The main purpose of the wulffnet cluster is to support synchrotron
related research programs that are conducted at Sector 5 of the
Advanced Photon Source. These include programs from biological
sciences to x-ray tomography. To support these programs LAM/MPI
as well as PVM are available on the cluster.
FFTW has also been installed
on the cluster. In addition, serial jobs can be submitted using
the Portable Batch System.
Computational Materials Science and X-ray Diffuse Scattering Calculations
The primary purpose of this project is to understand the two dimensional
structure of two dimensional surface alloys using a variety of techniques.
These techniques include measuring the x-ray diffuse scattering.
The diffuse program written by Dr. Brent Butler as well as the
discus program written by Dr. R.B. Neder and Dr. Th Proffen
are being evaluated for use on the cluster. This work is being funded
by the National Science Foundation DMR-0076063 and is a collaboration between
Dr. Mark Asta
, his group at Northwestern, Dr. Denis Keane, and Dr. John Quintana.
The cluster is also being used to run an
ab initio molecular dynamics program
to model the
Pb/Ge interface system.
Ab Initio Crystal Structure Determination from Powder Diffraction Data
Dr. Richard Harlow (DuPont) has been collaborating with Dr. Armel Le Bail's
group on a MPI based version of the
for performing ab initio structure determinations. A version of this
code is currently being tested on the Wulffnet cluster.
DND-CAT has a dedicated x-ray tomography station in the rear of one
of its bending magnet enclosures. By collecting x-ray radiographs
of a sample as it is rotated through 180 degrees, the
three dimensional structure of
the sample interior can be reconstructed inside of computer memory.
Currently, the CCD used to collect data contains 1300 x 1340 pixels and
replaces an older 1K x 1K system. The cluster is used to reconstruct
the data from the various images.
DuPont works with tire companies to develop their 'Engineered Elastomer'
products for various end uses. A continuing challenge has been to define
the distribution of reinforcing fibers in rubber to be able to relate this
structural feature to process variables and end-use performance. Using
X-ray microtomography, DuPont has successfully produced 3D images of
individual Kevlar pulp fibers in rubber. Heretofore, the only way
to look at pulp distribution has been via microscopy and this only
produces 2D pictures. Fibers have typical diameters of 1 to 12 microns
and lengths of 0.5 mm. A three dimensional movie of a "master batch"
containg 23% fiber pulp in elastomer is available for download.
Genetic modifications in plants can lead to structural modifications
within a plants seeds. DuPont has been investigating changed in
arabidopsis seeds since its genetic code is completely known. Wild
type seeds with no genetic alterations are compared with seeds
that have genetic alterations made. A three dimensional movie
of three arabidopsis seeds mounted on a glass fiber is available
The images were provided by Dr. Randy Barton of DuPont and were prepared
by David E. Jones of DuPont Scientific Computing.
- Download a movie of a Kevlar reinforced elastomer composite.
In some sense, this is mostly associated with the Tomography project, but
other applications can use it as well. Large data sets can be transferred
onto or created on the Wulffnet Cluster so they can be backed up to CD-R
using the Plasmon CD Robot. In order to fit the most data on the CD's they can
be compressed using bzip2 .
The root of this is a simple script which creates a series of PBS jobs to
compress individual files on the clusters disks.
Wulffnet is currently being used as a test cluster for the
Midwest Center for Structural Genomics
through collaborations with Dr. Steve Weigand. Local users can learn more about the user of the
cluster for DND
Macromolecular Crystallography research.
John Quintana (firstname.lastname@example.org) / May 2001