pyiron.atomistics.volumetric package

Submodules

pyiron.atomistics.volumetric.generic module

class pyiron.atomistics.volumetric.generic.VolumetricData[source]

Bases: object

A new class to handle 3-dimensional volumetric data elegantly (charge densities, electrostatic potentials etc) based on the numpy.ndarray instance. This module is adapted from the pymatgen vasp VolumtricData class

http://pymatgen.org/_modules/pymatgen/io/vasp/outputs.html#VolumetricData

total_data

A 3D array containing the data

Type:numpy.ndarray
from_hdf(hdf5, group_name='volumetric_data')[source]

Recreating the VolumetricData instance by reading data from the HDF5 files

Parameters:
Returns:

The VolumetricData instance

Return type:

pyiron.atomistics.volumetric.generic.VolumetricData

get_average_along_axis(ind=2)[source]

Get the lateral average along a certain axis direction. This function is adapted from the pymatgen vasp VolumtricData class

http://pymatgen.org/_modules/pymatgen/io/vasp/outputs.html#VolumetricData.get_average_along_axis

Parameters:ind (int) – Index of axis (0, 1 and 2 for the x, y, and z axis respectively)
Returns:A 1D vector with the laterally averaged values of the volumetric data
Return type:numpy.ndarray
to_hdf(hdf5, group_name='volumetric_data')[source]

Writes the data as a group to a HDF5 file

Parameters:
total_data

The Nx x Ny x Nz sized array for the total data

Type:numpy.ndarray

Module contents