update_readme.py and so one

scripts/compilation/create_ninja_build.py

@@ -484,13 +484,14 @@ def get_program(path_module):
             return []
 
 
-def get_dict_binaries(mode):
+def get_dict_binaries(mode="production"):
     """
     Return a dict [module] = list_binaries
-    If a the production mode is enable only header module will produce binaries
+    If a the production mode is enable only header module
+    who will produce all binaries
 
     Example : The module Full_CI can produce the binary SCF
-    so you dont need to use at all the module Hartree-Fock
+    so you dont need to compile at all the module Hartree-Fock
     """
     d_binaries = defaultdict(list)
 
@@ -653,7 +654,6 @@ if __name__ == "__main__":
     d_irp = get_file_dependency(d_genealogy_path)
 
     d_binaries_production = get_dict_binaries(mode="production")
-    d_binaries_development = get_dict_binaries(mode="development")
 
     # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
     # M o d u l e _ t o _ i r p #
@@ -663,15 +663,7 @@ if __name__ == "__main__":
         l_module_to_irp = d_binaries_production.keys()
 
     elif arguments["--development"]:
-        l_module_to_irp = d_binaries_development.keys()
+        l_module_to_irp = d_genealogy_path.keys()
-
-    l_all_module = d_genealogy_path.keys()
-
-    for module in l_all_module:
-        # ~#~#~#~#~#~#~#~ #
-        # d o t _ t r e e #
-        # ~#~#~#~#~#~#~#~ #
-        l_string += ninja_dot_tree_build(module)
 
     for module_to_compile in l_module_to_irp:
 
@@ -689,6 +681,11 @@ if __name__ == "__main__":
         l_string += ninja_irpf90_make_build(module_to_compile, l_children,
                                             d_irp)
 
+        # ~#~#~#~#~#~#~#~ #
+        # d o t _ t r e e #
+        # ~#~#~#~#~#~#~#~ #
+        l_string += ninja_dot_tree_build(module_to_compile)
+
     # ~#~#~#~#~#~#~ #
     #  b i n a r y  #
     # ~#~#~#~#~#~#~ #

scripts/module/update_README.py

@@ -12,10 +12,11 @@ URL = "http://github.com/LCPQ/quantum_package/tree/master/src/"
 
 import os
 import subprocess
+from collections import namedtuple
 
 header = """
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 """
 
@@ -43,18 +44,19 @@ def fetch_splitted_data():
 
     return result
 
+
 def update_needed(data):
     """Read the NEEDED_CHILDREN_MODULES file, and replace the data with it.
     Create the links to the GitHub pages."""
 
-    file = open('NEEDED_CHILDREN_MODULES', 'r')
+    with open('NEEDED_CHILDREN_MODULES', 'r') as f:
-    modules = file.read()
+        modules = f.read()
-    file.close()
 
     header_image = ".. image:: tree_dependency.png\n\n"
 
-    if modules.strip() != "":
+    if modules.strip():
-        modules = ['* `%s <%s%s>`_' % (x, URL, x) for x in modules.split()]
+        modules = ['* `{0} <{1}>`_'.format(name, os.path.join(URL, name))
+                   for name in modules.split()]
         modules = "\n".join(modules)
         modules = Needed_key + header + header_image + modules + '\n\n'
 
@@ -70,71 +72,50 @@ def update_needed(data):
     return data
 
 
-def update_documentation(data):
-    """Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation"""
-
-    # If the file does not exist, don't do anything
-    try:
-        file = open('tags', 'r')
-    except:
-        return
-    tags = file.readlines()
-    file.close()
-
 def extract_doc(item):
     """Extracts the documentation contained in IRPF90_man file"""
-        file = open("IRPF90_man/%s.l" % (item), 'r')
+
-        lines = file.readlines()
+    with open("IRPF90_man/%s.l" % (item), 'r') as f:
-        file.close()
+        l_line = f.readlines()
+
     result = []
     inside = False
-        for line in lines:
+    for line in l_line:
         if not inside:
             inside = line.startswith(".SH Description")
         else:
             if line.startswith(".SH"):
                 break
-                result.append("  " + line.strip())
+            result.append("  {0}".format(line.strip()))
 
-        if result == []:
+    if not result:
         result = ["  Undocumented"]
+
     return "\n".join(result) + '\n'
 
-    items = []
-    dirname = os.path.basename(os.getcwd())
-    command = "git ls-tree --full-tree --name-only HEAD:src/%s"
-    command = command % (dirname)
-    try:
-        if dirname != 'src':
-            p = subprocess.Popen(command.split(), stdout=subprocess.PIPE)
-            tracked_files = p.stdout.read()
-        else:
-            tracked_files = ""
-        tracked_files = tracked_files.splitlines()
-    except:
-        tracked_files = []
-    for filename in tracked_files:
-        if filename.endswith('.irp.f'):
-            # Search for providers, subroutines and functions in each file using
-            # the tags file
-            search = "\t" + filename + "\t"
-            tmp = filter(lambda line: search in line, tags)
 
-            # Search for the documentation in the IRPF90_man directory
+def update_documentation(data):
-            for item in tmp:
+    """Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation"""
-                item, _, line = item.strip().split('\t')
-                doc = extract_doc(item)
-                items.append((item, filename, doc, line))
 
-    dirname = os.path.basename(os.getcwd())
+    IRP_info = namedtuple('IRP_info', ["name", "file", "line"])
-    # Write the documentation in the README
-    template = "`%(item)s <%(url)s%(dirname)s/%(filename)s#L%(line)s>`_\n%(doc)s\n"
 
-    documentation = Doc_key + header
+    # If the file does not exist, don't do anything
-    url = URL
+
-    for item, filename, doc, line in items:
+    with open('tags', 'r') as f:
-        documentation += template % locals()
+        l_info = [IRP_info(*i.split()) for i in f.readlines()
-    documentation += '\n\n'
+                  if "/" not in i.split()[1]]
+
+    l_line = []
+    module_name = os.path.basename(os.getcwd())
+
+    for irp in l_info:
+        url = os.path.join(URL, module_name, irp.file)
+        doc = extract_doc(irp.name)
+
+        l_line += ["`{0} <{1}#L{2}>`_".format(irp.name, url, irp.line), doc,
+                   ""]
+
+    documentation = Doc_key + header + "\n".join(l_line)
 
     has_doc = False
     for i in range(len(data)):
@@ -153,8 +134,6 @@ def git_add():
     git add README.rst
     throw an error if git is not precent"""
 
-    import subprocess
-
     try:
         # pipe output to /dev/null for silence
         null = open("/dev/null", "w")
@@ -167,6 +146,7 @@ def git_add():
 
 def main():
     data = fetch_splitted_data()
+
     data = update_documentation(data)
     data = update_needed(data)
     output = ''.join(data)

src/CAS_SD/README.rst

@@ -11,18 +11,67 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 `full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/cas_sd_selected.irp.f#L1>`_
   Undocumented
 
 
+`h_apply_cas_sd <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L406>`_
+  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_cas_sd_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cas_sd_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L263>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cas_sd_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1842>`_
+  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_cas_sd_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1358>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cas_sd_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1661>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cas_sd_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L1112>`_
+  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_cas_sd_selected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L594>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_cas_sd_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/H_apply.irp.f_shell_16#L917>`_
+  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 from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
 

src/CID_SC2_selected/README.rst

@@ -6,18 +6,33 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 `cisd_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CID_SC2_selected/cid_sc2_selection.irp.f#L1>`_
   Undocumented
 
 
+`h_apply_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/CID_SC2_selected/H_apply.irp.f_shell_9#L487>`_
+  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_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_SC2_selected/H_apply.irp.f_shell_9#L1>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CID_SC2_selected/H_apply.irp.f_shell_9#L306>`_
+  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 from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
 

src/CIS/README.rst

@@ -11,21 +11,37 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. 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#L406>`_
+  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#L263>`_
+  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
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
 

src/CISD_SC2_selected/README.rst

@@ -6,18 +6,67 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 `cisd_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/cisd_sc2_selection.irp.f#L1>`_
   Undocumented
 
 
+`h_apply_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1253>`_
+  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_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L767>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_pt2_en_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1946>`_
+  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_pt2_en_sc2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1460>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_pt2_en_sc2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1765>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1072>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L521>`_
+  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_sc2_selected_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L1>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_sc2_selected_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/H_apply.irp.f_shell_17#L326>`_
+  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 from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
 

src/DDCI_selected/README.rst

@@ -6,18 +6,50 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 `full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/ddci.irp.f#L1>`_
   Undocumented
 
 
+`h_apply_ddci_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L1267>`_
+  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_ddci_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L774>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_ddci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L1083>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_ddci_selection <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L528>`_
+  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_ddci_selection_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L1>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_ddci_selection_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/H_apply.irp.f_shell_15#L330>`_
+  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 from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
 

src/FCIdump/README.rst

@@ -8,18 +8,16 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. 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
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
 

src/Full_CI/README.rst

@@ -8,21 +8,156 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 `full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/full_ci_no_skip.irp.f#L1>`_
   Undocumented
 
+
+`h_apply_fci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L519>`_
+  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_fci_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_fci_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2712>`_
+  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_fci_mono_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2192>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_fci_mono_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2515>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_fci_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L324>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_fci_no_skip <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1974>`_
+  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_fci_no_skip_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1456>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_fci_no_skip_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1779>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_fci_pt2 <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1249>`_
+  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_fci_pt2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L765>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_fci_pt2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L1068>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_pt2_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4210>`_
+  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_pt2_mono_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3724>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_pt2_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4027>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_pt2_mono_di_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L5665>`_
+  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_pt2_mono_di_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L5181>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_pt2_mono_di_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L5484>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_select_mono_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3478>`_
+  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_select_mono_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L2958>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_select_mono_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L3281>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_select_mono_di_delta_rho <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4935>`_
+  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_select_mono_di_delta_rho_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4417>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_select_mono_di_delta_rho_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/H_apply.irp.f_shell_43#L4740>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
 `var_pt2_ratio_run <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/var_pt2_ratio.irp.f#L1>`_
   Undocumented
 
-
-
 Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
 

src/MP2/README.rst

@@ -6,18 +6,33 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
+
+`h_apply_mp2 <http://github.com/LCPQ/quantum_package/tree/master/src/MP2/H_apply.irp.f_shell_9#L485>`_
+  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_mp2_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/MP2/H_apply.irp.f_shell_9#L1>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_mp2_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/MP2/H_apply.irp.f_shell_9#L304>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
 
 `mp2 <http://github.com/LCPQ/quantum_package/tree/master/src/MP2/mp2.irp.f#L1>`_
   Undocumented
 
-
-
 Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
 

src/MRCC/README.rst

@@ -6,7 +6,7 @@ Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
 
@@ -18,7 +18,23 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
+
+`ci_eigenvectors_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L79>`_
+  Eigenvectors/values of the CI matrix
+
+
+`ci_eigenvectors_s2_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L80>`_
+  Eigenvectors/values of the CI matrix
+
+
+`ci_electronic_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L78>`_
+  Eigenvectors/values of the CI matrix
+
+
+`ci_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L145>`_
+  N_states lowest eigenvalues of the dressed CI matrix
+
 
 `davidson_diag_hjj_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/davidson.irp.f#L51>`_
   Davidson diagonalization with specific diagonal elements of the H matrix
@@ -40,6 +56,7 @@ Documentation
   .br
   Initial guess vectors are not necessarily orthonormal
 
+
 `davidson_diag_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/davidson.irp.f#L1>`_
   Davidson diagonalization.
   .br
@@ -58,6 +75,66 @@ Documentation
   .br
   Initial guess vectors are not necessarily orthonormal
 
+
+`delta_ij <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L43>`_
+  Dressing matrix in N_det basis
+
+
+`delta_ij_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L34>`_
+  Dressing matrix in SD basis
+
+
+`diagonalize_ci_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L160>`_
+  Replace the coefficients of the CI states by the coefficients of the
+  eigenstates of the CI matrix
+
+
+`dressing_type <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L26>`_
+  [ Simple | MRCC ]
+
+
+`find_triples_and_quadruples <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L202>`_
+  Undocumented
+
+
+`h_apply_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L986>`_
+  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_mrcc_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L575>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_mrcc_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L840>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_mrcc_simple <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L412>`_
+  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_mrcc_simple_diexc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L1>`_
+  Generate all double excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_apply_mrcc_simple_monoexc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/H_apply.irp.f_shell_31#L266>`_
+  Generate all single excitations of key_in using the bit masks of holes and
+  particles.
+  Assume N_int is already provided.
+
+
+`h_matrix_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L63>`_
+  Dressed H with Delta_ij
+
+
 `h_u_0_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/davidson.irp.f#L355>`_
   Computes v_0 = H|u_0>
   .br
@@ -65,60 +142,35 @@ Documentation
   .br
   H_jj : array of <j|H|j>
 
-`mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L1>`_
-  Undocumented
-
-`run <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L10>`_
-  Undocumented
-
-`run_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L42>`_
-  Undocumented
-
-`run_mrcc_test <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L29>`_
-  Undocumented
-
-`find_triples_and_quadruples <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L202>`_
-  Undocumented
-
-`mrcc_dress <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L15>`_
-  Undocumented
-
-`mrcc_dress_simple <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L156>`_
-  Undocumented
-
-`psi_cas_lock <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L3>`_
-  Locks on CAS determinants to fill delta_ij
-
-`ci_eigenvectors_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L79>`_
-  Eigenvectors/values of the CI matrix
-
-`ci_eigenvectors_s2_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L80>`_
-  Eigenvectors/values of the CI matrix
-
-`ci_electronic_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L78>`_
-  Eigenvectors/values of the CI matrix
-
-`ci_energy_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L145>`_
-  N_states lowest eigenvalues of the dressed CI matrix
-
-`delta_ij <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L43>`_
-  Dressing matrix in N_det basis
-
-`delta_ij_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L34>`_
-  Dressing matrix in SD basis
-
-`diagonalize_ci_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L160>`_
-  Replace the coefficients of the CI states by the coefficients of the
-  eigenstates of the CI matrix
-
-`dressing_type <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L26>`_
-  [ Simple | MRCC ]
-
-`h_matrix_dressed <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L63>`_
-  Dressed H with Delta_ij
 
 `lambda_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_utils.irp.f#L2>`_
   cm/<Psi_0|H|D_m>
 
 
+`mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L1>`_
+  Undocumented
+
+
+`mrcc_dress <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L15>`_
+  Undocumented
+
+
+`mrcc_dress_simple <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L156>`_
+  Undocumented
+
+
+`psi_cas_lock <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc_dress.irp.f#L3>`_
+  Locks on CAS determinants to fill delta_ij
+
+
+`run <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L10>`_
+  Undocumented
+
+
+`run_mrcc <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L42>`_
+  Undocumented
+
+
+`run_mrcc_test <http://github.com/LCPQ/quantum_package/tree/master/src/MRCC/mrcc.irp.f#L29>`_
+  Undocumented
 

src/Molden/README.rst

@@ -6,30 +6,32 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. 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
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
 

src/Pseudo/README.rst

@@ -2,25 +2,66 @@
 Pseudo Module
 =============
 
-Documentation
-=============
-
-.. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
-
-
-
 Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
 
-.. image:: tree_dependancy.png
+.. image:: tree_dependency.png
 
-<<<<<<< HEAD
-=======
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
->>>>>>> LCPQ-master
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
 
+Documentation
+=============
+
+.. Do not edit this section. It was auto-generated from the
+.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+
+`do_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L248>`_
+  Using pseudo potential integral of not
+
+
+`pseudo_dz_k <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L204>`_
+  test
+
+
+`pseudo_dz_kl <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L94>`_
+  test
+
+
+`pseudo_grid_rmax <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L6>`_
+  R_maxof the QMC grid
+
+
+`pseudo_grid_size <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L160>`_
+  Nb of points of the QMC grid
+
+
+`pseudo_klocmax <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L116>`_
+  test
+
+
+`pseudo_kmax <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L72>`_
+  test
+
+
+`pseudo_lmax <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L138>`_
+  test
+
+
+`pseudo_n_k <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L226>`_
+  test
+
+
+`pseudo_n_kl <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L182>`_
+  test
+
+
+`pseudo_v_k <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L28>`_
+  test
+
+
+`pseudo_v_kl <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L50>`_
+  test
+

src/QmcChem/README.rst

@@ -6,7 +6,7 @@ Documentation
 =============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 `ao_pseudo_grid <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pot_ao_pseudo_ints.irp.f#L225>`_
   Grid points for f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \chi_i^{A} (r-r_A) d\Omega_C
@@ -14,40 +14,46 @@ Documentation
   <img src="http://latex.codecogs.com/gif.latex?f(|r-r_A|)&space;=&space;\int&space;Y_{lm}^{C}&space;(|r-r_C|,&space;\Omega_C)&space;\chi_i^{A}&space;(r-r_A)&space;d\Omega_C"
   title="f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \chi_i^{A} (r-r_A) d\Omega_C" />
 
+
 `aux_pseudo_integral <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pot_ao_pseudo_ints.irp.f#L1>`_
   Pseudo-potential
 
+
 `aux_pseudo_integral_local <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pot_ao_pseudo_ints.irp.f#L15>`_
   Local pseudo-potential
 
+
 `aux_pseudo_integral_non_local <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pot_ao_pseudo_ints.irp.f#L121>`_
   Local pseudo-potential
 
+
 `mo_pseudo_grid <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pot_ao_pseudo_ints.irp.f#L276>`_
   Grid points for f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \phi_i^{A} (r-r_A) d\Omega_C
   .br
   <img src="http://latex.codecogs.com/gif.latex?f(|r-r_A|)&space;=&space;\int&space;Y_{lm}^{C}&space;(|r-r_C|,&space;\Omega_C)&space;\chi_i^{A}&space;(r-r_A)&space;d\Omega_C"
   title="f(|r-r_A|) = \int Y_{lm}^{C} (|r-r_C|, \Omega_C) \chi_i^{A} (r-r_A) d\Omega_C" />
 
-`test_pseudo_grid_ao <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pot_ao_pseudo_ints.irp.f#L321>`_
-  Undocumented
 
 `pseudo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pseudo.irp.f#L12>`_
   Pseudo-potential expressed in the basis of ao products
 
-`write_pseudopotential <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pseudo.irp.f#L1>`_
-  Write the pseudo_potential into the EZFIO file
 
 `save_for_qmc <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/save_for_qmcchem.irp.f#L1>`_
   Undocumented
 
 
+`test_pseudo_grid_ao <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pot_ao_pseudo_ints.irp.f#L321>`_
+  Undocumented
+
+
+`write_pseudopotential <http://github.com/LCPQ/quantum_package/tree/master/src/QmcChem/pseudo.irp.f#L1>`_
+  Write the pseudo_potential into the EZFIO file
 
 Needed Modules
 ==============
 
 .. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
+.. by the `update_README.py` script.
 
 .. image:: tree_dependency.png