Welcome to exatomic

This notebook demonstrates some basics of working with exatomic.



In [1]:

    
import exatomic
exatomic.__version__









    Out[1]:





'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



In [2]:

    
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)



In [3]:

    
uni = exatomic.Universe()
uni









    Out[3]:





<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



In [4]:

    
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

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



In [5]:

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

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



In [6]:

    
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



In [7]:

    
uni.atom_two

Note again that distances are in atomic units



In [8]:

    
uni.molecule

Center of masses can also be computed



In [9]:

    
uni.compute_molecule_com()



In [10]:

    
uni.molecule



In [ ]:



In [ ]:

	atom0	atom1	dr	bond
two
0	0	1	0.68	True