sisl.io.siesta.pdosSileSiesta

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

Bases: SileSiesta

Projected DOS file with orbital information

Data file containing the PDOS as calculated by Siesta.

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([as_dataarray])

Returns data associated with the PDOS file

read_fermi_level()

Returns the fermi-level

read_geometry()

Read the geometry with coordinates and correct orbital counts

write(*args, **kwargs)

Generic write method which should be overloaded in child-classes

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(as_dataarray=False)[source]

Returns data associated with the PDOS file

For spin-polarized calculations the returned values are up/down, orbitals, energy. For non-collinear calculations the returned values are sum/x/y/z, orbitals, energy.

Parameters:

as_dataarray (bool, optional) – If True the returned PDOS is a xarray.DataArray with energy, spin and orbital information as coordinates in the data. The geometry, unit and Fermi level are stored as attributes in the DataArray.

Returns:

  • geom (Geometry instance with positions, atoms and orbitals.)

  • E (the energies at which the PDOS has been evaluated at (if Fermi-level present in file energies are shifted to \(E - E_F = 0\)).)

  • PDOS (an array of DOS with dimensions (nspin, geom.no, len(E)) (with different spin-components) or (geom.no, len(E)) (spin-symmetric).)

  • DataArray (if as_dataarray is True, only this data array is returned, in this case all data can be post-processed using the xarray selection routines.)

read_fermi_level()[source]

Returns the fermi-level

read_geometry()[source]

Read the geometry with coordinates and correct orbital counts

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.