airsspy 0.1.1

No project description provided

airsspy

Package to help working with the Ab initio Random Structure Searching (AIRSS) using Atomic simulation environment (ase). AIRSS is a open source code licensed under GPLv2, this package does not contain any source code of AIRSS nor links to it.

What this does

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

Try interactively

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!

Requirements

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

Usage

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()

Limitations

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.