Suport pseudo in qp_create

ocaml/qp_create_ezfio_from_xyz.ml

@@ -13,10 +13,12 @@ let spec =
      ~doc:"int Total charge of the molecule. Default is 0."
   +> flag "m" (optional_with_default 1 int)
      ~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1."
+  +> flag "p" (optional_with_default 1 int)
+     ~doc:"Using pseudo potentiel or not"
   +> anon ("xyz_file" %: string)
 ;;
 
-let run ?o b c m xyz_file =
+let run ?o b c m p xyz_file =
 
   (* Read molecule *)
   let molecule =
@@ -60,8 +62,12 @@ let run ?o b c m xyz_file =
       | None -> (* Principal basis *)
         let basis = elem_and_basis_name in
         let command =
+          if (p = 0) then  
             Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename 
               ^ "\" \"" ^ basis ^"\""
+          else
+            Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename 
+              ^ "\" \"" ^ basis ^"\" pseudo"
         in
         begin
           let filename = 
@@ -247,6 +253,9 @@ let run ?o b c m xyz_file =
   ~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_expo) ;
 
 
+  (* Doesn't work... *)
+  (*  if p = 1 then Qpackage.root ^ "scripts/pseudo/put_pseudo_in_ezfio.py" ezfio_file.to_string; *)
+
   match Input.Ao_basis.read () with
   | None -> failwith "Error in basis"
   | Some x -> Input.Ao_basis.write x
@@ -266,8 +275,8 @@ elements can be defined as follows:
 
       ")
     spec
-    (fun o b c m xyz_file () ->
+    (fun o b c m p xyz_file () ->
-       run ?o b c m xyz_file )
+       run ?o b c m p xyz_file )
 ;;
 
 let () =

scripts/get_basis.sh

@@ -50,6 +50,6 @@ if [[ -z $pseudo ]]
 then
     ${EMSL_API_ROOT}/EMSL_api.py get_basis_data --treat_l --save --path="${tmpfile}" --basis="${basis}"
 else
-    ${EMSL_API_ROOT}/EMSL_api.py get_basis_data --treat_l  --save --path="${tmpfile}" --basis="${basis}" --db_path="${EMSL_API_ROOT}/db/Pseudo.db"
+    ${EMSL_API_ROOT}/EMSL_api.py get_basis_data --save --path="${tmpfile}" --basis="${basis}" --db_path="${EMSL_API_ROOT}/db/Pseudo.db"
 fi
 

scripts/pseudo/put_pseudo_in_ezfio.py

@@ -311,11 +311,11 @@ if __name__ == "__main__":
     # ~#~#~#~#~ #
 
     klocmax = max([len(i) for i in v_k])
-    ezfio.pseudo_klocmax = klocmax
+    ezfio.pseudo_intergrals_klocmax = klocmax
 
-    ezfio.pseudo_v_k = zip(*v_k)
+    ezfio.pseudo_intergrals_v_k = zip(*v_k)
-    ezfio.pseudo_n_k = zip(*n_k)
+    ezfio.pseudo_intergrals_n_k = zip(*n_k)
-    ezfio.pseudo_dz_k = zip(*dz_k)
+    ezfio.pseudo_intergrals_dz_k = zip(*dz_k)
 
     # ~#~#~#~#~#~#~#~#~ #
     # N o n _ L o c a l #
@@ -324,13 +324,15 @@ if __name__ == "__main__":
     lmax = max([len(i) for i in v_kl])
     kmax = max([len(sublist) for list_ in v_kl for sublist in list_])
 
-    ezfio.pseudo_lmaxpo = lmax
+    ezfio.pseudo_intergrals_lmaxpo = lmax
-    ezfio.pseudo_kmax = kmax
+    ezfio.pseudo_intergrals_kmax = kmax
 
     v_kl = make_it_square(v_kl, [lmax, kmax])
     n_kl = make_it_square(n_kl, [lmax, kmax], int)
     dz_kl = make_it_square(dz_kl, [lmax, kmax])
 
-    ezfio.pseudo_v_kl = zip(*v_kl)
+    ezfio.pseudo_intergrals_v_kl = zip(*v_kl)
-    ezfio.pseudo_n_kl = zip(*n_kl)
+    ezfio.pseudo_intergrals_n_kl = zip(*n_kl)
-    ezfio.pseudo_dz_kl = zip(*dz_kl)
+    ezfio.pseudo_intergrals_dz_kl = zip(*dz_kl)
+
+    ezfio.pseudo_intergrals_do_pseudo = True

src/Pseudo_integrals/pot_ao_ints_pseudo.irp.f

@@ -25,13 +25,13 @@
   integer, allocatable ::  n_k(:,:)
   double precision, allocatable ::  v_k(:,:), dz_k(:,:)
 
-  call ezfio_get_pseudo_klocmax(klocmax)
+  call ezfio_get_pseudo_integrals_klocmax(klocmax)
 
   allocate(n_k(nucl_num,klocmax),v_k(nucl_num,klocmax), dz_k(nucl_num,klocmax))
 
-  call ezfio_get_pseudo_v_k(v_k)
+  call ezfio_get_pseudo_integrals_v_k(v_k)
-  call ezfio_get_pseudo_n_k(n_k)
+  call ezfio_get_pseudo_integrals_n_k(n_k)
-  call ezfio_get_pseudo_dz_k(dz_k)
+  call ezfio_get_pseudo_integrals_dz_k(dz_k)
 
   !! Dump array 
   integer, allocatable ::  n_k_dump(:)
@@ -50,16 +50,16 @@
   integer, allocatable ::  n_kl(:,:,:)
   double precision, allocatable ::  v_kl(:,:,:), dz_kl(:,:,:) 
 
-  call ezfio_get_pseudo_lmaxpo(lmax)
+  call ezfio_get_pseudo_integrals_lmaxpo(lmax)
-  call ezfio_get_pseudo_kmax(kmax)
+  call ezfio_get_pseudo_integrals_kmax(kmax)
   !lmax plus one -> lmax
   lmax = lmax - 1 
  
   allocate(n_kl(nucl_num,kmax,0:lmax), v_kl(nucl_num,kmax,0:lmax), dz_kl(nucl_num,kmax,0:lmax)) 
 
-  call ezfio_get_pseudo_n_kl(n_kl)
+  call ezfio_get_pseudo_integrals_n_kl(n_kl)
-  call ezfio_get_pseudo_v_kl(v_kl)
+  call ezfio_get_pseudo_integrals_v_kl(v_kl)
-  call ezfio_get_pseudo_dz_kl(dz_kl)
+  call ezfio_get_pseudo_integrals_dz_kl(dz_kl)
 
 
   !! Dump array 

src/Pseudo_integrals/pseudo.ezfio_config

@@ -1,10 +1,10 @@
-pseudo
+pseudo_integrals
     klocmax     integer
-    v_k         double precision (nuclei_nucl_num,pseudo_klocmax)
+    v_k         double precision (nuclei_nucl_num,pseudo_integrals_klocmax)
-    n_k         integer (nuclei_nucl_num,pseudo_klocmax)
+    n_k         integer (nuclei_nucl_num,pseudo_integrals_klocmax)
-    dz_k        double precision (nuclei_nucl_num,pseudo_klocmax)
+    dz_k        double precision (nuclei_nucl_num,pseudo_integrals_klocmax)
     lmaxpo      integer
     kmax        integer
-    v_kl        double precision (nuclei_nucl_num,pseudo_kmax,pseudo_lmaxpo)
+    v_kl        double precision (nuclei_nucl_num,pseudo_integrals_kmax,pseudo_integrals_lmaxpo)
-    n_kl        integer (nuclei_nucl_num,pseudo_kmax,pseudo_lmaxpo)
+    n_kl        integer (nuclei_nucl_num,pseudo_integrals_kmax,pseudo_integrals_lmaxpo)
-    dz_kl       double precision (nuclei_nucl_num,pseudo_kmax,pseudo_lmaxpo)
+    dz_kl       double precision (nuclei_nucl_num,pseudo_integrals_kmax,pseudo_integrals_lmaxpo)