Research Initiative


Site Design:
 Jeff Frey

Copyright © 2002

Resources - Hardware, Software, & Links

All of the work done by the Nanosciences group is computationally intensive; as a result, some relatively powerful hardware is in our possession.

Lohengrin - 8 processor SGI Origin 2100
Lohengrin is the main workhorse used for our computational efforts. It was purchased early in 2001 and was very quickly put to work. Some of the hardware specifics for this machine:
  • Eight (8) R12000 MIPS processors (350 MHz IP27)
  • 6144 MB (6 GB) RAM
  • 8.0 GB system disk
  • 17.0 GB user disk space
  • 61.0 GB calculational scratch disk space

The two main commercial packages we use (Gaussian and WIEN) are available on Lohengrin. Some of the home-brew code listed below is also available.

Grommet - 8 processor SGI Origin 2000
Grommet is shared between several departments on campus and thus is not used exclusively for our work. Visit the Grommet web page for more information on the projects both completed and in-progress on that machine, as well as the hardware and software specifics. You can also find why this beast is called Grommet!
The Grommet Home Page

Grendel - 4-node Beowulf Cluster
Grendel was born late in 2000 as a four-node Beowulf cluster. The basic hardware specs for the nodes:

Master Node:
  • Dual 800 MHz Pentium III
  • 768 MB RAM
  • 36 GB NFS-shared SCSI scratch disk
  • 10 GB local IDE system disk
Slave Nodes:
  • Dual 800 MHz Pentium III
  • 768 MB RAM
  • 10 GB local IDE system disk

The cluster is connected via 100 MBit ethernet cards in the nodes and a 100MBit switch. We are planning on adding to the cluster soon to expand the number of slave nodes and alleviate some latency problems with the NFS sharing on the master node. The original cluster was configured for us by PSSC Labs.

Currently, Grendel can run Gaussian98 (parallel over two processors on a single node) and some truly-parallel home-brew codes. The compilers of the Portland Group are available as well as standard MPI and the LINDA MPI libraries.
The Portland Group
PSSC Labs, Beowulf specialists
Notes on implementing Grendel

Commercial Software
Some of the computational details involved in the various projects on which group members are working require the use of commercial code packages.

Most of the computational work done on molecular systems within the Hartree-Fock, post Hartree-Fock, and Density Functional theories is done using this staple of quantum chemistry. While we do have access to several prior versions of the package, most of our work is done on Gaussian98 version A11, the most current public release.
Visit the Gaussian web site

Periodic chemical systems (like carbon nanotubes, for instance) are treated computationally as bulk material using the WIEN97 (version 10) solid-state code package. This package treats a given system within Density Functional Theory using full-potential atomic cores and a linearized augmented planewave basis (the FP-LAPW method).
Visit the WIEN web site

Home-Brew Code  

Commercial code packages cannot always satisfy our computational needs; in such cases we tend to write our own code to get the job done. Some of the code that has been developed by members of the group may be of general interest, while some may be very specialized to a single task. Whatever the case, this is where we make public a selection of our coding efforts.

UDSKIP [J. Boshoff]

A program to calculate theoretical Powder X-Ray diffraction patterns of ultra-small zeolite crystals. After the original SKIP algorithm described by Schlenker & Peterson in Journal of Applied Crystallography (1996 29, 178-185).
Installation instructions (coming soon)
Download full source (tarred/gzipped)
More about this program
More code by the author

TubeGen 3.1 [J. Frey]
A new release of the TubeGen program. Generates flat and rolled lattices in either fractional (WIEN 97 input format) or Cartesian (Gaussian 98 input format) coordinates. Rolled lattices are generated as either a hexagonal or a cubic crystal cell. Also allows the generation of arrays of unit cells, replicating the unit cell in each coordiate direction. Please read the User's Guide for more information.

This release features an updated tube-rolling procedure which accounts for warping of the carbon-carbon bonds as the flat graphite lattice is made into a cylinder.

TubeGen Online - Web-Based App

Diamond Online - Web-Based App

Graphite Online - Web-Based App

Download full source (tarred/gzipped)

Go to the TubeGen web site

View the User's Guide

More code by the author

STIGMA 1.0 [J. Frey]
STIGMA (Scanning Tunneling Imaging by Gaussian Molecular orbital Analysis) uses wavefunction information produced by Gaussian 98 and the Tersoff-Hamann s-wave-tip model to create an STM image of the system. Constant-height and constant-current images can be produced. The STIGMA code is available for download; instructions regarding this can be found at the STIGMA page (cited below).


STIGMA Online Manual

More code by the author

Off-Site Links
Here you'll find links to other sites of "nano interest."

Web Links
Purdue NanoHub: Online simulation tools
National Nanotechnology Initiative: U.S. government site for nanotech interests
MIT Tech Review Article: Nanotech article in which we get mentioned!