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Code Issues Releases Wiki Activity

Remove makefile.depend dependancy !

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This commit is contained in:
Thomas Applencourt 2015-05-27 11:02:13 +02:00
parent af1acde61f
commit ba49beff36
19 changed files with 157 additions and 265 deletions
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142
scripts/compilation/create_ninja_build.py
View File

@ -3,6 +3,7 @@
import os
import sys
import glob
from os.path import join
@ -18,10 +19,12 @@ from collections import namedtuple
Path = namedtuple('Path', ['abs', 'rel'])
EZ_config_path = namedtuple('EZ_config', ['path_in_module', 'path_in_ezfio'])
EZ_handler = namedtuple('EZ_handler', ['ez_module', 'ez_cfg', 'ez_interface', 'ez_config', 'ez_default', 'ez_ocaml'])
EZ_handler = namedtuple('EZ_handler', ['ez_module', 'ez_cfg',
'ez_interface', 'ez_config',
'ez_default', 'ez_ocaml'])
try:
from module_handler import module_genealogy
from module_handler import module_genealogy, file_dependancy
from cache import cache
from read_compilation_cfg import get_compilation_option
except ImportError:
@ -29,43 +32,10 @@ except ImportError:
sys.exit(1)
# _
# |\/| _. | _ _|_ o | _ _| _ ._ ._ _|
# | | (_| |< (/_ | | | (/_ o (_| (/_ |_) | | (_|
#
def ninja_makefile_depend_rule():
# Rule
l_string = ["rule build_makefile.depend"]
l_string += [" command = module_handler.py save_makefile_depend $module/NEEDED_CHILDREN_MODULES"]
l_string += [""]
return l_string
def ninja_makefile_depend_build(l_all_needed_molule, path_module):
l_makefile = [join(i.abs, "Makefile") for i in l_all_needed_molule]
# Build
path_mkdepend = join(path_module.abs, "Makefile.depend")
str_l_makefile = " ".join(l_makefile)
l_string = ["build {0}: build_makefile.depend {1}".format(path_mkdepend,
str_l_makefile)]
l_string += [" module = {0}".format(path_module.abs)]
l_string += [""]
return l_string
import glob
# _ __ _ ___ _ _
# |_ / |_ | / \ _ _|_ _
# |_ /_ | _|_ \_/ o (_ | (_|
# _|
def get_l_module_with_ezfio_cfg():
from os import listdir
from os.path import isfile, join
@ -213,13 +183,13 @@ def ninja_ezfio_config_build(l_ezfio_config):
return l_string
def ninja_ezfio_rule():
def ninja_ezfio_rule(pwd_config_file):
# Rule
l_string = ["rule build_ezfio"]
l_flag = []
for flag in ["FC", "FCFLAGS", "IRPF90"]:
str_ = "export {0}='{1}'".format(flag, get_compilation_option(flag))
str_ = "export {0}='{1}'".format(flag, get_compilation_option(pwd_config_file, flag))
l_flag.append(str_)
l_cmd = ["cd {0}".format(qpackage_root_ezfio)] + l_flag + ["make", "make Python"]
@ -297,9 +267,7 @@ def dict_needed_modules(l_module_to_compile):
for module_rel in l_module_to_compile:
module_abs = join(qpackage_root_src, module_rel)
path_neeeded_module = join(module_abs, "NEEDED_CHILDREN_MODULES")
d[Path(module_abs, module_rel)] = [Path(join(qpackage_root_src, m_children), m_children) for m_children in module_genealogy(path_neeeded_module)]
d[Path(module_abs, module_rel)] = [Path(join(qpackage_root_src, m_children), m_children) for m_children in module_genealogy(module_rel)]
return d
@ -319,32 +287,28 @@ def get_irp_dependancy(d_info_module):
return d_irp
def ninja_irpf90_make_rule():
def ninja_irpf90_make_rule(pwd_config_file):
# Rule
l_string = ["pool irp_pool"]
l_string += [" depth = 1"]
l_string += [""]
l_string += ["rule build_irpf90.make"]
l_string += [" command = cd $module ; irpf90 $include_dir $irpf90_flag"]
flag = get_compilation_option(pwd_config_file, "IRPF90_FLAGS")
l_cmd = ["cd $module",
"export SRC=$src",
"export OBJ=$obj",
"irpf90 $include_dir irpf90_flag = {0}".format(flag)]
l_string += [" command = {0}".format(" ; ".join(l_cmd))]
l_string += [" pool = irp_pool"]
l_string += [""]
return l_string
def ninja_create_l_irp_build(d_irp):
l_string = []
for m, l_irp in d_irp.iteritems():
dep = " ".join(l_irp)
l_string += ["build l_irp_{0}: phony {1}".format(m, dep)]
l_string += [""]
return l_string
def ninja_irpf90_make_build(l_all_needed_molule,
path_module,
d_irp):
@ -357,28 +321,32 @@ def ninja_irpf90_make_build(l_all_needed_molule,
str_l_irp_need = " ".join(l_irp_need)
path_makefiledepend = join(path_module.abs, "Makefile.depend")
if l_all_needed_molule:
str_l_destination = "l_symlink_{0}".format(path_module.rel)
str_depend = "{0} {1} {2}".format(str_l_irp_need,
path_makefiledepend,
str_l_destination)
else:
str_depend = "{0} {1}".format(str_l_irp_need,
path_makefiledepend)
str_l_destination)
else:
str_depend = "{0}".format(str_l_irp_need)
# Build
l_string = ["build {0}: build_irpf90.make {1}".format(path_irpf90_make,
str_depend)]
l_string += [" module = {0}".format(path_module.abs)]
# Env
l_src, l_obj = file_dependancy(path_module.rel)
str_src = " ".join(l_src)
str_obj = " ".join(l_obj)
l_string += [" src = '{0}'".format(str_src)]
l_string += [" obj = '{0}'".format(str_obj)]
# Option
str_include_dir = " ".join(["-I {0}".format(m.rel) for m in l_all_needed_molule])
l_string += [" include_dir = {0}".format(str_include_dir)]
l_string += [" irpf90_flag = {0}".format("--align=32 --openmp")]
l_string += [""]
return l_string
@ -388,6 +356,8 @@ def ninja_readme_rule():
l_string = ["rule build_readme"]
l_string += [" command = cd $module ; update_README.py"]
# Trick to not remove the update_README when cleaning
l_string += [" generator = 1"]
l_string += [""]
return l_string
@ -439,7 +409,7 @@ def get_ml_file(l_util, l_qp):
def ninja_ocaml_rule():
# Rule
cmd = " command = cd {0} ; make -j 1 $native ; touch $native; ln -sf $native $binary"
cmd = " command = cd {0} ; make -j 1 $native && touch $native && ln -sf $native $binary"
l_string = ["rule build_ocaml"]
l_string += [cmd.format(qpackage_root_ocaml)]
@ -522,16 +492,36 @@ def get_program(path_module):
return []
def ninja_binary_rule():
# Rule
def ninja_binary_rule(pwd_config_file):
l_flag = []
for flag in ["FC", "FCFLAGS"]:
str_ = "export {0}='{1}'".format(flag, get_compilation_option(pwd_config_file, flag))
l_flag.append(str_)
mkl = get_compilation_option(pwd_config_file, "MKL")
ezfio = join(qpackage_root_ezfio, "lib", "libezfio_irp.a")
str_ = "export LIB='{0} {1}'".format(mkl, ezfio)
l_flag.append(str_)
l_cmd = ["cd $module"] + l_flag + ["export SRC=$src",
"export OBJ=$obj",
"make -f irpf90.make -j 1 $binary && touch $binary"]
l_string = ["rule build_binary"]
l_string += [" command = cd $module ; make -j 1 $binary ; touch $binary"]
l_string += [" command = {0}".format(" ; ".join(l_cmd))]
l_string += [""]
return l_string
def ninja_binary_build(l_bin, path_module):
def ninja_binary_build(l_bin, path_module, l_children):
l_src, l_obj = file_dependancy(path_module.rel)
str_src = " ".join(l_src)
str_obj = " ".join(l_obj)
if not l_bin:
return []
@ -550,6 +540,8 @@ def ninja_binary_build(l_bin, path_module):
l_string += [" module = {0}".format(path_module.abs)]
l_string += [" binary = {0}".format(path)]
l_string += [" src = '{0}'".format(str_src)]
l_string += [" obj = '{0}'".format(str_obj)]
l_string += [""]
str_l_abs_bin = " ".join(l_abs_bin)
@ -577,22 +569,24 @@ def ninja_build_executable_list(l_module):
return l_string
if __name__ == "__main__":
pwd_config_file = sys.argv[1]
# _
# |_) | _
# | \ |_| | (/_
#
l_string = ninja_makefile_depend_rule()
l_string += ninja_ezfio_cfg_rule()
l_string = ninja_ezfio_cfg_rule()
l_string += ninja_symlink_rule()
l_string += ninja_irpf90_make_rule()
l_string += ninja_irpf90_make_rule(pwd_config_file)
l_string += ninja_readme_rule()
l_string += ninja_binary_rule()
l_string += ninja_binary_rule(pwd_config_file)
l_string += ninja_ezfio_config_rule()
l_string += ninja_ezfio_rule()
l_string += ninja_ezfio_rule(pwd_config_file)
# l_string += ninja_ocaml_rule()
@ -630,8 +624,6 @@ if __name__ == "__main__":
l_source, l_destination = get_source_destination(l_children, module)
l_string += ninja_makefile_depend_build(l_children, module)
# irpf90.make
l_string += ninja_symlink_build(l_source, l_destination, module)
@ -640,7 +632,7 @@ if __name__ == "__main__":
# ninja_binary
l_binary = get_program(module)
l_string += ninja_binary_build(l_binary, module)
l_string += ninja_binary_build(l_binary, module, l_children)
if l_binary:
l_module_with_binary.append(module.rel)

28
scripts/compilation/read_compilation_cfg.py
View File

@ -3,30 +3,23 @@
import os
import ConfigParser
import sys
from cache import cache
qpackage_root = os.environ['QPACKAGE_ROOT']
Config = ConfigParser.ConfigParser()
pwd = os.path.join(qpackage_root, "scripts/compilation/compilation.cfg")
Config.read(pwd)
@cache
def get_l_option_section():
return [o for o in ['OPENMP', 'PROFILE', 'DEBUG'] if Config.getboolean("OPTION", o)]
def get_l_option_section(config):
return [o for o in ['OPENMP', 'PROFILE', 'DEBUG'] if config.getboolean("OPTION", o)]
@cache
def get_compilation_option(name):
def get_compilation_option(pwd_cfg, flag_name):
l_option_section = get_l_option_section()
config = ConfigParser.ConfigParser()
config.read(pwd_cfg)
l_option_section = get_l_option_section(config)
l = []
for section in ["COMMON"] + l_option_section:
try:
l.extend(Config.get(section, name).split())
l.extend(config.get(section, flag_name).split())
except ConfigParser.NoOptionError:
pass
@ -34,6 +27,7 @@ def get_compilation_option(name):
if __name__ == '__main__':
name = sys.argv[1]
qpackage_root = os.environ['QPACKAGE_ROOT']
pwd_cfg = os.path.join(qpackage_root, "scripts/compilation/compilation_ifort.cfg")
print get_compilation_option(name)
print get_compilation_option(pwd_cfg, "FC")

173
scripts/module/module_handler.py
View File

@ -8,8 +8,6 @@ of a NEEDED_CHILDREN_MODULES file
Usage:
module_handler.py print_genealogy [<NEEDED_CHILDREN_MODULES>]
module_handler.py save_makefile_depend [<NEEDED_CHILDREN_MODULES>]
module_handler.py create_symlink [<NEEDED_CHILDREN_MODULES>]
module_handler.py create_png [<NEEDED_CHILDREN_MODULES>]
Options:
@ -25,10 +23,25 @@ from docopt import docopt
import os
import sys
import os.path
from cache import cache
from collections import namedtuple
Dependancy = namedtuple('Dependancy', ['src', 'obj'])
Module_info = namedtuple('Module_info', ['l_children', 'l_dependancy'])
@cache
def get_list_from_makefile(data, sep):
# Split for sep
dump = [l.split(sep)[1] for l in data if l.startswith(sep)]
# Delete the empy one
l_unique = [k for k in map(str.strip, dump) if k]
# Return the flat one (if multi in l_unique)
l_flat = [j for i in l_unique for j in i.split()]
return l_flat
# Canot cache for a fucking raison
def get_dict_genealogy():
"""Loop over MODULE in QPACKAGE_ROOT/src, open all the NEEDED_CHILDREN_MODULES
and create a dict[MODULE] = [sub module needed, ...]
@ -44,43 +57,32 @@ def get_dict_genealogy():
with open(os.path.join(dir_, o, "NEEDED_CHILDREN_MODULES"), "r") as f:
l_children = f.read().split()
except IOError:
pass
else:
d_ref[o] = l_children
continue
try:
with open(os.path.join(dir_, o, "Makefile"), "r") as f:
data = f.readlines()
l_depend = Dependancy(get_list_from_makefile(data, "SRC="),
get_list_from_makefile(data, "OBJ="))
except IOError:
l_depend = []
d_ref[o] = Module_info(l_children, l_depend)
return d_ref
def module_genealogy(path):
"""
Take a name of a NEEDED_CHILDREN_MODULES
and return a list of all the {sub, subsub, ...}children
"""
try:
with open(path, "r") as f:
l_children = f.read().split()
except IOError as e:
print >> sys.stderr, e
sys.exit(1)
else:
needed_module = get_it_and_children(l_children)
return needed_module
def get_it_and_children(l_module):
def him_and_all_children(d_ref, l_module):
"""
From a list of module return the module and all of the genealogy
"""
d_ref = get_dict_genealogy()
l = []
for module in l_module:
if module not in l:
l.append(module)
try:
l.extend(get_it_and_children(d_ref[module]))
l.extend(him_and_all_children(d_ref, d_ref[module].l_children))
except KeyError:
print >> sys.stderr, "`{0}` in not a good submodule name".format(module)
print >> sys.stderr, "Check the corresponding NEEDED_CHILDREN_MODULES"
@ -89,96 +91,28 @@ def get_it_and_children(l_module):
return list(set(l))
def get_all_children(l_module):
def module_genealogy(module_name):
"""
From a list of module return all the genealogy
Take a name of a NEEDED_CHILDREN_MODULES
and return a list of all the {sub, subsub, ...}children
"""
it_and_all = get_it_and_children(l_module)
return [children for children in it_and_all if children not in l_module]
def reduce_(l_module):
"""
Take a l_module and try to find the lower combinaitions
of module with the same genealogy
"""
import itertools
d_ref = get_dict_genealogy()
target_genealogy = sorted(get_all_children(l_module))
for i in xrange(len(d_ref)):
for c in itertools.combinations(d_ref, i):
guess_genealogy = sorted(get_it_and_children(d_ref, c))
if target_genealogy == guess_genealogy:
return c
return him_and_all_children(d_ref, d_ref[module_name].l_children)
def get_list_depend(l_module):
"""
transform
def file_dependancy(module_name):
SRC = Utils.f90 test.f90
OBJ = IRPF90_temp/map_module.o
d_ref = get_dict_genealogy()
l_src, l_obj = d_ref[module_name].l_dependancy
into
l_children_module = him_and_all_children(d_ref, d_ref[module_name].l_children)
for module in l_children_module:
l_src_dump, l_obj_dump = d_ref[module].l_dependancy
l_src.extend("{0}/{1}".format(module, i) for i in l_src_dump)
l_obj.extend("IRPF90_temp/{0}/{1}".format(module, os.path.basename(i)) for i in l_obj_dump)
['Utils/map_module.f90','test.f90']
['IRPF90_tmp/Utils/map_module.o']
"""
def get_list(sep):
# Split for sep
dump = [l.split(sep)[1] for l in data if l.startswith(sep)]
# Delete the empy one
l_unique = [k for k in map(str.strip, dump) if k]
# Return the flat one (if multi in l_unique)
l_flat = [j for i in l_unique for j in i.split()]
return l_flat
qpackage_root = os.environ['QPACKAGE_ROOT']
dir_ = os.path.join(qpackage_root, 'src')
l_src = []
l_obj = []
for module in l_module:
path = os.path.join(dir_, module, "Makefile")
with open(path, 'r') as f:
data = f.readlines()
l_src.extend("{0}/{1}".format(module, i) for i in get_list("SRC="))
l_obj.extend(["IRPF90_temp/{0}/{1}".format(module, os.path.basename(i))
for i in get_list("OBJ=")])
return l_src, l_obj
def save_makefile_depend(l_src, l_obj, dir_):
header = "# This file was created by the module_handler.py script. Do not modify it by hand."
try:
with open("Makefile.depend", "r") as f:
old_output = f.read()
except IOError:
old_output = None
output = "\n".join([header,
"\n",
"SRC+= {0}".format(" ".join(l_src)),
"OBJ+= {0}".format(" ".join(l_obj)),
"\n"])
if output != old_output:
with open(os.path.join(dir_,"Makefile.depend"), "w+") as f:
f.write(output)
return Dependancy(l_src, l_obj)
def create_png_from_path(path):
@ -210,7 +144,7 @@ def create_png(l_module):
edge = pydot.Edge(module, children)
graph.add_edge(edge)
# Recurs
draw_module_edge(children, d_ref[children])
draw_module_edge(children, d_ref[children].l_children)
all_ready_done.append(module)
# Init
@ -221,7 +155,7 @@ def create_png(l_module):
for module in l_module:
node_a = pydot.Node(module, fontcolor="red")
graph.add_node(node_a)
draw_module_edge(module, d_ref[module])
draw_module_edge(module, d_ref[module].l_children)
# Save
path = '{0}.png'.format("tree_dependancy")
@ -247,22 +181,5 @@ if __name__ == '__main__':
l_all_needed_molule = module_genealogy(path_file)
print " ".join(sorted(l_all_needed_molule))
if arguments['create_symlink']:
src = os.getcwd()
for link_name in module_genealogy(path_file) + ["include"]:
source = os.path.join("/home/razoa/quantum_package/src/",
link_name)
try:
os.symlink(source, link_name)
except OSError:
pass
if arguments['save_makefile_depend']:
l_all_needed_molule = module_genealogy(path_file)
l_src, l_obj = get_list_depend(l_all_needed_molule)
save_makefile_depend(l_src, l_obj, dir_)
if arguments["create_png"]:
create_png_from_path(path_file)

6
src/AOs/README.rst
View File

@ -28,7 +28,7 @@ Assumptions
===========
.. Do not edit this section. It was auto-generated from the
.. update_README.py.
.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
* The AO coefficients in the EZFIO files are not necessarily normalized and are normalized after reading
@ -37,7 +37,7 @@ Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. update_README.py.
.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
.. image:: tree_dependancy.png
@ -48,7 +48,7 @@ Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. update_README.py.
.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
`ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L1>`_
Overlap between atomic basis functions:

6
src/Bitmask/README.rst
View File

@ -22,7 +22,7 @@ Assumptions
===========
.. Do not edit this section. It was auto-generated from the
.. update_README.py.
.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
``bit_kind_shift``, ``bit_kind_size`` and ``bit_kind`` are coherent:
@ -38,7 +38,7 @@ Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. update_README.py.
.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
.. image:: tree_dependancy.png
@ -48,7 +48,7 @@ Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. update_README.py.
.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
`is_a_two_holes_two_particles <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L206>`_
Undocumented

6
src/Determinants/README.rst
View File

@ -15,7 +15,7 @@ Assumptions
===========
.. Do not edit this section. It was auto-generated from the
.. update_README.py.
.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
* The MOs are orthonormal
* All the determinants have the same number of electrons
@ -30,7 +30,7 @@ Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. update_README.py.
.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
.. image:: tree_dependancy.png
@ -41,7 +41,7 @@ Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. update_README.py.
.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
`copy_h_apply_buffer_to_wf <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/H_apply.irp.f#L103>`_
Copies the H_apply buffer to psi_coef.

6
src/Electrons/README.rst
View File

@ -10,7 +10,7 @@ Assumptions
===========
.. Do not edit this section. It was auto-generated from the
.. update_README.py.
.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
* ``elec_num`` >= 0
* ``elec_alpha_num`` >= 0
@ -22,7 +22,7 @@ Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. update_README.py.
.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
.. image:: tree_dependancy.png
@ -32,7 +32,7 @@ Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. update_README.py.
.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
`elec_alpha_num <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/electrons.irp.f#L1>`_
Numbers of alpha ("up") , beta ("down") and total electrons

2
src/Ezfio_files/README.rst
View File

@ -9,7 +9,7 @@ Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. update_README.py.
.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
`ezfio_filename <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files/ezfio.irp.f#L1>`_
Name of EZFIO file. It is obtained from the QPACKAGE_INPUT environment

4
src/FCIdump/README.rst
View File

@ -8,7 +8,7 @@ Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. update_README.py.
.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
`fcidump <http://github.com/LCPQ/quantum_package/tree/master/src/FCIdump/fcidump.irp.f#L1>`_
Undocumented
@ -19,7 +19,7 @@ Needed Modules
==============
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src/Generators_CAS/README.rst
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@ -7,7 +7,7 @@ Assumptions
===========
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The active space is defined by the ``reference_bitmask``.
@ -16,7 +16,7 @@ Documentation
=============
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`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L3>`_
Number of generator detetrminants
@ -41,7 +41,7 @@ Needed Modules
==============
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.. NEEDED_MODULES_CHILDREN file by the `update_README.py` script.
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src/Integrals_Bielec/README.rst
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@ -14,7 +14,7 @@ Needed Modules
==============
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@ -26,7 +26,7 @@ Documentation
=============
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`ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/ao_bi_integrals.irp.f#L1>`_
integral of the AO basis <ik|jl> or (ij|kl)

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src/Integrals_Monoelec/README.rst
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@ -2,7 +2,7 @@ Needed Modules
==============
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@ -13,7 +13,7 @@ Documentation
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`ao_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/ao_mono_ints.irp.f#L1>`_
array of the mono electronic hamiltonian on the AOs basis

4
src/MOGuess/README.rst
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@ -16,7 +16,7 @@ Documentation
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`h_core_guess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/H_CORE_guess.irp.f#L1>`_
Undocumented

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src/MOs/README.rst
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===========
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ASSUMPTONS
==========
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@ -45,7 +45,7 @@ Documentation
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`cholesky_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/cholesky_mo.irp.f#L1>`_
Cholesky decomposition of AO Density matrix to

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src/Makefile.common
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# Include the user's config
include $(QPACKAGE_ROOT)/src/Makefile.config
# Define the Makefile common variables
EZFIO_DIR=$(QPACKAGE_ROOT)/EZFIO
EZFIO=$(EZFIO_DIR)/lib/libezfio_irp.a
LIB+=$(EZFIO) $(MKL)
IRPF90+=$(patsubst %, -I %, $(INCLUDE_DIRS)) $(IRPF90_FLAGS)
include Makefile.depend
include irpf90.make

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src/Molden/README.rst
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`print_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Molden/print_mo.irp.f#L1>`_
Undocumented
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src/Nuclei/README.rst
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@ -20,7 +20,7 @@ Documentation
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`element_name <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L215>`_
Array of the name of element, sorted by nuclear charge (integer)

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src/Pseudo/README.rst
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@ -14,7 +14,7 @@ Needed Modules
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src/Utils/README.rst
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`apply_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L168>`_
Apply the rotation found by find_rotation