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Code Issues Releases Wiki Activity

Fix #82

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This commit is contained in:
Thomas Applencourt 2015-06-24 11:33:27 +02:00
parent b815828f38
commit 95c7861cbc
6 changed files with 115 additions and 80 deletions
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19
scripts/compilation/qp_create_ninja.py
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@ -474,21 +474,27 @@ def ninja_readme_rule():
For not dealted the readme when ninja -t clean and the generator option For not dealted the readme when ninja -t clean and the generator option
""" """
l_string = ["rule build_readme", l_string = ["rule build_readme",
" command = cd $module_abs ; update_README.py", " command = cd $module_abs ; update_README.py $module_root",
" generator = 1", ""] " generator = 1", ""]
return l_string return l_string
def ninja_readme_build(path_module): def ninja_readme_build(path_module, d_irp):
""" """
Rule for creation the readme Rule for creation the readme
""" """
path_irp_man = join(path_module.abs, "irpf90.make")
dict_root = module_instance.dict_root
dict_root_module_path = dict_module_genelogy_path(dict_root)
root_module = dict_root_module_path[module]
l_depend = d_irp[path_module]["l_depend"]
path_readme = join(path_module.abs, "README.rst") path_readme = join(path_module.abs, "README.rst")
l_string = ["build {0}: build_readme {1}".format(path_readme, l_string = ["build {0}: build_readme {1}".format(path_readme,
path_irp_man), " ".join(l_depend)),
" module_root = {0}".format(root_module.abs),
" module_abs = {0}".format(path_module.abs), " module_abs = {0}".format(path_module.abs),
" module_rel = {0}".format(path_module.rel), ""] " module_rel = {0}".format(path_module.rel), ""]
@ -533,7 +539,7 @@ def get_dict_binaries(l_module, mode="production"):
Example : The module Full_CI can produce the binary SCF Example : The module Full_CI can produce the binary SCF
so you dont need to compile at all the module Hartree-Fock so you dont need to compile at all the module Hartree-Fock
But you need to change the path acordingle But you need to change the path acordingly
Full_CI/Hartree-Fock/SCF Full_CI/Hartree-Fock/SCF
""" """
d_binaries = defaultdict(list) d_binaries = defaultdict(list)
@ -824,6 +830,7 @@ if __name__ == "__main__":
# d o t _ t r e e & r e a d m e # # d o t _ t r e e & r e a d m e #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ # # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
l_string += ninja_dot_tree_build(module, l_module) l_string += ninja_dot_tree_build(module, l_module)
l_string += ninja_readme_build(module, d_irp)
# ~#~#~#~#~#~#~#~#~#~#~#~#~ # # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# M o d u l e _ t o _ i r p # # M o d u l e _ t o _ i r p #
@ -860,8 +867,6 @@ if __name__ == "__main__":
l_string += ninja_irpf90_make_build(module_to_compile, l_children, l_string += ninja_irpf90_make_build(module_to_compile, l_children,
d_irp) d_irp)
l_string += ninja_readme_build(module_to_compile)
l_string += ninja_binaries_build(module_to_compile, l_children, l_string += ninja_binaries_build(module_to_compile, l_children,
d_binaries) d_binaries)

42
scripts/module/update_README.py
View File

@ -13,6 +13,26 @@ URL = "http://github.com/LCPQ/quantum_package/tree/master/src/"
import os import os
import subprocess import subprocess
from collections import namedtuple from collections import namedtuple
import sys
"""
NEED to call in a module
First arg can be the root parent
"""
try:
ROOT_module = os.path.realpath(sys.argv[1])
except:
ROOT_module = os.getcwd()
if ROOT_module != os.getcwd:
change = True
else:
change = False
MODULE_NAME = os.path.basename(os.getcwd())
print MODULE_NAME
print ROOT_module
header = """ header = """
.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
@ -71,7 +91,8 @@ def update_needed(data):
def extract_doc(item): def extract_doc(item):
"""Extracts the documentation contained in IRPF90_man file""" """Extracts the documentation contained in IRPF90_man file"""
with open("IRPF90_man/%s.l" % (item), 'r') as f: path = os.path.join(ROOT_module, "IRPF90_man/%s.l" % (item))
with open(path, 'r') as f:
l_line = f.readlines() l_line = f.readlines()
result = [] result = []
@ -97,15 +118,24 @@ def update_documentation(data):
# If the file does not exist, don't do anything # If the file does not exist, don't do anything
with open('tags', 'r') as f: path = os.path.join(ROOT_module, "tags")
l_info = [IRP_info(*i.split()) for i in f.readlines()
if "/" not in i.split()[1]] with open(path, 'r') as f:
dump = f.readlines()
l_info = []
for i in dump:
name, f, ligne = i.split()
if not change and "/" not in i:
l_info.append(IRP_info(name, f, ligne))
elif change and MODULE_NAME in i:
l_info.append(IRP_info(name, f.split("/")[-1], ligne))
l_line = [] l_line = []
module_name = os.path.basename(os.getcwd())
for irp in l_info: for irp in l_info:
url = os.path.join(URL, module_name, irp.file) url = os.path.join(URL, MODULE_NAME, irp.file)
doc = extract_doc(irp.name) doc = extract_doc(irp.name)
l_line += ["`{0} <{1}#L{2}>`_".format(irp.name, url, irp.line), doc, l_line += ["`{0} <{1}#L{2}>`_".format(irp.name, url, irp.line), doc,

62
src/AO_Basis/README.rst
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@ -46,135 +46,135 @@ Documentation
.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. by the `update_README.py` script. .. by the `update_README.py` script.
`ao_coef <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L62>`_ `ao_coef <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L62>`_
AO Coefficients, read from input. Those should not be used directly, as AO Coefficients, read from input. Those should not be used directly, as
the MOs are expressed on the basis of **normalized** AOs. the MOs are expressed on the basis of **normalized** AOs.
`ao_coef_normalized <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L84>`_ `ao_coef_normalized <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L84>`_
Coefficients including the AO normalization Coefficients including the AO normalization
`ao_coef_normalized_ordered <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L107>`_ `ao_coef_normalized_ordered <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L107>`_
Sorted primitives to accelerate 4 index MO transformation Sorted primitives to accelerate 4 index MO transformation
`ao_coef_normalized_ordered_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L133>`_ `ao_coef_normalized_ordered_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L133>`_
Transposed ao_coef_normalized_ordered Transposed ao_coef_normalized_ordered
`ao_expo <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L41>`_ `ao_expo <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L41>`_
AO Exponents read from input AO Exponents read from input
`ao_expo_ordered <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L108>`_ `ao_expo_ordered <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L108>`_
Sorted primitives to accelerate 4 index MO transformation Sorted primitives to accelerate 4 index MO transformation
`ao_expo_ordered_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L147>`_ `ao_expo_ordered_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L147>`_
Transposed ao_expo_ordered Transposed ao_expo_ordered
`ao_l <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L162>`_ `ao_l <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L162>`_
ao_l = l value of the AO: a+b+c in x^a y^b z^c ao_l = l value of the AO: a+b+c in x^a y^b z^c
`ao_l_char <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L163>`_ `ao_l_char <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L163>`_
ao_l = l value of the AO: a+b+c in x^a y^b z^c ao_l = l value of the AO: a+b+c in x^a y^b z^c
`ao_l_char_space <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L311>`_ `ao_l_char_space <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L311>`_
Undocumented Undocumented
`ao_md5 <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L403>`_ `ao_md5 <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L403>`_
MD5 key characteristic of the AO basis MD5 key characteristic of the AO basis
`ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L209>`_ `ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L209>`_
Index of the nuclei on which the ao is centered Index of the nuclei on which the ao is centered
`ao_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L1>`_ `ao_num <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L1>`_
Number of atomic orbitals Number of atomic orbitals
`ao_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L2>`_ `ao_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L2>`_
Number of atomic orbitals Number of atomic orbitals
`ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L1>`_ `ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ao_overlap.irp.f#L1>`_
Overlap between atomic basis functions: Overlap between atomic basis functions:
:math:`\int \chi_i(r) \chi_j(r) dr)` :math:`\int \chi_i(r) \chi_j(r) dr)`
`ao_overlap_abs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L65>`_ `ao_overlap_abs <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ao_overlap.irp.f#L65>`_
Overlap between absolute value of atomic basis functions: Overlap between absolute value of atomic basis functions:
:math:`\int |\chi_i(r)| |\chi_j(r)| dr)` :math:`\int |\chi_i(r)| |\chi_j(r)| dr)`
`ao_overlap_x <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L2>`_ `ao_overlap_x <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ao_overlap.irp.f#L2>`_
Overlap between atomic basis functions: Overlap between atomic basis functions:
:math:`\int \chi_i(r) \chi_j(r) dr)` :math:`\int \chi_i(r) \chi_j(r) dr)`
`ao_overlap_y <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L3>`_ `ao_overlap_y <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ao_overlap.irp.f#L3>`_
Overlap between atomic basis functions: Overlap between atomic basis functions:
:math:`\int \chi_i(r) \chi_j(r) dr)` :math:`\int \chi_i(r) \chi_j(r) dr)`
`ao_overlap_z <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L4>`_ `ao_overlap_z <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ao_overlap.irp.f#L4>`_
Overlap between atomic basis functions: Overlap between atomic basis functions:
:math:`\int \chi_i(r) \chi_j(r) dr)` :math:`\int \chi_i(r) \chi_j(r) dr)`
`ao_power <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L19>`_ `ao_power <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L19>`_
Powers of x,y and z read from input Powers of x,y and z read from input
`ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L177>`_ `ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L177>`_
Number of primitives per atomic orbital Number of primitives per atomic orbital
`ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L199>`_ `ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L199>`_
Undocumented Undocumented
`ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L200>`_ `ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L200>`_
Undocumented Undocumented
`l_to_charater <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L218>`_ `l_to_charater <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L218>`_
character corresponding to the "L" value of an AO orbital character corresponding to the "L" value of an AO orbital
`n_aos_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L231>`_ `n_aos_max <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L231>`_
Number of AOs per atom Number of AOs per atom
`n_pt_max_i_x <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/dimensions_integrals.irp.f#L2>`_ `n_pt_max_i_x <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/dimensions_integrals.irp.f#L2>`_
Undocumented Undocumented
`n_pt_max_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/dimensions_integrals.irp.f#L1>`_ `n_pt_max_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/dimensions_integrals.irp.f#L1>`_
Undocumented Undocumented
`nucl_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L244>`_ `nucl_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L244>`_
List of AOs attached on each atom List of AOs attached on each atom
`nucl_list_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L262>`_ `nucl_list_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L262>`_
Index of the shell type Aos and of the corresponding Aos Index of the shell type Aos and of the corresponding Aos
Per convention, for P,D,F and G AOs, we take the index Per convention, for P,D,F and G AOs, we take the index
of the AO with the the corresponding power in the "X" axis of the AO with the the corresponding power in the "X" axis
`nucl_n_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L230>`_ `nucl_n_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L230>`_
Number of AOs per atom Number of AOs per atom
`nucl_num_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L263>`_ `nucl_num_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/aos.irp.f#L263>`_
Index of the shell type Aos and of the corresponding Aos Index of the shell type Aos and of the corresponding Aos
Per convention, for P,D,F and G AOs, we take the index Per convention, for P,D,F and G AOs, we take the index
of the AO with the the corresponding power in the "X" axis of the AO with the the corresponding power in the "X" axis

2
src/Bitmask/README.rst
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@ -42,7 +42,7 @@ Needed Modules
.. image:: tree_dependency.png .. image:: tree_dependency.png
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_ * `MO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis>`_
Documentation Documentation
============= =============

40
src/MO_Basis/README.rst
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@ -38,7 +38,7 @@ Needed Modules
.. image:: tree_dependency.png .. image:: tree_dependency.png
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_ * `AO_Basis <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_ * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
Documentation Documentation
@ -47,16 +47,16 @@ Documentation
.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. by the `update_README.py` script. .. by the `update_README.py` script.
`ao_to_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L126>`_ `ao_to_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L136>`_
Transform A from the AO basis to the MO basis Transform A from the AO basis to the MO basis
`cholesky_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/cholesky_mo.irp.f#L1>`_ `cholesky_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/cholesky_mo.irp.f#L1>`_
Cholesky decomposition of AO Density matrix to Cholesky decomposition of AO Density matrix to
generate MOs generate MOs
`mix_mo_jk <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L210>`_ `mix_mo_jk <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L220>`_
subroutine that rotates the jth MO with the kth MO subroutine that rotates the jth MO with the kth MO
to give two new MO's that are to give two new MO's that are
'+' = 1/sqrt(2) (|j> + |k>) '+' = 1/sqrt(2) (|j> + |k>)
@ -65,70 +65,70 @@ Documentation
by convention, the '-' MO is in the greater index (max(j,k)) by convention, the '-' MO is in the greater index (max(j,k))
`mo_as_eigvectors_of_mo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L24>`_ `mo_as_eigvectors_of_mo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L24>`_
Undocumented Undocumented
`mo_as_eigvectors_of_mo_matrix_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L62>`_ `mo_as_eigvectors_of_mo_matrix_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L62>`_
Undocumented Undocumented
`mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L28>`_ `mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L28>`_
Molecular orbital coefficients on AO basis set Molecular orbital coefficients on AO basis set
mo_coef(i,j) = coefficient of the ith ao on the jth mo mo_coef(i,j) = coefficient of the ith ao on the jth mo
mo_label : Label characterizing the MOS (local, canonical, natural, etc) mo_label : Label characterizing the MOS (local, canonical, natural, etc)
`mo_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L71>`_ `mo_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L81>`_
Molecular orbital coefficients on AO basis set Molecular orbital coefficients on AO basis set
`mo_density_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/cholesky_mo.irp.f#L44>`_ `mo_density_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/cholesky_mo.irp.f#L44>`_
Density matrix in MO basis Density matrix in MO basis
`mo_density_matrix_virtual <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/cholesky_mo.irp.f#L64>`_ `mo_density_matrix_virtual <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/cholesky_mo.irp.f#L64>`_
Density matrix in MO basis (virtual MOs) Density matrix in MO basis (virtual MOs)
`mo_label <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L29>`_ `mo_label <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L63>`_
Molecular orbital coefficients on AO basis set Molecular orbital coefficients on AO basis set
mo_coef(i,j) = coefficient of the ith ao on the jth mo mo_coef(i,j) = coefficient of the ith ao on the jth mo
mo_label : Label characterizing the MOS (local, canonical, natural, etc) mo_label : Label characterizing the MOS (local, canonical, natural, etc)
`mo_occ <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L102>`_ `mo_occ <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L112>`_
MO occupation numbers MO occupation numbers
`mo_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mo_overlap.irp.f#L2>`_ `mo_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mo_overlap.irp.f#L2>`_
Undocumented Undocumented
`mo_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L144>`_ `mo_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L144>`_
Undocumented Undocumented
`mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L152>`_ `mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L162>`_
Transform A from the MO basis to the AO basis Transform A from the MO basis to the AO basis
`mo_to_ao_no_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L184>`_ `mo_to_ao_no_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L194>`_
Transform A from the MO basis to the S^-1 AO basis Transform A from the MO basis to the S^-1 AO basis
`mo_tot_num <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L1>`_ `mo_tot_num <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L1>`_
Total number of molecular orbitals and the size of the keys corresponding Total number of molecular orbitals and the size of the keys corresponding
`mo_tot_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L18>`_ `mo_tot_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L18>`_
Aligned variable for dimensioning of arrays Aligned variable for dimensioning of arrays
`s_mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L89>`_ `s_mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L99>`_
Product S.C where S is the overlap matrix in the AO basis and C the mo_coef matrix. Product S.C where S is the overlap matrix in the AO basis and C the mo_coef matrix.
`save_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L1>`_ `save_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/utils.irp.f#L1>`_
Undocumented Undocumented

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src/Nuclei/README.rst
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@ -23,68 +23,68 @@ Documentation
.. Do not edit this section. It was auto-generated from the .. Do not edit this section. It was auto-generated from the
.. by the `update_README.py` script. .. by the `update_README.py` script.
`element_name <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L215>`_ `element_name <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L172>`_
Array of the name of element, sorted by nuclear charge (integer) Array of the name of element, sorted by nuclear charge (integer)
`nucl_charge <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L23>`_ `nucl_charge <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/ezfio_interface.irp.f#L24>`_
Nuclear charges Nuclear charges
`nucl_coord <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L55>`_ `nucl_coord <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L12>`_
Nuclear coordinates in the format (:, {x,y,z}) Nuclear coordinates in the format (:, {x,y,z})
`nucl_coord_transp <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L110>`_ `nucl_coord_transp <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L67>`_
Transposed array of nucl_coord Transposed array of nucl_coord
`nucl_dist <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L129>`_ `nucl_dist <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L86>`_
nucl_dist : Nucleus-nucleus distances nucl_dist : Nucleus-nucleus distances
nucl_dist_2 : Nucleus-nucleus distances squared nucl_dist_2 : Nucleus-nucleus distances squared
nucl_dist_vec : Nucleus-nucleus distances vectors nucl_dist_vec : Nucleus-nucleus distances vectors
`nucl_dist_2 <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L125>`_ `nucl_dist_2 <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L82>`_
nucl_dist : Nucleus-nucleus distances nucl_dist : Nucleus-nucleus distances
nucl_dist_2 : Nucleus-nucleus distances squared nucl_dist_2 : Nucleus-nucleus distances squared
nucl_dist_vec : Nucleus-nucleus distances vectors nucl_dist_vec : Nucleus-nucleus distances vectors
`nucl_dist_vec_x <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L126>`_ `nucl_dist_vec_x <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L83>`_
nucl_dist : Nucleus-nucleus distances nucl_dist : Nucleus-nucleus distances
nucl_dist_2 : Nucleus-nucleus distances squared nucl_dist_2 : Nucleus-nucleus distances squared
nucl_dist_vec : Nucleus-nucleus distances vectors nucl_dist_vec : Nucleus-nucleus distances vectors
`nucl_dist_vec_y <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L127>`_ `nucl_dist_vec_y <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L84>`_
nucl_dist : Nucleus-nucleus distances nucl_dist : Nucleus-nucleus distances
nucl_dist_2 : Nucleus-nucleus distances squared nucl_dist_2 : Nucleus-nucleus distances squared
nucl_dist_vec : Nucleus-nucleus distances vectors nucl_dist_vec : Nucleus-nucleus distances vectors
`nucl_dist_vec_z <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L128>`_ `nucl_dist_vec_z <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L85>`_
nucl_dist : Nucleus-nucleus distances nucl_dist : Nucleus-nucleus distances
nucl_dist_2 : Nucleus-nucleus distances squared nucl_dist_2 : Nucleus-nucleus distances squared
nucl_dist_vec : Nucleus-nucleus distances vectors nucl_dist_vec : Nucleus-nucleus distances vectors
`nucl_label <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L41>`_ `nucl_label <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/ezfio_interface.irp.f#L6>`_
Nuclear labels Nuclear labels
`nucl_num <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L1>`_ `nucl_num <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/ezfio_interface.irp.f#L46>`_
Number of nuclei Number of nuclei
`nucl_num_aligned <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L2>`_ `nucl_num_aligned <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L1>`_
Number of nuclei Number of nuclei algined
`nuclear_repulsion <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L187>`_ `nuclear_repulsion <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L144>`_
Nuclear repulsion energy Nuclear repulsion energy
`positive_charge_barycentre <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L171>`_ `positive_charge_barycentre <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L128>`_
Centroid of the positive charges Centroid of the positive charges