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

property atoms

The structure related to the volumeric data

Returns

The structure associated with the data

Return type

pyiron.atomistics.structure.Atoms

cylindrical_average_potential(structure, spherical_center, axis_of_cyl, rad=2, fwhm=0.529177)[source]

Calculates the cylindrical average about a given point in space

Parameters

  • structure (pyiron.atomistics.structure.Atoms) – Input structure

  • spherical_center (list/numpy.ndarray) – position of spherical_center in direct coordinate

  • rad (float) – radius of sphere to be considered in Angstrom (recommended value: 2)

  • fwhm (float) – Full width half maximum of gaussian function in Angstrom (recommended value: 0.529177)

  • axis_of_cyl (int) – Axis of cylinder (0 (x) or 1 (y) or 2 (z))

Returns

Cylindrical average at the target center

Return type

float

static dist_between_two_grid_points(target_grid_point, n_grid_at_center, lattice, grid_shape)[source]

Calculates the distance between a target grid point and another grid point

Parameters

  • target_grid_point (numpy.ndarray/list) – Target grid point

  • n_grid_at_center (numpy.ndarray/list) – coordinate of center of sphere

  • lattice (numpy.ndarray/list) – lattice vector

  • grid_shape (tuple/list/numpy.ndarray) – size of grid

Returns

Distance between target grid and center of sphere in angstrom

Return type

float

static dist_between_two_grid_points_cyl(target_grid_point, n_grid_at_center, lattice, grid_shape, direction_of_cyl)[source]

Distance between a target grid point and the center of a cylinder

Parameters

  • target_grid_point (numpy.ndarray/list) – Target grid point

  • n_grid_at_center (numpy.ndarray/list) – coordinate of center of sphere

  • lattice (numpy.ndarray/list) – lattice vector

  • grid_shape (tuple/list/numpy.ndarray) – size of grid

  • direction_of_cyl (int) – Axis of cylinder (0 (x) or 1 (y) or 2 (z))

Returns

Distance between target grid and in-plane center of cylinder

Return type

float

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

static gauss_f(d, fwhm=0.529177)[source]

Generates a Gaussian distribution for a given distance and full width half maximum value

Parameters

  • d (float) – distance between target point and reference point

  • fwhm (float) – Full width half maximum in angstrom

Returns

Gaussian reduction constant

Return type

float

get_average_along_axis(ind=2)[source]

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

read_cube_file(filename='cube_file.cube')[source]

Generate data from a CUBE file

Parameters

filename (str) – Filename to parse

spherical_average_potential(structure, spherical_center, rad=2, fwhm=0.529177)[source]

Calculates the spherical average about a given point in space

Parameters

  • structure (pyiron.atomistics.structure.Atoms) – Input structure

  • spherical_center (list/numpy.ndarray) – position of spherical_center in direct coordinate

  • rad (float) – radius of sphere to be considered in Angstrom (recommended value: 2)

  • fwhm (float) – Full width half maximum of gaussian function in Angstrom (recommended value: 0.529177)

Returns

Spherical average at the target center

Return type

float

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

Writes the data as a group to a HDF5 file

Parameters
property total_data

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

Type

numpy.ndarray

write_cube_file(filename='cube_file.cube', cell_scaling=1.0)[source]

Write the volumetric data into the CUBE file format

Parameters

  • filename (str) – Filename

  • cell_scaling (float) – Scale the cell by this fraction

write_vasp_volumetric(filename='CHGCAR', normalize=False)[source]

Writes volumetric data into a VASP CHGCAR format

Parameters

  • filename (str) – Filename of the new file

  • normalize (bool) – True if the data is to be normalized by the volume