sisl.io.siesta.xvSileSiesta

class sisl.io.siesta.xvSileSiesta(filename, *args, **kwargs)

Bases: SileSiesta

Geometry file

Methods

close()
dir_file([filename, filename_base])	File of the current Sile
read(*args, **kwargs)	Generic read method which should be overloaded in child-classes
read_data()	Returns an array with the velocities from the XV file
read_geometry([velocity, species_Z])	Returns a Geometry object from the XV file
read_lattice()	Returns Lattice object from the XV file
read_velocity()	Returns an array with the velocities from the XV file
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes
write_geometry(geometry[, fmt, velocity])	Writes the geometry to the contained file
base_file	File of the current Sile
file	File of the current Sile

class InfoAttr(attr, regex, parser, doc='', updatable=False, default=None, found=False)

Bases: object

Holder for parsing lines and extracting information from text files

This consists of:

attr:

the name of the attribute This will be the sile.info. access point.

regex:

the regular expression used to match a line. If a str, it will be compiled as is to a regex pattern. regex.match(line) will be used to check if the value should be updated.

parser:

if regex.match(line) returns a match that is true, then this parser will be executed. The parser must be a function accepting two arguments:

def parser(attr, match)

where attr is this object, and match is the match done on the line. (Note that match.string will return the full line used to match against).

updatable:

control whether a new match on the line will update using parser. If false, only the first match will update the value

default:

the default value of the attribute

found:

whether the value has been found in the file.

__init__(attr, regex, parser, doc='', updatable=False, default=None, found=False)

attr

copy()

doc

documentation()

Returns a documentation string for this object

found

parser

process(line)

regex

updatable

value

__init__(filename, mode='r', *args, **kwargs)

Just to pass away the args and kwargs

property base_file

File of the current Sile

close()

dir_file(filename=None, filename_base='')

File of the current Sile

property file

File of the current Sile

plot

Handles all plotting possibilities for a class

read(*args, **kwargs)

Generic read method which should be overloaded in child-classes

Parameters

kwargs – keyword arguments will try and search for the attribute read_<> and call it with the remaining **kwargs as arguments.

read_data()

Returns an array with the velocities from the XV file

Return type

velocity

read_geometry(velocity=False, species_Z=False)

Returns a Geometry object from the XV file

Parameters

• species_Z (bool, optional) – if True the atomic numbers are the species indices (useful when reading the ChemicalSpeciesLabel block simultaneously).

• velocity (bool, optional) – also return the velocities in the file

Returns

• Geometry

• velocity (only if velocity is true.)

read_lattice()

Returns Lattice object from the XV file

read_velocity()

Returns an array with the velocities from the XV file

Return type

velocity

write(*args, **kwargs)

Generic write method which should be overloaded in child-classes

Parameters

**kwargs – keyword arguments will try and search for the attribute write_ and call it with the remaining **kwargs as arguments.

write_geometry(geometry, fmt='.9f', velocity=None)

Writes the geometry to the contained file

Parameters

• geometry (Geometry) – geometry to write in the XV file

• fmt (str, optional) – the precision used for writing the XV file

• velocity (numpy.ndarray, optional) – velocities to write in the XV file (will be zero if not specified). Units input must be in Ang/fs.