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
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
Returns the fermi-level
Read the geometry with coordinates and correct orbital counts
write
(*args, **kwargs)Generic write method which should be overloaded in child-classes
File of the current Sile
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(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.)
- 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.