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update_readme.py and so one

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This commit is contained in:
Thomas Applencourt 2015-06-04 12:09:28 +02:00
parent 81ca7f2545
commit 30df5835a1
14 changed files with 564 additions and 177 deletions
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23
scripts/compilation/create_ninja_build.py
View File

@ -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_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)
l_module_to_irp = d_genealogy_path.keys()
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 #
# ~#~#~#~#~#~#~ #

108
scripts/module/update_README.py
View File

@ -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')
modules = file.read()
file.close()
with open('NEEDED_CHILDREN_MODULES', 'r') as f:
modules = f.read()
header_image = ".. image:: tree_dependency.png\n\n"
if modules.strip() != "":
modules = ['* `%s <%s%s>`_' % (x, URL, x) for x in modules.split()]
if modules.strip():
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 extract_doc(item):
"""Extracts the documentation contained in IRPF90_man file"""
with open("IRPF90_man/%s.l" % (item), 'r') as f:
l_line = f.readlines()
result = []
inside = False
for line in l_line:
if not inside:
inside = line.startswith(".SH Description")
else:
if line.startswith(".SH"):
break
result.append(" {0}".format(line.strip()))
if not result:
result = [" Undocumented"]
return "\n".join(result) + '\n'
def update_documentation(data):
"""Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation"""
IRP_info = namedtuple('IRP_info', ["name", "file", "line"])
# 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()
file.close()
result = []
inside = False
for line in lines:
if not inside:
inside = line.startswith(".SH Description")
else:
if line.startswith(".SH"):
break
result.append(" " + line.strip())
with open('tags', 'r') as f:
l_info = [IRP_info(*i.split()) for i in f.readlines()
if "/" not in i.split()[1]]
if result == []:
result = [" Undocumented"]
return "\n".join(result) + '\n'
l_line = []
module_name = os.path.basename(os.getcwd())
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)
for irp in l_info:
url = os.path.join(URL, module_name, irp.file)
doc = extract_doc(irp.name)
# Search for the documentation in the IRPF90_man directory
for item in tmp:
item, _, line = item.strip().split('\t')
doc = extract_doc(item)
items.append((item, filename, doc, line))
l_line += ["`{0} <{1}#L{2}>`_".format(irp.name, url, irp.line), doc,
""]
dirname = os.path.basename(os.getcwd())
# Write the documentation in the README
template = "`%(item)s <%(url)s%(dirname)s/%(filename)s#L%(line)s>`_\n%(doc)s\n"
documentation = Doc_key + header
url = URL
for item, filename, doc, line in items:
documentation += template % locals()
documentation += '\n\n'
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)

53
src/CAS_SD/README.rst
View File

@ -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

19
src/CID_SC2_selected/README.rst
View File

@ -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

24
src/CIS/README.rst
View File

@ -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

53
src/CISD_SC2_selected/README.rst
View File

@ -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

36
src/DDCI_selected/README.rst
View File

@ -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

6
src/FCIdump/README.rst
View File

@ -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

143
src/Full_CI/README.rst
View File

@ -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

23
src/MP2/README.rst
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@ -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

158
src/MRCC/README.rst
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@ -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

10
src/Molden/README.rst
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@ -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

67
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@ -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

18
src/QmcChem/README.rst
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@ -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