Atoms Python Library
PyAtoms is now deprecated and has been replaced by quippy.
I've written a simple Python packaged called PyAtoms for playing with atomic configurations interactively. It works with the extended XYZ file format, and can also write files in AtomEye CFG format, and read CASTEP .cell and .geom files.
There's also written a simple wrapper to communicate with an AtomEye process. This is useful as it lets you manipulate the atoms structure programatically at the same time as visualising it.
The packages is designed to be used interactively from within a python console, or, even better, from ipython. The PyAtoms package is also used by some of my XYZ scripts.
Requirements
You need to have the following packages installed to use these modules.
And for the AtomEye interface you also need
Usage Example
Here's an example of a python console session using the Atoms and AtomEye modules.
1 from pyatoms import * # Load PyAtoms modules
2
3 a = Atoms('filepot.xyz') # Load from an extended XYZ file
4
5 a.add_property('norm2_pos',norm2(a.pos))
6
7 a.write_xyz('out.xyz') # Write it to a new file
8
9 print count(a.pos[:,1] < 0) # How many atoms with x < 0?
10
11 b = a.filter(a.pos[:,0] < 0) # Make a new atoms object
12 # containing just these atoms
13
14 as = [a for a in frame_reader('movie.xyz')] # Load a list of Atoms
15
16 from pyatoms.atomeye import * # Load the AtomEye module
17
18 ae = AtomEye() # Initialise from a list of Atoms
19 ae.view(as[0],align='CoM') # Show first frame, centre on centre of mass
20 ae.animate(as) # Animate configs from list
Download
You can get the latest development version of PyAtoms here