python-ase

ASE is an Atomistic Simulation Environment written in Python

Introduction

The python-ase package is a powerful atomistic simulation system written in Python. It is written in the form of several modules which makes the program easy to use in scripts and quite customizable and very flexible. The program is rather easy to use as well with three main ways of using the program including a GUI, a GPAW command line tool and an interface for use with python scripts.  The program contains a wealth of numerical algorithms and simulation tools that make it very useful for very complex simulations.

Usage of python-ase at RCC

The python-ase utilities and python packages are installed system wise in the following directories:

/usr/bin
/usr/lib/python2.7/site-packages/ase

 E.g.,

$ ls /usr/bin/ase*
 ase-build  ase-db  ase-gui  ase-info  ase-run  aserver

To Use the ase-build Command

 $ ase-build [options] name/input-file [output-file]

To Use other python-ase Command Line Tools

python-ase has a number of other available command line tools as well. Documentation and tutorials on how to use these can be found at the official website's Tutorials page under the "Command Line Tools" section.

To Use python-ase from a Script

python-ase modules can be loaded on the HPC system by simply using import commands in your python script. See the Tutorials under the ASE section for details and examples.

To Use python-ase in GUI Mode

python-ase also has a user-friendly GUI which is available on the HPC system. For examples on how to use the GUI and for guidelines on how to use and interact with the program in GUI mode, please refer to ase-gui section of the Tutorials where you will find a wealth of examples on this functionality.