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ASE

From CRC Wiki

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