
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subroutine save_wavefunction_general_unormalized(ndet,nstates,psidet,dim_psicoef,psicoef)
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implicit none
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BEGIN_DOC
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! Save the wave function into the |EZFIO| file
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END_DOC
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use bitmasks
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include 'constants.include.F'
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integer, intent(in) :: ndet,nstates,dim_psicoef
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integer(bit_kind), intent(in) :: psidet(N_int,2,ndet)
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double precision, intent(in) :: psicoef(dim_psicoef,nstates)
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integer*8, allocatable :: psi_det_save(:,:,:)
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double precision, allocatable :: psi_coef_save(:,:)
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double precision :: accu_norm
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integer :: i,j,k, ndet_qp_edit
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if (mpi_master) then
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ndet_qp_edit = min(ndet,N_det_qp_edit)
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call ezfio_set_determinants_N_int(N_int)
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call ezfio_set_determinants_bit_kind(bit_kind)
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call ezfio_set_determinants_N_det(ndet)
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call ezfio_set_determinants_N_det_qp_edit(ndet_qp_edit)
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call ezfio_set_determinants_n_states(nstates)
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call ezfio_set_determinants_mo_label(mo_label)
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allocate (psi_det_save(N_int,2,ndet))
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do i=1,ndet
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do j=1,2
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do k=1,N_int
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psi_det_save(k,j,i) = transfer(psidet(k,j,i),1_8)
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enddo
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enddo
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enddo
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call ezfio_set_determinants_psi_det(psi_det_save)
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call ezfio_set_determinants_psi_det_qp_edit(psi_det_save)
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deallocate (psi_det_save)
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allocate (psi_coef_save(ndet,nstates))
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do k=1,nstates
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do i=1,ndet
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psi_coef_save(i,k) = psicoef(i,k)
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enddo
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enddo
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call ezfio_set_determinants_psi_coef(psi_coef_save)
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deallocate (psi_coef_save)
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allocate (psi_coef_save(ndet_qp_edit,nstates))
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do k=1,nstates
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do i=1,ndet_qp_edit
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psi_coef_save(i,k) = psicoef(i,k)
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enddo
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enddo
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call ezfio_set_determinants_psi_coef_qp_edit(psi_coef_save)
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deallocate (psi_coef_save)
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call write_int(6,ndet,'Saved determinants')
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endif
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end
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subroutine save_wavefunction_specified(ndet,nstates,psidet,psicoef,ndetsave,index_det_save)
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subroutine save_wavefunction_specified(ndet,nstates,psidet,psicoef,ndetsave,index_det_save)
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implicit none
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implicit none
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BEGIN_DOC
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BEGIN_DOC
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