pyiron.sphinx.volumetric_data module

class pyiron.sphinx.volumetric_data.SphinxVolumetricData[source]

Bases: pyiron.atomistics.volumetric.generic.VolumetricData

General class for parsing and manipulating volumetric static within Sphinx.

The basic idea of the Base class is adapted from the pymatgen vasp VolumetricData class:

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

property diff_data

Volumtric difference data (3D)

Type

numpy.ndarray

from_file(filename, normalize=True)[source]

Parses volumetric data from a sphinx binary (.sxb) file.

Parameters
  • filename (str) – Path of file to parse

  • normalize (boolean) – Flag to normalize by the volume of the cell

from_hdf(hdf5, group_name='volumetric_data')[source]

Extract a VolumetricData instance from an HDF5 file.

Parameters
  • hdf5 (pyiron_base.generic.hdfio.ProjectHDFio) – The HDF file/path to read the data

  • group_name (str) – The name of the group under which the data have been stored

Returns

The

VolumetricData instance

Return type

pyiron.atomistics.volumetric.generic.VolumetricData

to_hdf(hdf5, group_name='volumetric_data')[source]

Writes the data as a group to a HDF5 file

Parameters
  • hdf5 (pyiron_base.generic.hdfio.ProjectHDFio) – The HDF file/path to write the data

  • group_name (str) – The name of the group under which the data must be stored

property total_data

Total volumtric data (3D)

Type

numpy.ndarray