zhubonan / airsspy Goto Github PK

A package to help working with the Ab initio Random Structure Searching (AIRSS) using Atomic simulation environment (ase). Supports building a search seed for AIRSS in a interactive python environments. One of the important steps for performing a successful search with AIRSS is to have sensible seed for generating random structures, which are subsequently relaxed using the method of choice. In general, AIRSS only relies on a few simple parameters to generate random structure, such as numbers of atoms, numbers of species and cell volume. However, for complicated search involving surfaces and/or interfaces, hand-building seed files becomes a tedious or impossible job to do. ASE has a suite of tools for manipulate atomic structure which can be very helpful for building structures, and here, for building search seeds.

AIRSS is a open source code licensed under GPLv2, this package does not contain any source code of AIRSS nor links to it.

• Allow preparing seed for AIRSS using ASE's atoms interface
• Allow ase's calculators to be used in AIRSS to do relaxations

Interactive jupyter notebook examples can be found in the examples folder. Click the binder badge above to launch these examples in a pre-built environment and try it in your browser!

• ase: The atomic simulation environment
• castepinput: A light weight writer/reader for the input files of CASTEP.

The package can be installed from pypi together with the dependencies:

pip install airsspy

Alternative, one can also install directly from the repository (defaults to the master branch):

pip install git+https://github.com/zhubonan/airsspy

Assuming you are familiar with ase, python and has some basic knowledge of AIRSS. To prepare a seed for generating a sensible random structure:

from airsspy import SeedAtoms
seed = SeedAtoms('C6')
seed.buiid.varvol = 20
seed.build.symmops = (2, 4)

# Can also access per `atom` tags/ketwords just like in ASE
for i in range(0, 6, 2):
    atom = seed[i]
    atom.tagname = 'CX'
    atom.posamp = 2

To write the seed file onto the disk:

atoms.write_seed('C6.cell')
# With IPython
# Use the buildcell executable to generate the file
!buildcell < C6.cell > C6-rand.cell

To generate a cell we can create a Buildcell instance, which is helping wrapper to the buildcell program of AIRSS:

from airsspy import Buildcell
buidcell = Buildcell(seed)
random_atoms = builcell.generate()

A shortcut is also available as an method of the SeedAtoms:

random_atoms = seed.build_random_atoms()

Due to the lack of timeout argument of Popen.communicate in python 2.7, communication with the buildcell is not available. Hence, direct generation and retrieval of the random structure are not supported in python. However, it is still possible to write the seed out and call the program externally.