Welcome to exatomic

This notebook demonstrates some basics of working with exatomic.

import exatomic
exatomic.__version__

'0.3.11'

• Getting help in the Jupyter notebook is easy, just put a “?” after a class or function.

• Don’t forget to use tab to help with syntax completion

exatomic.Universe?

• The Universe object contains all of the information about a simulation, nuclear coordinates, orbitals, etc.

• Data is stored in pandas DataFrames (see pandas for more information)

uni = exatomic.Universe()
uni

<exatomic.core.universe.Universe at 0x7f77da0bd630>

• Empty universes can be useful…but it is more interesting with data

• Note that exatomic uses Hartree atomic units

atom = exatomic.Atom.from_dict({'x': [0.0, 0.0], 'y': [0.0, 0.0], 'z': [-0.34, 0.34],
                                'symbol': ["H", "H"], 'frame': [0, 0]})
uni = exatomic.Universe(atom=atom)
uni.atom

	frame	symbol	x	y	z
atom
0	0	H	0.0	0.0	-0.34
1	0	H	0.0	0.0	0.34

• The frame column is how we track state (e.g. time, theory, etc.)

• The simplest dataframe is the frame object which by default only contains the number of atoms

uni.frame    # This was computed on-the-fly as we didn't instantiate it above

	atom_count
frame
0	2

• Visualization of this simple universe can be accomplished directly in the notebook

exatomic.UniverseWidget(uni)

• In building the visualization, bonds were automatically computed

• For small systems this is the default behavior, but for large systems it is not

uni.atom_two

	atom0	atom1	dr	bond
two
0	0	1	0.68	True

• Note again that distances are in atomic units

uni.molecule

	H	mass
molecule
0	2	2.015882

• Center of masses can also be computed

uni.compute_molecule_com()

uni.molecule

	H	mass	cx	cy	cz
molecule
0	2	2.015882	0.0	0.0	0.0