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This page shows some of the programs I use in my research on a daily basis.


Programs

  1. ATAT (Axel van de Walle)

  2. OVITO (Alex Stukowski)

  3.   LAMMPS (developed at Sandia National Lab)

  4. Bayesian design of experiments (Jesper Kristensen)


For more of my programs please visit my “blog” page. You will find a link to it in the top menu.

Go to ATAT’s homepage (opens new window)http://www.brown.edu/Departments/Engineering/Labs/avdw/atat/http://www.brown.edu/Departments/Engineering/Labs/avdw/atat/shapeimage_2_link_0

ATAT can be used to cluster expand properties of alloys. Typically this would be, but is not limited to, quantum mechanical energies of alloys. It has many nice features and is well developed. It can perform post-processing tasks as well. For instance, it can construct phase diagrams including configurational, vibrational, and electronic degrees of freedom. Please visit the ATAT homepage for more info on how to download the code and/or access the manual.

If you have any questions about a project you are working on, and want to know if ATAT can solve it in its current stage, please feel free to contact me.


I spent ~6 months going through the code carefully line by line understanding the theory of cluster expansions through Dr. Walle’s code. This helped me for my first paper where I needed to use certain classes from this code to interface with a sequential Monte Carlo sampler (you will find a link to this paper under “Publications...” in the menu at the top).

  1. OVITO (by Alexander Stukowski)

Go to OVITO’s homepage (opens new window)http://www.ovito.org/http://www.ovito.org/shapeimage_3_link_0

I have used OVITO to visualize structures created with LAMMPS. It reads “dump” files when given in this format (this is not the only format it can read):
dump myOvito all custom 1 dump.ovito.* id type xs ys zs


Also, I have used it for visualizing clusters found by ATAT in 3D structures. I will tell you how, in the next program in this list.


A particular feature in OVITO I found very helpful: the generation and visualization of bonds of given lengths just from the atomic coordinates (i.e. you do not need to provide bond information yourself). It has other nice features as well.

  1. Bayesian design of experiments

This is a Python package with multiple classes to perform bayesian design of experiments in the context of alloy modeling.


We are currently finishing up a journal article on this. I will make the code available asap.

External Programs

My Software

Jesper Toft Kristensen

  1. ATAT (by Axel van de Walle)

  1. Convert POSCAR to str.out

I have discussed how this program works in my blog (see top menu).

  1. LAMMPS (Sandia national lab)

LAMMPS is a molecular dynamics simulator. I am currently using this and will write more on this as my current project evolves. It is installed on both the Olympus and Hopper supercomputers.

  1. Double check output from Enumlib

I have discussed how this program works in my blog (see top menu).

Contact

CV

  1. Parsing ATAT output with Python

I am writing some Python parsing tools for ATAT.


Recently, I have written a Python class which can help you parse the “clusters.out” file from ATAT.


Simply put the class in your own project and parse the clusters file! Add whatever other functionalities you would like of course.


Download the Parse clusters.out with Python class.

Unzip and follow the README file.

Also, see this html file: Example of clusters.out parser


Please contact me if you have difficulties using this class or if you discover bugs.


Required Python modules:

os, sys, numpy and monty


p.s. I really recommend using Python in a virtual environment using pip (or easy_install) to easily obtain any package, including the above listed.