A lot of cleaning

.gitignore

@@ -8,3 +8,4 @@ bin/
 lib/
 config/qp_create_ninja.pickle
 src/*/.gitignore
+ezfio_interface.irp.f

ocaml/qp_export.ml

@@ -0,0 +1,176 @@
+open Core
+open Qptypes
+
+let get_data () =
+  let mos = 
+    Input.Mo_basis.read ()
+  in
+  let molecule =
+    let e = 
+      match Input.Electrons.read () with
+      | Some x -> x
+      | None -> failwith "No electrons"
+    in
+    { Molecule.nuclei =
+        begin
+          match Input.Nuclei_by_hand.read () with
+          | None -> failwith "No nuclei"
+          | Some l -> Input.Nuclei_by_hand.to_atom_list l
+        end ;
+      Molecule.elec_alpha = e.Input.Electrons.elec_alpha_num ;
+      Molecule.elec_beta  = e.Input.Electrons.elec_beta_num  ;
+    }
+  in
+  let charge = 
+    Molecule.get_charge molecule
+    |> Charge.to_int
+  and mult = 
+    Molecule.get_multiplicity molecule
+    |> Multiplicity.to_int
+  in 
+  let hf =
+    if mult = 0 then "RHF" else "ROHF"
+  in
+  let guess = 
+    if mos = None then `Huckel else `Read
+  in
+  (mos, molecule, charge, mult, hf, guess)
+
+
+
+
+let run_g09 () =
+  let (mos, molecule, charge, mult, hf, guess) =
+    get_data ()
+  in
+  let guess = 
+    match guess with
+    | `Read -> "cards"
+    | `Huckel -> "huckel"
+  in
+  let result = [
+    Printf.sprintf "# %s/Gen guess=%s" hf guess;
+    "" ;
+    Molecule.name molecule ;
+    "" ;
+    Printf.sprintf "%d %d" charge mult ;
+    Printf.sprintf "%s" (
+      match String.split ~on:'\n' @@ Molecule.to_xyz molecule  with
+      | _ :: _ :: rest -> String.concat ~sep:"\n" rest
+      | _ -> assert false
+    );
+    "";
+    begin
+      match Input.Ao_basis.read () with
+      | Some x -> Input.Ao_basis.to_basis x
+      | None -> failwith "No basis"
+    end 
+    |> Basis.to_string ~fmt:Gto.Gaussian ~ele_array:(List.map ~f:(fun x -> x.Atom.element)
+                                                       molecule.Molecule.nuclei |> Array.of_list) ;
+    "";
+    begin
+      match mos with
+      | None -> ""
+      | Some mos' -> 
+        begin
+          Printf.sprintf "(E20.12)\n%s\n    0" 
+            ( 
+              Array.map mos'.Input.Mo_basis.mo_coef ~f:(fun x -> 
+                  Array.map x ~f:(fun y -> Printf.sprintf "%20.12E" (MO_coef.to_float y))
+                  |> Array.to_list
+                  |> String.concat ~sep:"\n")
+              |> Array.mapi ~f:(fun i -> Printf.sprintf "%5d\n%s" (i+1))
+              |> Array.to_list
+              |> String.concat ~sep:"\n"
+            )
+        end
+    end;
+    "" ; "" ;
+    "" ; "" ;
+  ]
+  in
+  List.iter ~f:(fun x -> print_endline x) result
+
+
+
+
+let run_gamess () =
+  failwith "Not yet implemented"
+(* TODO
+  let (mos, molecule, charge, mult, hf, guess) =
+    get_data ()
+  in
+  let guess = 
+    match guess with
+    | `Read -> "MOREAD"
+    | `Huckel -> "HUCKEL"
+  in
+  and coord  =
+    Printf.sprintf "%s" (
+      match String.split ~on:'\n' @@ Molecule.to_xyz molecule  with
+      | _ :: _ :: rest -> String.concat ~sep:"\n" rest
+      | _ -> assert false
+    );
+  and basis  =
+    begin
+      match !read_data.basis with
+      | None |> failwith "No basis set defined in command line"
+      | Some b |> b
+    end
+  and typ    = !read_data.typ
+  and vecfile =
+    begin
+      match !read_data.filename with
+      | None |> ""
+      | Some filename |> filename
+    end
+  and nstate = !read_data.nstate
+  and guess  = !read_data.guess
+  in
+
+  let system =
+    Gamess.{ mult ; charge ; basis ; coord }
+  in
+  Gamess.create_input ~vecfile ~system ~guess ~nstate typ
+  |> print_endline 
+*)
+
+
+let spec =
+  let open Command.Spec in
+  empty
+  +> flag "-gamess" no_arg ~doc:"GAMESS(US) input"
+  +> flag "-g09" no_arg ~doc:"Gaussian 09 input"
+  +> anon ("ezfio_file" %: string)
+
+let command = 
+  Command.basic_spec
+  ~summary: "Quantum Package command"
+  ~readme:(fun () -> 
+      "
+Exports the computed data for other programs.
+      ")
+  spec
+  (fun gamess g09 ezfio_file () -> 
+    let count_flags l =
+        List.fold_left ~f:(fun a x -> 
+            if x then a+1 else a) ~init:0 l
+    in
+    let () =
+      match count_flags [ g09 ; gamess ] with
+      | 0  -> raise (Invalid_argument "No file format specified")
+      | 1  -> ()
+      | _  -> raise (Invalid_argument "Too many file formats specified")
+    in
+    Ezfio.set_file ezfio_file;
+    if g09 then
+      run_g09 ()
+    else if gamess then
+      run_gamess ()
+  )
+
+    
+let () = 
+  Command.run command;
+  exit 0
+   

plugins/FCIdump/NEEDED_CHILDREN_MODULES

@@ -1 +0,0 @@
-Determinants DavidsonUndressed 

plugins/FCIdump/README.rst

@@ -1,44 +0,0 @@
-==============
-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
-.. by the `update_README.py` script.
-
-`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
-.. by the `update_README.py` script.
-
-.. image:: tree_dependency.png
-
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-
-Needed Modules
-==============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-.. image:: tree_dependency.png
-
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-
-Documentation
-=============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-`fcidump <http://github.com/LCPQ/quantum_package/tree/master/plugins/FCIdump/fcidump.irp.f#L1>`_
-  Undocumented
-

plugins/Molden/.gitignore

@@ -1,19 +0,0 @@
-# Automatically created by $QP_ROOT/scripts/module/module_handler.py 
-.ninja_deps
-.ninja_log
-AO_Basis
-Electrons
-Ezfio_files
-IRPF90_man
-IRPF90_temp
-MO_Basis
-MPI
-Makefile
-Makefile.depend
-Nuclei
-Utils
-ezfio_interface.irp.f
-irpf90.make
-irpf90_entities
-print_mo
-tags

plugins/Molden/NEEDED_CHILDREN_MODULES

@@ -1 +0,0 @@
-MO_Basis Utils 

plugins/Molden/README.rst

@@ -1,76 +0,0 @@
-=============
-Molden Module
-=============
-
-Documentation
-=============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-`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
-.. by the `update_README.py` script.
-
-.. image:: tree_dependency.png
-
-* `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-
-Needed Modules
-==============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-.. image:: tree_dependency.png
-
-* `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-
-Documentation
-=============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-`print_mos <http://github.com/LCPQ/quantum_package/tree/master/plugins/Molden/print_mo.irp.f#L1>`_
-  Undocumented
-
-
-`write_ao_basis <http://github.com/LCPQ/quantum_package/tree/master/plugins/Molden/print_mo.irp.f#L63>`_
-  Undocumented
-
-
-`write_geometry <http://github.com/LCPQ/quantum_package/tree/master/plugins/Molden/print_mo.irp.f#L45>`_
-  Undocumented
-
-
-`write_intro_gamess <http://github.com/LCPQ/quantum_package/tree/master/plugins/Molden/print_mo.irp.f#L26>`_
-  Undocumented
-
-
-`write_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/plugins/Molden/print_mo.irp.f#L112>`_
-  Undocumented
-

plugins/eginer/Determinant_tools/README.rst

@@ -0,0 +1,12 @@
+=================
+Determinant_tools
+=================
+
+Needed Modules
+==============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+Documentation
+=============
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.

plugins/eginer/multistate/NEED

@@ -0,0 +1 @@
+DavidsonUndressed

plugins/eginer/multistate/README.rst

@@ -1,6 +1,6 @@
-=========
+==========
-dress_zmq
+multistate
-=========
+==========
 
 Needed Modules
 ==============

plugins/eginer/multistate/multistate.main.irp.f

@@ -0,0 +1,38 @@
+program multistate
+  implicit none
+  BEGIN_DOC
+! TODO
+  END_DOC
+  print *, '  _/                              '
+  print *, ' -:\_?,     _Jm####La             '
+  print *, 'J"(:" >  _]#AZ#Z#UUZ##,           '
+  print *, '_,::./   %(|i%12XmX1*1XL      _?, '
+  print *, '  \..\ _\(vmWQwodY+ia%lnL  _",/ ( '
+  print *, '   .:< ]J=mQD?WXn<uQWmmvd, -.-:=!'
+  print *, '   "{Z jC]QW|=3Zv)Bi3BmXv3  =   _7'
+  print *, '    ]h[Z6)WQ;)jZs]C;|$BZv+, : ./  '
+  print *, '    -#sJX%$Wmm#ev]hinW#Xi:` c ;   '
+  print *, '     #X#X23###1}vI$WWmX1>|,)nr"   '
+  print *, '     4XZ#Xov1v}=)vnXAX1nnv;1n"    '
+  print *, '     ]XX#ZXoovvvivnnnlvvo2*i7     '
+  print *, '     "23Z#1S2oo2XXSnnnoSo2>v"     '
+  print *, '      miX#L -~`""!!1}oSoe|i7      '
+  print *, '      4cn#m,        v221=|v[      '
+  print *, '      ]hI3Zma,;..__wXSe=+vo       '
+  print *, '      ]Zov*XSUXXZXZXSe||vo2       '
+  print *, '      ]Z#><iiii|i||||==vn2(       '
+  print *, '      ]Z#i<ii||+|=||=:{no2[       '
+  print *, '      ]ZUsiiiiivi|=||=vo22[       '
+  print *, '      ]XZvlliiIi|i=|+|vooo        '
+  print *, '      =v1llli||||=|||||lii(       '
+  print *, '      ]iillii||||||||=>=|<        '
+  print *, '      -ziiiii||||||+||==+>        '
+  print *, '       -%|+++||=|=+|=|==/         '
+  print *, '        -a>====+|====-:-          '
+  print *, '          "~,- --   /-            '
+  print *, '            -.     )>             '
+  print *, '           .~      +-             '
+  print *, '           . .... : .             '
+  print *, '            -------~              '
+  print *, ''
+end

scripts/compilation/qp_create_ninja.py

@@ -81,6 +81,7 @@ def real_join(*args):
 #  _
 # |_ ._           _. ._ o  _. |_  |  _   _
 # |_ | | \/   \/ (_| |  | (_| |_) | (/_ _>
+#
 def ninja_create_env_variable(pwd_config_file):
     """
     Return some ninja variable with the env variable expanded
@@ -335,6 +336,7 @@ def ninja_symlink_build(path_module, l_symlink):
 #    _  o _|_ o  _  ._   _  ._ _
 # o (_| |  |_ | (_| | | (_) | (/_
 #    _|          _|
+#
 def ninja_gitignore_rule():
     """
     Return the command to create the gitignore
@@ -368,6 +370,7 @@ def ninja_gitignore_build(path_module, d_binaries, l_symlink):
 # o ._ ._ _|_ (_| / \   ._ _   _. |   _
 # | |  |_) |    | \_/ o | | | (_| |< (/_
 #      |
+#
 def get_l_file_for_module(path_module):
     '''
     return the list of irp.f in a module
@@ -514,41 +517,6 @@ def ninja_irpf90_make_build(path_module, l_needed_molule, d_irp):
     return l_string
 
 
-def ninja_readme_rule():
-    """
-    Rule for creation the readme.
-    For not dealted the readme when ninja -t clean and the generator option
-    """
-    l_string = ["rule build_readme",
-                "   command = qp_update_readme.py $module_abs --root_module $module_root",
-                "   description = update_README $module_rel",
-                "   generator = 1", ""]
-
-    return l_string
-
-
-def ninja_readme_build(path_module, d_irp, dict_root_path):
-    """
-    Rule for creation the readme
-    """
-    path_readme = join(path_module.abs, "README.rst")
-    root_module = dict_root_path[module]
-
-    tags = join(root_module.abs, "tags")
-    str_depend = " ".join(d_irp[path_module]["l_depend"])
-
-    tree = join(path_module.abs, "tree_dependency.png")
-
-    l_string = ["build {0}: build_readme {1} {2} {3}".format(path_readme,
-                                                             tags,
-                                                             str_depend,
-                                                             tree),
-                "   module_root = {0}".format(root_module.abs),
-                "   module_abs = {0}".format(path_module.abs),
-                "   module_rel = {0}".format(path_module.rel), ""]
-
-    return l_string
-
 
 #  _
 # |_) o ._   _. ._
@@ -685,47 +653,10 @@ def ninja_module_build(path_module, d_binaries):
     l_abs_bin = [binary.abs for binary in d_binaries[path_module]]
 
     path_readme = os.path.join(path_module.abs, "README.rst")
-    path_png = os.path.join(path_module.abs, "tree_dependency.png")
 
-    l_string = ["build module_{0}: phony {1} {2} {3}".format(path_module.rel,
+    l_string = ["build module_{0}: phony {1} {2}".format(path_module.rel,
                                                              " ".join(l_abs_bin),
-                                                             path_readme,
+                                                             path_readme), ""]
-                                                             path_png), ""]
-
-    return l_string
-
-
-# ___
-#  | ._ _   _     _|  _  ._   _  ._   _|  _  ._   _ o  _   _
-#  | | (/_ (/_   (_| (/_ |_) (/_ | | (_| (/_ | | (_ | (/_ _>
-#                        |
-def ninja_dot_tree_rule():
-    """
-    Rule for creating the binaries
-    """
-    # ~#~#~ #
-    # c m d #
-    # ~#~#~ #
-
-    l_cmd = ["cd $module_abs", "module_handler.py create_png"]
-
-    l_string = [
-        "rule build_dot_tree", "   command = {0}".format(" ; ".join(l_cmd)),
-        "   generator = 1",
-        "   description = Generating Png representation of the Tree Dependencies of $module_rel",
-        ""
-    ]
-
-    return l_string
-
-
-def ninja_dot_tree_build(path_module, l_module):
-
-    path_tree = join(path_module.abs, "tree_dependency.png")
-    l_dep = [join(path.abs, "NEEDED_CHILDREN_MODULES") for path in l_module]
-    l_string = ["build {0}: build_dot_tree {1}".format(path_tree, " ".join(l_dep)),
-                "   module_abs = {0}".format(path_module.abs),
-                "   module_rel = {0}".format(path_module.rel), ""]
 
     return l_string
 
@@ -847,7 +778,6 @@ if __name__ == "__main__":
     l_string += ninja_symlink_rule()
 
     l_string += ninja_irpf90_make_rule()
-    l_string += ninja_readme_rule()
     l_string += ninja_gitignore_rule()
 
     l_string += ninja_binaries_rule()
@@ -855,8 +785,6 @@ if __name__ == "__main__":
     l_string += ninja_ezfio_config_rule()
     l_string += ninja_ezfio_rule()
 
-    l_string += ninja_dot_tree_rule()
-
     #  _
     # |_)     o |  _|    _   _  ._   _  ._ _. |
     # |_) |_| | | (_|   (_| (/_ | | (/_ | (_| |
@@ -892,22 +820,9 @@ if __name__ == "__main__":
     # M o d u l e _ t o _ i r p #
     # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
 
-    if arguments["--production"]:
+    d_binaries = get_dict_binaries(l_all_module, mode="development")
+    l_module = d_binaries.keys()
 
-        d_binaries = get_dict_binaries(l_all_module, mode="production")
-        l_module = d_binaries.keys()
-
-    elif arguments["--development"]:
-
-        d_binaries = get_dict_binaries(l_all_module, mode="development")
-        l_module = d_binaries.keys()
-
-        for module in l_all_module:
-            # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
-            # d o t _ t r e e  & r e a d  m e #
-            # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
-            l_string += ninja_dot_tree_build(module, l_all_module)
-            l_string += ninja_readme_build(module, d_irp, dict_root_path)
 
     # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
     # C h e c k _ c o h e r e n c y #
@@ -936,6 +851,9 @@ if __name__ == "__main__":
 
     for module_to_compile in l_module:
     
+        if module_to_compile.rel == "dummy":
+                continue
+
         # ~#~#~#~#~#~#~#~ #
         #  S y m l i n k  #
         # ~#~#~#~#~#~#~#~ #
@@ -953,14 +871,13 @@ if __name__ == "__main__":
         l_string += ninja_binaries_build(module_to_compile, l_children,
                                          d_binaries)
 
-        if arguments["--development"]:
 
-            l_string += ninja_module_build(module_to_compile, d_binaries)
+        l_string += ninja_module_build(module_to_compile, d_binaries)
 
-            l_string += ninja_gitignore_build(module_to_compile, d_binaries,
+        l_string += ninja_gitignore_build(module_to_compile, d_binaries,
-                                              l_symlink)
+                                            l_symlink)
 
-            save_subninja_file(module_to_compile)
+        save_subninja_file(module_to_compile)
 
     # ~#~#~#~#~ #
     # S a v e s #

scripts/ezfio_interface/ezfio_generate_provider.py

@@ -26,6 +26,7 @@ BEGIN_PROVIDER [ %(type)s, %(name)s %(size)s ]
     %(test_null_size)s
     call ezfio_has_%(ezfio_dir)s_%(ezfio_name)s(has)
     if (has) then
+      write(6,'(A)') '.. >>>>> [ IO READ: %(name)s ] <<<<< ..'
       call ezfio_get_%(ezfio_dir)s_%(ezfio_name)s(%(name)s)
     else
       print *, '%(ezfio_dir)s/%(ezfio_name)s not found in EZFIO file'
@@ -89,9 +90,6 @@ END_PROVIDER
         name = self.name
         l_write = ["",
                    "  call write_time(%(output)s)",
-                   "  if (mpi_master) then",
-                   "    write(%(output)s, *) 'Read  %(name)s'",
-                   "  endif", 
                    ""]
 
         self.write = "\n".join(l_write) % locals()

scripts/module/module_handler.py

@@ -10,11 +10,10 @@ Usage:
     module_handler.py create_git_ignore     [<module_name>...]
 
 Options:
-    print_descendant         Print the genealogy of the NEEDED_CHILDREN_MODULES
+    print_descendant        Print the genealogy of the needed modules
-                                 aka (children, subchildren, etc)
     create_png              Create a png of the file
-    NEEDED_CHILDREN_MODULES The path of NEEDED_CHILDREN_MODULES
+    NEED                    The path of NEED file.
-                                by default try to open the file in the current path
+                            by default try to open the file in the current path
 """
 import os
 import sys
@@ -30,13 +29,11 @@ except ImportError:
 
 
 def is_module(path_module_rel):
-    return os.path.isfile(os.path.join(QP_SRC, path_module_rel,
+    return os.path.isfile(os.path.join(QP_SRC, path_module_rel, "NEED"))
-                                       "NEEDED_CHILDREN_MODULES"))
 
 
 def is_plugin(path_module_rel):
-    return os.path.isfile(os.path.join(QP_PLUGINS, path_module_rel,
+    return os.path.isfile(os.path.join(QP_PLUGINS, path_module_rel, "NEED"))
-                                       "NEEDED_CHILDREN_MODULES"))
 
 
 def is_exe(fpath):
@@ -44,7 +41,7 @@ def is_exe(fpath):
 
 
 def get_dict_child(l_root_abs=None):
-    """Loop over MODULE in  QP_ROOT/src, open all the NEEDED_CHILDREN_MODULES
+    """Loop over MODULE in  QP_ROOT/src, open all the NEED
     and create a dict[MODULE] = [sub module needed, ...]
     """
     d_ref = dict()
@@ -57,7 +54,7 @@ def get_dict_child(l_root_abs=None):
 
             module_abs = os.path.join(root_abs, module_rel)
             try:
-                path_file = os.path.join(module_abs, "NEEDED_CHILDREN_MODULES")
+                path_file = os.path.join(module_abs, "NEED")
 
                 with open(path_file, "r") as f:
                     l_children = f.read().split()
@@ -131,7 +128,7 @@ class ModuleHandler():
                 d[module_name] = get_l_module_descendant(d_child,
                                                          d_child[module_name])
             except KeyError:
-                print "Check NEEDED_CHILDREN_MODULES for {0}".format(
+                print "Check NEED for {0}".format(
                     module_name)
                 sys.exit(1)
 
@@ -238,7 +235,7 @@ if __name__ == '__main__':
     for module in l_module:
         if not is_module(module):
             print "{0} is not a valide module. Abort".format(module)
-            print "No NEEDED_CHILDREN_MODULES in it"
+            print "No NEED in it"
             sys.exit(1)
 
     m = ModuleHandler()

scripts/module/qp_module.py

@@ -20,7 +20,6 @@ try:
     from docopt import docopt
     from module_handler import ModuleHandler, get_dict_child
     from module_handler import get_l_module_descendant
-    from qp_update_readme import D_KEY
     from qp_path import QP_SRC, QP_PLUGINS, QP_ROOT
 except ImportError:
     print "Please check if you have sourced the ${QP_ROOT}/quantum_package.rc"
@@ -40,7 +39,7 @@ def save_new_module(path, l_child):
         print "The module ({0}) already exists...".format(path)
         sys.exit(1)
 
-    with open(os.path.join(path, "NEEDED_CHILDREN_MODULES"), "w") as f:
+    with open(os.path.join(path, "NEED"), "w") as f:
         f.write(" ".join(l_child))
         f.write("\n")
 
@@ -54,49 +53,15 @@ def save_new_module(path, l_child):
 
     with open(os.path.join(path, "README.rst"), "w") as f:
         f.write(header + "\n")
-        f.write(D_KEY["needed_module"])
-        f.write(D_KEY["documentation"])
 
-    with open(os.path.join(path, "%s.main.irp.f"%(module_name) ), "w") as f:
+    with open(os.path.join(path, "%s.irp.f"%(module_name) ), "w") as f:
         f.write("program {0}".format(module_name) )
         f.write("""
   implicit none
   BEGIN_DOC
 ! TODO
   END_DOC
-  print *, '  _/                              '
+  print *, 'Hello world'
-  print *, ' -:\_?,     _Jm####La             '
-  print *, 'J"(:" >  _]#AZ#Z#UUZ##,           '
-  print *, '_,::./   %(|i%12XmX1*1XL      _?, '
-  print *, '  \..\ _\(vmWQwodY+ia%lnL  _",/ ( '
-  print *, '   .:< ]J=mQD?WXn<uQWmmvd, -.-:=!\'
-  print *, '   "{Z jC]QW|=3Zv)Bi3BmXv3  =   _7'
-  print *, '    ]h[Z6)WQ;)jZs]C;|$BZv+, : ./  '
-  print *, '    -#sJX%$Wmm#ev]hinW#Xi:` c ;   '
-  print *, '     #X#X23###1}vI$WWmX1>|,)nr"   '
-  print *, '     4XZ#Xov1v}=)vnXAX1nnv;1n"    '
-  print *, '     ]XX#ZXoovvvivnnnlvvo2*i7     '
-  print *, '     "23Z#1S2oo2XXSnnnoSo2>v"     '
-  print *, '      miX#L -~`""!!1}oSoe|i7      '
-  print *, '      4cn#m,        v221=|v[      '
-  print *, '      ]hI3Zma,;..__wXSe=+vo       '
-  print *, '      ]Zov*XSUXXZXZXSe||vo2       '
-  print *, '      ]Z#><iiii|i||||==vn2(       '
-  print *, '      ]Z#i<ii||+|=||=:{no2[       '
-  print *, '      ]ZUsiiiiivi|=||=vo22[       '
-  print *, '      ]XZvlliiIi|i=|+|vooo        '
-  print *, '      =v1llli||||=|||||lii(       '
-  print *, '      ]iillii||||||||=>=|<        '
-  print *, '      -ziiiii||||||+||==+>        '
-  print *, '       -%|+++||=|=+|=|==/         '
-  print *, '        -a>====+|====-:-          '
-  print *, '          "~,- --   /-            '
-  print *, '            -.     )>             '
-  print *, '           .~      +-             '
-  print *, '           . .... : .             '
-  print *, '            -------~              '
-  print *, ''
-end
 """)
 
 def main(arguments):

src/AO_Basis/README.rst

@@ -30,231 +30,3 @@ Assumptions
 * The AO coefficients in the EZFIO files are not necessarily normalized and are normalized after reading
 
 
-Needed Modules
-==============
-
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-.. image:: tree_dependency.png
-
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-
-Needed Modules
-==============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-.. image:: tree_dependency.png
-
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-
-Documentation
-=============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-`ao_cartesian <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ezfio_interface.irp.f#L65>`_
-  If true, use AOs in Cartesian coordinates (6d,10f,...)
-
-
-`ao_coef <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ezfio_interface.irp.f#L25>`_
-  Primitive coefficients, read from input. Those should not be used directly, as the MOs are expressed on the basis of **normalized** AOs.
-
-
-`ao_coef_normalization_factor <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L23>`_
-  Coefficients including the AO normalization
-
-
-`ao_coef_normalization_libint_factor <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L59>`_
-  Coefficients including the AO normalization
-
-
-`ao_coef_normalized <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L22>`_
-  Coefficients including the AO normalization
-
-
-`ao_coef_normalized_ordered <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L92>`_
-  Sorted primitives to accelerate 4 index MO transformation
-
-
-`ao_coef_normalized_ordered_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L118>`_
-  Transposed ao_coef_normalized_ordered
-
-
-`ao_expo <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ezfio_interface.irp.f#L143>`_
-  Exponents for each primitive of each AO
-
-
-`ao_expo_ordered <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L93>`_
-  Sorted primitives to accelerate 4 index MO transformation
-
-
-`ao_expo_ordered_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L132>`_
-  Transposed ao_expo_ordered
-
-
-`ao_l <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L146>`_
-  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/AO_Basis/aos.irp.f#L148>`_
-  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/AO_Basis/aos.irp.f#L282>`_
-  Undocumented
-
-
-`ao_l_max <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L147>`_
-  ao_l = l value of the AO: a+b+c in x^a y^b z^c
-
-
-`ao_md5 <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ezfio_interface.irp.f#L6>`_
-  MD5 key, specific of the AO basis
-
-
-`ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ezfio_interface.irp.f#L123>`_
-  Index of the nucleus on which the AO is centered
-
-
-`ao_num <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ezfio_interface.irp.f#L84>`_
-  number of AOs
-
-
-`ao_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L1>`_
-  Number of atomic orbitals align
-
-
-`ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/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/AO_Basis/ao_overlap.irp.f#L75>`_
-  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/AO_Basis/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/AO_Basis/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/AO_Basis/ao_overlap.irp.f#L4>`_
-  Overlap between atomic basis functions:
-  :math:`\int \chi_i(r) \chi_j(r) dr)`
-
-
-`ao_power <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ezfio_interface.irp.f#L45>`_
-  Powers of x, y and z for each AO
-
-
-`ao_power_index <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L171>`_
-  Unique index given to a triplet of powers:
-  .br
-  1/2 (l-n_x)*(l-n_x+1) + n_z + 1
-
-
-`ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ezfio_interface.irp.f#L103>`_
-  Number of primitives per atomic orbital
-
-
-`ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L12>`_
-  Undocumented
-
-
-`ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L161>`_
-  Number of primitives per atomic orbital aligned
-
-
-`ao_value <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos_value.irp.f#L1>`_
-  return the value of the ith ao at point r
-
-
-`cart_to_sphe_0 <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/spherical_to_cartesian.irp.f#L7>`_
-  Spherical -> Cartesian Transformation matrix for l=0
-
-
-`cart_to_sphe_1 <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/spherical_to_cartesian.irp.f#L18>`_
-  Spherical -> Cartesian Transformation matrix for l=1
-
-
-`cart_to_sphe_2 <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/spherical_to_cartesian.irp.f#L31>`_
-  Spherical -> Cartesian Transformation matrix for l=2
-
-
-`cart_to_sphe_3 <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/spherical_to_cartesian.irp.f#L49>`_
-  Spherical -> Cartesian Transformation matrix for l=3
-
-
-`cart_to_sphe_4 <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/spherical_to_cartesian.irp.f#L75>`_
-  Spherical -> Cartesian Transformation matrix for l=4
-
-
-`cart_to_sphe_5 <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/spherical_to_cartesian.irp.f#L113>`_
-  Spherical -> Cartesian Transformation matrix for l=5
-
-
-`cart_to_sphe_6 <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/spherical_to_cartesian.irp.f#L169>`_
-  Spherical -> Cartesian Transformation matrix for l=6
-
-
-`cart_to_sphe_7 <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/spherical_to_cartesian.irp.f#L249>`_
-  Spherical -> Cartesian Transformation matrix for l=7
-
-
-`cart_to_sphe_8 <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/spherical_to_cartesian.irp.f#L361>`_
-  Spherical -> Cartesian Transformation matrix for l=8
-
-
-`cart_to_sphe_9 <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/spherical_to_cartesian.irp.f#L512>`_
-  Spherical -> Cartesian Transformation matrix for l=9
-
-
-`give_all_aos_at_r <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos_value.irp.f#L34>`_
-  gives the values of aos at a given point r
-
-
-`l_to_charater <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L185>`_
-  character corresponding to the "L" value of an AO orbital
-
-
-`n_aos_max <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L202>`_
-  Number of AOs per atom
-
-
-`n_pt_max_i_x <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/dimensions_integrals.irp.f#L2>`_
-  Undocumented
-
-
-`n_pt_max_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/dimensions_integrals.irp.f#L1>`_
-  Undocumented
-
-
-`nucl_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L215>`_
-  List of AOs attached on each atom
-
-
-`nucl_list_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L233>`_
-  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/AO_Basis/aos.irp.f#L201>`_
-  Number of AOs per atom
-
-
-`nucl_num_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L234>`_
-  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
-

src/AO_one_e_integrals/README.rst

@@ -4,11 +4,3 @@ AO_one_e_integrals
 
 All the one-electron integrals in AO basis are here.
 
-Needed Modules
-==============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-Documentation
-=============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.

src/Bitmask/README.rst

@@ -33,461 +33,3 @@ Assumptions
 
 
 
-
-Needed Modules
-==============
-
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-.. image:: tree_dependency.png
-
-* `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
-
-Needed Modules
-==============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-.. image:: tree_dependency.png
-
-* `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
-
-Documentation
-=============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-`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#L65>`_
-  Transform a bit string to a string for printing
-
-
-`cas_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L307>`_
-  Bitmasks for CAS reference determinants. (N_int, alpha/beta, CAS reference)
-
-
-`closed_shell_ref_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L631>`_
-  Undocumented
-
-
-`core_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L558>`_
-  Core + deleted orbitals bitmask
-
-
-`core_inact_act_bitmask_4 <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L46>`_
-  Undocumented
-
-
-`core_inact_virt_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L526>`_
-  Reunion of the inactive and virtual bitmasks
-
-
-`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.
-
-
-`debug_spindet <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L155>`_
-  Subroutine to print the content of a determinant in '+-' notation and
-  hexadecimal representation.
-
-
-`full_ijkl_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L18>`_
-  Bitmask to include all possible MOs
-
-
-`full_ijkl_bitmask_4 <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L35>`_
-  Undocumented
-
-
-`generators_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L220>`_
-  Bitmasks for generator determinants.
-  (N_int, alpha/beta, hole/particle, generator).
-  .br
-  3rd index is :
-  .br
-  * 1 : hole     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
-  .br
-  * 5 : hole     for 2nd exc of double
-  .br
-  * 6 : particle for 2nd exc of double
-  .br
-
-
-`generators_bitmask_restart <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L161>`_
-  Bitmasks for generator determinants.
-  (N_int, alpha/beta, hole/particle, generator).
-  .br
-  3rd index is :
-  .br
-  * 1 : hole     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
-  .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#L71>`_
-  Hartree Fock bit mask
-
-
-`i_bitmask_gen <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L575>`_
-  Current bitmask for the generators
-
-
-`inact_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L348>`_
-  inact_bitmask : Bitmask of the inactive orbitals which are supposed to be doubly excited
-  in post CAS methods
-  n_inact_orb   : Number of inactive orbitals
-  virt_bitmask  : Bitmaks of vritual orbitals which are supposed to be recieve electrons
-  in post CAS methods
-  n_virt_orb    : Number of virtual orbitals
-
-
-`inact_virt_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L525>`_
-  Reunion of the inactive and virtual bitmasks
-
-
-`index_holes_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/modify_bitmasks.irp.f#L260>`_
-  Index of the holes in the generators_bitmasks
-
-
-`index_particl_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/modify_bitmasks.irp.f#L271>`_
-  Index of the holes in the generators_bitmasks
-
-
-`initialize_bitmask_to_restart_ones <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/modify_bitmasks.irp.f#L3>`_
-  Initialization of the generators_bitmask to the restart bitmask
-
-
-`is_a_1h <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L499>`_
-  Undocumented
-
-
-`is_a_1h1p <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L466>`_
-  Undocumented
-
-
-`is_a_1h2p <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L477>`_
-  Undocumented
-
-
-`is_a_1p <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L510>`_
-  Undocumented
-
-
-`is_a_2h <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L532>`_
-  Undocumented
-
-
-`is_a_2h1p <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L488>`_
-  Undocumented
-
-
-`is_a_2p <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L521>`_
-  Undocumented
-
-
-`is_a_two_holes_two_particles <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L212>`_
-  logical function that returns True if the determinant 'key_in'
-  belongs to the 2h-2p excitation class of the DDCI space
-  this is calculated using the CAS_bitmask that defines the active
-  orbital space, the inact_bitmasl that defines the inactive oribital space
-  and the virt_bitmask that defines the virtual orbital space
-
-
-`is_i_in_virtual <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L543>`_
-  Undocumented
-
-
-`is_the_hole_in_det <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/find_hole.irp.f#L1>`_
-  Undocumented
-
-
-`is_the_particl_in_det <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/find_hole.irp.f#L29>`_
-  Undocumented
-
-
-`list_act <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L609>`_
-  list_act(i) = index of the ith active orbital
-  .br
-  list_act_reverse : reverse list of active orbitals
-  list_act_reverse(i) = 0 ::> not an active
-  list_act_reverse(i) = k ::> IS the kth active orbital
-
-
-`list_act_reverse <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L610>`_
-  list_act(i) = index of the ith active orbital
-  .br
-  list_act_reverse : reverse list of active orbitals
-  list_act_reverse(i) = 0 ::> not an active
-  list_act_reverse(i) = k ::> IS the kth active orbital
-
-
-`list_core <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L540>`_
-  List of the core orbitals that are never excited in post CAS method
-
-
-`list_core_inact <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L440>`_
-  Undocumented
-
-
-`list_core_inact_act <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L495>`_
-  Undocumented
-
-
-`list_core_inact_act_reverse <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L496>`_
-  Undocumented
-
-
-`list_core_inact_reverse <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L441>`_
-  Undocumented
-
-
-`list_core_reverse <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L541>`_
-  List of the core orbitals that are never excited in post CAS method
-
-
-`list_inact <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L399>`_
-  list_inact : List of the inactive orbitals which are supposed to be doubly excited
-  in post CAS methods
-  list_virt  : List of vritual orbitals which are supposed to be recieve electrons
-  in post CAS methods
-  list_inact_reverse : reverse list of inactive orbitals
-  list_inact_reverse(i) = 0 ::> not an inactive
-  list_inact_reverse(i) = k ::> IS the kth inactive
-  list_virt_reverse : reverse list of virtual orbitals
-  list_virt_reverse(i) = 0 ::> not an virtual
-  list_virt_reverse(i) = k ::> IS the kth virtual
-
-
-`list_inact_reverse <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L401>`_
-  list_inact : List of the inactive orbitals which are supposed to be doubly excited
-  in post CAS methods
-  list_virt  : List of vritual orbitals which are supposed to be recieve electrons
-  in post CAS methods
-  list_inact_reverse : reverse list of inactive orbitals
-  list_inact_reverse(i) = 0 ::> not an inactive
-  list_inact_reverse(i) = k ::> IS the kth inactive
-  list_virt_reverse : reverse list of virtual orbitals
-  list_virt_reverse(i) = 0 ::> not an virtual
-  list_virt_reverse(i) = k ::> IS the kth virtual
-
-
-`list_to_bitstring <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L29>`_
-  Returns the physical string "string(N_int,2)" from the array of
-  occupations "list(N_int*bit_kind_size,2)
-
-
-`list_virt <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L400>`_
-  list_inact : List of the inactive orbitals which are supposed to be doubly excited
-  in post CAS methods
-  list_virt  : List of vritual orbitals which are supposed to be recieve electrons
-  in post CAS methods
-  list_inact_reverse : reverse list of inactive orbitals
-  list_inact_reverse(i) = 0 ::> not an inactive
-  list_inact_reverse(i) = k ::> IS the kth inactive
-  list_virt_reverse : reverse list of virtual orbitals
-  list_virt_reverse(i) = 0 ::> not an virtual
-  list_virt_reverse(i) = k ::> IS the kth virtual
-
-
-`list_virt_reverse <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L402>`_
-  list_inact : List of the inactive orbitals which are supposed to be doubly excited
-  in post CAS methods
-  list_virt  : List of vritual orbitals which are supposed to be recieve electrons
-  in post CAS methods
-  list_inact_reverse : reverse list of inactive orbitals
-  list_inact_reverse(i) = 0 ::> not an inactive
-  list_inact_reverse(i) = k ::> IS the kth inactive
-  list_virt_reverse : reverse list of virtual orbitals
-  list_virt_reverse(i) = 0 ::> not an virtual
-  list_virt_reverse(i) = k ::> IS the kth virtual
-
-
-`modify_bitmasks_for_hole <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/modify_bitmasks.irp.f#L25>`_
-  modify the generators_bitmask in order that one can only excite
-  the electrons occupying i_hole
-
-
-`modify_bitmasks_for_hole_in_out <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/modify_bitmasks.irp.f#L60>`_
-  modify the generators_bitmask in order that one can only excite
-  the electrons occupying i_hole
-
-
-`modify_bitmasks_for_particl <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/modify_bitmasks.irp.f#L83>`_
-  modify the generators_bitmask in order that one can only excite
-  the electrons to the orbital i_part
-
-
-`n_act_orb <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L596>`_
-  number of active orbitals
-
-
-`n_cas_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L277>`_
-  Number of bitmasks for CAS
-
-
-`n_core_inact_act_orb <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L481>`_
-  Reunion of the core, inactive and active bitmasks
-
-
-`n_core_inact_orb <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L458>`_
-  Undocumented
-
-
-`n_core_orb <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L559>`_
-  Core + deleted orbitals bitmask
-
-
-`n_core_orb_allocate <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L654>`_
-  Undocumented
-
-
-`n_generators_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L97>`_
-  Number of bitmasks for generators
-
-
-`n_generators_bitmask_restart <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L128>`_
-  Number of bitmasks for generators
-
-
-`n_inact_orb <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L350>`_
-  inact_bitmask : Bitmask of the inactive orbitals which are supposed to be doubly excited
-  in post CAS methods
-  n_inact_orb   : Number of inactive orbitals
-  virt_bitmask  : Bitmaks of vritual orbitals which are supposed to be recieve electrons
-  in post CAS methods
-  n_virt_orb    : Number of virtual orbitals
-
-
-`n_inact_orb_allocate <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L659>`_
-  Undocumented
-
-
-`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_virt_orb <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L351>`_
-  inact_bitmask : Bitmask of the inactive orbitals which are supposed to be doubly excited
-  in post CAS methods
-  n_inact_orb   : Number of inactive orbitals
-  virt_bitmask  : Bitmaks of vritual orbitals which are supposed to be recieve electrons
-  in post CAS methods
-  n_virt_orb    : Number of virtual orbitals
-
-
-`n_virt_orb_allocate <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L664>`_
-  Undocumented
-
-
-`number_of_holes <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L2>`_
-  Function that returns the number of holes in the inact space
-
-
-`number_of_holes_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L408>`_
-  function that returns the number of holes in the inact space
-
-
-`number_of_particles <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L107>`_
-  function that returns the number of particles in the virtual space
-
-
-`number_of_particles_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L438>`_
-  function that returns the number of particles in the inact space
-
-
-`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
-
-
-`print_generators_bitmasks_holes <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/modify_bitmasks.irp.f#L169>`_
-  Undocumented
-
-
-`print_generators_bitmasks_holes_for_one_generator <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/modify_bitmasks.irp.f#L213>`_
-  Undocumented
-
-
-`print_generators_bitmasks_particles <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/modify_bitmasks.irp.f#L191>`_
-  Undocumented
-
-
-`print_generators_bitmasks_particles_for_one_generator <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/modify_bitmasks.irp.f#L236>`_
-  Undocumented
-
-
-`print_spindet <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L171>`_
-  Subroutine to print the content of a determinant using the '+-' notation
-
-
-`ref_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L89>`_
-  Reference bit mask, used in Slater rules, chosen as Hartree-Fock bitmask
-
-
-`reunion_of_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L512>`_
-  Reunion of the inactive, active and virtual bitmasks
-
-
-`reunion_of_cas_inact_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L641>`_
-  Reunion of the inactive, active and virtual bitmasks
-
-
-`reunion_of_core_inact_act_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L480>`_
-  Reunion of the core, inactive and active bitmasks
-
-
-`reunion_of_core_inact_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L467>`_
-  Reunion of the core and inactive and virtual bitmasks
-
-
-`set_bitmask_hole_as_input <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/modify_bitmasks.irp.f#L144>`_
-  set the generators_bitmask for the holes
-  as the input_bimask
-
-
-`set_bitmask_particl_as_input <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/modify_bitmasks.irp.f#L119>`_
-  set the generators_bitmask for the particles
-  as the input_bimask
-
-
-`unpaired_alpha_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L584>`_
-  Bitmask reprenting the unpaired alpha electrons in the HF_bitmask
-
-
-`virt_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L349>`_
-  inact_bitmask : Bitmask of the inactive orbitals which are supposed to be doubly excited
-  in post CAS methods
-  n_inact_orb   : Number of inactive orbitals
-  virt_bitmask  : Bitmaks of vritual orbitals which are supposed to be recieve electrons
-  in post CAS methods
-  n_virt_orb    : Number of virtual orbitals
-
-
-`virt_bitmask_4 <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L57>`_
-  Undocumented
-

src/CIS/README.rst

@@ -7,85 +7,3 @@ Assumptions
 * The molecular orbitals are assumed orthonormal
 
 
-Documentation
-=============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-`cis <http://github.com/LCPQ/quantum_package/tree/master/src/CIS/super_ci.irp.f#L1>`_
-  Undocumented
-
-
-`h_apply_cis <http://github.com/LCPQ/quantum_package/tree/master/src/CIS/H_apply.irp.f_shell_8#L414>`_
-  Calls H_apply on the HF determinant and selects all connected single and double
-  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
-
-
-`h_apply_cis_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CIS/H_apply.irp.f_shell_8#L1>`_
-  Generate all double excitations of key_in using the bit masks of holes and
-  particles.
-  Assume N_int is already provided.
-
-
-`h_apply_cis_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CIS/H_apply.irp.f_shell_8#L269>`_
-  Generate all single excitations of key_in using the bit masks of holes and
-  particles.
-  Assume N_int is already provided.
-
-
-`super_ci <http://github.com/LCPQ/quantum_package/tree/master/src/CIS/super_ci.irp.f#L9>`_
-  Undocumented
-
-Needed Modules
-==============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-.. image:: tree_dependency.png
-
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
-* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
-
-Needed Modules
-==============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-.. image:: tree_dependency.png
-
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full>`_
-* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod>`_
-
-Documentation
-=============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-`cis <http://github.com/LCPQ/quantum_package/tree/master/plugins/CIS/super_ci.irp.f#L1>`_
-  Undocumented
-
-
-`h_apply_cis <http://github.com/LCPQ/quantum_package/tree/master/plugins/CIS/H_apply.irp.f_shell_8#L414>`_
-  Calls H_apply on the HF determinant and selects all connected single and double
-  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
-
-
-`h_apply_cis_diexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CIS/H_apply.irp.f_shell_8#L1>`_
-  Generate all double excitations of key_in using the bit masks of holes and
-  particles.
-  Assume N_int is already provided.
-
-
-`h_apply_cis_monoexc <http://github.com/LCPQ/quantum_package/tree/master/plugins/CIS/H_apply.irp.f_shell_8#L269>`_
-  Generate all single excitations of key_in using the bit masks of holes and
-  particles.
-  Assume N_int is already provided.
-
-
-`super_ci <http://github.com/LCPQ/quantum_package/tree/master/plugins/CIS/super_ci.irp.f#L9>`_
-  Undocumented
-

src/CISD/README.rst

@@ -9,77 +9,4 @@ This is a test directory which builds a CISD by setting the follwoing rules:
 
 These rules are set in the ``H_apply.irp.f`` file.
 
-Needed Modules
-==============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-.. image:: tree_dependency.png
-
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
-* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
-
-Documentation
-=============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-`h_apply_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_8#L414>`_
-  Calls H_apply on the HF determinant and selects all connected single and double
-  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
-
-
-`h_apply_cisd_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_8#L1>`_
-  Generate all double excitations of key_in using the bit masks of holes and
-  particles.
-  Assume N_int is already provided.
-
-
-`h_apply_cisd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD/H_apply.irp.f_shell_8#L269>`_
-  Generate all single excitations of key_in using the bit masks of holes and
-  particles.
-  Assume N_int is already provided.
-
-Needed Modules
-==============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-.. image:: tree_dependency.png
-
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/plugins/Selectors_full>`_
-* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/plugins/SingleRefMethod>`_
-
-Documentation
-=============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-h_apply_cisd
-  Calls H_apply on the HF determinant and selects all connected single and double
-  excitations (of the same symmetry). Auto-generated by the ``generate_h_apply`` script.
-
-
-h_apply_cisd_diexc
-  Undocumented
-
-
-h_apply_cisd_diexcorg
-  Generate all double excitations of key_in using the bit masks of holes and
-  particles.
-  Assume N_int is already provided.
-
-
-h_apply_cisd_diexcp
-  Undocumented
-
-
-h_apply_cisd_monoexc
-  Generate all single excitations of key_in using the bit masks of holes and
-  particles.
-  Assume N_int is already provided.
 

src/Davidson/README.rst

@@ -7,325 +7,3 @@ be defined and the DavidsonDressed module should be used. If no dressing is requ
 the Davidson module should be used, and it has a default null dressing vector.
 
 
-Needed Modules
-==============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-.. image:: tree_dependency.png
-
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-
-Documentation
-=============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-`ci_eigenvectors <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/diagonalize_CI.irp.f#L23>`_
-  Eigenvectors/values of the CI matrix
-
-
-`ci_eigenvectors_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/diagonalize_CI.irp.f#L24>`_
-  Eigenvectors/values of the CI matrix
-
-
-`ci_electronic_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/diagonalize_CI.irp.f#L22>`_
-  Eigenvectors/values of the CI matrix
-
-
-`ci_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/diagonalize_CI.irp.f#L2>`_
-  N_states lowest eigenvalues of the CI matrix
-
-
-`davidson_collector <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/davidson_parallel.irp.f#L235>`_
-  Undocumented
-
-
-`davidson_converged <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/parameters.irp.f#L9>`_
-  True if the Davidson algorithm is converged
-
-
-`davidson_criterion <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/parameters.irp.f#L1>`_
-  Can be : [  energy  | residual | both | wall_time | cpu_time | iterations ]
-
-
-`davidson_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/diagonalization.irp.f#L1>`_
-  Davidson diagonalization.
-  .br
-  dets_in : bitmasks corresponding to determinants
-  .br
-  u_in : guess coefficients on the various states. Overwritten
-  on exit
-  .br
-  dim_in : leftmost dimension of u_in
-  .br
-  sze : Number of determinants
-  .br
-  N_st : Number of eigenstates
-  .br
-  iunit : Unit number for the I/O
-  .br
-  Initial guess vectors are not necessarily orthonormal
-
-
-`davidson_diag_hjj <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/diagonalization.irp.f#L273>`_
-  Davidson diagonalization with specific diagonal elements of the H matrix
-  .br
-  H_jj : specific diagonal H matrix elements to diagonalize de Davidson
-  .br
-  dets_in : bitmasks corresponding to determinants
-  .br
-  u_in : guess coefficients on the various states. Overwritten
-  on exit
-  .br
-  dim_in : leftmost dimension of u_in
-  .br
-  sze : Number of determinants
-  .br
-  N_st : Number of eigenstates
-  .br
-  N_st_diag : Number of states in which H is diagonalized
-  .br
-  iunit : Unit for the I/O
-  .br
-  Initial guess vectors are not necessarily orthonormal
-
-
-`davidson_diag_hjj_sjj <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/diagonalization_hs2.irp.f#L52>`_
-  Davidson diagonalization with specific diagonal elements of the H matrix
-  .br
-  H_jj : specific diagonal H matrix elements to diagonalize de Davidson
-  .br
-  S2_out : Output : s^2
-  .br
-  dets_in : bitmasks corresponding to determinants
-  .br
-  u_in : guess coefficients on the various states. Overwritten
-  on exit
-  .br
-  dim_in : leftmost dimension of u_in
-  .br
-  sze : Number of determinants
-  .br
-  N_st : Number of eigenstates
-  .br
-  N_st_diag : Number of states in which H is diagonalized. Assumed > sze
-  .br
-  iunit : Unit for the I/O
-  .br
-  Initial guess vectors are not necessarily orthonormal
-
-
-`davidson_diag_hs2 <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/diagonalization_hs2.irp.f#L1>`_
-  Davidson diagonalization.
-  .br
-  dets_in : bitmasks corresponding to determinants
-  .br
-  u_in : guess coefficients on the various states. Overwritten
-  on exit
-  .br
-  dim_in : leftmost dimension of u_in
-  .br
-  sze : Number of determinants
-  .br
-  N_st : Number of eigenstates
-  .br
-  iunit : Unit number for the I/O
-  .br
-  Initial guess vectors are not necessarily orthonormal
-
-
-`davidson_pull_results <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/davidson_parallel.irp.f#L192>`_
-  Undocumented
-
-
-`davidson_push_results <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/davidson_parallel.irp.f#L149>`_
-  Undocumented
-
-
-`davidson_run_slave <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/davidson_parallel.irp.f#L22>`_
-  Undocumented
-
-
-`davidson_slave <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/davidson_slave.irp.f#L1>`_
-  Undocumented
-
-
-`davidson_slave_inproc <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/davidson_parallel.irp.f#L5>`_
-  Undocumented
-
-
-`davidson_slave_tcp <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/davidson_parallel.irp.f#L13>`_
-  Undocumented
-
-
-`davidson_slave_work <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/davidson_parallel.irp.f#L55>`_
-  Undocumented
-
-
-`davidson_sze_max <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/ezfio_interface.irp.f#L6>`_
-  Number of micro-iterations before re-contracting
-
-
-`det_inf <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/diagonalization.irp.f#L52>`_
-  Ordering function for determinants
-
-
-`diag_and_save <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/diagonalize_restart_and_save_one_state.irp.f#L1>`_
-  Undocumented
-
-
-`diagonalize_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/diagonalize_CI.irp.f#L154>`_
-  Replace the coefficients of the CI states by the coefficients of the
-  eigenstates of the CI matrix
-
-
-`disk_based_davidson <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/ezfio_interface.irp.f#L101>`_
-  If true, disk space is used to store the vectors
-
-
-`distributed_davidson <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/ezfio_interface.irp.f#L44>`_
-  If true, use the distributed algorithm
-
-
-`find_reference <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/find_reference.irp.f#L1>`_
-  Undocumented
-
-
-`first_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/guess_lowest_state.irp.f#L1>`_
-  Select all the determinants with the lowest energy as a starting point.
-
-
-`h_s2_u_0_nstates <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/u0Hu0_old.irp.f#L231>`_
-  Computes v_0 = H|u_0> and s_0 = S^2 |u_0>
-  .br
-  n : number of determinants
-  .br
-  H_jj : array of <j|H|j>
-  .br
-  S2_jj : array of <j|S^2|j>
-
-
-`h_s2_u_0_nstates_openmp <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/u0Hu0.irp.f#L11>`_
-  Computes v_0 = H|u_0> and s_0 = S^2 |u_0>
-  .br
-  Assumes that the determinants are in psi_det
-  .br
-  istart, iend, ishift, istep are used in ZMQ parallelization.
-
-
-`h_s2_u_0_nstates_openmp_work <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/u0Hu0.irp.f#L65>`_
-  Computes v_t = H|u_t> and s_t = S^2 |u_t>
-  .br
-  Default should be 1,N_det,0,1
-
-
-`h_s2_u_0_nstates_openmp_work_1 <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/u0Hu0.irp.f_template_454#L3>`_
-  Computes v_t = H|u_t> and s_t = S^2 |u_t>
-  .br
-  Default should be 1,N_det,0,1
-
-
-`h_s2_u_0_nstates_openmp_work_2 <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/u0Hu0.irp.f_template_454#L357>`_
-  Computes v_t = H|u_t> and s_t = S^2 |u_t>
-  .br
-  Default should be 1,N_det,0,1
-
-
-`h_s2_u_0_nstates_openmp_work_3 <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/u0Hu0.irp.f_template_454#L711>`_
-  Computes v_t = H|u_t> and s_t = S^2 |u_t>
-  .br
-  Default should be 1,N_det,0,1
-
-
-`h_s2_u_0_nstates_openmp_work_4 <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/u0Hu0.irp.f_template_454#L1065>`_
-  Computes v_t = H|u_t> and s_t = S^2 |u_t>
-  .br
-  Default should be 1,N_det,0,1
-
-
-`h_s2_u_0_nstates_openmp_work_n_int <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/u0Hu0.irp.f_template_454#L1419>`_
-  Computes v_t = H|u_t> and s_t = S^2 |u_t>
-  .br
-  Default should be 1,N_det,0,1
-
-
-`h_s2_u_0_nstates_test <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/u0Hu0_old.irp.f#L460>`_
-  Undocumented
-
-
-`h_s2_u_0_nstates_zmq <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/davidson_parallel.irp.f#L275>`_
-  Computes v_0 = H|u_0> and s_0 = S^2 |u_0>
-  .br
-  n : number of determinants
-  .br
-  H_jj : array of <j|H|j>
-  .br
-  S2_jj : array of <j|S^2|j>
-
-
-`h_u_0_nstates <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/u0Hu0_old.irp.f#L2>`_
-  Computes v_0 = H|u_0>
-  .br
-  n : number of determinants
-  .br
-  H_jj : array of <j|H|j>
-  .br
-
-
-`n_states_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/ezfio_interface.irp.f#L82>`_
-  Number of states to consider during the Davdison diagonalization
-
-
-`nthreads_davidson <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/davidson_parallel.irp.f#L418>`_
-  Number of threads for Davdison
-
-
-`print_h_matrix_restart <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/print_H_matrix_restart.irp.f#L1>`_
-  Undocumented
-
-
-`provide_everything <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/davidson_slave.irp.f#L29>`_
-  Undocumented
-
-
-`psi_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/u0Hu0.irp.f#L1>`_
-  Energy of the current wave function
-
-
-`routine <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/print_H_matrix_restart.irp.f#L9>`_
-  Undocumented
-
-
-`sort_dets_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/diagonalization.irp.f#L219>`_
-  Uncodumented : TODO
-
-
-`sort_dets_ab_v <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/diagonalization.irp.f#L149>`_
-  Uncodumented : TODO
-
-
-`sort_dets_ba_v <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/diagonalization.irp.f#L120>`_
-  Uncodumented : TODO
-
-
-`state_following <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/ezfio_interface.irp.f#L25>`_
-  If true, the states are re-ordered to match the input states
-
-
-`tamiser <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/diagonalization.irp.f#L77>`_
-  Uncodumented : TODO
-
-
-`threshold_davidson <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/ezfio_interface.irp.f#L63>`_
-  Thresholds of Davidson's algorithm
-
-
-`u_0_h_u_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Davidson/diagonalization_hs2.irp.f#L447>`_
-  Computes e_0 = <u_0|H|u_0>/<u_0|u_0>
-  .br
-  n : number of determinants
-  .br
-

src/DavidsonDressed/README.rst

@@ -4,11 +4,3 @@ DavidsonDressed
 
 Davidson with single-column dressing
 
-Needed Modules
-==============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-Documentation
-=============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.

src/DavidsonUndressed/README.rst

@@ -4,11 +4,3 @@ DavidsonUndressed
 
 Module for main files with undressed Davidson
 
-Needed Modules
-==============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-Documentation
-=============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.

src/DavidsonUndressed/davidson_slave.irp.f

@@ -1,124 +0,0 @@
-program selection_slave
-  implicit none
-  BEGIN_DOC
-! Helper program to compute the PT2 in distributed mode.
-  END_DOC
-
-  call omp_set_nested(.false.)
-  read_wf = .False.
-  distributed_davidson = .False.
-  SOFT_TOUCH read_wf distributed_davidson
-  call provide_everything
-  call switch_qp_run_to_master
-  call run_wf
-end
-
-subroutine provide_everything
-  PROVIDE H_apply_buffer_allocated mo_bielec_integrals_in_map psi_det_sorted_bit n_states zmq_context N_states_diag
-  PROVIDE mo_tot_num N_int ci_energy mpi_master zmq_state zmq_context
-  PROVIDE psi_det psi_coef state_average_weight 
-  PROVIDE N_det 
-end
-
-subroutine run_wf
-  use f77_zmq
-  
-  implicit none
-  IRP_IF MPI
-    include 'mpif.h'
-  IRP_ENDIF
-
-  integer(ZMQ_PTR), external :: new_zmq_to_qp_run_socket
-  integer(ZMQ_PTR) :: zmq_to_qp_run_socket
-  double precision :: energy(N_states)
-  character*(64) :: states(3)
-  character*(64) :: old_state
-  integer :: rc, i, ierr
-  double precision :: t0, t1
-  
-  integer, external              :: zmq_get_dvector, zmq_get_N_det_generators 
-  integer, external              :: zmq_get8_dvector
-  integer, external              :: zmq_get_ivector
-  integer, external              :: zmq_get_psi, zmq_get_N_det_selectors, zmq_get_psi_bilinear
-  integer, external              :: zmq_get_psi_notouch
-  integer, external              :: zmq_get_N_states_diag
-
-  zmq_context = f77_zmq_ctx_new ()
-  states(1) = 'davidson'
-  old_state = 'Waiting'
-
-  zmq_to_qp_run_socket = new_zmq_to_qp_run_socket()
-
-  PROVIDE psi_det psi_coef state_average_weight mpi_master
-  PROVIDE zmq_state N_det 
-  PROVIDE N_states N_states_diag psi_energy
-
-  IRP_IF MPI
-    call MPI_BARRIER(MPI_COMM_WORLD, ierr)
-  IRP_ENDIF
-  do
-
-    if (mpi_master) then
-      call wait_for_states(states,zmq_state,size(states))
-      if (zmq_state(1:64) == old_state(1:64)) then
-        call sleep(1)
-        cycle
-      else
-        old_state(1:64) = zmq_state(1:64)
-      endif
-      print *,  trim(zmq_state)
-    endif
-
-    IRP_IF MPI_DEBUG
-      print *,  irp_here, mpi_rank
-      call MPI_BARRIER(MPI_COMM_WORLD, ierr)
-    IRP_ENDIF
-    IRP_IF MPI
-      call MPI_BCAST (zmq_state, 128, MPI_CHARACTER, 0, MPI_COMM_WORLD, ierr)
-      if (ierr /= MPI_SUCCESS) then
-        print *,  irp_here, 'error in broadcast of zmq_state'
-      endif
-    IRP_ENDIF
-
-    if(zmq_state(1:7) == 'Stopped') then
-      exit
-    endif
-
-
-    if (zmq_state(1:8) == 'davidson') then
-
-      ! Davidson
-      ! --------
-
-      call wall_time(t0)
-      if (zmq_get_N_states_diag(zmq_to_qp_run_socket,1) == -1) cycle
-      if (zmq_get_psi(zmq_to_qp_run_socket,1) == -1) cycle
-      if (zmq_get_dvector(zmq_to_qp_run_socket,1,'energy',energy,N_states_diag) == -1) cycle
-
-      call wall_time(t1)
-      if (mpi_master) then
-        call write_double(6,(t1-t0),'Broadcast time')
-      endif
-
-      call omp_set_nested(.True.)
-      call davidson_slave_tcp(0)
-      call omp_set_nested(.False.)
-      print *,  'Davidson done'
-      IRP_IF MPI
-        call MPI_BARRIER(MPI_COMM_WORLD, ierr)
-        if (ierr /= MPI_SUCCESS) then
-          print *,  irp_here, 'error in barrier'
-        endif
-      IRP_ENDIF
-      print *,  'All Davidson done'
-
-    endif
-
-  end do
-  IRP_IF MPI
-    call MPI_finalize(ierr)
-  IRP_ENDIF
-end
-
-
-

src/DavidsonUndressed/print_energy.irp.f

@@ -1,27 +0,0 @@
-program print_energy
- implicit none
- read_wf = .true.
- touch read_wf
- provide mo_bielec_integrals_in_map psi_coef psi_det psi_bilinear_matrix_transp_values
- double precision :: time1, time0
- call wall_time(time0)
- call routine
- call wall_time(time1)
- print *,  'Wall time :' , time1 - time0
-end
-
-subroutine routine
- implicit none
- integer :: i,j
- double precision :: accu,hij
-
- print*, 'psi_energy          = ',psi_energy + nuclear_repulsion
- accu = 0.d0
-! do i = 1,N_det
-!  do j = 1,N_det
-!   call i_H_j(psi_det(1,1,j),psi_det(1,1,i),N_int,hij)
-!   accu += psi_coef(i,1) * psi_coef(j,1) * hij
-!  enddo
-! enddo
-! print*, 'accu                = ',accu + nuclear_repulsion
-end

src/Determinants/truncate_wf.irp.f

@@ -1,91 +0,0 @@
-program s2_eig_restart
- implicit none
- read_wf = .True.
- if (s2_eig) then
-  call routine_s2
- else
-  call routine
- endif
-end
-
-subroutine routine
- implicit none
- integer :: ndet_max
- print*, 'Max number of determinants ?'
- read(5,*)ndet_max
- integer(bit_kind), allocatable :: psi_det_tmp(:,:,:)
- double precision, allocatable :: psi_coef_tmp(:,:)
- allocate(psi_det_tmp(N_int,2,ndet_max),psi_coef_tmp(ndet_max, N_states))
- 
- integer :: i,j
- double precision :: accu(N_states)
- accu = 0.d0
- do i = 1, ndet_max
-  do j = 1, N_int
-   psi_det_tmp(j,1,i) = psi_det_sorted(j,1,i)
-   psi_det_tmp(j,2,i) = psi_det_sorted(j,2,i)
-  enddo
-  do j = 1, N_states
-   psi_coef_tmp(i,j) = psi_coef_sorted(i,j)
-   accu(j) += psi_coef_tmp(i,j) **2
-  enddo
- enddo
- do j = 1, N_states
-  accu(j) = 1.d0/dsqrt(accu(j))
- enddo
- do j = 1, N_states
-  do i = 1, ndet_max
-   psi_coef_tmp(i,j) = psi_coef_tmp(i,j) * accu(j)
-  enddo
- enddo
-
- call save_wavefunction_general(ndet_max,N_states,psi_det_tmp,size(psi_coef_tmp,1),psi_coef_tmp)
- 
-end
-
-subroutine routine_s2
- implicit none
- integer :: ndet_max
- double precision :: wmin
- integer(bit_kind), allocatable :: psi_det_tmp(:,:,:)
- double precision, allocatable :: psi_coef_tmp(:,:)
- integer :: i,j,k
- double precision :: accu(N_states)
-
- print*, 'Min weight of the occupation pattern ?'
- read(5,*) wmin
-
- ndet_max = 0
- do i=1,N_det
-   if (maxval(weight_occ_pattern( det_to_occ_pattern(i),:)) < wmin) cycle
-   ndet_max = ndet_max+1
- enddo
-
- allocate(psi_det_tmp(N_int,2,ndet_max),psi_coef_tmp(ndet_max, N_states))
- 
- accu = 0.d0
- k=0
- do i = 1, N_det
-  if (maxval(weight_occ_pattern( det_to_occ_pattern(i),:)) < wmin) cycle
-  k = k+1
-  do j = 1, N_int
-   psi_det_tmp(j,1,k) = psi_det(j,1,i)
-   psi_det_tmp(j,2,k) = psi_det(j,2,i)
-  enddo
-  do j = 1, N_states
-   psi_coef_tmp(k,j) = psi_coef(i,j)
-   accu(j) += psi_coef_tmp(k,j) **2
-  enddo
- enddo
- do j = 1, N_states
-  accu(j) = 1.d0/dsqrt(accu(j))
- enddo
- do j = 1, N_states
-  do i = 1, ndet_max
-   psi_coef_tmp(i,j) = psi_coef_tmp(i,j) * accu(j)
-  enddo
- enddo
-
- call save_wavefunction_general(ndet_max,N_states,psi_det_tmp,size(psi_coef_tmp,1),psi_coef_tmp)
- 
-end

src/Dressing/EZFIO.cfg.example

@@ -0,0 +1,18 @@
+[thresh_dressed_ci]
+type: Threshold
+doc: Threshold on the convergence of the dressed CI energy
+interface: ezfio,provider,ocaml
+default: 1.e-5
+
+[n_it_max_dressed_ci]
+type: Strictly_positive_int
+doc: Maximum number of dressed CI iterations
+interface: ezfio,provider,ocaml
+default: 10
+
+[dress_relative_error]
+type: Normalized_float
+doc: Stop stochastic PT2 when the relative error is smaller than PT2_relative_error
+interface: ezfio,provider,ocaml
+default: 0.001
+

src/Dressing/README.rst

@@ -0,0 +1,4 @@
+=========
+dress_zmq
+=========
+

src/Electrons/README.rst

@@ -18,44 +18,3 @@ Assumptions
 * ``elec_alpha_num`` >= ``elec_beta_num``
 
 
-Needed Modules
-==============
-
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-.. image:: tree_dependency.png
-
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-
-Needed Modules
-==============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-.. image:: tree_dependency.png
-
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-
-Documentation
-=============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-`elec_alpha_num <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/ezfio_interface.irp.f#L25>`_
-  Numbers of electrons alpha ("up")
-
-
-`elec_beta_num <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/ezfio_interface.irp.f#L6>`_
-  Numbers of electrons beta ("down")
-
-
-`elec_num <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/electrons.irp.f#L1>`_
-  Numbers of alpha ("up") , beta ("down") and total electrons
-
-
-`elec_num_tab <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/electrons.irp.f#L2>`_
-  Numbers of alpha ("up") , beta ("down") and total electrons
-

src/Ezfio_files/README.rst

@@ -5,280 +5,4 @@ Ezfio_files Module
 This modules essentially contains the name of the EZFIO directory in the
 ``ezfio_filename`` variable. This is read as the first argument of the
 command-line, or as the ``QP_INPUT`` environment variable.
-Documentation
-=============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-`ezfio_filename <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/ezfio.irp.f#L1>`_
-  Name of EZFIO file. It is obtained from the QPACKAGE_INPUT environment
-  variable if it is set, or as the 1st argument of the command line.
-
-
-`getunitandopen <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/get_unit_and_open.irp.f#L1>`_
-  :f:
-  file name
-  .br
-  :mode:
-  'R' : READ, UNFORMATTED
-  'W' : WRITE, UNFORMATTED
-  'r' : READ, FORMATTED
-  'w' : WRITE, FORMATTED
-  'a' : APPEND, FORMATTED
-  'x' : READ/WRITE, FORMATTED
-  .br
-
-
-`output_ao_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L1>`_
-  Output file for AO_Basis
-
-
-`output_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L21>`_
-  Output file for Bitmask
-
-
-`output_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L41>`_
-  Output file for CAS_SD
-
-
-`output_cis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L61>`_
-  Output file for CIS
-
-
-`output_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L81>`_
-  Output file for CISD
-
-
-`output_cisd_selected <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L101>`_
-  Output file for CISD_selected
-
-
-`output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L2>`_
-  Initial CPU and wall times when printing in the output files
-
-
-`output_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L121>`_
-  Output file for Determinants
-
-
-`output_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
-  Output file for Electrons
-
-
-`output_ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
-  Output file for Ezfio_files
-
-
-`output_full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
-  Output file for Full_CI
-
-
-`output_generators_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
-  Output file for Generators_CAS
-
-
-`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
-  Output file for Generators_full
-
-
-`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
-  Output file for Hartree_Fock
-
-
-`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
-  Output file for Integrals_Bielec
-
-
-`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
-  Output file for Integrals_Monoelec
-
-
-`output_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
-  Output file for MO_Basis
-
-
-`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
-  Output file for MOGuess
-
-
-`output_mrcc_cassd <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L341>`_
-  Output file for MRCC_CASSD
-
-
-`output_mrcc_utils_new <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L361>`_
-  Output file for MRCC_Utils_new
-
-
-`output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L381>`_
-  Output file for Nuclei
-
-
-`output_perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L401>`_
-  Output file for Perturbation
-
-
-`output_properties <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L421>`_
-  Output file for Properties
-
-
-`output_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L441>`_
-  Output file for Pseudo
-
-
-`output_psiref_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L461>`_
-  Output file for Psiref_CAS
-
-
-`output_psiref_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L481>`_
-  Output file for Psiref_Utils
-
-
-`output_qmcchem <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L501>`_
-  Output file for QmcChem
-
-
-`output_selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L521>`_
-  Output file for Selectors_full
-
-
-`output_singlerefmethod <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L541>`_
-  Output file for SingleRefMethod
-
-
-`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L561>`_
-  Output file for Utils
-
-
-`output_wall_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/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/Ezfio_files/output.irp.f#L88>`_
-  Write an logical value in output
-
-
-`write_double <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L58>`_
-  Write a double precision value in output
-
-
-`write_int <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L73>`_
-  Write an integer value in output
-
-
-`write_time <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L42>`_
-  Write a time stamp in the output for chronological reconstruction
-
-
-Documentation
-=============
-.. Do not edit this section It was auto-generated
-.. by the `update_README.py` script.
-
-
-`ezfio_filename <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/ezfio.irp.f#L1>`_
-  Name of EZFIO file. It is obtained from the QPACKAGE_INPUT environment
-  variable if it is set, or as the 1st argument of the command line.
-
-
-`ezfio_work_dir <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/ezfio.irp.f#L34>`_
-  EZFIO/work/
-
-
-`getunitandopen <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/get_unit_and_open.irp.f#L1>`_
-  :f:
-  file name
-  .br
-  :mode:
-  'R' : READ, UNFORMATTED
-  'W' : WRITE, UNFORMATTED
-  'r' : READ, FORMATTED
-  'w' : WRITE, FORMATTED
-  'a' : APPEND, FORMATTED
-  'x' : READ/WRITE, FORMATTED
-  .br
-
-
-output_ao_basis
-  Output file for AO_Basis
-
-
-output_bitmask
-  Output file for Bitmask
-
-
-`output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L2>`_
-  Initial CPU and wall times when printing in the output files
-
-
-output_davidson
-  Output file for Davidson
-
-
-output_determinants
-  Output file for Determinants
-
-
-output_electrons
-  Output file for Electrons
-
-
-output_ezfio_files
-  Output file for Ezfio_files
-
-
-output_hartree_fock
-  Output file for Hartree_Fock
-
-
-output_integrals_bielec
-  Output file for Integrals_Bielec
-
-
-output_integrals_monoelec
-  Output file for Integrals_Monoelec
-
-
-output_mo_basis
-  Output file for MO_Basis
-
-
-output_moguess
-  Output file for MOGuess
-
-
-output_nuclei
-  Output file for Nuclei
-
-
-output_pseudo
-  Output file for Pseudo
-
-
-output_utils
-  Output file for Utils
-
-
-`output_wall_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L1>`_
-  Initial CPU and wall times when printing in the output files
-
-
-output_zmq
-  Output file for ZMQ
-
-
-`write_bool <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L88>`_
-  Write an logical value in output
-
-
-`write_double <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L58>`_
-  Write a double precision value in output
-
-
-`write_int <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L73>`_
-  Write an integer value in output
-
-
-`write_time <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f#L42>`_
-  Write a time stamp in the output for chronological reconstruction
 

src/FCI/EZFIO.cfg

@@ -2,37 +2,12 @@
 type: double precision
 doc: Calculated Selected FCI energy
 interface: ezfio
+size: (determinants.n_states)
 
 [energy_pt2]
 type: double precision
 doc: Calculated FCI energy + PT2
 interface: ezfio
+size: (determinants.n_states)
 
-[iterative_save]
-type: integer
-doc: Save data at each iteration :  1(Append) | 2(Overwrite) | 3(NoSave)
-interface: ezfio,ocaml
-default: 2
 
-[n_iter]
-interface: ezfio
-doc: number of iterations
-type:integer
-
-[n_det_iter]
-interface: ezfio
-doc: number of determinants at iteration
-type: integer
-size: (full_ci_zmq.n_iter)
- 
-[energy_iter]
-interface: ezfio
-doc: The energy without a pt2 correction for n_det
-type: double precision 
-size: (determinants.n_states,full_ci_zmq.n_iter)
-
-[pt2_iter]
-interface: ezfio
-doc: The pt2 correction for n_det
-type: double precision 
-size: (determinants.n_states,full_ci_zmq.n_iter)

src/FCI/FCI.irp.f

@@ -12,7 +12,6 @@ program fci_zmq
   logical                        :: has
   double precision               :: relative_error
   integer                        :: N_states_p
-  character*(512)                :: fmt
 
   relative_error=PT2_relative_error
 
@@ -86,66 +85,12 @@ program fci_zmq
 
       N_states_p = min(N_det,N_states)
 
-      print *, ''
+      call ezfio_set_fci_energy_pt2(CI_energy+pt2)
-      print '(A,I12)',  'Summary at N_det = ', N_det
-      print '(A)',      '-----------------------------------'
-      print *, ''
       call write_double(6,correlation_energy_ratio, 'Correlation ratio')
-      print *, ''
+      call print_summary(CI_energy,pt2,error)
-
+      call save_iterations(CI_energy,pt2,N_det) 
-      write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))'
+      call print_extrapolated_energy(CI_energy,pt2)
-      write(*,fmt)
+      N_iter += 1
-      write(fmt,*) '(12X,', N_states_p, '(6X,A7,1X,I6,10X))'
-      write(*,fmt) ('State',k, k=1,N_states_p)
-      write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))'
-      write(*,fmt)
-      write(fmt,*) '(A12,', N_states_p, '(1X,F14.8,15X))'
-      write(*,fmt) '# E          ', CI_energy(1:N_states_p)
-      if (N_states_p > 1) then
-        write(*,fmt) '# Excit. (au)', CI_energy(1:N_states_p)-CI_energy(1)
-        write(*,fmt) '# Excit. (eV)', (CI_energy(1:N_states_p)-CI_energy(1))*27.211396641308d0
-      endif
-      write(fmt,*) '(A12,', 2*N_states_p, '(1X,F14.8))'
-      write(*,fmt) '# PT2'//pt2_string, (pt2(k), error(k), k=1,N_states_p)
-      write(*,'(A)') '#'
-      write(*,fmt) '# E+PT2      ', (CI_energy(k)+pt2(k),error(k), k=1,N_states_p)
-      if (N_states_p > 1) then
-        write(*,fmt) '# Excit. (au)', ( (CI_energy(k)+pt2(k)-CI_energy(1)-pt2(1)), &
-          dsqrt(error(k)*error(k)+error(1)*error(1)), k=1,N_states_p)
-        write(*,fmt) '# Excit. (eV)', ( (CI_energy(k)+pt2(k)-CI_energy(1)-pt2(1))*27.211396641308d0, &
-          dsqrt(error(k)*error(k)+error(1)*error(1))*27.211396641308d0, k=1,N_states_p)
-      endif
-      write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))'
-      write(*,fmt)
-      print *,  ''
-
-      print *,  'N_det             = ', N_det
-      print *,  'N_states          = ', N_states
-      print*,   'correlation_ratio = ', correlation_energy_ratio
-
-      do k=1, N_states_p
-        print*,'State ',k
-        print *,  'PT2             = ', pt2(k)
-        print *,  'E               = ', CI_energy(k)
-        print *,  'E+PT2'//pt2_string//'   = ', CI_energy(k)+pt2(k), ' +/- ', error(k)
-      enddo
-
-      print *,  '-----'
-      if(N_states.gt.1)then
-        print *, 'Variational Energy difference (au | eV)'
-        do i=2, N_states_p
-          print*,'Delta E = ', (CI_energy(i) - CI_energy(1)), &
-            (CI_energy(i) - CI_energy(1)) * 27.211396641308d0
-        enddo
-        print *,  '-----'
-        print*, 'Variational + perturbative Energy difference (au | eV)'
-        do i=2, N_states_p
-          print*,'Delta E = ', (CI_energy(i)+ pt2(i) - (CI_energy(1) + pt2(1))), &
-            (CI_energy(i)+ pt2(i) - (CI_energy(1) + pt2(1))) * 27.211396641308d0
-        enddo
-      endif
-      call ezfio_set_full_ci_zmq_energy_pt2(CI_energy(1)+pt2(1))
-      call dump_fci_iterations_value(N_det,CI_energy,pt2) 
 
       n_det_before = N_det
       if (s2_eig) then
@@ -168,7 +113,7 @@ program fci_zmq
       end if
       call diagonalize_CI
       call save_wavefunction
-      call ezfio_set_full_ci_zmq_energy(CI_energy(1))
+      call ezfio_set_fci_energy(CI_energy)
     enddo
   endif
 
@@ -176,8 +121,8 @@ program fci_zmq
       threshold_davidson = threshold_davidson_in
       call diagonalize_CI
       call save_wavefunction
-      call ezfio_set_full_ci_zmq_energy(CI_energy(1))
+      call ezfio_set_fci_energy(CI_energy)
-      call ezfio_set_full_ci_zmq_energy_pt2(CI_energy(1)+pt2(1))
+      call ezfio_set_fci_energy_pt2(CI_energy+pt2)
   endif
 
   if (do_pt2) then
@@ -189,52 +134,16 @@ program fci_zmq
     threshold_selectors = threshold_selectors_save
     threshold_generators = threshold_generators_save
     SOFT_TOUCH threshold_selectors threshold_generators
-    call ezfio_set_full_ci_zmq_energy(CI_energy(1))
+    call ezfio_set_fci_energy(CI_energy)
-    call ezfio_set_full_ci_zmq_energy_pt2(CI_energy(1)+pt2(1))
+    call ezfio_set_fci_energy_pt2(CI_energy+pt2)
   endif
   print *,  'N_det             = ', N_det
   print *,  'N_states          = ', N_states
   print*,   'correlation_ratio = ', correlation_energy_ratio
 
 
-  call dump_fci_iterations_value(N_det,CI_energy,pt2) 
+  call save_iterations(CI_energy,pt2,N_det) 
-
-  print *, ''
-  print '(A,I12)',  'Summary at N_det = ', N_det
-  print '(A)',      '-----------------------------------'
-  print *, ''
   call write_double(6,correlation_energy_ratio, 'Correlation ratio')
-  print *, ''
+  call print_summary(CI_energy,pt2,error)
-
-
-  N_states_p = min(N_det,N_states)
-  print *,  ''
-  write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))'
-  write(*,fmt)
-  write(fmt,*) '(12X,', N_states_p, '(6X,A7,1X,I6,10X))'
-  write(*,fmt) ('State',k, k=1,N_states_p)
-  write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))'
-  write(*,fmt)
-  write(fmt,*) '(A12,', N_states_p, '(1X,F14.8,15X))'
-  write(*,fmt) '# E          ', CI_energy(1:N_states_p)
-  if (N_states_p > 1) then
-    write(*,fmt) '# Excit. (au)', CI_energy(1:N_states_p)-CI_energy(1)
-    write(*,fmt) '# Excit. (eV)', (CI_energy(1:N_states_p)-CI_energy(1))*27.211396641308d0
-  endif
-  write(fmt,*) '(A12,', 2*N_states_p, '(1X,F14.8))'
-  write(*,fmt) '# PT2'//pt2_string, (pt2(k), error(k), k=1,N_states_p)
-  write(*,'(A)') '#'
-  write(*,fmt) '# E+PT2      ', (CI_energy(k)+pt2(k),error(k), k=1,N_states_p)
-  if (N_states_p > 1) then
-    write(*,fmt) '# Excit. (au)', ( (CI_energy(k)+pt2(k)-CI_energy(1)-pt2(1)), &
-      dsqrt(error(k)*error(k)+error(1)*error(1)), k=1,N_states_p)
-    write(*,fmt) '# Excit. (eV)', ( (CI_energy(k)+pt2(k)-CI_energy(1)-pt2(1))*27.211396641308d0, &
-      dsqrt(error(k)*error(k)+error(1)*error(1))*27.211396641308d0, k=1,N_states_p)
-  endif
-  write(fmt,*) '(''# ============'',', N_states_p, '(1X,''=============================''))'
-  write(*,fmt)
-  print *,  ''
-
-
 
 end