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show_atoms

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show_atoms#

abtem.visualize.visualizations.show_atoms(atoms, plane='xy', ax=None, scale=0.75, title=None, numbering=False, show_periodic=False, figsize=None, legend=False, merge=0.01, tight_limits=False, show_cell=None, **kwargs)[source]#

Display 2D projection of atoms as a matplotlib plot.

Parameters:

  • atoms (ase.Atoms) – The atoms to be shown.

  • plane (str, two float) – The projection plane given as a concatenation of ‘x’ ‘y’ and ‘z’, e.g. ‘xy’, or as two floats representing the azimuth and elevation angles of the viewing direction [degrees], e.g. (45, 45).

  • ax (matplotlib.axes.Axes, optional) – If given the plots are added to the axes.

  • scale (float) – Factor scaling their covalent radii for the atom display sizes (default is 0.75).

  • title (str) – Title of the displayed image. Default is None.

  • numbering (bool) – Display the index of the Atoms as a number. Default is False.

  • show_periodic (bool) – If True, show the periodic images of the atoms at the cell boundary.

  • figsize (two int, optional) – The figure size given as width and height in inches, passed to matplotlib.pyplot.figure.

  • legend (bool) – If True, add a legend indicating the color of the atomic species.

  • merge (float) – To speed up plotting large numbers of atoms, those closer than the given value [Å] are merged.

  • tight_limits (bool) – If True the limits of the plot are adjusted

  • kwargs (Keyword arguments for matplotlib.collections.PatchCollection.)

Return type:

matplotlib.figure.Figure, matplotlib.axes.Axes

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