File IO Module#

class nexus.fileio.TextFile(filepath=None)[source]#

Bases: DevBase

Methods

`append`(value)
`class_error`(message[, header, exit, trace, ...])	Report an error relating to a class.
`close`()
`error`(message[, header, exit, trace])	Report an error inside a class.
`find`(a, *kw)
`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
flush
get
get_optional
get_path
get_required
inverse
items
last
lines
list_optional
load
log
move
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
open
path_exists
random_key
read
read_byte
readline
readtokens
readtokensf
resize
rfind
seek
select_random
serial
set
set_optional
set_path
shallow_copy
size
tell
to_dict
to_obj
tokens
transfer_from
transfer_to
tree
tuple
values
write
write_byte

open(filepath)[source]#

lines()[source]#

tokens()[source]#

readtokens(s=None)[source]#

readtokensf(s=None, *formats)[source]#

close()[source]#

seek(pos, whence=0, start=None, end=None)[source]#

readline(s=None)[source]#

read(num=None)[source]#

find(*a, **kw)[source]#

flush(*a, **kw)[source]#

move(dest, src, count)[source]#

read_byte()[source]#

resize(newsize)[source]#

rfind(*a, **kw)[source]#

size()[source]#

tell()[source]#

write(string)[source]#

write_byte(byte)[source]#

class nexus.fileio.StandardFile(filepath=None)[source]#

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
check_valid
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
is_valid
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
path_exists
random_key
read
read_text
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
validity_checks
values
write
write_text

sftype = ''#

read(filepath)[source]#

write(filepath=None)[source]#

is_valid()[source]#

check_valid(header=None)[source]#

validity_checks()[source]#

read_text(text)[source]#

write_text()[source]#

class nexus.fileio.XsfFile(filepath=None, order=None)[source]#

Bases: StandardFile

Methods

`append`(value)
`change_units`(in_unit, out_unit)
`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`()
`incorporate_structure`(structure)
`interpolate_plane`(r1, r2, r3[, density, ...])
`keys`()
`line_data`(dim[, density])
`list`(*keys)
`norm`([density, vnorm])
`open_log`(filepath)
`read_text`(text[, order])
`remove_ghost`([density])
`save`([fpath])
`sorted_keys`()
`warn`(msg[, indent])	Warning from inside a Nexus class.
`write_text`()

add
add_density
add_optional
add_to_image
check_required
check_types
check_types_optional
check_valid
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
dimension
extract
extract_optional
get
get_density
get_optional
get_path
get_required
has_animation
has_bands
has_data
has_structure
initialized
inverse
is_valid
items
last
line_plot
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
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
validity_checks
values
write
write_band
write_coord
write_data
write_vec

sftype = 'xsf'#

filetypes = {'axsf', 'bxsf', 'xsf'}#

periodicities = {'crystal', 'molecule', 'polymer', 'slab'}#

dimensions = crystal int molecule int polymer int slab int #

add_to_image(image, name, value)[source]#

read_text(text, order=None)[source]#

write_text()[source]#

write_coord(image=None, index='')[source]#

write_vec(name, vec, index='')[source]#

write_data()[source]#

write_band()[source]#

dimension()[source]#

initialized()[source]#

has_animation()[source]#

has_bands()[source]#

has_structure()[source]#

has_data()[source]#

validity_checks()[source]#

incorporate_structure(structure)[source]#

add_density(cell, density, name='density', corner=None, grid=None, centered=False, add_ghost=False)[source]#

get_density()[source]#

change_units(in_unit, out_unit)[source]#

remove_ghost(density=None)[source]#

norm(density=None, vnorm=True)[source]#

line_data(dim, density=None)[source]#

line_plot(dim, filepath)[source]#

interpolate_plane(r1, r2, r3, density=None, meshsize=50, fill_value=0)[source]#

class nexus.fileio.PoscarFile(filepath=None)[source]#

Bases: StandardFile

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
assign_defaults
check_required
check_types
check_types_optional
check_valid
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
incorporate_xsf
inverse
is_valid
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
path_exists
random_key
read
read_text
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
validity_checks
values
write
write_text

sftype = 'POSCAR'#

assign_defaults()[source]#

validity_checks()[source]#

read_text(text)[source]#

write_text()[source]#

incorporate_xsf(xsf)[source]#

class nexus.fileio.ChgcarFile(filepath=None)[source]#

Bases: StandardFile

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
check_valid
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
incorporate_xsf
inverse
is_valid
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
path_exists
random_key
read
read_text
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
validity_checks
values
write
write_text

sftype = 'CHGCAR'#

validity_checks()[source]#

read_text(text)[source]#

write_text()[source]#

incorporate_xsf(xsf)[source]#

nexus.fileio.read_poscar_chgcar(host, text)[source]#