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Merge branch 'master' of github.com:scemama/quantum_package

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This commit is contained in:
Anthony Scemama 2015-05-04 19:24:25 +02:00
commit ac285a09d9
224 changed files with 7130 additions and 2183 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

30
data/ezfio_defaults/WILL_BE_DELETED.ezfio_default
View File

@ -1,19 +1,19 @@
bielec_integrals
read_ao_integrals False
read_mo_integrals False
write_ao_integrals False
write_mo_integrals False
read_ao_integrals false
read_mo_integrals false
write_ao_integrals false
write_mo_integrals false
threshold_ao 1.e-15
threshold_mo 1.e-15
direct False
direct false
cis_dressed
n_state_cis 10
n_core_cis 0
n_act_cis mo_basis_mo_tot_num
mp2_dressing False
standard_doubles True
en_2_2 False
mp2_dressing false
standard_doubles true
en_2_2 false
determinants
n_states 1
@ -21,27 +21,27 @@ determinants
n_det_max_jacobi 1000
threshold_generators 0.99
threshold_selectors 0.999
read_wf False
s2_eig False
only_single_double_dm False
read_wf false
s2_eig false
only_single_double_dm false
full_ci
n_det_max_fci 10000
n_det_max_fci_property 50000
pt2_max 1.e-4
do_pt2_end True
do_pt2_end true
var_pt2_ratio 0.75
cas_sd
n_det_max_cas_sd 100000
pt2_max 1.e-4
do_pt2_end True
do_pt2_end true
var_pt2_ratio 0.75
all_singles
n_det_max_fci 50000
pt2_max 1.e-8
do_pt2_end False
do_pt2_end false
hartree_fock
n_it_scf_max 200
@ -55,7 +55,7 @@ cisd_selected
cisd_sc2_selected
n_det_max_cisd_sc2 10000
pt2_max 1.e-4
do_pt2_end True
do_pt2_end true
properties
z_one_point 3.9

9
data/ezfio_defaults/determinants.ezfio_default
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@ -1,9 +0,0 @@
determinants
n_states 1
n_states_diag determinants_n_states
n_det_max_jacobi 1000
threshold_generators 0.99
threshold_selectors 0.999
read_wf false
s2_eig false
only_single_double_dm false

2
data/ezfio_defaults/properties.ezfio_default
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@ -1,2 +0,0 @@
properties
z_one_point 3.9

4
ocaml/.merlin Normal file
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@ -0,0 +1,4 @@
PKG core ZMQ cryptokit
B _build/

2
ocaml/Input.ml
View File

@ -4,7 +4,7 @@ open Core.Std;;
include Input_ao_basis;;
include Input_bitmasks;;
include Input_determinants;;
include Input_determinants_by_hand;;
include Input_electrons;;
include Input_mo_basis;;
include Input_nuclei;;

158
ocaml/Input_determinants.ml → ocaml/Input_determinants_by_hand.ml
View File

@ -2,20 +2,14 @@ open Qptypes;;
open Qputils;;
open Core.Std;;
module Determinants : sig
module Determinants_by_hand : sig
type t =
{ n_int : N_int_number.t;
bit_kind : Bit_kind.t;
mo_label : MO_label.t;
n_det : Det_number.t;
n_states : States_number.t;
n_states_diag : States_number.t;
n_det_max_jacobi : Strictly_positive_int.t;
threshold_generators : Threshold.t;
threshold_selectors : Threshold.t;
read_wf : bool;
expected_s2 : Positive_float.t;
s2_eig : bool;
psi_coef : Det_coef.t array;
psi_det : Determinant.t array;
} with sexp
@ -28,16 +22,10 @@ end = struct
type t =
{ n_int : N_int_number.t;
bit_kind : Bit_kind.t;
mo_label : MO_label.t;
n_det : Det_number.t;
n_states : States_number.t;
n_states_diag : States_number.t;
n_det_max_jacobi : Strictly_positive_int.t;
threshold_generators : Threshold.t;
threshold_selectors : Threshold.t;
read_wf : bool;
expected_s2 : Positive_float.t;
s2_eig : bool;
psi_coef : Det_coef.t array;
psi_det : Determinant.t array;
} with sexp
@ -77,22 +65,6 @@ end = struct
|> Ezfio.set_determinants_bit_kind
;;
let read_mo_label () =
if (not (Ezfio.has_determinants_mo_label ())) then
Ezfio.get_mo_basis_mo_label ()
|> Ezfio.set_determinants_mo_label
;
Ezfio.get_determinants_mo_label ()
|> MO_label.of_string
;;
let write_mo_label l =
MO_label.to_string l
|> Ezfio.set_determinants_mo_label
;;
let read_n_det () =
if not (Ezfio.has_determinants_n_det ()) then
Ezfio.set_determinants_n_det 1
@ -138,67 +110,6 @@ end = struct
Ezfio.set_determinants_n_states_diag (max n_states n)
;;
let read_n_det_max_jacobi () =
if not (Ezfio.has_determinants_n_det_max_jacobi ()) then
get_default "n_det_max_jacobi"
|> Int.of_string
|> Ezfio.set_determinants_n_det_max_jacobi
;
Ezfio.get_determinants_n_det_max_jacobi ()
|> Strictly_positive_int.of_int
;;
let write_n_det_max_jacobi n =
Strictly_positive_int.to_int n
|> Ezfio.set_determinants_n_det_max_jacobi
;;
let read_threshold_generators () =
if not (Ezfio.has_determinants_threshold_generators ()) then
get_default "threshold_generators"
|> Float.of_string
|> Ezfio.set_determinants_threshold_generators
;
Ezfio.get_determinants_threshold_generators ()
|> Threshold.of_float
;;
let write_threshold_generators t =
Threshold.to_float t
|> Ezfio.set_determinants_threshold_generators
;;
let read_threshold_selectors () =
if not (Ezfio.has_determinants_threshold_selectors ()) then
get_default "threshold_selectors"
|> Float.of_string
|> Ezfio.set_determinants_threshold_selectors
;
Ezfio.get_determinants_threshold_selectors ()
|> Threshold.of_float
;;
let write_threshold_selectors t =
Threshold.to_float t
|> Ezfio.set_determinants_threshold_selectors
;;
let read_read_wf () =
if not (Ezfio.has_determinants_read_wf ()) then
get_default "read_wf"
|> Bool.of_string
|> Ezfio.set_determinants_read_wf
;
Ezfio.get_determinants_read_wf ()
;;
let write_read_wf = Ezfio.set_determinants_read_wf ;;
let read_expected_s2 () =
if not (Ezfio.has_determinants_expected_s2 ()) then
begin
@ -219,19 +130,6 @@ end = struct
|> Ezfio.set_determinants_expected_s2
;;
let read_s2_eig () =
if not (Ezfio.has_determinants_s2_eig ()) then
get_default "s2_eig"
|> Bool.of_string
|> Ezfio.set_determinants_s2_eig
;
Ezfio.get_determinants_s2_eig ()
;;
let write_s2_eig = Ezfio.set_determinants_s2_eig ;;
let read_psi_coef () =
if not (Ezfio.has_determinants_psi_coef ()) then
begin
@ -315,16 +213,10 @@ end = struct
Some
{ n_int = read_n_int () ;
bit_kind = read_bit_kind () ;
mo_label = read_mo_label () ;
n_det = read_n_det () ;
n_states = read_n_states () ;
n_states_diag = read_n_states_diag () ;
n_det_max_jacobi = read_n_det_max_jacobi () ;
threshold_generators = read_threshold_generators () ;
threshold_selectors = read_threshold_selectors () ;
read_wf = read_read_wf () ;
expected_s2 = read_expected_s2 () ;
s2_eig = read_s2_eig () ;
psi_coef = read_psi_coef () ;
psi_det = read_psi_det () ;
}
@ -334,31 +226,19 @@ end = struct
let write { n_int ;
bit_kind ;
mo_label ;
n_det ;
n_states ;
n_states_diag ;
n_det_max_jacobi ;
threshold_generators ;
threshold_selectors ;
read_wf ;
expected_s2 ;
s2_eig ;
psi_coef ;
psi_det ;
} =
write_n_int n_int ;
write_bit_kind bit_kind;
write_mo_label mo_label;
write_n_det n_det;
write_n_states n_states;
write_n_states_diag ~n_states:n_states n_states_diag;
write_n_det_max_jacobi n_det_max_jacobi;
write_threshold_generators threshold_generators;
write_threshold_selectors threshold_selectors;
write_read_wf read_wf;
write_expected_s2 expected_s2;
write_s2_eig s2_eig;
write_psi_coef ~n_det:n_det psi_coef ~n_states:n_states;
write_psi_det ~n_int:n_int ~n_det:n_det psi_det;
;;
@ -399,35 +279,17 @@ end = struct
|> String.concat_array ~sep:"\n"
in
Printf.sprintf "
Read the current wave function ::
read_wf = %s
Label of the MOs on which the determinants were computed ::
mo_label = %s
Force the selected wave function to be an eigenfunction of S^2.
If true, input the expected value of S^2 ::
s2_eig = %s
expected_s2 = %s
Thresholds on generators and selectors (fraction of the norm) ::
threshold_generators = %s
threshold_selectors = %s
Number of requested states, and number of states used for the
Davidson diagonalization ::
n_states = %s
n_states_diag = %s
Maximum size of the Hamiltonian matrix that will be fully diagonalized ::
n_det_max_jacobi = %s
Number of determinants ::
n_det = %s
@ -436,15 +298,9 @@ Determinants ::
%s
"
(b.read_wf |> Bool.to_string)
(b.mo_label |> MO_label.to_string)
(b.s2_eig |> Bool.to_string)
(b.expected_s2 |> Positive_float.to_string)
(b.threshold_generators |> Threshold.to_string)
(b.threshold_selectors |> Threshold.to_string)
(b.n_states |> States_number.to_string)
(b.n_states_diag |> States_number.to_string)
(b.n_det_max_jacobi |> Strictly_positive_int.to_string)
(b.n_det |> Det_number.to_string)
det_text
|> Rst_string.of_string
@ -456,31 +312,19 @@ Determinants ::
Printf.sprintf "
n_int = %s
bit_kind = %s
mo_label = \"%s\"
n_det = %s
n_states = %s
n_states_diag = %s
n_det_max_jacobi = %s
threshold_generators = %s
threshold_selectors = %s
read_wf = %s
expected_s2 = %s
s2_eig = %s
psi_coef = %s
psi_det = %s
"
(b.n_int |> N_int_number.to_string)
(b.bit_kind |> Bit_kind.to_string)
(b.mo_label |> MO_label.to_string)
(b.n_det |> Det_number.to_string)
(b.n_states |> States_number.to_string)
(b.n_states_diag |> States_number.to_string)
(b.n_det_max_jacobi |> Strictly_positive_int.to_string)
(b.threshold_generators |> Threshold.to_string)
(b.threshold_selectors |> Threshold.to_string)
(b.read_wf |> Bool.to_string)
(b.expected_s2 |> Positive_float.to_string)
(b.s2_eig |> Bool.to_string)
(b.psi_coef |> Array.to_list |> List.map ~f:Det_coef.to_string
|> String.concat ~sep:", ")
(b.psi_det |> Array.to_list |> List.map ~f:(Determinant.to_string

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
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@ -5,18 +5,20 @@ open Core.Std;;
let spec =
let open Command.Spec in
empty
+> flag "o" (optional string)
+> flag "o" (optional string)
~doc:"file Name of the created EZFIO file."
+> flag "b" (required string)
~doc:"string Name of basis set."
+> flag "c" (optional_with_default 0 int)
~doc:"int Total charge of the molecule. Default is 0."
+> flag "m" (optional_with_default 1 int)
+> flag "m" (optional_with_default 1 int)
~doc:"int Spin multiplicity (2S+1) of the molecule. Default is 1."
+> flag "p" (optional_with_default 0 int)
~doc:"Using pseudo. Default is not (aka 0)"
+> 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 =
@ -60,8 +62,12 @@ let run ?o b c m xyz_file =
| None -> (* Principal basis *)
let basis = elem_and_basis_name in
let command =
if (p = 0) then
Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename
^ "\" \"" ^ basis ^"\""
else
Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename
^ "\" \"" ^ basis ^"\" pseudo"
in
begin
let filename =
@ -247,6 +253,9 @@ 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 = 1 then Qpackage.root ^ "scripts/pseudo/put_pseudo_in_ezfio.py" ezfio_file.to_string; *)
match Input.Ao_basis.read () with
| None -> failwith "Error in basis"
| Some x -> Input.Ao_basis.write x
@ -266,8 +275,8 @@ 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
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@ -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

@ -70,9 +70,9 @@ def is_bool(str_):
Take a string, if is a bool return the conversion into
fortran and ocaml.
"""
if "true" in str_.lower():
if "true" in str_.strip().lower():
return Type(None, "true", ".True.")
elif "false" in str_.lower():
elif "false" in str_.strip().lower():
return Type(None, "false", ".False")
else:
raise TypeError
@ -112,6 +112,8 @@ def get_type_dict():
# ~#~#~#~#~#~#~#~ #
fancy_type['integer'] = Type(None, "int", "integer")
fancy_type['integer*8'] = Type(None, "int", "integer*8")
fancy_type['int'] = Type(None, "int", "integer")
fancy_type['float'] = Type(None, "float", "double precision")
@ -121,7 +123,7 @@ def get_type_dict():
fancy_type['bool'] = Type(None, "bool", "logical")
fancy_type['character*(32)'] = Type(None, "string", "character*(32)")
fancy_type['character*(60)'] = Type(None, "string", "character*(60)")
fancy_type['character*(64)'] = Type(None, "string", "character*(68)")
fancy_type['character*(256)'] = Type(None, "string", "character*(256)")
# ~#~#~#~#~#~#~#~ #
@ -203,7 +205,7 @@ def get_dict_config_file(config_file_path, module_lower):
- ezfio_name : Will be the name of the file
- ezfio_dir : Will be the folder who containt the ezfio_name
* /ezfio_dir/ezfio_name
* equal to MODULE_lower name for the moment.
* equal to MODULE_lower name by default.
- interface : The provider is a imput or a output
- default : The default value /!\ stored in a Type named type!
if interface == output
@ -216,7 +218,7 @@ def get_dict_config_file(config_file_path, module_lower):
d = defaultdict(dict)
l_info_required = ["doc", "interface"]
l_info_optional = ["ezfio_name", "size"]
l_info_optional = ["ezfio_dir", "ezfio_name", "size"]
# ~#~#~#~#~#~#~#~#~#~#~ #
# L o a d _ C o n f i g #
@ -238,10 +240,8 @@ def get_dict_config_file(config_file_path, module_lower):
pvd = section.lower()
# Create the dictionary who containt the value per default
d_default = {"ezfio_name": pvd}
# Set the ezfio_dir
d[pvd]["ezfio_dir"] = module_lower
d_default = {"ezfio_name": pvd,
"ezfio_dir": module_lower}
# Check if type if avalaible
type_ = config_file.get(section, "type")
@ -269,7 +269,7 @@ def get_dict_config_file(config_file_path, module_lower):
d[pvd][option] = d_default[option]
# If interface is input we need a default value information
if d[pvd]["interface"] == "input":
if d[pvd]["interface"].lower() == "input":
try:
default_raw = config_file.get(section, "default")
except ConfigParser.NoOptionError:
@ -294,6 +294,7 @@ def create_ezfio_provider(dict_ezfio_cfg):
default
size}
create the a list who containt all the code for the provider
output = output_dict_info['ezfio_dir'
return [code, ...]
"""
from ezfio_generate_provider import EZFIO_Provider

8
scripts/ezfio_interface/ezfio_generate_ocaml.py
View File

@ -1,7 +1,13 @@
#!/usr/bin/env python
"""
This programme generate all the
ocaml template needed by qp_edit
You can see `ezfio_generate_provider.py`
for an example of utilisation
"""
import sys
import os
# If type in **kwargs
from ei_handler import Type

2
scripts/ezfio_interface/ezfio_generate_provider.py
View File

@ -45,7 +45,7 @@ END_PROVIDER
self.set_write()
for v in self.values:
if not v:
msg = "Error : %s is not set in ezfio_with_default.py" % (v)
msg = "Error : %s is not set in EZFIO.cfg" % (v)
print >>sys.stderr, msg
sys.exit(1)
return self.data % self.__dict__

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

36
scripts/ezfio_interface/qp_convert_ezfio_v1_to_v2.sh Executable file
View File

@ -0,0 +1,36 @@
#!/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
echo "Will tranform qp_v1.*_ezfio to qp_v2.*_ezfio"
echo "All action are irrevocable! And is by choice"
echo "You need to stop to use a old version! Plz..."
echo "Change thresh_SCF > thresh_scf0"
mv $1/hartree_Fock/thresh_SCF $1/hartree_fock/thresh_scf 2> /dev/null
# Set disk_acess
echo "Change {read,write}_ao_integrals > disk_access_ao_integrals"
biint=$1/bielec_integrals
if [[ -f $biint/read_ao_integrals ]]; then
if [[ `cat $1/bielec_integrals/read_ao_integrals` -eq "T" ]]
then
echo "Read" > $biint/disk_access_ao_integrals
elif [[ `cat $biint/write_ao_integrals` -eq "T" ]]
then
echo "Write" > $biint/disk_access_ao_integrals
else
echo "None" > $biint/disk_access_ao_integrals
fi
rm $biint/read_ao_integrals $biint/write_ao_integrals $biint/write_ao_intergals 2> /dev/null
fi
echo "Done"

302
scripts/ezfio_interface/qp_convert_output_to_ezfio.py Executable file
View File

@ -0,0 +1,302 @@
#!/usr/bin/env python
"""
This function acceep
Usage:
qp_convert_output_to_ezfio.py <file.out> [--ezfio=<folder.ezfio>]
Option:
file.out is the file to check (like gamess.out)
folder.ezfio is the name you whant for the ezfio
(by default is file.out.ezfio)
"""
import sys
import os
from functools import reduce
# ~#~#~#~#~#~#~#~ #
# Add to the path #
# ~#~#~#~#~#~#~#~ #
try:
QPACKAGE_ROOT = os.environ["QPACKAGE_ROOT"]
except:
print "Error: QPACKAGE_ROOT environment variable not found."
sys.exit(1)
else:
sys.path = [QPACKAGE_ROOT + "/EZFIO/Python",
QPACKAGE_ROOT + "/resultsFile",
QPACKAGE_ROOT + "/scripts"] + sys.path
# ~#~#~#~#~#~ #
# I m p o r t #
# ~#~#~#~#~#~ #
from ezfio import ezfio
try:
from resultsFile import *
except:
print "Error: resultsFile Python library not installed"
sys.exit(1)
from docopt import docopt
# _
# |_ ._ _ _|_ o _ ._
# | |_| | | (_ |_ | (_) | |
#
def write_ezfio(res, filename):
res.clean_uncontractions()
ezfio.set_file(filename)
# _
# |_ | _ _ _|_ ._ _ ._ _
# |_ | (/_ (_ |_ | (_) | | _>
#
ezfio.set_electrons_elec_alpha_num(res.num_alpha)
ezfio.set_electrons_elec_beta_num(res.num_beta)
#
# |\ | _ | _ o
# | \| |_| (_ | (/_ |
#
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
charge = []
coord_x = []
coord_y = []
coord_z = []
# ~#~#~#~#~#~#~ #
# P a r s i n g #
# ~#~#~#~#~#~#~ #
for a in res.geometry:
charge.append(a.charge)
if res.units == 'BOHR':
coord_x.append(a.coord[0])
coord_y.append(a.coord[1])
coord_z.append(a.coord[2])
else:
coord_x.append(a.coord[0] / a0)
coord_y.append(a.coord[1] / a0)
coord_z.append(a.coord[2] / a0)
# ~#~#~#~#~ #
# W r i t e #
# ~#~#~#~#~ #
ezfio.set_nuclei_nucl_num(len(res.geometry))
ezfio.set_nuclei_nucl_charge(charge)
# Transformt H1 into H
import re
p = re.compile(ur'(\d*)$')
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)
# _
# /\ _ _ |_) _. _ o _
# /--\ (_) _> |_) (_| _> | _>
#
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
import string
at = []
num_prim = []
power_x = []
power_y = []
power_z = []
coefficient = []
exponent = []
res.clean_contractions()
res.convert_to_cartesian()
# ~#~#~#~#~#~#~ #
# P a r s i n g #
# ~#~#~#~#~#~#~ #
for b in res.basis:
c = b.center
for i, atom in enumerate(res.geometry):
if atom.coord == c:
at.append(i + 1)
num_prim.append(len(b.prim))
s = b.sym
power_x.append(string.count(s, "x"))
power_y.append(string.count(s, "y"))
power_z.append(string.count(s, "z"))
coefficient.append(b.coef)
exponent.append([p.expo for p in b.prim])
# ~#~#~#~#~ #
# W r i t e #
# ~#~#~#~#~ #
ezfio.set_ao_basis_ao_num(len(res.basis))
ezfio.set_ao_basis_ao_nucl(at)
ezfio.set_ao_basis_ao_prim_num(num_prim)
ezfio.set_ao_basis_ao_power(power_x + power_y + power_z)
# ~#~#~#~#~#~#~ #
# P a r s i n g #
# ~#~#~#~#~#~#~ #
prim_num_max = ezfio.get_ao_basis_ao_prim_num_max()
for i in range(len(res.basis)):
coefficient[
i] += [0. for j in range(len(coefficient[i]), prim_num_max)]
exponent[i] += [0. for j in range(len(exponent[i]), prim_num_max)]
coefficient = reduce(lambda x, y: x + y, coefficient, [])
exponent = reduce(lambda x, y: x + y, exponent, [])
coef = []
expo = []
for i in range(prim_num_max):
for j in range(i, len(coefficient), prim_num_max):
coef.append(coefficient[j])
expo.append(exponent[j])
# ~#~#~#~#~ #
# W r i t e #
# ~#~#~#~#~ #
ezfio.set_ao_basis_ao_coef(coef)
ezfio.set_ao_basis_ao_expo(expo)
ezfio.set_ao_basis_ao_basis("Read by resultsFile")
# _
# |\/| _ _ |_) _. _ o _
# | | (_) _> |_) (_| _> | _>
#
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
MoTag = res.determinants_mo_type
ezfio.set_mo_basis_mo_label('Orthonormalized')
MO_type = MoTag
allMOs = res.mo_sets[MO_type]
# ~#~#~#~#~#~#~ #
# P a r s i n g #
# ~#~#~#~#~#~#~ #
try:
closed = [(allMOs[i].eigenvalue, i) for i in res.closed_mos]
active = [(allMOs[i].eigenvalue, i) for i in res.active_mos]
virtual = [(allMOs[i].eigenvalue, i) for i in res.virtual_mos]
except:
closed = []
virtual = []
active = [(allMOs[i].eigenvalue, i) for i in range(len(allMOs))]
closed = map(lambda x: x[1], closed)
active = map(lambda x: x[1], active)
virtual = map(lambda x: x[1], virtual)
MOindices = closed + active + virtual
MOs = []
for i in MOindices:
MOs.append(allMOs[i])
mo_tot_num = len(MOs)
while len(MOindices) < mo_tot_num:
MOindices.append(len(MOindices))
MOmap = list(MOindices)
for i in range(len(MOindices)):
MOmap[i] = MOindices.index(i)
energies = []
for i in xrange(mo_tot_num):
energies.append(MOs[i].eigenvalue)
if res.occ_num is not None:
OccNum = []
for i in MOindices:
OccNum.append(res.occ_num[MO_type][i])
while len(OccNum) < mo_tot_num:
OccNum.append(0.)
MoMatrix = []
sym0 = [i.sym for i in res.mo_sets[MO_type]]
sym = [i.sym for i in res.mo_sets[MO_type]]
for i in xrange(len(sym)):
sym[MOmap[i]] = sym0[i]
MoMatrix = []
for i in xrange(len(MOs)):
m = MOs[i]
for coef in m.vector:
MoMatrix.append(coef)
while len(MoMatrix) < len(MOs[0].vector) ** 2:
MoMatrix.append(0.)
# ~#~#~#~#~ #
# W r i t e #
# ~#~#~#~#~ #
ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
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)
file_path = os.path.expandvars(file_path)
file_path = os.path.abspath(file_path)
return file_path
if __name__ == '__main__':
arguments = docopt(__doc__)
file_ = get_full_path(arguments['<file.out>'])
if arguments["--ezfio"]:
ezfio_file = get_full_path(arguments["--ezfio"])
else:
ezfio_file = "{0}.ezfio".format(file_)
try:
res_file = getFile(file_)
except:
raise
else:
print file_, 'recognized as', str(res_file).split('.')[-1].split()[0]
write_ezfio(res_file, ezfio_file)

24
scripts/ezfio_interface/qp_edit_template
View File

@ -4,14 +4,16 @@ open Core.Std;;
(** Interactive editing of the input.
@author A. Scemama
WARNING
This file is autogenerad by
`${{QP_ROOT}}/script/ezfio_interface/ei_handler.py`
*)
(** Keywords used to define input sections *)
type keyword =
| Ao_basis
| Determinants
| Determinants_by_hand
| Electrons
| Mo_basis
| Nuclei
@ -20,11 +22,11 @@ type keyword =
let keyword_to_string = function
| Ao_basis -> "AO basis"
| Determinants -> "Determinants"
| Electrons -> "Electrons"
| Mo_basis -> "MO basis"
| Nuclei -> "Molecule"
| Ao_basis -> "AO basis"
| Determinants_by_hand -> "Determinants_by_hand"
| Electrons -> "Electrons"
| Mo_basis -> "MO basis"
| Nuclei -> "Molecule"
{keywords_to_string}
;;
@ -72,8 +74,8 @@ let get s =
f Nuclei.(read, to_rst)
| Ao_basis ->
f Ao_basis.(read, to_rst)
| Determinants ->
f Determinants.(read, to_rst)
| Determinants_by_hand ->
f Determinants_by_hand.(read, to_rst)
{section_to_rst}
end
with
@ -114,7 +116,7 @@ let set str s =
match s with
{write}
| Electrons -> write Electrons.(of_rst, write) s
| Determinants -> write Determinants.(of_rst, write) s
| Determinants_by_hand -> write Determinants_by_hand.(of_rst, write) s
| Nuclei -> write Nuclei.(of_rst, write) s
| Ao_basis -> () (* TODO *)
| Mo_basis -> () (* TODO *)
@ -162,7 +164,7 @@ let run check_only ezfio_filename =
Electrons ;
{tasks}
Mo_basis;
Determinants ;
Determinants_by_hand ;
]
in

27
scripts/ezfio_interface/upgrade_1.0_2.0.sh Executable file
View File

@ -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

18
scripts/ezfio_with_default.py
View File

@ -90,13 +90,19 @@ END_PROVIDER
self.default = t
def get_default(self):
filename = '/'.join( [os.environ['QPACKAGE_ROOT'], 'data',
'ezfio_defaults',
'WILL_BE_DELETED.ezfio_default'] )
mypath = '/'.join( [os.environ['QPACKAGE_ROOT'], 'data',
'ezfio_defaults'] )
from os import listdir
from os.path import isfile, join
onlyfiles = [ join(mypath,f) for f in listdir(mypath) if isfile(join(mypath,f)) ]
lines = []
for filename in onlyfiles:
file = open(filename,'r')
lines.extend(file.readlines())
file.close()
file = open(filename,'r')
lines = file.readlines()
file.close()
k=-1
# Search directory
for k,line in enumerate(lines):

12
scripts/generate_h_apply.py
View File

@ -1,7 +1,7 @@
#!/usr/bin/env python
import os
file = open(os.environ["QPACKAGE_ROOT"]+'/src/Dets/H_apply_template.f','r')
file = open(os.environ["QPACKAGE_ROOT"]+'/src/Determinants/H_apply_template.f','r')
template = file.read()
file.close()
@ -104,7 +104,7 @@ class H_apply(object):
endif
SOFT_TOUCH psi_det psi_coef N_det
"""
s["printout_now"] = """write(output_Dets,*) &
s["printout_now"] = """write(output_determinants,*) &
100.*float(i_generator)/float(N_det_generators), '% in ', wall_1-wall_0, 's'"""
self.data = s
@ -211,9 +211,9 @@ class H_apply(object):
delta_pt2(k) = 0.d0
pt2_old(k) = 0.d0
enddo
write(output_Dets,'(A12, X, A8, 3(2X, A9), 2X, A8, 2X, A8, 2X, A8)') &
write(output_determinants,'(A12, X, A8, 3(2X, A9), 2X, A8, 2X, A8, 2X, A8)') &
'N_generators', 'Norm', 'Delta PT2', 'PT2', 'Est. PT2', 'secs'
write(output_Dets,'(A12, X, A8, 3(2X, A9), 2X, A8, 2X, A8, 2X, A8)') &
write(output_determinants,'(A12, X, A8, 3(2X, A9), 2X, A8, 2X, A8, 2X, A8)') &
'============', '========', '=========', '=========', '=========', &
'========='
"""
@ -226,7 +226,7 @@ class H_apply(object):
"""
self.data["printout_now"] = """
do k=1,N_st
write(output_Dets,'(I10, 4(2X, F9.6), 2X, F8.1)') &
write(output_determinants,'(I10, 4(2X, F9.6), 2X, F8.1)') &
i_generator, norm_psi(k), delta_pt2(k), pt2(k), &
pt2(k)/(norm_psi(k)*norm_psi(k)), &
wall_1-wall_0
@ -258,7 +258,7 @@ class H_apply(object):
! SOFT_TOUCH psi_det psi_coef N_det
selection_criterion_min = min(selection_criterion_min, maxval(select_max))*0.1d0
selection_criterion = selection_criterion_min
call write_double(output_Dets,selection_criterion,'Selection criterion')
call write_double(output_determinants,selection_criterion,'Selection criterion')
"""
self.data["keys_work"] = """
e_2_pert_buffer = 0.d0

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
View File

@ -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

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

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 +13,9 @@ source ${QPACKAGE_ROOT}/scripts/qp_include.sh
function do_clean()
{
rm -rf -- \
IRPF90_temp IRPF90_man Makefile.depend $(cat NEEDED_MODULES) include \
ezfio_interface.irp.f irpf90.make irpf90_entities tags $(ls_exe)
IRPF90_temp IRPF90_man Makefile.depend \
$(module_handler.py print_genealogy) include \
ezfio_interface.irp.f irpf90.make irpf90_entities tags $(ls_exe) *.mod
}
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

202
scripts/module/module_handler.py Executable file
View File

@ -0,0 +1,202 @@
#!/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 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
@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_intergrals_klocmax = klocmax
ezfio.pseudo_intergrals_v_k = zip(*v_k)
ezfio.pseudo_intergrals_n_k = zip(*n_k)
ezfio.pseudo_intergrals_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_intergrals_lmaxpo = lmax
ezfio.pseudo_intergrals_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_intergrals_v_kl = zip(*v_kl)
ezfio.pseudo_intergrals_n_kl = zip(*n_kl)
ezfio.pseudo_intergrals_dz_kl = zip(*dz_kl)
ezfio.pseudo_intergrals_do_pseudo = True

210
scripts/qp_convert.py
View File

@ -1,210 +0,0 @@
#!/usr/bin/env python
import sys,os
try:
QPACKAGE_ROOT = os.environ["QPACKAGE_ROOT"]
except:
print "Error: QPACKAGE_ROOT environment variable not found."
sys.exit(1)
sys.path = [ QPACKAGE_ROOT+"/EZFIO/Python", QPACKAGE_ROOT+"/resultsFile" ]+sys.path
from ezfio import ezfio
import ezfio as ez
print "EZFIO: ", os.path.dirname(ez.__file__)
try:
from resultsFile import *
except:
print "Error: resultsFile Python library not installed"
sys.exit(1)
def write_ezfioFile(res,filename):
res.clean_uncontractions()
ezfio.set_file(filename)
# Electrons
ezfio.set_electrons_elec_alpha_num(res.num_alpha)
ezfio.set_electrons_elec_beta_num(res.num_beta)
# Nuclei
ezfio.set_nuclei_nucl_num(len(res.geometry))
charge = []
coord = []
coord_x = []
coord_y = []
coord_z = []
for a in res.geometry:
charge.append(a.charge)
if res.units == 'BOHR':
coord_x.append(a.coord[0])
coord_y.append(a.coord[1])
coord_z.append(a.coord[2])
else:
coord_x.append(a.coord[0]/a0)
coord_y.append(a.coord[1]/a0)
coord_z.append(a.coord[2]/a0)
ezfio.set_nuclei_nucl_charge(charge)
label = map(lambda x: x.name, res.geometry)
ezfio.set_nuclei_nucl_label(label)
ezfio.set_nuclei_nucl_coord(coord_x+coord_y+coord_z)
# Basis
basis = res.uncontracted_basis
geom = res.geometry
res.clean_contractions()
# AO Basis
import string
at = []
num_prim = []
magnetic_number = []
angular_number = []
power_x = []
power_y = []
power_z = []
coefficient = []
exponent = []
res.convert_to_cartesian()
for b in res.basis:
c = b.center
for i,atom in enumerate(res.geometry):
if atom.coord == c:
at.append(i+1)
num_prim.append(len(b.prim))
s = b.sym
power_x.append( string.count(s,"x") )
power_y.append( string.count(s,"y") )
power_z.append( string.count(s,"z") )
coefficient.append( b.coef )
exponent.append( [ p.expo for p in b.prim ] )
ezfio.set_ao_basis_ao_num(len(res.basis))
ezfio.set_ao_basis_ao_nucl(at)
ezfio.set_ao_basis_ao_prim_num(num_prim)
ezfio.set_ao_basis_ao_power(power_x+power_y+power_z)
prim_num_max = ezfio.get_ao_basis_ao_prim_num_max()
len_res_basis = len(res.basis)
for i in range(len(res.basis)):
coefficient[i] += [ 0. for j in range(len(coefficient[i]),prim_num_max) ]
exponent[i] += [ 0. for j in range(len(exponent[i]),prim_num_max) ]
coefficient = reduce(lambda x, y: x+y, coefficient, [])
exponent = reduce(lambda x, y: x+y, exponent, [])
coef = []
expo = []
for i in range(prim_num_max):
for j in range(i,len(coefficient),prim_num_max):
coef.append ( coefficient[j] )
expo.append ( exponent[j] )
ezfio.set_ao_basis_ao_coef(coef)
ezfio.set_ao_basis_ao_expo(expo)
ezfio.set_ao_basis_ao_basis("Read by resultsFile")
# MO
MoTag = res.determinants_mo_type
ezfio.set_mo_basis_mo_label('Orthonormalized')
MO_type = MoTag
allMOs = res.mo_sets[MO_type]
try:
closed = [ (allMOs[i].eigenvalue,i) for i in res.closed_mos ]
active = [ (allMOs[i].eigenvalue,i) for i in res.active_mos ]
virtual =[ (allMOs[i].eigenvalue,i) for i in res.virtual_mos ]
except:
closed = []
virtual = []
active = [ (allMOs[i].eigenvalue,i) for i in range(len(allMOs)) ]
# closed.sort()
# active.sort()
# virtual.sort()
closed = map( lambda x: x[1], closed)
active = map( lambda x: x[1], active)
virtual = map( lambda x: x[1], virtual)
MOindices = closed + active + virtual
MOs = []
for i in MOindices:
MOs.append(allMOs[i])
mo_tot_num = len(MOs)
while len(MOindices) < mo_tot_num:
MOindices.append(len(MOindices))
MOmap = list(MOindices)
for i in range(len(MOindices)):
MOmap[i] = MOindices.index(i)
energies = []
for i in xrange(mo_tot_num):
energies.append(MOs[i].eigenvalue)
if res.occ_num is not None:
OccNum = []
for i in MOindices:
OccNum.append(res.occ_num[MO_type][i])
while len(OccNum) < mo_tot_num:
OccNum.append(0.)
MoMatrix = []
sym0 = [ i.sym for i in res.mo_sets[MO_type] ]
sym = [ i.sym for i in res.mo_sets[MO_type] ]
for i in xrange(len(sym)):
sym[MOmap[i]] = sym0[i]
MoMatrix = []
for i in xrange(len(MOs)):
m = MOs[i]
for coef in m.vector:
MoMatrix.append(coef)
while len(MoMatrix) < len(MOs[0].vector)**2:
MoMatrix.append(0.)
mo = []
for i in MOindices:
mo.append(res.mo_sets[MoTag][i])
if len(mo) < mo_tot_num:
newmo = orbital()
newmo.eigenvalue = 0.
newmo.vector = [0. for i in range(mo_tot_num)]
newmo.vector[len(mo)] = 1.
while len(mo) < mo_tot_num:
mo.append(newmo)
Energies = [ m.eigenvalue for m in mo ]
ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
ezfio.set_mo_basis_mo_occ(OccNum)
ezfio.set_mo_basis_mo_coef(MoMatrix)
if __name__ == '__main__':
# Check command line
det_threshold = 0.
if len(sys.argv) == 2:
State=0
elif len(sys.argv) == 3:
State=int(sys.argv[2])
else:
print "usage: "+sys.argv[0]+" file.out [state]"
sys.exit(2)
firstArg = sys.argv[1]
file = getFile(firstArg)
print firstArg, 'recognized as', str(file).split('.')[-1].split()[0]
filename = firstArg+".ezfio"
write_ezfioFile(file,filename)

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

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

43
setup_environment.sh
View File

@ -17,8 +17,10 @@ export QPACKAGE_ROOT=\$( cd \$(dirname "\${BASH_SOURCE}") ; pwd -P )
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

93
src/AOs/README.rst
View File

@ -17,21 +17,19 @@ 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 +37,7 @@ 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 +65,41 @@ 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 +109,35 @@ 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

309
src/AOs/aos.irp.f
View File

@ -1,152 +1,171 @@
BEGIN_PROVIDER [ integer, ao_num ]
&BEGIN_PROVIDER [ integer, ao_num_align ]
implicit none
implicit none
BEGIN_DOC
! Number of atomic orbitals
END_DOC
BEGIN_DOC
! Number of atomic orbitals
END_DOC
ao_num = -1
PROVIDE ezfio_filename
call ezfio_get_ao_basis_ao_num(ao_num)
if (ao_num <= 0) then
stop 'Number of contracted gaussians should be > 0'
endif
integer :: align_double
ao_num_align = align_double(ao_num)
ao_num = -1
PROVIDE ezfio_filename
call ezfio_get_ao_basis_ao_num(ao_num)
if (ao_num <= 0) then
stop 'Number of contracted gaussians should be > 0'
endif
integer :: align_double
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) ]
implicit none
BEGIN_DOC
! Coefficients, exponents and powers of x,y and z
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
ibuffer = 0
call ezfio_get_ao_basis_ao_power(ibuffer)
ao_power = 0
do j = 1, 3
do i = 1, ao_num
ao_power(i,j) = ibuffer(i,j)
enddo
enddo
ao_expo = 0.d0
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(i,j) = buffer(i,j)
enddo
enddo
ao_coef = 0.d0
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(i,j) = buffer(i,j)
enddo
enddo
deallocate(buffer)
! Normalization of the AO coefficients
! ------------------------------------
double precision :: norm, norm2,overlap_x,overlap_y,overlap_z,C_A(3)
integer :: l, powA(3), nz
nz=100
C_A(1) = 0.d0
C_A(2) = 0.d0
C_A(3) = 0.d0
do i=1,ao_num
powA(1) = ao_power(i,1)
powA(2) = ao_power(i,2)
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)
enddo
enddo
! Sorting of the exponents for efficient integral calculations
integer :: iorder(ao_prim_num_max)
double precision :: d(ao_prim_num_max,2)
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)
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)
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) ]
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
BEGIN_PROVIDER [ integer, ao_power, (ao_num_align,3) ]
implicit none
BEGIN_DOC
! Powers of x,y and z read from input
END_DOC
PROVIDE ezfio_filename
integer :: i,j,k
integer, allocatable :: ibuffer(:,:)
allocate ( ibuffer(ao_num,3) )
ibuffer = 0
call ezfio_get_ao_basis_ao_power(ibuffer)
ao_power = 0
do j = 1, 3
do i = 1, ao_num
ao_power(i,j) = ibuffer(i,j)
enddo
enddo
deallocate(ibuffer)
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, (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)
do j = 1, ao_prim_num_max
do i = 1, ao_num
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)
do j = 1, ao_prim_num_max
do i = 1, ao_num
ao_coef(i,j) = buffer(i,j)
enddo
enddo
deallocate(buffer)
END_PROVIDER
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
C_A(3) = 0.d0
do i=1,ao_num
powA(1) = ao_power(i,1)
powA(2) = ao_power(i,2)
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_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
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_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_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_normalized_ordered_transp, (ao_prim_num_max_align,ao_num) ]
implicit none
BEGIN_DOC
! Transposed ao_coef_normalized_ordered
END_DOC
integer :: i,j
do j=1, ao_num
do i=1, ao_prim_num_max
ao_coef_normalized_ordered_transp(i,j) = ao_coef_normalized_ordered(j,i)
enddo
enddo
END_PROVIDER
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

9
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
=============

58
src/Bielec_integrals/ao_bi_integrals.irp.f
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@ -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))

1
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@ -0,0 +1 @@
MOs

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

6
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
=============

1
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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 Dets 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>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_

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 Dets 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>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
Documentation
=============

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CID_selected

2
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@ -1,2 +0,0 @@
AOs Bielec_integrals Bitmask CISD CISD_selected Dets 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>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
* `CID_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected>`_

1
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Perturbation CID

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

18
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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>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
* `CID <http://github.com/LCPQ/quantum_package/tree/master/src/CID>`_

1
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Selectors_full SingleRefMethod

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13
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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>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

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@ -1,2 +0,0 @@
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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>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
Documentation
=============

1
src/CISD_SC2_selected/NEEDED_CHILDREN_MODULES Normal file
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@ -0,0 +1 @@
CISD_selected

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

18
src/CISD_SC2_selected/README.rst
View File

@ -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>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_

1
src/CISD_selected/NEEDED_CHILDREN_MODULES Normal file
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@ -0,0 +1 @@
Perturbation CISD

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

18
src/CISD_selected/README.rst
View File

@ -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>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_

1
src/DDCI_selected/NEEDED_CHILDREN_MODULES Normal file
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@ -0,0 +1 @@
Perturbation Selectors_full Generators_CAS

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

16
src/DDCI_selected/README.rst
View File

@ -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>`_
* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_

0
src/Dets/ASSUMPTIONS.rst → src/Determinants/ASSUMPTIONS.rst
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103
src/Determinants/EZFIO.cfg Normal file
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@ -0,0 +1,103 @@
[N_states]
type: States_number
doc: Number of states to consider
interface: input
default: 1
[N_det_max_jacobi]
type: Strictly_positive_int
doc: Maximum number of determinants diagonalized by Jacobi
interface: input
default: 1000
[read_wf]
type: logical
doc: If true, read the wave function from the EZFIO file
interface: input
default: False
[only_single_double_dm]
type: logical
doc: If true, The One body DM is calculated with ignoring the Double<->Doubles extra diag elements
interface: input
default: False
[s2_eig]
type: logical
doc: Force the wave function to be an eigenfunction of S^2
interface: input
default: False
[threshold_generators]
type: Threshold
doc: Thresholds on generators (fraction of the norm)
interface: input
default: 0.99
[threshold_selectors]
type: Threshold
doc: Thresholds on selectors (fraction of the norm)
interface: input
default: 0.999
# Only create the ezfio_config, (no Input_* and no PROVIDER)
[n_states_diag]
type: integer
doc: n_states_diag
interface: Ocaml
[n_int]
interface: OCaml
doc: n_int
type: N_int_number
[bit_kind]
interface: OCaml
doc: bit_kind
type: Bit_kind
[mo_label]
interface: OCaml
doc: o_label
type: character*(64)
[n_det]
interface: OCaml
doc: n_det
type: integer
[psi_coef]
interface: OCaml
doc: psi_coef
type: double precision
size: (determinants_n_det,determinants_n_states)
[psi_det]
interface: OCaml
doc: psi_det
type: integer*8
size: (determinants_n_int*determinants_bit_kind/8,2,determinants_n_det)
[det_num]
interface: OCaml
doc: det_num
type: integer
[det_occ]
interface: OCaml
doc: det_occ
type: integer
size: (electrons_elec_alpha_num,determinants_det_num,2)
[det_coef]
interface: OCaml
doc: det_coef
type: double precision
size: (determinants_det_num)
[expected_s2]
interface: OCaml
doc: expcted_s2
type: double precision

35
src/Dets/H_apply.irp.f → src/Determinants/H_apply.irp.f
View File

@ -181,8 +181,43 @@ subroutine copy_H_apply_buffer_to_wf
call normalize(psi_coef,N_det)
SOFT_TOUCH N_det psi_det psi_coef
call debug_unicity_of_determinants
end
subroutine debug_unicity_of_determinants
implicit none
BEGIN_DOC
! This subroutine checks that there are no repetitions in the wave function
END_DOC
logical :: same, failed
integer :: i,k
print *, "======= DEBUG UNICITY ========="
failed = .False.
do i=2,N_det
same = .True.
do k=1,N_int
if ( psi_det_sorted_bit(k,1,i) /= psi_det_sorted_bit(k,1,i-1) ) then
same = .False.
exit
endif
if ( psi_det_sorted_bit(k,2,i) /= psi_det_sorted_bit(k,2,i-1) ) then
same = .False.
exit
endif
enddo
if (same) then
failed = .True.
call debug_det(psi_det_sorted_bit(1,1,i))
endif
enddo
if (failed) then
print *, '======= Determinants not unique : Failed ! ========='
stop
else
print *, '======= Determinants are unique : OK ! ========='
endif
end
subroutine fill_H_apply_buffer_no_selection(n_selected,det_buffer,Nint,iproc)
use bitmasks

0
src/Dets/H_apply_template.f → src/Determinants/H_apply_template.f
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0
src/Dets/Makefile → src/Determinants/Makefile
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1
src/Determinants/NEEDED_CHILDREN_MODULES Normal file
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@ -0,0 +1 @@
Bielec_integrals

324
src/Dets/README.rst → 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
=============
@ -49,26 +40,29 @@ Documentation
.. Do not edit this section. It was auto-generated from the
.. NEEDED_MODULES file.
`copy_h_apply_buffer_to_wf <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L100>`_
`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.
After calling this subroutine, N_det, psi_det and psi_coef need to be touched
`fill_h_apply_buffer_no_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L187>`_
`debug_unicity_of_determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L187>`_
This subroutine checks that there are no repetitions in the wave function
`fill_h_apply_buffer_no_selection <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L222>`_
Fill the H_apply buffer with determiants for CISD
`h_apply_buffer_allocated <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L15>`_
`h_apply_buffer_allocated <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/H_apply.irp.f#L15>`_
Buffer of determinants/coefficients/perturbative energy for H_apply.
Uninitialized. Filled by H_apply subroutines.
`h_apply_buffer_lock <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L16>`_
`h_apply_buffer_lock <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/H_apply.irp.f#L16>`_
Buffer of determinants/coefficients/perturbative energy for H_apply.
Uninitialized. Filled by H_apply subroutines.
`resize_h_apply_buffer <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/H_apply.irp.f#L48>`_
`resize_h_apply_buffer <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/H_apply.irp.f#L48>`_
Undocumented
`cisd_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/SC2.irp.f#L1>`_
`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)
.br
dets_in : bitmasks corresponding to determinants
@ -84,25 +78,25 @@ Documentation
.br
Initial guess vectors are not necessarily orthonormal
`connected_to_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L155>`_
`connected_to_ref <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/connected_to_ref.irp.f#L155>`_
Undocumented
`connected_to_ref_by_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L253>`_
`connected_to_ref_by_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/connected_to_ref.irp.f#L253>`_
Undocumented
`det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L1>`_
`det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/connected_to_ref.irp.f#L1>`_
Return an integer*8 corresponding to a determinant index for searching
`get_index_in_psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L48>`_
`get_index_in_psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/connected_to_ref.irp.f#L48>`_
Returns the index of the determinant in the ``psi_det_sorted_bit`` array
`is_in_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L34>`_
`is_in_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/connected_to_ref.irp.f#L34>`_
True if the determinant ``det`` is in the wave function
`occ_pattern_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/connected_to_ref.irp.f#L17>`_
`occ_pattern_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/connected_to_ref.irp.f#L17>`_
Return an integer*8 corresponding to a determinant index for searching
`do_mono_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/create_excitations.irp.f#L1>`_
`do_mono_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/create_excitations.irp.f#L1>`_
Apply the mono excitation operator : a^{dager}_(i_particle) a_(i_hole) of spin = ispin
on key_in
ispin = 1 == alpha
@ -110,13 +104,13 @@ Documentation
i_ok = 1 == the excitation is possible
i_ok = -1 == the excitation is not possible
`davidson_converged <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L382>`_
`davidson_converged <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/davidson.irp.f#L382>`_
True if the Davidson algorithm is converged
`davidson_criterion <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L372>`_
`davidson_criterion <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/davidson.irp.f#L372>`_
Can be : [ energy | residual | both | wall_time | cpu_time | iterations ]
`davidson_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L18>`_
`davidson_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/davidson.irp.f#L18>`_
Davidson diagonalization.
.br
dets_in : bitmasks corresponding to determinants
@ -134,7 +128,7 @@ Documentation
.br
Initial guess vectors are not necessarily orthonormal
`davidson_diag_hjj <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L68>`_
`davidson_diag_hjj <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/davidson.irp.f#L68>`_
Davidson diagonalization with specific diagonal elements of the H matrix
.br
H_jj : specific diagonal H matrix elements to diagonalize de Davidson
@ -154,49 +148,49 @@ Documentation
.br
Initial guess vectors are not necessarily orthonormal
`davidson_iter_max <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L1>`_
`davidson_iter_max <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/davidson.irp.f#L1>`_
Max number of Davidson iterations
`davidson_sze_max <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L9>`_
`davidson_sze_max <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/davidson.irp.f#L9>`_
Max number of Davidson sizes
`davidson_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/davidson.irp.f#L373>`_
`davidson_threshold <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/davidson.irp.f#L373>`_
Can be : [ energy | residual | both | wall_time | cpu_time | iterations ]
`one_body_dm_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L164>`_
`one_body_dm_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L164>`_
One-body density matrix
`one_body_dm_mo_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L1>`_
`one_body_dm_mo_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L1>`_
Alpha and beta one-body density matrix for each state
`one_body_dm_mo_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L2>`_
`one_body_dm_mo_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L2>`_
Alpha and beta one-body density matrix for each state
`one_body_single_double_dm_mo_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L80>`_
`one_body_single_double_dm_mo_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L80>`_
Alpha and beta one-body density matrix for each state
`one_body_single_double_dm_mo_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L81>`_
`one_body_single_double_dm_mo_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L81>`_
Alpha and beta one-body density matrix for each state
`one_body_spin_density_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L172>`_
`one_body_spin_density_mo <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L172>`_
rho(alpha) - rho(beta)
`save_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L196>`_
`save_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L196>`_
Save natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis
`set_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L180>`_
`set_natural_mos <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L180>`_
Set natural orbitals, obtained by diagonalization of the one-body density matrix in the MO basis
`state_average_weight <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/density_matrix.irp.f#L207>`_
`state_average_weight <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/density_matrix.irp.f#L207>`_
Weights in the state-average calculation of the density matrix
`det_svd <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/det_svd.irp.f#L1>`_
`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/Dets/determinants.irp.f#L426>`_
`filter_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L426>`_
Returns a determinant with only the 3 highest electrons
`int_of_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L391>`_
`int_of_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L391>`_
Returns an integer*8 as :
.br
|_<--- 21 bits ---><--- 21 bits ---><--- 21 bits --->|
@ -207,158 +201,158 @@ Documentation
in descending order
.br
`max_degree_exc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L32>`_
`max_degree_exc <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L32>`_
Maximum degree of excitation in the wf
`n_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L3>`_
`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/Dets/determinants.irp.f#L276>`_
`psi_average_norm_contrib <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L276>`_
Contribution of determinants to the state-averaged density
`psi_average_norm_contrib_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L306>`_
`psi_average_norm_contrib_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L306>`_
Wave function sorted by determinants contribution to the norm (state-averaged)
`psi_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L230>`_
`psi_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L230>`_
The wave function coefficients. Initialized with Hartree-Fock if the EZFIO file
is empty
`psi_coef_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L305>`_
`psi_coef_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L305>`_
Wave function sorted by determinants contribution to the norm (state-averaged)
`psi_coef_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L453>`_
`psi_coef_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L453>`_
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/Dets/determinants.irp.f#L336>`_
`psi_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L336>`_
Determinants on which we apply <i|H|psi> for perturbation.
They are sorted by determinants interpreted as integers. Useful
to accelerate the search of a random determinant in the wave
function.
`psi_det <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L65>`_
`psi_det <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L65>`_
The wave function determinants. Initialized with Hartree-Fock if the EZFIO file
is empty
`psi_det_size <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L47>`_
`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/Dets/determinants.irp.f#L304>`_
`psi_det_sorted <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L304>`_
Wave function sorted by determinants contribution to the norm (state-averaged)
`psi_det_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L452>`_
`psi_det_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L452>`_
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/Dets/determinants.irp.f#L335>`_
`psi_det_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L335>`_
Determinants on which we apply <i|H|psi> for perturbation.
They are sorted by determinants interpreted as integers. Useful
to accelerate the search of a random determinant in the wave
function.
`psi_det_sorted_next_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L454>`_
`psi_det_sorted_next_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L454>`_
Determinants on which we apply <i|H|j>.
They are sorted by the 3 highest electrons in the alpha part,
then by the 3 highest electrons in the beta part to accelerate
the research of connected determinants.
`read_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L583>`_
`read_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L583>`_
Reads the determinants from the EZFIO file
`save_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L630>`_
`save_wavefunction <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L630>`_
Save the wave function into the EZFIO file
`save_wavefunction_general <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L649>`_
`save_wavefunction_general <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L649>`_
Save the wave function into the EZFIO file
`save_wavefunction_unsorted <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L640>`_
`save_wavefunction_unsorted <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L640>`_
Save the wave function into the EZFIO file
`sort_dets_by_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L474>`_
`sort_dets_by_3_highest_electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L474>`_
Determinants on which we apply <i|H|j>.
They are sorted by the 3 highest electrons in the alpha part,
then by the 3 highest electrons in the beta part to accelerate
the research of connected determinants.
`sort_dets_by_det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants.irp.f#L349>`_
`sort_dets_by_det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants.irp.f#L349>`_
Determinants are sorted are sorted according to their det_search_key.
Useful to accelerate the search of a random determinant in the wave
function.
`double_exc_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants_bitmasks.irp.f#L40>`_
`double_exc_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants_bitmasks.irp.f#L40>`_
double_exc_bitmask(:,1,i) is the bitmask for holes of excitation 1
double_exc_bitmask(:,2,i) is the bitmask for particles of excitation 1
double_exc_bitmask(:,3,i) is the bitmask for holes of excitation 2
double_exc_bitmask(:,4,i) is the bitmask for particles of excitation 2
for a given couple of hole/particle excitations i.
`n_double_exc_bitmasks <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants_bitmasks.irp.f#L31>`_
`n_double_exc_bitmasks <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants_bitmasks.irp.f#L31>`_
Number of double excitation bitmasks
`n_single_exc_bitmasks <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants_bitmasks.irp.f#L8>`_
`n_single_exc_bitmasks <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants_bitmasks.irp.f#L8>`_
Number of single excitation bitmasks
`single_exc_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/determinants_bitmasks.irp.f#L17>`_
`single_exc_bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/determinants_bitmasks.irp.f#L17>`_
single_exc_bitmask(:,1,i) is the bitmask for holes
single_exc_bitmask(:,2,i) is the bitmask for particles
for a given couple of hole/particle excitations i.
`ci_eigenvectors <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L37>`_
`ci_eigenvectors <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI.irp.f#L37>`_
Eigenvectors/values of the CI matrix
`ci_eigenvectors_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L38>`_
`ci_eigenvectors_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI.irp.f#L38>`_
Eigenvectors/values of the CI matrix
`ci_electronic_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L36>`_
`ci_electronic_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI.irp.f#L36>`_
Eigenvectors/values of the CI matrix
`ci_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L18>`_
`ci_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI.irp.f#L18>`_
N_states lowest eigenvalues of the CI matrix
`diag_algorithm <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI.irp.f#L1>`_
`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/Dets/diagonalize_CI.irp.f#L96>`_
`diagonalize_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI.irp.f#L96>`_
Replace the coefficients of the CI states by the coefficients of the
eigenstates of the CI matrix
`ci_sc2_eigenvectors <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L27>`_
`ci_sc2_eigenvectors <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_SC2.irp.f#L27>`_
Eigenvectors/values of the CI matrix
`ci_sc2_electronic_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L26>`_
`ci_sc2_electronic_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_SC2.irp.f#L26>`_
Eigenvectors/values of the CI matrix
`ci_sc2_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L1>`_
`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/Dets/diagonalize_CI_SC2.irp.f#L46>`_
`diagonalize_ci_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_SC2.irp.f#L46>`_
Replace the coefficients of the CI states_diag by the coefficients of the
eigenstates of the CI matrix
`threshold_convergence_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_SC2.irp.f#L18>`_
`threshold_convergence_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_SC2.irp.f#L18>`_
convergence of the correlation energy of SC2 iterations
`ci_eigenvectors_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L2>`_
`ci_eigenvectors_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_mono.irp.f#L2>`_
Eigenvectors/values of the CI matrix
`ci_eigenvectors_s2_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L3>`_
`ci_eigenvectors_s2_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_mono.irp.f#L3>`_
Eigenvectors/values of the CI matrix
`ci_electronic_energy_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/diagonalize_CI_mono.irp.f#L1>`_
`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/Dets/diagonalize_CI_mono.irp.f#L59>`_
`diagonalize_ci_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/diagonalize_CI_mono.irp.f#L59>`_
Replace the coefficients of the CI states by the coefficients of the
eigenstates of the CI matrix
`apply_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/excitations_utils.irp.f#L1>`_
`apply_mono <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/excitations_utils.irp.f#L1>`_
Undocumented
`filter_connected <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L2>`_
`filter_connected <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/filter_connected.irp.f#L2>`_
Filters out the determinants that are not connected by H
.br
returns the array idx which contains the index of the
@ -369,7 +363,7 @@ Documentation
.br
idx(0) is the number of determinants that interact with key1
`filter_connected_davidson <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L163>`_
`filter_connected_davidson <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/filter_connected.irp.f#L163>`_
Filters out the determinants that are not connected by H
returns the array idx which contains the index of the
determinants in the array key1 that interact
@ -378,7 +372,7 @@ Documentation
idx(0) is the number of determinants that interact with key1
key1 should come from psi_det_sorted_ab.
`filter_connected_i_h_psi0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L293>`_
`filter_connected_i_h_psi0 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/filter_connected.irp.f#L293>`_
returns the array idx which contains the index of the
.br
determinants in the array key1 that interact
@ -387,7 +381,7 @@ Documentation
.br
idx(0) is the number of determinants that interact with key1
`filter_connected_i_h_psi0_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L392>`_
`filter_connected_i_h_psi0_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/filter_connected.irp.f#L392>`_
standard filter_connected_i_H_psi but returns in addition
.br
the array of the index of the non connected determinants to key1
@ -398,7 +392,7 @@ Documentation
.br
to repeat the excitations
`filter_connected_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/filter_connected.irp.f#L101>`_
`filter_connected_sorted_ab <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/filter_connected.irp.f#L101>`_
Filters out the determinants that are not connected by H
returns the array idx which contains the index of the
determinants in the array key1 that interact
@ -407,197 +401,197 @@ Documentation
.br
Determinants are taken from the psi_det_sorted_ab array
`put_gess <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/guess_triplet.irp.f#L1>`_
`put_gess <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/guess_triplet.irp.f#L1>`_
Undocumented
`det_to_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L2>`_
`det_to_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/occ_pattern.irp.f#L2>`_
Transform a determinant to an occupation pattern
`make_s2_eigenfunction <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L251>`_
`make_s2_eigenfunction <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/occ_pattern.irp.f#L251>`_
Undocumented
`n_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L143>`_
`n_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/occ_pattern.irp.f#L143>`_
array of the occ_pattern present in the wf
psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation
psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation
`occ_pattern_to_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L42>`_
`occ_pattern_to_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/occ_pattern.irp.f#L42>`_
Generate all possible determinants for a give occ_pattern
`occ_pattern_to_dets_size <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L20>`_
`occ_pattern_to_dets_size <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/occ_pattern.irp.f#L20>`_
Number of possible determinants for a given occ_pattern
`psi_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L142>`_
`psi_occ_pattern <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/occ_pattern.irp.f#L142>`_
array of the occ_pattern present in the wf
psi_occ_pattern(:,1,j) = jth occ_pattern of the wave function : represent all the single occupation
psi_occ_pattern(:,2,j) = jth occ_pattern of the wave function : represent all the double occupation
`rec_occ_pattern_to_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/occ_pattern.irp.f#L102>`_
`rec_occ_pattern_to_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/occ_pattern.irp.f#L102>`_
Undocumented
`n_states_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/options.irp.f#L40>`_
`n_states_diag <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/options.irp.f#L1>`_
Number of states to consider for the diagonalization
`pouet <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/program_beginer_determinants.irp.f#L1>`_
`pouet <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/program_beginer_determinants.irp.f#L1>`_
Undocumented
`routine <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/program_beginer_determinants.irp.f#L7>`_
`routine <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/program_beginer_determinants.irp.f#L7>`_
Undocumented
`idx_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L5>`_
`idx_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L5>`_
CAS wave function, defined from the application of the CAS bitmask on the
determinants. idx_cas gives the indice of the CAS determinant in psi_det.
`idx_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L62>`_
`idx_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L62>`_
Set of determinants which are not part of the CAS, defined from the application
of the CAS bitmask on the determinants.
idx_non_cas gives the indice of the determinant in psi_det.
`n_det_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L6>`_
`n_det_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L6>`_
CAS wave function, defined from the application of the CAS bitmask on the
determinants. idx_cas gives the indice of the CAS determinant in psi_det.
`n_det_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L63>`_
`n_det_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L63>`_
Set of determinants which are not part of the CAS, defined from the application
of the CAS bitmask on the determinants.
idx_non_cas gives the indice of the determinant in psi_det.
`psi_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L3>`_
`psi_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L3>`_
CAS wave function, defined from the application of the CAS bitmask on the
determinants. idx_cas gives the indice of the CAS determinant in psi_det.
`psi_cas_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L4>`_
`psi_cas_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L4>`_
CAS wave function, defined from the application of the CAS bitmask on the
determinants. idx_cas gives the indice of the CAS determinant in psi_det.
`psi_cas_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L47>`_
`psi_cas_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L47>`_
CAS determinants sorted to accelerate the search of a random determinant in the wave
function.
`psi_cas_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L46>`_
`psi_cas_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L46>`_
CAS determinants sorted to accelerate the search of a random determinant in the wave
function.
`psi_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L60>`_
`psi_non_cas <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L60>`_
Set of determinants which are not part of the CAS, defined from the application
of the CAS bitmask on the determinants.
idx_non_cas gives the indice of the determinant in psi_det.
`psi_non_cas_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L61>`_
`psi_non_cas_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L61>`_
Set of determinants which are not part of the CAS, defined from the application
of the CAS bitmask on the determinants.
idx_non_cas gives the indice of the determinant in psi_det.
`psi_non_cas_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L100>`_
`psi_non_cas_coef_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L100>`_
CAS determinants sorted to accelerate the search of a random determinant in the wave
function.
`psi_non_cas_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/psi_cas.irp.f#L99>`_
`psi_non_cas_sorted_bit <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/psi_cas.irp.f#L99>`_
CAS determinants sorted to accelerate the search of a random determinant in the wave
function.
`bi_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L5>`_
`bi_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ref_bitmask.irp.f#L5>`_
Energy of the reference bitmask used in Slater rules
`kinetic_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L3>`_
`kinetic_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ref_bitmask.irp.f#L3>`_
Energy of the reference bitmask used in Slater rules
`mono_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L2>`_
`mono_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ref_bitmask.irp.f#L2>`_
Energy of the reference bitmask used in Slater rules
`nucl_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L4>`_
`nucl_elec_ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ref_bitmask.irp.f#L4>`_
Energy of the reference bitmask used in Slater rules
`ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/ref_bitmask.irp.f#L1>`_
`ref_bitmask_energy <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/ref_bitmask.irp.f#L1>`_
Energy of the reference bitmask used in Slater rules
`expected_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L48>`_
`expected_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/s2.irp.f#L48>`_
Expected value of S2 : S*(S+1)
`get_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L1>`_
`get_s2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/s2.irp.f#L1>`_
Returns <S^2>
`get_s2_u0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L82>`_
`get_s2_u0 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/s2.irp.f#L82>`_
Undocumented
`s2_values <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L67>`_
`s2_values <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/s2.irp.f#L67>`_
array of the averaged values of the S^2 operator on the various states
`s_z <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L36>`_
`s_z <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/s2.irp.f#L36>`_
z component of the Spin
`s_z2_sz <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/s2.irp.f#L37>`_
`s_z2_sz <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/s2.irp.f#L37>`_
z component of the Spin
`prog_save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_casino.irp.f#L266>`_
`prog_save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_for_casino.irp.f#L266>`_
Undocumented
`save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_casino.irp.f#L1>`_
`save_casino <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_for_casino.irp.f#L1>`_
Undocumented
`save_dets_qmcchem <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_for_qmcchem.irp.f#L1>`_
`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/Dets/save_for_qmcchem.irp.f#L48>`_
`save_for_qmc <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_for_qmcchem.irp.f#L48>`_
Undocumented
`save_natorb <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/save_natorb.irp.f#L1>`_
`save_natorb <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/save_natorb.irp.f#L1>`_
Undocumented
`a_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L962>`_
`a_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L962>`_
Needed for diag_H_mat_elem
`ac_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1007>`_
`ac_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L1007>`_
Needed for diag_H_mat_elem
`decode_exc <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L76>`_
`decode_exc <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L76>`_
Decodes the exc arrays returned by get_excitation.
h1,h2 : Holes
p1,p2 : Particles
s1,s2 : Spins (1:alpha, 2:beta)
degree : Degree of excitation
`det_connections <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1139>`_
`det_connections <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L1139>`_
Build connection proxy between determinants
`diag_h_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L900>`_
`diag_h_mat_elem <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L900>`_
Computes <i|H|i>
`get_double_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L141>`_
`get_double_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L141>`_
Returns the two excitation operators between two doubly excited determinants and the phase
`get_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L30>`_
`get_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L30>`_
Returns the excitation operators between two determinants and the phase
`get_excitation_degree <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1>`_
`get_excitation_degree <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L1>`_
Returns the excitation degree between two determinants
`get_excitation_degree_vector <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L816>`_
`get_excitation_degree_vector <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L816>`_
Applies get_excitation_degree to an array of determinants
`get_mono_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L274>`_
`get_mono_excitation <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L274>`_
Returns the excitation operator between two singly excited determinants and the phase
`get_occ_from_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1055>`_
`get_occ_from_key <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L1055>`_
Returns a list of occupation numbers from a bitstring
`h_u_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1071>`_
`h_u_0 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L1071>`_
Computes v_0 = H|u_0>
.br
n : number of determinants
.br
H_jj : array of <j|H|j>
`i_h_j <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L355>`_
`i_h_j <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L355>`_
Returns <i|H|j> where i and j are determinants
`i_h_j_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L492>`_
`i_h_j_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L492>`_
Returns <i|H|j> where i and j are determinants
`i_h_psi <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L631>`_
`i_h_psi <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L631>`_
<key|H|psi> for the various Nstates
`i_h_psi_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L713>`_
`i_h_psi_sc2 <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L713>`_
<key|H|psi> for the various Nstate
.br
returns in addition
@ -610,7 +604,7 @@ Documentation
.br
to repeat the excitations
`i_h_psi_sc2_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L760>`_
`i_h_psi_sc2_verbose <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L760>`_
<key|H|psi> for the various Nstate
.br
returns in addition
@ -623,73 +617,73 @@ Documentation
.br
to repeat the excitations
`i_h_psi_sec_ord <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L666>`_
`i_h_psi_sec_ord <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L666>`_
<key|H|psi> for the various Nstates
`n_con_int <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/slater_rules.irp.f#L1131>`_
`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/Dets/spindeterminants.irp.f#L473>`_
`create_wf_of_psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L473>`_
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/Dets/spindeterminants.irp.f#L528>`_
`generate_all_alpha_beta_det_products <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L528>`_
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/Dets/spindeterminants.irp.f#L131>`_
`get_index_in_psi_det_alpha_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L131>`_
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/Dets/spindeterminants.irp.f#L212>`_
`get_index_in_psi_det_beta_unique <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L212>`_
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/Dets/spindeterminants.irp.f#L54>`_
`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/Dets/spindeterminants.irp.f#L91>`_
`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/Dets/spindeterminants.irp.f#L25>`_
`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/Dets/spindeterminants.irp.f#L53>`_
`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/Dets/spindeterminants.irp.f#L39>`_
`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/Dets/spindeterminants.irp.f#L90>`_
`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/Dets/spindeterminants.irp.f#L568>`_
`psi_svd_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L568>`_
SVD wave function
`psi_svd_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L569>`_
`psi_svd_beta <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L569>`_
SVD wave function
`psi_svd_coefs <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L570>`_
`psi_svd_coefs <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L570>`_
SVD wave function
`psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L457>`_
`psi_svd_matrix <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L457>`_
Matrix of wf coefficients. Outer product of alpha and beta determinants
`psi_svd_matrix_columns <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L398>`_
`psi_svd_matrix_columns <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L398>`_
Matrix of wf coefficients. Outer product of alpha and beta determinants
`psi_svd_matrix_rows <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L397>`_
`psi_svd_matrix_rows <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L397>`_
Matrix of wf coefficients. Outer product of alpha and beta determinants
`psi_svd_matrix_values <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L396>`_
`psi_svd_matrix_values <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L396>`_
Matrix of wf coefficients. Outer product of alpha and beta determinants
`spin_det_search_key <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/spindeterminants.irp.f#L9>`_
`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/Dets/spindeterminants.irp.f#L294>`_
`write_spindeterminants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/spindeterminants.irp.f#L294>`_
Undocumented
`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/truncate_wf.irp.f#L1>`_
`cisd <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/truncate_wf.irp.f#L1>`_
Undocumented
`h_matrix_all_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets/utils.irp.f#L1>`_
`h_matrix_all_dets <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/utils.irp.f#L1>`_
H matrix on the basis of the slater determinants defined by psi_det

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