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Merge pull request #64 from TApplencourt/master

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Pseudo! ❤️
This commit is contained in:
Anthony Scemama 2015-05-11 11:19:55 +02:00
commit 97b740cc8a
187 changed files with 6221 additions and 1737 deletions
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2
Makefile
View File

@ -45,5 +45,5 @@ ocaml:
veryclean:
rm -rf EZFIO
$(MAKE) EZFIO
rm -rf resultsFile
$(MAKE) -C src veryclean

4
ocaml/.merlin Normal file
View File

@ -0,0 +1,4 @@
PKG core ZMQ cryptokit
B _build/

2
ocaml/Makefile
View File

@ -35,7 +35,7 @@ default: $(ALL_TESTS) $(ALL_EXE) .gitignore
executables: $(QPACKAGE_ROOT)/data/executables
$(QPACKAGE_ROOT)/data/executables:
$(QPACKAGE_ROOT)/scripts/create_executables_list.sh
$(QPACKAGE_ROOT)/scripts/create/create_executables_list.sh
external_libs:
opam install cryptokit core

19
ocaml/qp_create_ezfio_from_xyz.ml
View File

@ -13,10 +13,12 @@ let spec =
~doc:"int Total charge of the molecule. Default is 0."
+> flag "m" (optional_with_default 1 int)
~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1."
+> flag "p" no_arg
~doc:"Using pseudo."
+> anon ("xyz_file" %: string)
;;
let run ?o b c m xyz_file =
let run ?o b c m p xyz_file =
(* Read molecule *)
let molecule =
@ -60,6 +62,10 @@ let run ?o b c m xyz_file =
| None -> (* Principal basis *)
let basis = elem_and_basis_name in
let command =
if (p) then
Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename
^ "\" \"" ^ basis ^"\" pseudo"
else
Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename
^ "\" \"" ^ basis ^"\""
in
@ -247,6 +253,13 @@ let run ?o b c m xyz_file =
~rank:2 ~dim:[| ao_num ; ao_prim_num_max |] ~data:ao_expo) ;
(* Doesn't work... *)
if (p) then
begin
Qpackage.root ^ "/scripts/pseudo/put_pseudo_in_ezfio.py " ^ ezfio_file
|> Sys.command_exn
end;
match Input.Ao_basis.read () with
| None -> failwith "Error in basis"
| Some x -> Input.Ao_basis.write x
@ -266,8 +279,8 @@ elements can be defined as follows:
")
spec
(fun o b c m xyz_file () ->
run ?o b c m xyz_file )
(fun o b c m p xyz_file () ->
run ?o b c m p xyz_file )
;;
let () =

1
scripts/.gitignore vendored
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@ -1,2 +1,3 @@
*.pyc
*.pyo
docopt.py

63
scripts/check_dependencies.sh
View File

@ -1,63 +0,0 @@
#!/bin/bash
#
# usage:
# check_dependencies.sh MOs AOs Electrons
#
# Checks that the list of dependencies given in
# argument is consistent. If the dependencies
# are OK the exit code is 0, otherwise it is 1.
# If no argument is given, the dependencies are
# read in the Makefile.
# Thu Apr 3 01:44:23 CEST 2014
if [[ -z ${QPACKAGE_ROOT} ]]
then
print "The QPACKAGE_ROOT environment variable is not set."
print "Please reload the quantum_package.rc file."
exit -1
fi
source ${QPACKAGE_ROOT}/scripts/qp_include.sh
if [[ -z $1 ]]
then
exit 0
fi
if [[ $1 == "-" ]]
then
COMMAND_LINE=$(cat NEEDED_MODULES)
else
COMMAND_LINE=$(unique_list $@)
fi
for d in $COMMAND_LINE
do
if [[ ! -d ${QPACKAGE_ROOT}/src/$d ]]
then
echo Error: Directory $d does not exist
exit 2
fi
done
DEPS_LONG=""
for i in $COMMAND_LINE
do
DEPS_LONG+=" $i "
DEPS_LONG+=$(cat "${QPACKAGE_ROOT}/src/${i}/NEEDED_MODULES")
done
DEPS=$(unique_list $DEPS_LONG)
if [[ ! "$COMMAND_LINE" == "$DEPS" ]]
then
DEPS=$(${QPACKAGE_ROOT}/scripts/check_dependencies.sh ${DEPS})
fi
echo "$DEPS"
if [[ "$COMMAND_LINE" == "$DEPS" ]]
then
exit 0
else
exit 1
fi

590
scripts/docopt.py
View File

@ -1,590 +0,0 @@
"""Pythonic command-line interface parser that will make you smile.
* http://docopt.org
* Repository and issue-tracker: https://github.com/docopt/docopt
* Licensed under terms of MIT license (see LICENSE-MIT)
* Copyright (c) 2013 Vladimir Keleshev, vladimir@keleshev.com
"""
import sys
import re
__all__ = ['docopt']
__version__ = '0.6.1'
class DocoptLanguageError(Exception):
"""Error in construction of usage-message by developer."""
class DocoptExit(SystemExit):
"""Exit in case user invoked program with incorrect arguments."""
usage = ''
def __init__(self, message=''):
SystemExit.__init__(self, (message + '\n' + self.usage).strip())
class Pattern(object):
def __eq__(self, other):
return repr(self) == repr(other)
def __hash__(self):
return hash(repr(self))
def fix(self):
self.fix_identities()
self.fix_repeating_arguments()
return self
def fix_identities(self, uniq=None):
"""Make pattern-tree tips point to same object if they are equal."""
if not hasattr(self, 'children'):
return self
uniq = list(set(self.flat())) if uniq is None else uniq
for i, child in enumerate(self.children):
if not hasattr(child, 'children'):
assert child in uniq
self.children[i] = uniq[uniq.index(child)]
else:
child.fix_identities(uniq)
def fix_repeating_arguments(self):
"""Fix elements that should accumulate/increment values."""
either = [list(child.children) for child in transform(self).children]
for case in either:
for e in [child for child in case if case.count(child) > 1]:
if isinstance(
e,
Argument) or isinstance(
e,
Option) and e.argcount:
if e.value is None:
e.value = []
elif not isinstance(e.value, list):
e.value = e.value.split()
if isinstance(
e,
Command) or isinstance(
e,
Option) and e.argcount == 0:
e.value = 0
return self
def transform(pattern):
"""Expand pattern into an (almost) equivalent one, but with single Either.
Example: ((-a | -b) (-c | -d)) => (-a -c | -a -d | -b -c | -b -d)
Quirks: [-a] => (-a), (-a...) => (-a -a)
"""
result = []
groups = [[pattern]]
while groups:
children = groups.pop(0)
parents = [Required, Optional, OptionsShortcut, Either, OneOrMore]
if any(t in map(type, children) for t in parents):
child = [c for c in children if type(c) in parents][0]
children.remove(child)
if isinstance(child, Either):
for c in child.children:
groups.append([c] + children)
elif isinstance(child, OneOrMore):
groups.append(child.children * 2 + children)
else:
groups.append(child.children + children)
else:
result.append(children)
return Either(*[Required(*e) for e in result])
class LeafPattern(Pattern):
"""Leaf/terminal node of a pattern tree."""
def __init__(self, name, value=None):
self.name, self.value = name, value
def __repr__(self):
return '%s(%r, %r)' % (self.__class__.__name__, self.name, self.value)
def flat(self, *types):
return [self] if not types or type(self) in types else []
def match(self, left, collected=None):
collected = [] if collected is None else collected
pos, match = self.single_match(left)
if match is None:
return False, left, collected
left_ = left[:pos] + left[pos + 1:]
same_name = [a for a in collected if a.name == self.name]
if type(self.value) in (int, list):
if isinstance(self.value, int):
increment = 1
else:
increment = ([match.value] if isinstance(match.value, str)
else match.value)
if not same_name:
match.value = increment
return True, left_, collected + [match]
same_name[0].value += increment
return True, left_, collected
return True, left_, collected + [match]
class BranchPattern(Pattern):
"""Branch/inner node of a pattern tree."""
def __init__(self, *children):
self.children = list(children)
def __repr__(self):
return '%s(%s)' % (self.__class__.__name__,
', '.join(repr(a) for a in self.children))
def flat(self, *types):
if type(self) in types:
return [self]
return sum([child.flat(*types) for child in self.children], [])
class Argument(LeafPattern):
def single_match(self, left):
for n, pattern in enumerate(left):
if isinstance(pattern, Argument):
return n, Argument(self.name, pattern.value)
return None, None
@classmethod
def parse(class_, source):
name = re.findall('(<\S*?>)', source)[0]
value = re.findall('\[default: (.*)\]', source, flags=re.I)
return class_(name, value[0] if value else None)
class Command(Argument):
def __init__(self, name, value=False):
self.name, self.value = name, value
def single_match(self, left):
for n, pattern in enumerate(left):
if isinstance(pattern, Argument):
if pattern.value == self.name:
return n, Command(self.name, True)
else:
break
return None, None
class Option(LeafPattern):
def __init__(self, short=None, long=None, argcount=0, value=False):
assert argcount in (0, 1)
self.short, self.long, self.argcount = short, long, argcount
self.value = None if value is False and argcount else value
@classmethod
def parse(class_, option_description):
short, long, argcount, value = None, None, 0, False
options, _, description = option_description.strip().partition(' ')
options = options.replace(',', ' ').replace('=', ' ')
for s in options.split():
if s.startswith('--'):
long = s
elif s.startswith('-'):
short = s
else:
argcount = 1
if argcount:
matched = re.findall('\[default: (.*)\]', description, flags=re.I)
value = matched[0] if matched else None
return class_(short, long, argcount, value)
def single_match(self, left):
for n, pattern in enumerate(left):
if self.name == pattern.name:
return n, pattern
return None, None
@property
def name(self):
return self.long or self.short
def __repr__(self):
return 'Option(%r, %r, %r, %r)' % (self.short, self.long,
self.argcount, self.value)
class Required(BranchPattern):
def match(self, left, collected=None):
collected = [] if collected is None else collected
l = left
c = collected
for pattern in self.children:
matched, l, c = pattern.match(l, c)
if not matched:
return False, left, collected
return True, l, c
class Optional(BranchPattern):
def match(self, left, collected=None):
collected = [] if collected is None else collected
for pattern in self.children:
m, left, collected = pattern.match(left, collected)
return True, left, collected
class OptionsShortcut(Optional):
"""Marker/placeholder for [options] shortcut."""
class OneOrMore(BranchPattern):
def match(self, left, collected=None):
assert len(self.children) == 1
collected = [] if collected is None else collected
l = left
c = collected
l_ = None
matched = True
times = 0
while matched:
# could it be that something didn't match but changed l or c?
matched, l, c = self.children[0].match(l, c)
times += 1 if matched else 0
if l_ == l:
break
l_ = l
if times >= 1:
return True, l, c
return False, left, collected
class Either(BranchPattern):
def match(self, left, collected=None):
collected = [] if collected is None else collected
outcomes = []
for pattern in self.children:
matched, _, _ = outcome = pattern.match(left, collected)
if matched:
outcomes.append(outcome)
if outcomes:
return min(outcomes, key=lambda outcome: len(outcome[1]))
return False, left, collected
class Tokens(list):
def __init__(self, source, error=DocoptExit):
self += source.split() if hasattr(source, 'split') else source
self.error = error
@staticmethod
def from_pattern(source):
source = re.sub(r'([\[\]\(\)\|]|\.\.\.)', r' \1 ', source)
source = [s for s in re.split('\s+|(\S*<.*?>)', source) if s]
return Tokens(source, error=DocoptLanguageError)
def move(self):
return self.pop(0) if len(self) else None
def current(self):
return self[0] if len(self) else None
def parse_long(tokens, options):
"""long ::= '--' chars [ ( ' ' | '=' ) chars ] ;"""
long, eq, value = tokens.move().partition('=')
assert long.startswith('--')
value = None if eq == value == '' else value
similar = [o for o in options if o.long == long]
if tokens.error is DocoptExit and similar == []: # if no exact match
similar = [o for o in options if o.long and o.long.startswith(long)]
if len(similar) > 1: # might be simply specified ambiguously 2+ times?
raise tokens.error('%s is not a unique prefix: %s?' %
(long, ', '.join(o.long for o in similar)))
elif len(similar) < 1:
argcount = 1 if eq == '=' else 0
o = Option(None, long, argcount)
options.append(o)
if tokens.error is DocoptExit:
o = Option(None, long, argcount, value if argcount else True)
else:
o = Option(similar[0].short, similar[0].long,
similar[0].argcount, similar[0].value)
if o.argcount == 0:
if value is not None:
raise tokens.error('%s must not have an argument' % o.long)
else:
if value is None:
if tokens.current() in [None, '--']:
raise tokens.error('%s requires argument' % o.long)
value = tokens.move()
if tokens.error is DocoptExit:
o.value = value if value is not None else True
return [o]
def parse_shorts(tokens, options):
"""shorts ::= '-' ( chars )* [ [ ' ' ] chars ] ;"""
token = tokens.move()
assert token.startswith('-') and not token.startswith('--')
left = token.lstrip('-')
parsed = []
while left != '':
short, left = '-' + left[0], left[1:]
similar = [o for o in options if o.short == short]
if len(similar) > 1:
raise tokens.error('%s is specified ambiguously %d times' %
(short, len(similar)))
elif len(similar) < 1:
o = Option(short, None, 0)
options.append(o)
if tokens.error is DocoptExit:
o = Option(short, None, 0, True)
else: # why copying is necessary here?
o = Option(short, similar[0].long,
similar[0].argcount, similar[0].value)
value = None
if o.argcount != 0:
if left == '':
if tokens.current() in [None, '--']:
raise tokens.error('%s requires argument' % short)
value = tokens.move()
else:
value = left
left = ''
if tokens.error is DocoptExit:
o.value = value if value is not None else True
parsed.append(o)
return parsed
def parse_pattern(source, options):
tokens = Tokens.from_pattern(source)
result = parse_expr(tokens, options)
if tokens.current() is not None:
raise tokens.error('unexpected ending: %r' % ' '.join(tokens))
return Required(*result)
def parse_expr(tokens, options):
"""expr ::= seq ( '|' seq )* ;"""
seq = parse_seq(tokens, options)
if tokens.current() != '|':
return seq
result = [Required(*seq)] if len(seq) > 1 else seq
while tokens.current() == '|':
tokens.move()
seq = parse_seq(tokens, options)
result += [Required(*seq)] if len(seq) > 1 else seq
return [Either(*result)] if len(result) > 1 else result
def parse_seq(tokens, options):
"""seq ::= ( atom [ '...' ] )* ;"""
result = []
while tokens.current() not in [None, ']', ')', '|']:
atom = parse_atom(tokens, options)
if tokens.current() == '...':
atom = [OneOrMore(*atom)]
tokens.move()
result += atom
return result
def parse_atom(tokens, options):
"""atom ::= '(' expr ')' | '[' expr ']' | 'options'
| long | shorts | argument | command ;
"""
token = tokens.current()
result = []
if token in '([':
tokens.move()
matching, pattern = {'(': [')', Required], '[': [']', Optional]}[token]
result = pattern(*parse_expr(tokens, options))
if tokens.move() != matching:
raise tokens.error("unmatched '%s'" % token)
return [result]
elif token == 'options':
tokens.move()
return [OptionsShortcut()]
elif token.startswith('--') and token != '--':
return parse_long(tokens, options)
elif token.startswith('-') and token not in ('-', '--'):
return parse_shorts(tokens, options)
elif token.startswith('<') and token.endswith('>') or token.isupper():
return [Argument(tokens.move())]
else:
return [Command(tokens.move())]
def parse_argv(tokens, options, options_first=False):
"""Parse command-line argument vector.
If options_first:
argv ::= [ long | shorts ]* [ argument ]* [ '--' [ argument ]* ] ;
else:
argv ::= [ long | shorts | argument ]* [ '--' [ argument ]* ] ;
"""
parsed = []
while tokens.current() is not None:
if tokens.current() == '--':
return parsed + [Argument(None, v) for v in tokens]
elif tokens.current().startswith('--'):
parsed += parse_long(tokens, options)
elif tokens.current().startswith('-') and tokens.current() != '-':
parsed += parse_shorts(tokens, options)
elif options_first:
return parsed + [Argument(None, v) for v in tokens]
else:
parsed.append(Argument(None, tokens.move()))
return parsed
def parse_defaults(doc):
defaults = []
for s in parse_section('options:', doc):
# FIXME corner case "bla: options: --foo"
_, _, s = s.partition(':') # get rid of "options:"
split = re.split('\n[ \t]*(-\S+?)', '\n' + s)[1:]
split = [s1 + s2 for s1, s2 in zip(split[::2], split[1::2])]
options = [Option.parse(s) for s in split if s.startswith('-')]
defaults += options
return defaults
def parse_section(name, source):
pattern = re.compile('^([^\n]*' + name + '[^\n]*\n?(?:[ \t].*?(?:\n|$))*)',
re.IGNORECASE | re.MULTILINE)
return [s.strip() for s in pattern.findall(source)]
def formal_usage(section):
_, _, section = section.partition(':') # drop "usage:"
pu = section.split()
return '( ' + ' '.join(') | (' if s == pu[0] else s for s in pu[1:]) + ' )'
def extras(help, version, options, doc):
if help and any((o.name in ('-h', '--help')) and o.value for o in options):
print(doc.strip("\n"))
sys.exit()
if version and any(o.name == '--version' and o.value for o in options):
print(version)
sys.exit()
class Dict(dict):
def __repr__(self):
return '{%s}' % ',\n '.join('%r: %r' % i for i in sorted(self.items()))
def docopt(doc, argv=None, help=True, version=None, options_first=False):
"""Parse `argv` based on command-line interface described in `doc`.
`docopt` creates your command-line interface based on its
description that you pass as `doc`. Such description can contain
--options, <positional-argument>, commands, which could be
[optional], (required), (mutually | exclusive) or repeated...
Parameters
----------
doc : str
Description of your command-line interface.
argv : list of str, optional
Argument vector to be parsed. sys.argv[1:] is used if not
provided.
help : bool (default: True)
Set to False to disable automatic help on -h or --help
options.
version : any object
If passed, the object will be printed if --version is in
`argv`.
options_first : bool (default: False)
Set to True to require options precede positional arguments,
i.e. to forbid options and positional arguments intermix.
Returns
-------
args : dict
A dictionary, where keys are names of command-line elements
such as e.g. "--verbose" and "<path>", and values are the
parsed values of those elements.
Example
-------
>>> from docopt import docopt
>>> doc = '''
... Usage:
... my_program tcp <host> <port> [--timeout=<seconds>]
... my_program serial <port> [--baud=<n>] [--timeout=<seconds>]
... my_program (-h | --help | --version)
...
... Options:
... -h, --help Show this screen and exit.
... --baud=<n> Baudrate [default: 9600]
... '''
>>> argv = ['tcp', '127.0.0.1', '80', '--timeout', '30']
>>> docopt(doc, argv)
{'--baud': '9600',
'--help': False,
'--timeout': '30',
'--version': False,
'<host>': '127.0.0.1',
'<port>': '80',
'serial': False,
'tcp': True}
See also
--------
* For video introduction see http://docopt.org
* Full documentation is available in README.rst as well as online
at https://github.com/docopt/docopt#readme
"""
argv = sys.argv[1:] if argv is None else argv
usage_sections = parse_section('usage:', doc)
if len(usage_sections) == 0:
raise DocoptLanguageError('"usage:" (case-insensitive) not found.')
if len(usage_sections) > 1:
raise DocoptLanguageError('More than one "usage:" (case-insensitive).')
DocoptExit.usage = usage_sections[0]
options = parse_defaults(doc)
pattern = parse_pattern(formal_usage(DocoptExit.usage), options)
# [default] syntax for argument is disabled
# for a in pattern.flat(Argument):
# same_name = [d for d in arguments if d.name == a.name]
# if same_name:
# a.value = same_name[0].value
argv = parse_argv(Tokens(argv), list(options), options_first)
pattern_options = set(pattern.flat(Option))
for options_shortcut in pattern.flat(OptionsShortcut):
doc_options = parse_defaults(doc)
options_shortcut.children = list(set(doc_options) - pattern_options)
# if any_options:
# options_shortcut.children += [Option(o.short, o.long, o.argcount)
# for o in argv if type(o) is Option]
extras(help, version, argv, doc)
matched, left, collected = pattern.fix().match(argv)
if matched and left == []: # better error message if left?
return Dict((a.name, a.value) for a in (pattern.flat() + collected))
raise DocoptExit()

21
scripts/ezfio_interface/ei_handler.py
View File

@ -62,6 +62,9 @@ import ConfigParser
from collections import defaultdict
from collections import namedtuple
from qp_utils import cache
Type = namedtuple('Type', 'fancy ocaml fortran')
@ -78,6 +81,7 @@ def is_bool(str_):
raise TypeError
@cache
def get_type_dict():
"""
This function makes the correspondance between the type of value read in
@ -89,17 +93,7 @@ def get_type_dict():
# ~#~#~#~#~ #
# P i c l e #
# ~#~#~#~#~ #
import cPickle as pickle
from os import listdir
qpackage_root = os.environ['QPACKAGE_ROOT']
fancy_type_pickle = qpackage_root + "/scripts/ezfio_interface/fancy_type.p"
if fancy_type_pickle in listdir(os.getcwd()):
fancy_type = pickle.load(open(fancy_type_pickle, "rb"))
return fancy_type
# ~#~#~#~ #
# I n i t #
@ -148,9 +142,7 @@ def get_type_dict():
b = r.find('let untouched = "')
e = r.find(';;', b)
l_un = [
i for i in r[
b:e].splitlines() if i.strip().startswith("module")]
l_un = [i for i in r[b:e].splitlines() if i.strip().startswith("module")]
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# q p _ t y p e s _ g e n e r a t e #
@ -174,9 +166,6 @@ def get_type_dict():
# ~#~#~#~#~#~#~#~ #
# F i n a l i z e #
# ~#~#~#~#~#~#~#~ #
pickle.dump(dict(fancy_type), open(fancy_type_pickle, "wb"))
return dict(fancy_type)

0
scripts/prepare_ezfio.sh → scripts/ezfio_interface/prepare_ezfio.sh
View File

12
scripts/ezfio_interface/qp_convert_output_to_ezfio.py
View File

@ -105,7 +105,7 @@ def write_ezfio(res, filename):
# Transformt H1 into H
import re
p = re.compile(ur'(\d*)$')
label = [p.sub("", x.name) for x in res.geometry]
label = [p.sub("", x.name).capitalize() for x in res.geometry]
ezfio.set_nuclei_nucl_label(label)
ezfio.set_nuclei_nucl_coord(coord_x + coord_y + coord_z)
@ -265,6 +265,16 @@ def write_ezfio(res, filename):
ezfio.set_mo_basis_mo_occ(OccNum)
ezfio.set_mo_basis_mo_coef(MoMatrix)
# ______ _
# | ___ \ | |
# | |_/ /__ ___ _ _ __| | ___
# | __/ __|/ _ \ | | |/ _` |/ _ \
# | | \__ \ __/ |_| | (_| | (_) |
# \_| |___/\___|\__,_|\__,_|\___/
#
ezfio.set_pseudo_integrals_do_pseudo(False)
def get_full_path(file_path):
file_path = os.path.expanduser(file_path)

27
scripts/ezfio_interface/upgrade_1.0_2.0.sh Executable file
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@ -0,0 +1,27 @@
#!/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

2
scripts/generate_h_apply.py
View File

@ -141,7 +141,7 @@ class H_apply(object):
def set_filter_2h_2p(self):
self["filter2h2p"] = """
! ! DIR$ FORCEINLINE
if(is_a_two_holes_two_particles(key))cycle
if (is_a_two_holes_two_particles(key)) cycle
"""

11
scripts/get_basis.sh
View File

@ -42,9 +42,14 @@ then
echo "ERROR"
exit 1
fi
${EMSL_API_ROOT}/EMSL_api.py get_basis_data --treat_l --save --path="${tmpfile}" --basis="${basis}" $atoms
pseudo="$1"
shift
if [[ -z $pseudo ]]
then
${EMSL_API_ROOT}/EMSL_api.py get_basis_data --treat_l --save --path="${tmpfile}" --basis="${basis}"
else
${EMSL_API_ROOT}/EMSL_api.py get_basis_data --save --path="${tmpfile}" --basis="${basis}" --db_path="${EMSL_API_ROOT}/db/Pseudo.db"
fi

4
scripts/install_curl.sh → scripts/install/install_curl.sh
View File

@ -8,8 +8,8 @@ CURL_URL="http://qmcchem.ups-tlse.fr/files/scemama/${CURL}.tar.bz2"
if [[ -z ${QPACKAGE_ROOT} ]]
then
print "The QPACKAGE_ROOT environment variable is not set."
print "Please reload the quantum_package.rc file."
echo "The QPACKAGE_ROOT environment variable is not set."
echo "Please reload the quantum_package.rc file."
exit -1
fi

21
scripts/install/install_docopt.sh Executable file
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@ -0,0 +1,21 @@
#!/bin/bash
#
# Installs docopt
# lundi 27 avril 2015, 16:51:34 (UTC+0200)
DOCOPT="docopt.py"
DOCOPT_URL="https://raw.githubusercontent.com/docopt/docopt/master/${DOCOPT}"
if [[ -z ${QPACKAGE_ROOT} ]]
then
echo "The QPACKAGE_ROOT environment variable is not set."
echo "Please reload the quantum_package.rc file."
exit -1
fi
cd ${QPACKAGE_ROOT}
rm -f -- scripts/${DOCOPT}{,c}
${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${DOCOPT_URL} ${DOCOPT}
mv ${DOCOPT} scripts/${DOCOPT}

4
scripts/install_emsl.sh → scripts/install/install_emsl.sh
View File

@ -8,8 +8,8 @@ URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz"
if [[ -z ${QPACKAGE_ROOT} ]]
then
print "The QPACKAGE_ROOT environment variable is not set."
print "Please reload the quantum_package.rc file."
echo "The QPACKAGE_ROOT environment variable is not set."
echo "Please reload the quantum_package.rc file."
exit -1
fi

4
scripts/install_ezfio.sh → scripts/install/install_ezfio.sh
View File

@ -8,8 +8,8 @@ URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz"
if [[ -z ${QPACKAGE_ROOT} ]]
then
print "The QPACKAGE_ROOT environment variable is not set."
print "Please reload the quantum_package.rc file."
echo "The QPACKAGE_ROOT environment variable is not set."
echo "Please reload the quantum_package.rc file."
exit -1
fi

0
scripts/install_irpf90.sh → scripts/install/install_irpf90.sh
View File

0
scripts/install_m4.sh → scripts/install/install_m4.sh
View File

0
scripts/install_ocaml.sh → scripts/install/install_ocaml.sh
View File

1
scripts/install_resultsFile.sh → scripts/install/install_resultsFile.sh
View File

@ -16,6 +16,7 @@ fi
cd ${QPACKAGE_ROOT}
rm -rf resultsFile-master
${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/resultsFile.tar.gz
tar -zxf resultsFile.tar.gz && rm resultsFile.tar.gz ||exit 1
mv resultsFile-master resultsFile

0
scripts/install_zlib.sh → scripts/install/install_zlib.sh
View File

4
scripts/build_modules.sh → scripts/module/build_modules.sh
View File

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

5
scripts/clean_modules.sh → scripts/module/clean_modules.sh
View File

@ -13,8 +13,11 @@ source ${QPACKAGE_ROOT}/scripts/qp_include.sh
function do_clean()
{
rm -rf -- \
IRPF90_temp IRPF90_man Makefile.depend $(cat NEEDED_MODULES) include \
IRPF90_temp IRPF90_man Makefile.depend \
$(module_handler.py print_genealogy) include \
ezfio_interface.irp.f irpf90.make irpf90_entities tags $(ls_exe) *.mod
touch -c EZFIO.cfg *.ezfio_config
}
if [[ -z $1 ]]

0
scripts/create_Makefile.sh → scripts/module/create_Makefile.sh
View File

0
scripts/create_Makefile_depend.sh → scripts/module/create_Makefile_depend.sh
View File

8
scripts/create_Needed_modules.sh → scripts/module/create_Needed_modules.sh
View File

@ -14,7 +14,9 @@ source ${QPACKAGE_ROOT}/scripts/qp_include.sh
check_current_dir_is_module
OUTPUT=$(${QPACKAGE_ROOT}/scripts/check_dependencies.sh $@)
echo ${OUTPUT} > NEEDED_MODULES
OUTPUT=$(module_handler.py check_dependencies $@)
if [[ $? -eq 0 ]]
then
echo $@ > NEEDED_CHILDREN_MODULES
fi

0
scripts/create_executables_list.sh → scripts/module/create_executables_list.sh
View File

0
scripts/create_gitignore.sh → scripts/module/create_gitignore.sh
View File

0
scripts/create_rst_templates.sh → scripts/module/create_rst_templates.sh
View File

185
scripts/module/module_handler.py Executable file
View File

@ -0,0 +1,185 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Create the NEEDED_MODULE
aka the genealogy (children module, subchildren module and so on),
of a NEEDED_CHILDREN_MODULES file
Usage:
module_handler.py print_genealogy [<NEEDED_CHILDREN_MODULES>]
module_handler.py check_dependencies [<module_name>...]
module_handler.py create_png [<NEEDED_CHILDREN_MODULES>]
Options:
print_genealogy Print the genealogy of the NEEDED_CHILDREN_MODULES
aka (children, subchildren, etc)
create_png Create a png of the file
NEEDED_CHILDREN_MODULES The path of NEEDED_CHILDREN_MODULES
by default try to open the file in the current path
"""
from docopt import docopt
import os
import sys
import os.path
from qp_utils import cache
@cache
def get_dict_genealogy():
"""Loop over MODULE in QPACKAGE_ROOT/src, open all the NEEDED_CHILDREN_MODULES
and create a dict[MODULE] = [sub module needed, ...]
"""
d_ref = dict()
qpackage_root = os.environ['QPACKAGE_ROOT']
dir_ = os.path.join(qpackage_root, 'src')
for o in os.listdir(dir_):
try:
with open(os.path.join(dir_, o, "NEEDED_CHILDREN_MODULES"), "r") as f:
l_children = f.read().split()
except IOError:
pass
else:
d_ref[o] = l_children
return d_ref
def module_genealogy(path):
"""
Take a name of a NEEDED_CHILDREN_MODULES
and return a list of all the {sub, subsub, ...}children
"""
try:
with open(path, "r") as f:
l_children = f.read().split()
except IOError as e:
print >> sys.stderr, e
sys.exit(1)
else:
needed_module = get_it_and_children(l_children)
return needed_module
def get_it_and_children(l_module):
"""
From a list of module return the module and all of the genealogy
"""
d_ref = get_dict_genealogy()
l = []
for module in l_module:
if module not in l:
l.append(module)
try:
l.extend(get_it_and_children(d_ref[module]))
except KeyError:
print >> sys.stderr, "`{0}` in not a good submodule name".format(module)
print >> sys.stderr, "Check the corresponding NEEDED_CHILDREN_MODULES"
sys.exit(1)
return list(set(l))
def get_all_children(l_module):
"""
From a list of module return all the genealogy
"""
it_and_all = get_it_and_children(l_module)
return [children for children in it_and_all if children not in l_module]
def reduce_(l_module):
"""
Take a l_module and try to find the lower combinaitions
of module with the same genealogy
"""
import itertools
d_ref = get_dict_genealogy()
target_genealogy = sorted(get_all_children(l_module))
for i in xrange(len(d_ref)):
for c in itertools.combinations(d_ref, i):
guess_genealogy = sorted(get_it_and_children(d_ref, c))
if target_genealogy == guess_genealogy:
return c
def create_png_from_path(path):
" Change a path like this into a module list"
"path = /home/razoa/quantum_package/src/Molden/NEEDED_CHILDREN_MODULES"
l_module = os.path.split(path)[0].split("/")[-1]
create_png([l_module])
def create_png(l_module):
"""Create the png of the dependancy tree for a l_module"""
# Init
import pydot
all_ready_done = []
def draw_module_edge(module, l_children):
"Draw all the module recursifly"
if module not in all_ready_done:
for children in l_children:
# Add Edge
edge = pydot.Edge(module, children)
graph.add_edge(edge)
# Recurs
draw_module_edge(children, d_ref[children])
all_ready_done.append(module)
# Init
graph = pydot.Dot(graph_type='digraph')
d_ref = get_dict_genealogy()
# Create all the edge
for module in l_module:
node_a = pydot.Node(module, fontcolor="red")
graph.add_node(node_a)
draw_module_edge(module, d_ref[module])
# Save
path = '{0}.png'.format("_".join(l_module))
print "png saved in {0}".format(path)
graph.write_png(path)
if __name__ == '__main__':
arguments = docopt(__doc__)
if not arguments['<NEEDED_CHILDREN_MODULES>']:
dir_ = os.getcwd()
path = os.path.join(dir_, "NEEDED_CHILDREN_MODULES")
else:
path = os.path.abspath(arguments['<NEEDED_CHILDREN_MODULES>'])
path = os.path.expanduser(path)
path = os.path.expandvars(path)
if arguments['print_genealogy']:
l_all_needed_molule = module_genealogy(path)
print " ".join(sorted(l_all_needed_molule))
elif arguments["check_dependencies"]:
l_module = arguments['<module_name>']
if l_module:
l_all_needed_molule = get_it_and_children(l_module)
else:
l_all_needed_molule = module_genealogy(path)
elif arguments["create_png"]:
create_png_from_path(path)

2125
scripts/module/pydot.py Normal file
View File

File diff suppressed because it is too large Load Diff

10
scripts/create_module.sh → scripts/module/qp_create_module.sh
View File

@ -71,7 +71,7 @@ debug "Module does not already exist: OK"
# Set up dependencies
ALL_MODULES="${NEEDED_MODULES}"
ALL_MODULES="$(cat NEEDED_MODULES)"
echo "Select which modules you are sure you will need: (press q to quit)"
NEEDED_MODULES=""
select M in ${ALL_MODULES}
@ -117,7 +117,7 @@ debug "Module directory is created."
# Create the Makefile
"${QPACKAGE_ROOT}/scripts/create_Makefile.sh" || fail "Unable to create Makefile"
"${QPACKAGE_ROOT}/scripts/module/create_Makefile.sh" || fail "Unable to create Makefile"
if [[ ! -f Makefile ]]
then
fail "Makefile was not created"
@ -125,8 +125,8 @@ fi
debug "Makefile created"
# Create the NEEDED_MODULES file
"${QPACKAGE_ROOT}/scripts/create_Needed_modules.sh" ${NEEDED_MODULES} || fail "Unable to create the NEEDED_MODULES file"
if [[ ! -f NEEDED_MODULES ]]
"${QPACKAGE_ROOT}/scripts/module/create_Needed_modules.sh" ${NEEDED_MODULES} || fail "Unable to create the NEEDED_MODULES file"
if [[ ! -f NEEDED_CHILDREN_MODULES ]]
then
fail "NEEDED_MODULES was not created"
fi
@ -135,7 +135,7 @@ debug "NEEDED_MODULES created"
# Create rst templates
"${QPACKAGE_ROOT}/scripts/create_rst_templates.sh" || fail "Unable to create rst templates"
"${QPACKAGE_ROOT}/scripts/module/create_rst_templates.sh" || fail "Unable to create rst templates"
# Update module list in main NEEDED_MODULES

118
scripts/pseudo/elts_num_ele.py Normal file
View File

@ -0,0 +1,118 @@
name_to_elec = {"H": 1,
"He": 2,
"Li": 3,
"Be": 4,
"B": 5,
"C": 6,
"N": 7,
"O": 8,
"F": 9,
"Ne": 10,
"Na": 11,
"Mg": 12,
"Al": 13,
"Si": 14,
"P": 15,
"S": 16,
"Cl": 17,
"Ar": 18,
"K": 19,
"Ca": 20,
"Sc": 21,
"Ti": 22,
"V": 23,
"Cr": 24,
"Mn": 25,
"Fe": 26,
"Co": 27,
"Ni": 28,
"Cu": 29,
"Zn": 30,
"Ga": 31,
"Ge": 32,
"As": 33,
"Se": 34,
"Br": 35,
"Kr": 36,
"Rb": 37,
"Sr": 38,
"Y": 39,
"Zr": 40,
"Nb": 41,
"Mo": 42,
"Tc": 43,
"Ru": 44,
"Rh": 45,
"Pd": 46,
"Ag": 47,
"Cd": 48,
"In": 49,
"Sn": 50,
"Sb": 51,
"Te": 52,
"I": 53,
"Xe": 54,
"Cs": 55,
"Ba": 56,
"La": 57,
"Ce": 58,
"Pr": 59,
"Nd": 60,
"Pm": 61,
"Sm": 62,
"Eu": 63,
"Gd": 64,
"Tb": 65,
"Dy": 66,
"Ho": 67,
"Er": 68,
"Tm": 69,
"Yb": 70,
"Lu": 71,
"Hf": 72,
"Ta": 73,
"W": 74,
"Re": 75,
"Os": 76,
"Ir": 77,
"Pt": 78,
"Au": 79,
"Hg": 80,
"Tl": 81,
"Pb": 82,
"Bi": 83,
"Po": 84,
"At": 85,
"Rn": 86,
"Fr": 87,
"Ra": 88,
"Ac": 89,
"Th": 90,
"Pa": 91,
"U": 92,
"Np": 93,
"Pu": 94,
"Am": 95,
"Cm": 96,
"Bk": 97,
"Cf": 98,
"Es": 99,
"Fm": 100,
"Md": 101,
"No": 102,
"Lr": 103,
"Rf": 104,
"Db": 105,
"Sg": 106,
"Bh": 107,
"Hs": 108,
"Mt": 109,
"Ds": 110,
"Rg": 111,
"Cn": 112,
"Uut": 113,
"Fl": 114,
"Uup": 115,
"Lv": 116,
"Uus": 117,
"Uuo": 118}

338
scripts/pseudo/put_pseudo_in_ezfio.py Executable file
View File

@ -0,0 +1,338 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Create the pseudo potential for a given atom
Usage:
put_pseudo_in_ezfio.py <ezfio_path>
Help:
atom is the Abreviation of the atom
"""
import os
import sys
from docopt import docopt
from subprocess import Popen, PIPE
qpackage_root = os.environ['QPACKAGE_ROOT']
EZFIO = "{0}/EZFIO".format(qpackage_root)
sys.path = [EZFIO + "/Python"] + sys.path
from ezfio import ezfio
import re
p = re.compile(ur'\|(\d+)><\d+\|')
def get_pseudo_str(l_atom):
"""
Run EMSL_local for geting the str of the speudo potential
str_ele :
Element Symbol: Na
Number of replaced protons: 10
Number of projectors: 2
Pseudopotential data:
Local component:
Coeff. r^n Exp.
1.00000000 -1 5.35838717
5.35838717 1 3.67918975
-2.07764789 0 1.60507673
Non-local component:
Coeff. r^n Exp. Proj.
10.69640234 0 1.32389367 |0><0|
10.11238853 0 1.14052020 |1><1|
"""
EMSL_root = "{0}/EMSL_Basis/".format(qpackage_root)
EMSL_path = "{0}/EMSL_api.py".format(EMSL_root)
db_path = "{0}/db/Pseudo.db".format(EMSL_root)
str_ = ""
for a in l_atom:
l_cmd_atom = ["--atom", a]
l_cmd_head = [EMSL_path, "get_basis_data",
"--db_path", db_path,
"--basis", "BFD-Pseudo"]
process = Popen(l_cmd_head + l_cmd_atom, stdout=PIPE, stderr=PIPE)
stdout, _ = process.communicate()
str_ += stdout.strip() + "\n"
return str_
def get_v_n_dz_local(str_ele):
"""
From a str_ele of the pseudo (aka only one ele in the str)
get the list ussefull for the Local potential : v_k n_k and dz_k
"""
l_v_k = []
l_n_k = []
l_dz_k = []
for l in str_ele.splitlines():
try:
v, n, dz = l.split()
v = float(v)
n = int(n)
dz = float(dz)
except ValueError:
pass
else:
l_v_k.append(v)
l_n_k.append(n)
l_dz_k.append(dz)
return l_v_k, l_n_k, l_dz_k
def get_v_n_dz_l_nonlocal(str_ele):
"""
From a str_ele of the pseudo (aka only one ele in the str)
get the list ussefull for the non Local potential
v_kl (v, l)
n_k (v, l)
dz_k (dz ,l)
"""
l_v_kl = []
l_n_kl = []
l_dz_kl = []
for l in str_ele.splitlines():
try:
v, n, dz, proj = l.split()
v = float(v)
n = int(n)
dz = float(dz)
l = int(p.match(proj).group(1))
except ValueError:
pass
else:
l_v_kl.append([v])
l_n_kl.append([n])
l_dz_kl.append([dz])
if not l_v_kl:
l_v_kl.append([0.])
l_n_kl.append([0])
l_dz_kl.append([0.])
return l_v_kl, l_n_kl, l_dz_kl
def get_zeff_alpha_beta(str_ele):
"""
Return the the zeff, alpha num elec and beta num elec
Assert ezfio_set_file alredy defined
"""
import re
# ___
# | ._ o _|_
# _|_ | | | |_
#
# ~#~#~#~#~#~#~ #
# s t r _ e l e #
# ~#~#~#~#~#~#~ #
# m = re.search('Element Symbol: ([a-zA-Z]+)', str_ele)
# name = m.group(1).capitalize()
name = str_ele.split("\n")[0].strip().capitalize()
m = re.search('Number of replaced protons: (\d+)', str_ele)
z_remove = int(m.group(1))
# _
# |_) _. ._ _ _
# | (_| | _> (/_
#
from elts_num_ele import name_to_elec
z = name_to_elec[name]
z_eff = z - z_remove
alpha = (z_remove / 2)
beta = (z_remove / 2)
# _
# |_) _ _|_ ._ ._
# | \ (/_ |_ |_| | | |
#
return [z_eff, alpha, beta]
def add_zero(array, size, type):
for add in xrange(len(array), size):
array.append([type(0)])
return array
def make_it_square(matrix, dim, type=float):
"""
matix the matrix to squate
dim array [lmax, kmax]
type the null value you want
[[[28.59107316], [19.37583724]], [[50.25646328]]]
=>
[[[28.59107316], [19.37583724]], [[50.25646328], [0.0]]]
"""
lmax = dim[0]
kmax = dim[1]
for l_list in matrix:
l_list = add_zero(l_list, lmax, type)
for k_list in list_:
k_list = add_zero(k_list, kmax, type)
return matrix
if __name__ == "__main__":
arguments = docopt(__doc__)
# ___
# | ._ o _|_
# _|_ | | | |_
#
# ~#~#~#~#~ #
# E Z F I O #
# ~#~#~#~#~ #
ezfio_path = arguments["<ezfio_path>"]
ezfio_path = os.path.expanduser(ezfio_path)
ezfio_path = os.path.expandvars(ezfio_path)
ezfio_path = os.path.abspath(ezfio_path)
ezfio.set_file("{0}".format(ezfio_path))
# ~#~#~#~#~#~#~#~#~#~#~ #
# P s e u d o _ d a t a #
# ~#~#~#~#~#~#~#~#~#~#~ #
l_ele = ezfio.get_nuclei_nucl_label()
str_ = get_pseudo_str(l_ele)
# _
# |_) _. ._ _ _
# | (_| | _> (/_
#
l_str_ele = [str_ele for str_ele in str_.split("Element Symbol: ")
if str_ele]
for i in "l_zeff v_k n_k dz_k v_kl n_kl dz_kl".split():
exec("{0} = []".format(i))
alpha_tot = 0
beta_tot = 0
for str_ele in l_str_ele:
# ~#~#~#~#~ #
# S p l i t #
# ~#~#~#~#~ #
l = str_ele.find("Local component:")
nl = str_ele.find("Non-local component")
# ~#~#~#~#~ #
# L o c a l #
# ~#~#~#~#~ #
l_v, l_n, l_dz = get_v_n_dz_local(str_ele[l:nl])
v_k.append(l_v)
n_k.append(l_n)
dz_k.append(l_dz)
# ~#~#~#~#~#~#~#~#~ #
# N o n _ L o c a l #
# ~#~#~#~#~#~#~#~#~ #
l_v_kl, l_n_kl, l_dz_kl = get_v_n_dz_l_nonlocal(str_ele[nl:])
v_kl.append(l_v_kl)
n_kl.append(l_n_kl)
dz_kl.append(l_dz_kl)
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Z _ e f f , a l p h a / b e t a _ e l e c #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
zeff, alpha, beta = get_zeff_alpha_beta(str_ele)
alpha_tot += alpha
beta_tot += beta
l_zeff.append(zeff)
# _
# /\ _| _| _|_ _ _ _ _|_ o _
# /--\ (_| (_| |_ (_) (/_ /_ | | (_)
#
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
# Z _ e f f , a l p h a / b e t a _ e l e c #
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
ezfio.nuclei_nucl_charge = l_zeff
alpha_tot = ezfio.get_electrons_elec_alpha_num() - alpha_tot
beta_tot = ezfio.get_electrons_elec_beta_num() - beta_tot
ezfio.electrons_elec_alpha_num = alpha_tot
ezfio.electrons_elec_beta_num = beta_tot
# Change all the array 'cause EZFIO
# v_kl (v, l) => v_kl(l,v)
# v_kl => zip(*_v_kl)
# [[7.0, 79.74474797, -49.45159098], [1.0, 5.41040609, -4.60151975]]
# [(7.0, 1.0), (79.74474797, 5.41040609), (-49.45159098, -4.60151975)]
# ~#~#~#~#~ #
# L o c a l #
# ~#~#~#~#~ #
klocmax = max([len(i) for i in v_k])
ezfio.pseudo_integrals_klocmax = klocmax
ezfio.pseudo_integrals_v_k = zip(*v_k)
ezfio.pseudo_integrals_n_k = zip(*n_k)
ezfio.pseudo_integrals_dz_k = zip(*dz_k)
# ~#~#~#~#~#~#~#~#~ #
# N o n _ L o c a l #
# ~#~#~#~#~#~#~#~#~ #
lmax = max([len(i) for i in v_kl])
kmax = max([len(sublist) for list_ in v_kl for sublist in list_])
ezfio.pseudo_integrals_lmaxpo = lmax
ezfio.pseudo_integrals_kmax = kmax
v_kl = make_it_square(v_kl, [lmax, kmax])
n_kl = make_it_square(n_kl, [lmax, kmax], int)
dz_kl = make_it_square(dz_kl, [lmax, kmax])
ezfio.pseudo_integrals_v_kl = zip(*v_kl)
ezfio.pseudo_integrals_n_kl = zip(*n_kl)
ezfio.pseudo_integrals_dz_kl = zip(*dz_kl)
ezfio.pseudo_integrals_do_pseudo = True

5
scripts/qp_include.sh
View File

@ -35,9 +35,10 @@ function check_current_dir_is_module()
exit -1
fi
}
if [[ -f NEEDED_MODULES ]]
if [[ -f NEEDED_CHILDREN_MODULES ]]
then
NEEDED_MODULES=$(cat NEEDED_MODULES)
NEEDED_MODULES=$(module_handler.py print_genealogy NEEDED_CHILDREN_MODULES)
fi
# List of executables in the current directory

17
scripts/qp_utils.py Normal file
View File

@ -0,0 +1,17 @@
from functools import wraps
def cache(func):
"""
A decorator for lazy evaluation off true function
"""
saved = {}
@wraps(func)
def newfunc(*args):
if args in saved:
return saved[args]
result = func(*args)
saved[args] = result
return result
return newfunc

8
scripts/run_Makefile_common.sh
View File

@ -14,7 +14,7 @@ check_current_dir_is_module
# Check if the NEEDED_MODULES file is consistent
INCLUDE_DIRS="${NEEDED_MODULES} include"
NEEDED_MODULES_OK=$( ${QPACKAGE_ROOT}/scripts/check_dependencies.sh ${NEEDED_MODULES} )
NEEDED_MODULES_OK=$(module_handler.py check_dependencies ${NEEDED_MODULES} )
if [[ $? -ne 0 ]]
then
error "
@ -28,7 +28,7 @@ fi
# Check if README.rst exists
if [[ ! -f README.rst ]]
then
${QPACKAGE_ROOT}/scripts/create_rst_templates.sh
${QPACKAGE_ROOT}/scripts/module/create_rst_templates.sh
error "
README.rst was not present, so I created a
default one for you.
@ -62,7 +62,7 @@ then
fi
# Update Makefile.depend
${QPACKAGE_ROOT}/scripts/create_Makefile_depend.sh
${QPACKAGE_ROOT}/scripts/module/create_Makefile_depend.sh
# Update EZFIO interface
${QPACKAGE_ROOT}/scripts/ezfio_interface/ei_handler.py
${QPACKAGE_ROOT}/scripts/ezfio_interface/ei_handler.py

4
scripts/run_Makefile_global.sh
View File

@ -52,7 +52,7 @@ ${IRPF90_VERSION}.
IRPF90 version >= ${IRPF90_REQUIRED_VERSION} is required.
To upgrade IRPF90, run :
${QPACKAGE_ROOT}/scripts/upgrade_irpf90.sh
${QPACKAGE_ROOT}/scripts/upgrade/upgrade_irpf90.sh
"
else
info "irpf90 version is OK"
@ -75,7 +75,7 @@ then
Current EZFIO version : ${EZFIO_VERSION}
EZFIO version >= ${EZFIO_REQUIRED_VERSION} is required.
To upgrade EZFIO, run :
${QPACKAGE_ROOT}/scripts/upgrade_ezfio.sh
${QPACKAGE_ROOT}/scripts/upgrade/upgrade_ezfio.sh
"
else
info "EZFIO version is OK"

2
scripts/update_README.py
View File

@ -83,7 +83,7 @@ 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_CHILDREN_MODULES', 'r')
modules = file.read()
file.close()

2
scripts/upgrade_ezfio.sh → scripts/upgrade/upgrade_ezfio.sh
View File

@ -12,7 +12,7 @@ fi
cd -- ${QPACKAGE_ROOT}
mv -- ${QPACKAGE_ROOT}/EZFIO ${QPACKAGE_ROOT}/EZFIO.old
${QPACKAGE_ROOT}/scripts/install_ezfio.sh
${QPACKAGE_ROOT}/scripts/install/install_ezfio.sh
if [[ $? -eq 0 ]]
then

2
scripts/upgrade_irpf90.sh → scripts/upgrade/upgrade_irpf90.sh
View File

@ -12,7 +12,7 @@ fi
cd -- ${QPACKAGE_ROOT}
mv -f -- ${QPACKAGE_ROOT}/irpf90 ${QPACKAGE_ROOT}/irpf90.old
${QPACKAGE_ROOT}/scripts/install_irpf90.sh
${QPACKAGE_ROOT}/scripts/install/install_irpf90.sh
if [[ $? -eq 0 ]]
then

45
setup_environment.sh
View File

@ -12,13 +12,15 @@ QPACKAGE_ROOT="$( cd "$(dirname "$BASH_SOURCE")" ; pwd -P )"
cat << EOF > quantum_package.rc
export IRPF90="${IRPF90}"
export QPACKAGE_ROOT=\$( cd \$(dirname "\${BASH_SOURCE}") ; pwd -P )
export IRPF90="\${QPACKAGE_ROOT}/bin/irpf90"
export LD_LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LD_LIBRARY_PATH}
export LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LIBRARY_PATH}
export C_INCLUDE_PATH="\${QPACKAGE_ROOT}"/include:\${C_INCLUDE_PATH}
export PYTHONPATH=\${PYTHONPATH}:"\${QPACKAGE_ROOT}"/scripts:"\${QPACKAGE_ROOT}"/scripts/ezfio_interface
export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/scripts:"\${QPACKAGE_ROOT}"/scripts/ezfio_interface
export PYTHONPATH=\${PYTHONPATH}\$(find "\${QPACKAGE_ROOT}"/scripts -type d -printf ":%p")
export PATH=\${PATH}\$(find "\${QPACKAGE_ROOT}"/scripts -type d -printf ":%p")
export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/bin
export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/ocaml
source "\${QPACKAGE_ROOT}"/bin/irpman &> /dev/null
@ -28,37 +30,29 @@ EOF
source quantum_package.rc
echo "${BLUE}===== Installing IRPF90 ===== ${BLACK}"
${QPACKAGE_ROOT}/scripts/install_irpf90.sh | tee install_irpf90.log
if [[ ! -d ${QPACKAGE_ROOT}/irpf90 ]]
then
echo $RED "Error in IRPF90 installation" $BLACK
exit 1
fi
if [[ ! -x ${QPACKAGE_ROOT}/bin/irpf90 ]]
then
echo $RED "Error in IRPF90 installation" $BLACK
exit 1
fi
if [[ ! -x ${QPACKAGE_ROOT}/bin/irpman ]]
${QPACKAGE_ROOT}/scripts/install/install_irpf90.sh | tee ${QPACKAGE_ROOT}/install_logs/install_irpf90.log
if [[ ! -d ${QPACKAGE_ROOT}/irpf90 ]] || [[ ! -x ${QPACKAGE_ROOT}/bin/irpf90 ]] || [[ ! -x ${QPACKAGE_ROOT}/bin/irpman ]]
then
echo $RED "Error in IRPF90 installation" $BLACK
exit 1
fi
mkdir -p ${QPACKAGE_ROOT}/install_logs
echo "${BLUE}===== Installing Zlib ===== ${BLACK}"
${QPACKAGE_ROOT}/scripts/install_zlib.sh | tee install_zlib.log
${QPACKAGE_ROOT}/scripts/install/install_zlib.sh | tee ${QPACKAGE_ROOT}/install_logs/install_zlib.log
echo "${BLUE}===== Installing Curl ===== ${BLACK}"
${QPACKAGE_ROOT}/scripts/install_curl.sh | tee install_curl.log
${QPACKAGE_ROOT}/scripts/install/install_curl.sh | tee ${QPACKAGE_ROOT}/install_logs/install_curl.log
echo "${BLUE}===== Installing M4 ===== ${BLACK}"
${QPACKAGE_ROOT}/scripts/install_m4.sh | tee install_m4.log
${QPACKAGE_ROOT}/scripts/install/install_m4.sh | tee ${QPACKAGE_ROOT}/install_logs/install_m4.log
echo "${BLUE}===== Installing Docopt ===== ${BLACK}"
${QPACKAGE_ROOT}/scripts/install/install_docopt.sh | tee ${QPACKAGE_ROOT}/install_logs/install_docopt.log
echo "${BLUE}===== Installing EMSL Basis set library ===== ${BLACK}"
${QPACKAGE_ROOT}/scripts/install_emsl.sh | tee install_emsl.log
${QPACKAGE_ROOT}/scripts/install/install_emsl.sh | tee ${QPACKAGE_ROOT}/install_logs/install_emsl.log
if [[ ! -d ${QPACKAGE_ROOT}/EMSL_Basis ]]
then
@ -68,7 +62,7 @@ fi
echo "${BLUE}===== Installing EZFIO ===== ${BLACK}"
${QPACKAGE_ROOT}/scripts/install_ezfio.sh | tee install_ezfio.log
${QPACKAGE_ROOT}/scripts/install/install_ezfio.sh | tee ${QPACKAGE_ROOT}/install_logs/install_ezfio.log
if [[ ! -d ${QPACKAGE_ROOT}/EZFIO ]]
then
echo $RED "Error in EZFIO installation" $BLACK
@ -78,7 +72,7 @@ fi
echo "${BLUE}===== Installing Ocaml compiler and libraries ===== ${BLACK}"
rm -f -- ocaml/Qptypes.ml
${QPACKAGE_ROOT}/scripts/install_ocaml.sh | tee install_ocaml.log
${QPACKAGE_ROOT}/scripts/install/install_ocaml.sh | tee ${QPACKAGE_ROOT}/install_logs/install_ocaml.log
if [[ ! -f ${QPACKAGE_ROOT}/ocaml/Qptypes.ml ]]
then
@ -87,7 +81,7 @@ then
fi
echo "${BLUE}===== Installing resultsFile Python library ===== ${BLACK}"
${QPACKAGE_ROOT}/scripts/install_resultsFile.sh
${QPACKAGE_ROOT}/scripts/install/install_resultsFile.sh
if [[ ! -d ${QPACKAGE_ROOT}/resultsFile ]]
then
echo $RED "Error in resultsFile installation" $BLACK
@ -106,8 +100,7 @@ source ${QPACKAGE_ROOT}/quantum_package.rc
" $BLACK
mkdir -p ${QPACKAGE_ROOT}/install_logs
mv ${QPACKAGE_ROOT}/*.log ${QPACKAGE_ROOT}/install_logs/
if [[ $1 == "--robot" ]] ;
then

7
src/AOs/ASSUMPTIONS.rst
View File

@ -1,8 +1 @@
* The atomic orbitals are normalized:
.. math::
\int \left(\chi_i({\bf r}) \right)^2 dr = 1
* The AO coefficients in the EZFIO files are not necessarily normalized and are normalized after reading
* The AO coefficients and exponents are ordered in increasing order of exponents

1
src/AOs/NEEDED_CHILDREN_MODULES Normal file
View File

@ -0,0 +1 @@
Nuclei

2
src/AOs/NEEDED_MODULES
View File

@ -1,2 +0,0 @@
Ezfio_files Nuclei Output Utils

91
src/AOs/README.rst
View File

@ -17,20 +17,20 @@ The AO coefficients are normalized as:
{\tilde c}_{ki} = \frac{c_{ki}}{ \int \left( (x-X_A)^a (y-Y_A)^b (z-Z_A)^c e^{-\gamma_{ki} |{\bf r} - {\bf R}_A|^2} \right)^2} dr
Warning: ``ao_coef`` contains the AO coefficients given in input. These do not
include the normalization constant of the AO. The ``ao_coef_normalized`` includes
this normalization factor.
The AOs are also sorted by increasing exponent to accelerate the calculation of
the two electron integrals.
Assumptions
===========
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
* The atomic orbitals are normalized:
.. math::
\int \left(\chi_i({\bf r}) \right)^2 dr = 1
* The AO coefficients in the EZFIO files are not necessarily normalized and are normalized after reading
* The AO coefficients and exponents are ordered in increasing order of exponents
Needed Modules
@ -39,10 +39,7 @@ Needed Modules
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
* `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>`_
Documentation
=============
@ -70,45 +67,41 @@ Documentation
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 <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L62>`_
AO Coefficients, read from input. Those should not be used directly, as
the MOs are expressed on the basis of **normalized** AOs.
`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_normalized <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L84>`_
Coefficients including the AO normalization
`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_coef_normalized_ordered <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L107>`_
Sorted primitives to accelerate 4 index MO transformation
`ao_coef_normalized_ordered_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L133>`_
Transposed ao_coef_normalized_ordered
`ao_expo <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L41>`_
AO Exponents read from input
`ao_expo_ordered <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L108>`_
Sorted primitives to accelerate 4 index MO transformation
`ao_expo_ordered_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L147>`_
Transposed ao_expo_ordered
`ao_l <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L162>`_
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_expo_transp <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L158>`_
Transposed ao_coef and ao_expo
`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_char <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L163>`_
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>`_
`ao_l_char_space <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L311>`_
Undocumented
`ao_md5 <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L400>`_
`ao_md5 <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L403>`_
MD5 key characteristic of the AO basis
`ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L207>`_
`ao_nucl <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L209>`_
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>`_
@ -118,35 +111,35 @@ Documentation
Number of atomic orbitals
`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
Powers of x,y and z read from input
`ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L175>`_
`ao_prim_num <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L177>`_
Number of primitives per atomic orbital
`ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L197>`_
`ao_prim_num_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L199>`_
Undocumented
`ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L198>`_
`ao_prim_num_max_align <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L200>`_
Undocumented
`l_to_charater <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L216>`_
`l_to_charater <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L218>`_
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>`_
`n_aos_max <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L231>`_
Number of AOs per atom
`nucl_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L242>`_
`nucl_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L244>`_
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>`_
`nucl_list_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L262>`_
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>`_
`nucl_n_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L230>`_
Number of AOs per atom
`nucl_num_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L261>`_
`nucl_num_shell_aos <http://github.com/LCPQ/quantum_package/tree/master/src/AOs/aos.irp.f#L263>`_
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

20
src/AOs/ao_overlap.irp.f
View File

@ -21,8 +21,8 @@
!$OMP overlap_x,overlap_y, overlap_z, overlap, &
!$OMP alpha, beta,i,j,c) &
!$OMP SHARED(nucl_coord,ao_power,ao_prim_num, &
!$OMP ao_overlap_x,ao_overlap_y,ao_overlap_z,ao_overlap,ao_num,ao_coef_transp,ao_nucl, &
!$OMP ao_expo_transp,dim1)
!$OMP ao_overlap_x,ao_overlap_y,ao_overlap_z,ao_overlap,ao_num,ao_coef_normalized_ordered_transp,ao_nucl, &
!$OMP ao_expo_ordered_transp,dim1)
do j=1,ao_num
A_center(1) = nucl_coord( ao_nucl(j), 1 )
A_center(2) = nucl_coord( ao_nucl(j), 2 )
@ -44,12 +44,12 @@
power_B(2) = ao_power( i, 2 )
power_B(3) = ao_power( i, 3 )
do n = 1,ao_prim_num(j)
alpha = ao_expo_transp(n,j)
alpha = ao_expo_ordered_transp(n,j)
!DEC$ VECTOR ALIGNED
do l = 1, ao_prim_num(i)
beta = ao_expo_transp(l,i)
beta = ao_expo_ordered_transp(l,i)
call overlap_gaussian_xyz(A_center,B_center,alpha,beta,power_A,power_B,overlap_x,overlap_y,overlap_z,overlap,dim1)
c = ao_coef_transp(n,j) * ao_coef_transp(l,i)
c = ao_coef_normalized_ordered_transp(n,j) * ao_coef_normalized_ordered_transp(l,i)
ao_overlap(i,j) += c * overlap
ao_overlap_x(i,j) += c * overlap_x
ao_overlap_y(i,j) += c * overlap_y
@ -84,8 +84,8 @@ BEGIN_PROVIDER [ double precision, ao_overlap_abs,(ao_num_align,ao_num) ]
!$OMP overlap_x,overlap_y, overlap_z, overlap, &
!$OMP alpha, beta,i,j,dx) &
!$OMP SHARED(nucl_coord,ao_power,ao_prim_num, &
!$OMP ao_overlap_abs,ao_num,ao_coef_transp,ao_nucl, &
!$OMP ao_expo_transp,dim1,lower_exp_val)
!$OMP ao_overlap_abs,ao_num,ao_coef_normalized_ordered_transp,ao_nucl, &
!$OMP ao_expo_ordered_transp,dim1,lower_exp_val)
do j=1,ao_num
A_center(1) = nucl_coord( ao_nucl(j), 1 )
A_center(2) = nucl_coord( ao_nucl(j), 2 )
@ -104,14 +104,14 @@ BEGIN_PROVIDER [ double precision, ao_overlap_abs,(ao_num_align,ao_num) ]
power_B(2) = ao_power( i, 2 )
power_B(3) = ao_power( i, 3 )
do n = 1,ao_prim_num(j)
alpha = ao_expo_transp(n,j)
alpha = ao_expo_ordered_transp(n,j)
!DEC$ VECTOR ALIGNED
do l = 1, ao_prim_num(i)
beta = ao_expo_transp(l,i)
beta = ao_expo_ordered_transp(l,i)
call overlap_x_abs(A_center(1),B_center(1),alpha,beta,power_A(1),power_B(1),overlap_x,lower_exp_val,dx,dim1)
call overlap_x_abs(A_center(2),B_center(2),alpha,beta,power_A(2),power_B(2),overlap_y,lower_exp_val,dx,dim1)
call overlap_x_abs(A_center(3),B_center(3),alpha,beta,power_A(3),power_B(3),overlap_z,lower_exp_val,dx,dim1)
ao_overlap_abs(i,j) += abs(ao_coef_transp(n,j) * ao_coef_transp(l,i)) * overlap_x * overlap_y * overlap_z
ao_overlap_abs(i,j) += abs(ao_coef_normalized_ordered_transp(n,j) * ao_coef_normalized_ordered_transp(l,i)) * overlap_x * overlap_y * overlap_z
enddo
enddo
enddo

147
src/AOs/aos.irp.f
View File

@ -3,7 +3,7 @@
implicit none
BEGIN_DOC
! Number of atomic orbitals
! Number of atomic orbitals
END_DOC
ao_num = -1
@ -16,21 +16,16 @@
ao_num_align = align_double(ao_num)
END_PROVIDER
BEGIN_PROVIDER [ integer, ao_power, (ao_num_align,3) ]
&BEGIN_PROVIDER [ double precision, ao_expo, (ao_num_align,ao_prim_num_max) ]
&BEGIN_PROVIDER [ double precision, ao_coef, (ao_num_align,ao_prim_num_max) ]
BEGIN_PROVIDER [ integer, ao_power, (ao_num_align,3) ]
implicit none
BEGIN_DOC
! Coefficients, exponents and powers of x,y and z
! Powers of x,y and z read from input
END_DOC
PROVIDE ezfio_filename
double precision, allocatable :: buffer(:,:)
allocate ( buffer(ao_num,ao_prim_num_max) )
integer :: ibuffer(ao_num,3)
integer :: i,j,k
character*(128) :: give_ao_character_space
integer, allocatable :: ibuffer(:,:)
allocate ( ibuffer(ao_num,3) )
ibuffer = 0
call ezfio_get_ao_basis_ao_power(ibuffer)
ao_power = 0
@ -39,6 +34,20 @@ END_PROVIDER
ao_power(i,j) = ibuffer(i,j)
enddo
enddo
deallocate(ibuffer)
END_PROVIDER
BEGIN_PROVIDER [ double precision, ao_expo, (ao_num_align,ao_prim_num_max) ]
implicit none
BEGIN_DOC
! AO Exponents read from input
END_DOC
PROVIDE ezfio_filename
double precision, allocatable :: buffer(:,:)
allocate ( buffer(ao_num,ao_prim_num_max) )
integer :: i,j,k
ao_expo = 0.d0
buffer = 0.d0
call ezfio_get_ao_basis_ao_expo(buffer)
@ -47,7 +56,20 @@ END_PROVIDER
ao_expo(i,j) = buffer(i,j)
enddo
enddo
deallocate(buffer)
END_PROVIDER
BEGIN_PROVIDER [ double precision, ao_coef, (ao_num_align,ao_prim_num_max) ]
implicit none
BEGIN_DOC
! AO Coefficients, read from input. Those should not be used directly, as
! the MOs are expressed on the basis of **normalized** AOs.
END_DOC
PROVIDE ezfio_filename
double precision, allocatable :: buffer(:,:)
allocate ( buffer(ao_num,ao_prim_num_max) )
integer :: i,j,k
ao_coef = 0.d0
buffer = 0.d0
call ezfio_get_ao_basis_ao_coef(buffer)
@ -56,13 +78,17 @@ END_PROVIDER
ao_coef(i,j) = buffer(i,j)
enddo
enddo
deallocate(buffer)
END_PROVIDER
! Normalization of the AO coefficients
! ------------------------------------
BEGIN_PROVIDER [ double precision, ao_coef_normalized, (ao_num_align,ao_prim_num_max) ]
implicit none
BEGIN_DOC
! Coefficients including the AO normalization
END_DOC
double precision :: norm, norm2,overlap_x,overlap_y,overlap_z,C_A(3)
integer :: l, powA(3), nz
integer :: i,j
nz=100
C_A(1) = 0.d0
C_A(2) = 0.d0
@ -73,80 +99,73 @@ END_PROVIDER
powA(3) = ao_power(i,3)
do j=1,ao_prim_num(i)
call overlap_gaussian_xyz(C_A,C_A,ao_expo(i,j),ao_expo(i,j),powA,powA,overlap_x,overlap_y,overlap_z,norm,nz)
ao_coef(i,j) = ao_coef(i,j)/sqrt(norm)
ao_coef_normalized(i,j) = ao_coef(i,j)/sqrt(norm)
enddo
enddo
END_PROVIDER
BEGIN_PROVIDER [ double precision, ao_coef_normalized_ordered, (ao_num_align,ao_prim_num_max) ]
&BEGIN_PROVIDER [ double precision, ao_expo_ordered, (ao_num_align,ao_prim_num_max) ]
implicit none
BEGIN_DOC
! Sorted primitives to accelerate 4 index MO transformation
END_DOC
! Sorting of the exponents for efficient integral calculations
integer :: iorder(ao_prim_num_max)
double precision :: d(ao_prim_num_max,2)
integer :: i,j
do i=1,ao_num
do j=1,ao_prim_num(i)
iorder(j) = j
d(j,1) = ao_expo(i,j)
d(j,2) = ao_coef(i,j)
d(j,2) = ao_coef_normalized(i,j)
enddo
call dsort(d(1,1),iorder,ao_prim_num(i))
call dset_order(d(1,2),iorder,ao_prim_num(i))
do j=1,ao_prim_num(i)
ao_expo(i,j) = d(j,1)
ao_coef(i,j) = d(j,2)
ao_expo_ordered(i,j) = d(j,1)
ao_coef_normalized_ordered(i,j) = d(j,2)
enddo
enddo
END_PROVIDER
BEGIN_PROVIDER [ double precision, ao_coef_transp, (ao_prim_num_max_align,ao_num) ]
&BEGIN_PROVIDER [ double precision, ao_expo_transp, (ao_prim_num_max_align,ao_num) ]
BEGIN_PROVIDER [ double precision, ao_coef_normalized_ordered_transp, (ao_prim_num_max_align,ao_num) ]
implicit none
BEGIN_DOC
! Transposed ao_coef and ao_expo
! Transposed ao_coef_normalized_ordered
END_DOC
integer :: i,j
do j=1, ao_num
do i=1, ao_prim_num_max
ao_coef_transp(i,j) = ao_coef(j,i)
ao_expo_transp(i,j) = ao_expo(j,i)
ao_coef_normalized_ordered_transp(i,j) = ao_coef_normalized_ordered(j,i)
enddo
enddo
END_PROVIDER
BEGIN_PROVIDER [ double precision, ao_coef_unnormalized, (ao_num_align,ao_prim_num_max) ]
&BEGIN_PROVIDER [ double precision, ao_expo_unsorted, (ao_num_align,ao_prim_num_max) ]
&BEGIN_PROVIDER [ integer, ao_l, (ao_num) ]
BEGIN_PROVIDER [ double precision, ao_expo_ordered_transp, (ao_prim_num_max_align,ao_num) ]
implicit none
BEGIN_DOC
! Transposed ao_expo_ordered
END_DOC
integer :: i,j
do j=1, ao_num
do i=1, ao_prim_num_max
ao_expo_ordered_transp(i,j) = ao_expo_ordered(j,i)
enddo
enddo
END_PROVIDER
BEGIN_PROVIDER [ integer, ao_l, (ao_num) ]
&BEGIN_PROVIDER [ character*(128), ao_l_char, (ao_num) ]
implicit none
BEGIN_DOC
! 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
END_DOC
PROVIDE ezfio_filename
double precision, allocatable :: buffer(:,:)
allocate ( buffer(ao_num,ao_prim_num_max) )
integer :: i,j,k
character*(128) :: give_ao_character_space
buffer = 0.d0
call ezfio_get_ao_basis_ao_expo(buffer)
do j = 1, ao_prim_num_max
do i = 1, ao_num
ao_expo_unsorted(i,j) = buffer(i,j)
enddo
enddo
buffer = 0.d0
call ezfio_get_ao_basis_ao_coef(buffer)
do j = 1, ao_prim_num_max
do i = 1, ao_num
ao_coef_unnormalized(i,j) = buffer(i,j)
enddo
enddo
deallocate(buffer)
integer :: i
do i=1,ao_num
ao_l(i) = ao_power(i,1) + ao_power(i,2) + ao_power(i,3)
ao_l_char(i) = l_to_charater(ao_l(i))
@ -154,23 +173,6 @@ END_PROVIDER
END_PROVIDER
BEGIN_PROVIDER [ double precision, ao_coef_transp, (ao_prim_num_max_align,ao_num) ]
&BEGIN_PROVIDER [ double precision, ao_expo_transp, (ao_prim_num_max_align,ao_num) ]
implicit none
BEGIN_DOC
! Transposed ao_coef and ao_expo
END_DOC
integer :: i,j
do j=1, ao_num
do i=1, ao_prim_num_max
ao_coef_transp(i,j) = ao_coef(j,i)
ao_expo_transp(i,j) = ao_expo(j,i)
enddo
enddo
END_PROVIDER
BEGIN_PROVIDER [ integer, ao_prim_num, (ao_num_align) ]
implicit none
@ -303,10 +305,10 @@ END_PROVIDER
enddo
enddo
END_PROVIDER
END_PROVIDER
BEGIN_PROVIDER [ character*(4), ao_l_char_space, (ao_num) ]
BEGIN_PROVIDER [ character*(4), ao_l_char_space, (ao_num) ]
implicit none
integer :: i
character*(4) :: give_ao_character_space
@ -397,6 +399,7 @@ END_PROVIDER
ao_l_char_space(i) = give_ao_character_space
enddo
END_PROVIDER
BEGIN_PROVIDER [ character*(32), ao_md5 ]
BEGIN_DOC
! MD5 key characteristic of the AO basis

1
src/Bielec_integrals/NEEDED_CHILDREN_MODULES Normal file
View File

@ -0,0 +1 @@
MonoInts Bitmask

1
src/Bielec_integrals/NEEDED_MODULES
View File

@ -1 +0,0 @@
AOs Bitmask Electrons Ezfio_files MOs Nuclei Output Utils MonoInts

47
src/Bielec_integrals/README.rst
View File

@ -16,15 +16,8 @@ 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>`_
* `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>`_
* `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>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
Documentation
=============
@ -36,7 +29,7 @@ Documentation
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/Bielec_integrals/ao_bi_integrals.irp.f#L490>`_
`ao_bielec_integral_schwartz <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L491>`_
Needed to compute Schwartz inequalities
`ao_bielec_integral_schwartz_accel <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L107>`_
@ -53,48 +46,48 @@ Documentation
`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/Bielec_integrals/ao_bi_integrals.irp.f#L653>`_
`eri <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L654>`_
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/Bielec_integrals/ao_bi_integrals.irp.f#L515>`_
`general_primitive_integral <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L516>`_
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/Bielec_integrals/ao_bi_integrals.irp.f#L851>`_
`give_polynom_mult_center_x <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L852>`_
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/Bielec_integrals/ao_bi_integrals.irp.f#L772>`_
`i_x1_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L773>`_
recursive function involved in the bielectronic integral
`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L914>`_
`i_x1_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L915>`_
recursive function involved in the bielectronic integral
`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1034>`_
`i_x1_pol_mult_a1 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1035>`_
recursive function involved in the bielectronic integral
`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1088>`_
`i_x1_pol_mult_a2 <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1089>`_
recursive function involved in the bielectronic integral
`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L948>`_
`i_x1_pol_mult_recurs <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L949>`_
recursive function involved in the bielectronic integral
`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L807>`_
`i_x2_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L808>`_
recursive function involved in the bielectronic integral
`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1150>`_
`i_x2_pol_mult <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L1151>`_
recursive function involved in the bielectronic integral
`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L698>`_
`integrale_new <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L699>`_
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/Bielec_integrals/ao_bi_integrals.irp.f#L837>`_
`n_pt_sup <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/ao_bi_integrals.irp.f#L838>`_
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)
@ -172,32 +165,32 @@ Documentation
`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/Bielec_integrals/mo_bi_integrals.irp.f#L464>`_
`mo_bielec_integral_jj <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) = 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/Bielec_integrals/mo_bi_integrals.irp.f#L466>`_
`mo_bielec_integral_jj_anti <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L467>`_
mo_bielec_integral_jj(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_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L326>`_
`mo_bielec_integral_jj_anti_from_ao <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals/mo_bi_integrals.irp.f#L327>`_
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_exchange <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) = K_ij
mo_bielec_integral_jj_anti(i,j) = J_ij - K_ij
`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_exchange_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_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 <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

59
src/Bielec_integrals/ao_bi_integrals.irp.f
View File

@ -42,24 +42,24 @@ double precision function ao_bielec_integral(i,j,k,l)
do p = 1, ao_prim_num(i)
double precision :: coef1
coef1 = ao_coef_transp(p,i)
coef1 = ao_coef_normalized_ordered_transp(p,i)
do q = 1, ao_prim_num(j)
double precision :: coef2
coef2 = coef1*ao_coef_transp(q,j)
coef2 = coef1*ao_coef_normalized_ordered_transp(q,j)
double precision :: p_inv,q_inv
call give_explicit_poly_and_gaussian(P_new,P_center,pp,fact_p,iorder_p,&
ao_expo_transp(p,i),ao_expo_transp(q,j), &
ao_expo_ordered_transp(p,i),ao_expo_ordered_transp(q,j), &
I_power,J_power,I_center,J_center,dim1)
p_inv = 1.d0/pp
do r = 1, ao_prim_num(k)
double precision :: coef3
coef3 = coef2*ao_coef_transp(r,k)
coef3 = coef2*ao_coef_normalized_ordered_transp(r,k)
do s = 1, ao_prim_num(l)
double precision :: coef4
coef4 = coef3*ao_coef_transp(s,l)
coef4 = coef3*ao_coef_normalized_ordered_transp(s,l)
double precision :: general_primitive_integral
call give_explicit_poly_and_gaussian(Q_new,Q_center,qq,fact_q,iorder_q,&
ao_expo_transp(r,k),ao_expo_transp(s,l), &
ao_expo_ordered_transp(r,k),ao_expo_ordered_transp(s,l), &
K_power,L_power,K_center,L_center,dim1)
q_inv = 1.d0/qq
integral = general_primitive_integral(dim1, &
@ -82,15 +82,15 @@ double precision function ao_bielec_integral(i,j,k,l)
double precision :: ERI
do p = 1, ao_prim_num(i)
coef1 = ao_coef_transp(p,i)
coef1 = ao_coef_normalized_ordered_transp(p,i)
do q = 1, ao_prim_num(j)
coef2 = coef1*ao_coef_transp(q,j)
coef2 = coef1*ao_coef_normalized_ordered_transp(q,j)
do r = 1, ao_prim_num(k)
coef3 = coef2*ao_coef_transp(r,k)
coef3 = coef2*ao_coef_normalized_ordered_transp(r,k)
do s = 1, ao_prim_num(l)
coef4 = coef3*ao_coef_transp(s,l)
coef4 = coef3*ao_coef_normalized_ordered_transp(s,l)
integral = ERI( &
ao_expo_transp(p,i),ao_expo_transp(q,j),ao_expo_transp(r,k),ao_expo_transp(s,l),&
ao_expo_ordered_transp(p,i),ao_expo_ordered_transp(q,j),ao_expo_ordered_transp(r,k),ao_expo_ordered_transp(s,l),&
I_power(1),J_power(1),K_power(1),L_power(1), &
I_power(2),J_power(2),K_power(2),L_power(2), &
I_power(3),J_power(3),K_power(3),L_power(3))
@ -149,12 +149,12 @@ double precision function ao_bielec_integral_schwartz_accel(i,j,k,l)
schwartz_kl(0,0) = 0.d0
do r = 1, ao_prim_num(k)
coef1 = ao_coef_transp(r,k)*ao_coef_transp(r,k)
coef1 = ao_coef_normalized_ordered_transp(r,k)*ao_coef_normalized_ordered_transp(r,k)
schwartz_kl(0,r) = 0.d0
do s = 1, ao_prim_num(l)
coef2 = coef1 * ao_coef_transp(s,l) * ao_coef_transp(s,l)
coef2 = coef1 * ao_coef_normalized_ordered_transp(s,l) * ao_coef_normalized_ordered_transp(s,l)
call give_explicit_poly_and_gaussian(Q_new,Q_center,qq,fact_q,iorder_q,&
ao_expo_transp(r,k),ao_expo_transp(s,l), &
ao_expo_ordered_transp(r,k),ao_expo_ordered_transp(s,l), &
K_power,L_power,K_center,L_center,dim1)
q_inv = 1.d0/qq
schwartz_kl(s,r) = general_primitive_integral(dim1, &
@ -168,13 +168,13 @@ double precision function ao_bielec_integral_schwartz_accel(i,j,k,l)
do p = 1, ao_prim_num(i)
double precision :: coef1
coef1 = ao_coef_transp(p,i)
coef1 = ao_coef_normalized_ordered_transp(p,i)
do q = 1, ao_prim_num(j)
double precision :: coef2
coef2 = coef1*ao_coef_transp(q,j)
coef2 = coef1*ao_coef_normalized_ordered_transp(q,j)
double precision :: p_inv,q_inv
call give_explicit_poly_and_gaussian(P_new,P_center,pp,fact_p,iorder_p,&
ao_expo_transp(p,i),ao_expo_transp(q,j), &
ao_expo_ordered_transp(p,i),ao_expo_ordered_transp(q,j), &
I_power,J_power,I_center,J_center,dim1)
p_inv = 1.d0/pp
schwartz_ij = general_primitive_integral(dim1, &
@ -189,16 +189,16 @@ double precision function ao_bielec_integral_schwartz_accel(i,j,k,l)
cycle
endif
double precision :: coef3
coef3 = coef2*ao_coef_transp(r,k)
coef3 = coef2*ao_coef_normalized_ordered_transp(r,k)
do s = 1, ao_prim_num(l)
double precision :: coef4
if (schwartz_kl(s,r)*schwartz_ij < thresh) then
cycle
endif
coef4 = coef3*ao_coef_transp(s,l)
coef4 = coef3*ao_coef_normalized_ordered_transp(s,l)
double precision :: general_primitive_integral
call give_explicit_poly_and_gaussian(Q_new,Q_center,qq,fact_q,iorder_q,&
ao_expo_transp(r,k),ao_expo_transp(s,l), &
ao_expo_ordered_transp(r,k),ao_expo_ordered_transp(s,l), &
K_power,L_power,K_center,L_center,dim1)
q_inv = 1.d0/qq
integral = general_primitive_integral(dim1, &
@ -222,12 +222,12 @@ double precision function ao_bielec_integral_schwartz_accel(i,j,k,l)
schwartz_kl(0,0) = 0.d0
do r = 1, ao_prim_num(k)
coef1 = ao_coef_transp(r,k)*ao_coef_transp(r,k)
coef1 = ao_coef_normalized_ordered_transp(r,k)*ao_coef_normalized_ordered_transp(r,k)
schwartz_kl(0,r) = 0.d0
do s = 1, ao_prim_num(l)
coef2 = coef1*ao_coef_transp(s,l)*ao_coef_transp(s,l)
coef2 = coef1*ao_coef_normalized_ordered_transp(s,l)*ao_coef_normalized_ordered_transp(s,l)
schwartz_kl(s,r) = ERI( &
ao_expo_transp(r,k),ao_expo_transp(s,l),ao_expo_transp(r,k),ao_expo_transp(s,l),&
ao_expo_ordered_transp(r,k),ao_expo_ordered_transp(s,l),ao_expo_ordered_transp(r,k),ao_expo_ordered_transp(s,l),&
K_power(1),L_power(1),K_power(1),L_power(1), &
K_power(2),L_power(2),K_power(2),L_power(2), &
K_power(3),L_power(3),K_power(3),L_power(3)) * &
@ -238,11 +238,11 @@ double precision function ao_bielec_integral_schwartz_accel(i,j,k,l)
enddo
do p = 1, ao_prim_num(i)
coef1 = ao_coef_transp(p,i)
coef1 = ao_coef_normalized_ordered_transp(p,i)
do q = 1, ao_prim_num(j)
coef2 = coef1*ao_coef_transp(q,j)
coef2 = coef1*ao_coef_normalized_ordered_transp(q,j)
schwartz_ij = ERI( &
ao_expo_transp(p,i),ao_expo_transp(q,j),ao_expo_transp(p,i),ao_expo_transp(q,j),&
ao_expo_ordered_transp(p,i),ao_expo_ordered_transp(q,j),ao_expo_ordered_transp(p,i),ao_expo_ordered_transp(q,j),&
I_power(1),J_power(1),I_power(1),J_power(1), &
I_power(2),J_power(2),I_power(2),J_power(2), &
I_power(3),J_power(3),I_power(3),J_power(3))*coef2*coef2
@ -253,14 +253,14 @@ double precision function ao_bielec_integral_schwartz_accel(i,j,k,l)
if (schwartz_kl(0,r)*schwartz_ij < thresh) then
cycle
endif
coef3 = coef2*ao_coef_transp(r,k)
coef3 = coef2*ao_coef_normalized_ordered_transp(r,k)
do s = 1, ao_prim_num(l)
if (schwartz_kl(s,r)*schwartz_ij < thresh) then
cycle
endif
coef4 = coef3*ao_coef_transp(s,l)
coef4 = coef3*ao_coef_normalized_ordered_transp(s,l)
integral = ERI( &
ao_expo_transp(p,i),ao_expo_transp(q,j),ao_expo_transp(r,k),ao_expo_transp(s,l),&
ao_expo_ordered_transp(p,i),ao_expo_ordered_transp(q,j),ao_expo_ordered_transp(r,k),ao_expo_ordered_transp(s,l),&
I_power(1),J_power(1),K_power(1),L_power(1), &
I_power(2),J_power(2),K_power(2),L_power(2), &
I_power(3),J_power(3),K_power(3),L_power(3))
@ -481,6 +481,7 @@ IRP_ENDIF COARRAY
ao_bielec_integrals_in_map = .True.
if (write_ao_integrals) then
call dump_ao_integrals(trim(ezfio_filename)//'/work/ao_integrals.bin')
call ezfio_set_bielec_integrals_disk_access_ao_integrals(.True.)
endif
END_PROVIDER

1
src/Bielec_integrals/mo_bi_integrals.irp.f
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@ -312,6 +312,7 @@ IRP_ENDIF
if (write_mo_integrals) then
call dump_mo_integrals(trim(ezfio_filename)//'/work/mo_integrals.bin')
call ezfio_set_bielec_integrals_disk_access_mo_integrals(.True.)
endif

1
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@ -0,0 +1 @@
MOs

1
src/Bitmask/NEEDED_MODULES
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@ -1 +0,0 @@
AOs Electrons Ezfio_files MOs Nuclei Output Utils

13
src/Bitmask/README.rst
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@ -40,13 +40,7 @@ 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>`_
Documentation
=============
@ -134,6 +128,10 @@ Documentation
Subroutine to print the content of a determinant in '+-' notation and
hexadecimal representation.
`debug_spindet <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L155>`_
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>`_
Returns the physical string "string(N_int,2)" from the array of
occupations "list(N_int*bit_kind_size,2)
@ -141,5 +139,8 @@ Documentation
`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
`print_spindet <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L171>`_
Subroutine to print the content of a determinant using the '+-' notation

35
src/Bitmask/bitmasks_routines.irp.f
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@ -126,7 +126,7 @@ subroutine debug_det(string,Nint)
END_DOC
integer, intent(in) :: Nint
integer(bit_kind), intent(in) :: string(Nint,2)
character*(512) :: output(2)
character*(2048) :: output(2)
call bitstring_to_hexa( output(1), string(1,1), Nint )
call bitstring_to_hexa( output(2), string(1,2), Nint )
print *, trim(output(1)) , '|', trim(output(2))
@ -143,7 +143,7 @@ subroutine print_det(string,Nint)
END_DOC
integer, intent(in) :: Nint
integer(bit_kind), intent(in) :: string(Nint,2)
character*(512) :: output(2)
character*(2048) :: output(2)
call bitstring_to_str( output(1), string(1,1), Nint )
call bitstring_to_str( output(2), string(1,2), Nint )
@ -151,3 +151,34 @@ subroutine print_det(string,Nint)
print *, trim(output(2))
end
subroutine debug_spindet(string,Nint)
use bitmasks
implicit none
BEGIN_DOC
! Subroutine to print the content of a determinant in '+-' notation and
! hexadecimal representation.
END_DOC
integer, intent(in) :: Nint
integer(bit_kind), intent(in) :: string(Nint,2)
character*(2048) :: output(1)
call bitstring_to_hexa( output(1), string(1,1), Nint )
print *, trim(output(1))
call print_spindet(string,Nint)
end
subroutine print_spindet(string,Nint)
use bitmasks
implicit none
BEGIN_DOC
! Subroutine to print the content of a determinant using the '+-' notation
END_DOC
integer, intent(in) :: Nint
integer(bit_kind), intent(in) :: string(Nint,2)
character*(2048) :: output(1)
call bitstring_to_str( output(1), string(1,1), Nint )
print *, trim(output(1))
end

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@ -0,0 +1 @@
Perturbation Selectors_full Generators_CAS

2
src/CAS_SD/NEEDED_MODULES
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@ -1,2 +0,0 @@
AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Generators_CAS Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils

16
src/CAS_SD/README.rst
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@ -24,21 +24,7 @@ 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>`_
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
* `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>`_
* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_

22
src/CAS_SD/cas_sd.irp.f
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@ -1,6 +1,7 @@
program full_ci
implicit none
integer :: i,k
integer :: N_det_old
double precision, allocatable :: pt2(:), norm_pert(:), H_pert_diag(:)
@ -9,6 +10,7 @@ program full_ci
allocate (pt2(N_st), norm_pert(N_st),H_pert_diag(N_st))
character*(64) :: perturbation
N_det_old = 0
pt2 = 1.d0
diag_algorithm = "Lapack"
if (N_det > n_det_max_cas_sd) then
@ -29,6 +31,7 @@ program full_ci
endif
do while (N_det < n_det_max_cas_sd.and.maxval(abs(pt2(1:N_st))) > pt2_max)
N_det_old = N_det
call H_apply_CAS_SD(pt2, norm_pert, H_pert_diag, N_st)
PROVIDE psi_coef
@ -53,10 +56,11 @@ program full_ci
if (abort_all) then
exit
endif
if (N_det == N_det_old) then
exit
endif
enddo
! Check that it is a CAS-SD
logical :: in_cas
integer :: exc_max, degree_min
exc_max = 0
print *, 'CAS determinants : ', N_det_generators
@ -69,18 +73,4 @@ program full_ci
print *, ''
enddo
print *, 'Max excitation degree in the CAS :', exc_max
do i=1,N_det
in_cas = .False.
degree_min = 1000
do k=1,N_det_generators
call get_excitation_degree(psi_det_generators(1,1,k),psi_det(1,1,i),degree,N_int)
degree_min = min(degree_min,degree)
enddo
if (degree_min > 2) then
print *, 'Error : This is not a CAS-SD : '
print *, 'Excited determinant:', degree_min
call debug_det(psi_det(1,1,k),N_int)
stop
endif
enddo
end

36
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@ -50,14 +50,30 @@ program full_ci
print *, 'E = ', CI_energy
print *, 'E+PT2 = ', CI_energy+pt2
print *, '-----'
call ezfio_set_full_ci_energy(CI_energy)
call ezfio_set_cas_sd_energy(CI_energy(1))
if (abort_all) then
exit
endif
enddo
call diagonalize_CI
if(do_pt2_end)then
print*,'Last iteration only to compute the PT2'
threshold_selectors = 1.d0
threshold_generators = 0.999d0
call H_apply_CAS_SD_PT2(pt2, norm_pert, H_pert_diag, N_st)
print *, 'Final step'
print *, 'N_det = ', N_det
print *, 'N_states = ', N_states
print *, 'PT2 = ', pt2
print *, 'E = ', CI_energy
print *, 'E+PT2 = ', CI_energy+pt2
print *, '-----'
call ezfio_set_cas_sd_energy_pt2(CI_energy(1)+pt2(1))
endif
! Check that it is a CAS-SD
logical :: in_cas
integer :: exc_max, degree_min
exc_max = 0
print *, 'CAS determinants : ', N_det_cas
@ -70,18 +86,4 @@ program full_ci
print *, ''
enddo
print *, 'Max excitation degree in the CAS :', exc_max
do i=1,N_det
in_cas = .False.
degree_min = 1000
do k=1,N_det_cas
call get_excitation_degree(psi_cas(1,1,k),psi_det(1,1,i),degree,N_int)
degree_min = min(degree_min,degree)
enddo
if (degree_min > 2) then
print *, 'Error : This is not a CAS-SD : '
print *, 'Excited determinant:', degree_min
call debug_det(psi_det(1,1,k),N_int)
stop
endif
enddo
end

1
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@ -0,0 +1 @@
Selectors_full SingleRefMethod

3
src/CID/NEEDED_MODULES
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@ -1,3 +0,0 @@
AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils

13
src/CID/README.rst
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@ -15,21 +15,8 @@ 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>`_
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
* `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>`_
Documentation
=============

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@ -0,0 +1 @@
CID_selected

2
src/CID_SC2_selected/NEEDED_MODULES
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@ -1,2 +0,0 @@
AOs Bielec_integrals Bitmask CISD CISD_selected Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils

20
src/CID_SC2_selected/README.rst
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@ -19,23 +19,5 @@ 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>`_
* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
* `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
* `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>`_
* `CID_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected>`_

1
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@ -0,0 +1 @@
Perturbation CID

2
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@ -1,2 +0,0 @@
AOs Bielec_integrals Bitmask CISD Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils

18
src/CID_selected/README.rst
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@ -22,22 +22,6 @@ 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>`_
* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
* `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>`_
* `CID <http://github.com/LCPQ/quantum_package/tree/master/src/CID>`_

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Selectors_full SingleRefMethod

2
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AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils

13
src/CIS/README.rst
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@ -31,19 +31,6 @@ 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>`_
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
* `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>`_

1
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Selectors_full SingleRefMethod

2
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@ -1,2 +0,0 @@
AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils

13
src/CISD/README.rst
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@ -15,21 +15,8 @@ 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>`_
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
* `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>`_
Documentation
=============

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CISD_selected

2
src/CISD_SC2_selected/NEEDED_MODULES
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@ -1,2 +0,0 @@
AOs Bielec_integrals Bitmask CISD CISD_selected Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils

18
src/CISD_SC2_selected/README.rst
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@ -19,23 +19,5 @@ 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>`_
* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
* `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
* `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>`_

1
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Perturbation CISD

2
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@ -1,2 +0,0 @@
AOs Bielec_integrals Bitmask CISD Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils

18
src/CISD_selected/README.rst
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@ -28,22 +28,6 @@ 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>`_
* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
* `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>`_
* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_

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Perturbation Selectors_full Generators_CAS

2
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@ -1,2 +0,0 @@
AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Generators_CAS Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils

16
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@ -19,21 +19,7 @@ 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>`_
* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
* `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>`_
* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_

83
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@ -53,13 +53,17 @@ subroutine resize_H_apply_buffer(new_size,iproc)
double precision, pointer :: buffer_e2(:,:)
integer :: i,j,k
integer :: Ndet
BEGIN_DOC
! Resizes the H_apply buffer of proc iproc. The buffer lock should
! be set before calling this function.
END_DOC
PROVIDE H_apply_buffer_allocated
ASSERT (new_size > 0)
ASSERT (iproc >= 0)
ASSERT (iproc < nproc)
call omp_set_lock(H_apply_buffer_lock(1,iproc))
allocate ( buffer_det(N_int,2,new_size), &
buffer_coef(new_size,N_states), &
buffer_e2(new_size,N_states) )
@ -93,7 +97,6 @@ subroutine resize_H_apply_buffer(new_size,iproc)
H_apply_buffer(iproc)%sze = new_size
H_apply_buffer(iproc)%N_det = min(new_size,H_apply_buffer(iproc)%N_det)
call omp_unset_lock(H_apply_buffer_lock(1,iproc))
end
@ -101,8 +104,7 @@ subroutine copy_H_apply_buffer_to_wf
use omp_lib
implicit none
BEGIN_DOC
! Copies the H_apply buffer to psi_coef. You need to touch psi_det, psi_coef and N_det
! after calling this function.
! Copies the H_apply buffer to psi_coef.
! After calling this subroutine, N_det, psi_det and psi_coef need to be touched
END_DOC
integer(bit_kind), allocatable :: buffer_det(:,:,:)
@ -181,8 +183,77 @@ subroutine copy_H_apply_buffer_to_wf
call normalize(psi_coef,N_det)
SOFT_TOUCH N_det psi_det psi_coef
logical :: found_duplicates
call remove_duplicates_in_psi_det(found_duplicates)
end
subroutine remove_duplicates_in_psi_det(found_duplicates)
implicit none
logical, intent(out) :: found_duplicates
BEGIN_DOC
! Removes duplicate determinants in the wave function.
END_DOC
integer :: i,j,k
integer(bit_kind), allocatable :: bit_tmp(:)
logical,allocatable :: duplicate(:)
allocate (duplicate(N_det), bit_tmp(N_det))
do i=1,N_det
integer, external :: det_search_key
!$DIR FORCEINLINE
bit_tmp(i) = det_search_key(psi_det_sorted_bit(1,1,i),N_int)
duplicate(i) = .False.
enddo
do i=1,N_det-1
if (duplicate(i)) then
cycle
endif
j = i+1
do while (bit_tmp(j)==bit_tmp(i))
if (duplicate(j)) then
j += 1
cycle
endif
duplicate(j) = .True.
do k=1,N_int
if ( (psi_det_sorted_bit(k,1,i) /= psi_det_sorted_bit(k,1,j) ) &
.or. (psi_det_sorted_bit(k,2,i) /= psi_det_sorted_bit(k,2,j) ) ) then
duplicate(j) = .False.
exit
endif
enddo
j += 1
if (j > N_det) then
exit
endif
enddo
enddo
found_duplicates = .False.
do i=1,N_det
if (duplicate(i)) then
found_duplicates = .True.
exit
endif
enddo
if (found_duplicates) then
call write_bool(output_determinants,found_duplicates,'Found duplicate determinants')
k=0
do i=1,N_det
if (.not.duplicate(i)) then
k += 1
psi_det(:,:,k) = psi_det_sorted_bit (:,:,i)
psi_coef(k,:) = psi_coef_sorted_bit(i,:)
endif
enddo
N_det = k
TOUCH N_det psi_det psi_coef
endif
deallocate (duplicate,bit_tmp)
end
subroutine fill_H_apply_buffer_no_selection(n_selected,det_buffer,Nint,iproc)
use bitmasks
@ -196,11 +267,11 @@ subroutine fill_H_apply_buffer_no_selection(n_selected,det_buffer,Nint,iproc)
integer :: i,j,k
integer :: new_size
PROVIDE H_apply_buffer_allocated
call omp_set_lock(H_apply_buffer_lock(1,iproc))
new_size = H_apply_buffer(iproc)%N_det + n_selected
if (new_size > H_apply_buffer(iproc)%sze) then
call resize_h_apply_buffer(max(2*H_apply_buffer(iproc)%sze,new_size),iproc)
endif
call omp_set_lock(H_apply_buffer_lock(1,iproc))
do i=1,H_apply_buffer(iproc)%N_det
ASSERT (sum(popcnt(H_apply_buffer(iproc)%det(:,1,i)) )== elec_alpha_num)
ASSERT (sum(popcnt(H_apply_buffer(iproc)%det(:,2,i))) == elec_beta_num)
@ -215,7 +286,7 @@ subroutine fill_H_apply_buffer_no_selection(n_selected,det_buffer,Nint,iproc)
enddo
do j=1,N_states
do i=1,N_selected
H_apply_buffer(iproc)%coef(i,j) = 0.d0
H_apply_buffer(iproc)%coef(i+H_apply_buffer(iproc)%N_det,j) = 0.d0
enddo
enddo
H_apply_buffer(iproc)%N_det = new_size

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Bielec_integrals

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AOs Bielec_integrals Bitmask Electrons Ezfio_files MonoInts MOs Nuclei Output Utils

102
src/Determinants/README.rst
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@ -32,16 +32,7 @@ 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>`_
* `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>`_
Documentation
=============
@ -49,12 +40,11 @@ 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/Determinants/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.
`copy_h_apply_buffer_to_wf <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/H_apply.irp.f#L103>`_
Copies the H_apply buffer to psi_coef.
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/Determinants/H_apply.irp.f#L187>`_
`fill_h_apply_buffer_no_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/H_apply.irp.f#L258>`_
Fill the H_apply buffer with determiants for CISD
`h_apply_buffer_allocated <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/H_apply.irp.f#L15>`_
@ -65,8 +55,12 @@ Documentation
Buffer of determinants/coefficients/perturbative energy for H_apply.
Uninitialized. Filled by H_apply subroutines.
`remove_duplicates_in_psi_det <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/H_apply.irp.f#L190>`_
Removes duplicate determinants in the wave function.
`resize_h_apply_buffer <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/H_apply.irp.f#L48>`_
Undocumented
Resizes the H_apply buffer of proc iproc. The buffer lock should
be set before calling this function.
`cisd_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/SC2.irp.f#L1>`_
CISD+SC2 method :: take off all the disconnected terms of a CISD (selected or not)
@ -193,10 +187,10 @@ Documentation
`det_svd <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/det_svd.irp.f#L1>`_
Computes the SVD of the Alpha x Beta determinant coefficient matrix
`filter_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L426>`_
`filter_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L423>`_
Returns a determinant with only the 3 highest electrons
`int_of_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L391>`_
`int_of_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L388>`_
Returns an integer*8 as :
.br
|_<--- 21 bits ---><--- 21 bits ---><--- 21 bits --->|
@ -213,26 +207,26 @@ Documentation
`n_det <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L3>`_
Number of determinants in the wave function
`psi_average_norm_contrib <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L276>`_
`psi_average_norm_contrib <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L273>`_
Contribution of determinants to the state-averaged density
`psi_average_norm_contrib_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L306>`_
`psi_average_norm_contrib_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L303>`_
Wave function sorted by determinants contribution to the norm (state-averaged)
`psi_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L230>`_
`psi_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L227>`_
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/Determinants/determinants.irp.f#L305>`_
`psi_coef_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L302>`_
Wave function sorted by determinants contribution to the norm (state-averaged)
`psi_coef_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L453>`_
`psi_coef_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L450>`_
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_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L336>`_
`psi_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L333>`_
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
@ -245,46 +239,46 @@ Documentation
`psi_det_size <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L47>`_
Size of the psi_det/psi_coef arrays
`psi_det_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L304>`_
`psi_det_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L301>`_
Wave function sorted by determinants contribution to the norm (state-averaged)
`psi_det_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L452>`_
`psi_det_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L449>`_
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_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L335>`_
`psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L332>`_
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/Determinants/determinants.irp.f#L454>`_
`psi_det_sorted_next_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L451>`_
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/Determinants/determinants.irp.f#L583>`_
`read_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L580>`_
Reads the determinants from the EZFIO file
`save_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L630>`_
`save_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L627>`_
Save the wave function into the EZFIO file
`save_wavefunction_general <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L649>`_
`save_wavefunction_general <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L646>`_
Save the wave function into the EZFIO file
`save_wavefunction_unsorted <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L640>`_
`save_wavefunction_unsorted <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L637>`_
Save the wave function into the EZFIO file
`sort_dets_by_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L474>`_
`sort_dets_by_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L471>`_
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/Determinants/determinants.irp.f#L349>`_
`sort_dets_by_det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L346>`_
Determinants are sorted are sorted according to their det_search_key.
Useful to accelerate the search of a random determinant in the wave
function.
@ -322,7 +316,7 @@ Documentation
`diag_algorithm <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI.irp.f#L1>`_
Diagonalization algorithm (Davidson or Lapack)
`diagonalize_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI.irp.f#L96>`_
`diagonalize_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI.irp.f#L100>`_
Replace the coefficients of the CI states by the coefficients of the
eigenstates of the CI matrix
@ -335,7 +329,7 @@ Documentation
`ci_sc2_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_SC2.irp.f#L1>`_
N_states_diag lowest eigenvalues of the CI matrix
`diagonalize_ci_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_SC2.irp.f#L46>`_
`diagonalize_ci_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_SC2.irp.f#L45>`_
Replace the coefficients of the CI states_diag by the coefficients of the
eigenstates of the CI matrix
@ -351,7 +345,7 @@ Documentation
`ci_electronic_energy_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_mono.irp.f#L1>`_
Eigenvectors/values of the CI matrix
`diagonalize_ci_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_mono.irp.f#L59>`_
`diagonalize_ci_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_mono.irp.f#L73>`_
Replace the coefficients of the CI states by the coefficients of the
eigenstates of the CI matrix
@ -538,7 +532,7 @@ Documentation
`save_dets_qmcchem <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_for_qmcchem.irp.f#L1>`_
Undocumented
`save_for_qmc <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_for_qmcchem.irp.f#L48>`_
`save_for_qmc <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_for_qmcchem.irp.f#L46>`_
Undocumented
`save_natorb <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_natorb.irp.f#L1>`_
@ -629,61 +623,49 @@ Documentation
`n_con_int <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L1131>`_
Number of integers to represent the connections between determinants
`create_wf_of_psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L473>`_
`create_wf_of_psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L483>`_
Matrix of wf coefficients. Outer product of alpha and beta determinants
`generate_all_alpha_beta_det_products <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L528>`_
`generate_all_alpha_beta_det_products <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L538>`_
Create a wave function from all possible alpha x beta determinants
`get_index_in_psi_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L131>`_
`get_index_in_psi_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L139>`_
Returns the index of the determinant in the ``psi_det_alpha_unique`` array
`get_index_in_psi_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L212>`_
`get_index_in_psi_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L221>`_
Returns the index of the determinant in the ``psi_det_beta_unique`` array
`n_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L54>`_
Unique alpha determinants
`n_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L91>`_
Unique beta determinants
`psi_det_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L25>`_
List of alpha determinants of psi_det
`psi_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L53>`_
Unique alpha determinants
`psi_det_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L39>`_
List of beta determinants of psi_det
`psi_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L90>`_
Unique beta determinants
`psi_svd_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L568>`_
`psi_svd_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L578>`_
SVD wave function
`psi_svd_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L569>`_
`psi_svd_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L579>`_
SVD wave function
`psi_svd_coefs <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L570>`_
`psi_svd_coefs <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L580>`_
SVD wave function
`psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L457>`_
`psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L467>`_
Matrix of wf coefficients. Outer product of alpha and beta determinants
`psi_svd_matrix_columns <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L398>`_
`psi_svd_matrix_columns <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L407>`_
Matrix of wf coefficients. Outer product of alpha and beta determinants
`psi_svd_matrix_rows <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L397>`_
`psi_svd_matrix_rows <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L406>`_
Matrix of wf coefficients. Outer product of alpha and beta determinants
`psi_svd_matrix_values <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L396>`_
`psi_svd_matrix_values <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L405>`_
Matrix of wf coefficients. Outer product of alpha and beta determinants
`spin_det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L9>`_
Return an integer*8 corresponding to a determinant index for searching
`write_spindeterminants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L294>`_
`write_spindeterminants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L303>`_
Undocumented
`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/truncate_wf.irp.f#L1>`_

3
src/Determinants/determinants.irp.f
View File

@ -147,9 +147,7 @@ END_PROVIDER
!$DIR FORCEINLINE
bit_tmp(i) = occ_pattern_search_key(psi_occ_pattern(1,1,i),N_int)
enddo
print*,'passed 1'
call i8sort(bit_tmp,iorder,N_det)
print*,'passed 2'
!DIR$ IVDEP
do i=1,N_det
do k=1,N_int
@ -189,7 +187,6 @@ END_PROVIDER
endif
enddo
enddo
print*,'passed 3'
N_occ_pattern=0
do i=1,N_det

18
src/Determinants/diagonalize_CI.irp.f
View File

@ -66,6 +66,7 @@ END_PROVIDER
enddo
integer :: i_state
double precision :: s2
if (s2_eig) then
i_state = 0
do j=1,N_det
call get_s2_u0(psi_det,eigenvectors(1,j),N_det,N_det,s2)
@ -81,13 +82,16 @@ END_PROVIDER
exit
endif
enddo
! if(i_state < min(N_states_diag,N_det))then
! print *, 'pb with the number of states'
! print *, 'i_state = ',i_state
! print *, 'N_states_diag ',N_states_diag
! print *,'stopping ...'
! stop
! endif
else
do j=1,N_states_diag
call get_s2_u0(psi_det,eigenvectors(1,j),N_det,N_det,s2)
do i=1,N_det
CI_eigenvectors(i,j) = eigenvectors(i,j)
enddo
CI_electronic_energy(j) = eigenvalues(j)
CI_eigenvectors_s2(j) = s2
enddo
endif
deallocate(eigenvectors,eigenvalues)
endif

3
src/Determinants/diagonalize_CI_SC2.irp.f
View File

@ -35,8 +35,7 @@ END_PROVIDER
do i=1,N_det
CI_SC2_eigenvectors(i,j) = psi_coef(i,j)
enddo
! TODO : check comment
! CI_SC2_electronic_energy(j) = CI_electronic_energy(j)
CI_SC2_electronic_energy(j) = CI_electronic_energy(j)
enddo
call CISD_SC2(psi_det,CI_SC2_eigenvectors,CI_SC2_electronic_energy, &

14
src/Determinants/diagonalize_CI_mono.irp.f
View File

@ -32,6 +32,7 @@
integer :: i_state
double precision :: s2
i_state = 0
if (s2_eig) then
do j=1,N_det
call get_s2_u0(psi_det,eigenvectors(1,j),N_det,N_det,s2)
if(dabs(s2-expected_s2).le.0.3d0)then
@ -51,6 +52,19 @@
exit
endif
enddo
else
do j=1,N_states_diag
call get_s2_u0(psi_det,eigenvectors(1,j),N_det,N_det,s2)
if(dabs(eigenvectors(1,j)).gt.0.9d0)then
i_state += 1
do i=1,N_det
CI_eigenvectors_mono(i,i_state) = eigenvectors(i,j)
enddo
CI_electronic_energy_mono(i_state) = eigenvalues(j)
CI_eigenvectors_s2_mono(i_state) = s2
endif
enddo
endif
deallocate(eigenvectors,eigenvalues)
endif

4
src/Determinants/filter_connected.irp.f
View File

@ -235,8 +235,8 @@ subroutine filter_connected_davidson(key1,key2,Nint,sze,idx)
else if (Nint==3) then
!DIR$ LOOP COUNT (1000)
i = idx(0)
!DIR$ LOOP COUNT (1000)
do j_int=1,N_con_int
itmp = det_connections(j_int,i)
do while (itmp /= 0_8)
@ -261,8 +261,8 @@ subroutine filter_connected_davidson(key1,key2,Nint,sze,idx)
else
!DIR$ LOOP COUNT (1000)
i = idx(0)
!DIR$ LOOP COUNT (1000)
do j_int=1,N_con_int
itmp = det_connections(j_int,i)
do while (itmp /= 0_8)

12
src/Determinants/s2.irp.f
View File

@ -88,19 +88,19 @@ subroutine get_s2_u0(psi_keys_tmp,psi_coefs_tmp,n,nmax,s2)
double precision, intent(out) :: s2
integer :: i,j,l
double precision :: s2_tmp
s2 = S_z2_Sz
s2 = 0.d0
!$OMP PARALLEL DO DEFAULT(NONE) &
!$OMP PRIVATE(i,j,s2_tmp) SHARED(n,psi_coefs_tmp,psi_keys_tmp,N_int) &
!$OMP REDUCTION(+:s2) SCHEDULE(dynamic)
do i = 1, n
do i=1,n
call get_s2(psi_keys_tmp(1,1,i),psi_keys_tmp(1,1,i),s2_tmp,N_int)
! print*,'s2_tmp = ',s2_tmp
do j = 1, n
s2 += psi_coefs_tmp(i)*psi_coefs_tmp(i)*s2_tmp
do j=i+1,n
call get_s2(psi_keys_tmp(1,1,i),psi_keys_tmp(1,1,j),s2_tmp,N_int)
if (s2_tmp == 0.d0) cycle
s2 += psi_coefs_tmp(i)*psi_coefs_tmp(j)*s2_tmp
s2 += (psi_coefs_tmp(i)+psi_coefs_tmp(i))*psi_coefs_tmp(j)*s2_tmp
enddo
enddo
!$OMP END PARALLEL DO
s2 += S_z2_Sz
end

2
src/Determinants/save_for_casino.irp.f
View File

@ -161,7 +161,7 @@ subroutine save_casino
if (ao_l(i) == ao_power(i,1)) then
do j=1,ao_prim_num(i)
l+=1
rtmp(l) = ao_coef(i,ao_prim_num(i)-j+1)
rtmp(l) = ao_coef_normalized(i,ao_prim_num(i))
enddo
endif
enddo

6
src/Determinants/save_for_qmcchem.irp.f
View File

@ -7,8 +7,6 @@ subroutine save_dets_qmcchem
integer, allocatable :: occ(:,:,:), occ_tmp(:,:)
!DIR$ ATTRIBUTES ALIGN : $IRP_ALIGN :: occ, occ_tmp
read_wf = .True.
TOUCH read_wf
call ezfio_set_determinants_det_num(N_det)
call ezfio_set_determinants_det_coef(psi_coef_sorted(1,1))
@ -46,6 +44,8 @@ subroutine save_dets_qmcchem
end
program save_for_qmc
call save_dets_qmcchem
read_wf = .True.
TOUCH read_wf
! call save_dets_qmcchem
call write_spindeterminants
end

194
src/Determinants/spindeterminants.irp.f
View File

@ -50,80 +50,88 @@ BEGIN_PROVIDER [ integer(bit_kind), psi_det_beta, (N_int,psi_det_size) ]
enddo
END_PROVIDER
BEGIN_PROVIDER [ integer(bit_kind), psi_det_alpha_unique, (N_int,psi_det_size) ]
&BEGIN_PROVIDER [ integer, N_det_alpha_unique ]
BEGIN_TEMPLATE
BEGIN_PROVIDER [ integer(bit_kind), psi_det_$alpha_unique, (N_int,psi_det_size) ]
&BEGIN_PROVIDER [ integer, N_det_$alpha_unique ]
implicit none
BEGIN_DOC
! Unique alpha determinants
! Unique $alpha determinants
END_DOC
integer :: i,k
integer :: i,j,k
integer, allocatable :: iorder(:)
integer*8, allocatable :: bit_tmp(:)
integer*8 :: last_key
integer*8, external :: spin_det_search_key
logical,allocatable :: duplicate(:)
allocate ( iorder(N_det), bit_tmp(N_det))
allocate ( iorder(N_det), bit_tmp(N_det), duplicate(N_det) )
do i=1,N_det
iorder(i) = i
bit_tmp(i) = spin_det_search_key(psi_det_alpha(1,i),N_int)
bit_tmp(i) = spin_det_search_key(psi_det_$alpha(1,i),N_int)
enddo
call i8sort(bit_tmp,iorder,N_det)
N_det_alpha_unique = 0
N_det_$alpha_unique = 0
last_key = 0_8
do i=1,N_det
if (bit_tmp(i) /= last_key) then
last_key = bit_tmp(i)
N_det_alpha_unique += 1
N_det_$alpha_unique += 1
do k=1,N_int
psi_det_alpha_unique(k,N_det_alpha_unique) = psi_det_alpha(k,iorder(i))
psi_det_$alpha_unique(k,N_det_$alpha_unique) = psi_det_$alpha(k,iorder(i))
enddo
duplicate(i) = .False.
enddo
j=1
do i=1,N_det_$alpha_unique-1
if (duplicate(i)) then
cycle
endif
j = i+1
do while (bit_tmp(j)==bit_tmp(i))
if (duplicate(j)) then
j += 1
cycle
endif
duplicate(j) = .True.
do k=1,N_int
if (psi_det_$alpha_unique(k,i) /= psi_det_$alpha_unique(k,j)) then
duplicate(j) = .False.
exit
endif
enddo
deallocate (iorder, bit_tmp)
END_PROVIDER
BEGIN_PROVIDER [ integer(bit_kind), psi_det_beta_unique, (N_int,psi_det_size) ]
&BEGIN_PROVIDER [ integer, N_det_beta_unique ]
implicit none
BEGIN_DOC
! Unique beta determinants
END_DOC
integer :: i,k
integer, allocatable :: iorder(:)
integer*8, allocatable :: bit_tmp(:)
integer*8 :: last_key
integer*8, external :: spin_det_search_key
allocate ( iorder(N_det), bit_tmp(N_det))
do i=1,N_det
iorder(i) = i
bit_tmp(i) = spin_det_search_key(psi_det_beta(1,i),N_int)
enddo
call i8sort(bit_tmp,iorder,N_det)
N_det_beta_unique = 0
last_key = 0_8
do i=1,N_det
if (bit_tmp(i) /= last_key) then
last_key = bit_tmp(i)
N_det_beta_unique += 1
do k=1,N_int
psi_det_beta_unique(k,N_det_beta_unique) = psi_det_beta(k,iorder(i))
enddo
j+=1
if (j > N_det_$alpha_unique) then
exit
endif
enddo
enddo
deallocate (iorder, bit_tmp)
j=1
do i=2,N_det_$alpha_unique
if (duplicate(i)) then
cycle
else
j += 1
psi_det_$alpha_unique(:,j) = psi_det_$alpha_unique(:,i)
endif
enddo
N_det_$alpha_unique = j
deallocate (iorder, bit_tmp, duplicate)
END_PROVIDER
SUBST [ alpha ]
alpha ;;
beta ;;
END_TEMPLATE
@ -150,6 +158,7 @@ integer function get_index_in_psi_det_alpha_unique(key,Nint)
!DIR$ FORCEINLINE
det_ref = spin_det_search_key(key,Nint)
!DIR$ FORCEINLINE
det_search = spin_det_search_key(psi_det_alpha_unique(1,1),Nint)
@ -337,52 +346,52 @@ subroutine write_spindeterminants
call ezfio_set_spindeterminants_psi_coef_matrix_rows(psi_svd_matrix_rows)
call ezfio_set_spindeterminants_psi_coef_matrix_columns(psi_svd_matrix_columns)
integer :: n_svd_coefs
double precision :: norm, f
f = 1.d0/dble(N_states)
norm = 1.d0
do n_svd_coefs=1,N_det_alpha_unique
do k=1,N_states
norm -= psi_svd_coefs(n_svd_coefs,k)*psi_svd_coefs(n_svd_coefs,k)
enddo
if (norm < 1.d-4) then
exit
endif
enddo
n_svd_coefs -= 1
call ezfio_set_spindeterminants_n_svd_coefs(n_svd_coefs)
double precision, allocatable :: dtmp(:,:,:)
allocate(dtmp(N_det_alpha_unique,n_svd_coefs,N_states))
do k=1,N_states
do j=1,n_svd_coefs
do i=1,N_det_alpha_unique
dtmp(i,j,k) = psi_svd_alpha(i,j,k)
enddo
enddo
enddo
call ezfio_set_spindeterminants_psi_svd_alpha(dtmp)
deallocate(dtmp)
allocate(dtmp(N_det_beta_unique,n_svd_coefs,N_states))
do k=1,N_states
do j=1,n_svd_coefs
do i=1,N_det_beta_unique
dtmp(i,j,k) = psi_svd_beta(i,j,k)
enddo
enddo
enddo
call ezfio_set_spindeterminants_psi_svd_beta(dtmp)
deallocate(dtmp)
allocate(dtmp(n_svd_coefs,N_states,1))
do k=1,N_states
do j=1,n_svd_coefs
dtmp(j,k,1) = psi_svd_coefs(j,k)
enddo
enddo
call ezfio_set_spindeterminants_psi_svd_coefs(dtmp)
deallocate(dtmp)
! integer :: n_svd_coefs
! double precision :: norm, f
! f = 1.d0/dble(N_states)
! norm = 1.d0
! do n_svd_coefs=1,N_det_alpha_unique
! do k=1,N_states
! norm -= psi_svd_coefs(n_svd_coefs,k)*psi_svd_coefs(n_svd_coefs,k)
! enddo
! if (norm < 1.d-4) then
! exit
! endif
! enddo
! n_svd_coefs -= 1
! call ezfio_set_spindeterminants_n_svd_coefs(n_svd_coefs)
!
! double precision, allocatable :: dtmp(:,:,:)
! allocate(dtmp(N_det_alpha_unique,n_svd_coefs,N_states))
! do k=1,N_states
! do j=1,n_svd_coefs
! do i=1,N_det_alpha_unique
! dtmp(i,j,k) = psi_svd_alpha(i,j,k)
! enddo
! enddo
! enddo
! call ezfio_set_spindeterminants_psi_svd_alpha(dtmp)
! deallocate(dtmp)
!
! allocate(dtmp(N_det_beta_unique,n_svd_coefs,N_states))
! do k=1,N_states
! do j=1,n_svd_coefs
! do i=1,N_det_beta_unique
! dtmp(i,j,k) = psi_svd_beta(i,j,k)
! enddo
! enddo
! enddo
! call ezfio_set_spindeterminants_psi_svd_beta(dtmp)
! deallocate(dtmp)
!
! allocate(dtmp(n_svd_coefs,N_states,1))
! do k=1,N_states
! do j=1,n_svd_coefs
! dtmp(j,k,1) = psi_svd_coefs(j,k)
! enddo
! enddo
! call ezfio_set_spindeterminants_psi_svd_coefs(dtmp)
! deallocate(dtmp)
end
@ -439,6 +448,7 @@ BEGIN_PROVIDER [ double precision, psi_svd_matrix_values, (N_det,N_states) ]
do k=1,N_det
i = get_index_in_psi_det_alpha_unique(psi_det(1,1,k),N_int)
j = get_index_in_psi_det_beta_unique (psi_det(1,2,k),N_int)
do l=1,N_states
psi_svd_matrix_values(k,l) = psi_coef(k,l)
enddo

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