NSC's Summer Internship Contest 2013

In today’s science, one controls material construction down to the level of individual atoms. Fantastic experiments are conducted where e.g. one can take snapshots of individual proteins as they fold or place atoms in patterns on surfaces (as illustrated in the figure). Many of these experiments are very complex and correct interpretations of signals often require supporting calculations, solving the fundamental laws of physics.

atoms on a surface spelling IBM

The simulation of material properties on the atomic scale leads to matrix equations of grand sizes, requiring the world’s largest computers to be solved. This is where centers like National Supercomputer Centre play an important role to service researchers with high-performance computing (HPC) facilities.

Many times, computational costs can be reduced by the simplest of considerations before running a simulation on thousands of processors. Let us consider the geometry of the famous Buckminster fullerene, the soccer ball molecule composed of 60 carbons.

C60 fullerene

As can be seen in the figure, this molecular structure is highly symmetric. The task of this year’s contest is to write a program that, given a list of xyz­‐coordinates, identifies as many symmetry operations as possible. You only need to consider: mirror planes, 180-degree rotations, and inversions. Your program should, given an arbitrary initial molecular orientation and translation, reorient the molecule and deliver a list of coordinates that manifests the identified symmetry operations in the Cartesian coordinate system. E.g. if your program detects a rotation axis, then reorient the molecule so that it is centered in origin and the rotation axis becomes equal to any one of the Cartesian axes.

Contributions are to be sent to Peter Larsson and will be evaluated by Soon-­Heum Ko.

The deadline for submission is April 21st.

Please include the source code and instructions on how to compile and run the program. You may write the program in any reasonbly common programming language that can be compiled or interpreted on recent versions of Linux, Mac OS X, or Windows. MATLAB and Mathematica are also ok, but please check with us before using any other commercial programming environment.

The criteria for selecting a winning contribution are:

  • Functionality
  • Efficiency
  • Elegance
  • Readability

Tip: The file containing the coordinates is in xyz-format and can be visualized and rotated in 3D by using a program such as Jmol.

Good Luck!

Page last modified: 2013-04-03 12:20
For more information contact us at info@nsc.liu.se.