sisl.io.siesta.tshsSileSiesta

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

Bases: onlysSileSiesta

Geometry, Hamiltonian and overlap matrix file

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()	Query the Fermi-level contained in the file
read_geometry([basis])	Returns Geometry object from a TranSiesta file
read_hamiltonian([geometry])	Electronic structure from the siesta.TSHS file
read_lattice()	Returns a Lattice object from a TranSiesta file
read_overlap(**kwargs)	Returns the overlap matrix from the TranSiesta file
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes
write_hamiltonian(H, **kwargs)	Writes the Hamiltonian to a siesta.TSHS file
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_fermi_level() → float

Query the Fermi-level contained in the file

Returns:

fermi-level of the system

Return type:

float

read_geometry(basis: Atoms | None = None)

Returns Geometry object from a TranSiesta file

Parameters:

basis (Atoms | None)

read_hamiltonian(geometry=None, **kwargs) → Hamiltonian

Electronic structure from the siesta.TSHS file

The TSHS file format does not contain exact orbital information. When reading the Hamiltonian directly using this class one will find wrong orbital information. In such cases it may be beneficial to pass the geometry argument to override the contained geometry.

The orbital order is unaltered but the atomic and orbital information will be somewhat arbitrary.

Parameters:

geometry (Geometry, optional) – override the contained geometry in the returned Hamiltonian. Useful when reading files directly using this class.

Return type:

Hamiltonian

Examples

Reading the Hamiltonian using the tshsSileSiesta backend through the fdf sile. Since the fdf file will try and read the basis sets using other files than the TSHS.

>>> H = sisl.get_sile("RUN.fdf").read_hamiltonian(order="TSHS")

An equivalent, but different way would be:

>>> geom = sisl.get_sile("RUN.fdf").read_geometry()
>>> H = sisl.get_sile("siesta.TSHS").read_hamiltonian(geometry=geom)

read_lattice() → Lattice

Returns a Lattice object from a TranSiesta file

Return type:

Lattice

read_overlap(**kwargs) → Overlap

Returns the overlap matrix from the TranSiesta 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.

write_hamiltonian(H, **kwargs)

Writes the Hamiltonian to a siesta.TSHS file