ASE

What is ASE?

ASE is an Atomistic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. It has a graphical user-interface that allows users to visualize, manipulate, and render molecular systems and atoms objects. It also allows to setup and run a number of calculations and can be used to transfer between different file formats.

Some features of the software:

  • Total energy calculations
  • Geometry optimization
  • Different boundary conditions (finite, slab, bulk)
  • X-Ray Absorption Spectroscopy (XAS)
  • ...

To know more about it, please visit official site ASE.

Basic Usage

ASE environment can be set with the following module command:

module load ase

A small job can be run by using python interpreter as:

python input.py

However, we strongly recommend to use batch script to run jobs on compute nodes.

Submitting a job to SGE

#!/bin/csh

#$ -M netid@nd.edu       # Email address for job notification
#$ -m abe                # Send mail when job begins, ends and aborts
#$ -pe smp 1             # Specify parallel environment and legal core size
#$ -q long               # Specify queue
#$ -N job_name           # Specify job name

module load ase

echo "Job Started at:"
date

python input.py 

echo "Job Ended at:"
date

ASE-GUI can be opened by loading its module as:

module load ase
ase-gui &

Test Examples

An example, including job-scripts and instructions of how to run it, tested on CRC resources is available at /opt/crc/gpaw/Examples. Please follow "README" file to run examples located at:

  • Calculation of Absorption Energy @ /opt/crc/ase/Examples/AdsorptionEnergy

More tutorials can be found at ASE official site ASE-tutorial.

Further Information

ASE User's Documentation

See the official website: ASE