cube_files
- class DataCube(mol: Mole, box: ndarray, origin: ndarray, data: ndarray)[source]
A data cube, containing a field on a cartesian grid, spanning a molecule.
- __init__(mol: Mole, box: ndarray, origin: ndarray, data: ndarray)[source]
Initialize a DataCube.
- Parameters:
mol – The pyscf molecule.
box – The vectors spanning the box, defining x y and z directions.
origin – The origin of the box.
data – The data, shape (nx, ny, nz).
- classmethod from_file(filename: str | IO, is_tiling_unit_cell=False) DataCube[source]
Read a cube file. Adapted from pyscf.tools.cubegen.Cube.read. For details on the format see https://h5cube-spec.readthedocs.io/en/latest/cubeformat.html#cubeformat-dset-ids
- Parameters:
filename – The filename.
is_tiling_unit_cell – Whether to use an asymmetric mesh for tiling unit cells.
- Returns:
A DataCube object.
- classmethod from_fileobject(f: IO, is_tiling_unit_cell=False)[source]
Read a cube file. Adapted from pyscf.tools.cubegen.Cube.read. For details on the format see https://h5cube-spec.readthedocs.io/en/latest/cubeformat.html#cubeformat-dset-ids
- Parameters:
f – The file object.
is_tiling_unit_cell – Whether to use an asymmetric mesh for tiling unit cells.
- Returns:
A DataCube object.
- classmethod from_function(mol: Mole, func: callable, resolution: float = None, margin: float = 3.0, block_size: int = 16384)[source]
Create a DataCube by evaluating a given function on a cartesian grid spanning a molecule.
- Parameters:
mol – The pyscf molecule.
func – The function to evaluate on the grid. Must take an array of positions of shape (n, 3) as input.
resolution – The resolution of the grid in Bohr.
margin – The margin of the box.
block_size – The blocksize for the evaluation. Defaults to 16384.