https://github.com/zhubonan/airsspy
Python bindings for the `buildcell` program for Ab Initio Random Structure Searching (AIRSS)
Science Score: 26.0%
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Low similarity (12.9%) to scientific vocabulary
Keywords
Repository
Python bindings for the `buildcell` program for Ab Initio Random Structure Searching (AIRSS)
Basic Info
Statistics
- Stars: 19
- Watchers: 1
- Forks: 2
- Open Issues: 4
- Releases: 1
Topics
Metadata Files
README.md
airsspy
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.
What this does
- Allow preparing seed for AIRSS using ASE's
atomsinterface - 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!
Dependences
- ase: The atomic simulation environment
- castepinput: A light weight writer/reader for the input files of CASTEP.
Installation
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
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:
```python 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:
```python 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:
python
from airsspy import Buildcell
buidcell = Buildcell(seed)
random_atoms = builcell.generate()
A shortcut is also available as an method of the SeedAtoms:
python
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.
Owner
- Name: Bonan Zhu
- Login: zhubonan
- Kind: user
- Location: London, UK
- Company: University College London
- Website: zhubonan.github.io
- Twitter: 1stbz
- Repositories: 74
- Profile: https://github.com/zhubonan
Postdoctoral Research Fellow at University College London, Computational Material Scientist, Topic Editor at Journal of Open Source Software (JOSS)
GitHub Events
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- Watch event: 3
Last Year
- Watch event: 3
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Bonan Zhu | z****n@o****u | 46 |
| Bonan Zhu | z****n@o****m | 21 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 9 months ago
All Time
- Total issues: 3
- Total pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 3
- Total pull request authors: 1
- Average comments per issue: 1.33
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ndhamrai (1)
- dirocCen (1)
- YuanbinLiu (1)
Pull Request Authors
- lamdalamda (2)
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Packages
- Total packages: 1
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Total downloads:
- pypi 47 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 4
- Total maintainers: 1
pypi.org: airsspy
A wrapper for using AIRSS with python and ase.
- Homepage: https://github.com/zhubonan/airsspy
- Documentation: https://airsspy.readthedocs.io/
- License: gpl-2.0
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Latest release: 0.1.3
published almost 5 years ago
Rankings
Maintainers (1)
Dependencies
- ase *
- castepinput *