sisl.io.siesta.hsxSileSiesta

class sisl.io.siesta.hsxSileSiesta(filename, mode='r', *args, **kwargs)

Bases: SileBinSiesta

Hamiltonian and overlap matrix file

This file does not contain all information regarding the system.

To ensure no errors are being raised one should pass a Geometry with correct number of atoms and correct number of supercells. The number of orbitals will be updated in the returned matrices geometry.

>>> hsx = hsxSileSiesta("siesta.HSX")
>>> HS = hsx.read_hamiltonian() # may fail
>>> HS = hsx.read_hamiltonian(geometry=<>) # should run correctly if above satisfied

Users are adviced to use the tshsSileSiesta instead since that correctly contains all information.

Methods

base_directory([relative_to])

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

dir_file([filename, filename_base])

File of the current Sile

read(*args, **kwargs)

Generic read method which should be overloaded in child-classes

read_fermi_level(**kwargs)

Reads the fermi level in the file

read_geometry(**kwargs)

Read the geometry from the file

read_hamiltonian(**kwargs)

Returns the electronic structure from the siesta.TSHS file

read_overlap(**kwargs)

Returns the electronic structure from the siesta.TSHS file

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

version

The version of the file

__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

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_fermi_level(**kwargs)[source]

Reads the fermi level in the file

Only valid for files created by Siesta >=5.

read_geometry(**kwargs)[source]

Read the geometry from the file

This will always work on new files Siesta >=5, but only sometimes on older versions of the HSX file format.

read_hamiltonian(**kwargs)[source]

Returns the electronic structure from the siesta.TSHS file

read_overlap(**kwargs)[source]

Returns the electronic structure from the siesta.TSHS file

property version: int

The version of the file

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.