sisl.physics.dynmat module

Dynamical matrix.

class sisl.physics.dynmat.DynamicalMatrix(geom, nnzpr=None, orthogonal=True, spin=1, dtype=None, *args, **kwargs)

Bases: sisl.physics.hamiltonian.Hamiltonian

Dynamical matrix of a geometry

Attributes

D
H
S
dtype	Return data type of Hamiltonian (and overlap matrix)
finalized	Whether the contained data is finalized and non-used elements have been removed
geom	Return the attached geometry
geometry	Return the attached geometry
nnz	Returns number of non-zero elements in the tight-binding model
no	Returns number of orbitals as used when the object was created
orthogonal	Return whether the Hamiltonian is orthogonal
spin	Return number of spin-components in Hamiltonian

Methods

Dk([k, dtype])	Return the Hamiltonian in a scipy.sparse.csr_matrix at k.
construct(func[, na_iR, method, eta])	Automatically construct the Hamiltonian model based on a function that does the setting up of the Hamiltonian
copy([dtype])	Return a copy of the Hamiltonian object
correct_Newton()	Sometimes the dynamical matrix does not obey Newtons laws.
create_construct(dR, param)	Returns a simple function for passing to the construct function.
cut(seps, axis, *args, **kwargs)	Cuts the tight-binding model into different parts.
eigh([k, atoms, eigvals_only, overwrite_a, ...])	Returns the eigenvalues of the Hamiltonian
eigsh([k, n, atoms, eigvals_only])	Returns a subset of eigenvalues of the Hamiltonian (default 10)
eliminate_zeros()	Removes all zero elememts from the sparse matrix
empty([keep])	See SparseCSR.empty for details
finalize()	Finalizes the tight-binding model
fromsp(geom, H[, S])	Returns a tight-binding model from a preset H, S and Geometry
iter([local])	Iterations of the orbital space in the geometry, two indices from loop
iter_nnz([atom, orbital])	Iterations of the non-zero elements, returns a tuple of orbital and coupling orbital
read(sile, *args, **kwargs)	Reads Hamiltonian from Sile using read_H.
remove(atom)	Remove atom from the Hamiltonian.
repeat(reps, axis)	Returns a repeated tight-binding model for this, much like the Geometry
reset([nnzpr, orthogonal, spin, dtype])	The sparsity pattern is cleaned and every thing is reset.
spsame(other)	Compare two Hamiltonians and check whether they have the same entries.
sub(atom)	Returns a subset of atoms from the geometry.
sub_supercell(sc)	Creates a new object with only the given supercells
tile(reps, axis)	Returns a tiled tight-binding model for this, much like the Geometry
tocsr(index[, isc])	Return a scipy.sparse.csr_matrix from the specified index
write(sile, *args, **kwargs)	Writes a tight-binding model to the Sile as implemented in the Sile.write_hamiltonian method

Create tight-binding model from geometry

Initializes a tight-binding model using the geom object as the underlying geometry for the tight-binding parameters.

Attributes

D
H
S
dtype	Return data type of Hamiltonian (and overlap matrix)
finalized	Whether the contained data is finalized and non-used elements have been removed
geom	Return the attached geometry
geometry	Return the attached geometry
nnz	Returns number of non-zero elements in the tight-binding model
no	Returns number of orbitals as used when the object was created
orthogonal	Return whether the Hamiltonian is orthogonal
spin	Return number of spin-components in Hamiltonian

Methods

Dk([k, dtype])	Return the Hamiltonian in a scipy.sparse.csr_matrix at k.
construct(func[, na_iR, method, eta])	Automatically construct the Hamiltonian model based on a function that does the setting up of the Hamiltonian
copy([dtype])	Return a copy of the Hamiltonian object
correct_Newton()	Sometimes the dynamical matrix does not obey Newtons laws.
create_construct(dR, param)	Returns a simple function for passing to the construct function.
cut(seps, axis, *args, **kwargs)	Cuts the tight-binding model into different parts.
eigh([k, atoms, eigvals_only, overwrite_a, ...])	Returns the eigenvalues of the Hamiltonian
eigsh([k, n, atoms, eigvals_only])	Returns a subset of eigenvalues of the Hamiltonian (default 10)
eliminate_zeros()	Removes all zero elememts from the sparse matrix
empty([keep])	See SparseCSR.empty for details
finalize()	Finalizes the tight-binding model
fromsp(geom, H[, S])	Returns a tight-binding model from a preset H, S and Geometry
iter([local])	Iterations of the orbital space in the geometry, two indices from loop
iter_nnz([atom, orbital])	Iterations of the non-zero elements, returns a tuple of orbital and coupling orbital
read(sile, *args, **kwargs)	Reads Hamiltonian from Sile using read_H.
remove(atom)	Remove atom from the Hamiltonian.
repeat(reps, axis)	Returns a repeated tight-binding model for this, much like the Geometry
reset([nnzpr, orthogonal, spin, dtype])	The sparsity pattern is cleaned and every thing is reset.
spsame(other)	Compare two Hamiltonians and check whether they have the same entries.
sub(atom)	Returns a subset of atoms from the geometry.
sub_supercell(sc)	Creates a new object with only the given supercells
tile(reps, axis)	Returns a tiled tight-binding model for this, much like the Geometry
tocsr(index[, isc])	Return a scipy.sparse.csr_matrix from the specified index
write(sile, *args, **kwargs)	Writes a tight-binding model to the Sile as implemented in the Sile.write_hamiltonian method

D

Dk(k=(0, 0, 0), dtype=None)

Return the Hamiltonian in a scipy.sparse.csr_matrix at k.

Parameters:

k: ``array_like``, `[0,0,0]`

k-point

dtype : numpy.dtype

default to numpy.complex128

correct_Newton()

Sometimes the dynamical matrix does not obey Newtons laws.

We correct the dynamical matrix by imposing zero force.

Correcting for Newton forces the matrix to be finalized.