sisl (sisl)

sisl is an electronic structure package which may interact with tight-binding and DFT matrices alike.

Below a set of classes that are the basis of everything in sisl is present.

Generic classes

PeriodicTable	Periodic table for creating an Atom, or retrieval of atomic information via atomic numbers
Atom(Z[, R, orbs, mass, tag])	Atomic information, mass, name number of orbitals and ranges
Atoms([atom, na])	A list-like object to contain a list of different atoms with minimum data duplication.
Geometry(xyz[, atom, sc])	Holds atomic information, coordinates, species, lattice vectors
SuperCell(cell[, nsc])	Object to retain a super-cell and its nested values.
Grid(shape[, bc, sc, dtype, geom])	Object to retain grid information

Below are a group of advanced classes rarely needed. A lot of the sub-classes extend these classes, or use them intrinsically. However, they are not necessarily intended for users use.

Advanced classes

Quaternion([angle, v, rad])	Quaternion object to enable easy rotational quantities.
SparseCSR(arg1[, dim, dtype, nnzpr, nnz])	A compressed sparse row matrix, slightly different than scipy.sparse.csr_matrix.
SparseAtom(geom[, dim, dtype, nnzpr])	Sparse object with number of rows equal to the total number of atoms in the Geometry
SparseOrbital(geom[, dim, dtype, nnzpr])	Sparse object with number of rows equal to the total number of orbitals in the Geometry
Selector([routines, ordered])	Base class for implementing a selector of class routines

Atom(Z[, R, orbs, mass, tag])	Atomic information, mass, name number of orbitals and ranges
Atoms([atom, na])	A list-like object to contain a list of different atoms with minimum data duplication.
BaseSile	Base class for all sisl files
BrillouinZone(obj)	A class to construct Brillouin zone related quantities
Cube(edge_length[, center])	A cuboid/rectangular prism (P4) with all-equi faces
Cuboid(edge_length[, center])	A cuboid/rectangular prism (P4) with equi-opposite faces
DensityMatrix(geom[, dim, dtype, nnzpr])	DensityMatrix object containing the density matrix elements
DynamicalMatrix	alias of Hessian
Ellipsoid(x, y, z[, center])	3D Ellipsoid shape
EnergyDensityMatrix(geom[, dim, dtype, nnzpr])	EnergyDensityMatrix object containing the energy density matrix elements
Geometry(xyz[, atom, sc])	Holds atomic information, coordinates, species, lattice vectors
Grid(shape[, bc, sc, dtype, geom])	Object to retain grid information
Hamiltonian(geom[, dim, dtype, nnzpr])	Object containing the coupling constants between orbitals.
Hessian(geom[, dim, dtype, nnzpr])	Dynamical matrix of a geometry
MonkhorstPackBZ(obj, nkpt[, symmetry, ...])	Create a Monkhorst-Pack grid for the Brillouin zone
PathBZ(obj, point, division[, name])	Create a path in the Brillouin zone for plotting band-structures etc.
PeriodicTable	Periodic table for creating an Atom, or retrieval of atomic information via atomic numbers
Quaternion([angle, v, rad])	Quaternion object to enable easy rotational quantities.
RecursiveSI(spgeom, infinite[, eta, bloch])	Self-energy object using the Lopez-Sancho Lopez-Sancho algorithm
Selector([routines, ordered])	Base class for implementing a selector of class routines
SelfEnergy(*args, **kwargs)	Self-energy object able to calculate the dense self-energy for a given sparse matrix
SemiInfinite(spgeom, infinite[, eta, bloch])	Self-energy object able to calculate the dense self-energy for a given SparseGeometry in a semi-infinite chain.
Shape(center)	Baseclass for shapes
Sile(filename[, mode, comment])	Base class for ASCII files
SileBin(filename[, mode])	Base class for binary files
SileCDF(filename[, mode, lvl, access, _open])	Base class for NetCDF files
SparseAtom(geom[, dim, dtype, nnzpr])	Sparse object with number of rows equal to the total number of atoms in the Geometry
SparseCSR(arg1[, dim, dtype, nnzpr, nnz])	A compressed sparse row matrix, slightly different than scipy.sparse.csr_matrix.
SparseOrbital(geom[, dim, dtype, nnzpr])	Sparse object with number of rows equal to the total number of orbitals in the Geometry
SparseOrbitalBZ(geom[, dim, dtype, nnzpr])	Sparse object containing the orbital connections in a Brillouin zone
SparseOrbitalBZSpin(geom[, dim, dtype, nnzpr])	Sparse object containing the orbital connections in a Brillouin zone with possible spin-components
Sphere(radius[, center])
Spheroid(a, b[, axis, center])	3D spheroid shape
Spin([kind, dtype])	Spin class to determine configurations and spin components.
SuperCell(cell[, nsc])	Object to retain a super-cell and its nested values.
SuperCellChild	Class to be inherited by using the self.sc as a SuperCell object
TightBinding	alias of Hamiltonian
TimeSelector([routines, ordered])	Routine performance selector based on timings for the routines

add_sile(ending, cls[, case, gzip, _parent_cls])	Add files to the global lookup table
cite()
get_sile(file, *args, **kwargs)	Retrieve an object from the global lookup table via filename and the extension
get_sile_class(file, *args, **kwargs)	Retrieve a class from the global lookup table via filename and the extension
get_siles([attrs])	Retrieve all files with specific attributes or methods
ispmatrix(matrix[, map_row, map_col])	Iterator for iterating rows and columns for non-zero elements in a scipy.sparse.*_matrix (or SparseCSR)
ispmatrixd(matrix[, map_row, map_col])	Iterator for iterating rows, columns and data for non-zero elements in a scipy.sparse.*_matrix (or SparseCSR)
plot(obj, *args, **kwargs)
sgeom([geom, argv, ret_geometry])	Main script for sgeom.
sgrid([grid, argv, ret_grid])	Main script for sgrid.
unit_convert(fr, to[, opts, tbl])	Factor that takes ‘fr’ to the units of ‘to’.
unit_default(group[, tbl])	The default unit of the unit group group.
unit_group(unit[, tbl])	The group of units that unit belong to

SileError(value[, obj])

Define an error object related to the Sile objects