tsgfSileSiesta

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

Bases: sisl.io.siesta._gfSileSiesta

Surface Green function file containing, Hamiltonian, overlap matrix and self-energies

Do not mix read and write statements when using this code. Complete one or the other before doing the other thing. Fortran does not allow the same file opened twice, if this is needed you are recommended to make a symlink to the file and thus open two different files.

This small snippet reads/writes the GF file

>>> with sisl.io.tsgfSileSiesta('hello.GF') as f:
...    nspin, no, k, E = f.read_header()
...    for ispin, new_k, k, E in f:
...        if new_k:
...            H, S = f.read_hamiltonian()
...        SeHSE = f.read_self_energy()

To write a file do:

>>> with sisl.io.tsgfSileSiesta('hello.GF') as f:
...    f.write_header(sisl.MonkhorstPack(...), E)
...    for ispin, new_k, k, E in f:
...        if new_k:
...            f.write_hamiltonian(H, S)
...        f.write_self_energy(SeHSE)

Attributes

__dict__

__doc__

__module__

__weakref__

list of weak references to the object (if defined)

_write_default

_write_default_only

base_file

File of the current Sile

file

File of the current Sile

Methods

Eindex(E)

Return the closest energy index corresponding to the energy E

HkSk([k, spin])

Retrieve H and S for the given k-point

_ArgumentParser_args_single()

Default arguments for the Sile

__delattr__

Implement delattr(self, name).

__dir__

Default dir() implementation.

__enter__()

Opens the output file and returns it self

__eq__

Return self==value.

__exit__(type, value, traceback)

__format__

Default object formatter.

__ge__

Return self>=value.

__getattr__(name)

Override to check the handle

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(filename[, mode])

Initialize self.

__init_subclass__

This method is called when a class is subclassed.

__iter__()

Iterate through the energies and k-points that this GF file is associated with

__le__

Return self<=value.

__len__()

__lt__

Return self<value.

__ne__

Return self!=value.

__new__

Create and return a new object.

__reduce__

Helper for pickle.

__reduce_ex__

Helper for pickle.

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__

Size of object in memory, in bytes.

__str__()

Return a representation of the Sile

__subclasshook__

Abstract classes can override this to customize issubclass().

_base_file(f)

Make f refer to the file with the appropriate base directory

_base_setup(*args, **kwargs)

Setup the Sile after initialization

_close_gf()

_is_open()

_open_gf(mode[, rewind])

_setup(*args, **kwargs)

Simple setup that needs to be overwritten

_step_counter(method, **kwargs)

Method for stepping values must be called before doing the actual read to check correct values

dir_file([filename])

File of the current Sile

disk_usage()

Calculate the estimated size of the resulting file

exist()

Query whether the file exists

kindex(k)

Return the index of the k-point that is closests to the queried k-point (in reduced coordinates)

read(*args, **kwargs)

Generic read method which should be overloaded in child-classes

read_hamiltonian()

Return current Hamiltonian and overlap matrix from the GF file

read_header()

Read the header of the file and open it for reading subsequently

read_self_energy()

Read the currently reached bulk self-energy

self_energy(E[, k, spin])

Retrieve self-energy for a given energy-point and k-point

write(*args, **kwargs)

Generic write method which should be overloaded in child-classes

write_hamiltonian(H[, S])

Write the current energy, k-point and H and S to the file

write_header(bz, E[, mu, obj])

Write to the binary file the header of the file

write_self_energy(SE)

Write the current self energy, k-point and H and S to the file
Eindex(E)

Return the closest energy index corresponding to the energy E

Parameters

E (float or int) – if int, return it-self, else return the energy index which is closests to the energy.

HkSk(k=0, 0, 0, spin=0)

Retrieve H and S for the given k-point

Parameters

  • k (int or array_like of float, optional) – k-point to read the corresponding Hamiltonian and overlap matrices for. If a specific k-point is passed kindex will be used to find the corresponding index.

  • spin (int, optional) – spin-index for the Hamiltonian and overlap matrices

property base_file

File of the current Sile

dir_file(filename=None)

File of the current Sile

disk_usage()

Calculate the estimated size of the resulting file

Returns

Return type

estimated disk-space used in GB

exist()

Query whether the file exists

property file

File of the current Sile

kindex(k)

Return the index of the k-point that is closests to the queried k-point (in reduced coordinates)

Parameters

k (array_like of float or int) – the queried k-point in reduced coordinates \(]-0.5;0.5]\). If int return it-self.

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_hamiltonian()

Return current Hamiltonian and overlap matrix from the GF file

Returns

  • complex128 (Hamiltonian matrix)

  • complex128 (Overlap matrix)

read_header()

Read the header of the file and open it for reading subsequently

NOTES: this method may change in the future

Returns

  • nspin (number of spin-components stored (1 or 2))

  • no_u (size of the matrices returned)

  • k (k points in the GF file)

  • E (energy points in the GF file)

read_self_energy()

Read the currently reached bulk self-energy

The returned self-energy is:

\[\boldsymbol \Sigma_{\mathrm{bulk}}(E) = \mathbf S E - \mathbf H - \boldsymbol \Sigma(E)\]
Returns

complex128

Return type

Self-energy matrix

self_energy(E, k=0, spin=0)

Retrieve self-energy for a given energy-point and k-point

Parameters

  • E (int or float) – energy to retrieve self-energy at

  • k (int or array_like of float, optional) – k-point to retrieve k-point at

  • spin (int, optional) – spin-index to retrieve self-energy at

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, S=None)

Write the current energy, k-point and H and S to the file

Parameters

  • H (matrix) – a square matrix corresponding to the Hamiltonian

  • S (matrix, optional) – a square matrix corresponding to the overlap, for efficiency reasons it may be advantageous to specify this argument for orthogonal cells.

write_header(bz, E, mu=0.0, obj=None)

Write to the binary file the header of the file

Parameters

  • bz (BrillouinZone) – contains the k-points, the weights and possibly the parent Hamiltonian (if obj is None)s

  • E (array_like of cmplx or float) – the energy points. If obj is an instance of SelfEnergy where an associated eta is defined then E may be float, otherwise it has to be a complex array.

  • mu (float, optional) – chemical potential in the file

  • obj (.., optional) – an object that contains the Hamiltonian definitions, defaults to bz.parent

write_self_energy(SE)

Write the current self energy, k-point and H and S to the file

The self-energy must correspond to the bulk self-energy

\[\boldsymbol \Sigma_{\mathrm{bulk}}(E) = \mathbf S E - \mathbf H - \boldsymbol \Sigma(E)\]
Parameters

SE (matrix) – a square matrix corresponding to the self-energy (Green function)