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.
ASE environment can be set with the following module command:
module load ase
A small job can be run by using python interpreter as:
However, we strongly recommend to use batch script to run jobs on compute nodes.
Submitting a job to SGE
#!/bin/csh #$ -M email@example.com # 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 &
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.
See the official website: ASE