Working with ASE

The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.

Using the ase.build.nanotube() as an example of using calculating the scattering directly from an ase.Atoms object.

>>> from javelin.fourier import Fourier  # doctest: +SKIP
>>> from ase.build import nanotube  # doctest: +SKIP
>>> cnt = nanotube(6, 0, length=4)  # doctest: +SKIP
>>> print(cnt)  # doctest: +SKIP
Atoms(symbols='C96', pbc=[False, False, True], cell=[0.0, 0.0, 17.04])
>>> cnt_four = Fourier()  # doctest: +SKIP
>>> cnt_four.grid.bins = 201, 201  # doctest: +SKIP
>>> cnt_four.grid.r1 = -3, 3  # doctest: +SKIP
>>> cnt_four.grid.r2 = -3, 3  # doctest: +SKIP
>>> results = cnt_four.calc(cnt)  # doctest: +SKIP
Working on atom number 6 Total atoms: 96
>>> results.plot(vmax=2e5)  # doctest: +SKIP
<matplotlib.collections.QuadMesh object at ...>

(Source code, png, hires.png, pdf)

Convert structure from ASE to javelin

A ase.Atoms can be converted to javelin.structure.Structure simply by initializing the javelin structure from the ASE atoms.

>>> print(cnt)  # doctest: +SKIP
Atoms(symbols='C96', pbc=[False, False, True], cell=[0.0, 0.0, 17.04])
>>> type(cnt)  # doctest: +SKIP
<class 'ase.atoms.Atoms'>
>>> from javelin.structure import Structure  # doctest: +SKIP
>>> javelin_cnt = Structure(cnt)  # doctest: +SKIP
>>> print(javelin_cnt)  # doctest: +SKIP
Structure(C96, a=1, b=1, c=17.04, alpha=90.0, beta=90.0, gamma=90.0)
>>> type(javelin_cnt)  # doctest: +SKIP
<class 'javelin.structure.Structure'>

Convert structure from javelin to ASE

To convert javelin.structure.Structure to ase.Atoms you can use javelin.structure.Structure.to_ase().

>>> from javelin.io import read_stru  # doctest: +SKIP
>>> pzn = read_stru('../../tests/data/pzn.stru')  # doctest: +SKIP
Found a = 4.06, b = 4.06, c = 4.06, alpha = 90.0, beta = 90.0, gamma = 90.0
Read in these atoms:
O     9
Pb    3
Nb    2
Zn    1
Name: symbol, dtype: int64
>>> print(pzn)  # doctest: +SKIP
Structure(O9Pb3Nb2Zn1, a=4.06, b=4.06, c=4.06, alpha=90.0, beta=90.0, gamma=90.0)
>>> type(pzn)  # doctest: +SKIP
<class 'javelin.structure.Structure'>
>>> pzn_ase = pzn.to_ase()  # doctest: +SKIP
>>> print(pzn_ase)  # doctest: +SKIP
Atoms(symbols='PbNbO3PbZnO3PbNbO3', pbc=False, cell=[4.06, 4.06, 4.06])
>>> type(pzn_ase)  # doctest: +SKIP
<class 'ase.atoms.Atoms'>

Visualization with ASE

The javelin.structure.Structure has enough api compatibility with ase.Atoms that it can be used with some of ASE’s visulization tools.

An example using ASE’s matplotlib interface.

>>> from javelin.io import read_stru  # doctest: +SKIP
>>> from ase.visualize.plot import plot_atoms  # doctest: +SKIP
>>> pzn = read_stru('../../tests/data/pzn.stru')  # doctest: +SKIP
>>> print(pzn)  # doctest: +SKIP
Structure(O9Pb3Nb2Zn1, a=4.06, b=4.06, c=4.06, alpha=90.0, beta=90.0, gamma=90.0)
>>> plot_atoms(pzn, radii=0.3)  # doctest: +SKIP
<matplotlib.axes._subplots.AxesSubplot object at ...>

(Source code, png, hires.png, pdf)

To use all of ASE’s visualization tools, such as ase.gui, VMD, Avogadro, or ParaView, first Convert structure from javelin to ASE.

>>> from ase.visualize import view  # doctest: +SKIP
>>> pzn_ase = pzn.to_ase()  # doctest: +SKIP
>>> view(pzn_ase)  # doctest: +SKIP
>>> view(pzn_ase, viewer='vmd')  # doctest: +SKIP
>>> view(pzn_ase, viewer='avogadro')  # doctest: +SKIP
>>> view(pzn_ase, viewer='paraview')  # doctest: +SKIP

File IO

ase.io has extensive support for file-formats that can be utilized by javelin. For example reading in ‘.cif’ files using ase.io.read()

>>> from javelin.structure import Structure  # doctest: +SKIP
>>> from ase.io import read  # doctest: +SKIP
>>> graphite = Structure(read('tests/data/graphite.cif'))  # doctest: +SKIP
>>> print(graphite)  # doctest: +SKIP
Structure(C4, a=2.456, b=2.456, c=6.696, alpha=90.0, beta=90.0, gamma=119.99999999999999)
>>> type(graphite)  # doctest: +SKIP
<class 'javelin.structure.Structure'>
>>> PbTe = Structure(read('tests/data/PbTe.cif'))  # doctest: +SKIP
>>> print(PbTe)  # doctest: +SKIP
Structure(Pb4Te4, a=6.461, b=6.461, c=6.461, alpha=90.0, beta=90.0, gamma=90.0)
>>> type(PbTe)  # doctest: +SKIP
<class 'javelin.structure.Structure'>

ASE can also be used to write file to many file-formats using ase.io.write()

>>> from ase.io import write  # doctest: +SKIP
>>> write('output.xyz', graphite.to_ase())  # doctest: +SKIP
>>> write('output.png', graphite.to_ase())  # doctest: +SKIP