Merge pull request #8 from TApplencourt/master

Merge
2024-12-31 16:45:54 +01:00 · 2015-04-13 13:44:22 +02:00 · 2015-04-13 13:44:22 +02:00 · 70de4546b8
commit 70de4546b8
parent 5962aff7ee 323da5e449
78 changed files with 2361 additions and 1222 deletions
--- a/.gitattributes
+++ b/.gitattributes
@ -0,0 +1,5 @@
+*.irp.f linguist-language=IRPF90
+*.f linguist-language=Fortran
+*.ml linguist-language=Ocaml
+*.sh linguist-language=Bash
+*.py linguist-language=Python
--- a/INSTALL.md
+++ b/INSTALL.md
@ -6,8 +6,9 @@
 * m4
 * GNU make
 * Fortran compiler (ifort or gfortran are tested)
-* Python >= 2.7
+* Python >= 2.6
 * Bash
+* Patch (for opam)


 ## Standard installation
--- a/data/ezfio_defaults/WILL_BE_DELETED.ezfio_default
+++ b/data/ezfio_defaults/WILL_BE_DELETED.ezfio_default
@ -32,16 +32,17 @@ full_ci
  do_pt2_end                 True
  var_pt2_ratio              0.75

+cas_sd
+  n_det_max_cas_sd           100000
+  pt2_max                    1.e-4
+  do_pt2_end                 True
+  var_pt2_ratio              0.75
+
 all_singles
  n_det_max_fci              50000
  pt2_max                    1.e-8
  do_pt2_end                 False

-cassd  
-  n_det_max_cassd            10000
-  pt2_max                    1.e-4
-  do_pt2_end                 True
-                            
 hartree_fock
  n_it_scf_max               200
  thresh_scf                 1.e-10
--- a/data/ezfio_defaults/determinants.ezfio_default
+++ b/data/ezfio_defaults/determinants.ezfio_default
@ -4,6 +4,6 @@ determinants
  n_det_max_jacobi           1000
  threshold_generators       0.99
  threshold_selectors        0.999
-  read_wf                    False
-  s2_eig                     False
-  only_single_double_dm      False
+  read_wf                    false
+  s2_eig                     false
+  only_single_double_dm      false
--- a/ocaml/Makefile
+++ b/ocaml/Makefile
@ -25,9 +25,12 @@ default: $(ALL_TESTS) $(ALL_EXE) .gitignore

 .gitignore: $(MLFILES)
 	@for i in .gitignore ezfio.ml Qptypes.ml qptypes_generator.byte _build $(ALL_EXE) $(ALL_TESTS) \
-	$(patsubst %.ml,%,$(wildcard test_*.ml)) $(patsubst %.ml,%,$(wildcard qp_*.ml)) ; do \
+	$(patsubst %.ml,%,$(wildcard test_*.ml)) $(patsubst %.ml,%,$(wildcard qp_*.ml)) \
+	$(shell grep Input Input_auto_generated.ml | awk '{print $$2 ".ml"}') \
+	Input_auto_generated.ml;\
+	do \
 	   echo $$i ; \
-	done >> .gitignore
+	done > .gitignore

 executables: $(QPACKAGE_ROOT)/data/executables

--- a/ocaml/Qpackage.ml
+++ b/ocaml/Qpackage.ml
@ -94,7 +94,7 @@ let get_ezfio_default_in_file ~directory ~data ~filename =
            match (String.lsplit2 ~on:' ' (String.strip line)) with
              | Some (l,r) -> 
                if (l = data) then 
-                  String.lowercase (String.strip r)
+                  String.strip r
                else
                  find_data rest
              | None -> raise Not_found
--- a/ocaml/qp_run.ml
+++ b/ocaml/qp_run.ml
@ -20,6 +20,10 @@ let run exe ezfio_file =
  Printf.printf "===============\nQuantum Package\n===============\n\n";
  Printf.printf "Date : %s\n\n%!" (Time.to_string time_start);

+  match (Sys.command ("qp_edit -c "^ezfio_file)) with
+  | 0 -> ()
+  | i -> failwith "Error: Input inconsistent\n";
+  ;
  let exe =
    match (List.find ~f:(fun (x,_) -> x = exe) executables) with
    | None -> assert false
--- a/ocaml/qptypes_generator.ml
+++ b/ocaml/qptypes_generator.ml
@ -150,15 +150,12 @@ end = struct

  let to_string = function
  | Huckel -> \"Huckel\"
-  | HCore  -> \"HCore\"
+  | HCore  -> \"Hcore\"

  let of_string  s = 
-    let s = 
-      String.lowercase s
-    in
    match s with
-    | \"huckel\" -> Huckel
-    | \"hcore\"  -> HCore
+    | \"Huckel\" -> Huckel
+    | \"Hcore\"  -> HCore
    | _ -> failwith (\"Wrong Guess type : \"^s)

 end
@ -179,13 +176,10 @@ end = struct
  | Write  -> \"Write\"
  | None   -> \"None\"
  let of_string  s = 
-    let s = 
-      String.lowercase s
-    in
    match s with
-    | \"read\"  -> Read
-    | \"write\" -> Write
-    | \"none\"  -> None
+    | \"Read\"  -> Read
+    | \"Write\" -> Write
+    | \"None\"  -> None
    | _ -> failwith (\"Wrong IO type : \"^s)

 end
--- a/ocaml/test_input.ml
+++ b/ocaml/test_input.ml
@ -1,177 +0,0 @@
-open Qptypes;;
-
-let test_ao () =
-  Ezfio.set_file "F2.ezfio" ;
-  let b = match Input.Ao_basis.read () with
-  | Some x -> x
-  | None   -> assert false
-  in
-  print_endline (Input.Ao_basis.to_string b);
-  print_endline (Input.Ao_basis.to_rst b |> Rst_string.to_string);
-;;
-
-let test_bielec_intergals () =
-  Ezfio.set_file "F2.ezfio" ;
-  let b = match Input.Bielec_integrals.read () with
-  | Some x -> x
-  | None   -> assert false
-  in
-  let output = Input.Bielec_integrals.to_string b
-  in
-  print_endline output;
-  let rst = Input.Bielec_integrals.to_rst b in
-  let b2 = match Input.Bielec_integrals.of_rst rst with
-  | Some x -> x
-  | None -> assert false
-  in
-  if (b = b2) then
-    print_endline "OK"
-  else
-    print_endline "rst failed";
-;;
-
-let test_bitmasks () =
-  Ezfio.set_file "F2.ezfio" ;
-  let b = match Input.Bitmasks.read () with
-  | Some x -> x
-  | None   -> assert false
-  in
-  print_endline (Input.Bitmasks.to_string b);
-;;
-
-
-let test_dets () =
-  Ezfio.set_file "F2.ezfio" ;
-  let b = match Input.Determinants.read () with
-  | Some x -> x
-  | None -> assert false
-  in
-  print_endline (Input.Determinants.to_rst b |> Rst_string.to_string ) ;
-  print_endline (Input.Determinants.sexp_of_t b |> Sexplib.Sexp.to_string ) ;
-  let rst = Input.Determinants.to_rst b in
-  let b2 = match Input.Determinants.of_rst rst with
-  | Some x -> x
-  | None -> assert false
-  in
-  if (b2 = b) then
-    print_endline "OK"
-  else
-    print_endline "Failed"
-;;
-
-let test_cisd_sc2 () =
-  Ezfio.set_file "F2.ezfio" ;
-  let b = match Input.Cisd_sc2_selected.read () with
-  | Some x -> x
-  | None   -> assert false
-  in
-  print_endline (Input.Cisd_sc2_selected.to_string b);
-  let rst = Input.Cisd_sc2_selected.to_rst b in
-  let b2 = match Input.Cisd_sc2_selected.of_rst rst with
-  | Some x -> x
-  | None -> assert false
-  in
-  if (b = b2) then
-    print_endline "OK"
-  else
-    print_endline "rst failed";
-
-;;
-
-let test_electrons () =
-  Ezfio.set_file "F2.ezfio" ;
-  let b = match Input.Electrons.read () with
-  | Some x -> x
-  | None   -> assert false
-  in
-  print_endline (Input.Electrons.to_string b);
-  let rst = Input.Electrons.to_rst b in
-  let b2 = match Input.Electrons.of_rst rst with
-  | Some x -> x
-  | None -> assert false
-  in
-  if (b = b2) then
-    print_endline "OK"
-  else
-    print_endline "Failed in rst"
-;;
-
-let test_fci () =
-  Ezfio.set_file "F2.ezfio" ;
-  let b = match Input.Full_ci.read () with
-  | Some x -> x
-  | None   -> assert false
-  in
-  print_endline (Input.Full_ci.to_string b);
-  let rst = Input.Full_ci.to_rst b in
-  let b2 = match Input.Full_ci.of_rst rst with
-  | Some x -> x
-  | None -> assert false
-  in
-  print_endline (Input.Full_ci.to_string b);
-  if (b = b2) then
-    print_endline "OK"
-  else
-    print_endline "Failed in rst"
-;;
-
-let test_hf () =
-  Ezfio.set_file "F2.ezfio" ;
-  let b = match Input.Hartree_fock.read () with
-  | Some x -> x
-  | None   -> assert false
-  in
-  print_endline (Input.Hartree_fock.to_string b);
-  let rst = Input.Hartree_fock.to_rst b in
-  let b2 = match Input.Hartree_fock.of_rst rst with
-  | Some x -> x
-  | None -> assert false
-  in
-  print_endline (Input.Hartree_fock.to_string b);
-  if (b = b2) then
-    print_endline "OK"
-  else
-    print_endline "Failed in rst"
-;;
-
-let test_mo () =
-  Ezfio.set_file "F2.ezfio" ;
-  let b = match Input.Mo_basis.read () with
-  | Some x -> x
-  | None   -> assert false
-  in
-  print_endline (Input.Mo_basis.to_string b);
-;;
-
-let test_nucl () =
-  Ezfio.set_file "F2.ezfio" ;
-  let b = match Input.Nuclei.read () with
-  | Some x -> x
-  | None   -> assert false
-  in
-  let rst = Input.Nuclei.to_rst b in
-  let b2 = match Input.Nuclei.of_rst rst with
-  | Some x -> x
-  | None -> assert false
-  in
-  print_endline (Input.Nuclei.to_string b);
-  if (b = b2) then
-    print_endline "OK"
-  else
-    print_endline "Failed in rst"
-;;
-
-(*
-test_ao ();;
-test_bitmasks ();
-test_cis ();
-test_cisd_sc2 ();
-test_dets ();
-test_hf ();;
-test_mo ();;
-test_nucl ();
-test_bielec_intergals ();;
-test_electrons();
-*)
-test_dets ();
-
--- a/scripts/build_modules.sh
+++ b/scripts/build_modules.sh
@ -30,6 +30,7 @@ Build failed for module $MODULE
 "
    fi
  fi
+  ${QPACKAGE_ROOT}/scripts/create_gitignore.sh
  cd ${OLDPWD}
 done
 ${QPACKAGE_ROOT}/scripts/create_executables_list.sh
--- a/scripts/create_gitignore.sh
+++ b/scripts/create_gitignore.sh
@ -35,4 +35,4 @@ then
 fi

 find . -type l | sed "s@./@@" >> .gitignore
-
+find . -type f -executable -print | sed "s@./@@" >> .gitignore
--- a/scripts/create_rst_templates.sh
+++ b/scripts/create_rst_templates.sh
@ -12,6 +12,8 @@ fi
 source ${QPACKAGE_ROOT}/scripts/qp_include.sh

 check_current_dir_is_module
+MODULE=$(basename $PWD)
+

 README="True"
 if [[ -f README.rst ]]
--- a/scripts/ezfio_interface/ei_handler.py
+++ b/scripts/ezfio_interface/ei_handler.py
@ -12,8 +12,8 @@ By default all the option are executed.
 Options:
    -h --help
    --path             The path of the `EZFIO.cfg`, by default will look in the ${pwd}
-    --irpf90           Create the `ezfio_interface.ipf90`
-                             who containt all the provider needed
+    --irpf90           Create the `ezfio_interface.irpf90`
+                             which contains all the providers needed
                             (aka all with the `interface: input` parameter)
                             in `${pwd}`
    --ezfio_config     Create the `${module_lower}_ezfio_interface_config` in
@ -28,7 +28,7 @@ Options:
 Format specification :
    [provider_name]  | the name of the provider in irp.f90
    doc:{str}        | Is the doc
-    Type:{str}       | Is a fancy_type support by the ocaml
+    Type:{str}       | Is a fancy_type supported by the ocaml
    ezfio_name:{str} | Will be the name of the file for the ezfio
                       (optional by default is the name of the provider)
    interface:{str}  | The provider is a imput or a output
@ -67,13 +67,13 @@ Type = namedtuple('Type', 'fancy ocaml fortran')

 def is_bool(str_):
    """
-    Take a string, if is a bool return the convert into
-        fortran and ocaml one.
+    Take a string, if is a bool return the conversion into
+        fortran and ocaml.
    """
-    if str_.lower() in ['true', '.true.']:
-        return Type(None, "True", ".True.")
-    elif str_.lower() in ['false', '.False.']:
-        return Type(None, "False", ".False")
+    if "true" in str_.lower():
+        return Type(None, "true", ".True.")
+    elif "false" in str_.lower():
+        return Type(None, "false", ".False")
    else:
        raise TypeError

@ -81,7 +81,7 @@ def is_bool(str_):
 def get_type_dict():
    """
    This function makes the correspondance between the type of value read in
-    ezfio.cfg into the f90 and Ocam Type
+    ezfio.cfg into the f90 and Ocaml Type
    return fancy_type[fancy_type] = namedtuple('Type', 'ocaml fortran')
    For example fancy_type['Ndet'].fortran = interger
                                  .ocaml   = int
@ -154,7 +154,7 @@ def get_type_dict():
    # q p _ t y p e s _ g e n e r a t e #
    # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #

-    # Read the fancy_type, the ocaml. and convert the ocam to the fortran
+    # Read the fancy_type, the ocaml. and convert the ocaml to the fortran
    for i in l_gen + l_un:
        str_fancy_type = i.split()[1].strip()
        str_ocaml_type = i.split()[3]
@ -507,6 +507,9 @@ def create_ocaml_input(dict_ezfio_cfg, module_lower):
            l_type.append(v["type"])
            l_doc.append(v["doc"])

+    if not l_ezfio_name:
+        raise ValueError
+
    e_glob = EZFIO_ocaml(l_ezfio_name=l_ezfio_name,
                         l_type=l_type,
                         l_doc=l_doc)
@ -602,6 +605,49 @@ def save_ocaml_input(module_lower, str_ocaml_input):
            f.write(str_ocaml_input)


+def get_l_module_lower():
+    """
+    Get all module who have EZFIO.cfg with input data
+        (NB `search` in all the ligne and `match` only in one)
+    """
+
+    # ~#~#~#~ #
+    # I n i t #
+    # ~#~#~#~ #
+
+    mypath = "{0}/src".format(os.environ['QPACKAGE_ROOT'])
+
+    # ~#~#~#~#~#~#~#~ #
+    # L _ f o l d e r #
+    # ~#~#~#~#~#~#~#~ #
+
+    from os import listdir
+    from os.path import isdir, join, exists
+
+    l_folder = [f for f in listdir(mypath) if isdir(join(mypath, f))]
+
+    # ~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
+    # L _ m o d u l e _ l o w e r #
+    # ~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
+
+    l_module_lower = []
+    import re
+    p = re.compile(ur'interface:\s+input')
+
+    for f in l_folder:
+        path = "{0}/{1}/EZFIO.cfg".format(mypath, f)
+        if exists(path):
+            with open(path, 'r') as file_:
+                if p.search(file_.read()):
+                    l_module_lower.append(f.lower())
+
+    # ~#~#~#~#~#~ #
+    # R e t u r n #
+    # ~#~#~#~#~#~ #
+
+    return l_module_lower
+
+
 def create_ocaml_input_global():
    """
    Check for all the EZFIO.cfg get the module lower
@ -612,15 +658,7 @@ def create_ocaml_input_global():
    #  I n i t #
    # ~#~#~#~# #

-    from os import listdir
-    from os.path import isdir, join, exists
-
-    mypath = "{0}/src".format(os.environ['QPACKAGE_ROOT'])
-
-    onlyfodler = [f for f in listdir(mypath) if isdir(join(mypath, f))]
-
-    l_module_lower = [f.lower() for f in onlyfodler
-                      if exists("{0}/{1}/EZFIO.cfg".format(mypath, f))]
+    l_module_lower = get_l_module_lower()

    # ~#~#~#~#~#~#~#~# #
    #  C r e a t i o n #
@ -761,8 +799,12 @@ if __name__ == "__main__":
    # O c a m l #
    # ~#~#~#~#~#~#
    if do_all or arguments["--ocaml"]:
-        str_ocaml_input = create_ocaml_input(dict_ezfio_cfg, module_lower)
-        save_ocaml_input(module_lower, str_ocaml_input)
+        try:
+            str_ocaml_input = create_ocaml_input(dict_ezfio_cfg, module_lower)
+        except ValueError:
+            pass
+        else:
+            save_ocaml_input(module_lower, str_ocaml_input)

    # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
    # e z f i o _ d e f a u l t #
--- a/scripts/ezfio_with_default.py
+++ b/scripts/ezfio_with_default.py
@ -90,19 +90,14 @@ END_PROVIDER
    self.default = t

  def get_default(self):
+    filename = '/'.join( [os.environ['QPACKAGE_ROOT'], 'data',
+                          'ezfio_defaults',
+                          'WILL_BE_DELETED.ezfio_default'] )

-    from os import listdir
-    from os.path import isfile, join
-
-    mypath = '/'.join( [os.environ['QPACKAGE_ROOT'], 'data', 'ezfio_defaults','/'])
-    onlyfiles = [ f for f in listdir(mypath) if isfile(join(mypath,f)) ]
-
-    lines= []
-    for filename in onlyfiles: 
-      file = open(mypath+filename,'r')
-      lines.extend(file.readlines()[:])
-      file.close()
-
+    file = open(filename,'r')
+    lines = file.readlines()
+    file.close()
+    k=-1
    # Search directory
    for k,line in enumerate(lines):
      if line[0] != ' ':
@ -120,16 +115,21 @@ END_PROVIDER
        break
    v = buffer[1]
    name = self.name
+    true = True
+    false= False
    try:
+      true = True
+      false = False
      v_eval = eval(v)
+    except:
+      v = "call ezfio_get_%(v)s(%(name)s)"%locals()
+    else:
      if type(v_eval) == bool:
        v = '.%s.'%(v)
      elif type(v_eval) == float:
        v = v.replace('e','d')
        v = v.replace('E','D')
      v = "%(name)s = %(v)s"%locals()
-    except:
-      v = "call ezfio_get_%(v)s(%(name)s)"%locals()
    self.default = v


--- a/scripts/generate_h_apply.py
+++ b/scripts/generate_h_apply.py
@ -53,7 +53,7 @@ class H_apply(object):
        !$OMP  N_elec_in_key_hole_2,ia_ja_pairs)               &
        !$OMP SHARED(key_in,N_int,elec_num_tab,mo_tot_num,           &
        !$OMP  hole_1, particl_1, hole_2, particl_2,                 &
-        !$OMP  elec_alpha_num,i_generator)"""
+        !$OMP  elec_alpha_num,i_generator) FIRSTPRIVATE(iproc)"""
    s["omp_end_parallel"] = "!$OMP END PARALLEL"
    s["omp_master"]       = "!$OMP MASTER"
    s["omp_end_master"]   = "!$OMP END MASTER"
--- a/scripts/qp_convert.py
+++ b/scripts/qp_convert.py
@ -53,16 +53,68 @@ def write_ezfioFile(res,filename):
  basis = res.uncontracted_basis
  geom  = res.geometry

+  res.clean_contractions()
+  # AO Basis
+  import string
+  at = []
+  num_prim = []
+  magnetic_number = []
+  angular_number = []
+  power_x = []
+  power_y = []
+  power_z = []
+  coefficient = []
+  exponent = []
+  res.convert_to_cartesian()
+  for b in res.basis:
+    c = b.center
+    for i,atom in enumerate(res.geometry):
+      if atom.coord == c:
+         at.append(i+1)
+    num_prim.append(len(b.prim))
+    s = b.sym
+    power_x.append( string.count(s,"x") )
+    power_y.append( string.count(s,"y") )
+    power_z.append( string.count(s,"z") )
+    coefficient.append(  b.coef )
+    exponent.append( [ p.expo for p in b.prim ] )
+  ezfio.set_ao_basis_ao_num(len(res.basis))
+  ezfio.set_ao_basis_ao_nucl(at)
+  ezfio.set_ao_basis_ao_prim_num(num_prim)
+  ezfio.set_ao_basis_ao_power(power_x+power_y+power_z)
+  prim_num_max = ezfio.get_ao_basis_ao_prim_num_max()
+  len_res_basis = len(res.basis)
+  for i in range(len(res.basis)):
+    coefficient[i] += [ 0. for j in range(len(coefficient[i]),prim_num_max) ]
+    exponent[i]    += [ 0. for j in range(len(exponent[i]),prim_num_max) ]
+  coefficient = reduce(lambda x, y: x+y, coefficient, [])
+  exponent = reduce(lambda x, y: x+y, exponent, [])
+  coef = []
+  expo = []
+  for i in range(prim_num_max):
+   for j in range(i,len(coefficient),prim_num_max):
+    coef.append ( coefficient[j] )
+    expo.append ( exponent[j] )
+  ezfio.set_ao_basis_ao_coef(coef)
+  ezfio.set_ao_basis_ao_expo(expo)
+  ezfio.set_ao_basis_ao_basis("Read by resultsFile")
+
+
 # MO 
  MoTag = res.determinants_mo_type
  ezfio.set_mo_basis_mo_label('Orthonormalized')
  MO_type = MoTag
-  allMOs = res.uncontracted_mo_sets[MO_type]
+  allMOs = res.mo_sets[MO_type]


-  closed = [ (allMOs[i].eigenvalue,i) for i  in res.closed_mos ]
-  active = [ (allMOs[i].eigenvalue,i) for i  in res.active_mos ]
-  virtual =[ (allMOs[i].eigenvalue,i) for i  in res.virtual_mos ]
+  try:
+    closed = [ (allMOs[i].eigenvalue,i) for i  in res.closed_mos ]
+    active = [ (allMOs[i].eigenvalue,i) for i  in res.active_mos ]
+    virtual =[ (allMOs[i].eigenvalue,i) for i  in res.virtual_mos ]
+  except:
+    closed = []
+    virtual = []
+    active = [ (allMOs[i].eigenvalue,i) for i in range(len(allMOs)) ]

 # closed.sort()
 # active.sort()
@ -111,117 +163,6 @@ def write_ezfioFile(res,filename):
  while len(MoMatrix) < len(MOs[0].vector)**2:
    MoMatrix.append(0.)

-  ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
-  ezfio.set_mo_basis_mo_occ(OccNum)
-
-
-  res.clean_contractions()
-  # AO Basis
-  import string
-  at = []
-  num_prim = []
-  magnetic_number = []
-  angular_number = []
-  power_x = []
-  power_y = []
-  power_z = []
-  coefficient = []
-  exponent = []
-  res.convert_to_cartesian()
-  for b in res.basis:
-    c = b.center
-    for i,atom in enumerate(res.geometry):
-      if atom.coord == c:
-         at.append(i+1)
-    num_prim.append(len(b.prim))
-    s = b.sym
-    power_x.append( string.count(s,"x") )
-    power_y.append( string.count(s,"y") )
-    power_z.append( string.count(s,"z") )
-    coefficient.append(  b.coef )
-    exponent.append( [ p.expo for p in b.prim ] )
-  ezfio.set_ao_basis_ao_num(len(res.basis))
-  ezfio.set_ao_basis_ao_nucl(at)
-  ezfio.set_ao_basis_ao_prim_num(num_prim)
-  ezfio.set_ao_basis_ao_power(power_x+power_y+power_z)
-  prim_num_max = ezfio.get_ao_basis_ao_prim_num_max()
-  len_res_basis = len(res.basis)
-  for i in range(len(res.basis)):
-    coefficient[i] += [ 0. for j in range(len(coefficient[i]),prim_num_max) ]
-    exponent[i]    += [ 0. for j in range(len(exponent[i]),prim_num_max) ]
-  coefficient = reduce(lambda x, y: x+y, coefficient, [])
-  exponent = reduce(lambda x, y: x+y, exponent, [])
-  coef = []
-  expo = []
-  for i in range(prim_num_max):
-   for j in range(i,len(coefficient),prim_num_max):
-    coef.append ( coefficient[j] )
-    expo.append ( exponent[j] )
-  ezfio.set_ao_basis_ao_coef(coef)
-  ezfio.set_ao_basis_ao_expo(expo)
-  ezfio.set_ao_basis_ao_basis("Read by resultsFile")
-
-# Apply threshold to determinants
-  if len(res.determinants) == 1:
-    sorted_determinants = [ (-1.,1.,res.determinants[0]) ]
-  else:
-    sorted_determinants = []
-    for i,j in zip(res.det_coefficients[0],res.determinants):
-      sorted_determinants.append((-abs(i),i,j))
-  sorted_determinants.sort()
-  norm = 0.0
-  for length, (a,b,c) in enumerate(sorted_determinants):
-    if -a < det_threshold:
-      length -=1
-      break
-    norm += a**2
-  norm = sqrt(norm)
-  length += 1
-  for i in xrange(length):
-    a = sorted_determinants[i]
-    sorted_determinants[i] = (a[0],a[1]/norm,a[2])
-  sorted_determinants = sorted_determinants[:length]
-
-# MOs
-  mo_tot_num = len(res.mo_sets[MoTag])
-  closed_mos = res.closed_mos
-  active_mos = res.active_mos
-  virtual_mos = res.virtual_mos
-  to_remove = []
-  to_add = []
-  for i in active_mos:
-    found = False
-    for (a,b,c) in sorted_determinants:
-      if i in c['alpha']+c['beta']:
-        found = True
-        break
-    if not found:
-      to_remove.append(i)
-      to_add.append(i)
-  virtual_mos = to_add + virtual_mos
-  for i in active_mos:
-    always = True
-    for (a,b,c) in sorted_determinants:
-      if not (i in c['alpha'] and i in c['beta']):
-        always = False
-        break
-    if always:
-      to_remove.append(i)
-      closed_mos.append(i)
-  for i in to_remove:
-    active_mos.remove(i)
-
-
-  MOindices = closed_mos + active_mos + virtual_mos
-  while len(MOindices) < mo_tot_num:
-    MOindices.append(len(MOindices))
-  MOmap = list(MOindices)
-  for i in range(len(MOindices)):
-    MOmap[i] = MOindices.index(i)
-
-
-  ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
-
  mo = []
  for i in MOindices:
    mo.append(res.mo_sets[MoTag][i])
@ -234,35 +175,11 @@ def write_ezfioFile(res,filename):
    while len(mo) < mo_tot_num:
      mo.append(newmo)
  Energies  = [ m.eigenvalue for m in mo ]
-
-  if res.occ_num is not None:
-    OccNum    = []
-    for i in MOindices:
-      OccNum.append(res.occ_num[MoTag][i])
-
-    while len(OccNum) < mo_tot_num:
-      OccNum.append(0.)
-    ezfio.set_mo_basis_mo_occ(OccNum)
-
-  cls = [ "v" for i in mo ]
-  for i in closed_mos:
-    cls[MOmap[i]] = 'c'
-  for i in active_mos:
-    cls[MOmap[i]] = 'a'
-
-  sym0 = [ i.sym for i in res.mo_sets[MoTag] ]
-  sym  = [ i.sym for i in res.mo_sets[MoTag] ]
-  for i in xrange(len(sym)):
-    sym[MOmap[i]] = sym0[i]
-
-  MoMatrix = []
-  for m in mo:
-     for coef in m.vector:
-         MoMatrix.append(coef)
-  while len(MoMatrix) < len(mo[0].vector)**2:
-    MoMatrix.append(0.)
+  
+  ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
+  ezfio.set_mo_basis_mo_occ(OccNum)
  ezfio.set_mo_basis_mo_coef(MoMatrix)
-  del MoMatrix
+



--- a/scripts/update_README.py
+++ b/scripts/update_README.py
@ -1,16 +1,16 @@
 #!/usr/bin/env python

 """Updates the README.rst file as the include directive is disabled on GitHub."""
-__date__     = "Thu Apr  3 23:06:18 CEST 2014"
+__date__ = "Thu Apr  3 23:06:18 CEST 2014"
 __author__ = "Anthony Scemama <scemama@irsamc.ups-tlse.fr>"


-README="README.rst"
-Assum_key="Assumptions\n===========\n"
-Needed_key="Needed Modules\n==============\n"
-Doc_key="Documentation\n=============\n"
-Sentinel="@@$%&@@"
-URL="http://github.com/LCPQ/quantum_package/tree/master/src/"
+README = "README.rst"
+Assum_key = "Assumptions\n===========\n"
+Needed_key = "Needed Modules\n==============\n"
+Doc_key = "Documentation\n=============\n"
+Sentinel = "@@$%&@@"
+URL = "http://github.com/LCPQ/quantum_package/tree/master/src/"

 import os
 import subprocess
@ -22,30 +22,30 @@ header = """
 """

 try:
-# subprocess.check_output("git status".split())
-# has_git = True
-  pass
+    # subprocess.check_output("git status".split())
+    has_git = True
 except OSError:
-  has_git = False
+    has_git = False
+

 def fetch_splitted_data():
    """Read the README.rst file and split it in strings:
    * The description
    * The assumptions
-    * The documentation 
+    * The documentation
    * The needed modules
    The result is given as a list of strings
    """

-    file = open(README,'r')
+    file = open(README, 'r')
    data = file.read()
    file.close()

    # Place sentinels
-    data = data.replace(Assum_key,Sentinel+Assum_key)
-    data = data.replace(Doc_key,Sentinel+Doc_key)
-    data = data.replace(Needed_key,Sentinel+Needed_key)
-    
+    data = data.replace(Assum_key, Sentinel + Assum_key)
+    data = data.replace(Doc_key, Sentinel + Doc_key)
+    data = data.replace(Needed_key, Sentinel + Needed_key)
+
    # Now Split data using the sentinels
    result = data.split(Sentinel)

@ -56,9 +56,9 @@ def update_assumptions(data):
    """Read the ASSUMPTIONS.rst file, and replace the data with it."""

    try:
-        file = open('ASSUMPTIONS.rst','r')
+        file = open('ASSUMPTIONS.rst', 'r')
    except IOError:
-        file = open('ASSUMPTIONS.rst','w')
+        file = open('ASSUMPTIONS.rst', 'w')
        assumptions = ""
    else:
        assumptions = file.read()
@ -74,7 +74,7 @@ def update_assumptions(data):
            data[i] = assumptions

    if not has_assumptions:
-        data.insert(1,assumptions)
+        data.insert(1, assumptions)

    return data

@ -83,12 +83,12 @@ def update_needed(data):
    """Read the NEEDED_MODULES file, and replace the data with it.
    Create the links to the GitHub pages."""

-    file = open('NEEDED_MODULES','r')
+    file = open('NEEDED_MODULES', 'r')
    modules = file.read()
    file.close()

    if modules.strip() != "":
-        modules = [ '* `%s <%s%s>`_'%(x,URL,x) for x in  modules.split() ]
+        modules = ['* `%s <%s%s>`_' % (x, URL, x) for x in modules.split()]
        modules = "\n".join(modules)
        modules = Needed_key + header + modules + '\n\n'

@ -105,112 +105,114 @@ def update_needed(data):


 def update_documentation(data):
-  """Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation"""
+    """Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation"""

-  # If the file does not exist, don't do anything
-  try:
-    file = open('tags','r')
-  except:
-    return
-  tags = file.readlines()
-  file.close()
-
-  def extract_doc(item):
-    """Extracts the documentation contained in IRPF90_man file"""
-    file = open("IRPF90_man/%s.l"%(item),'r')
-    lines = file.readlines()
+    # If the file does not exist, don't do anything
+    try:
+        file = open('tags', 'r')
+    except:
+        return
+    tags = file.readlines()
    file.close()
-    result = []
-    inside = False
-    for line in lines:
-      if not inside:
-        inside = line.startswith(".SH Description")
-      else:
-        if line.startswith(".SH"):
-          break
-        result.append("  "+line.strip())

-    if result == []:
-      result = ["  Undocumented"]
-    return "\n".join(result)+'\n'
-            
-        
-  
-  items = []
-  dirname = os.path.basename(os.getcwd())
-  command = "git ls-tree --full-tree --name-only HEAD:src/%s"
-  command = command%(dirname)
-  try:
-    if dirname != 'src':
-      p = subprocess.Popen(command.split(),stdout=subprocess.PIPE)
-      tracked_files = p.stdout.read()
-    else:
-      tracked_files = ""
-    tracked_files = tracked_files.splitlines()
-  except:
-    tracked_files = []
-  for filename in tracked_files:
-      if filename.endswith('.irp.f'):
-          # Search for providers, subroutines and functions in each file using
-          # the tags file
-          search = "\t"+filename+"\t"
-          tmp = filter(lambda line: search in line, tags)
+    def extract_doc(item):
+        """Extracts the documentation contained in IRPF90_man file"""
+        file = open("IRPF90_man/%s.l" % (item), 'r')
+        lines = file.readlines()
+        file.close()
+        result = []
+        inside = False
+        for line in lines:
+            if not inside:
+                inside = line.startswith(".SH Description")
+            else:
+                if line.startswith(".SH"):
+                    break
+                result.append("  " + line.strip())

-          # Search for the documentation in the IRPF90_man directory
-          for item in tmp :
-              item, _, line = item.strip().split('\t')
-              doc = extract_doc(item)
-              items.append( (item, filename, doc, line) )
+        if result == []:
+            result = ["  Undocumented"]
+        return "\n".join(result) + '\n'

-  dirname = os.path.basename(os.getcwd())
-  # Write the documentation in the README
-  template = "`%(item)s <%(url)s%(dirname)s/%(filename)s#L%(line)s>`_\n%(doc)s\n"
+    items = []
+    dirname = os.path.basename(os.getcwd())
+    command = "git ls-tree --full-tree --name-only HEAD:src/%s"
+    command = command % (dirname)
+    try:
+        if dirname != 'src':
+            p = subprocess.Popen(command.split(), stdout=subprocess.PIPE)
+            tracked_files = p.stdout.read()
+        else:
+            tracked_files = ""
+        tracked_files = tracked_files.splitlines()
+    except:
+        tracked_files = []
+    for filename in tracked_files:
+        if filename.endswith('.irp.f'):
+                    # Search for providers, subroutines and functions in each file using
+                    # the tags file
+            search = "\t" + filename + "\t"
+            tmp = filter(lambda line: search in line, tags)

-  documentation = Doc_key + header 
-  url = URL
-  for item, filename, doc, line in items:
-    documentation += template%locals()
-  documentation += '\n\n'
+            # Search for the documentation in the IRPF90_man directory
+            for item in tmp:
+                item, _, line = item.strip().split('\t')
+                doc = extract_doc(item)
+                items.append((item, filename, doc, line))

-  has_doc = False
-  for i in range(len(data)):
-      if data[i].startswith(Doc_key):
-          has_doc = True
-          data[i] = documentation
+    dirname = os.path.basename(os.getcwd())
+    # Write the documentation in the README
+    template = "`%(item)s <%(url)s%(dirname)s/%(filename)s#L%(line)s>`_\n%(doc)s\n"

-  if not has_doc:
-      data.append(documentation)
+    documentation = Doc_key + header
+    url = URL
+    for item, filename, doc, line in items:
+        documentation += template % locals()
+    documentation += '\n\n'

-  return data
+    has_doc = False
+    for i in range(len(data)):
+        if data[i].startswith(Doc_key):
+            has_doc = True
+            data[i] = documentation
+
+    if not has_doc:
+        data.append(documentation)
+
+    return data


 def git_add():
    """Executes:
    git add README.rst
-    if git is present on the machine."""
-    command = "git add "+README
-    os.system(command+" &> /dev/null")
+    throw an error if git is not precent"""
+
+    import subprocess
+
+    try:
+        # pipe output to /dev/null for silence
+        null = open("/dev/null", "w")
+        subprocess.Popen("git add README.rst", stdout=null, stderr=null)
+        null.close()
+
+    except OSError:
+        raise


 def main():
-    if not has_git:
-        return
    data = fetch_splitted_data()
    data = update_assumptions(data)
    data = update_documentation(data)
    data = update_needed(data)
    output = ''.join(data)
-    
-    file = open(README,'w')
-    file.write(output)
-    file.close()

-    git_add()
+    with open(README, 'w') as f:
+        f.write(output)

+    try:
+        git_add()
+    except OSError:
+        pass

 if __name__ == '__main__':
-    try:
-      main()
-    except:
-      pass
-
+    main()
--- a/setup_environment.sh
+++ b/setup_environment.sh
@ -50,16 +50,6 @@ then
 fi


-echo "${BLUE}===== Installing EZFIO ===== ${BLACK}"
-${QPACKAGE_ROOT}/scripts/install_ezfio.sh | tee install_ezfio.log
-
-if [[ ! -d ${QPACKAGE_ROOT}/EZFIO ]]
-then
-  echo $RED "Error in EZFIO installation" $BLACK
-  exit 1
-fi
-
-
 echo "${BLUE}===== Installing Zlib ===== ${BLACK}"
 ${QPACKAGE_ROOT}/scripts/install_zlib.sh       | tee install_zlib.log

--- a/src/AOs/README.rst
+++ b/src/AOs/README.rst
@ -50,21 +50,65 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.

+`ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L1>`_
+  Overlap between atomic basis functions:
+  :math:`\int \chi_i(r) \chi_j(r) dr)`
+
+`ao_overlap_abs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L65>`_
+  Overlap between absolute value of atomic basis functions:
+  :math:`\int |\chi_i(r)| |\chi_j(r)| dr)`
+
+`ao_overlap_x <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L2>`_
+  Overlap between atomic basis functions:
+  :math:`\int \chi_i(r) \chi_j(r) dr)`
+
+`ao_overlap_y <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L3>`_
+  Overlap between atomic basis functions:
+  :math:`\int \chi_i(r) \chi_j(r) dr)`
+
+`ao_overlap_z <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L4>`_
+  Overlap between atomic basis functions:
+  :math:`\int \chi_i(r) \chi_j(r) dr)`
+
 `ao_coef <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L21>`_
  Coefficients, exponents and powers of x,y and z
-  ao_coef(i,j) = coefficient of the jth primitive on the ith ao

-`ao_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L96>`_
+`ao_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L157>`_
  Transposed ao_coef and ao_expo

+`ao_coef_unnormalized <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L116>`_
+  Coefficients, exponents and powers of x,y and z as in the EZFIO file
+  ao_coef(i,j) = coefficient of the jth primitive on the ith ao
+  ao_l = l value of the AO: a+b+c in x^a y^b z^c
+
 `ao_expo <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L20>`_
  Coefficients, exponents and powers of x,y and z
-  ao_coef(i,j) = coefficient of the jth primitive on the ith ao

-`ao_expo_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L97>`_
+`ao_expo_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L158>`_
  Transposed ao_coef and ao_expo

-`ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L146>`_
+`ao_expo_unsorted <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L117>`_
+  Coefficients, exponents and powers of x,y and z as in the EZFIO file
+  ao_coef(i,j) = coefficient of the jth primitive on the ith ao
+  ao_l = l value of the AO: a+b+c in x^a y^b z^c
+
+`ao_l <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L118>`_
+  Coefficients, exponents and powers of x,y and z as in the EZFIO file
+  ao_coef(i,j) = coefficient of the jth primitive on the ith ao
+  ao_l = l value of the AO: a+b+c in x^a y^b z^c
+
+`ao_l_char <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L119>`_
+  Coefficients, exponents and powers of x,y and z as in the EZFIO file
+  ao_coef(i,j) = coefficient of the jth primitive on the ith ao
+  ao_l = l value of the AO: a+b+c in x^a y^b z^c
+
+`ao_l_char_space <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L309>`_
+  Undocumented
+
+`ao_md5 <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L400>`_
+  MD5 key characteristic of the AO basis
+
+`ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L207>`_
  Index of the nuclei on which the ao is centered

 `ao_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L1>`_
@ -75,16 +119,37 @@ Documentation

 `ao_power <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L19>`_
  Coefficients, exponents and powers of x,y and z
-  ao_coef(i,j) = coefficient of the jth primitive on the ith ao

-`ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L114>`_
+`ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L175>`_
  Number of primitives per atomic orbital

-`ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L136>`_
+`ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L197>`_
  Undocumented

-`ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L137>`_
+`ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L198>`_
  Undocumented

+`l_to_charater <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L216>`_
+  character corresponding to the "L" value of an AO orbital
+
+`n_aos_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L229>`_
+  Number of AOs per atom
+
+`nucl_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L242>`_
+  List of AOs attached on each atom
+
+`nucl_list_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L260>`_
+  Index of the shell type Aos and of the corresponding Aos
+  Per convention, for P,D,F and G AOs, we take the index
+  of the AO with the the corresponding power in the "X" axis
+
+`nucl_n_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L228>`_
+  Number of AOs per atom
+
+`nucl_num_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L261>`_
+  Index of the shell type Aos and of the corresponding Aos
+  Per convention, for P,D,F and G AOs, we take the index
+  of the AO with the the corresponding power in the "X" axis
+


--- a/src/Bielec_integrals/EZFIO.cfg
+++ b/src/Bielec_integrals/EZFIO.cfg
@ -7,26 +7,26 @@ ezfio_name: direct

 [disk_access_mo_integrals]
 type: Disk_access
-doc: Write, Read, None for  MO integrals from disk (EZFIO folder)
+doc: Read/Write MO integrals from/to disk [ Write | Read | None ] 
 interface: input
 default: None

 [disk_access_ao_integrals]
 type: Disk_access
-doc: Write or Read or None for AO integrals from disk (EZFIO folder)
+doc: Read/Write AO integrals from/to disk [ Write | Read | None ] 
 interface: input
 default: None

 [ao_integrals_threshold]
 type: Threshold
-doc: If <pq|rs> < ao_integrals_threshold then <pq|rs> is null
+doc: If |<pq|rs>| < ao_integrals_threshold then <pq|rs> is zero
 interface: input
 default: 1.e-15
 ezfio_name: threshold_ao

 [mo_integrals_threshold]
 type: Threshold
-doc: If <ij|kl> < ao_integrals_threshold then <pq|rs> is null
+doc: If |<ij|kl>| < ao_integrals_threshold then <pq|rs> is zero
 interface: input
 default: 1.e-15
-ezfio_name: threshold_mo
+ezfio_name: threshold_mo
--- a/src/Bielec_integrals/README.rst
+++ b/src/Bielec_integrals/README.rst
@ -32,152 +32,193 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.

-`ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L1>`_
+`ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1>`_
  integral of the AO basis <ik|jl> or (ij|kl)
  i(r1) j(r1) 1/r12 k(r2) l(r2)

-`ao_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L350>`_
-  Needed to compuet Schwartz inequalities
+`ao_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L490>`_
+  Needed to compute Schwartz inequalities

-`ao_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L188>`_
+`ao_bielec_integral_schwartz_accel <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L107>`_
+  integral of the AO basis <ik|jl> or (ij|kl)
+  i(r1) j(r1) 1/r12 k(r2) l(r2)
+
+`ao_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L322>`_
  Map of Atomic integrals
  i(r1) j(r2) 1/r12 k(r1) l(r2)

-`compute_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L147>`_
+`ao_l4 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L279>`_
+  Computes the product of l values of i,j,k,and l
+
+`compute_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L290>`_
  Compute AO 1/r12 integrals for all i and fixed j,k,l

-`eri <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L511>`_
+`eri <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L653>`_
  ATOMIC PRIMTIVE bielectronic integral between the 4 primitives ::
  primitive_1 = x1**(a_x) y1**(a_y) z1**(a_z) exp(-alpha * r1**2)
  primitive_2 = x1**(b_x) y1**(b_y) z1**(b_z) exp(- beta * r1**2)
  primitive_3 = x2**(c_x) y2**(c_y) z2**(c_z) exp(-delta * r2**2)
  primitive_4 = x2**(d_x) y2**(d_y) z2**(d_z) exp(- gama * r2**2)

-`general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L376>`_
+`general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L515>`_
  Computes the integral <pq|rs> where p,q,r,s are Gaussian primitives

-`give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L656>`_
+`give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L851>`_
  subroutine that returns the explicit polynom in term of the "t"
  variable of the following polynomw :
  I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q)

-`i_x1_new <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L600>`_
+`i_x1_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L772>`_
  recursive function involved in the bielectronic integral

-`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L719>`_
+`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L914>`_
  recursive function involved in the bielectronic integral

-`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L839>`_
+`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1034>`_
  recursive function involved in the bielectronic integral

-`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L893>`_
+`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1088>`_
  recursive function involved in the bielectronic integral

-`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L753>`_
+`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L948>`_
  recursive function involved in the bielectronic integral

-`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L623>`_
+`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L807>`_
  recursive function involved in the bielectronic integral

-`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L955>`_
+`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1150>`_
  recursive function involved in the bielectronic integral

-`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L555>`_
+`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L698>`_
  calculate the integral of the polynom ::
  I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q)
  between ( 0 ; 1)

-`n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L642>`_
-  Returns the upper boundary of the degree of the polynom involved in the
+`n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L837>`_
+  Returns the upper boundary of the degree of the polynomial involved in the
  bielctronic integral :
  Ix(a_x,b_x,c_x,d_x) * Iy(a_y,b_y,c_y,d_y) * Iz(a_z,b_z,c_z,d_z)

-`gauleg <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/gauss_legendre.irp.f#L20>`_
+`gauleg <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/gauss_legendre.irp.f#L29>`_
  Gauss-Legendre

-`gauleg_t2 <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/gauss_legendre.irp.f#L1>`_
+`gauleg_t2 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/gauss_legendre.irp.f#L10>`_
  t_w(i,1,k) = w(i)
  t_w(i,2,k) = t(i)

-`gauleg_w <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/gauss_legendre.irp.f#L2>`_
+`gauleg_w <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/gauss_legendre.irp.f#L11>`_
  t_w(i,1,k) = w(i)
  t_w(i,2,k) = t(i)

-`ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L6>`_
+`n_pt_max_integrals_16 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/gauss_legendre.irp.f#L1>`_
+  Aligned n_pt_max_integrals
+
+`ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L6>`_
  AO integrals

-`bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L17>`_
+`bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L19>`_
  Undocumented

-`clear_ao_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L128>`_
+`bielec_integrals_index_reverse <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L36>`_
+  Undocumented
+
+`clear_ao_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L223>`_
  Frees the memory of the AO map

-`clear_mo_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L285>`_
+`clear_mo_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L399>`_
  Frees the memory of the MO map

-`get_ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L33>`_
+`get_ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L113>`_
  Gets one AO bi-electronic integral from the AO map

-`get_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L51>`_
+`get_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L137>`_
  Gets multiple AO bi-electronic integral from the AO map .
  All i are retrieved for j,k,l fixed.

-`get_ao_bielec_integrals_non_zero <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L84>`_
+`get_ao_bielec_integrals_non_zero <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L172>`_
  Gets multiple AO bi-electronic integral from the AO map .
  All non-zero i are retrieved for j,k,l fixed.

-`get_ao_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L120>`_
+`get_ao_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L214>`_
  Returns the number of elements in the AO map

-`get_mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L184>`_
+`get_mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L281>`_
  Returns one integral <ij|kl> in the MO basis

-`get_mo_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L213>`_
+`get_mo_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L310>`_
  Returns multiple integrals <ij|kl> in the MO basis, all
  i for j,k,l fixed.

-`get_mo_bielec_integrals_existing_ik <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L235>`_
+`get_mo_bielec_integrals_existing_ik <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L341>`_
  Returns multiple integrals <ij|kl> in the MO basis, all
+  i(1)j(1) 1/r12 k(2)l(2)
  i for j,k,l fixed.

-`get_mo_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L277>`_
+`get_mo_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L391>`_
  Return the number of elements in the MO map

-`insert_into_ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L153>`_
+`insert_into_ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L250>`_
  Create new entry into AO map

-`insert_into_mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L168>`_
+`insert_into_mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L265>`_
  Create new entry into MO map, or accumulate in an existing entry

-`mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L201>`_
+`mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L298>`_
  Returns one integral <ij|kl> in the MO basis

-`mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L142>`_
+`mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L237>`_
  MO integrals

-`add_integrals_to_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L40>`_
+`add_integrals_to_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L42>`_
  Adds integrals to tha MO map according to some bitmask

-`mo_bielec_integral_jj <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L314>`_
+`mo_bielec_integral_jj <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L464>`_
  mo_bielec_integral_jj(i,j) = J_ij
-  mo_bielec_integral_jj_exchange(i,j) = J_ij
+  mo_bielec_integral_jj_exchange(i,j) = K_ij
  mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij

-`mo_bielec_integral_jj_anti <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L316>`_
+`mo_bielec_integral_jj_anti <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L466>`_
  mo_bielec_integral_jj(i,j) = J_ij
-  mo_bielec_integral_jj_exchange(i,j) = J_ij
+  mo_bielec_integral_jj_exchange(i,j) = K_ij
  mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij

-`mo_bielec_integral_jj_exchange <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L315>`_
+`mo_bielec_integral_jj_anti_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L326>`_
+  mo_bielec_integral_jj_from_ao(i,j) = J_ij
+  mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
+  mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
+
+`mo_bielec_integral_jj_exchange <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L465>`_
  mo_bielec_integral_jj(i,j) = J_ij
-  mo_bielec_integral_jj_exchange(i,j) = J_ij
+  mo_bielec_integral_jj_exchange(i,j) = K_ij
  mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij

-`mo_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L21>`_
+`mo_bielec_integral_jj_exchange_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L325>`_
+  mo_bielec_integral_jj_from_ao(i,j) = J_ij
+  mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
+  mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
+
+`mo_bielec_integral_jj_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L324>`_
+  mo_bielec_integral_jj_from_ao(i,j) = J_ij
+  mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
+  mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
+
+`mo_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L22>`_
  If True, the map of MO bielectronic integrals is provided

-`mo_bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L1>`_
+`mo_bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L1>`_
  Computes an unique index for i,j,k,l integrals

+`read_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/read_write.irp.f#L1>`_
+  One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
+
+`read_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/read_write.irp.f#L2>`_
+  One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
+
+`write_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/read_write.irp.f#L3>`_
+  One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
+
+`write_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/read_write.irp.f#L4>`_
+  One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
+


--- a/src/Bielec_integrals/map_integrals.irp.f
+++ b/src/Bielec_integrals/map_integrals.irp.f
@ -368,11 +368,11 @@ subroutine get_mo_bielec_integrals_existing_ik(j,l,sze,out_array,map)
  enddo

  logical :: integral_is_in_map
-  if (cache_key_kind == 8) then
+  if (key_kind == 8) then
    call i8radix_sort(hash,iorder,kk,-1)
-  else if (cache_key_kind == 4) then
+  else if (key_kind == 4) then
    call iradix_sort(hash,iorder,kk,-1)
-  else if (cache_key_kind == 2) then
+  else if (key_kind == 2) then
    call i2radix_sort(hash,iorder,kk,-1)
  endif

--- a/src/Bitmask/README.rst
+++ b/src/Bitmask/README.rst
@ -54,6 +54,24 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.

+`is_a_two_holes_two_particles <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L206>`_
+  Undocumented
+
+`number_of_holes <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L1>`_
+  Undocumented
+
+`number_of_holes_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L394>`_
+  Undocumented
+
+`number_of_particles <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L103>`_
+  Undocumented
+
+`number_of_particles_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L422>`_
+  Undocumented
+
+`cas_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L173>`_
+  Bitmasks for CAS reference determinants. (N_int, alpha/beta, CAS reference)
+
 `cis_ijkl_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L32>`_
  Bitmask to include all possible single excitations from Hartree-Fock

@ -61,23 +79,35 @@ Documentation
  Bitmask to include all possible MOs

 `generators_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L100>`_
-  Bitmasks for generator determinants. (N_int, alpha/beta, hole/particle, generator).
+  Bitmasks for generator determinants.
+  (N_int, alpha/beta, hole/particle, generator).
+  .br
  3rd index is :
+  .br
  * 1 : hole     for single exc
-  * 1 : particle for single exc
+  .br
+  * 2 : particle for single exc
+  .br
  * 3 : hole     for 1st exc of double
+  .br
  * 4 : particle for 1st exc of double
-  * 5 : hole     for 2dn exc of double
-  * 6 : particle for 2dn exc of double
+  .br
+  * 5 : hole     for 2nd exc of double
+  .br
+  * 6 : particle for 2nd exc of double
+  .br

 `hf_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L44>`_
  Hartree Fock bit mask

-`i_bitmask_gen <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L186>`_
+`i_bitmask_gen <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L211>`_
  Current bitmask for the generators

-`i_bitmask_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L194>`_
-  Current bitmask for the reference
+`inact_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L193>`_
+  Bitmasks for the inactive orbitals that are excited in post CAS method
+
+`n_cas_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L143>`_
+  Number of bitmasks for CAS

 `n_generators_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L70>`_
  Number of bitmasks for generators
@ -85,36 +115,31 @@ Documentation
 `n_int <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L3>`_
  Number of 64-bit integers needed to represent determinants as binary strings

-`n_reference_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L134>`_
-  Number of bitmasks for reference
-
 `ref_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L62>`_
  Reference bit mask, used in Slater rules, chosen as Hartree-Fock bitmask

-`reference_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L164>`_
-  Bitmasks for reference determinants. (N_int, alpha/beta, hole/particle, reference)
+`virt_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L194>`_
+  Bitmasks for the inactive orbitals that are excited in post CAS method

-`bitstring_to_hexa <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L95>`_
+`bitstring_to_hexa <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L98>`_
  Transform a bit string to a string in hexadecimal format for printing

 `bitstring_to_list <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L1>`_
  Gives the inidices(+1) of the bits set to 1 in the bit string

-`bitstring_to_str <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L62>`_
+`bitstring_to_str <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L65>`_
  Transform a bit string to a string for printing

-`debug_det <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L117>`_
-  Undocumented
+`debug_det <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L120>`_
+  Subroutine to print the content of a determinant in '+-' notation and
+  hexadecimal representation.

 `list_to_bitstring <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L29>`_
-  return the physical string "string(N_int,2)" from the array of occupations "list(N_int*bit_kind_size,2)
-  list
-  <== ipos ==>
-  |
-  v
-  string :|------------------------|-------------------------|------------------------|
-  <==== bit_kind_size ====> <==== bit_kind_size ====> <==== bit_kind_size ====>
-  {        iint            } {         iint         } {         iint         }
+  Returns the physical string "string(N_int,2)" from the array of
+  occupations "list(N_int*bit_kind_size,2)
+
+`print_det <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L138>`_
+  Subroutine to print the content of a determinant using the '+-' notation



--- a/src/Bitmask/bitmasks.irp.f
+++ b/src/Bitmask/bitmasks.irp.f
@ -123,7 +123,6 @@ BEGIN_PROVIDER [ integer(bit_kind), generators_bitmask, (N_int,2,6,N_generators_

 call ezfio_has_bitmasks_generators(exists)
 if (exists) then
-   print*,'EXIST !!'
   call ezfio_get_bitmasks_generators(generators_bitmask)
 else
   integer :: k, ispin
@ -181,7 +180,6 @@ BEGIN_PROVIDER [ integer(bit_kind), cas_bitmask, (N_int,2,N_cas_bitmask) ]
 PROVIDE ezfio_filename

 call ezfio_has_bitmasks_cas(exists)
- print*,'exists = ',exists
 if (exists) then
   call ezfio_get_bitmasks_cas(cas_bitmask)
 else
--- a/src/CAS_SD_selected/ASSUMPTIONS.rst
+++ b/src/CAS_SD_selected/ASSUMPTIONS.rst
--- a/src/CAS_SD/EZFIO.cfg
+++ b/src/CAS_SD/EZFIO.cfg
@ -0,0 +1,36 @@
+[N_det_max_cas_sd]
+type: Det_number_max
+doc: Max number of determinants in the wave function
+interface: input
+default: 10000
+
+[do_pt2_end]
+type: logical
+doc: If true, compute the PT2 at the end of the selection
+interface: input
+default: True
+
+[PT2_max]
+type: PT2_energy
+doc: The selection process stops when the largest PT2 (for all the state is lower
+     than pt2_max in absolute value
+interface: input
+default: 0.0001
+
+[var_pt2_ratio]
+type: Normalized_float
+doc: The selection process stops when the energy ratio variational/(variational+PT2)
+     is equal to var_pt2_ratio
+interface: input
+default: 0.75
+
+[energy]
+type: double precision
+doc: "Calculated CAS-SD energy"
+interface: output
+
+[energy_pt2]
+type: double precision
+doc: "Calculated selected CAS-SD energy with PT2 correction"
+interface: output
+
--- a/src/CAS_SD_selected/H_apply.irp.f
+++ b/src/CAS_SD_selected/H_apply.irp.f
@ -2,11 +2,14 @@ use bitmasks
 BEGIN_SHELL [ /usr/bin/env python ]
 from generate_h_apply import *

-s = H_apply("FCI")
+s = H_apply("CAS_SD")
+print s
+
+s = H_apply("CAS_SD_selected")
 s.set_selection_pt2("epstein_nesbet_2x2")
 print s

-s = H_apply("FCI_PT2")
+s = H_apply("CAS_SD_PT2")
 s.set_perturbation("epstein_nesbet_2x2")
 print s

--- a/src/CAS_SD_selected/Makefile
+++ b/src/CAS_SD_selected/Makefile
--- a/src/CAS_SD_selected/NEEDED_MODULES
+++ b/src/CAS_SD_selected/NEEDED_MODULES
--- a/src/CAS_SD/README.rst
+++ b/src/CAS_SD/README.rst
@ -0,0 +1,44 @@
+======================
+CAS_SD_selected Module
+======================
+
+Selected CAS + SD module.
+
+1) Set the different MO classes using the ``qp_set_mo_class`` command
+2) Run the selected CAS+SD program
+
+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/cas_sd_selected.irp.f#L1>`_
+  Undocumented
+
+
+
+Needed Modules
+==============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
+* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
+* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
+* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
+* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
+* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
+* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
+* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
+* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
+* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
+* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+
--- a/src/CAS_SD_selected/cas_sd.irp.f
+++ b/src/CAS_SD_selected/cas_sd.irp.f
@ -11,12 +11,12 @@ program full_ci
  
  pt2 = 1.d0
  diag_algorithm = "Lapack"
-  if (N_det > n_det_max_fci) then
+  if (N_det > n_det_max_cas_sd) then
    call diagonalize_CI
    call save_wavefunction
    psi_det = psi_det_sorted
    psi_coef = psi_coef_sorted
-    N_det = n_det_max_fci
+    N_det = n_det_max_cas_sd
    soft_touch N_det psi_det psi_coef
    call diagonalize_CI
    call save_wavefunction
@ -28,17 +28,17 @@ program full_ci
    print *,  '-----'
  endif

-  do while (N_det < n_det_max_fci.and.maxval(abs(pt2(1:N_st))) > pt2_max)
-    call H_apply_FCI(pt2, norm_pert, H_pert_diag,  N_st)
+  do while (N_det < n_det_max_cas_sd.and.maxval(abs(pt2(1:N_st))) > pt2_max)
+    call H_apply_CAS_SD(pt2, norm_pert, H_pert_diag,  N_st)

    PROVIDE  psi_coef
    PROVIDE  psi_det
    PROVIDE  psi_det_sorted

-    if (N_det > n_det_max_fci) then
+    if (N_det > n_det_max_cas_sd) then
       psi_det = psi_det_sorted
       psi_coef = psi_coef_sorted
-       N_det = n_det_max_fci
+       N_det = n_det_max_cas_sd
       soft_touch N_det psi_det psi_coef
    endif
    call diagonalize_CI
@ -60,7 +60,7 @@ program full_ci
  integer :: exc_max, degree_min
  exc_max = 0
  print *,  'CAS determinants : ', N_det_generators
-  do i=1,N_det_generators
+  do i=1,min(N_det_generators,10)
    do k=i,N_det_generators
      call get_excitation_degree(psi_det_generators(1,1,k),psi_det_generators(1,1,i),degree,N_int)
      exc_max = max(exc_max,degree)
--- a/src/CAS_SD/cas_sd_selected.irp.f
+++ b/src/CAS_SD/cas_sd_selected.irp.f
@ -0,0 +1,87 @@
+program full_ci
+  implicit none
+  integer                        :: i,k
+
+  
+  double precision, allocatable  :: pt2(:), norm_pert(:), H_pert_diag(:)
+  integer                        :: N_st, degree
+  N_st = N_states
+  allocate (pt2(N_st), norm_pert(N_st),H_pert_diag(N_st))
+  character*(64)                 :: perturbation
+  PROVIDE N_det_cas
+  
+  pt2 = 1.d0
+  diag_algorithm = "Lapack"
+  if (N_det > n_det_max_cas_sd) then
+    call diagonalize_CI
+    call save_wavefunction
+    psi_det = psi_det_sorted
+    psi_coef = psi_coef_sorted
+    N_det = n_det_max_cas_sd
+    soft_touch N_det psi_det psi_coef
+    call diagonalize_CI
+    call save_wavefunction
+    print *,  'N_det    = ', N_det
+    print *,  'N_states = ', N_states
+    print *,  'PT2      = ', pt2
+    print *,  'E        = ', CI_energy
+    print *,  'E+PT2    = ', CI_energy+pt2
+    print *,  '-----'
+  endif
+
+  do while (N_det < n_det_max_cas_sd.and.maxval(abs(pt2(1:N_st))) > pt2_max)
+    call H_apply_CAS_SD_selected(pt2, norm_pert, H_pert_diag,  N_st)
+
+    PROVIDE  psi_coef
+    PROVIDE  psi_det
+    PROVIDE  psi_det_sorted
+
+    if (N_det > n_det_max_cas_sd) then
+       psi_det = psi_det_sorted
+       psi_coef = psi_coef_sorted
+       N_det = n_det_max_cas_sd
+       soft_touch N_det psi_det psi_coef
+    endif
+    call diagonalize_CI
+    call save_wavefunction
+    print *,  'N_det    = ', N_det
+    print *,  'N_states = ', N_states
+    print *,  'PT2      = ', pt2
+    print *,  'E        = ', CI_energy
+    print *,  'E+PT2    = ', CI_energy+pt2
+    print *,  '-----'
+    call ezfio_set_full_ci_energy(CI_energy)
+    if (abort_all) then
+      exit
+    endif
+  enddo
+
+  ! Check that it is a CAS-SD
+  logical :: in_cas
+  integer :: exc_max, degree_min
+  exc_max = 0
+  print *,  'CAS determinants : ', N_det_cas
+  do i=1,min(N_det_cas,10)
+    do k=i,N_det_cas
+      call get_excitation_degree(psi_cas(1,1,k),psi_cas(1,1,i),degree,N_int)
+      exc_max = max(exc_max,degree)
+    enddo
+    call debug_det(psi_cas(1,1,i),N_int)
+    print *,  ''
+  enddo
+  print *,  'Max excitation degree in the CAS :', exc_max
+  do i=1,N_det
+    in_cas = .False.
+    degree_min = 1000
+    do k=1,N_det_cas
+      call get_excitation_degree(psi_cas(1,1,k),psi_det(1,1,i),degree,N_int)
+      degree_min = min(degree_min,degree)
+    enddo
+    if (degree_min > 2) then
+        print *,  'Error : This is not a CAS-SD : '
+        print *,  'Excited determinant:', degree_min
+        call debug_det(psi_det(1,1,k),N_int)
+        stop
+    endif
+  enddo
+end
--- a/src/CAS_SD_selected/README.rst
+++ b/src/CAS_SD_selected/README.rst
@ -1,5 +0,0 @@
-======================
-CAS_SD_selected Module
-======================
-
-Selected CAS + SD module
--- a/src/CAS_SD_selected/options.irp.f
+++ b/src/CAS_SD_selected/options.irp.f
@ -1,32 +0,0 @@
-BEGIN_SHELL [ /usr/bin/python ]
-from ezfio_with_default import EZFIO_Provider
-T = EZFIO_Provider()
-T.set_type      ( "integer" )
-T.set_name      ( "N_det_max_fci" )
-T.set_doc       ( "Max number of determinants in the wave function" )
-T.set_ezfio_dir ( "full_ci" )
-T.set_ezfio_name( "N_det_max_fci" )
-T.set_output    ( "output_full_ci" )
-print T
-
-T.set_type      ( "logical" )
-T.set_name      ( "do_pt2_end" )
-T.set_doc       ( "If true, compute the PT2 at the end of the selection" )
-T.set_ezfio_name( "do_pt2_end" )
-print T
-
-T.set_type      ( "double precision" )
-T.set_name      ( "pt2_max" )
-T.set_doc       ( """The selection process stops when the largest PT2 (for all the states) 
-is lower than pt2_max in absolute value""" )
-T.set_ezfio_name( "pt2_max" )
-print T
-
-T.set_type      ( "double precision" )
-T.set_name      ( "var_pt2_ratio" )
-T.set_doc       ( """The selection process stops when the energy ratio variational/(variational+PT2)
-is equal to var_pt2_ratio""" )
-T.set_ezfio_name( "var_pt2_ratio" )
-print T
-END_SHELL
-
--- a/src/CID/README.rst
+++ b/src/CID/README.rst
@ -16,19 +16,20 @@ Needed Modules
 .. NEEDED_MODULES file.

 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_

 Documentation
 =============
--- a/src/CID_SC2_selected/README.rst
+++ b/src/CID_SC2_selected/README.rst
@ -20,20 +20,21 @@ Needed Modules
 .. NEEDED_MODULES file.

 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
-* `SC2 <http://github.com/LCPQ/quantum_package/tree/master/src/SC2>`_
 * `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
--- a/src/CID_selected/README.rst
+++ b/src/CID_selected/README.rst
@ -23,19 +23,21 @@ Needed Modules
 .. NEEDED_MODULES file.

 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_

--- a/src/CIS/README.rst
+++ b/src/CIS/README.rst
@ -32,17 +32,18 @@ Needed Modules
 .. NEEDED_MODULES file.

 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_

--- a/src/CISD/README.rst
+++ b/src/CISD/README.rst
@ -16,19 +16,20 @@ Needed Modules
 .. NEEDED_MODULES file.

 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_

 Documentation
 =============
--- a/src/CISD/cisd.irp.f
+++ b/src/CISD/cisd.irp.f
@ -13,6 +13,7 @@ program cisd
   print *,  'E_corr  = ',CI_electronic_energy(i) - ref_bitmask_energy
  enddo

+  call save_wavefunction
 ! call CISD_SC2(psi_det,psi_coef,eigvalues,size(psi_coef,1),N_det,N_states,N_int)
 ! do i = 1, N_states
 !  print*,'eigvalues(i) = ',eigvalues(i)
--- a/src/CISD_SC2_selected/EZFIO.cfg
+++ b/src/CISD_SC2_selected/EZFIO.cfg
@ -1,6 +1,6 @@
 [N_det_max_cisd_sc2]
 type: Det_number_max
-doc: Get n_det_max_cisd_sc2 from EZFIO file
+doc: Max number of determinants
 interface: input
 default: 10000

@ -8,12 +8,12 @@ default: 10000
 type: logical
 doc: If true, compute the PT2 at the end of the selection
 interface: input
-default: true
+default: True

 [PT2_max]
 type: PT2_energy
-doc: The selection process stops when the largest PT2 (for all the state) is lower
-     than pt2_max in absolute value
+doc: The selection process stops when the largest PT2 (for all the states) is lower
+     than abs(pt2_max)
 interface: input
 default: 0.0001

--- a/src/CISD_SC2_selected/README.rst
+++ b/src/CISD_SC2_selected/README.rst
@ -8,6 +8,9 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.

+`cisd_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/cisd_sc2_selection.irp.f#L1>`_
+  Undocumented
+


 Needed Modules
@ -17,20 +20,21 @@ Needed Modules
 .. NEEDED_MODULES file.

 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
-* `SC2 <http://github.com/LCPQ/quantum_package/tree/master/src/SC2>`_
 * `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
--- a/src/CISD_selected/README.rst
+++ b/src/CISD_selected/README.rst
@ -14,6 +14,12 @@ Documentation
 `cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/cisd_selection.irp.f#L1>`_
  Undocumented

+`n_det_max_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/options.irp.f#L1>`_
+  Get n_det_max_cisd from EZFIO file
+
+`pt2_max <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/options.irp.f#L18>`_
+  Get pt2_max from EZFIO file
+


 Needed Modules
@ -23,19 +29,21 @@ Needed Modules
 .. NEEDED_MODULES file.

 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_

--- a/src/DDCI_selected/README.rst
+++ b/src/DDCI_selected/README.rst
@ -2,3 +2,38 @@
 DDCI_selected Module
 ====================

+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/ddci.irp.f#L1>`_
+  Undocumented
+
+
+
+Needed Modules
+==============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
+* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
+* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
+* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
+* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
+* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
+* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
+* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
+* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
+* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
+* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+
--- a/src/Dets/H_apply_template.f
+++ b/src/Dets/H_apply_template.f
@ -1,4 +1,4 @@
-subroutine $subroutine_diexc(key_in, hole_1,particl_1, hole_2, particl_2, i_generator, iproc $parameters )
+subroutine $subroutine_diexc(key_in, hole_1,particl_1, hole_2, particl_2, i_generator, iproc_in $parameters )
  use omp_lib
  use bitmasks
  implicit none
@ -14,7 +14,7 @@ subroutine $subroutine_diexc(key_in, hole_1,particl_1, hole_2, particl_2, i_gene
  integer(bit_kind),allocatable  :: keys_out(:,:,:)
  integer(bit_kind), intent(in)  :: hole_1(N_int,2), particl_1(N_int,2)
  integer(bit_kind), intent(in)  :: hole_2(N_int,2), particl_2(N_int,2)
-  integer, intent(in)            :: iproc
+  integer, intent(in)            :: iproc_in
  integer(bit_kind), allocatable :: hole_save(:,:)
  integer(bit_kind), allocatable :: key(:,:),hole(:,:), particle(:,:)
  integer(bit_kind), allocatable :: hole_tmp(:,:), particle_tmp(:,:)
@ -30,6 +30,7 @@ subroutine $subroutine_diexc(key_in, hole_1,particl_1, hole_2, particl_2, i_gene
  integer, allocatable           :: ia_ja_pairs(:,:,:)
  integer, allocatable           :: ib_jb_pairs(:,:)
  double precision               :: diag_H_mat_elem
+  integer                        :: iproc
  integer(omp_lock_kind), save   :: lck, ifirst=0
  if (ifirst == 0) then
 !$    call omp_init_lock(lck)
@ -38,12 +39,13 @@ subroutine $subroutine_diexc(key_in, hole_1,particl_1, hole_2, particl_2, i_gene
  
  logical :: check_double_excitation 
  check_double_excitation = .True.
-
+  iproc = iproc_in


  $initialization
  
  $omp_parallel
+!$ iproc = omp_get_thread_num()
  allocate (keys_out(N_int,2,size_max), hole_save(N_int,2),          &
      key(N_int,2),hole(N_int,2), particle(N_int,2), hole_tmp(N_int,2),&
      particle_tmp(N_int,2), occ_particle(N_int*bit_kind_size,2),    &
@ -248,7 +250,7 @@ subroutine $subroutine_diexc(key_in, hole_1,particl_1, hole_2, particl_2, i_gene
  $finalization
 end

-subroutine $subroutine_monoexc(key_in, hole_1,particl_1,i_generator,iproc $parameters )
+subroutine $subroutine_monoexc(key_in, hole_1,particl_1,i_generator,iproc_in $parameters )
  use omp_lib
  use bitmasks
  implicit none
@ -262,7 +264,7 @@ subroutine $subroutine_monoexc(key_in, hole_1,particl_1,i_generator,iproc $param
  integer          ,intent(in)   :: i_generator
  integer(bit_kind),intent(in)   :: key_in(N_int,2)
  integer(bit_kind),intent(in)   :: hole_1(N_int,2), particl_1(N_int,2)
-  integer, intent(in)            :: iproc
+  integer, intent(in)            :: iproc_in
  integer(bit_kind),allocatable  :: keys_out(:,:,:)
  integer(bit_kind),allocatable  :: hole_save(:,:)
  integer(bit_kind),allocatable  :: key(:,:),hole(:,:), particle(:,:)
@ -281,8 +283,11 @@ subroutine $subroutine_monoexc(key_in, hole_1,particl_1,i_generator,iproc $param
  logical, allocatable           :: array_pairs(:,:)
  double precision               :: diag_H_mat_elem
  integer(omp_lock_kind), save   :: lck, ifirst=0
+  integer                        :: iproc

  logical :: check_double_excitation 
+  iproc = iproc_in
+
  check_double_excitation = .True.
  $check_double_excitation

@ -295,6 +300,7 @@ subroutine $subroutine_monoexc(key_in, hole_1,particl_1,i_generator,iproc $param
  $initialization
  
  $omp_parallel
+!$ iproc = omp_get_thread_num()
  allocate (keys_out(N_int,2,size_max), hole_save(N_int,2),          &
      key(N_int,2),hole(N_int,2), particle(N_int,2), hole_tmp(N_int,2),&
      particle_tmp(N_int,2), occ_particle(N_int*bit_kind_size,2),    &
@ -396,7 +402,8 @@ subroutine $subroutine($params_main)
  integer                        :: iproc

  $initialization
-  PROVIDE H_apply_buffer_allocated mo_bielec_integrals_in_map
+  PROVIDE H_apply_buffer_allocated mo_bielec_integrals_in_map psi_det_generators psi_coef_generators
+
  
  nmax = mod( N_det_generators,nproc )
 
@ -406,6 +413,7 @@ subroutine $subroutine($params_main)

  call wall_time(wall_0)

+  iproc = 0
  allocate( mask(N_int,2,6) )
  do i_generator=1,nmax

@ -443,12 +451,12 @@ subroutine $subroutine($params_main)
     call $subroutine_diexc(psi_det_generators(1,1,i_generator),      &
         mask(1,1,d_hole1), mask(1,1,d_part1),                        &
         mask(1,1,d_hole2), mask(1,1,d_part2),                        &
-         i_generator, 0 $params_post)
+         i_generator, iproc $params_post)
    endif
    if($do_mono_excitations)then
     call $subroutine_monoexc(psi_det_generators(1,1,i_generator),    &
         mask(1,1,s_hole ), mask(1,1,s_part ),                        &
-         i_generator, 0 $params_post)
+         i_generator, iproc $params_post)
    endif
    call wall_time(wall_1)
    $printout_always
@ -463,7 +471,6 @@ subroutine $subroutine($params_main)
  !$OMP PARALLEL DEFAULT(SHARED) &
  !$OMP PRIVATE(i_generator,wall_1,wall_0,ispin,k,mask,iproc) 
  call wall_time(wall_0)
-  iproc = 0
  !$ iproc = omp_get_thread_num()
  allocate( mask(N_int,2,6) )
  !$OMP DO SCHEDULE(dynamic,1)
--- a/src/Dets/README.rst
+++ b/src/Dets/README.rst
@ -33,11 +33,10 @@ Needed Modules
 .. NEEDED_MODULES file.

 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
@ -50,18 +49,23 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.

-`copy_h_apply_buffer_to_wf <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L95>`_
+`copy_h_apply_buffer_to_wf <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L100>`_
  Copies the H_apply buffer to psi_coef. You need to touch psi_det, psi_coef and N_det
  after calling this function.
+  After calling this subroutine, N_det, psi_det and psi_coef need to be touched

-`fill_h_apply_buffer_no_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L181>`_
+`fill_h_apply_buffer_no_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L187>`_
  Fill the H_apply buffer with determiants for CISD

-`h_apply_buffer_allocated <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L14>`_
+`h_apply_buffer_allocated <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L15>`_
  Buffer of determinants/coefficients/perturbative energy for H_apply.
  Uninitialized. Filled by H_apply subroutines.

-`resize_h_apply_buffer <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L45>`_
+`h_apply_buffer_lock <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L16>`_
+  Buffer of determinants/coefficients/perturbative energy for H_apply.
+  Uninitialized. Filled by H_apply subroutines.
+
+`resize_h_apply_buffer <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L48>`_
  Undocumented

 `cisd_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/SC2.irp.f#L1>`_
@ -80,26 +84,43 @@ Documentation
  .br
  Initial guess vectors are not necessarily orthonormal

-`repeat_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/SC2.irp.f#L220>`_
+`connected_to_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L155>`_
  Undocumented

-`connected_to_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L95>`_
+`connected_to_ref_by_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L253>`_
  Undocumented

-`det_is_not_or_may_be_in_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L191>`_
+`det_is_not_or_may_be_in_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L359>`_
  If true, det is not in ref
  If false, det may be in ref

-`is_in_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L1>`_
-  Undocumented
+`det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L1>`_
+  Return an integer*8 corresponding to a determinant index for searching

-`key_pattern_not_in_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L225>`_
+`get_index_in_psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L48>`_
+  Returns the index of the determinant in the ``psi_det_sorted_bit`` array
+
+`is_in_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L34>`_
+  True if the determinant ``det`` is in the wave function
+
+`key_pattern_not_in_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L393>`_
  Min and max values of the integers of the keys of the reference

-`davidson_converged <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L383>`_
+`occ_pattern_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L17>`_
+  Return an integer*8 corresponding to a determinant index for searching
+
+`do_mono_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/create_excitations.irp.f#L1>`_
+  Apply the mono excitation operator : a^{dager}_(i_particle) a_(i_hole) of spin = ispin
+  on key_in
+  ispin = 1  == alpha
+  ispin = 2  == beta
+  i_ok = 1  == the excitation is possible
+  i_ok = -1 == the excitation is not possible
+
+`davidson_converged <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L382>`_
  True if the Davidson algorithm is converged

-`davidson_criterion <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L373>`_
+`davidson_criterion <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L372>`_
  Can be : [  energy  | residual | both | wall_time | cpu_time | iterations ]

 `davidson_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L18>`_
@ -146,10 +167,10 @@ Documentation
 `davidson_sze_max <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L9>`_
  Max number of Davidson sizes

-`davidson_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L374>`_
+`davidson_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L373>`_
  Can be : [  energy  | residual | both | wall_time | cpu_time | iterations ]

-`one_body_dm_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L73>`_
+`one_body_dm_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L164>`_
  One-body density matrix

 `one_body_dm_mo_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L1>`_
@ -158,63 +179,162 @@ Documentation
 `one_body_dm_mo_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L2>`_
  Alpha and beta one-body density matrix for each state

-`save_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L97>`_
+`one_body_single_double_dm_mo_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L80>`_
+  Alpha and beta one-body density matrix for each state
+
+`one_body_single_double_dm_mo_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L81>`_
+  Alpha and beta one-body density matrix for each state
+
+`one_body_spin_density_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L172>`_
+  rho(alpha) - rho(beta)
+
+`save_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L196>`_
  Save natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis

-`set_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L81>`_
+`set_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L180>`_
  Set natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis

-`state_average_weight <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L108>`_
+`state_average_weight <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L207>`_
  Weights in the state-average calculation of the density matrix

-`det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L295>`_
-  Return an integer*8 corresponding to a determinant index for searching
+`det_svd <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/det_svd.irp.f#L1>`_
+  Computes the SVD of the Alpha x Beta determinant coefficient matrix
+
+`create_wf_of_psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L741>`_
+  Matrix of wf coefficients. Outer product of alpha and beta determinants
+
+`filter_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L552>`_
+  Returns a determinant with only the 3 highest electrons
+
+`generate_all_alpha_beta_det_products <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L796>`_
+  Create a wave function from all possible alpha x beta determinants
+
+`int_of_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L517>`_
+  Returns an integer*8 as :
+  .br
+  |_<--- 21 bits ---><--- 21 bits ---><--- 21 bits --->|
+  .br
+  |0<---   i1    ---><---   i2    ---><---   i3    --->|
+  .br
+  It encodes the value of the indices of the 3 highest MOs
+  in descending order
+  .br
+
+`max_degree_exc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L32>`_
+  Maximum degree of excitation in the wf

 `n_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L3>`_
  Number of determinants in the wave function

-`psi_average_norm_contrib <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L208>`_
+`n_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L348>`_
+  Unique alpha determinants
+
+`n_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L385>`_
+  Unique beta determinants
+
+`psi_average_norm_contrib <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L276>`_
  Contribution of determinants to the state-averaged density

-`psi_average_norm_contrib_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L229>`_
+`psi_average_norm_contrib_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L432>`_
  Wave function sorted by determinants contribution to the norm (state-averaged)

-`psi_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L153>`_
+`psi_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L230>`_
  The wave function coefficients. Initialized with Hartree-Fock if the EZFIO file
  is empty

-`psi_coef_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L228>`_
+`psi_coef_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L431>`_
  Wave function sorted by determinants contribution to the norm (state-averaged)

-`psi_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L259>`_
-  Determinants on which we apply <i|H|psi> for perturbation.
-  o They are sorted by determinants interpreted as integers. Useful
-  to accelerate the search of a determinant
+`psi_coef_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L579>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.

-`psi_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L53>`_
+`psi_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L462>`_
+  Determinants on which we apply <i|H|psi> for perturbation.
+  They are sorted by determinants interpreted as integers. Useful
+  to accelerate the search of a random determinant in the wave
+  function.
+
+`psi_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L65>`_
  The wave function determinants. Initialized with Hartree-Fock if the EZFIO file
  is empty

-`psi_det_size <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L35>`_
+`psi_det_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L319>`_
+  List of alpha determinants of psi_det
+
+`psi_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L347>`_
+  Unique alpha determinants
+
+`psi_det_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L333>`_
+  List of beta determinants of psi_det
+
+`psi_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L384>`_
+  Unique beta determinants
+
+`psi_det_size <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L47>`_
  Size of the psi_det/psi_coef arrays

-`psi_det_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L227>`_
+`psi_det_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L430>`_
  Wave function sorted by determinants contribution to the norm (state-averaged)

-`psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L258>`_
-  Determinants on which we apply <i|H|psi> for perturbation.
-  o They are sorted by determinants interpreted as integers. Useful
-  to accelerate the search of a determinant
+`psi_det_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L578>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.

-`read_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L104>`_
+`psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L461>`_
+  Determinants on which we apply <i|H|psi> for perturbation.
+  They are sorted by determinants interpreted as integers. Useful
+  to accelerate the search of a random determinant in the wave
+  function.
+
+`psi_det_sorted_next_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L580>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
+
+`psi_svd_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L826>`_
+  SVD wave function
+
+`psi_svd_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L827>`_
+  SVD wave function
+
+`psi_svd_coefs <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L828>`_
+  SVD wave function
+
+`psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L709>`_
+  Matrix of wf coefficients. Outer product of alpha and beta determinants
+
+`read_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L880>`_
  Reads the determinants from the EZFIO file

-`save_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L310>`_
+`save_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L927>`_
  Save the wave function into the EZFIO file

-`save_wavefunction_general <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L319>`_
+`save_wavefunction_general <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L946>`_
  Save the wave function into the EZFIO file

+`save_wavefunction_unsorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L937>`_
+  Save the wave function into the EZFIO file
+
+`sort_dets_by_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L600>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
+
+`sort_dets_by_det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L475>`_
+  Determinants are sorted are sorted according to their det_search_key.
+  Useful to accelerate the search of a random determinant in the wave
+  function.
+
+`spin_det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L303>`_
+  Return an integer*8 corresponding to a determinant index for searching
+
 `double_exc_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants_bitmasks.irp.f#L40>`_
  double_exc_bitmask(:,1,i) is the bitmask for holes of excitation 1
  double_exc_bitmask(:,2,i) is the bitmask for particles of excitation 1
@ -233,10 +353,13 @@ Documentation
  single_exc_bitmask(:,2,i) is the bitmask for particles
  for a given couple of hole/particle excitations i.

-`ci_eigenvectors <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L36>`_
+`ci_eigenvectors <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L37>`_
  Eigenvectors/values of the CI matrix

-`ci_electronic_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L35>`_
+`ci_eigenvectors_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L38>`_
+  Eigenvectors/values of the CI matrix
+
+`ci_electronic_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L36>`_
  Eigenvectors/values of the CI matrix

 `ci_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L18>`_
@ -245,7 +368,7 @@ Documentation
 `diag_algorithm <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L1>`_
  Diagonalization algorithm (Davidson or Lapack)

-`diagonalize_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L73>`_
+`diagonalize_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L96>`_
  Replace the coefficients of the CI states by the coefficients of the
  eigenstates of the CI matrix

@ -256,15 +379,31 @@ Documentation
  Eigenvectors/values of the CI matrix

 `ci_sc2_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L1>`_
-  N_states lowest eigenvalues of the CI matrix
+  N_states_diag lowest eigenvalues of the CI matrix

 `diagonalize_ci_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L46>`_
-  Replace the coefficients of the CI states by the coefficients of the
+  Replace the coefficients of the CI states_diag by the coefficients of the
  eigenstates of the CI matrix

 `threshold_convergence_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L18>`_
  convergence of the correlation energy of SC2 iterations

+`ci_eigenvectors_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L2>`_
+  Eigenvectors/values of the CI matrix
+
+`ci_eigenvectors_s2_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L3>`_
+  Eigenvectors/values of the CI matrix
+
+`ci_electronic_energy_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L1>`_
+  Eigenvectors/values of the CI matrix
+
+`diagonalize_ci_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L59>`_
+  Replace the coefficients of the CI states by the coefficients of the
+  eigenstates of the CI matrix
+
+`apply_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/excitations_utils.irp.f#L1>`_
+  Undocumented
+
 `filter_connected <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L2>`_
  Filters out the determinants that are not connected by H
  .br
@ -276,9 +415,16 @@ Documentation
  .br
  idx(0) is the number of determinants that interact with key1

-`filter_connected_davidson <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L101>`_
+`filter_connected_davidson <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L163>`_
  Filters out the determinants that are not connected by H
+  returns the array idx which contains the index of the
+  determinants in the array key1 that interact
+  via the H operator with key2.
  .br
+  idx(0) is the number of determinants that interact with key1
+  key1 should come from psi_det_sorted_ab.
+
+`filter_connected_i_h_psi0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L293>`_
  returns the array idx which contains the index of the
  .br
  determinants in the array key1 that interact
@ -287,16 +433,7 @@ Documentation
  .br
  idx(0) is the number of determinants that interact with key1

-`filter_connected_i_h_psi0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L233>`_
-  returns the array idx which contains the index of the
-  .br
-  determinants in the array key1 that interact
-  .br
-  via the H operator with key2.
-  .br
-  idx(0) is the number of determinants that interact with key1
-
-`filter_connected_i_h_psi0_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L332>`_
+`filter_connected_i_h_psi0_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L392>`_
  standard filter_connected_i_H_psi but returns in addition
  .br
  the array of the index of the non connected determinants to key1
@ -307,31 +444,156 @@ Documentation
  .br
  to repeat the excitations

+`filter_connected_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L101>`_
+  Filters out the determinants that are not connected by H
+  returns the array idx which contains the index of the
+  determinants in the array key1 that interact
+  via the H operator with key2.
+  idx(0) is the number of determinants that interact with key1
+  .br
+  Determinants are taken from the psi_det_sorted_ab array
+
+`put_gess <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/guess_triplet.irp.f#L1>`_
+  Undocumented
+
+`det_to_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L2>`_
+  Transform a determinant to an occupation pattern
+
+`make_s2_eigenfunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L251>`_
+  Undocumented
+
+`n_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L143>`_
+  array of the occ_pattern present in the wf
+  psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation
+  psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation
+
+`occ_pattern_to_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L42>`_
+  Generate all possible determinants for a give occ_pattern
+
+`occ_pattern_to_dets_size <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L20>`_
+  Number of possible determinants for a given occ_pattern
+
+`psi_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L142>`_
+  array of the occ_pattern present in the wf
+  psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation
+  psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation
+
+`rec_occ_pattern_to_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L102>`_
+  Undocumented
+
+`n_states_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/options.irp.f#L40>`_
+  Number of states to consider for the diagonalization
+
+`pouet <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/program_beginer_determinants.irp.f#L1>`_
+  Undocumented
+
+`routine <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/program_beginer_determinants.irp.f#L7>`_
+  Undocumented
+
+`idx_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L5>`_
+  CAS wave function, defined from the application of the CAS bitmask on the
+  determinants. idx_cas gives the indice of the CAS determinant in psi_det.
+
+`idx_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L62>`_
+  Set of determinants which are not part of the CAS, defined from the application
+  of the CAS bitmask on the determinants.
+  idx_non_cas gives the indice of the determinant in psi_det.
+
+`n_det_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L6>`_
+  CAS wave function, defined from the application of the CAS bitmask on the
+  determinants. idx_cas gives the indice of the CAS determinant in psi_det.
+
+`n_det_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L63>`_
+  Set of determinants which are not part of the CAS, defined from the application
+  of the CAS bitmask on the determinants.
+  idx_non_cas gives the indice of the determinant in psi_det.
+
+`psi_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L3>`_
+  CAS wave function, defined from the application of the CAS bitmask on the
+  determinants. idx_cas gives the indice of the CAS determinant in psi_det.
+
+`psi_cas_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L4>`_
+  CAS wave function, defined from the application of the CAS bitmask on the
+  determinants. idx_cas gives the indice of the CAS determinant in psi_det.
+
+`psi_cas_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L47>`_
+  CAS determinants sorted to accelerate the search of a random determinant in the wave
+  function.
+
+`psi_cas_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L46>`_
+  CAS determinants sorted to accelerate the search of a random determinant in the wave
+  function.
+
+`psi_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L60>`_
+  Set of determinants which are not part of the CAS, defined from the application
+  of the CAS bitmask on the determinants.
+  idx_non_cas gives the indice of the determinant in psi_det.
+
+`psi_non_cas_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L61>`_
+  Set of determinants which are not part of the CAS, defined from the application
+  of the CAS bitmask on the determinants.
+  idx_non_cas gives the indice of the determinant in psi_det.
+
+`psi_non_cas_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L100>`_
+  CAS determinants sorted to accelerate the search of a random determinant in the wave
+  function.
+
+`psi_non_cas_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L99>`_
+  CAS determinants sorted to accelerate the search of a random determinant in the wave
+  function.
+
+`bi_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L5>`_
+  Energy of the reference bitmask used in Slater rules
+
+`kinetic_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L3>`_
+  Energy of the reference bitmask used in Slater rules
+
+`mono_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L2>`_
+  Energy of the reference bitmask used in Slater rules
+
+`nucl_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L4>`_
+  Energy of the reference bitmask used in Slater rules
+
+`ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L1>`_
+  Energy of the reference bitmask used in Slater rules
+
+`expected_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L48>`_
+  Expected value of S2 : S*(S+1)
+
 `get_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L1>`_
  Returns <S^2>

-`get_s2_u0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L46>`_
+`get_s2_u0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L82>`_
  Undocumented

+`s2_values <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L67>`_
+  array of the averaged values of the S^2 operator on the various states
+
 `s_z <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L36>`_
-  Undocumented
+  z component of the Spin

 `s_z2_sz <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L37>`_
+  z component of the Spin
+
+`prog_save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_casino.irp.f#L266>`_
+  Undocumented
+
+`save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_casino.irp.f#L1>`_
  Undocumented

 `save_dets_qmcchem <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_qmcchem.irp.f#L1>`_
  Undocumented

-`save_for_qmc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_qmcchem.irp.f#L37>`_
+`save_for_qmc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_qmcchem.irp.f#L48>`_
  Undocumented

 `save_natorb <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_natorb.irp.f#L1>`_
  Undocumented

-`a_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L721>`_
+`a_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L962>`_
  Needed for diag_H_mat_elem

-`ac_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L766>`_
+`ac_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1007>`_
  Needed for diag_H_mat_elem

 `decode_exc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L76>`_
@ -341,10 +603,10 @@ Documentation
  s1,s2 : Spins (1:alpha, 2:beta)
  degree : Degree of excitation

-`det_connections <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L898>`_
-  .br
+`det_connections <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1139>`_
+  Build connection proxy between determinants

-`diag_h_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L659>`_
+`diag_h_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L900>`_
  Computes <i|H|i>

 `get_double_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L141>`_
@ -356,16 +618,16 @@ Documentation
 `get_excitation_degree <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1>`_
  Returns the excitation degree between two determinants

-`get_excitation_degree_vector <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L575>`_
+`get_excitation_degree_vector <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L816>`_
  Applies get_excitation_degree to an array of determinants

 `get_mono_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L274>`_
  Returns the excitation operator between two singly excited determinants and the phase

-`get_occ_from_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L814>`_
+`get_occ_from_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1055>`_
  Returns a list of occupation numbers from a bitstring

-`h_u_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L830>`_
+`h_u_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1071>`_
  Computes v_0 = H|u_0>
  .br
  n : number of determinants
@ -375,10 +637,13 @@ Documentation
 `i_h_j <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L355>`_
  Returns <i|H|j> where i and j are determinants

-`i_h_psi <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L491>`_
+`i_h_j_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L492>`_
+  Returns <i|H|j> where i and j are determinants
+
+`i_h_psi <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L631>`_
  <key|H|psi> for the various Nstates

-`i_h_psi_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L527>`_
+`i_h_psi_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L713>`_
  <key|H|psi> for the various Nstate
  .br
  returns in addition
@ -391,11 +656,33 @@ Documentation
  .br
  to repeat the excitations

-`n_con_int <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L890>`_
+`i_h_psi_sc2_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L760>`_
+  <key|H|psi> for the various Nstate
+  .br
+  returns in addition
+  .br
+  the array of the index of the non connected determinants to key1
+  .br
+  in order to know what double excitation can be repeated on key1
+  .br
+  idx_repeat(0) is the number of determinants that can be used
+  .br
+  to repeat the excitations
+
+`i_h_psi_sec_ord <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L666>`_
+  <key|H|psi> for the various Nstates
+
+`n_con_int <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1131>`_
  Number of integers to represent the connections between determinants

+`write_spindeterminants <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L1>`_
+  Undocumented
+
+`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/truncate_wf.irp.f#L1>`_
+  Undocumented
+
 `h_matrix_all_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/utils.irp.f#L1>`_
-  H matrix on the basis of the slater deter;inants defined by psi_det
+  H matrix on the basis of the slater determinants defined by psi_det



--- a/src/Dets/connected_to_ref.irp.f
+++ b/src/Dets/connected_to_ref.irp.f
@ -95,9 +95,9 @@ integer function get_index_in_psi_det_sorted_bit(key,Nint)
  enddo
  i += 1

-!  if (i > N_det) then
-!    return
-!  endif
+  if (i > N_det) then
+    return
+  endif

  !DIR$ FORCEINLINE
  do while (det_search_key(psi_det_sorted_bit(1,1,i),Nint) == det_ref)
@ -116,39 +116,39 @@ integer function get_index_in_psi_det_sorted_bit(key,Nint)
      enddo
      if (is_in_wavefunction) then
        get_index_in_psi_det_sorted_bit = i
-        exit
-!        return
+!        exit
+        return
      endif
    endif
    i += 1
    if (i > N_det) then
-      exit
-!      return
+!      exit
+      return
    endif
    
  enddo

 ! DEBUG is_in_wf
- if (is_in_wavefunction) then
-   degree = 1
-   do i=1,N_det
-     integer                        :: degree
-     call get_excitation_degree(key,psi_det(1,1,i),degree,N_int)
-     if (degree == 0) then
-       exit
-     endif
-   enddo
-   if (degree /=0) then
-     stop 'pouet 1'
-   endif
- else
-   do i=1,N_det
-     call get_excitation_degree(key,psi_det(1,1,i),degree,N_int)
-     if (degree == 0) then
-       stop 'pouet 2'
-     endif
-   enddo
- endif
+! if (is_in_wavefunction) then
+!   degree = 1
+!   do i=1,N_det
+!     integer                        :: degree
+!     call get_excitation_degree(key,psi_det(1,1,i),degree,N_int)
+!     if (degree == 0) then
+!       exit
+!     endif
+!   enddo
+!   if (degree /=0) then
+!     stop 'pouet 1'
+!   endif
+! else
+!   do i=1,N_det
+!     call get_excitation_degree(key,psi_det(1,1,i),degree,N_int)
+!     if (degree == 0) then
+!       stop 'pouet 2'
+!     endif
+!   enddo
+! endif
 ! END DEBUG is_in_wf
 end

--- a/src/Dets/det_svd.irp.f
+++ b/src/Dets/det_svd.irp.f
@ -3,7 +3,7 @@ program det_svd
  BEGIN_DOC
 ! Computes the SVD of the Alpha x Beta determinant coefficient matrix
  END_DOC
-  integer                        :: i,j
+  integer                        :: i,j,k

  read_wf = .True.
  TOUCH read_wf
@ -40,17 +40,22 @@ program det_svd
  print *,  'N_det_alpha = ', N_det_alpha_unique
  print *,  'N_det_beta  = ', N_det_beta_unique
  print *,  ''
-
-!  do i=1,N_det_alpha_unique
-!    do j=1,N_det_beta_unique
-!      print *,  i,j,psi_svd_matrix(i,j,:)
-!    enddo
-!  enddo
-
  print *,  ''
+  call diagonalize_ci
  print *,  'Energy = ', ci_energy
+
+  do i=1,N_det_alpha_unique
+    do j=1,N_det_beta_unique
+      do k=1,N_states
+        if (dabs(psi_svd_matrix(i,j,k)) < 1.d-15) then
+          psi_svd_matrix(i,j,k) = 0.d0
+        endif
+      enddo
+    enddo
+  enddo
+
  print *,  ''
  print *,  psi_svd_coefs(1:20,1)
-!  call save_wavefunction
+  call save_wavefunction

 end
--- a/src/Dets/determinants.irp.f
+++ b/src/Dets/determinants.irp.f
@ -467,33 +467,52 @@ END_PROVIDER
 ! to accelerate the search of a random determinant in the wave
 ! function.
 END_DOC
+
+ call sort_dets_by_det_search_key(N_det, psi_det, psi_coef, &
+   psi_det_sorted_bit, psi_coef_sorted_bit)
+END_PROVIDER
+
+subroutine sort_dets_by_det_search_key(Ndet, det_in, coef_in, det_out, coef_out)
+  use bitmasks
+  implicit none
+  integer, intent(in) :: Ndet
+  integer(bit_kind), intent(in)  :: det_in  (N_int,2,psi_det_size)
+  double precision , intent(in)  :: coef_in(psi_det_size,N_states)
+  integer(bit_kind), intent(out) :: det_out (N_int,2,psi_det_size)
+  double precision , intent(out) :: coef_out(psi_det_size,N_states)
+ BEGIN_DOC
+ ! Determinants are sorted are sorted according to their det_search_key.
+ ! Useful to accelerate the search of a random determinant in the wave
+ ! function.
+ END_DOC
 integer :: i,j,k
 integer, allocatable ::  iorder(:)
 integer*8, allocatable :: bit_tmp(:)
 integer*8, external :: det_search_key

- allocate ( iorder(N_det), bit_tmp(N_det) )
+ allocate ( iorder(Ndet), bit_tmp(Ndet) )

- do i=1,N_det
+ do i=1,Ndet
   iorder(i) = i
   !$DIR FORCEINLINE
-   bit_tmp(i) = det_search_key(psi_det(1,1,i),N_int)
+   bit_tmp(i) = det_search_key(det_in(1,1,i),N_int)
 enddo
- call i8sort(bit_tmp,iorder,N_det)
+ call i8sort(bit_tmp,iorder,Ndet)
 !DIR$ IVDEP
- do i=1,N_det
+ do i=1,Ndet
  do j=1,N_int
-    psi_det_sorted_bit(j,1,i) = psi_det(j,1,iorder(i))
-    psi_det_sorted_bit(j,2,i) = psi_det(j,2,iorder(i))
+    det_out(j,1,i) = det_in(j,1,iorder(i))
+    det_out(j,2,i) = det_in(j,2,iorder(i))
  enddo
  do k=1,N_states
-    psi_coef_sorted_bit(i,k) = psi_coef(iorder(i),k)
+    coef_out(i,k) = coef_in(iorder(i),k)
  enddo
 enddo

 deallocate(iorder, bit_tmp)

-END_PROVIDER
+end
+

 subroutine int_of_3_highest_electrons( det_in, res, Nint )
  implicit none
--- a/src/Dets/psi_cas.irp.f
+++ b/src/Dets/psi_cas.irp.f
@ -0,0 +1,114 @@
+use bitmasks
+
+ BEGIN_PROVIDER [ integer(bit_kind), psi_cas, (N_int,2,psi_det_size) ]
+&BEGIN_PROVIDER [ double precision, psi_cas_coef,  (psi_det_size,n_states) ]
+&BEGIN_PROVIDER [ integer, idx_cas, (psi_det_size) ]
+&BEGIN_PROVIDER [ integer, N_det_cas ]
+  implicit none
+  BEGIN_DOC
+  ! CAS wave function, defined from the application of the CAS bitmask on the 
+  ! determinants. idx_cas gives the indice of the CAS determinant in psi_det.
+  END_DOC
+  integer                        :: i, k, l
+  logical                        :: good
+  N_det_cas = 0
+  do i=1,N_det
+    do l=1,n_cas_bitmask
+      good = .True.
+      do k=1,N_int
+        good = good .and. (                                          &
+            iand(not(cas_bitmask(k,1,l)), psi_det(k,1,i)) ==         &
+            iand(not(cas_bitmask(k,1,l)), psi_det(k,1,1)) ) .and. (  &
+            iand(not(cas_bitmask(k,2,l)), psi_det(k,2,i)) ==         &
+            iand(not(cas_bitmask(k,2,l)), psi_det(k,2,1)) )
+      enddo
+      if (good) then
+        exit
+      endif
+    enddo
+    if (good) then
+      N_det_cas = N_det_cas+1
+      do k=1,N_int
+        psi_cas(k,1,N_det_cas) = psi_det(k,1,i)
+        psi_cas(k,2,N_det_cas) = psi_det(k,2,i)
+      enddo
+      idx_cas(N_det_cas) = i
+      do k=1,N_states
+        psi_cas_coef(N_det_cas,k) = psi_coef(i,k)
+      enddo
+    endif
+  enddo
+  call write_int(output_dets,N_det_cas, 'Number of determinants in the CAS')
+
+END_PROVIDER
+
+
+ BEGIN_PROVIDER [ integer(bit_kind), psi_cas_sorted_bit, (N_int,2,psi_det_size) ]
+&BEGIN_PROVIDER [ double precision, psi_cas_coef_sorted_bit, (psi_det_size,N_states) ]
+ implicit none
+ BEGIN_DOC
+ ! CAS determinants sorted to accelerate the search of a random determinant in the wave
+ ! function.
+ END_DOC
+ call sort_dets_by_det_search_key(N_det_cas, psi_cas, psi_cas_coef, &
+     psi_cas_sorted_bit, psi_cas_coef_sorted_bit)
+
+END_PROVIDER
+
+
+
+ BEGIN_PROVIDER [ integer(bit_kind), psi_non_cas,  (N_int,2,psi_det_size) ]
+&BEGIN_PROVIDER [ double precision, psi_non_cas_coef, (psi_det_size,n_states) ]
+&BEGIN_PROVIDER [ integer, idx_non_cas,  (psi_det_size) ]
+&BEGIN_PROVIDER [ integer, N_det_non_cas ]
+ implicit none
+ BEGIN_DOC
+  ! Set of determinants which are not part of the CAS, defined from the application
+  ! of the CAS bitmask on the determinants. 
+  ! idx_non_cas gives the indice of the determinant in psi_det.
+ END_DOC
+ integer                        :: i_non_cas,j,k
+ integer                        :: degree
+ logical                        :: in_cas
+ i_non_cas =0
+ do k=1,N_det
+   in_cas = .False.
+   do j=1,N_det_cas
+     call get_excitation_degree(psi_cas(1,1,j), psi_det(1,1,k), degree, N_int)
+     if (degree == 0) then
+       in_cas = .True.
+       exit
+     endif
+   enddo
+   if (.not.in_cas) then
+     double precision :: hij
+     i_non_cas += 1
+     do j=1,N_int
+       psi_non_cas(j,1,i_non_cas) = psi_det(j,1,k)
+       psi_non_cas(j,2,i_non_cas) = psi_det(j,2,k)
+     enddo
+     do j=1,N_states
+       psi_non_cas_coef(i_non_cas,j) = psi_coef(k,j)
+     enddo
+     idx_non_cas(i_non_cas) = k
+   endif
+ enddo
+ N_det_non_cas = i_non_cas
+END_PROVIDER
+
+ BEGIN_PROVIDER [ integer(bit_kind), psi_non_cas_sorted_bit, (N_int,2,psi_det_size) ]
+&BEGIN_PROVIDER [ double precision, psi_non_cas_coef_sorted_bit, (psi_det_size,N_states) ]
+ implicit none
+ BEGIN_DOC
+ ! CAS determinants sorted to accelerate the search of a random determinant in the wave
+ ! function.
+ END_DOC
+ call sort_dets_by_det_search_key(N_det_cas, psi_non_cas, psi_non_cas_coef, &
+     psi_non_cas_sorted_bit, psi_non_cas_coef_sorted_bit)
+
+END_PROVIDER
+
+
+
+
+
--- a/src/Dets/save_for_qmcchem.irp.f
+++ b/src/Dets/save_for_qmcchem.irp.f
@ -42,8 +42,10 @@ subroutine save_dets_qmcchem
 enddo
 close(31)
 call system('gzip -f '//trim(ezfio_filename)//'/mo_basis/mo_classif')
+
 end

 program save_for_qmc
  call save_dets_qmcchem
+ call write_spindeterminants
 end
--- a/src/Dets/spindeterminants.ezfio_config
+++ b/src/Dets/spindeterminants.ezfio_config
@ -7,4 +7,8 @@ spindeterminants
  psi_det_alpha   integer*8 (spindeterminants_n_int*spindeterminants_bit_kind/8,spindeterminants_n_det_alpha)
  psi_det_beta    integer*8 (spindeterminants_n_int*spindeterminants_bit_kind/8,spindeterminants_n_det_beta)
  psi_coef_matrix double precision (spindeterminants_n_det_alpha,spindeterminants_n_det_beta,spindeterminants_n_states)
+  n_svd_coefs     integer
+  psi_svd_alpha   double precision (spindeterminants_n_det_alpha,spindeterminants_n_svd_coefs,spindeterminants_n_states)
+  psi_svd_beta    double precision (spindeterminants_n_det_beta,spindeterminants_n_svd_coefs,spindeterminants_n_states)
+  psi_svd_coefs   double precision (spindeterminants_n_svd_coefs,spindeterminants_n_states)

--- a/src/Dets/spindeterminants.irp.f
+++ b/src/Dets/spindeterminants.irp.f
@ -26,7 +26,7 @@ subroutine write_spindeterminants
  enddo
  call ezfio_set_spindeterminants_psi_det_alpha(psi_det_alpha_unique)
  deallocate(tmpdet)
-
+  
  allocate(tmpdet(N_int2,N_det_beta_unique))
  do i=1,N_det_beta_unique
    do k=1,N_int
@ -38,7 +38,54 @@ subroutine write_spindeterminants
  enddo
  call ezfio_set_spindeterminants_psi_det_beta(psi_det_beta_unique)
  deallocate(tmpdet)
-
+  
  call ezfio_set_spindeterminants_psi_coef_matrix(psi_svd_matrix)
+  
+  integer                        :: n_svd_coefs
+  double precision               :: norm, f
+  f = 1.d0/dble(N_states)
+  norm = 1.d0
+  do n_svd_coefs=1,N_det_alpha_unique
+    do k=1,N_states
+      norm -= psi_svd_coefs(n_svd_coefs,k)*psi_svd_coefs(n_svd_coefs,k)
+    enddo
+    if (norm < 1.d-6) then
+      exit
+    endif
+  enddo
+  n_svd_coefs -= 1
+  call ezfio_set_spindeterminants_n_svd_coefs(n_svd_coefs)
+  
+  double precision, allocatable  :: dtmp(:,:,:)
+  allocate(dtmp(N_det_alpha_unique,n_svd_coefs,N_states))
+  do k=1,N_states
+    do j=1,n_svd_coefs
+      do i=1,N_det_alpha_unique
+        dtmp(i,j,k) = psi_svd_alpha(i,j,k)
+      enddo
+    enddo
+  enddo
+  call ezfio_set_spindeterminants_psi_svd_alpha(dtmp)
+  deallocate(dtmp)
+
+  allocate(dtmp(N_det_beta_unique,n_svd_coefs,N_states))
+  do k=1,N_states
+    do j=1,n_svd_coefs
+      do i=1,N_det_beta_unique
+        dtmp(i,j,k) = psi_svd_beta(i,j,k)
+      enddo
+    enddo
+  enddo
+  call ezfio_set_spindeterminants_psi_svd_beta(dtmp)
+  deallocate(dtmp)
+
+  allocate(dtmp(n_svd_coefs,N_states,1))
+  do k=1,N_states
+    do j=1,n_svd_coefs
+        dtmp(j,k,1) = psi_svd_coefs(j,k)
+    enddo
+  enddo
+  call ezfio_set_spindeterminants_psi_svd_coefs(dtmp)
+  deallocate(dtmp)

 end
--- a/src/FCIdump/README.rst
+++ b/src/FCIdump/README.rst
@ -4,3 +4,32 @@ FCIdump Module

 Interface for the `NECI <https://github.com/ghb24/NECI_STABLE>`_ Full-CI QMC program.

+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+`fcidump <http://github.com/LCPQ/quantum_package/tree/master/src/FCIdump/fcidump.irp.f#L1>`_
+  Undocumented
+
+
+
+Needed Modules
+==============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
+* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
+* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
+* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
+* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
+* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
+* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
+* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
+* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+
--- a/src/Full_CI/EZFIO.cfg
+++ b/src/Full_CI/EZFIO.cfg
@ -14,7 +14,7 @@ default: 10000
 type: logical
 doc: If true, compute the PT2 at the end of the selection
 interface: input
-default: true
+default: True

 [PT2_max]
 type: PT2_energy
@ -32,11 +32,11 @@ default: 0.75

 [energy]
 type: double precision
-doc: "Calculated Full CI energy"
+doc: Calculated Selected FCI energy
 interface: output

 [energy_pt2]
 type: double precision
-doc: "Calculated Full CI energy"
+doc: Calculated FCI energy + PT2
 interface: output

--- a/src/Full_CI/README.rst
+++ b/src/Full_CI/README.rst
@ -10,7 +10,10 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.

-`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/full_ci.irp.f#L1>`_
+`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/full_ci_no_skip.irp.f#L1>`_
+  Undocumented
+
+`var_pt2_ratio_run <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/var_pt2_ratio.irp.f#L1>`_
  Undocumented


@ -22,18 +25,20 @@ Needed Modules
 .. NEEDED_MODULES file.

 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_

--- a/src/Generators_CAS/README.rst
+++ b/src/Generators_CAS/README.rst
@ -3,3 +3,55 @@ Generators_CAS Module
 =====================

 The generator determinants are those filtered by the ``cas_bitmask`` mask.
+Assumptions
+===========
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+The active space is defined by the ``reference_bitmask``.
+
+
+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L3>`_
+  Number of generator detetrminants
+
+`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L35>`_
+  For Single reference wave functions, the generator is the
+  Hartree-Fock determinant
+
+`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L34>`_
+  For Single reference wave functions, the generator is the
+  Hartree-Fock determinant
+
+`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L78>`_
+  Memo to skip useless selectors
+
+`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L70>`_
+  Size of the select_max array
+
+
+
+Needed Modules
+==============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
+* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
+* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
+* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
+* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
+* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
+* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
+* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
+* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+
--- a/src/Generators_CAS/generators.irp.f
+++ b/src/Generators_CAS/generators.irp.f
@ -62,7 +62,6 @@ END_PROVIDER
        psi_det_generators(k,2,m) = psi_det(k,2,i)
      enddo
      psi_coef_generators(m,:) = psi_coef(m,:)
-!     call debug_det(psi_det_generators(1,1,m),N_int)
    endif
  enddo
  
--- a/src/Generators_full/README.rst
+++ b/src/Generators_full/README.rst
@ -11,20 +11,26 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.

-`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L22>`_
+`degree_max_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L55>`_
+  Max degree of excitation (respect to HF) of the generators
+
+`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L15>`_
  For Single reference wave functions, the number of generators is 1 : the
  Hartree-Fock determinant

-`psi_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L44>`_
+`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L38>`_
  For Single reference wave functions, the generator is the
  Hartree-Fock determinant

-`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L60>`_
+`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L37>`_
+  For Single reference wave functions, the generator is the
+  Hartree-Fock determinant
+
+`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L78>`_
  Memo to skip useless selectors

-`threshold_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L3>`_
-  Percentage of the norm of the state-averaged wave function to
-  consider for the generators
+`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L70>`_
+  Size of the select_max array



@ -35,12 +41,13 @@ Needed Modules
 .. NEEDED_MODULES file.

 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
--- a/src/Hartree_Fock/README.rst
+++ b/src/Hartree_Fock/README.rst
@ -11,11 +11,12 @@ Needed Modules
 .. NEEDED_MODULES file.

 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
@ -36,16 +37,16 @@ Documentation
 `fock_matrix_alpha_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L83>`_
  Alpha Fock matrix in AO basis set

-`fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L194>`_
+`fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L231>`_
  Fock matrix on the MO basis

-`fock_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L242>`_
+`fock_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L289>`_
  Fock matrix in AO basis set

 `fock_matrix_beta_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L84>`_
  Alpha Fock matrix in AO basis set

-`fock_matrix_beta_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L214>`_
+`fock_matrix_beta_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L251>`_
  Fock matrix on the MO basis

 `fock_matrix_diag_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L2>`_
@ -78,24 +79,30 @@ Documentation
  K = Fb - Fa
  .br

-`fock_mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L285>`_
+`fock_mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L332>`_
  Undocumented

-`hf_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L233>`_
+`hf_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L270>`_
  Hartree-Fock energy

 `hf_density_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L27>`_
-  Density matrix in the AO basis
+  S^-1 Density matrix in the AO basis S^-1

 `hf_density_matrix_ao_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L1>`_
-  Alpha density matrix in the AO basis
+  S^-1 x Alpha density matrix in the AO basis x S^-1

 `hf_density_matrix_ao_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L14>`_
-  Beta density matrix in the AO basis
+  S^-1 Beta density matrix in the AO basis x S^-1

-`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L7>`_
+`guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Huckel_guess.irp.f#L1>`_
  Undocumented

+`create_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L8>`_
+  Create an MO guess if no MOs are present in the EZFIO directory
+
+`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L33>`_
+  Run SCF calculation
+
 `scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L2>`_
  Undocumented

@ -105,7 +112,7 @@ Documentation
 `diagonal_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L1>`_
  Diagonal Fock matrix in the MO basis

-`diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L57>`_
+`diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L67>`_
  diagonal element of the fock matrix calculated as the sum over all the interactions
  with all the electrons in the RHF determinant
  diagonal_Fock_matrix_mo_sum(i) = sum_{j=1, N_elec} 2 J_ij -K_ij
@ -113,20 +120,8 @@ Documentation
 `eigenvectors_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L2>`_
  Diagonal Fock matrix in the MO basis

-`bi_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L5>`_
-  Energy of the reference bitmask used in Slater rules
-
-`kinetic_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L3>`_
-  Energy of the reference bitmask used in Slater rules
-
-`mono_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L2>`_
-  Energy of the reference bitmask used in Slater rules
-
-`nucl_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L4>`_
-  Energy of the reference bitmask used in Slater rules
-
-`ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L1>`_
-  Energy of the reference bitmask used in Slater rules
+`huckel_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/huckel.irp.f#L1>`_
+  Build the MOs using the extended Huckel model



--- a/src/MOs/README.rst
+++ b/src/MOs/README.rst
@ -23,11 +23,11 @@ Needed Modules
 .. NEEDED_MODULES file.

 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_

 Documentation
 =============
@ -45,29 +45,58 @@ Documentation
 `mo_density_matrix_virtual <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/cholesky_mo.irp.f#L64>`_
  Density matrix in MO basis (virtual MOs)

-`mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L22>`_
+`mo_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mo_overlap.irp.f#L2>`_
+  Undocumented
+
+`ao_to_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L126>`_
+  Transform A from the AO basis to the MO basis
+
+`mix_mo_jk <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L210>`_
+  subroutine that rotates the jth MO with the kth MO
+  to give two new MO's that are
+  '+' = 1/sqrt(2) (|j> + |k>)
+  '-' = 1/sqrt(2) (|j> - |k>)
+  by convention, the '+' MO is in the lower index (min(j,k))
+  by convention, the '-' MO is in the greater index (max(j,k))
+
+`mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L28>`_
  Molecular orbital coefficients on AO basis set
  mo_coef(i,j) = coefficient of the ith ao on the jth mo
  mo_label : Label characterizing the MOS (local, canonical, natural, etc)

-`mo_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L60>`_
+`mo_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L71>`_
  Molecular orbital coefficients on AO basis set

-`mo_label <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L23>`_
+`mo_label <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L29>`_
  Molecular orbital coefficients on AO basis set
  mo_coef(i,j) = coefficient of the ith ao on the jth mo
  mo_label : Label characterizing the MOS (local, canonical, natural, etc)

-`mo_occ <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L78>`_
+`mo_occ <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L102>`_
  MO occupation numbers

+`mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L152>`_
+  Transform A from the MO basis to the AO basis
+
+`mo_to_ao_no_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L184>`_
+  Transform A from the MO basis to the S^-1 AO basis
+
 `mo_tot_num <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L1>`_
  Total number of molecular orbitals and the size of the keys corresponding

-`mo_tot_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L12>`_
+`mo_tot_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L18>`_
  Aligned variable for dimensioning of arrays

-`mo_as_eigvectors_of_mo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L22>`_
+`s_mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L89>`_
+  Product S.C where S is the overlap matrix in the AO basis and C the mo_coef matrix.
+
+`mo_as_eigvectors_of_mo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L24>`_
+  Undocumented
+
+`mo_as_eigvectors_of_mo_matrix_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L62>`_
+  Undocumented
+
+`mo_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L144>`_
  Undocumented

 `save_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L1>`_
--- a/src/MP2/README.rst
+++ b/src/MP2/README.rst
@ -8,7 +8,7 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.

-`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/MP2/mp2.irp.f#L1>`_
+`mp2 <http://github.com/LCPQ/quantum_package/tree/master/src/MP2/mp2.irp.f#L1>`_
  Undocumented


@ -20,18 +20,20 @@ Needed Modules
 .. NEEDED_MODULES file.

 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

--- a/src/MRCC/EZFIO.cfg
+++ b/src/MRCC/EZFIO.cfg
@ -0,0 +1,4 @@
+[energy]
+type: double precision
+doc: Calculated MRCC energy
+interface: output
--- a/src/MRCC/H_apply.irp.f
+++ b/src/MRCC/H_apply.irp.f
@ -2,13 +2,13 @@ use bitmasks
 BEGIN_SHELL [ /usr/bin/env python ]
 from generate_h_apply import *

-s = H_apply("mrcc")
+s = H_apply("mrcc_simple")
 s.data["parameters"] = ", delta_ij_sd_, Ndet_sd"
 s.data["declarations"] += """
    integer, intent(in) :: Ndet_sd
    double precision, intent(in) :: delta_ij_sd_(Ndet_sd,Ndet_sd,*)
 """
-s.data["keys_work"] = "call mrcc_dress(delta_ij_sd_,Ndet_sd,i_generator,key_idx,keys_out,N_int,iproc)"
+s.data["keys_work"] = "call mrcc_dress_simple(delta_ij_sd_,Ndet_sd,i_generator,key_idx,keys_out,N_int,iproc)"
 s.data["params_post"] += ", delta_ij_sd_, Ndet_sd"
 s.data["params_main"] += "delta_ij_sd_, Ndet_sd"
 s.data["decls_main"] += """
@ -18,8 +18,14 @@ s.data["decls_main"] += """
 s.data["finalization"] = ""
 s.data["copy_buffer"] = ""
 s.data["generate_psi_guess"] = ""
-s.data["size_max"] = "256"
+s.data["size_max"] = "3072"
+print s

+
+
+
+s.data["subroutine"] = "H_apply_mrcc"
+s.data["keys_work"] = "call mrcc_dress(delta_ij_sd_,Ndet_sd,i_generator,key_idx,keys_out,N_int,iproc)"
 print s

 END_SHELL
--- a/src/MRCC/NEEDED_MODULES
+++ b/src/MRCC/NEEDED_MODULES
@ -1,2 +1,2 @@
-AOs Bielec_integrals Bitmask CAS_SD_selected Dets Electrons Ezfio_files Generators_CAS Generators_full Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils
+AOs Bielec_integrals Bitmask Dets Electrons Ezfio_files Generators_full Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils

--- a/src/MRCC/README.rst
+++ b/src/MRCC/README.rst
@ -1,14 +1,91 @@
-4.142795384334731
+===========
+MRCC Module
+===========

-4.695183071437694E-002
- Determinant           64
- ---------------------------------------------
- 000000000000002E|000000000000002E
- |-+++-+----------------------------------------------------------|
- |-+++-+----------------------------------------------------------|
+Needed Modules
+==============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
+* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
+* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
+* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
+* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
+* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
+* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
+* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
+* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
+* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
+* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+
+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+`mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L1>`_
+  Undocumented
+
+`run <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L10>`_
+  Undocumented
+
+`run_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L42>`_
+  Undocumented
+
+`run_mrcc_test <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L29>`_
+  Undocumented
+
+`find_triples_and_quadruples <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L202>`_
+  Undocumented
+
+`mrcc_dress <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L15>`_
+  Undocumented
+
+`mrcc_dress_simple <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L156>`_
+  Undocumented
+
+`psi_cas_lock <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L3>`_
+  Locks on CAS determinants to fill delta_ij
+
+`ci_eigenvectors_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L79>`_
+  Eigenvectors/values of the CI matrix
+
+`ci_eigenvectors_s2_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L80>`_
+  Eigenvectors/values of the CI matrix
+
+`ci_electronic_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L78>`_
+  Eigenvectors/values of the CI matrix
+
+`ci_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L132>`_
+  N_states lowest eigenvalues of the dressed CI matrix
+
+`delta_ij <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L43>`_
+  Dressing matrix in N_det basis
+
+`delta_ij_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L34>`_
+  Dressing matrix in SD basis
+
+`diagonalize_ci_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L147>`_
+  Replace the coefficients of the CI states by the coefficients of the
+  eigenstates of the CI matrix
+
+`dressing_type <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L26>`_
+  [ Simple | MRCC ]
+
+`h_matrix_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L63>`_
+  Dressed H with Delta_ij
+
+`lambda_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L2>`_
+  cm/<Psi_0|H|D_m>

-CAS-SD: -4.14214374069306
-      : -4.14230904320551

-E0 = -11.5634986758976

--- a/src/MRCC/mrcc.irp.f
+++ b/src/MRCC/mrcc.irp.f
@ -3,41 +3,65 @@ program mrcc
  read_wf = .True.
  TOUCH read_wf
  call run
+  call run_mrcc
+!  call run_mrcc_test
 end

 subroutine run
  implicit none

-  print *, N_det
-  print *, N_det_cas
-  print *, N_det_sd
-
-!  call update_generators
-  integer :: i
+  integer :: i,j
  print *,  'CAS'
  print *,  '==='
  do i=1,N_det_cas
-    print *,  psi_cas_coefs(i,:)
+    print *,  psi_cas_coef(i,:)
    call debug_det(psi_cas(1,1,i),N_int)
  enddo

 !  print *,  'SD'
 !  print *,  '=='
-!  do i=1,N_det_sd
-!    print *,  psi_sd_coefs(i,:)
-!    call debug_det(psi_sd(1,1,i),N_int)
-!  enddo
-!
-  print *,  'MRCC'
-  print *,  '===='
-  print *,  ci_energy(:)
-  print *,  h_matrix_all_dets(3,3), delta_ij(3,3,1)
-  print *,  h_matrix_all_dets(3,3), delta_ij(3,3,1)
-  print *,  ci_energy_dressed(:)
-!  print *,  'max', maxval(delta_ij_sd)
-!  print *,  'min', minval(delta_ij_sd)
-!
-!  do i=1,N_det
-!     print '(10(F10.6,X))',  delta_ij(i,1:N_det,1)
+!  do i=1,N_det_non_cas
+!    print *,  psi_non_cas_coef(i,:)
+!    call debug_det(psi_non_cas(1,1,i),N_int)
 !  enddo
+  call write_double(6,ci_energy(1),"Initial CI energy")
+end
+subroutine run_mrcc_test
+  implicit none
+  integer :: i,j
+  double precision :: pt2
+  pt2 = 0.d0
+  do j=1,N_det
+   do i=1,N_det
+     pt2 += psi_coef(i,1)*psi_coef(j,1) * delta_ij(i,j,1)
+   enddo
+  enddo
+  print *,  ci_energy(1)
+  print *,  ci_energy(1)+pt2
+end
+subroutine run_mrcc
+  implicit none
+  integer :: i,j
+
+  double precision :: E_new, E_old, delta_e
+  integer :: iteration
+  E_new = 0.d0
+  delta_E = 1.d0
+  iteration = 0
+  do while (delta_E > 1.d-8)
+    iteration += 1
+    print *,  '===========================' 
+    print *,  'MRCC Iteration', iteration
+    print *,  '===========================' 
+    print *,  ''
+    E_old = sum(ci_energy_dressed)
+    call write_double(6,ci_energy_dressed(1),"MRCC energy")
+    call diagonalize_ci_dressed
+    E_new = sum(ci_energy_dressed)
+    delta_E = dabs(E_new - E_old)
+  enddo
+  call write_double(6,ci_energy_dressed(1),"Final MRCC energy")
+  call ezfio_set_mrcc_energy(ci_energy_dressed(1))
+!  call save_wavefunction
+
 end
--- a/src/MRCC/mrcc_dress.irp.f
+++ b/src/MRCC/mrcc_dress.irp.f
@ -1,15 +1,169 @@
-subroutine mrcc_dress(delta_ij_sd_,Ndet_sd,i_generator,n_selected,det_buffer,Nint,iproc)
+use omp_lib
+
+BEGIN_PROVIDER [ integer(omp_lock_kind), psi_cas_lock, (psi_det_size) ]
+ implicit none
+ BEGIN_DOC
+ ! Locks on CAS determinants to fill delta_ij
+ END_DOC
+ integer :: i
+ do i=1,psi_det_size
+   call omp_init_lock( psi_cas_lock(i) )
+ enddo
+
+END_PROVIDER
+
+subroutine mrcc_dress(delta_ij_,Ndet,i_generator,n_selected,det_buffer,Nint,iproc)
 use bitmasks
 implicit none

  integer, intent(in)            :: i_generator,n_selected, Nint, iproc
-  integer, intent(in) :: Ndet_sd
-  double precision, intent(inout) :: delta_ij_sd_(Ndet_sd,Ndet_sd,*)
+  integer, intent(in) :: Ndet
+  double precision, intent(inout) :: delta_ij_(Ndet,Ndet,*)
+
+  integer(bit_kind), intent(in)  :: det_buffer(Nint,2,n_selected)
+  integer                        :: i,j,k,l
+  integer                        :: degree_alpha(psi_det_size)
+  integer                        :: idx_alpha(0:psi_det_size)
+  logical                        :: good
+
+  integer(bit_kind)              :: tq(Nint,2,n_selected)
+  integer                        :: N_tq, c_ref ,degree
+  integer                        :: connected_to_ref
+
+  double precision               :: hIk, hla, hIl, dIk(N_states), dka(N_states), dIa(N_states)
+  double precision, allocatable  :: dIa_hla(:,:)
+  double precision               :: haj, phase, phase2
+  double precision               :: f(N_states), ci_inv(N_states)
+  integer                        :: exc(0:2,2,2)
+  integer                        :: h1,h2,p1,p2,s1,s2
+  integer(bit_kind)              :: tmp_det(Nint,2)
+  integer                        :: iint, ipos
+  integer                        :: i_state, k_sd, l_sd, i_I, i_alpha
+
+  call find_triples_and_quadruples(i_generator,n_selected,det_buffer,Nint,tq,N_tq)
+
+  allocate (dIa_hla(N_states,Ndet))
+
+  ! |I>
+
+  ! |alpha>
+  do i_alpha=1,N_tq
+    call get_excitation_degree_vector(psi_non_cas,tq(1,1,i_alpha),degree_alpha,Nint,N_det_non_cas,idx_alpha)
+
+    ! |I>
+    do i_I=1,N_det_cas
+       ! Find triples and quadruple grand parents
+       call get_excitation_degree(tq(1,1,i_alpha),psi_cas(1,1,i_I),degree,Nint)
+       if (degree > 4) then
+         cycle
+       endif
+
+       do i_state=1,N_states
+         dIa(i_state) = 0.d0
+       enddo
+
+       ! <I|  <>  |alpha>
+       do k_sd=1,idx_alpha(0)
+         call get_excitation_degree(psi_cas(1,1,i_I),psi_non_cas(1,1,idx_alpha(k_sd)),degree,Nint)
+         if (degree > 2) then
+           cycle
+         endif
+         ! <I| /k\ |alpha>
+         ! <I|H|k>
+         call i_h_j(psi_cas(1,1,i_I),psi_non_cas(1,1,idx_alpha(k_sd)),Nint,hIk)
+         do i_state=1,N_states
+           dIk(i_state) = hIk * lambda_mrcc(i_state,idx_alpha(k_sd))
+         enddo
+         ! |l> = Exc(k -> alpha) |I>
+         call get_excitation(psi_non_cas(1,1,idx_alpha(k_sd)),tq(1,1,i_alpha),exc,degree,phase,Nint)
+         call decode_exc(exc,degree,h1,p1,h2,p2,s1,s2)
+         do k=1,N_int
+           tmp_det(k,1) = psi_cas(k,1,i_I)
+           tmp_det(k,2) = psi_cas(k,2,i_I)
+         enddo
+         ! Hole (see list_to_bitstring)
+         iint = ishft(h1-1,-bit_kind_shift) + 1
+         ipos = h1-ishft((iint-1),bit_kind_shift)-1
+         tmp_det(iint,s1) = ibclr(tmp_det(iint,s1),ipos)
+
+         ! Particle
+         iint = ishft(p1-1,-bit_kind_shift) + 1
+         ipos = p1-ishft((iint-1),bit_kind_shift)-1
+         tmp_det(iint,s1) = ibset(tmp_det(iint,s1),ipos)
+         if (degree_alpha(k_sd) == 2) then
+           ! Hole (see list_to_bitstring)
+           iint = ishft(h2-1,-bit_kind_shift) + 1
+           ipos = h2-ishft((iint-1),bit_kind_shift)-1
+           tmp_det(iint,s2) = ibclr(tmp_det(iint,s2),ipos)
+
+           ! Particle
+           iint = ishft(p2-1,-bit_kind_shift) + 1
+           ipos = p2-ishft((iint-1),bit_kind_shift)-1
+           tmp_det(iint,s2) = ibset(tmp_det(iint,s2),ipos)
+         endif
+         
+         ! <I| \l/ |alpha>
+         do i_state=1,N_states
+           dka(i_state) = 0.d0
+         enddo
+         do l_sd=k_sd+1,idx_alpha(0)
+           call get_excitation_degree(tmp_det,psi_non_cas(1,1,idx_alpha(l_sd)),degree,Nint)
+           if (degree == 0) then
+             call get_excitation(psi_cas(1,1,i_I),psi_non_cas(1,1,idx_alpha(l_sd)),exc,degree,phase2,Nint)
+             call i_h_j(psi_cas(1,1,i_I),psi_non_cas(1,1,idx_alpha(l_sd)),Nint,hIl)
+             do i_state=1,N_states
+               dka(i_state) = hIl * lambda_mrcc(i_state,idx_alpha(l_sd)) * phase * phase2
+             enddo
+             exit
+           endif
+         enddo
+         do i_state=1,N_states
+           dIa(i_state) = dIa(i_state) + dIk(i_state) * dka(i_state) 
+         enddo
+       enddo
+
+       do i_state=1,N_states
+         ci_inv(i_state) = 1.d0/psi_cas_coef(i_I,i_state)
+       enddo
+       do l_sd=1,idx_alpha(0)
+         k_sd = idx_alpha(l_sd)
+         call i_h_j(tq(1,1,i_alpha),psi_non_cas(1,1,idx_alpha(l_sd)),Nint,hla)
+         do i_state=1,N_states
+           dIa_hla(i_state,k_sd) = dIa(i_state) * hla
+         enddo
+       enddo
+       call omp_set_lock( psi_cas_lock(i_I) )
+       do l_sd=1,idx_alpha(0)
+         k_sd = idx_alpha(l_sd)
+         do i_state=1,N_states
+           delta_ij_(idx_non_cas(k_sd),idx_cas(i_I),i_state) += dIa_hla(i_state,k_sd)
+           delta_ij_(idx_cas(i_I),idx_non_cas(k_sd),i_state) += dIa_hla(i_state,k_sd)
+           delta_ij_(idx_cas(i_I),idx_cas(i_I),i_state) -= dIa_hla(i_state,k_sd) * ci_inv(i_state) * psi_non_cas_coef(k_sd,i_state)
+         enddo
+       enddo
+       call omp_unset_lock( psi_cas_lock(i_I) )
+    enddo
+  enddo
+  deallocate (dIa_hla)
+end
+
+
+
+
+
+
+
+subroutine mrcc_dress_simple(delta_ij_non_cas_,Ndet_non_cas,i_generator,n_selected,det_buffer,Nint,iproc)
+ use bitmasks
+ implicit none
+
+  integer, intent(in)            :: i_generator,n_selected, Nint, iproc
+  integer, intent(in) :: Ndet_non_cas
+  double precision, intent(inout) :: delta_ij_non_cas_(Ndet_non_cas,Ndet_non_cas,*)

  integer(bit_kind), intent(in)  :: det_buffer(Nint,2,n_selected)
  integer                        :: i,j,k,m
  integer                        :: new_size
-  logical                        :: is_in_wavefunction
  integer                        :: degree(psi_det_size)
  integer                        :: idx(0:psi_det_size)
  logical                        :: good
@ -18,6 +172,51 @@ subroutine mrcc_dress(delta_ij_sd_,Ndet_sd,i_generator,n_selected,det_buffer,Nin
  integer                        :: N_tq, c_ref
  integer                        :: connected_to_ref

+  call find_triples_and_quadruples(i_generator,n_selected,det_buffer,Nint,tq,N_tq)
+
+  ! Compute <k|H|a><a|H|j> / (E0 - Haa)
+  double precision :: hka, haa
+  double precision :: haj
+  double precision :: f(N_states)
+
+  do i=1,N_tq
+    call get_excitation_degree_vector(psi_non_cas,tq(1,1,i),degree,Nint,Ndet_non_cas,idx)
+    call i_h_j(tq(1,1,i),tq(1,1,i),Nint,haa)
+    do m=1,N_states
+      f(m) = 1.d0/(ci_electronic_energy(m)-haa)
+    enddo
+    do k=1,idx(0)
+      call i_h_j(tq(1,1,i),psi_non_cas(1,1,idx(k)),Nint,hka)
+      do j=k,idx(0)
+        call i_h_j(tq(1,1,i),psi_non_cas(1,1,idx(j)),Nint,haj)
+        do m=1,N_states
+          delta_ij_non_cas_(idx(k), idx(j),m) += haj*hka* f(m)
+          delta_ij_non_cas_(idx(j), idx(k),m) += haj*hka* f(m)
+        enddo
+      enddo 
+    enddo
+  enddo
+end
+
+
+subroutine find_triples_and_quadruples(i_generator,n_selected,det_buffer,Nint,tq,N_tq)
+ use bitmasks
+ implicit none
+
+  integer, intent(in)            :: i_generator,n_selected, Nint
+
+  integer(bit_kind), intent(in)  :: det_buffer(Nint,2,n_selected)
+  integer                        :: i,j,k,m
+  logical                        :: is_in_wavefunction
+  integer                        :: degree(psi_det_size)
+  integer                        :: idx(0:psi_det_size)
+  logical                        :: good
+
+  integer(bit_kind), intent(out) :: tq(Nint,2,n_selected)
+  integer, intent(out)           :: N_tq
+  integer                        :: c_ref
+  integer                        :: connected_to_ref
+
  N_tq = 0
  do i=1,N_selected
    c_ref = connected_to_ref(det_buffer(1,1,i),psi_det_generators,Nint, &
@ -48,143 +247,11 @@ subroutine mrcc_dress(delta_ij_sd_,Ndet_sd,i_generator,n_selected,det_buffer,Nin
    endif
  enddo

-  ! Compute <k|H|a><a|H|j> / (E0 - Haa)
-  double precision :: hka, haa
-  double precision :: haj
-  double precision :: f(N_states)
-
-  do i=1,N_tq
-    call get_excitation_degree_vector(psi_sd,tq(1,1,i),degree,Nint,Ndet_sd,idx)
-    call i_h_j(tq(1,1,i),tq(1,1,i),Nint,haa)
-    do m=1,N_states
-      f(m) = 1.d0/(ci_electronic_energy(m)-haa)
-    enddo
-    do k=1,idx(0)
-      call i_h_j(tq(1,1,i),psi_sd(1,1,idx(k)),Nint,hka)
-      do j=k,idx(0)
-        call i_h_j(tq(1,1,i),psi_sd(1,1,idx(j)),Nint,haj)
-        do m=1,N_states
-          delta_ij_sd_(idx(k), idx(j),m) += haj*hka* f(m)
-          delta_ij_sd_(idx(j), idx(k),m) += haj*hka* f(m)
-        enddo
-      enddo 
-    enddo
-  enddo
 end

-BEGIN_PROVIDER [ double precision, delta_ij_sd, (N_det_sd, N_det_sd,N_states) ]
- implicit none
- BEGIN_DOC
- ! Dressing matrix in SD basis
- END_DOC
- delta_ij_sd = 0.d0
- call H_apply_mrcc(delta_ij_sd,N_det_sd)
-
-END_PROVIDER
-
-BEGIN_PROVIDER [ double precision, delta_ij, (N_det,N_det,N_states) ]
- implicit none
- BEGIN_DOC
- ! Dressing matrix in N_det basis
- END_DOC
- integer :: i,j,m
- delta_ij = 0.d0
- do m=1,N_states
-  do j=1,N_det_sd
-   do i=1,N_det_sd
-     delta_ij(idx_sd(i),idx_sd(j),m) = delta_ij_sd(i,j,m) 
-   enddo
-  enddo
- enddo
-END_PROVIDER
-
-BEGIN_PROVIDER [ double precision, h_matrix_dressed, (N_det,N_det) ]
- implicit none
- BEGIN_DOC
- ! Dressed H with Delta_ij
- END_DOC
- integer                        :: i, j
- do j=1,N_det
-   do i=1,N_det
-     h_matrix_dressed(i,j) = h_matrix_all_dets(i,j) + delta_ij(i,j,1)
-     if (i==j) then
-       print *,  i, delta_ij(i,j,1), h_matrix_all_dets(i,j) 
-     endif
-   enddo
- enddo
-
-END_PROVIDER


- BEGIN_PROVIDER [ double precision, CI_electronic_energy_dressed, (N_states_diag) ]
-&BEGIN_PROVIDER [ double precision, CI_eigenvectors_dressed, (N_det,N_states_diag) ]
-&BEGIN_PROVIDER [ double precision, CI_eigenvectors_s2_dressed, (N_states_diag) ]
-  implicit none
-  BEGIN_DOC
-  ! Eigenvectors/values of the CI matrix
-  END_DOC
-  integer                        :: i,j
-  
-  do j=1,N_states_diag
-    do i=1,N_det
-      CI_eigenvectors_dressed(i,j) = psi_coef(i,j)
-    enddo
-  enddo
-  
-  if (diag_algorithm == "Davidson") then
-    
-    stop 'use Lapack'
-!    call davidson_diag(psi_det,CI_eigenvectors_dressed,CI_electronic_energy_dressed, &
-!        size(CI_eigenvectors_dressed,1),N_det,N_states_diag,N_int,output_Dets)
-    
-  else if (diag_algorithm == "Lapack") then
-    
-    double precision, allocatable  :: eigenvectors(:,:), eigenvalues(:)
-    allocate (eigenvectors(size(H_matrix_dressed,1),N_det))
-    allocate (eigenvalues(N_det))
-    call lapack_diag(eigenvalues,eigenvectors,                       &
-        H_matrix_dressed,size(H_matrix_dressed,1),N_det)
-    CI_electronic_energy_dressed(:) = 0.d0
-    do i=1,N_det
-       CI_eigenvectors_dressed(i,1) = eigenvectors(i,1)
-    enddo
-    integer :: i_state
-    double precision :: s2
-    i_state = 0
-    do j=1,N_det
-      call get_s2_u0(psi_det,eigenvectors(1,j),N_det,N_det,s2)
-      if(dabs(s2-expected_s2).le.0.3d0)then
-       i_state += 1
-       do i=1,N_det
-         CI_eigenvectors_dressed(i,i_state) = eigenvectors(i,j)
-       enddo
-       CI_electronic_energy_dressed(i_state) = eigenvalues(j)
-       CI_eigenvectors_s2_dressed(i_state) = s2
-      endif
-      if (i_state.ge.N_states_diag) then
-        exit
-      endif
-    enddo
-    deallocate(eigenvectors,eigenvalues)
-  endif
-  
-END_PROVIDER

-BEGIN_PROVIDER [ double precision, CI_energy_dressed, (N_states_diag) ]
-  implicit none
-  BEGIN_DOC
-  ! N_states lowest eigenvalues of the dressed CI matrix
-  END_DOC
-  
-  integer                        :: j
-  character*(8)                  :: st
-  call write_time(output_Dets)
-  do j=1,N_states_diag
-    CI_energy_dressed(j) = CI_electronic_energy_dressed(j) + nuclear_repulsion
-    write(st,'(I4)') j
-    call write_double(output_Dets,CI_energy(j),'Energy of state '//trim(st))
-    call write_double(output_Dets,CI_eigenvectors_s2(j),'S^2 of state '//trim(st))
-  enddo

-END_PROVIDER
+

--- a/src/MRCC/mrcc_utils.irp.f
+++ b/src/MRCC/mrcc_utils.irp.f
@ -1,150 +1,161 @@
- use bitmasks

-BEGIN_PROVIDER [ integer(bit_kind), cas_bitmask, (N_int,2,N_cas_bitmask) ]
- implicit none
- BEGIN_DOC
- ! Bitmasks for CAS reference determinants. (N_int, alpha/beta, CAS reference)
- END_DOC
- logical                        :: exists
- integer                        :: i
- PROVIDE ezfio_filename
-  
- call ezfio_has_bitmasks_cas(exists)
- if (exists) then                
-   call ezfio_get_bitmasks_cas(cas_bitmask)
- else
-   do i=1,N_cas_bitmask
-     cas_bitmask(:,:,i) = iand(not(HF_bitmask(:,:)),full_ijkl_bitmask(:,:))
-   enddo 
- endif  
-            
-END_PROVIDER
-
-BEGIN_PROVIDER [ integer, N_det_cas ]
-  implicit none
-  BEGIN_DOC
-  ! Number of generator detetrminants
-  END_DOC
-  integer                        :: i,k,l
-  logical                        :: good
-  call write_time(output_dets)
-  N_det_cas = 0
-  do i=1,N_det
-    do l=1,n_cas_bitmask
-      good = .True.
-      do k=1,N_int
-        good = good .and. (                                          &
-            iand(not(cas_bitmask(k,1,l)), psi_det(k,1,i)) ==         &
-            iand(not(cas_bitmask(k,1,l)), psi_det(k,1,1)) ) .and. (  &
-            iand(not(cas_bitmask(k,2,l)), psi_det(k,2,i)) ==         &
-            iand(not(cas_bitmask(k,2,l)), psi_det(k,2,1)) )
-      enddo
-      if (good) then
-        exit
-      endif
-    enddo
-    if (good) then
-      N_det_cas += 1
-    endif
-  enddo
-  N_det_cas = max(N_det_cas, 1)
-  call write_int(output_dets,N_det_cas, 'Number of determinants in the CAS')
-END_PROVIDER
-
- BEGIN_PROVIDER [ integer(bit_kind), psi_cas, (N_int,2,N_det_cas) ]
-&BEGIN_PROVIDER [ double precision, psi_cas_coefs,  (N_det_cas,n_states) ]
-&BEGIN_PROVIDER [ integer, idx_cas, (N_det_cas) ]
-  implicit none
-  BEGIN_DOC
-  ! For Single reference wave functions, the generator is the
-  ! Hartree-Fock determinant
-  END_DOC
-  integer                        :: i, k, l, m
-  logical                        :: good
-  m=0
-  do i=1,N_det
-    do l=1,n_cas_bitmask
-      good = .True.
-      do k=1,N_int
-        good = good .and. (                                          &
-            iand(not(cas_bitmask(k,1,l)), psi_det(k,1,i)) ==         &
-            iand(not(cas_bitmask(k,1,l)), psi_det(k,1,1)) ) .and. (  &
-            iand(not(cas_bitmask(k,2,l)), psi_det(k,2,i)) ==         &
-            iand(not(cas_bitmask(k,2,l)), psi_det(k,2,1)) )
-      enddo
-      if (good) then
-        exit
-      endif
-    enddo
-    if (good) then
-      m = m+1
-      do k=1,N_int
-        psi_cas(k,1,m) = psi_det(k,1,i)
-        psi_cas(k,2,m) = psi_det(k,2,i)
-      enddo
-      idx_cas(m) = i
-      do k=1,N_states
-        psi_cas_coefs(m,k) = psi_coef(i,k)
-      enddo
-    endif
-  enddo
-
-END_PROVIDER
-
-
-
-
- BEGIN_PROVIDER [ integer(bit_kind), psi_sd,  (N_int,2,N_det) ]
-&BEGIN_PROVIDER [ double precision, psi_sd_coefs, (N_det,n_states) ]
-&BEGIN_PROVIDER [ integer, idx_sd,  (N_det) ]
-&BEGIN_PROVIDER [ integer, N_det_sd]
- implicit none
- BEGIN_DOC
- ! SD
- END_DOC
- integer                        :: i_sd,j,k
- integer                        :: degree
- logical                        :: in_cas
- i_sd =0
- do k=1,N_det
-   in_cas = .False.
-   do j=1,N_det_cas
-     call get_excitation_degree(psi_cas(1,1,j), psi_det(1,1,k), degree, N_int)
-     if (degree == 0) then
-       in_cas = .True.
-       exit
-     endif
-   enddo
-   if (.not.in_cas) then
-     double precision :: hij
-     i_sd += 1
-     psi_sd(1:N_int,1:2,i_sd) = psi_det(1:N_int,1:2,k)
-     psi_sd_coefs(i_sd,1:N_states) = psi_coef(k,1:N_states)
-     idx_sd(i_sd) = k
-   endif
- enddo
- N_det_sd = i_sd
-END_PROVIDER
-
-BEGIN_PROVIDER [ double precision, lambda_mrcc, (psi_det_size,n_states) ]
+BEGIN_PROVIDER [ double precision, lambda_mrcc, (N_states,psi_det_size) ]
 implicit none
 BEGIN_DOC
 ! cm/<Psi_0|H|D_m>
 END_DOC
 integer :: i,k
 double precision :: ihpsi(N_states)
- do i=1,N_det_sd
-   call i_h_psi(psi_sd(1,1,i), psi_cas, psi_cas_coefs, N_int, N_det_cas, &
-     size(psi_cas_coefs,1), n_states, ihpsi)
+ do i=1,N_det_non_cas
+   call i_h_psi(psi_non_cas(1,1,i), psi_cas, psi_cas_coef, N_int, N_det_cas, &
+     size(psi_cas_coef,1), n_states, ihpsi)
   double precision :: hij
   do k=1,N_states
-     if (dabs(ihpsi(k)) < 1.d-6) then
-       lambda_mrcc(i,k) = 0.d0
+     if (dabs(ihpsi(k)) > 1.d-5) then
+       lambda_mrcc(k,i) = psi_non_cas_coef(i,k)/ihpsi(k)
+       lambda_mrcc(k,i) = min( lambda_mrcc (k,i),0.d0 )
     else
-       lambda_mrcc(i,k) = psi_sd_coefs(i,k)/ihpsi(k)
-       lambda_mrcc(i,k) = min( lambda_mrcc (i,k),0.d0 )
+       lambda_mrcc(k,i) = 0.d0
     endif
   enddo
 enddo
 END_PROVIDER

+
+
+BEGIN_PROVIDER [ character*(32), dressing_type ]
+ implicit none
+ BEGIN_DOC
+ ! [ Simple | MRCC ]
+ END_DOC
+ dressing_type = "MRCC"
+END_PROVIDER
+
+BEGIN_PROVIDER [ double precision, delta_ij_non_cas, (N_det_non_cas, N_det_non_cas,N_states) ]
+ implicit none
+ BEGIN_DOC
+ ! Dressing matrix in SD basis
+ END_DOC
+ delta_ij_non_cas = 0.d0
+ call H_apply_mrcc_simple(delta_ij_non_cas,N_det_non_cas)
+END_PROVIDER
+
+BEGIN_PROVIDER [ double precision, delta_ij, (N_det,N_det,N_states) ]
+ implicit none
+ BEGIN_DOC
+ ! Dressing matrix in N_det basis
+ END_DOC
+ integer :: i,j,m
+ delta_ij = 0.d0
+ if (dressing_type == "MRCC") then
+   call H_apply_mrcc(delta_ij,N_det)
+ else if (dressing_type == "Simple") then
+   do m=1,N_states
+    do j=1,N_det_non_cas
+     do i=1,N_det_non_cas
+       delta_ij(idx_non_cas(i),idx_non_cas(j),m) = delta_ij_non_cas(i,j,m) 
+     enddo
+    enddo
+   enddo
+ endif
+END_PROVIDER
+
+BEGIN_PROVIDER [ double precision, h_matrix_dressed, (N_det,N_det) ]
+ implicit none
+ BEGIN_DOC
+ ! Dressed H with Delta_ij
+ END_DOC
+ integer                        :: i, j
+ do j=1,N_det
+   do i=1,N_det
+     h_matrix_dressed(i,j) = h_matrix_all_dets(i,j) + delta_ij(i,j,1)
+   enddo
+ enddo
+
+END_PROVIDER
+
+
+ BEGIN_PROVIDER [ double precision, CI_electronic_energy_dressed, (N_states_diag) ]
+&BEGIN_PROVIDER [ double precision, CI_eigenvectors_dressed, (N_det,N_states_diag) ]
+&BEGIN_PROVIDER [ double precision, CI_eigenvectors_s2_dressed, (N_states_diag) ]
+  implicit none
+  BEGIN_DOC
+  ! Eigenvectors/values of the CI matrix
+  END_DOC
+  integer                        :: i,j
+  
+  do j=1,N_states_diag
+    do i=1,N_det
+      CI_eigenvectors_dressed(i,j) = psi_coef(i,j)
+    enddo
+  enddo
+  
+  if (diag_algorithm == "Davidson") then
+    
+    stop 'use Lapack'
+!    call davidson_diag(psi_det,CI_eigenvectors_dressed,CI_electronic_energy_dressed, &
+!        size(CI_eigenvectors_dressed,1),N_det,N_states_diag,N_int,output_Dets)
+    
+  else if (diag_algorithm == "Lapack") then
+    
+    double precision, allocatable  :: eigenvectors(:,:), eigenvalues(:)
+    allocate (eigenvectors(size(H_matrix_dressed,1),N_det))
+    allocate (eigenvalues(N_det))
+    call lapack_diag(eigenvalues,eigenvectors,                       &
+        H_matrix_dressed,size(H_matrix_dressed,1),N_det)
+    CI_electronic_energy_dressed(:) = 0.d0
+    do i=1,N_det
+       CI_eigenvectors_dressed(i,1) = eigenvectors(i,1)
+    enddo
+    integer :: i_state
+    double precision :: s2
+    i_state = 0
+    do j=1,N_det
+      call get_s2_u0(psi_det,eigenvectors(1,j),N_det,N_det,s2)
+      if(dabs(s2-expected_s2).le.0.3d0)then
+       i_state += 1
+       do i=1,N_det
+         CI_eigenvectors_dressed(i,i_state) = eigenvectors(i,j)
+       enddo
+       CI_electronic_energy_dressed(i_state) = eigenvalues(j)
+       CI_eigenvectors_s2_dressed(i_state) = s2
+      endif
+      if (i_state.ge.N_states_diag) then
+        exit
+      endif
+    enddo
+    deallocate(eigenvectors,eigenvalues)
+  endif
+  
+END_PROVIDER
+
+BEGIN_PROVIDER [ double precision, CI_energy_dressed, (N_states_diag) ]
+  implicit none
+  BEGIN_DOC
+  ! N_states lowest eigenvalues of the dressed CI matrix
+  END_DOC
+  
+  integer                        :: j
+  character*(8)                  :: st
+  call write_time(output_Dets)
+  do j=1,N_states_diag
+    CI_energy_dressed(j) = CI_electronic_energy_dressed(j) + nuclear_repulsion
+  enddo
+
+END_PROVIDER
+
+subroutine diagonalize_CI_dressed
+  implicit none
+  BEGIN_DOC
+!  Replace the coefficients of the CI states by the coefficients of the 
+!  eigenstates of the CI matrix
+  END_DOC
+  integer :: i,j
+  do j=1,N_states_diag
+    do i=1,N_det
+      psi_coef(i,j) = CI_eigenvectors_dressed(i,j)
+    enddo
+  enddo
+  SOFT_TOUCH psi_coef 
+
+end
--- a/src/Makefile
+++ b/src/Makefile
@ -16,6 +16,10 @@ default: ezfio

 veryclean:
 	$(QPACKAGE_ROOT)/scripts/clean_modules.sh $(ALL_MODULES)
+	# Define the dict [type in EZFIO.cfg] = ocaml type , f90 type
+	# If you change the qptypes_generator.ml, you need to rm this
+	# For simplicity add this to the veryclean rule
+	rm $(QPACKAGE_ROOT)/scripts/ezfio_interface/fancy_type.p

 $(ALL_MODULES): ezfio
 	$(QPACKAGE_ROOT)/scripts/build_modules.sh $@ 
--- a/src/Molden/README.rst
+++ b/src/Molden/README.rst
@ -2,3 +2,40 @@
 Molden Module
 =============

+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+`print_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Molden/print_mo.irp.f#L1>`_
+  Undocumented
+
+`write_ao_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Molden/print_mo.irp.f#L63>`_
+  Undocumented
+
+`write_geometry <http://github.com/LCPQ/quantum_package/tree/master/src/Molden/print_mo.irp.f#L45>`_
+  Undocumented
+
+`write_intro_gamess <http://github.com/LCPQ/quantum_package/tree/master/src/Molden/print_mo.irp.f#L26>`_
+  Undocumented
+
+`write_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Molden/print_mo.irp.f#L112>`_
+  Undocumented
+
+
+
+Needed Modules
+==============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES file.
+
+* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
+* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
+* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
+* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
+* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
+* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+
--- a/src/MonoInts/README.rst
+++ b/src/MonoInts/README.rst
@ -18,30 +18,10 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.

-`ao_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L122>`_
+`ao_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L1>`_
  array of the mono electronic hamiltonian on the AOs basis
  : sum of the kinetic and nuclear electronic potential

-`ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L1>`_
-  Overlap between atomic basis functions:
-  :math:`\int \chi_i(r) \chi_j(r) dr)`
-
-`ao_overlap_abs <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L65>`_
-  Overlap between absolute value of atomic basis functions:
-  :math:`\int |\chi_i(r)| |\chi_j(r)| dr)`
-
-`ao_overlap_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L2>`_
-  Overlap between atomic basis functions:
-  :math:`\int \chi_i(r) \chi_j(r) dr)`
-
-`ao_overlap_y <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L3>`_
-  Overlap between atomic basis functions:
-  :math:`\int \chi_i(r) \chi_j(r) dr)`
-
-`ao_overlap_z <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L4>`_
-  Overlap between atomic basis functions:
-  :math:`\int \chi_i(r) \chi_j(r) dr)`
-
 `check_ortho <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/check_orthonormality.irp.f#L1>`_
  Undocumented

@ -72,58 +52,63 @@ Documentation
  .br
  {\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle

-`ao_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_ao_ints.irp.f#L126>`_
+`ao_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_ao_ints.irp.f#L125>`_
  array of the priminitve basis kinetic integrals
  \langle \chi_i |\hat{T}| \chi_j \rangle

 `mo_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_mo_ints.irp.f#L1>`_
  Undocumented

-`mo_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/mo_mono_ints.irp.f#L35>`_
+`mo_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/mo_mono_ints.irp.f#L1>`_
  array of the mono electronic hamiltonian on the MOs basis
  : sum of the kinetic and nuclear electronic potential

-`mo_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/mo_mono_ints.irp.f#L1>`_
-  Undocumented
-
 `orthonormalize_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/orthonormalize.irp.f#L1>`_
  Undocumented

 `ao_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L1>`_
  interaction nuclear electron

-`give_polynom_mult_center_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L161>`_
+`ao_nucl_elec_integral_per_atom <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L67>`_
+  ao_nucl_elec_integral_per_atom(i,j,k) = -<AO(i)|1/|r-Rk|AO(j)>
+  where Rk is the geometry of the kth atom
+
+`give_polynom_mult_center_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L214>`_
  Undocumented

-`i_x1_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L289>`_
+`i_x1_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L342>`_
  Undocumented

-`i_x2_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L361>`_
+`i_x2_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L413>`_
  Undocumented

-`int_gaus_pol <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L432>`_
+`int_gaus_pol <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L484>`_
  Undocumented

-`nai_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L82>`_
+`nai_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L135>`_
  Undocumented

-`v_e_n <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L413>`_
+`v_e_n <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L465>`_
  Undocumented

-`v_phi <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L477>`_
+`v_phi <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L529>`_
  Undocumented

-`v_r <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L461>`_
+`v_r <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L513>`_
  Undocumented

-`v_theta <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L490>`_
+`v_theta <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L542>`_
  Undocumented

-`wallis <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L506>`_
+`wallis <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L558>`_
  Undocumented

 `mo_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_mo_ints.irp.f#L1>`_
-  Undocumented
+  interaction nuclear electron on the MO basis
+
+`mo_nucl_elec_integral_per_atom <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_mo_ints.irp.f#L30>`_
+  mo_nucl_elec_integral_per_atom(i,j,k) = -<MO(i)|1/|r-Rk|MO(j)>
+  where Rk is the geometry of the kth atom

 `save_ortho_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/save_ortho_mos.irp.f#L1>`_
  Undocumented
@ -173,7 +158,7 @@ Documentation
  array of the integrals of AO_i * y^2 AO_j
  array of the integrals of AO_i * z^2 AO_j

-`overlap_bourrin_deriv_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L359>`_
+`overlap_bourrin_deriv_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L365>`_
  Undocumented

 `overlap_bourrin_dipole <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L318>`_
@ -182,7 +167,7 @@ Documentation
 `overlap_bourrin_spread <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L265>`_
  Undocumented

-`overlap_bourrin_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L374>`_
+`overlap_bourrin_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L380>`_
  Undocumented

 `overlap_bourrin_x_abs <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L226>`_
--- a/src/NEEDED_MODULES
+++ b/src/NEEDED_MODULES
@ -1 +1 @@
-AOs Bielec_integrals Bitmask CID CID_SC2_selected CID_selected CIS CISD CISD_selected CISD_SC2_selected Dets Electrons Ezfio_files Full_CI Generators_full Hartree_Fock MOGuess MonoInts MOs MP2 Nuclei Output Selectors_full Utils Molden FCIdump Generators_CAS CAS_SD_selected DDCI_selected MRCC
+AOs Bielec_integrals Bitmask CID CID_SC2_selected CID_selected CIS CISD CISD_selected CISD_SC2_selected Dets Electrons Ezfio_files Full_CI Generators_full Hartree_Fock MOGuess MonoInts MOs MP2 Nuclei Output Selectors_full Utils Molden FCIdump Generators_CAS CAS_SD DDCI_selected MRCC
--- a/src/Nuclei/README.rst
+++ b/src/Nuclei/README.rst
@ -22,6 +22,9 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.

+`element_name <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L215>`_
+  Array of the name of element, sorted by nuclear charge (integer)
+
 `nucl_charge <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L23>`_
  Nuclear charges

@ -65,8 +68,11 @@ Documentation
 `nucl_num_aligned <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L2>`_
  Number of nuclei

-`nuclear_repulsion <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L171>`_
+`nuclear_repulsion <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L187>`_
  Nuclear repulsion energy

+`positive_charge_barycentre <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L171>`_
+  Centroid of the positive charges
+


--- a/src/Output/README.rst
+++ b/src/Output/README.rst
@ -39,5 +39,23 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.

+`output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L2>`_
+  Initial CPU and wall times when printing in the output files
+
+`output_wall_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L1>`_
+  Initial CPU and wall times when printing in the output files
+
+`write_bool <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L88>`_
+  Write an logical value in output
+
+`write_double <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L58>`_
+  Write a double precision value in output
+
+`write_int <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L73>`_
+  Write an integer value in output
+
+`write_time <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L42>`_
+  Write a time stamp in the output for chronological reconstruction
+


--- a/src/Selectors_full/README.rst
+++ b/src/Selectors_full/README.rst
@ -8,7 +8,18 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.

-`coef_hf_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L27>`_
+`coef_hf_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L28>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+`delta_e_per_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L33>`_
  energy of correlation per determinant respect to the Hartree Fock determinant
  .br
  for the all the double excitations in the selectors determinants
@ -28,7 +39,29 @@ Documentation
  .br
  n_double_selectors = number of double excitations in the selectors determinants

-`e_corr_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L28>`_
+`e_corr_double_only <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L34>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+`e_corr_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L31>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+`e_corr_second_order <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L35>`_
  energy of correlation per determinant respect to the Hartree Fock determinant
  .br
  for the all the double excitations in the selectors determinants
@ -48,6 +81,39 @@ Documentation
  .br
  n_double_selectors = number of double excitations in the selectors determinants

+`i_h_hf_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L32>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+`inv_selectors_coef_hf <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L29>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
+`inv_selectors_coef_hf_squared <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L30>`_
+  energy of correlation per determinant respect to the Hartree Fock determinant
+  .br
+  for the all the double excitations in the selectors determinants
+  .br
+  E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
+  .br
+  E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
+  .br
+  coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
+
 `n_double_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L5>`_
  degree of excitation respect to Hartree Fock for the wave function
  .br
@ -57,23 +123,40 @@ Documentation
  .br
  n_double_selectors = number of double excitations in the selectors determinants

-`n_det_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L26>`_
+`n_det_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L20>`_
  For Single reference wave functions, the number of selectors is 1 : the
  Hartree-Fock determinant

-`psi_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L48>`_
+`psi_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L42>`_
  Determinants on which we apply <i|H|psi> for perturbation.

-`psi_selectors_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L49>`_
+`psi_selectors_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L76>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
+
+`psi_selectors_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L43>`_
  Determinants on which we apply <i|H|psi> for perturbation.

-`psi_selectors_size <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L21>`_
+`psi_selectors_coef_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L77>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
+
+`psi_selectors_diag_h_mat <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L63>`_
+  Diagonal elements of the H matrix for each selectors
+
+`psi_selectors_next_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L78>`_
+  Determinants on which we apply <i|H|j>.
+  They are sorted by the 3 highest electrons in the alpha part,
+  then by the 3 highest electrons in the beta part to accelerate
+  the research of connected determinants.
+
+`psi_selectors_size <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L15>`_
  Undocumented

-`threshold_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L3>`_
-  Percentage of the norm of the state-averaged wave function to
-  consider for the selectors
-


 Needed Modules
@ -83,12 +166,13 @@ Needed Modules
 .. NEEDED_MODULES file.

 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
+* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
--- a/src/Utils/LinearAlgebra.irp.f
+++ b/src/Utils/LinearAlgebra.irp.f
@ -451,3 +451,6 @@ subroutine set_zero_extra_diag(i1,i2,matrix,lda,m)


 end
+
+
+
--- a/src/Utils/README.rst
+++ b/src/Utils/README.rst
@ -10,35 +10,104 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.

+`apply_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L168>`_
+  Apply the rotation found by find_rotation
+
+`find_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L149>`_
+  Find A.C = B
+
+`get_pseudo_inverse <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L95>`_
+  Find C = A^-1
+
+`lapack_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L247>`_
+  Diagonalize matrix H
+  .br
+  H is untouched between input and ouptut
+  .br
+  eigevalues(i) = ith lowest eigenvalue of the H matrix
+  .br
+  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
+  .br
+
+`lapack_diag_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L310>`_
+  Diagonalize matrix H
+  .br
+  H is untouched between input and ouptut
+  .br
+  eigevalues(i) = ith lowest eigenvalue of the H matrix
+  .br
+  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
+  .br
+
+`lapack_diagd <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L180>`_
+  Diagonalize matrix H
+  .br
+  H is untouched between input and ouptut
+  .br
+  eigevalues(i) = ith lowest eigenvalue of the H matrix
+  .br
+  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
+  .br
+
+`lapack_partial_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L376>`_
+  Diagonalize matrix H
+  .br
+  H is untouched between input and ouptut
+  .br
+  eigevalues(i) = ith lowest eigenvalue of the H matrix
+  .br
+  eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
+  .br
+
+`ortho_lowdin <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L1>`_
+  Compute C_new=C_old.S^-1/2 canonical orthogonalization.
+  .br
+  overlap : overlap matrix
+  .br
+  LDA : leftmost dimension of overlap array
+  .br
+  N : Overlap matrix is NxN (array is (LDA,N) )
+  .br
+  C : Coefficients of the vectors to orthogonalize. On exit,
+  orthogonal vectors
+  .br
+  LDC : leftmost dimension of C
+  .br
+  m : Coefficients matrix is MxN, ( array is (LDC,N) )
+  .br
+
+`set_zero_extra_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L433>`_
+  Undocumented
+
 `abort_all <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L1>`_
  If True, all the calculation is aborted

-`abort_here <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L10>`_
+`abort_here <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L11>`_
  If True, all the calculation is aborted

-`catch_signal <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L33>`_
+`catch_signal <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L30>`_
  What to do on Ctrl-C. If two Ctrl-C are pressed within 1 sec, the calculation if aborted.

-`trap_signals <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L18>`_
+`trap_signals <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L19>`_
  What to do when a signal is caught. Here, trap Ctrl-C and call the control_C subroutine.

-`add_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L243>`_
+`add_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L306>`_
  Add two polynomials
  D(t) =! D(t) +( B(t)+C(t))

-`add_poly_multiply <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L271>`_
+`add_poly_multiply <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L334>`_
  Add a polynomial multiplied by a constant
  D(t) =! D(t) +( cst * B(t))

-`f_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L345>`_
+`f_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L408>`_
  function that calculates the following integral
  \int_{\-infty}^{+\infty} x^n \exp(-p x^2) dx

-`gaussian_product <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L121>`_
+`gaussian_product <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L184>`_
  Gaussian product in 1D.
  e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}

-`gaussian_product_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L163>`_
+`gaussian_product_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L226>`_
  Gaussian product in 1D.
  e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}

@ -50,108 +119,148 @@ Documentation
  * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 )
  * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 )

+`give_explicit_poly_and_gaussian_double <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L122>`_
+  Transforms the product of
+  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3)
+  exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta) exp(-(r-Nucl_center)^2 gama
+  .br
+  into
+  fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 )
+  * [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 )
+  * [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 )
+
 `give_explicit_poly_and_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L1>`_
  Transform the product of
  (x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta)
  into
  fact_k  (x-x_P)^iorder(1)  (y-y_P)^iorder(2)  (z-z_P)^iorder(3) exp(-p(r-P)^2)

-`hermite <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L477>`_
+`hermite <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L540>`_
  Hermite polynomial

-`multiply_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L201>`_
+`multiply_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L264>`_
  Multiply two polynomials
  D(t) =! D(t) +( B(t)*C(t))

-`recentered_poly2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L300>`_
+`recentered_poly2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L363>`_
  Recenter two polynomials

-`rint <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L373>`_
+`rint <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L436>`_
  .. math::
  .br
  \int_0^1 dx \exp(-p x^2) x^n
  .br

-`rint1 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L533>`_
+`rint1 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L596>`_
  Standard version of rint

-`rint_large_n <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L502>`_
+`rint_large_n <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L565>`_
  Version of rint for large values of n

-`rint_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L421>`_
+`rint_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L484>`_
  Needed for the calculation of two-electron integrals.

+`overlap_a_b_c <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L35>`_
+  Undocumented
+
 `overlap_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L1>`_
  .. math::
  .br
  \sum_{-infty}^{+infty} (x-A_x)^ax (x-B_x)^bx exp(-alpha(x-A_x)^2) exp(-beta(x-B_X)^2) dx
  .br

-`overlap_gaussian_xyz <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L37>`_
+`overlap_gaussian_xyz <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L113>`_
  .. math::
  .br
  S_x = \int (x-A_x)^{a_x} exp(-\alpha(x-A_x)^2)  (x-B_x)^{b_x} exp(-beta(x-B_x)^2) dx \\
  S = S_x S_y S_z
  .br

-`overlap_x_abs <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L99>`_
+`overlap_x_abs <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L175>`_
  .. math                      ::
  .br
  \int_{-infty}^{+infty} (x-A_center)^(power_A) * (x-B_center)^power_B * exp(-alpha(x-A_center)^2) * exp(-beta(x-B_center)^2) dx
  .br

-`align_double <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L70>`_
+`progress_active <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L29>`_
+  Current status for displaying progress bars. Global variable.
+
+`progress_bar <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L27>`_
+  Current status for displaying progress bars. Global variable.
+
+`progress_timeout <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L28>`_
+  Current status for displaying progress bars. Global variable.
+
+`progress_title <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L31>`_
+  Current status for displaying progress bars. Global variable.
+
+`progress_value <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L30>`_
+  Current status for displaying progress bars. Global variable.
+
+`run_progress <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L45>`_
+  Display a progress bar with documentation of what is happening
+
+`start_progress <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L1>`_
+  Starts the progress bar
+
+`stop_progress <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L19>`_
+  Stop the progress bar
+
+`align_double <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L48>`_
  Compute 1st dimension such that it is aligned for vectorization.

-`all_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L1>`_
-  Dummy provider to provide all utils
-
-`approx_dble <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L299>`_
+`approx_dble <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L341>`_
  Undocumented

-`binom <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L52>`_
+`binom <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L31>`_
  Binomial coefficients

-`binom_func <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L21>`_
+`binom_func <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L1>`_
  .. math                       ::
  .br
  \frac{i!}{j!(i-j)!}
  .br

-`binom_transp <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L53>`_
+`binom_transp <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L32>`_
  Binomial coefficients

-`dble_fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L129>`_
+`dble_fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L137>`_
  n!!

-`fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L85>`_
+`dble_logfact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L171>`_
+  n!!
+
+`fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L63>`_
  n!

-`fact_inv <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L117>`_
+`fact_inv <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L125>`_
  1/n!

-`inv_int <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L176>`_
+`inv_int <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L218>`_
  1/i

-`normalize <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L275>`_
+`logfact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L93>`_
+  n!
+
+`normalize <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L317>`_
  Normalizes vector u
  u is expected to be aligned in memory.

-`nproc <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L202>`_
+`nproc <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L244>`_
  Number of current OpenMP threads

-`u_dot_u <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L244>`_
+`u_dot_u <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L286>`_
  Compute <u|u>

-`u_dot_v <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L218>`_
+`u_dot_v <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L260>`_
  Compute <u|v>

-`wall_time <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L187>`_
+`wall_time <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L229>`_
  The equivalent of cpu_time, but for the wall time.

-`write_git_log <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L162>`_
+`write_git_log <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L204>`_
  Write the last git commit in file iunit.



- 
+
				`@ -451,3 +451,6 @@ subroutine set_zero_extra_diag(i1,i2,matrix,lda,m)`


				`end`