pyiron_atomistics.atomistics.structure.structurestorage.StructurePlots

class pyiron_atomistics.atomistics.structure.structurestorage.StructurePlots(store: StructureStorage)

Bases: object

Simple interface to plot various properties of structures.

__init__(store: StructureStorage)

Methods

__init__(store)
atoms()	Plot a histogram of the number of atoms in each structure.
cell([angle_in_degrees])	Plot histograms of cell parameters.
concentration([elements])	Plot histograms of the concentrations in each structure.
coordination([num_shells, log, num_neighbors])	Plot histogram of coordination in neighbor shells.
distances([bins, num_neighbors, normalize])	Plot a histogram of the neighbor distances.
shell_distances([num_shells, num_neighbors])	Plot a violin plot of the neighbor distances in shells up to num_shells.
spacegroups([symprec])	Plot histograms of space groups and crystal systems.

atoms()

Plot a histogram of the number of atoms in each structure.

cell(angle_in_degrees=True)

Plot histograms of cell parameters.

Plotted are atomic volume, density, cell vector lengths and cell vector angles in separate subplots all on a log-scale.

Parameters:

angle_in_degrees (bool) – whether unit for angles is degree or radians

Returns:

contains the plotted information in the columns:

• a: length of first vector

• b: length of second vector

• c: length of third vector

• alpha: angle between first and second vector

• beta: angle between second and third vector

• gamma: angle between third and first vector

• V: volume of the cell

• N: number of atoms in the cell

Return type:

DataFrame

concentration(elements: List[str] = None, **kwargs) → DataFrame

Plot histograms of the concentrations in each structure.

Parameters:

• elements (list of str) – elements to plot the histograms for; default is for all elements in the container

• **kwargs – passed through to seaborn.histplot

Returns:

table of concentrations in each structure; column headers are the element names

Return type:

pandas.DataFrame

coordination(num_shells=4, log=True, num_neighbors=None)

Plot histogram of coordination in neighbor shells.

Computes one histogram of the number of neighbors in each neighbor shell up to num_shells and then plots them together.

If the underlying StructureStorage has a ‘shells’ array defined it is used, if not it is calculated on the fly.

Parameters:

• num_shells (int) – maximum shell to plot

• num_neighbors (int) – maximum number of neighbors to calculate, when ‘shells’ is not defined in storage, default is the value from the previous call or 36

• log (float) – plot histogram values on a log scale

distances(bins: int = 50, num_neighbors: int = None, normalize: bool = False)

Plot a histogram of the neighbor distances.

Setting normalize plots the radial distribution function.

Parameters:

• bins (int) – number of bins

• num_neighbors (int) – maximum number of neighbors to calculate, when ‘shells’ or ‘distances’ are not defined in storage default is the value from the previous call or 36

• normalize (bool) – normalize the distribution by the surface area of the radial bin, 4pi r^2

shell_distances(num_shells=4, num_neighbors=None)

Plot a violin plot of the neighbor distances in shells up to num_shells.

Parameters:

• num_shells (int) – maximum shell to plot

• num_neighbors (int) – maximum number of neighbors to calculate, when ‘shells’ or ‘distances’ are not defined in storage default is the value from the previous call or 36

spacegroups(symprec=0.001)

Plot histograms of space groups and crystal systems.

Spacegroups and crystal systems are plotted in separate subplots.

Parameters:

symprec (float) – precision of the symmetry search (passed to spglib)

Returns:

contains two columns “space_group”, “crystal_system”

for each structure

Return type:

DataFrame