minor modifs to merge

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
@@ -585,12 +595,16 @@ let run ?o b au c d m p cart xyz_file =
         let shell_prim_num =
           list_map List.length  lc
         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
           | [] -> List.rev accu
           | l::rest ->
-            let newcount = count+(List.length l) in
-            aux newcount (count::accu) rest
+            let new_l = make_list count accu (List.length l) in
+            aux (count+1) new_l rest
           in
           aux 1 [] lc
         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);
         Ezfio.set_basis_shell_ang_mom (Ezfio.ezfio_array_of_list
           ~rank:1 ~dim:[| shell_num |] ~data:ang_mom ) ;
-        Ezfio.set_basis_shell_prim_index (Ezfio.ezfio_array_of_list
-          ~rank:1 ~dim:[| shell_num |] ~data:shell_prim_idx) ;
+        Ezfio.set_basis_shell_index (Ezfio.ezfio_array_of_list
+          ~rank:1 ~dim:[| prim_num |] ~data:shell_idx) ;
         Ezfio.set_basis_basis_nucleus_index (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 
-            | [] -> []
-            | (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
-          )) ;
+          ~rank:1 ~dim:[| shell_num |]
+          ~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)
           ) []
@@ -675,10 +681,8 @@ let () =
   let open Command_line in
   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:
-
     -b \"cc-pcvdz | H:cc-pvdz | C: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.
 "   |> set_description_doc ;
     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.";
     ]
-    |> set_specs 
+    |> set_specs
   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
     | 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
 

src/basis/EZFIO.cfg

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

src/davidson/EZFIO.cfg

@@ -16,9 +16,3 @@ doc: If |true|, don't use denominator
 default: False
 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
-

src/determinants/determinants.irp.f

@@ -652,74 +652,6 @@ subroutine save_wavefunction_general_unormalized(ndet,nstates,psidet,dim_psicoef
 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)
   implicit none
   BEGIN_DOC