Fix README and graphiz

configure

@@ -61,7 +61,8 @@ d_dependency = {
     "gcc": [],
     "python": [],
     "ninja": ["gcc", "python"],
-    "make": []
+    "make": [],
+    "p_graphviz": ["python"]
 }
 
 from collections import namedtuple
@@ -126,10 +127,15 @@ ezfio = Info(
     description=' EZFIO',
     default_path=join(QP_ROOT_INSTALL, "EZFIO"))
 
+p_graphviz = Info(
+    url='https://github.com/xflr6/graphviz/archive/master.zip',
+    description=' Python library for graphviz',
+    default_path=join(QP_ROOT_INSTALL, "p_graphviz"))
+
 d_info = dict()
 
 for m in ["ocaml", "m4", "curl", "zlib", "path", "irpf90", "docopt",
-          "resultsFile", "ninja", "emsl", "ezfio"]:
+          "resultsFile", "ninja", "emsl", "ezfio", "p_graphviz"]:
     exec ("d_info['{0}']={0}".format(m))
 
 

install/scripts/install_p_graphviz.sh

@@ -0,0 +1,10 @@
+#!/bin/bash -x
+
+TARGET=p_graphviz
+
+function _install()
+{
+  cp -R ${BUILD} . || exit 1
+}
+
+source scripts/build.sh

plugins/Alavi/.gitignore

@@ -0,0 +1,23 @@
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
+IRPF90_temp
+IRPF90_man
+irpf90_entities
+tags
+irpf90.make
+Makefile
+Makefile.depend
+.ninja_log
+.ninja_deps
+ezfio_interface.irp.f
+Ezfio_files
+Determinants
+Integrals_Monoelec
+MO_Basis
+Utils
+Pseudo
+Bitmask
+AO_Basis
+Electrons
+Nuclei
+Integrals_Bielec
+alavi_graph

plugins/Alavi/NEEDED_CHILDREN_MODULES

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

plugins/Alavi/README.rst

@@ -0,0 +1,23 @@
+=====
+alavi
+=====
+
+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. by the `update_README.py` script.
+
+`alavi_graph <http://github.com/LCPQ/quantum_package/tree/master/src/Alavi/alavi_graph.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.pdf
+
+* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
+

plugins/Alavi/alavi_graph.irp.f

@@ -0,0 +1,28 @@
+program alavi_graph
+  implicit none
+  integer :: exc(0:2,2,2),h1,p1,h2,p2,s1,s2
+  double precision :: phase
+
+  read_wf = .True.
+  touch read_wf
+
+  integer :: k,degree
+  double precision :: hii
+
+  do k=1,N_det
+      call get_excitation_degree(psi_det(1,1,1),psi_det(1,1,k),degree,N_int)
+      call  i_H_j(psi_det(1,1,k),psi_det(1,1,k),N_int,hii) 
+      print*, k,abs(psi_coef(k,1)), hii,degree
+
+!      if (degree == 2) then
+!      	call get_excitation(psi_det(1,1,1),psi_det(1,1,k),exc,degree,phase,N_int)
+!      	call decode_exc(exc,degree,h1,p1,h2,p2,s1,s2)
+!		print*, h1,h2,hii, abs(psi_coef(k,1))
+!      endif
+!      
+
+
+  enddo
+end
+
+!plot "test.dat" u (abs($2)):(abs($3)):4  w p palette

plugins/All_singles/README.rst

@@ -1,4 +0,0 @@
-==================
-All_singles Module
-==================
-

plugins/CAS_SD/.gitignore

@@ -1,4 +1,4 @@
-# Automatically created by /home/scemama/quantum_package/scripts/module/module_handler.py 
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
 IRPF90_temp
 IRPF90_man
 irpf90_entities

plugins/CID_SC2_selected/.gitignore

@@ -6,7 +6,6 @@ tags
 irpf90.make
 Makefile
 Makefile.depend
-build.ninja
 .ninja_log
 .ninja_deps
 ezfio_interface.irp.f

plugins/CIS/.gitignore

@@ -6,7 +6,6 @@ tags
 irpf90.make
 Makefile
 Makefile.depend
-build.ninja
 .ninja_log
 .ninja_deps
 ezfio_interface.irp.f

plugins/CISD_SC2_selected/.gitignore

@@ -1,33 +1,31 @@
-#
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
-# Do not modify this file. Add your ignored files to the gitignore
-# (without the dot at the beginning) file.
-#
 IRPF90_temp
 IRPF90_man
-irpf90.make
-tags
-Makefile.depend
 irpf90_entities
-build.ninja
+tags
+irpf90.make
+Makefile
+Makefile.depend
 .ninja_log
 .ninja_deps
-Pseudo
+ezfio_interface.irp.f
-Integrals_Monoelec
-Bitmask
-Integrals_Bielec
-CISD_selected
-AOs
-Selectors_full
-MOs
-Hartree_Fock
-Perturbation
-CISD
-Determinants
-Electrons
-Utils
-Properties
-Nuclei
-MOGuess
-SingleRefMethod
 Ezfio_files
+Perturbation
+Determinants
+Integrals_Monoelec
+MO_Basis
+Selectors_full
+SingleRefMethod
+Utils
+Pseudo
+Properties
+Bitmask
+AO_Basis
+Electrons
+CISD_selected
+MOGuess
+CISD
+Nuclei
+Hartree_Fock
+Integrals_Bielec
 cisd_sc2_selection

plugins/Casino/README.rst

@@ -21,7 +21,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 

plugins/DDCI_selected/.gitignore

@@ -6,7 +6,6 @@ tags
 irpf90.make
 Makefile
 Makefile.depend
-build.ninja
 .ninja_log
 .ninja_deps
 ezfio_interface.irp.f

plugins/DensityMatrix/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Bitmask

plugins/FCIdump/.gitignore

@@ -6,7 +6,6 @@ tags
 irpf90.make
 Makefile
 Makefile.depend
-build.ninja
 .ninja_log
 .ninja_deps
 ezfio_interface.irp.f

plugins/Full_CI/README.rst

@@ -159,7 +159,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_

plugins/Generators_full/README.rst

@@ -43,7 +43,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_

plugins/Hartree_Fock/README.rst

@@ -10,7 +10,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Integrals_Bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec>`_
 * `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
@@ -29,16 +29,6 @@ Documentation
   Alpha Fock matrix in AO basis set
 
 
-`big <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/test.irp.f#L1>`_
-  Produce `Huckel` MO orbital
-  output:  mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
-  Produce `Hartree_Fock` MO orbital
-  output: mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
-  output: hartree_fock.energy
-  input: mo_basis.mo_coef
-  Run SCF calculation
-
-
 `create_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L13>`_
   Create an MO guess if no MOs are present in the EZFIO directory
 

plugins/MP2/.gitignore

@@ -6,7 +6,6 @@ tags
 irpf90.make
 Makefile
 Makefile.depend
-build.ninja
 .ninja_log
 .ninja_deps
 ezfio_interface.irp.f

plugins/MRCC/.gitignore

@@ -1,4 +1,4 @@
-# Automatically created by /home/scemama/quantum_package/scripts/module/module_handler.py 
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
 IRPF90_temp
 IRPF90_man
 irpf90_entities

plugins/MRCC/mrcc_utils.irp.f

@@ -17,7 +17,6 @@ do i=1,N_det_non_cas
    lambda_mrcc(k,i) = psi_non_cas_coef(i,k)/ihpsi(k)
     if (dabs(ihpsi(k)).le.1.d-3) then
       lambda_mrcc(k,i) = 1.d0 / (psi_cas_energy_diagonalized(k)-hii)
-      icount_manu = icount_manu+1
       cycle
     endif
    enddo

plugins/Molden/README.rst

@@ -33,7 +33,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

plugins/Perturbation/README.rst

@@ -356,7 +356,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_

plugins/Properties/README.rst

@@ -148,7 +148,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 

plugins/QmcChem/.gitignore

@@ -1,4 +1,4 @@
-# Automatically created by /home/scemama/quantum_package/scripts/module/module_handler.py 
+# Automatically created by /home/razoa/quantum_package/scripts/module/module_handler.py 
 IRPF90_temp
 IRPF90_man
 irpf90_entities

plugins/Selectors_full/README.rst

@@ -181,7 +181,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_

plugins/loc_cele/README.rst

@@ -16,7 +16,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
 

scripts/compilation/qp_create_ninja.py

@@ -530,7 +530,7 @@ def ninja_readme_build(path_module, d_irp, dict_root_path):
     tags = join(root_module.abs, "tags")
     str_depend = " ".join(d_irp[path_module]["l_depend"])
 
-    tree = join(root_module.abs, "tree_dependency.png")
+    tree = join(root_module.abs, "tree_dependency.pdf")
 
     l_string = ["build {0}: build_readme {1} {2} {3}".format(path_readme,
                                                              tags,
@@ -714,7 +714,7 @@ def ninja_dot_tree_rule():
 
 def ninja_dot_tree_build(path_module, l_module):
 
-    path_tree = join(path_module.abs, "tree_dependency.png")
+    path_tree = join(path_module.abs, "tree_dependency.pdf")
     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),
@@ -869,14 +869,7 @@ if __name__ == "__main__":
     dict_root = module_instance.dict_root
     dict_root_path = dict_module_genelogy_path(dict_root)
 
-    l_module = d_genealogy_path.keys()
+    l_all_module = d_genealogy_path.keys()
-
-    for module in l_module:
-        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
-        # d o t _ t r e e  & r e a d  m e #
-        # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
-        l_string += ninja_dot_tree_build(module, l_module)
-        l_string += ninja_readme_build(module, d_irp, dict_root_path)
 
     # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
     # M o d u l e _ t o _ i r p #
@@ -884,14 +877,21 @@ if __name__ == "__main__":
 
     if arguments["--production"]:
 
-        d_binaries = get_dict_binaries(l_module, mode="production")
+        d_binaries = get_dict_binaries(l_all_module, mode="production")
         l_module = d_binaries.keys()
 
     elif arguments["--development"]:
 
-        d_binaries = get_dict_binaries(l_module, mode="development")
+        d_binaries = get_dict_binaries(l_all_module, mode="development")
         l_module = d_binaries.keys()
 
+        for module in l_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)
+
     create_build_ninja_global(l_module)
 
     for module_to_compile in l_module:

scripts/module/module_handler.py

@@ -177,7 +177,7 @@ class ModuleHandler():
 
         # Init
         try:
-            import pydot
+            from graphviz import Digraph
         except:
             with open(path, 'a'):
                 os.utime(path, None)
@@ -191,23 +191,20 @@ class ModuleHandler():
             if module not in all_ready_done:
                 for children in l_children:
                     # Add Edge
-                    edge = pydot.Edge(module, children)
+                    graph.edge(module, children)
-                    graph.add_edge(edge)
                     # Recurs
                     draw_module_edge(children, d_ref[children])
                 all_ready_done.append(module)
 
-        graph = pydot.Dot(graph_type='digraph')
+        graph = Digraph(comment=l_module)
         d_ref = self.dict_child
 
         # Create all the edge
         for module in l_module:
-            node_a = pydot.Node(module, fontcolor="red")
+            graph.node(module, fontcolor="red")
-            graph.add_node(node_a)
             draw_module_edge(module, d_ref[module])
 
-        # Save
+        graph.render('tree_dependency')
-        graph.write_png(path)
 
 
 if __name__ == '__main__':

scripts/module/update_README.py

@@ -66,7 +66,7 @@ def update_needed(data):
     with open('NEEDED_CHILDREN_MODULES', 'r') as f:
         modules = f.read()
 
-    header_image = ".. image:: tree_dependency.png\n\n"
+    header_image = ".. image:: tree_dependency.pdf\n\n"
 
     if modules.strip():
         modules = ['* `{0} <{1}>`_'.format(name, os.path.join(URL, name))

scripts/utility/dot_parser.py

@@ -1,536 +0,0 @@
-# -*- coding: Latin-1 -*-
-"""Graphviz's dot language parser.
-
-The dotparser parses graphviz files in dot and dot files and transforms them
-into a class representation defined by pydot.
-
-The module needs pyparsing (tested with version 1.2.2) and pydot
-
-Author: Michael Krause <michael@krause-software.de>
-Fixes by: Ero Carrera <ero@dkbza.org>
-"""
-
-__author__ = ['Michael Krause', 'Ero Carrera']
-__license__ = 'MIT'
-
-import sys
-import glob
-import pydot
-import re
-import codecs
-
-from pyparsing import __version__ as pyparsing_version
-
-from pyparsing import (
-    nestedExpr, Literal, CaselessLiteral, Word, Upcase, OneOrMore, ZeroOrMore,
-    Forward, NotAny, delimitedList, oneOf, Group, Optional, Combine, alphas,
-    nums, restOfLine, cStyleComment, nums, alphanums, printables, empty,
-    quotedString, ParseException, ParseResults, CharsNotIn, _noncomma,
-    dblQuotedString, QuotedString, ParserElement)
-
-
-class P_AttrList:
-    def __init__(self, toks):
-
-        self.attrs = {}
-        i = 0
-
-        while i < len(toks):
-            attrname = toks[i]
-            if i + 2 < len(toks) and toks[i + 1] == '=':
-                attrvalue = toks[i + 2]
-                i += 3
-            else:
-                attrvalue = None
-                i += 1
-
-            self.attrs[attrname] = attrvalue
-
-    def __repr__(self):
-
-        return "%s(%r)" % (self.__class__.__name__, self.attrs)
-
-
-class DefaultStatement(P_AttrList):
-    def __init__(self, default_type, attrs):
-
-        self.default_type = default_type
-        self.attrs = attrs
-
-    def __repr__(self):
-
-        return "%s(%s, %r)" % (self.__class__.__name__, self.default_type,
-                               self.attrs)
-
-
-top_graphs = list()
-
-
-def push_top_graph_stmt(str, loc, toks):
-
-    attrs = {}
-    g = None
-
-    for element in toks:
-
-        if (isinstance(element, (ParseResults, tuple, list)) and
-            len(element) == 1 and isinstance(element[0], basestring)):
-
-            element = element[0]
-
-        if element == 'strict':
-            attrs['strict'] = True
-
-        elif element in ['graph', 'digraph']:
-
-            attrs = {}
-
-            g = pydot.Dot(graph_type=element, **attrs)
-            attrs['type'] = element
-
-            top_graphs.append(g)
-
-        elif isinstance(element, basestring):
-            g.set_name(element)
-
-        elif isinstance(element, pydot.Subgraph):
-
-            g.obj_dict['attributes'].update(element.obj_dict['attributes'])
-            g.obj_dict['edges'].update(element.obj_dict['edges'])
-            g.obj_dict['nodes'].update(element.obj_dict['nodes'])
-            g.obj_dict['subgraphs'].update(element.obj_dict['subgraphs'])
-
-            g.set_parent_graph(g)
-
-        elif isinstance(element, P_AttrList):
-            attrs.update(element.attrs)
-
-        elif isinstance(element, (ParseResults, list)):
-            add_elements(g, element)
-
-        else:
-            raise ValueError, "Unknown element statement: %r " % element
-
-    for g in top_graphs:
-        update_parent_graph_hierarchy(g)
-
-    if len(top_graphs) == 1:
-        return top_graphs[0]
-
-    return top_graphs
-
-
-def update_parent_graph_hierarchy(g, parent_graph=None, level=0):
-
-    if parent_graph is None:
-        parent_graph = g
-
-    for key_name in ('edges', ):
-
-        if isinstance(g, pydot.frozendict):
-            item_dict = g
-        else:
-            item_dict = g.obj_dict
-
-        if not item_dict.has_key(key_name):
-            continue
-
-        for key, objs in item_dict[key_name].items():
-            for obj in objs:
-                if 'parent_graph' in obj and obj['parent_graph'].get_parent_graph(
-                ) == g:
-                    if obj['parent_graph'] is g:
-                        pass
-                    else:
-                        obj['parent_graph'].set_parent_graph(parent_graph)
-
-                if key_name == 'edges' and len(key) == 2:
-                    for idx, vertex in enumerate(obj['points']):
-                        if isinstance(vertex, (pydot.Graph, pydot.Subgraph,
-                                               pydot.Cluster)):
-                            vertex.set_parent_graph(parent_graph)
-                        if isinstance(vertex, pydot.frozendict):
-                            if vertex['parent_graph'] is g:
-                                pass
-                            else:
-                                vertex['parent_graph'].set_parent_graph(
-                                    parent_graph)
-
-
-def add_defaults(element, defaults):
-
-    d = element.__dict__
-    for key, value in defaults.items():
-        if not d.get(key):
-            d[key] = value
-
-
-def add_elements(g, toks,
-                 defaults_graph=None,
-                 defaults_node=None,
-                 defaults_edge=None):
-
-    if defaults_graph is None:
-        defaults_graph = {}
-    if defaults_node is None:
-        defaults_node = {}
-    if defaults_edge is None:
-        defaults_edge = {}
-
-    for elm_idx, element in enumerate(toks):
-
-        if isinstance(element, (pydot.Subgraph, pydot.Cluster)):
-
-            add_defaults(element, defaults_graph)
-            g.add_subgraph(element)
-
-        elif isinstance(element, pydot.Node):
-
-            add_defaults(element, defaults_node)
-            g.add_node(element)
-
-        elif isinstance(element, pydot.Edge):
-
-            add_defaults(element, defaults_edge)
-            g.add_edge(element)
-
-        elif isinstance(element, ParseResults):
-
-            for e in element:
-                add_elements(g, [e], defaults_graph, defaults_node,
-                             defaults_edge)
-
-        elif isinstance(element, DefaultStatement):
-
-            if element.default_type == 'graph':
-
-                default_graph_attrs = pydot.Node('graph', **element.attrs)
-                g.add_node(default_graph_attrs)
-
-            elif element.default_type == 'node':
-
-                default_node_attrs = pydot.Node('node', **element.attrs)
-                g.add_node(default_node_attrs)
-
-            elif element.default_type == 'edge':
-
-                default_edge_attrs = pydot.Node('edge', **element.attrs)
-                g.add_node(default_edge_attrs)
-                defaults_edge.update(element.attrs)
-
-            else:
-                raise ValueError, "Unknown DefaultStatement: %s " % element.default_type
-
-        elif isinstance(element, P_AttrList):
-
-            g.obj_dict['attributes'].update(element.attrs)
-
-        else:
-            raise ValueError, "Unknown element statement: %r" % element
-
-
-def push_graph_stmt(str, loc, toks):
-
-    g = pydot.Subgraph('')
-    add_elements(g, toks)
-    return g
-
-
-def push_subgraph_stmt(str, loc, toks):
-
-    g = pydot.Subgraph('')
-    for e in toks:
-        if len(e) == 3:
-            e[2].set_name(e[1])
-            if e[0] == 'subgraph':
-                e[2].obj_dict['show_keyword'] = True
-            return e[2]
-        else:
-            if e[0] == 'subgraph':
-                e[1].obj_dict['show_keyword'] = True
-            return e[1]
-
-    return g
-
-
-def push_default_stmt(str, loc, toks):
-
-    # The pydot class instances should be marked as
-    # default statements to be inherited by actual
-    # graphs, nodes and edges.
-    #
-    default_type = toks[0][0]
-    if len(toks) > 1:
-        attrs = toks[1].attrs
-    else:
-        attrs = {}
-
-    if default_type in ['graph', 'node', 'edge']:
-        return DefaultStatement(default_type, attrs)
-    else:
-        raise ValueError, "Unknown default statement: %r " % toks
-
-
-def push_attr_list(str, loc, toks):
-
-    p = P_AttrList(toks)
-    return p
-
-
-def get_port(node):
-
-    if len(node) > 1:
-        if isinstance(node[1], ParseResults):
-            if len(node[1][0]) == 2:
-                if node[1][0][0] == ':':
-                    return node[1][0][1]
-
-    return None
-
-
-def do_node_ports(node):
-
-    node_port = ''
-    if len(node) > 1:
-        node_port = ''.join([str(a) + str(b) for a, b in node[1]])
-
-    return node_port
-
-
-def push_edge_stmt(str, loc, toks):
-
-    tok_attrs = [a for a in toks if isinstance(a, P_AttrList)]
-    attrs = {}
-    for a in tok_attrs:
-        attrs.update(a.attrs)
-
-    e = []
-
-    if isinstance(toks[0][0], pydot.Graph):
-
-        n_prev = pydot.frozendict(toks[0][0].obj_dict)
-    else:
-        n_prev = toks[0][0] + do_node_ports(toks[0])
-
-    if isinstance(toks[2][0], ParseResults):
-
-        n_next_list = [[n.get_name(), ] for n in toks[2][0]]
-        for n_next in [n for n in n_next_list]:
-            n_next_port = do_node_ports(n_next)
-            e.append(pydot.Edge(n_prev, n_next[0] + n_next_port, **attrs))
-
-    elif isinstance(toks[2][0], pydot.Graph):
-
-        e.append(pydot.Edge(n_prev, pydot.frozendict(toks[2][0].obj_dict), **
-                            attrs))
-
-    elif isinstance(toks[2][0], pydot.Node):
-
-        node = toks[2][0]
-
-        if node.get_port() is not None:
-            name_port = node.get_name() + ":" + node.get_port()
-        else:
-            name_port = node.get_name()
-
-        e.append(pydot.Edge(n_prev, name_port, **attrs))
-
-    elif isinstance(toks[2][0], type('')):
-
-        for n_next in [n for n in tuple(toks)[2::2]]:
-
-            if isinstance(n_next, P_AttrList) or not isinstance(n_next[0],
-                                                                type('')):
-                continue
-
-            n_next_port = do_node_ports(n_next)
-            e.append(pydot.Edge(n_prev, n_next[0] + n_next_port, **attrs))
-
-            n_prev = n_next[0] + n_next_port
-
-    else:
-        # UNEXPECTED EDGE TYPE
-        pass
-
-    return e
-
-
-def push_node_stmt(s, loc, toks):
-
-    if len(toks) == 2:
-        attrs = toks[1].attrs
-    else:
-        attrs = {}
-
-    node_name = toks[0]
-    if isinstance(node_name, list) or isinstance(node_name, tuple):
-        if len(node_name) > 0:
-            node_name = node_name[0]
-
-    n = pydot.Node(str(node_name), **attrs)
-    return n
-
-
-graphparser = None
-
-
-def graph_definition():
-
-    global graphparser
-
-    if not graphparser:
-
-        # punctuation
-        colon = Literal(":")
-        lbrace = Literal("{")
-        rbrace = Literal("}")
-        lbrack = Literal("[")
-        rbrack = Literal("]")
-        lparen = Literal("(")
-        rparen = Literal(")")
-        equals = Literal("=")
-        comma = Literal(",")
-        dot = Literal(".")
-        slash = Literal("/")
-        bslash = Literal("\\")
-        star = Literal("*")
-        semi = Literal(";")
-        at = Literal("@")
-        minus = Literal("-")
-
-        # keywords
-        strict_ = CaselessLiteral("strict")
-        graph_ = CaselessLiteral("graph")
-        digraph_ = CaselessLiteral("digraph")
-        subgraph_ = CaselessLiteral("subgraph")
-        node_ = CaselessLiteral("node")
-        edge_ = CaselessLiteral("edge")
-
-        # token definitions
-
-        identifier = Word(alphanums + "_.").setName("identifier")
-
-        double_quoted_string = QuotedString('"',
-                                            multiline=True,
-                                            unquoteResults=False
-                                            )  # dblQuotedString
-
-        alphastring_ = OneOrMore(CharsNotIn(_noncomma + ' '))
-
-        def parse_html(s, loc, toks):
-            return '<%s>' % ''.join(toks[0])
-
-        opener = '<'
-        closer = '>'
-        html_text = nestedExpr(opener, closer, (CharsNotIn(opener + closer)
-             )).setParseAction(parse_html).leaveWhitespace()
-
-        ID = (identifier | html_text | double_quoted_string |
-              #.setParseAction(strip_quotes) |
-              alphastring_).setName("ID")
-
-        float_number = Combine(
-            Optional(minus) + OneOrMore(Word(nums + "."))).setName(
-                "float_number")
-
-        righthand_id = (float_number | ID).setName("righthand_id")
-
-        port_angle = (at + ID).setName("port_angle")
-
-        port_location = (OneOrMore(Group(colon + ID)) |
-                         Group(colon + lparen + ID + comma + ID + rparen)
-                         ).setName("port_location")
-
-        port = (Group(port_location + Optional(port_angle)) |
-                Group(port_angle + Optional(port_location))).setName("port")
-
-        node_id = (ID + Optional(port))
-        a_list = OneOrMore(ID + Optional(equals + righthand_id) +
-                           Optional(comma.suppress())).setName("a_list")
-
-        attr_list = OneOrMore(
-            lbrack.suppress() + Optional(a_list) + rbrack.suppress()).setName(
-                "attr_list")
-
-        attr_stmt = (Group(graph_ | node_ | edge_) + attr_list).setName(
-            "attr_stmt")
-
-        edgeop = (Literal("--") | Literal("->")).setName("edgeop")
-
-        stmt_list = Forward()
-        graph_stmt = Group(
-            lbrace.suppress() + Optional(stmt_list) + rbrace.suppress() +
-            Optional(semi.suppress())).setName("graph_stmt")
-
-        edge_point = Forward()
-
-        edgeRHS = OneOrMore(edgeop + edge_point)
-        edge_stmt = edge_point + edgeRHS + Optional(attr_list)
-
-        subgraph = Group(subgraph_ + Optional(ID) + graph_stmt).setName(
-            "subgraph")
-
-        edge_point << Group(subgraph | graph_stmt |
-                            node_id).setName('edge_point')
-
-        node_stmt = (node_id + Optional(attr_list) + Optional(semi.suppress())
-                     ).setName("node_stmt")
-
-        assignment = (ID + equals + righthand_id).setName("assignment")
-        stmt = (assignment | edge_stmt | attr_stmt | subgraph | graph_stmt |
-                node_stmt).setName("stmt")
-        stmt_list << OneOrMore(stmt + Optional(semi.suppress()))
-
-        graphparser = OneOrMore((Optional(strict_) + Group(
-            (graph_ | digraph_)) + Optional(ID) + graph_stmt
-                                  ).setResultsName("graph"))
-
-        singleLineComment = Group("//" + restOfLine) | Group("#" + restOfLine)
-
-        # actions
-
-        graphparser.ignore(singleLineComment)
-        graphparser.ignore(cStyleComment)
-
-        assignment.setParseAction(push_attr_list)
-        a_list.setParseAction(push_attr_list)
-        edge_stmt.setParseAction(push_edge_stmt)
-        node_stmt.setParseAction(push_node_stmt)
-        attr_stmt.setParseAction(push_default_stmt)
-
-        subgraph.setParseAction(push_subgraph_stmt)
-        graph_stmt.setParseAction(push_graph_stmt)
-        graphparser.setParseAction(push_top_graph_stmt)
-
-    return graphparser
-
-
-def parse_dot_data(data):
-
-    global top_graphs
-
-    top_graphs = list()
-
-    if data.startswith(codecs.BOM_UTF8):
-        data = data.decode('utf-8')
-
-    try:
-
-        graphparser = graph_definition()
-
-        if pyparsing_version >= '1.2':
-            graphparser.parseWithTabs()
-
-        tokens = graphparser.parseString(data)
-
-        if len(tokens) == 1:
-            return tokens[0]
-        else:
-            return [g for g in tokens]
-
-    except ParseException, err:
-
-        print err.line
-        print " " * (err.column - 1) + "^"
-        print err
-        return None

src/AO_Basis/README.rst

@@ -36,7 +36,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 

src/Bitmask/README.rst

@@ -40,7 +40,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
 

src/Determinants/README.rst

@@ -32,7 +32,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Integrals_Monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec>`_
 * `Integrals_Bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec>`_

src/Electrons/README.rst

@@ -24,7 +24,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 

src/Ezfio_files/README.rst

@@ -30,15 +30,19 @@ Documentation
   .br
 
 
-`output_ao_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L1>`_
+`output_alavi <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L1>`_
+  Output file for Alavi
+
+
+`output_ao_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L21>`_
   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_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L41>`_
   Output file for Bitmask
 
 
-`output_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L41>`_
+`output_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L61>`_
   Output file for Casino
 
 
@@ -46,75 +50,75 @@ Documentation
   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#L61>`_
+`output_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L81>`_
   Output file for Determinants
 
 
-`output_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L81>`_
+`output_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L101>`_
   Output file for Electrons
 
 
-`output_ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L101>`_
+`output_ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L121>`_
   Output file for Ezfio_files
 
 
-`output_full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L121>`_
+`output_full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
   Output file for Full_CI
 
 
-`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L141>`_
+`output_generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
   Output file for Generators_full
 
 
-`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L161>`_
+`output_hartree_fock <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
   Output file for Hartree_Fock
 
 
-`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L181>`_
+`output_integrals_bielec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
   Output file for Integrals_Bielec
 
 
-`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L201>`_
+`output_integrals_monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
   Output file for Integrals_Monoelec
 
 
-`output_loc_cele <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L221>`_
+`output_loc_cele <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
   Output file for loc_cele
 
 
-`output_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L241>`_
+`output_mo_basis <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
   Output file for MO_Basis
 
 
-`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L261>`_
+`output_moguess <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
   Output file for MOGuess
 
 
-`output_molden <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L281>`_
+`output_molden <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
   Output file for Molden
 
 
-`output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L301>`_
+`output_nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
   Output file for Nuclei
 
 
-`output_perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L321>`_
+`output_perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L341>`_
   Output file for Perturbation
 
 
-`output_properties <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L341>`_
+`output_properties <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L361>`_
   Output file for Properties
 
 
-`output_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L361>`_
+`output_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L381>`_
   Output file for Pseudo
 
 
-`output_selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L381>`_
+`output_selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L401>`_
   Output file for Selectors_full
 
 
-`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L401>`_
+`output_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/output.irp.f_shell_40#L421>`_
   Output file for Utils
 
 

src/Integrals_Bielec/README.rst

@@ -16,7 +16,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo>`_
 * `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_

src/Integrals_Monoelec/README.rst

@@ -4,7 +4,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
 * `Pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo>`_

src/MOGuess/README.rst

@@ -8,7 +8,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Integrals_Monoelec <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec>`_
 

src/MOGuess/h_core_guess_routine.irp.f

@@ -0,0 +1,16 @@
+subroutine hcore_guess
+  BEGIN_DOC
+! Produce `H_core` MO orbital
+  END_DOC
+  implicit none
+  character*(64)                 :: label
+  mo_coef = ao_ortho_lowdin_coef
+  TOUCH mo_coef
+  label = "Guess"
+  call mo_as_eigvectors_of_mo_matrix(mo_mono_elec_integral,          &
+                                     size(mo_mono_elec_integral,1),  &
+                                     size(mo_mono_elec_integral,2),label)
+  print *,  'save mos'
+  call save_mos
+  SOFT_TOUCH mo_coef mo_label
+end

src/MO_Basis/README.rst

@@ -36,7 +36,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `AO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_

src/Nuclei/README.rst

@@ -12,7 +12,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

src/Pseudo/README.rst

@@ -8,7 +8,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. by the `update_README.py` script.
 
-.. image:: tree_dependency.png
+.. image:: tree_dependency.pdf
 
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_