Observables Module

class nexus.observables.VLog

Bases: DevBase

Methods

__call__(msg[, level, n, time, mem, width])	Call self as a function.
append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
check_required
check_types
check_types_optional
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
copy
copy_from
copy_to
data_repr
decrement
delete
delete_optional
delete_required
dict
extract
extract_optional
get
get_optional
get_path
get_required
increment
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
path_exists
random_key
select_random
serial
set
set_high
set_low
set_none
set_optional
set_path
set_verbosity
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

verbosity_levels = high                  int                    low                   int                    none                  int                 

increment(n=1)

decrement(n=1)

set_none()

set_low()

set_high()

set_verbosity(level)

nexus.observables.set_verbosity(level)

class nexus.observables.Missing

Bases: object

Methods

__call__(value)

Call self as a function.

class nexus.observables.AttributeProperties(**kwargs)

Bases: DevBase

Methods

append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
check_required
check_types
check_types_optional
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
copy
copy_from
copy_to
data_repr
delete
delete_optional
delete_required
dict
extract
extract_optional
get
get_optional
get_path
get_required
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
path_exists
random_key
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

class nexus.observables.DefinedAttributeBase(**values)

Bases: DevBase

Methods

append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
check_attributes
check_required
check_types
check_types_optional
check_unassigned
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
copy
copy_from
copy_to
data_repr
define_attributes
delete
delete_optional
delete_required
dict
extract
extract_optional
get
get_attribute
get_optional
get_path
get_required
has_attribute
initialize
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
obtain_attributes
path_exists
random_key
select_random
serial
set
set_attribute
set_attributes
set_default_attributes
set_optional
set_path
set_unassigned_default
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

classmethod set_unassigned_default(default)

classmethod define_attributes(*other_cls, **attribute_properties)

classmethod obtain_attributes(super_cls)

initialize(**values)

set_default_attributes()

set_attributes(**values)

check_attributes(exit=False)

check_unassigned(value)

set_attribute(name, value)

get_attribute(name, value=<nexus.observables.Missing object>, assigned=True)

has_attribute(name)

class nexus.observables.Observable(**values)

Bases: DefinedAttributeBase

Attributes:

unassigned_default

Methods

append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
check_attributes
check_required
check_types
check_types_optional
check_unassigned
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
copy
copy_from
copy_to
data_repr
define_attributes
delete
delete_optional
delete_required
dict
extract
extract_optional
get
get_attribute
get_optional
get_path
get_required
has_attribute
initialize
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
obtain_attributes
path_exists
random_key
select_random
serial
set
set_attribute
set_attributes
set_default_attributes
set_optional
set_path
set_unassigned_default
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

initialize(**values)

attribute_definitions = info                  AttributeProperties    initialized           AttributeProperties    structure             AttributeProperties 

deepcopy_attributes = {'structure'}

required_attributes = {}

sublevel_attributes = {'initialized', 'structure'}

toplevel_attributes = {'info'}

typed_attributes = {'info', 'initialized', 'structure'}

unassigned_default = None

class nexus.observables.ObservableWithComponents(**values)

Bases: Observable

Attributes:

component_names

default_component_name

unassigned_default

Methods

append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
check_attributes
check_required
check_types
check_types_optional
check_unassigned
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
component
components
copy
copy_from
copy_to
data_repr
default_component
define_attributes
delete
delete_optional
delete_required
dict
extract
extract_optional
get
get_attribute
get_optional
get_path
get_required
has_attribute
initialize
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
obtain_attributes
path_exists
process_component_name
random_key
select_random
serial
set
set_attribute
set_attributes
set_default_attributes
set_optional
set_path
set_unassigned_default
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

component_names = None

default_component_name = None

process_component_name(name)

default_component()

component(name)

components(names=None)

nexus.observables.read_eshdf_nofk_data(filename, Ef)

class nexus.observables.MomentumDistribution(**values)

Bases: ObservableWithComponents

Attributes:

unassigned_default

Methods

append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
backfold
check_attributes
check_required
check_types
check_types_optional
check_unassigned
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
component
components
copy
copy_from
copy_to
data_repr
default_component
define_attributes
delete
delete_optional
delete_required
dict
extract
extract_optional
filter_raw_data
get
get_attribute
get_optional
get_path
get_raw_data
get_required
has_attribute
initialize
inverse
items
last
list_optional
load
log
map_raw_data_onto_grid
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
obtain_attributes
path_exists
plot_directional_raw
plot_plane_contours
plot_radial_raw
process_component_name
random_key
select_random
serial
set
set_attribute
set_attributes
set_default_attributes
set_optional
set_path
set_unassigned_default
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

component_names = ('tot', 'pol', 'u', 'd')

default_component_name = 'tot'

get_raw_data()

filter_raw_data(filter_tol=1e-05, store=True)

map_raw_data_onto_grid(unfold=False, filter_tol=1e-05)

backfold()

plot_plane_contours(quantity=None, origin=None, a1=None, a2=None, a1_range=(0, 1), a2_range=(0, 1), grid_spacing=0.3, unit_in=False, unit_out=False, boundary=True)

plot_radial_raw(quants='all', kmax=None, fmt='b.', fig=True, show=True)

plot_directional_raw(kdir, quants='all', kmax=None, fmt='b.', fig=True, show=True, reflect=False)

attribute_definitions = d                     AttributeProperties    info                  AttributeProperties    initialized           AttributeProperties    kaxes                 AttributeProperties    pol                   AttributeProperties    raw                   AttributeProperties    raw_filter_tol        AttributeProperties    structure             AttributeProperties    tot                   AttributeProperties    u                     AttributeProperties 

deepcopy_attributes = {'structure'}

required_attributes = {}

sublevel_attributes = {'initialized', 'kaxes', 'raw_filter_tol', 'structure'}

toplevel_attributes = {'d', 'info', 'pol', 'raw', 'tot', 'u'}

typed_attributes = {'d', 'info', 'initialized', 'kaxes', 'pol', 'raw', 'raw_filter_tol', 'structure', 'tot', 'u'}

class nexus.observables.MomentumDistributionDFT(**values)

Bases: MomentumDistribution

Attributes:

unassigned_default

Methods

append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
backfold
check_attributes
check_required
check_types
check_types_optional
check_unassigned
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
component
components
copy
copy_from
copy_to
data_repr
default_component
define_attributes
delete
delete_optional
delete_required
dict
extract
extract_optional
filter_raw_data
get
get_attribute
get_optional
get_path
get_raw_data
get_required
has_attribute
initialize
inverse
items
last
list_optional
load
log
map_raw_data_onto_grid
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
obtain_attributes
path_exists
plot_directional_raw
plot_plane_contours
plot_radial_raw
process_component_name
random_key
read_eshdf
select_random
serial
set
set_attribute
set_attributes
set_default_attributes
set_optional
set_path
set_unassigned_default
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

read_eshdf(filepath, E_fermi=None, savefile=None, unfold=False, grid=True)

attribute_definitions = E_fermi               AttributeProperties    d                     AttributeProperties    info                  AttributeProperties    initialized           AttributeProperties    kaxes                 AttributeProperties    pol                   AttributeProperties    raw                   AttributeProperties    raw_filter_tol        AttributeProperties    structure             AttributeProperties    tot                   AttributeProperties    u                     AttributeProperties 

deepcopy_attributes = {'structure'}

required_attributes = {}

sublevel_attributes = {'E_fermi', 'initialized', 'kaxes', 'raw_filter_tol', 'structure'}

toplevel_attributes = {'d', 'info', 'pol', 'raw', 'tot', 'u'}

typed_attributes = {'E_fermi', 'd', 'info', 'initialized', 'kaxes', 'pol', 'raw', 'raw_filter_tol', 'structure', 'tot', 'u'}

class nexus.observables.MomentumDistributionQMC(**values)

Bases: MomentumDistribution

Attributes:

unassigned_default

Methods

append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
backfold
check_attributes
check_required
check_types
check_types_optional
check_unassigned
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
component
components
copy
copy_from
copy_to
data_repr
default_component
define_attributes
delete
delete_optional
delete_required
dict
extract
extract_optional
filter_raw_data
get
get_attribute
get_optional
get_path
get_raw_data
get_required
has_attribute
initialize
inverse
items
last
list_optional
load
log
map_raw_data_onto_grid
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
obtain_attributes
path_exists
plot_directional_raw
plot_plane_contours
plot_radial_raw
process_component_name
random_key
read_stat_h5
select_random
serial
set
set_attribute
set_attributes
set_default_attributes
set_optional
set_path
set_unassigned_default
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

read_stat_h5(*files, equil=0, savefile=None)

class nexus.observables.Density(**values)

Bases: ObservableWithComponents

Attributes:

unassigned_default

Methods

append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
change_density_units
change_distance_units
check_attributes
check_required
check_types
check_types_optional
check_unassigned
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
component
components
copy
copy_from
copy_to
cumulative_radial_density
data_repr
default_component
define_attributes
delete
delete_optional
delete_required
dict
extract
extract_optional
get
get_attribute
get_optional
get_path
get_required
has_attribute
initialize
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
norm
not_implemented
obj
obtain_attributes
path_exists
plot_radial_density
process_component_name
radial_density
random_key
read_xsf
save_radial_density
select_random
serial
set
set_attribute
set_attributes
set_default_attributes
set_optional
set_path
set_unassigned_default
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
volume_normalize
write

component_names = ('tot', 'pol', 'u', 'd')

default_component_name = 'tot'

read_xsf(filepath, component=None)

volume_normalize()

norm(component=None)

change_distance_units(units)

change_density_units(units)

radial_density(component=None, dr=0.01, ntheta=100, rmax=None, single=False, interp_kwargs=None, comps_return=False, species=None)

cumulative_radial_density(rdfs=None, comps_return=False, **kwargs)

plot_radial_density(component=None, show=True, cumulative=False, **kwargs)

save_radial_density(prefix, rdfs=None, **kwargs)

attribute_definitions = d                     AttributeProperties    density_units         AttributeProperties    distance_units        AttributeProperties    grid                  AttributeProperties    info                  AttributeProperties    initialized           AttributeProperties    pol                   AttributeProperties    raw                   AttributeProperties    structure             AttributeProperties    tot                   AttributeProperties    u                     AttributeProperties 

deepcopy_attributes = {'structure'}

required_attributes = {}

sublevel_attributes = {'density_units', 'distance_units', 'initialized', 'structure'}

toplevel_attributes = {'d', 'grid', 'info', 'pol', 'raw', 'tot', 'u'}

typed_attributes = {'d', 'density_units', 'distance_units', 'grid', 'info', 'initialized', 'pol', 'raw', 'structure', 'tot', 'u'}

class nexus.observables.ChargeDensity(**values)

Bases: Density

Attributes:

unassigned_default

Methods

append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
change_density_units
change_distance_units
check_attributes
check_required
check_types
check_types_optional
check_unassigned
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
component
components
copy
copy_from
copy_to
cumulative_radial_density
data_repr
default_component
define_attributes
delete
delete_optional
delete_required
dict
extract
extract_optional
get
get_attribute
get_optional
get_path
get_required
has_attribute
initialize
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
norm
not_implemented
obj
obtain_attributes
path_exists
plot_radial_density
process_component_name
radial_density
random_key
read_xsf
save_radial_density
select_random
serial
set
set_attribute
set_attributes
set_default_attributes
set_optional
set_path
set_unassigned_default
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
volume_normalize
write

class nexus.observables.EnergyDensity(**values)

Bases: Density

Attributes:

unassigned_default

Methods

append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
change_density_units
change_distance_units
check_attributes
check_required
check_types
check_types_optional
check_unassigned
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
component
components
copy
copy_from
copy_to
cumulative_radial_density
data_repr
default_component
define_attributes
delete
delete_optional
delete_required
dict
extract
extract_optional
get
get_attribute
get_optional
get_path
get_required
has_attribute
initialize
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
norm
not_implemented
obj
obtain_attributes
path_exists
plot_radial_density
process_component_name
radial_density
random_key
read_xsf
save_radial_density
select_random
serial
set
set_attribute
set_attributes
set_default_attributes
set_optional
set_path
set_unassigned_default
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
volume_normalize
write

class nexus.observables.StatFile(filepath=None, **read_kwargs)

Bases: DevBase

Methods

append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
check_required
check_types
check_types_optional
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
cls
condense_name
copy
copy_from
copy_to
data_repr
delete
delete_optional
delete_required
dict
extract
extract_optional
get
get_optional
get_path
get_required
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
observable_groups
path_exists
random_key
read
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

scalars = {'ElecElec', 'IonIon', 'KEcorr', 'Kinetic', 'LocalECP', 'LocalEnergy', 'LocalEnergy_sq', 'LocalPotential', 'MPC', 'NonLocalECP'}

observable_aliases = momentum_distribution  str                    nofk                  str                 

observable_classes = momentum_distribution  type                

observable_class_to_stat_group = MomentumDistributionQMC  str                 

read(filepath, observables='all')

condense_name(name)

alias = 'nofk'

cls

alias of MomentumDistributionQMC

name = 'momentum_distribution'

observable = 'momentum_distribution'

observable_groups(observable, single=False)