AtomsPlotter 0.3.3

Package for easy plotting of ASE atoms using matplotlib

Atoms_plotter

Package for plotting ASE atoms-objects using matplotlib. Can be used to create vector graphics, or used interactively in a jupyter-notebook.

Installation

clone repository into Atoms_plotter install with

cd Atoms_plotter
python3 -m pip install -e . 

Ideally with a development install (-e) so changes are easily updated.

Usage

• use installed entry point plot_atoms. See plot_atoms --help for options

In a python script

Initialize the class; set options either when initialising or modify class attributes.

from AtomsPlotter.atoms_plotter import atoms_plotter
from ase.io import read
from sys import argv
atoms=read(argv[1])
ap=atoms_plotter(atoms,show=True)
ap.plot()

In a jupyter-notebook

import ase
import ase.io
import matplotlib.pyplot
atoms=ase.io.read('CONTCAR')
%matplotlib widget #for interactive use
from AtomsPlotter.atoms_plotter import atoms_plotter

plotter=atoms_plotter(atoms=atoms, constraints=True)
plotter.dimension='3D'
plotter.atoms=atoms
plotter.plot()

some options

plotter.scale=70
plotter.bondlinewidth=2
plotter.colorbonds=True
plotter.constraints=False #draw constraints as x
plotter.draw_outline=True
plotter.repeat=[2,2]
plotter.use_bondorders=True #double/triple bonds
plotter.dimension='2D' #2D projection
plotter.plot()

#plot lewis-like structures. bonds as simple black lines, no atoms.

plotter.dimension='2D'
plotter.lewis=True
plotter.scale=0
plotter.atoms.rotate(90, 'z',rotate_cell=True)
plotter.view=2
plotter.plot()

Changelog

0.3.3

• Fix plot_atoms_2D / plot_atoms_3D colour assignment: elements missing from color_dict (e.g. Au, Pt) used to inherit the last-iterated atom's jmol colour because self.COLORS was rebuilt inside the per-atom loop with the outer-loop atomic number as the fallback. Now built once with a per-atom jmol fallback.
• Add Au (gold) to the default color_dict.
• Promote plot_atom_colorscaling to a real constructor keyword (plot_atom_colorscaling=False by default). Previously it was referenced from both render paths but the __init__ assignment was commented out, so any code that hit the color_dict=None branch raised AttributeError.
• Guard the z-fraction colour scaling against z_norm == 0 so flat (2-D) structures no longer divide by zero.
• Tidy four ruff E702 (semicolon-chained statements) in check_pbc.

(0.3.2 was prepared but never published — its scope is included in 0.3.3 above.)