iodata.utils module

Utility functions module.

class Cube(origin, axes, data)

Bases: object

The volumetric data from a cube (or similar) file.

origin

A 3D vector with the origin of the axes frame.

axes

A (3, 3) array where each row represents the spacing between two neighboring grid points along the first, second and third axis, respectively.

data

A (K, L, M) array of data on a uniform grid

__init__(origin, axes, data)

Method generated by attrs for class Cube.

Return type

None

axes: numpy.ndarray

data: numpy.ndarray

origin: numpy.ndarray

property shape

Shape of the rectangular grid.

exception FileFormatError

Bases: OSError

Raised when incorrect content is encountered when loading files.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args

characters_written

errno

POSIX exception code

filename

exception filename

filename2

second exception filename

strerror

exception strerror

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception FileFormatWarning

Bases: Warning

Raised when incorrect content is encountered and fixed when loading files.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class LineIterator(filename)

Bases: object

Iterator class for looping over lines and keeping track of the line number.

__init__(filename)

Initialize a LineIterator.

Parameters

filename (str) – The file that will be read.

back(line)

Go one line back and decrease the lineno attribute by one.

error(msg)

Raise an error while reading a file.

Parameters

msg (str) – Message to raise alongside filename and line number.

warn(msg)

Raise a warning while reading a file.

Parameters

msg (str) – Message to raise alongside filename and line number.

check_dm(dm, overlap, eps=0.0001, occ_max=1.0)

Check if the density matrix has eigenvalues in the proper range.

Parameters

• dm (ndarray) – The density matrix shape=(nbasis, nbasis), dtype=float

• overlap (ndarray) – The overlap matrix shape=(nbasis, nbasis), dtype=float

• eps (float) – The threshold on the eigenvalue inequalities.

• occ_max (float) – The maximum occupation.

Raises

ValueError – When the density matrix has wrong eigenvalues.

derive_naturals(dm, overlap)

Derive natural orbitals from a given density matrix.

Parameters

• dm (ndarray) – The density matrix. shape=(nbasis, nbasis)

• overlap (ndarray) – The overlap matrix shape=(nbasis, nbasis)

Return type

Tuple[ndarray, ndarray]

Returns

• coeffs – Orbital coefficients shape=(nbasis, nfn)

• occs – Orbital occupations shape=(nfn, )

set_four_index_element(four_index_object, i, j, k, l, value)

Assign values to a four index object, account for 8-fold index symmetry.

This function assumes physicists’ notation.

Parameters

• four_index_object (ndarray) – The four-index object. It will be written to. shape=(nbasis, nbasis, nbasis, nbasis), dtype=float

• i (int) – The indices to assign to.

• j (int) – The indices to assign to.

• k (int) – The indices to assign to.

• l (int) – The indices to assign to.

• value (float) – The value of the matrix element to store.

volume(cellvecs)

Calculate the (generalized) cell volume.

Parameters

cellvecs (ndarray) – A numpy matrix of shape (x,3) where x is in {1,2,3}. Each row is one cellvector.

Returns

In case of 3D, the cell volume. In case of 2D, the cell area. In case of 1D, the cell length.

Return type

volume