ASE

Software name: 
ASE
Policy 

ASE is available to users at HPC2N. See here for how to include acknowledgement of the use of this program into scientific papers.

General 

ASE is an Atomistic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. Read more about its features here.

Description 

ASE is an Atomic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. The ASE has been constructed with a number of “design goals” that make it:

  • Easy to use:

    Setting up an atomistic total energy calculation or molecular dynamics simulation with ASE is simple and straightforward. ASE can be used via a graphical user interface, Command line tools and the Python language. Python scripts are easy to follow. It is simple for new users to get access to all of the functionality of ASE.

  • Flexible:

    Since ASE is based on the Python scripting language it is possible to perform very complicated simulation tasks without any code modifications. For example, a sequence of calculations may be performed with the use of simple “for-loop” constructions. There exist ASE modules for performing many standard simulation tasks.

  • Customizable:

    The Python code in ASE is structured in modules intended for different purposes. There are ase.calculators for calculating energies, forces and stresses, ase.md and ase.optimize modules for controlling the motion of atoms, constraints objects and filters for performing nudged-elastic-band calculations etc. The modularity of the object-oriented code make it simple to contribute new functionality to ASE.

  • Pythonic:

    It fits nicely into the rest of the Python world with use of the popular NumPy package for numerical work (see Numeric arrays in Python for a short introduction). The use of the Python language allows ASE to be used both interactively as well as in scripts.

  • Open to participation:

    The CAMPOS Atomic Simulation Environment is released under the GNU Lesser General Public License version 2.1 or any later version. See the files COPYING and COPYING.LESSER which accompany the downloaded files, or see the license at GNU’s web server at http://www.gnu.org/licenses/. Everybody is invited to participate in using and developing the code.

Availability 

On HPC2N we have ASE available as a module on Abisko and Kebnekaise.

Usage at HPC2N 

To use ASE add it to your environment. Run this command to see which versions exist:

module spider ase 

The run "ml spider" on the version (ASE/version) to see how it is loaded and which prerequisites it has. Loading the module sets all needed environment variables as well as the path.

Use it like this in your submit file:

srun ase-run <your-ase-python-code>

or

srun ase-run [calculator] [task] [options] system(s)

Where

calculator: abinit, aims, asap, castep, dftb, elk, emt, exciting,
            fleur, gpaw, hotbit, jacapo, lammps, lj, morse, nwchem,
            siesta, turbomole or vasp.  Default value is emt.
task:       'molecule', 'bulk' or the name of Python script that instantiates
            a Task object.  Default value is 'molecule'.
systems:    chemical formulas or filenames of files containing the atomic
            structure.

 

See more help with

ase-run --help

after you have loaded the module.

Additional info 

More information can be found on the official website.

Updated: 2017-12-06, 15:21