sisl.io.siesta.xvSileSiesta

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

Bases: SileSiesta

Geometry file

Methods

base_directory([relative_to])

Retrieve the base directory of the file, relative to the path relative_to

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

base_directory(relative_to='.')

Retrieve the base directory of the file, relative to the path relative_to

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)[source]

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()[source]

Returns Lattice object from the XV file

read_velocity()[source]

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)[source]

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.