Fireball computation outputs

class fireballpy.outputs.OrbitalVector(*, vector, orbitals)

Object to manipulate the Eigenvectors in a computation.

This object adds the ability to select atoms and their orbitals with 2 index expressions. When accessing elements of the matrix one may use a [iatom, iorb] syntax.

• iatom: Refers to the index/indices of the atom.

• iorb: Refers to the orbital index/indices of the atom.

Following np.ndarray indexing, it is also valid to use expressions as [iatom], [iatom, iorb], where the absence of an index is assumed as a full selection. Slicing is supported in both the orbitals and atoms (when orbitals are not specified).

Parameters:

vectorNDArray

Matrix where each row/column represents an orbital.

orbitalsNDArray[int]

Array with the number of orbitals each atom has.

Attributes:

vectorNDArray

Matrix where each row/column represents an orbital.

orbitalsNDArray[int]

Array with the number of orbitals each atom has.

class fireballpy.outputs.OrbitalMatrix(*, matrix, orbitals)

Object to manipulate the Hamiltonian and Overlap matrix in a computation.

This object adds the ability to select atoms and their orbitals with 4 index expressions. When accessing elements of the matrix one may use a [iatom, jatom, iorb, jorb] syntax.

• iatom: Refers to the index/indices of the first atom (row).

• jatom: Refers to the index/indices of the second atom (column).

• iorb: Refers to the orbital index/indices of the first atom.

• jorb: Refers to the orbital index/indices of the second atom.

Following np.ndarray indexing, it is also valid to use expressions as [iatom], [iatom, jatom], [iatom, jatom, iorb], where the absence of an index is assumed as a full selection. Slicing is supported in both the orbitals and atoms (when orbitals are not specified).

Parameters:

matrixNDArray

Matrix where each row/column represents an orbital.

orbitalsNDArray[int]

Array with the number of orbitals each atom has.

Attributes:

matrixNDArray

Matrix where each row/column represents an orbital.

orbitalsNDArray[int]

Array with the number of orbitals each atom has.

fireballpy.outputs.get_eigenvectors(*, kpt=0, atoms=None, fbobj=None)

Function to extract the eigenvectors from Fireball.

This function accepts any fireballpy-like object and returns a numpy array with the eigenvectors for each eigenvalue as OrbitalVector instances. If they are desired as a matrix, it is better to obtain them directly from the computation API.

Parameters:

kptint

Index of the k-point to obtain the eigenvectors. By default takes the first (kpt = 0).

atomsase.Atoms | None

An ase.Atoms object with a Fireball attached as calculator. The SCF loop must be computed before. This parameter is not compatible with fbobj.

fbobjBaseFireball | None

Directly a low-level BaseFireball object. In general this is reserved only for advanced users. The SCF loop must be computed before. This parameter is not compatible with atoms.

Returns:

Eigenvectors

Numpy array with the eigenvectors as OrbitalVector.

Raises:

ValueError

If more than one fireballpy object is passed.

RuntimeError

If the SCF loop was not computed.

fireballpy.outputs.get_hamiltonian(*, atoms=None, fbobj=None)

Function to extract the hamiltonian and overlap matrices from Fireball.

This function accepts any fireballpy-like object and returns a named tuple with the hamiltonian and the overlap matrices as OrbitalMatrix instances.

Parameters:

atomsase.Atoms | None

An ase.Atoms object with a Fireball attached as calculator. The SCF loop must be computed before. This parameter is not compatible with fbobj.

fbobjBaseFireball | None

Directly a low-level BaseFireball object. In general this is reserved only for advanced users. The SCF loop must be computed before. This parameter is not compatible with atoms.

Returns:

Hamiltonian

Named tuple with the hamiltonian (.hamiltonian) and overlap (.overlap) matrices.

Raises:

ValueError

If more than one fireballpy object is passed.

RuntimeError

If the SCF loop was not computed.