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_basis(**kwargs)	Reads basis set and geometry information from the HSX file
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_lattice(**kwargs)	Read the lattice from the 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
plot	Handles all plotting possibilities for a class
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_basis(**kwargs) → Atoms

Reads basis set and geometry information from the HSX file

Return type:

Atoms

read_fermi_level(**kwargs) → float

Reads the fermi level in the file

Only valid for files created by Siesta >=5.

Return type:

float

read_geometry(**kwargs) → Geometry

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.

Return type:

Geometry

read_hamiltonian(**kwargs) → Hamiltonian

Returns the electronic structure from the siesta.TSHS file

Return type:

Hamiltonian

read_lattice(**kwargs) → Lattice

Read the lattice from the file

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

Return type:

Lattice

read_overlap(**kwargs) → Overlap

Returns the electronic structure from the siesta.TSHS file

Return type:

Overlap

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.