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Merge pull request #56 from TApplencourt/master

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Fix gitignore and update_readme
This commit is contained in:
Thomas Applencourt 2015-04-13 18:36:52 +02:00
commit cff8f0f56f
37 changed files with 1364 additions and 435 deletions
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7
ocaml/Makefile
View File

@ -25,9 +25,12 @@ default: $(ALL_TESTS) $(ALL_EXE) .gitignore
.gitignore: $(MLFILES)
@for i in .gitignore ezfio.ml Qptypes.ml qptypes_generator.byte _build $(ALL_EXE) $(ALL_TESTS) \
$(patsubst %.ml,%,$(wildcard test_*.ml)) $(patsubst %.ml,%,$(wildcard qp_*.ml)) ; do \
$(patsubst %.ml,%,$(wildcard test_*.ml)) $(patsubst %.ml,%,$(wildcard qp_*.ml)) \
$(shell grep Input Input_auto_generated.ml | awk '{print $$2 ".ml"}') \
Input_auto_generated.ml;\
do \
echo $$i ; \
done >> .gitignore
done > .gitignore
executables: $(QPACKAGE_ROOT)/data/executables

1
scripts/build_modules.sh
View File

@ -30,6 +30,7 @@ Build failed for module $MODULE
"
fi
fi
${QPACKAGE_ROOT}/scripts/create_gitignore.sh
cd ${OLDPWD}
done
${QPACKAGE_ROOT}/scripts/create_executables_list.sh

2
scripts/create_gitignore.sh
View File

@ -35,4 +35,4 @@ then
fi
find . -type l | sed "s@./@@" >> .gitignore
find . -type f -executable -print | sed "s@./@@" >> .gitignore

27
scripts/ezfio_interface/convert_ezfio.sh
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@ -1,27 +0,0 @@
#!/bin/bash
# Convert a old ezfio file (with option.irp.f ezfio_default)
# into a new EZFIO.cfg type
# Hartree Fock
# Changin the case, don't know if is needed or not
mv $1/Hartree_Fock $1/hartree_fock 2> /dev/null
mv $1/hartree_Fock/thresh_SCF $1/hartree_fock/thresh_scf 2> /dev/null
# BiInts
mv $1/bi_integrals $1/bielect_integrals 2> /dev/null
if [ -f $1/bielect_integrals/read_ao_integrals ]; then
if [ `cat $1/bielect_integrals/read_ao_integrals` -eq "True" ]
then
echo "Read" > $1/bielect_integrals/disk_access_ao_integrals
elif [ `cat bielect_integrals/write_ao_integrals` -eq "True" ]
then
echo "Write" > $1/bielect_integrals/disk_access_ao_integrals
else
echo "None" > $1/bielect_integrals/disk_access_ao_integrals
fi
fi

4
scripts/ezfio_interface/ei_handler.py
View File

@ -70,9 +70,9 @@ def is_bool(str_):
Take a string, if is a bool return the conversion into
fortran and ocaml.
"""
if str_.lower() in ['true', '.true.']:
if "true" in str_.lower():
return Type(None, "true", ".True.")
elif str_.lower() in ['false', '.false.']:
elif "false" in str_.lower():
return Type(None, "false", ".False")
else:
raise TypeError

212
scripts/update_README.py
View File

@ -1,16 +1,16 @@
#!/usr/bin/env python
"""Updates the README.rst file as the include directive is disabled on GitHub."""
__date__ = "Thu Apr 3 23:06:18 CEST 2014"
__date__ = "Thu Apr 3 23:06:18 CEST 2014"
__author__ = "Anthony Scemama <scemama@irsamc.ups-tlse.fr>"
README="README.rst"
Assum_key="Assumptions\n===========\n"
Needed_key="Needed Modules\n==============\n"
Doc_key="Documentation\n=============\n"
Sentinel="@@$%&@@"
URL="http://github.com/LCPQ/quantum_package/tree/master/src/"
README = "README.rst"
Assum_key = "Assumptions\n===========\n"
Needed_key = "Needed Modules\n==============\n"
Doc_key = "Documentation\n=============\n"
Sentinel = "@@$%&@@"
URL = "http://github.com/LCPQ/quantum_package/tree/master/src/"
import os
import subprocess
@ -22,30 +22,30 @@ header = """
"""
try:
# subprocess.check_output("git status".split())
# has_git = True
pass
# subprocess.check_output("git status".split())
has_git = True
except OSError:
has_git = False
has_git = False
def fetch_splitted_data():
"""Read the README.rst file and split it in strings:
* The description
* The assumptions
* The documentation
* The documentation
* The needed modules
The result is given as a list of strings
"""
file = open(README,'r')
file = open(README, 'r')
data = file.read()
file.close()
# Place sentinels
data = data.replace(Assum_key,Sentinel+Assum_key)
data = data.replace(Doc_key,Sentinel+Doc_key)
data = data.replace(Needed_key,Sentinel+Needed_key)
data = data.replace(Assum_key, Sentinel + Assum_key)
data = data.replace(Doc_key, Sentinel + Doc_key)
data = data.replace(Needed_key, Sentinel + Needed_key)
# Now Split data using the sentinels
result = data.split(Sentinel)
@ -56,9 +56,9 @@ def update_assumptions(data):
"""Read the ASSUMPTIONS.rst file, and replace the data with it."""
try:
file = open('ASSUMPTIONS.rst','r')
file = open('ASSUMPTIONS.rst', 'r')
except IOError:
file = open('ASSUMPTIONS.rst','w')
file = open('ASSUMPTIONS.rst', 'w')
assumptions = ""
else:
assumptions = file.read()
@ -74,7 +74,7 @@ def update_assumptions(data):
data[i] = assumptions
if not has_assumptions:
data.insert(1,assumptions)
data.insert(1, assumptions)
return data
@ -83,12 +83,12 @@ def update_needed(data):
"""Read the NEEDED_MODULES file, and replace the data with it.
Create the links to the GitHub pages."""
file = open('NEEDED_MODULES','r')
file = open('NEEDED_MODULES', 'r')
modules = file.read()
file.close()
if modules.strip() != "":
modules = [ '* `%s <%s%s>`_'%(x,URL,x) for x in modules.split() ]
modules = ['* `%s <%s%s>`_' % (x, URL, x) for x in modules.split()]
modules = "\n".join(modules)
modules = Needed_key + header + modules + '\n\n'
@ -105,112 +105,114 @@ def update_needed(data):
def update_documentation(data):
"""Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation"""
"""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()
# If the file does not exist, don't do anything
try:
file = open('tags', 'r')
except:
return
tags = 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())
if 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)
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())
# 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) )
if result == []:
result = [" Undocumented"]
return "\n".join(result) + '\n'
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"
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)
documentation = Doc_key + header
url = URL
for item, filename, doc, line in items:
documentation += template%locals()
documentation += '\n\n'
# 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))
has_doc = False
for i in range(len(data)):
if data[i].startswith(Doc_key):
has_doc = True
data[i] = documentation
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"
if not has_doc:
data.append(documentation)
documentation = Doc_key + header
url = URL
for item, filename, doc, line in items:
documentation += template % locals()
documentation += '\n\n'
return data
has_doc = False
for i in range(len(data)):
if data[i].startswith(Doc_key):
has_doc = True
data[i] = documentation
if not has_doc:
data.append(documentation)
return data
def git_add():
"""Executes:
git add README.rst
if git is present on the machine."""
command = "git add "+README
os.system(command+" &> /dev/null")
throw an error if git is not precent"""
import subprocess
try:
# pipe output to /dev/null for silence
null = open("/dev/null", "w")
subprocess.Popen("git add README.rst", stdout=null, stderr=null)
null.close()
except OSError:
raise
def main():
if not has_git:
return
data = fetch_splitted_data()
data = update_assumptions(data)
data = update_documentation(data)
data = update_needed(data)
output = ''.join(data)
file = open(README,'w')
file.write(output)
file.close()
git_add()
with open(README, 'w') as f:
f.write(output)
try:
git_add()
except OSError:
pass
if __name__ == '__main__':
try:
main()
except:
pass
main()

83
src/AOs/README.rst
View File

@ -50,21 +50,65 @@ Documentation
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/ao_overlap.irp.f#L1>`_
Overlap between atomic basis functions:
: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>`_
Overlap between absolute value of atomic basis functions:
: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>`_
Overlap between atomic basis functions:
: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>`_
Overlap between atomic basis functions:
: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>`_
Overlap between atomic basis functions:
:math:`\int \chi_i(r) \chi_j(r) dr)`
`ao_coef <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L21>`_
Coefficients, exponents and powers of x,y and z
ao_coef(i,j) = coefficient of the jth primitive on the ith ao
`ao_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L96>`_
`ao_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L157>`_
Transposed ao_coef and ao_expo
`ao_coef_unnormalized <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L116>`_
Coefficients, exponents and powers of x,y and z as in the EZFIO file
ao_coef(i,j) = coefficient of the jth primitive on the ith ao
ao_l = l value of the AO: a+b+c in x^a y^b z^c
`ao_expo <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L20>`_
Coefficients, exponents and powers of x,y and z
ao_coef(i,j) = coefficient of the jth primitive on the ith ao
`ao_expo_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L97>`_
`ao_expo_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L158>`_
Transposed ao_coef and ao_expo
`ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L146>`_
`ao_expo_unsorted <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L117>`_
Coefficients, exponents and powers of x,y and z as in the EZFIO file
ao_coef(i,j) = coefficient of the jth primitive on the ith ao
ao_l = l value of the AO: a+b+c in x^a y^b z^c
`ao_l <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L118>`_
Coefficients, exponents and powers of x,y and z as in the EZFIO file
ao_coef(i,j) = coefficient of the jth primitive on the ith ao
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#L119>`_
Coefficients, exponents and powers of x,y and z as in the EZFIO file
ao_coef(i,j) = coefficient of the jth primitive on the ith ao
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#L309>`_
Undocumented
`ao_md5 <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L400>`_
MD5 key characteristic of the AO basis
`ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L207>`_
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>`_
@ -75,16 +119,37 @@ Documentation
`ao_power <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L19>`_
Coefficients, exponents and powers of x,y and z
ao_coef(i,j) = coefficient of the jth primitive on the ith ao
`ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L114>`_
`ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L175>`_
Number of primitives per atomic orbital
`ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L136>`_
`ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L197>`_
Undocumented
`ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L137>`_
`ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L198>`_
Undocumented
`l_to_charater <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L216>`_
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#L229>`_
Number of AOs per atom
`nucl_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L242>`_
List of AOs attached on each atom
`nucl_list_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L260>`_
Index of the shell type Aos and of the corresponding Aos
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
`nucl_n_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L228>`_
Number of AOs per atom
`nucl_num_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L261>`_
Index of the shell type Aos and of the corresponding Aos
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

133
src/Bielec_integrals/README.rst
View File

@ -32,152 +32,193 @@ Documentation
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L1>`_
`ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1>`_
integral of the AO basis <ik|jl> or (ij|kl)
i(r1) j(r1) 1/r12 k(r2) l(r2)
`ao_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L350>`_
Needed to compuet Schwartz inequalities
`ao_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L490>`_
Needed to compute Schwartz inequalities
`ao_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L188>`_
`ao_bielec_integral_schwartz_accel <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L107>`_
integral of the AO basis <ik|jl> or (ij|kl)
i(r1) j(r1) 1/r12 k(r2) l(r2)
`ao_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L322>`_
Map of Atomic integrals
i(r1) j(r2) 1/r12 k(r1) l(r2)
`compute_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L147>`_
`ao_l4 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L279>`_
Computes the product of l values of i,j,k,and l
`compute_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L290>`_
Compute AO 1/r12 integrals for all i and fixed j,k,l
`eri <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L511>`_
`eri <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L653>`_
ATOMIC PRIMTIVE bielectronic integral between the 4 primitives ::
primitive_1 = x1**(a_x) y1**(a_y) z1**(a_z) exp(-alpha * r1**2)
primitive_2 = x1**(b_x) y1**(b_y) z1**(b_z) exp(- beta * r1**2)
primitive_3 = x2**(c_x) y2**(c_y) z2**(c_z) exp(-delta * r2**2)
primitive_4 = x2**(d_x) y2**(d_y) z2**(d_z) exp(- gama * r2**2)
`general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L376>`_
`general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L515>`_
Computes the integral <pq|rs> where p,q,r,s are Gaussian primitives
`give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L656>`_
`give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L851>`_
subroutine that returns the explicit polynom in term of the "t"
variable of the following polynomw :
I_x1(a_x, d_x,p,q) * I_x1(a_y, d_y,p,q) * I_x1(a_z, d_z,p,q)
`i_x1_new <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L600>`_
`i_x1_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L772>`_
recursive function involved in the bielectronic integral
`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L719>`_
`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L914>`_
recursive function involved in the bielectronic integral
`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L839>`_
`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1034>`_
recursive function involved in the bielectronic integral
`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L893>`_
`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1088>`_
recursive function involved in the bielectronic integral
`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L753>`_
`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L948>`_
recursive function involved in the bielectronic integral
`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L623>`_
`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L807>`_
recursive function involved in the bielectronic integral
`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L955>`_
`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1150>`_
recursive function involved in the bielectronic integral
`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L555>`_
`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L698>`_
calculate the integral of the polynom ::
I_x1(a_x+b_x, c_x+d_x,p,q) * I_x1(a_y+b_y, c_y+d_y,p,q) * I_x1(a_z+b_z, c_z+d_z,p,q)
between ( 0 ; 1)
`n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/ao_bi_integrals.irp.f#L642>`_
Returns the upper boundary of the degree of the polynom involved in the
`n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L837>`_
Returns the upper boundary of the degree of the polynomial involved in the
bielctronic integral :
Ix(a_x,b_x,c_x,d_x) * Iy(a_y,b_y,c_y,d_y) * Iz(a_z,b_z,c_z,d_z)
`gauleg <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/gauss_legendre.irp.f#L20>`_
`gauleg <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/gauss_legendre.irp.f#L29>`_
Gauss-Legendre
`gauleg_t2 <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/gauss_legendre.irp.f#L1>`_
`gauleg_t2 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/gauss_legendre.irp.f#L10>`_
t_w(i,1,k) = w(i)
t_w(i,2,k) = t(i)
`gauleg_w <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/gauss_legendre.irp.f#L2>`_
`gauleg_w <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/gauss_legendre.irp.f#L11>`_
t_w(i,1,k) = w(i)
t_w(i,2,k) = t(i)
`ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L6>`_
`n_pt_max_integrals_16 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/gauss_legendre.irp.f#L1>`_
Aligned n_pt_max_integrals
`ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L6>`_
AO integrals
`bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L17>`_
`bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L19>`_
Undocumented
`clear_ao_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L128>`_
`bielec_integrals_index_reverse <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L36>`_
Undocumented
`clear_ao_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L223>`_
Frees the memory of the AO map
`clear_mo_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L285>`_
`clear_mo_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L399>`_
Frees the memory of the MO map
`get_ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L33>`_
`get_ao_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L113>`_
Gets one AO bi-electronic integral from the AO map
`get_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L51>`_
`get_ao_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L137>`_
Gets multiple AO bi-electronic integral from the AO map .
All i are retrieved for j,k,l fixed.
`get_ao_bielec_integrals_non_zero <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L84>`_
`get_ao_bielec_integrals_non_zero <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L172>`_
Gets multiple AO bi-electronic integral from the AO map .
All non-zero i are retrieved for j,k,l fixed.
`get_ao_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L120>`_
`get_ao_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L214>`_
Returns the number of elements in the AO map
`get_mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L184>`_
`get_mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L281>`_
Returns one integral <ij|kl> in the MO basis
`get_mo_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L213>`_
`get_mo_bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L310>`_
Returns multiple integrals <ij|kl> in the MO basis, all
i for j,k,l fixed.
`get_mo_bielec_integrals_existing_ik <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L235>`_
`get_mo_bielec_integrals_existing_ik <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L341>`_
Returns multiple integrals <ij|kl> in the MO basis, all
i(1)j(1) 1/r12 k(2)l(2)
i for j,k,l fixed.
`get_mo_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L277>`_
`get_mo_map_size <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L391>`_
Return the number of elements in the MO map
`insert_into_ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L153>`_
`insert_into_ao_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L250>`_
Create new entry into AO map
`insert_into_mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L168>`_
`insert_into_mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L265>`_
Create new entry into MO map, or accumulate in an existing entry
`mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L201>`_
`mo_bielec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L298>`_
Returns one integral <ij|kl> in the MO basis
`mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/map_integrals.irp.f#L142>`_
`mo_integrals_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/map_integrals.irp.f#L237>`_
MO integrals
`add_integrals_to_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L40>`_
`add_integrals_to_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L42>`_
Adds integrals to tha MO map according to some bitmask
`mo_bielec_integral_jj <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L314>`_
`mo_bielec_integral_jj <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L464>`_
mo_bielec_integral_jj(i,j) = J_ij
mo_bielec_integral_jj_exchange(i,j) = J_ij
mo_bielec_integral_jj_exchange(i,j) = K_ij
mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij
`mo_bielec_integral_jj_anti <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L316>`_
`mo_bielec_integral_jj_anti <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L466>`_
mo_bielec_integral_jj(i,j) = J_ij
mo_bielec_integral_jj_exchange(i,j) = J_ij
mo_bielec_integral_jj_exchange(i,j) = K_ij
mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij
`mo_bielec_integral_jj_exchange <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L315>`_
`mo_bielec_integral_jj_anti_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L326>`_
mo_bielec_integral_jj_from_ao(i,j) = J_ij
mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
`mo_bielec_integral_jj_exchange <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L465>`_
mo_bielec_integral_jj(i,j) = J_ij
mo_bielec_integral_jj_exchange(i,j) = J_ij
mo_bielec_integral_jj_exchange(i,j) = K_ij
mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij
`mo_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L21>`_
`mo_bielec_integral_jj_exchange_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L325>`_
mo_bielec_integral_jj_from_ao(i,j) = J_ij
mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
`mo_bielec_integral_jj_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L324>`_
mo_bielec_integral_jj_from_ao(i,j) = J_ij
mo_bielec_integral_jj_exchange_from_ao(i,j) = J_ij
mo_bielec_integral_jj_anti_from_ao(i,j) = J_ij - K_ij
`mo_bielec_integrals_in_map <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L22>`_
If True, the map of MO bielectronic integrals is provided
`mo_bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts/mo_bi_integrals.irp.f#L1>`_
`mo_bielec_integrals_index <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L1>`_
Computes an unique index for i,j,k,l integrals
`read_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/read_write.irp.f#L1>`_
One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
`read_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/read_write.irp.f#L2>`_
One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
`write_ao_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/read_write.irp.f#L3>`_
One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals
`write_mo_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/read_write.irp.f#L4>`_
One level of abstraction for disk_access_ao_integrals and disk_access_mo_integrals

73
src/Bitmask/README.rst
View File

@ -54,6 +54,24 @@ Documentation
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`is_a_two_holes_two_particles <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L206>`_
Undocumented
`number_of_holes <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L1>`_
Undocumented
`number_of_holes_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L394>`_
Undocumented
`number_of_particles <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L103>`_
Undocumented
`number_of_particles_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmask_cas_routines.irp.f#L422>`_
Undocumented
`cas_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L173>`_
Bitmasks for CAS reference determinants. (N_int, alpha/beta, CAS reference)
`cis_ijkl_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L32>`_
Bitmask to include all possible single excitations from Hartree-Fock
@ -61,23 +79,35 @@ Documentation
Bitmask to include all possible MOs
`generators_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L100>`_
Bitmasks for generator determinants. (N_int, alpha/beta, hole/particle, generator).
Bitmasks for generator determinants.
(N_int, alpha/beta, hole/particle, generator).
.br
3rd index is :
.br
* 1 : hole for single exc
* 1 : particle for single exc
.br
* 2 : particle for single exc
.br
* 3 : hole for 1st exc of double
.br
* 4 : particle for 1st exc of double
* 5 : hole for 2dn exc of double
* 6 : particle for 2dn exc of double
.br
* 5 : hole for 2nd exc of double
.br
* 6 : particle for 2nd exc of double
.br
`hf_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L44>`_
Hartree Fock bit mask
`i_bitmask_gen <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L186>`_
`i_bitmask_gen <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L211>`_
Current bitmask for the generators
`i_bitmask_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L194>`_
Current bitmask for the reference
`inact_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L193>`_
Bitmasks for the inactive orbitals that are excited in post CAS method
`n_cas_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L143>`_
Number of bitmasks for CAS
`n_generators_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L70>`_
Number of bitmasks for generators
@ -85,36 +115,31 @@ Documentation
`n_int <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L3>`_
Number of 64-bit integers needed to represent determinants as binary strings
`n_reference_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L134>`_
Number of bitmasks for reference
`ref_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L62>`_
Reference bit mask, used in Slater rules, chosen as Hartree-Fock bitmask
`reference_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L164>`_
Bitmasks for reference determinants. (N_int, alpha/beta, hole/particle, reference)
`virt_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks.irp.f#L194>`_
Bitmasks for the inactive orbitals that are excited in post CAS method
`bitstring_to_hexa <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L95>`_
`bitstring_to_hexa <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L98>`_
Transform a bit string to a string in hexadecimal format for printing
`bitstring_to_list <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L1>`_
Gives the inidices(+1) of the bits set to 1 in the bit string
`bitstring_to_str <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L62>`_
`bitstring_to_str <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L65>`_
Transform a bit string to a string for printing
`debug_det <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L117>`_
Undocumented
`debug_det <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L120>`_
Subroutine to print the content of a determinant in '+-' notation and
hexadecimal representation.
`list_to_bitstring <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L29>`_
return the physical string "string(N_int,2)" from the array of occupations "list(N_int*bit_kind_size,2)
list
<== ipos ==>
|
v
string :|------------------------|-------------------------|------------------------|
<==== bit_kind_size ====> <==== bit_kind_size ====> <==== bit_kind_size ====>
{ iint } { iint } { iint }
Returns the physical string "string(N_int,2)" from the array of
occupations "list(N_int*bit_kind_size,2)
`print_det <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L138>`_
Subroutine to print the content of a determinant using the '+-' notation

2
src/CAS_SD/EZFIO.cfg
View File

@ -8,7 +8,7 @@ default: 10000
type: logical
doc: If true, compute the PT2 at the end of the selection
interface: input
default: true
default: True
[PT2_max]
type: PT2_energy

35
src/CAS_SD/README.rst
View File

@ -7,3 +7,38 @@ Selected CAS + SD module.
1) Set the different MO classes using the ``qp_set_mo_class`` command
2) Run the selected CAS+SD program
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/CAS_SD/cas_sd_selected.irp.f#L1>`_
Undocumented
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

5
src/CID/README.rst
View File

@ -16,19 +16,20 @@ Needed Modules
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
Documentation
=============

5
src/CID_SC2_selected/README.rst
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@ -20,20 +20,21 @@ Needed Modules
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
* `SC2 <http://github.com/LCPQ/quantum_package/tree/master/src/SC2>`_
* `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

6
src/CID_selected/README.rst
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@ -23,19 +23,21 @@ Needed Modules
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_

5
src/CIS/README.rst
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@ -32,17 +32,18 @@ Needed Modules
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_

5
src/CISD/README.rst
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@ -16,19 +16,20 @@ Needed Modules
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
Documentation
=============

2
src/CISD_SC2_selected/EZFIO.cfg
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@ -8,7 +8,7 @@ default: 10000
type: logical
doc: If true, compute the PT2 at the end of the selection
interface: input
default: true
default: True
[PT2_max]
type: PT2_energy

8
src/CISD_SC2_selected/README.rst
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@ -8,6 +8,9 @@ Documentation
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`cisd_sc2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected/cisd_sc2_selection.irp.f#L1>`_
Undocumented
Needed Modules
@ -17,20 +20,21 @@ Needed Modules
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
* `SC2 <http://github.com/LCPQ/quantum_package/tree/master/src/SC2>`_
* `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

12
src/CISD_selected/README.rst
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@ -14,6 +14,12 @@ Documentation
`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/cisd_selection.irp.f#L1>`_
Undocumented
`n_det_max_cisd <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/options.irp.f#L1>`_
Get n_det_max_cisd from EZFIO file
`pt2_max <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected/options.irp.f#L18>`_
Get pt2_max from EZFIO file
Needed Modules
@ -23,19 +29,21 @@ Needed Modules
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_

35
src/DDCI_selected/README.rst
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@ -2,3 +2,38 @@
DDCI_selected Module
====================
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/DDCI_selected/ddci.irp.f#L1>`_
Undocumented
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

427
src/Dets/README.rst
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@ -33,11 +33,10 @@ Needed Modules
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
@ -50,18 +49,23 @@ Documentation
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`copy_h_apply_buffer_to_wf <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L95>`_
`copy_h_apply_buffer_to_wf <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L100>`_
Copies the H_apply buffer to psi_coef. You need to touch psi_det, psi_coef and N_det
after calling this function.
After calling this subroutine, N_det, psi_det and psi_coef need to be touched
`fill_h_apply_buffer_no_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L181>`_
`fill_h_apply_buffer_no_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L187>`_
Fill the H_apply buffer with determiants for CISD
`h_apply_buffer_allocated <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L14>`_
`h_apply_buffer_allocated <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L15>`_
Buffer of determinants/coefficients/perturbative energy for H_apply.
Uninitialized. Filled by H_apply subroutines.
`resize_h_apply_buffer <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L45>`_
`h_apply_buffer_lock <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L16>`_
Buffer of determinants/coefficients/perturbative energy for H_apply.
Uninitialized. Filled by H_apply subroutines.
`resize_h_apply_buffer <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L48>`_
Undocumented
`cisd_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/SC2.irp.f#L1>`_
@ -80,26 +84,43 @@ Documentation
.br
Initial guess vectors are not necessarily orthonormal
`repeat_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/SC2.irp.f#L220>`_
`connected_to_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L155>`_
Undocumented
`connected_to_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L95>`_
`connected_to_ref_by_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L253>`_
Undocumented
`det_is_not_or_may_be_in_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L191>`_
`det_is_not_or_may_be_in_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L359>`_
If true, det is not in ref
If false, det may be in ref
`is_in_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L1>`_
Undocumented
`det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L1>`_
Return an integer*8 corresponding to a determinant index for searching
`key_pattern_not_in_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L225>`_
`get_index_in_psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L48>`_
Returns the index of the determinant in the ``psi_det_sorted_bit`` array
`is_in_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L34>`_
True if the determinant ``det`` is in the wave function
`key_pattern_not_in_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L393>`_
Min and max values of the integers of the keys of the reference
`davidson_converged <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L383>`_
`occ_pattern_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L17>`_
Return an integer*8 corresponding to a determinant index for searching
`do_mono_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/create_excitations.irp.f#L1>`_
Apply the mono excitation operator : a^{dager}_(i_particle) a_(i_hole) of spin = ispin
on key_in
ispin = 1 == alpha
ispin = 2 == beta
i_ok = 1 == the excitation is possible
i_ok = -1 == the excitation is not possible
`davidson_converged <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L382>`_
True if the Davidson algorithm is converged
`davidson_criterion <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L373>`_
`davidson_criterion <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L372>`_
Can be : [ energy | residual | both | wall_time | cpu_time | iterations ]
`davidson_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L18>`_
@ -146,10 +167,10 @@ Documentation
`davidson_sze_max <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L9>`_
Max number of Davidson sizes
`davidson_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L374>`_
`davidson_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L373>`_
Can be : [ energy | residual | both | wall_time | cpu_time | iterations ]
`one_body_dm_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L73>`_
`one_body_dm_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L164>`_
One-body density matrix
`one_body_dm_mo_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L1>`_
@ -158,63 +179,162 @@ Documentation
`one_body_dm_mo_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L2>`_
Alpha and beta one-body density matrix for each state
`save_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L97>`_
`one_body_single_double_dm_mo_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L80>`_
Alpha and beta one-body density matrix for each state
`one_body_single_double_dm_mo_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L81>`_
Alpha and beta one-body density matrix for each state
`one_body_spin_density_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L172>`_
rho(alpha) - rho(beta)
`save_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L196>`_
Save natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis
`set_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L81>`_
`set_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L180>`_
Set natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis
`state_average_weight <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L108>`_
`state_average_weight <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L207>`_
Weights in the state-average calculation of the density matrix
`det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L295>`_
Return an integer*8 corresponding to a determinant index for searching
`det_svd <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/det_svd.irp.f#L1>`_
Computes the SVD of the Alpha x Beta determinant coefficient matrix
`create_wf_of_psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L741>`_
Matrix of wf coefficients. Outer product of alpha and beta determinants
`filter_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L552>`_
Returns a determinant with only the 3 highest electrons
`generate_all_alpha_beta_det_products <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L796>`_
Create a wave function from all possible alpha x beta determinants
`int_of_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L517>`_
Returns an integer*8 as :
.br
|_<--- 21 bits ---><--- 21 bits ---><--- 21 bits --->|
.br
|0<--- i1 ---><--- i2 ---><--- i3 --->|
.br
It encodes the value of the indices of the 3 highest MOs
in descending order
.br
`max_degree_exc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L32>`_
Maximum degree of excitation in the wf
`n_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L3>`_
Number of determinants in the wave function
`psi_average_norm_contrib <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L208>`_
`n_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L348>`_
Unique alpha determinants
`n_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L385>`_
Unique beta determinants
`psi_average_norm_contrib <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L276>`_
Contribution of determinants to the state-averaged density
`psi_average_norm_contrib_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L229>`_
`psi_average_norm_contrib_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L432>`_
Wave function sorted by determinants contribution to the norm (state-averaged)
`psi_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L153>`_
`psi_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L230>`_
The wave function coefficients. Initialized with Hartree-Fock if the EZFIO file
is empty
`psi_coef_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L228>`_
`psi_coef_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L431>`_
Wave function sorted by determinants contribution to the norm (state-averaged)
`psi_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L259>`_
Determinants on which we apply <i|H|psi> for perturbation.
o They are sorted by determinants interpreted as integers. Useful
to accelerate the search of a determinant
`psi_coef_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L579>`_
Determinants on which we apply <i|H|j>.
They are sorted by the 3 highest electrons in the alpha part,
then by the 3 highest electrons in the beta part to accelerate
the research of connected determinants.
`psi_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L53>`_
`psi_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L462>`_
Determinants on which we apply <i|H|psi> for perturbation.
They are sorted by determinants interpreted as integers. Useful
to accelerate the search of a random determinant in the wave
function.
`psi_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L65>`_
The wave function determinants. Initialized with Hartree-Fock if the EZFIO file
is empty
`psi_det_size <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L35>`_
`psi_det_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L319>`_
List of alpha determinants of psi_det
`psi_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L347>`_
Unique alpha determinants
`psi_det_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L333>`_
List of beta determinants of psi_det
`psi_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L384>`_
Unique beta determinants
`psi_det_size <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L47>`_
Size of the psi_det/psi_coef arrays
`psi_det_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L227>`_
`psi_det_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L430>`_
Wave function sorted by determinants contribution to the norm (state-averaged)
`psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L258>`_
Determinants on which we apply <i|H|psi> for perturbation.
o They are sorted by determinants interpreted as integers. Useful
to accelerate the search of a determinant
`psi_det_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L578>`_
Determinants on which we apply <i|H|j>.
They are sorted by the 3 highest electrons in the alpha part,
then by the 3 highest electrons in the beta part to accelerate
the research of connected determinants.
`read_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L104>`_
`psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L461>`_
Determinants on which we apply <i|H|psi> for perturbation.
They are sorted by determinants interpreted as integers. Useful
to accelerate the search of a random determinant in the wave
function.
`psi_det_sorted_next_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L580>`_
Determinants on which we apply <i|H|j>.
They are sorted by the 3 highest electrons in the alpha part,
then by the 3 highest electrons in the beta part to accelerate
the research of connected determinants.
`psi_svd_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L826>`_
SVD wave function
`psi_svd_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L827>`_
SVD wave function
`psi_svd_coefs <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L828>`_
SVD wave function
`psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L709>`_
Matrix of wf coefficients. Outer product of alpha and beta determinants
`read_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L880>`_
Reads the determinants from the EZFIO file
`save_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L310>`_
`save_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L927>`_
Save the wave function into the EZFIO file
`save_wavefunction_general <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L319>`_
`save_wavefunction_general <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L946>`_
Save the wave function into the EZFIO file
`save_wavefunction_unsorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L937>`_
Save the wave function into the EZFIO file
`sort_dets_by_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L600>`_
Determinants on which we apply <i|H|j>.
They are sorted by the 3 highest electrons in the alpha part,
then by the 3 highest electrons in the beta part to accelerate
the research of connected determinants.
`sort_dets_by_det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L475>`_
Determinants are sorted are sorted according to their det_search_key.
Useful to accelerate the search of a random determinant in the wave
function.
`spin_det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L303>`_
Return an integer*8 corresponding to a determinant index for searching
`double_exc_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants_bitmasks.irp.f#L40>`_
double_exc_bitmask(:,1,i) is the bitmask for holes of excitation 1
double_exc_bitmask(:,2,i) is the bitmask for particles of excitation 1
@ -233,10 +353,13 @@ Documentation
single_exc_bitmask(:,2,i) is the bitmask for particles
for a given couple of hole/particle excitations i.
`ci_eigenvectors <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L36>`_
`ci_eigenvectors <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L37>`_
Eigenvectors/values of the CI matrix
`ci_electronic_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L35>`_
`ci_eigenvectors_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L38>`_
Eigenvectors/values of the CI matrix
`ci_electronic_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L36>`_
Eigenvectors/values of the CI matrix
`ci_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L18>`_
@ -245,7 +368,7 @@ Documentation
`diag_algorithm <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L1>`_
Diagonalization algorithm (Davidson or Lapack)
`diagonalize_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L73>`_
`diagonalize_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L96>`_
Replace the coefficients of the CI states by the coefficients of the
eigenstates of the CI matrix
@ -256,15 +379,31 @@ Documentation
Eigenvectors/values of the CI matrix
`ci_sc2_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L1>`_
N_states lowest eigenvalues of the CI matrix
N_states_diag lowest eigenvalues of the CI matrix
`diagonalize_ci_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L46>`_
Replace the coefficients of the CI states by the coefficients of the
Replace the coefficients of the CI states_diag by the coefficients of the
eigenstates of the CI matrix
`threshold_convergence_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L18>`_
convergence of the correlation energy of SC2 iterations
`ci_eigenvectors_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L2>`_
Eigenvectors/values of the CI matrix
`ci_eigenvectors_s2_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L3>`_
Eigenvectors/values of the CI matrix
`ci_electronic_energy_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L1>`_
Eigenvectors/values of the CI matrix
`diagonalize_ci_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L59>`_
Replace the coefficients of the CI states by the coefficients of the
eigenstates of the CI matrix
`apply_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/excitations_utils.irp.f#L1>`_
Undocumented
`filter_connected <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L2>`_
Filters out the determinants that are not connected by H
.br
@ -276,9 +415,16 @@ Documentation
.br
idx(0) is the number of determinants that interact with key1
`filter_connected_davidson <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L101>`_
`filter_connected_davidson <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L163>`_
Filters out the determinants that are not connected by H
returns the array idx which contains the index of the
determinants in the array key1 that interact
via the H operator with key2.
.br
idx(0) is the number of determinants that interact with key1
key1 should come from psi_det_sorted_ab.
`filter_connected_i_h_psi0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L293>`_
returns the array idx which contains the index of the
.br
determinants in the array key1 that interact
@ -287,16 +433,7 @@ Documentation
.br
idx(0) is the number of determinants that interact with key1
`filter_connected_i_h_psi0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L233>`_
returns the array idx which contains the index of the
.br
determinants in the array key1 that interact
.br
via the H operator with key2.
.br
idx(0) is the number of determinants that interact with key1
`filter_connected_i_h_psi0_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L332>`_
`filter_connected_i_h_psi0_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L392>`_
standard filter_connected_i_H_psi but returns in addition
.br
the array of the index of the non connected determinants to key1
@ -307,31 +444,156 @@ Documentation
.br
to repeat the excitations
`filter_connected_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L101>`_
Filters out the determinants that are not connected by H
returns the array idx which contains the index of the
determinants in the array key1 that interact
via the H operator with key2.
idx(0) is the number of determinants that interact with key1
.br
Determinants are taken from the psi_det_sorted_ab array
`put_gess <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/guess_triplet.irp.f#L1>`_
Undocumented
`det_to_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L2>`_
Transform a determinant to an occupation pattern
`make_s2_eigenfunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L251>`_
Undocumented
`n_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L143>`_
array of the occ_pattern present in the wf
psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation
psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation
`occ_pattern_to_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L42>`_
Generate all possible determinants for a give occ_pattern
`occ_pattern_to_dets_size <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L20>`_
Number of possible determinants for a given occ_pattern
`psi_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L142>`_
array of the occ_pattern present in the wf
psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation
psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation
`rec_occ_pattern_to_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L102>`_
Undocumented
`n_states_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/options.irp.f#L40>`_
Number of states to consider for the diagonalization
`pouet <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/program_beginer_determinants.irp.f#L1>`_
Undocumented
`routine <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/program_beginer_determinants.irp.f#L7>`_
Undocumented
`idx_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L5>`_
CAS wave function, defined from the application of the CAS bitmask on the
determinants. idx_cas gives the indice of the CAS determinant in psi_det.
`idx_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L62>`_
Set of determinants which are not part of the CAS, defined from the application
of the CAS bitmask on the determinants.
idx_non_cas gives the indice of the determinant in psi_det.
`n_det_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L6>`_
CAS wave function, defined from the application of the CAS bitmask on the
determinants. idx_cas gives the indice of the CAS determinant in psi_det.
`n_det_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L63>`_
Set of determinants which are not part of the CAS, defined from the application
of the CAS bitmask on the determinants.
idx_non_cas gives the indice of the determinant in psi_det.
`psi_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L3>`_
CAS wave function, defined from the application of the CAS bitmask on the
determinants. idx_cas gives the indice of the CAS determinant in psi_det.
`psi_cas_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L4>`_
CAS wave function, defined from the application of the CAS bitmask on the
determinants. idx_cas gives the indice of the CAS determinant in psi_det.
`psi_cas_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L47>`_
CAS determinants sorted to accelerate the search of a random determinant in the wave
function.
`psi_cas_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L46>`_
CAS determinants sorted to accelerate the search of a random determinant in the wave
function.
`psi_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L60>`_
Set of determinants which are not part of the CAS, defined from the application
of the CAS bitmask on the determinants.
idx_non_cas gives the indice of the determinant in psi_det.
`psi_non_cas_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L61>`_
Set of determinants which are not part of the CAS, defined from the application
of the CAS bitmask on the determinants.
idx_non_cas gives the indice of the determinant in psi_det.
`psi_non_cas_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L100>`_
CAS determinants sorted to accelerate the search of a random determinant in the wave
function.
`psi_non_cas_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L99>`_
CAS determinants sorted to accelerate the search of a random determinant in the wave
function.
`bi_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L5>`_
Energy of the reference bitmask used in Slater rules
`kinetic_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L3>`_
Energy of the reference bitmask used in Slater rules
`mono_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L2>`_
Energy of the reference bitmask used in Slater rules
`nucl_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L4>`_
Energy of the reference bitmask used in Slater rules
`ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L1>`_
Energy of the reference bitmask used in Slater rules
`expected_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L48>`_
Expected value of S2 : S*(S+1)
`get_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L1>`_
Returns <S^2>
`get_s2_u0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L46>`_
`get_s2_u0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L82>`_
Undocumented
`s2_values <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L67>`_
array of the averaged values of the S^2 operator on the various states
`s_z <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L36>`_
Undocumented
z component of the Spin
`s_z2_sz <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L37>`_
z component of the Spin
`prog_save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_casino.irp.f#L266>`_
Undocumented
`save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_casino.irp.f#L1>`_
Undocumented
`save_dets_qmcchem <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_qmcchem.irp.f#L1>`_
Undocumented
`save_for_qmc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_qmcchem.irp.f#L37>`_
`save_for_qmc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_qmcchem.irp.f#L48>`_
Undocumented
`save_natorb <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_natorb.irp.f#L1>`_
Undocumented
`a_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L721>`_
`a_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L962>`_
Needed for diag_H_mat_elem
`ac_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L766>`_
`ac_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1007>`_
Needed for diag_H_mat_elem
`decode_exc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L76>`_
@ -341,10 +603,10 @@ Documentation
s1,s2 : Spins (1:alpha, 2:beta)
degree : Degree of excitation
`det_connections <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L898>`_
.br
`det_connections <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1139>`_
Build connection proxy between determinants
`diag_h_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L659>`_
`diag_h_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L900>`_
Computes <i|H|i>
`get_double_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L141>`_
@ -356,16 +618,16 @@ Documentation
`get_excitation_degree <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1>`_
Returns the excitation degree between two determinants
`get_excitation_degree_vector <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L575>`_
`get_excitation_degree_vector <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L816>`_
Applies get_excitation_degree to an array of determinants
`get_mono_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L274>`_
Returns the excitation operator between two singly excited determinants and the phase
`get_occ_from_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L814>`_
`get_occ_from_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1055>`_
Returns a list of occupation numbers from a bitstring
`h_u_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L830>`_
`h_u_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1071>`_
Computes v_0 = H|u_0>
.br
n : number of determinants
@ -375,10 +637,13 @@ Documentation
`i_h_j <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L355>`_
Returns <i|H|j> where i and j are determinants
`i_h_psi <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L491>`_
`i_h_j_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L492>`_
Returns <i|H|j> where i and j are determinants
`i_h_psi <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L631>`_
<key|H|psi> for the various Nstates
`i_h_psi_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L527>`_
`i_h_psi_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L713>`_
<key|H|psi> for the various Nstate
.br
returns in addition
@ -391,11 +656,33 @@ Documentation
.br
to repeat the excitations
`n_con_int <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L890>`_
`i_h_psi_sc2_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L760>`_
<key|H|psi> for the various Nstate
.br
returns in addition
.br
the array of the index of the non connected determinants to key1
.br
in order to know what double excitation can be repeated on key1
.br
idx_repeat(0) is the number of determinants that can be used
.br
to repeat the excitations
`i_h_psi_sec_ord <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L666>`_
<key|H|psi> for the various Nstates
`n_con_int <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1131>`_
Number of integers to represent the connections between determinants
`write_spindeterminants <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L1>`_
Undocumented
`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/truncate_wf.irp.f#L1>`_
Undocumented
`h_matrix_all_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/utils.irp.f#L1>`_
H matrix on the basis of the slater deter;inants defined by psi_det
H matrix on the basis of the slater determinants defined by psi_det

29
src/FCIdump/README.rst
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@ -4,3 +4,32 @@ FCIdump Module
Interface for the `NECI <https://github.com/ghb24/NECI_STABLE>`_ Full-CI QMC program.
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`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 file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

2
src/Full_CI/EZFIO.cfg
View File

@ -14,7 +14,7 @@ default: 10000
type: logical
doc: If true, compute the PT2 at the end of the selection
interface: input
default: true
default: True
[PT2_max]
type: PT2_energy

11
src/Full_CI/README.rst
View File

@ -10,7 +10,10 @@ Documentation
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/full_ci.irp.f#L1>`_
`full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/full_ci_no_skip.irp.f#L1>`_
Undocumented
`var_pt2_ratio_run <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/var_pt2_ratio.irp.f#L1>`_
Undocumented
@ -22,18 +25,20 @@ Needed Modules
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_

52
src/Generators_CAS/README.rst
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@ -3,3 +3,55 @@ Generators_CAS Module
=====================
The generator determinants are those filtered by the ``cas_bitmask`` mask.
Assumptions
===========
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
The active space is defined by the ``reference_bitmask``.
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L3>`_
Number of generator detetrminants
`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L35>`_
For Single reference wave functions, the generator is the
Hartree-Fock determinant
`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L34>`_
For Single reference wave functions, the generator is the
Hartree-Fock determinant
`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L78>`_
Memo to skip useless selectors
`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS/generators.irp.f#L70>`_
Size of the select_max array
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

21
src/Generators_full/README.rst
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@ -11,20 +11,26 @@ Documentation
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L22>`_
`degree_max_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L55>`_
Max degree of excitation (respect to HF) of the generators
`n_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L15>`_
For Single reference wave functions, the number of generators is 1 : the
Hartree-Fock determinant
`psi_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L44>`_
`psi_coef_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L38>`_
For Single reference wave functions, the generator is the
Hartree-Fock determinant
`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L60>`_
`psi_det_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L37>`_
For Single reference wave functions, the generator is the
Hartree-Fock determinant
`select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L78>`_
Memo to skip useless selectors
`threshold_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L3>`_
Percentage of the norm of the state-averaged wave function to
consider for the generators
`size_select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L70>`_
Size of the select_max array
@ -35,12 +41,13 @@ Needed Modules
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_

45
src/Hartree_Fock/README.rst
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@ -11,11 +11,12 @@ Needed Modules
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
@ -36,16 +37,16 @@ Documentation
`fock_matrix_alpha_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L83>`_
Alpha Fock matrix in AO basis set
`fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L194>`_
`fock_matrix_alpha_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L231>`_
Fock matrix on the MO basis
`fock_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L242>`_
`fock_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L289>`_
Fock matrix in AO basis set
`fock_matrix_beta_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L84>`_
Alpha Fock matrix in AO basis set
`fock_matrix_beta_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L214>`_
`fock_matrix_beta_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L251>`_
Fock matrix on the MO basis
`fock_matrix_diag_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L2>`_
@ -78,24 +79,30 @@ Documentation
K = Fb - Fa
.br
`fock_mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L285>`_
`fock_mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L332>`_
Undocumented
`hf_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L233>`_
`hf_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L270>`_
Hartree-Fock energy
`hf_density_matrix_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L27>`_
Density matrix in the AO basis
S^-1 Density matrix in the AO basis S^-1
`hf_density_matrix_ao_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L1>`_
Alpha density matrix in the AO basis
S^-1 x Alpha density matrix in the AO basis x S^-1
`hf_density_matrix_ao_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/HF_density_matrix_ao.irp.f#L14>`_
Beta density matrix in the AO basis
S^-1 Beta density matrix in the AO basis x S^-1
`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L7>`_
`guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Huckel_guess.irp.f#L1>`_
Undocumented
`create_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L8>`_
Create an MO guess if no MOs are present in the EZFIO directory
`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L33>`_
Run SCF calculation
`scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L2>`_
Undocumented
@ -105,7 +112,7 @@ Documentation
`diagonal_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L1>`_
Diagonal Fock matrix in the MO basis
`diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L57>`_
`diagonal_fock_matrix_mo_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L67>`_
diagonal element of the fock matrix calculated as the sum over all the interactions
with all the electrons in the RHF determinant
diagonal_Fock_matrix_mo_sum(i) = sum_{j=1, N_elec} 2 J_ij -K_ij
@ -113,20 +120,8 @@ Documentation
`eigenvectors_fock_matrix_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/diagonalize_fock.irp.f#L2>`_
Diagonal Fock matrix in the MO basis
`bi_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L5>`_
Energy of the reference bitmask used in Slater rules
`kinetic_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L3>`_
Energy of the reference bitmask used in Slater rules
`mono_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L2>`_
Energy of the reference bitmask used in Slater rules
`nucl_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L4>`_
Energy of the reference bitmask used in Slater rules
`ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ref_bitmask.irp.f#L1>`_
Energy of the reference bitmask used in Slater rules
`huckel_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/huckel.irp.f#L1>`_
Build the MOs using the extended Huckel model

43
src/MOs/README.rst
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@ -23,11 +23,11 @@ Needed Modules
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
Documentation
=============
@ -45,29 +45,58 @@ Documentation
`mo_density_matrix_virtual <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/cholesky_mo.irp.f#L64>`_
Density matrix in MO basis (virtual MOs)
`mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L22>`_
`mo_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mo_overlap.irp.f#L2>`_
Undocumented
`ao_to_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L126>`_
Transform A from the AO basis to the MO basis
`mix_mo_jk <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L210>`_
subroutine that rotates the jth MO with the kth MO
to give two new MO's that are
'+' = 1/sqrt(2) (|j> + |k>)
'-' = 1/sqrt(2) (|j> - |k>)
by convention, the '+' MO is in the lower index (min(j,k))
by convention, the '-' MO is in the greater index (max(j,k))
`mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L28>`_
Molecular orbital coefficients on AO basis set
mo_coef(i,j) = coefficient of the ith ao on the jth mo
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#L60>`_
`mo_coef_transp <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L71>`_
Molecular orbital coefficients on AO basis set
`mo_label <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L23>`_
`mo_label <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L29>`_
Molecular orbital coefficients on AO basis set
mo_coef(i,j) = coefficient of the ith ao on the jth mo
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#L78>`_
`mo_occ <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L102>`_
MO occupation numbers
`mo_to_ao <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L152>`_
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>`_
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>`_
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#L12>`_
`mo_tot_num_align <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L18>`_
Aligned variable for dimensioning of arrays
`mo_as_eigvectors_of_mo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L22>`_
`s_mo_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/mos.irp.f#L89>`_
Product S.C where S is the overlap matrix in the AO basis and C the mo_coef matrix.
`mo_as_eigvectors_of_mo_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L24>`_
Undocumented
`mo_as_eigvectors_of_mo_matrix_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L62>`_
Undocumented
`mo_sort_by_observable <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L144>`_
Undocumented
`save_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MOs/utils.irp.f#L1>`_

8
src/MP2/README.rst
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@ -8,7 +8,7 @@ Documentation
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/MP2/mp2.irp.f#L1>`_
`mp2 <http://github.com/LCPQ/quantum_package/tree/master/src/MP2/mp2.irp.f#L1>`_
Undocumented
@ -20,18 +20,20 @@ Needed Modules
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

82
src/MRCC/README.rst
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@ -5,5 +5,87 @@ MRCC Module
Needed Modules
==============
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`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#L132>`_
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#L147>`_
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>

4
src/Makefile
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@ -16,6 +16,10 @@ default: ezfio
veryclean:
$(QPACKAGE_ROOT)/scripts/clean_modules.sh $(ALL_MODULES)
# Define the dict [type in EZFIO.cfg] = ocaml type , f90 type
# If you change the qptypes_generator.ml, you need to rm this
# For simplicity add this to the veryclean rule
rm $(QPACKAGE_ROOT)/scripts/ezfio_interface/fancy_type.p
$(ALL_MODULES): ezfio
$(QPACKAGE_ROOT)/scripts/build_modules.sh $@

37
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@ -2,3 +2,40 @@
Molden Module
=============
Documentation
=============
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`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 file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

63
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@ -18,30 +18,10 @@ Documentation
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`ao_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L122>`_
`ao_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L1>`_
array of the mono electronic hamiltonian on the AOs basis
: sum of the kinetic and nuclear electronic potential
`ao_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L1>`_
Overlap between atomic basis functions:
:math:`\int \chi_i(r) \chi_j(r) dr)`
`ao_overlap_abs <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L65>`_
Overlap between absolute value of atomic basis functions:
:math:`\int |\chi_i(r)| |\chi_j(r)| dr)`
`ao_overlap_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L2>`_
Overlap between atomic basis functions:
:math:`\int \chi_i(r) \chi_j(r) dr)`
`ao_overlap_y <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L3>`_
Overlap between atomic basis functions:
:math:`\int \chi_i(r) \chi_j(r) dr)`
`ao_overlap_z <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/ao_mono_ints.irp.f#L4>`_
Overlap between atomic basis functions:
:math:`\int \chi_i(r) \chi_j(r) dr)`
`check_ortho <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/check_orthonormality.irp.f#L1>`_
Undocumented
@ -72,58 +52,63 @@ Documentation
.br
{\tt ao_deriv2_x} = \langle \chi_i(x,y,z) \frac{\partial^2}{\partial x^2} |\chi_j (x,y,z) \rangle
`ao_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_ao_ints.irp.f#L126>`_
`ao_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_ao_ints.irp.f#L125>`_
array of the priminitve basis kinetic integrals
\langle \chi_i |\hat{T}| \chi_j \rangle
`mo_kinetic_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/kin_mo_ints.irp.f#L1>`_
Undocumented
`mo_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/mo_mono_ints.irp.f#L35>`_
`mo_mono_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/mo_mono_ints.irp.f#L1>`_
array of the mono electronic hamiltonian on the MOs basis
: sum of the kinetic and nuclear electronic potential
`mo_overlap <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/mo_mono_ints.irp.f#L1>`_
Undocumented
`orthonormalize_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/orthonormalize.irp.f#L1>`_
Undocumented
`ao_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L1>`_
interaction nuclear electron
`give_polynom_mult_center_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L161>`_
`ao_nucl_elec_integral_per_atom <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L67>`_
ao_nucl_elec_integral_per_atom(i,j,k) = -<AO(i)|1/|r-Rk|AO(j)>
where Rk is the geometry of the kth atom
`give_polynom_mult_center_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L214>`_
Undocumented
`i_x1_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L289>`_
`i_x1_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L342>`_
Undocumented
`i_x2_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L361>`_
`i_x2_pol_mult_mono_elec <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L413>`_
Undocumented
`int_gaus_pol <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L432>`_
`int_gaus_pol <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L484>`_
Undocumented
`nai_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L82>`_
`nai_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L135>`_
Undocumented
`v_e_n <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L413>`_
`v_e_n <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L465>`_
Undocumented
`v_phi <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L477>`_
`v_phi <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L529>`_
Undocumented
`v_r <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L461>`_
`v_r <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L513>`_
Undocumented
`v_theta <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L490>`_
`v_theta <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L542>`_
Undocumented
`wallis <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L506>`_
`wallis <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_ao_ints.irp.f#L558>`_
Undocumented
`mo_nucl_elec_integral <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_mo_ints.irp.f#L1>`_
Undocumented
interaction nuclear electron on the MO basis
`mo_nucl_elec_integral_per_atom <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/pot_mo_ints.irp.f#L30>`_
mo_nucl_elec_integral_per_atom(i,j,k) = -<MO(i)|1/|r-Rk|MO(j)>
where Rk is the geometry of the kth atom
`save_ortho_mos <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/save_ortho_mos.irp.f#L1>`_
Undocumented
@ -173,7 +158,7 @@ Documentation
array of the integrals of AO_i * y^2 AO_j
array of the integrals of AO_i * z^2 AO_j
`overlap_bourrin_deriv_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L359>`_
`overlap_bourrin_deriv_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L365>`_
Undocumented
`overlap_bourrin_dipole <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L318>`_
@ -182,7 +167,7 @@ Documentation
`overlap_bourrin_spread <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L265>`_
Undocumented
`overlap_bourrin_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L374>`_
`overlap_bourrin_x <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L380>`_
Undocumented
`overlap_bourrin_x_abs <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts/spread_dipole_ao.irp.f#L226>`_

8
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@ -22,6 +22,9 @@ Documentation
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`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)
`nucl_charge <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L23>`_
Nuclear charges
@ -65,8 +68,11 @@ Documentation
`nucl_num_aligned <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L2>`_
Number of nuclei
`nuclear_repulsion <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L171>`_
`nuclear_repulsion <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L187>`_
Nuclear repulsion energy
`positive_charge_barycentre <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L171>`_
Centroid of the positive charges

18
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@ -39,5 +39,23 @@ Documentation
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`output_cpu_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L2>`_
Initial CPU and wall times when printing in the output files
`output_wall_time_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L1>`_
Initial CPU and wall times when printing in the output files
`write_bool <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L88>`_
Write an logical value in output
`write_double <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L58>`_
Write a double precision value in output
`write_int <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L73>`_
Write an integer value in output
`write_time <http://github.com/LCPQ/quantum_package/tree/master/src/Output/output.irp.f#L42>`_
Write a time stamp in the output for chronological reconstruction

106
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@ -8,7 +8,18 @@ Documentation
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`coef_hf_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L27>`_
`coef_hf_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L28>`_
energy of correlation per determinant respect to the Hartree Fock determinant
.br
for the all the double excitations in the selectors determinants
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`delta_e_per_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L33>`_
energy of correlation per determinant respect to the Hartree Fock determinant
.br
for the all the double excitations in the selectors determinants
@ -28,7 +39,29 @@ Documentation
.br
n_double_selectors = number of double excitations in the selectors determinants
`e_corr_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L28>`_
`e_corr_double_only <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L34>`_
energy of correlation per determinant respect to the Hartree Fock determinant
.br
for the all the double excitations in the selectors determinants
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`e_corr_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L31>`_
energy of correlation per determinant respect to the Hartree Fock determinant
.br
for the all the double excitations in the selectors determinants
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`e_corr_second_order <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L35>`_
energy of correlation per determinant respect to the Hartree Fock determinant
.br
for the all the double excitations in the selectors determinants
@ -48,6 +81,39 @@ Documentation
.br
n_double_selectors = number of double excitations in the selectors determinants
`i_h_hf_per_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L32>`_
energy of correlation per determinant respect to the Hartree Fock determinant
.br
for the all the double excitations in the selectors determinants
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`inv_selectors_coef_hf <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L29>`_
energy of correlation per determinant respect to the Hartree Fock determinant
.br
for the all the double excitations in the selectors determinants
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`inv_selectors_coef_hf_squared <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L30>`_
energy of correlation per determinant respect to the Hartree Fock determinant
.br
for the all the double excitations in the selectors determinants
.br
E_corr_per_selectors(i) = <D_i|H|HF> * c(D_i)/c(HF) if |D_i> is a double excitation
.br
E_corr_per_selectors(i) = -1000.d0 if it is not a double excitation
.br
coef_hf_selector = coefficient of the Hartree Fock determinant in the selectors determinants
`n_double_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L5>`_
degree of excitation respect to Hartree Fock for the wave function
.br
@ -57,23 +123,40 @@ Documentation
.br
n_double_selectors = number of double excitations in the selectors determinants
`n_det_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L26>`_
`n_det_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L20>`_
For Single reference wave functions, the number of selectors is 1 : the
Hartree-Fock determinant
`psi_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L48>`_
`psi_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L42>`_
Determinants on which we apply <i|H|psi> for perturbation.
`psi_selectors_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L49>`_
`psi_selectors_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L76>`_
Determinants on which we apply <i|H|j>.
They are sorted by the 3 highest electrons in the alpha part,
then by the 3 highest electrons in the beta part to accelerate
the research of connected determinants.
`psi_selectors_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L43>`_
Determinants on which we apply <i|H|psi> for perturbation.
`psi_selectors_size <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L21>`_
`psi_selectors_coef_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L77>`_
Determinants on which we apply <i|H|j>.
They are sorted by the 3 highest electrons in the alpha part,
then by the 3 highest electrons in the beta part to accelerate
the research of connected determinants.
`psi_selectors_diag_h_mat <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L63>`_
Diagonal elements of the H matrix for each selectors
`psi_selectors_next_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L78>`_
Determinants on which we apply <i|H|j>.
They are sorted by the 3 highest electrons in the alpha part,
then by the 3 highest electrons in the beta part to accelerate
the research of connected determinants.
`psi_selectors_size <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L15>`_
Undocumented
`threshold_selectors <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L3>`_
Percentage of the norm of the state-averaged wave function to
consider for the selectors
Needed Modules
@ -83,12 +166,13 @@ Needed Modules
.. NEEDED_MODULES file.
* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_

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@ -10,35 +10,104 @@ Documentation
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`apply_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L168>`_
Apply the rotation found by find_rotation
`find_rotation <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L149>`_
Find A.C = B
`get_pseudo_inverse <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L95>`_
Find C = A^-1
`lapack_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L247>`_
Diagonalize matrix H
.br
H is untouched between input and ouptut
.br
eigevalues(i) = ith lowest eigenvalue of the H matrix
.br
eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
.br
`lapack_diag_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L310>`_
Diagonalize matrix H
.br
H is untouched between input and ouptut
.br
eigevalues(i) = ith lowest eigenvalue of the H matrix
.br
eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
.br
`lapack_diagd <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L180>`_
Diagonalize matrix H
.br
H is untouched between input and ouptut
.br
eigevalues(i) = ith lowest eigenvalue of the H matrix
.br
eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
.br
`lapack_partial_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L376>`_
Diagonalize matrix H
.br
H is untouched between input and ouptut
.br
eigevalues(i) = ith lowest eigenvalue of the H matrix
.br
eigvectors(i,j) = <i|psi_j> where i is the basis function and psi_j is the j th eigenvector
.br
`ortho_lowdin <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L1>`_
Compute C_new=C_old.S^-1/2 canonical orthogonalization.
.br
overlap : overlap matrix
.br
LDA : leftmost dimension of overlap array
.br
N : Overlap matrix is NxN (array is (LDA,N) )
.br
C : Coefficients of the vectors to orthogonalize. On exit,
orthogonal vectors
.br
LDC : leftmost dimension of C
.br
m : Coefficients matrix is MxN, ( array is (LDC,N) )
.br
`set_zero_extra_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/LinearAlgebra.irp.f#L433>`_
Undocumented
`abort_all <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L1>`_
If True, all the calculation is aborted
`abort_here <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L10>`_
`abort_here <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L11>`_
If True, all the calculation is aborted
`catch_signal <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L33>`_
`catch_signal <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L30>`_
What to do on Ctrl-C. If two Ctrl-C are pressed within 1 sec, the calculation if aborted.
`trap_signals <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L18>`_
`trap_signals <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/abort.irp.f#L19>`_
What to do when a signal is caught. Here, trap Ctrl-C and call the control_C subroutine.
`add_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L243>`_
`add_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L306>`_
Add two polynomials
D(t) =! D(t) +( B(t)+C(t))
`add_poly_multiply <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L271>`_
`add_poly_multiply <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L334>`_
Add a polynomial multiplied by a constant
D(t) =! D(t) +( cst * B(t))
`f_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L345>`_
`f_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L408>`_
function that calculates the following integral
\int_{\-infty}^{+\infty} x^n \exp(-p x^2) dx
`gaussian_product <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L121>`_
`gaussian_product <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L184>`_
Gaussian product in 1D.
e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}
`gaussian_product_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L163>`_
`gaussian_product_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L226>`_
Gaussian product in 1D.
e^{-a (x-x_A)^2} e^{-b (x-x_B)^2} = K_{ab}^x e^{-p (x-x_P)^2}
@ -50,108 +119,148 @@ Documentation
* [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 )
* [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 )
`give_explicit_poly_and_gaussian_double <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L122>`_
Transforms the product of
(x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3)
exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta) exp(-(r-Nucl_center)^2 gama
.br
into
fact_k * [ sum (l_x = 0,i_order(1)) P_new(l_x,1) * (x-P_center(1))^l_x ] exp (- p (x-P_center(1))^2 )
* [ sum (l_y = 0,i_order(2)) P_new(l_y,2) * (y-P_center(2))^l_y ] exp (- p (y-P_center(2))^2 )
* [ sum (l_z = 0,i_order(3)) P_new(l_z,3) * (z-P_center(3))^l_z ] exp (- p (z-P_center(3))^2 )
`give_explicit_poly_and_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L1>`_
Transform the product of
(x-x_A)^a(1) (x-x_B)^b(1) (x-x_A)^a(2) (y-y_B)^b(2) (z-z_A)^a(3) (z-z_B)^b(3) exp(-(r-A)^2 alpha) exp(-(r-B)^2 beta)
into
fact_k (x-x_P)^iorder(1) (y-y_P)^iorder(2) (z-z_P)^iorder(3) exp(-p(r-P)^2)
`hermite <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L477>`_
`hermite <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L540>`_
Hermite polynomial
`multiply_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L201>`_
`multiply_poly <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L264>`_
Multiply two polynomials
D(t) =! D(t) +( B(t)*C(t))
`recentered_poly2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L300>`_
`recentered_poly2 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L363>`_
Recenter two polynomials
`rint <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L373>`_
`rint <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L436>`_
.. math::
.br
\int_0^1 dx \exp(-p x^2) x^n
.br
`rint1 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L533>`_
`rint1 <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L596>`_
Standard version of rint
`rint_large_n <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L502>`_
`rint_large_n <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L565>`_
Version of rint for large values of n
`rint_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L421>`_
`rint_sum <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/integration.irp.f#L484>`_
Needed for the calculation of two-electron integrals.
`overlap_a_b_c <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L35>`_
Undocumented
`overlap_gaussian_x <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L1>`_
.. math::
.br
\sum_{-infty}^{+infty} (x-A_x)^ax (x-B_x)^bx exp(-alpha(x-A_x)^2) exp(-beta(x-B_X)^2) dx
.br
`overlap_gaussian_xyz <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L37>`_
`overlap_gaussian_xyz <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L113>`_
.. math::
.br
S_x = \int (x-A_x)^{a_x} exp(-\alpha(x-A_x)^2) (x-B_x)^{b_x} exp(-beta(x-B_x)^2) dx \\
S = S_x S_y S_z
.br
`overlap_x_abs <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L99>`_
`overlap_x_abs <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/one_e_integration.irp.f#L175>`_
.. math ::
.br
\int_{-infty}^{+infty} (x-A_center)^(power_A) * (x-B_center)^power_B * exp(-alpha(x-A_center)^2) * exp(-beta(x-B_center)^2) dx
.br
`align_double <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L70>`_
`progress_active <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L29>`_
Current status for displaying progress bars. Global variable.
`progress_bar <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L27>`_
Current status for displaying progress bars. Global variable.
`progress_timeout <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L28>`_
Current status for displaying progress bars. Global variable.
`progress_title <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L31>`_
Current status for displaying progress bars. Global variable.
`progress_value <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L30>`_
Current status for displaying progress bars. Global variable.
`run_progress <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L45>`_
Display a progress bar with documentation of what is happening
`start_progress <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L1>`_
Starts the progress bar
`stop_progress <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/progress.irp.f#L19>`_
Stop the progress bar
`align_double <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L48>`_
Compute 1st dimension such that it is aligned for vectorization.
`all_utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L1>`_
Dummy provider to provide all utils
`approx_dble <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L299>`_
`approx_dble <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L341>`_
Undocumented
`binom <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L52>`_
`binom <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L31>`_
Binomial coefficients
`binom_func <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L21>`_
`binom_func <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L1>`_
.. math ::
.br
\frac{i!}{j!(i-j)!}
.br
`binom_transp <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L53>`_
`binom_transp <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L32>`_
Binomial coefficients
`dble_fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L129>`_
`dble_fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L137>`_
n!!
`fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L85>`_
`dble_logfact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L171>`_
n!!
`fact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L63>`_
n!
`fact_inv <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L117>`_
`fact_inv <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L125>`_
1/n!
`inv_int <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L176>`_
`inv_int <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L218>`_
1/i
`normalize <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L275>`_
`logfact <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L93>`_
n!
`normalize <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L317>`_
Normalizes vector u
u is expected to be aligned in memory.
`nproc <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L202>`_
`nproc <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L244>`_
Number of current OpenMP threads
`u_dot_u <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L244>`_
`u_dot_u <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L286>`_
Compute <u|u>
`u_dot_v <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L218>`_
`u_dot_v <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L260>`_
Compute <u|v>
`wall_time <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L187>`_
`wall_time <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L229>`_
The equivalent of cpu_time, but for the wall time.
`write_git_log <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L162>`_
`write_git_log <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L204>`_
Write the last git commit in file iunit.