Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

New Chemistry Software Automatically Generates Computer Code

09.09.2003


A new software tool promises to aid scientists whose research has forced them to lead double lives - as computer programmers.


Ponnuswamy Sadayappan



The tool, called the Tensor Contraction Engine (TCE), automatically generates the computer code that chemists, physicists, and materials scientists need to model the structure and interaction of complex molecules, saving them weeks or even months of work.

By making the computer code more efficient, the TCE could even reduce the amount of time required for these projects at national laboratories and supercomputer centers around the country.


“With this tool, scientists can focus on their research rather than writing and debugging software,” said Ponnuswamy Sadayappan, professor of computer and information science at Ohio State University. “They can focus on innovation.”

Sadayappan leads the consortium that introduced a prototype of the TCE Sept. 7 at the national meeting of the American Chemical Society in New York. Partners on the project include Louisiana State University, Oak Ridge National Laboratory, Pacific Northwest National Laboratory, and University of Waterloo.

Once the software is fully developed, it could impact two
of the broadest areas of research in the physical sciences. Both computational chemistry and computational physics concern the behavior of atoms and molecules on very large scales, and they encompass a diverse array of specialties, such as atmospheric chemistry, protein structure, materials science, and industrial chemical processing.

This research also consumes a great deal of supercomputer time around the country. In a recent study, Sadayappan and his colleagues reported that computational chemistry and materials science projects accounted for some 85 percent of computer usage at the Pacific Northwest National Laboratory, 30 percent at the National Energy Research Scientific Computing Center at Lawrence Berkeley National Laboratory, and 50 percent of one computer system at the San Diego Supercomputer Center.

The reason: the interactions of atoms and molecules are so complex that scientists model them using elaborate mathematical matrices, or tensors, containing tens of millions to billions of elements. The modeling process involves dozens to hundreds of manipulations called tensor contractions, which are extremely complex and hard to program efficiently.

The tedious job often falls to graduate students and post-doctoral researchers, who labor for months to write the code before scientists can begin to do any actual research.

Once fully developed, the TCE will perform the task in hours, generating an efficient parallel program that uses a minimum amount of computer memory and fast communication between parallel processors on a supercomputer, Sadayappan said.

Given a mathematical description of a problem in computational chemistry or physics, the TCE generates code in the FORTRAN computer language, which is the most common language used for this kind of research. Scientists then plug that code into their own software programs.

Sadayappan got the idea for the TCE while collaborating on a particularly arduous electronic structure theory project with John Wilkins, an Ohio Eminent Scholar and professor of physics at Ohio State.

“Some problems cropped up during the course of that work that made us realize the magnitude of the challenges involved, and by the time it was all over we had the idea for a way to make things easier,” Sadayappan said.

At an annual workshop hosted by Russell Pitzer, professor of chemistry at Ohio State, Sadayappan discovered that some chemists had been thinking along similar lines. He joined with Pitzer and Gerald Baumgartner, an assistant professor of computer and information science with expertise in programming language design, and other chemists and computer scientists to form the consortium.

Partners outside of Ohio State include Jagannathan Ramanujam at Louisiana State University, David Bernholdt and Robert Harrison at Oak Ridge National Laboratory, Marcel Nooijen at the University of Waterloo, and So Hirata at Pacific Northwest National Laboratory. Bernholdt gave the first of the consortium’s presentations on the TCE at the American Chemical Society meeting Sunday.

“The success of such an endeavor requires a team with expertise in several disciplines,” said Sadayappan, “and we are fortunate to have that -- with world renowned quantum chemists Nooijen and Harrison, Bernholdt’s expertise in developing software interfaces, Ramanujam’s expertise in compilers, and Hirata’s ability to bridge computer science and chemistry, as evidenced by his prototype TCE.”

Sadayappan also emphasized the work that many postdoctoral researchers and students have contributed to the project, both in developing the ideas and implementing the software, which now contains almost 50,000 lines of code.

Now is the time for potential users of the TCE to join with the consortium and help shape the system’s functionality, Sadayappan said. Interested scientists should contact him to attend future project meetings and participate in dialogs concerning new features.

Development of the Tensor Contraction Engine was funded by the National Science Foundation through its Information Technology Research program, with the intention that the TCE source code will be made available to researchers. The consortium members from the national laboratories have been funded by the Department of Energy.


Contact: Ponnuswamy Sadayappan, (614) 292-0053;
Sadayappan.1@osu.edu

Written by Pam Frost Gorder, (614) 292-9475; Gorder.1@osu.edu

Pam Frost Gorder | Ohio State University
Further information:
http://www.osu.edu/researchnews/archive/tcengine1.htm
http://www.itr.nsf.gov/
http://www.energy.gov/engine/content.do

More articles from Information Technology:

nachricht The Flexible Grid Involves its Users
27.09.2016 | Fraunhofer-Institut für Angewandte Informationstechnik FIT

nachricht Optical fiber transmits one terabit per second – Novel modulation approach
16.09.2016 | Technische Universität München

All articles from Information Technology >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: First-Ever 3D Printed Excavator Project Advances Large-Scale Additive Manufacturing R&D

Heavy construction machinery is the focus of Oak Ridge National Laboratory’s latest advance in additive manufacturing research. With industry partners and university students, ORNL researchers are designing and producing the world’s first 3D printed excavator, a prototype that will leverage large-scale AM technologies and explore the feasibility of printing with metal alloys.

Increasing the size and speed of metal-based 3D printing techniques, using low-cost alloys like steel and aluminum, could create new industrial applications...

Im Focus: New welding process joins dissimilar sheets better

Friction stir welding is a still-young and thus often unfamiliar pressure welding process for joining flat components and semi-finished components made of light metals.
Scientists at the University of Stuttgart have now developed two new process variants that will considerably expand the areas of application for friction stir welding.
Technologie-Lizenz-Büro (TLB) GmbH supports the University of Stuttgart in patenting and marketing its innovations.

Friction stir welding is a still-young and thus often unfamiliar pressure welding process for joining flat components and semi-finished components made of...

Im Focus: First quantum photonic circuit with electrically driven light source

Optical quantum computers can revolutionize computer technology. A team of researchers led by scientists from Münster University and KIT now succeeded in putting a quantum optical experimental set-up onto a chip. In doing so, they have met one of the requirements for making it possible to use photonic circuits for optical quantum computers.

Optical quantum computers are what people are pinning their hopes on for tomorrow’s computer technology – whether for tap-proof data encryption, ultrafast...

Im Focus: OLED microdisplays in data glasses for improved human-machine interaction

The Fraunhofer Institute for Organic Electronics, Electron Beam and Plasma Technology FEP has been developing various applications for OLED microdisplays based on organic semiconductors. By integrating the capabilities of an image sensor directly into the microdisplay, eye movements can be recorded by the smart glasses and utilized for guidance and control functions, as one example. The new design will be debuted at Augmented World Expo Europe (AWE) in Berlin at Booth B25, October 18th – 19th.

“Augmented-reality” and “wearables” have become terms we encounter almost daily. Both can make daily life a little simpler and provide valuable assistance for...

Im Focus: Artificial Intelligence Helps in the Discovery of New Materials

With the help of artificial intelligence, chemists from the University of Basel in Switzerland have computed the characteristics of about two million crystals made up of four chemical elements. The researchers were able to identify 90 previously unknown thermodynamically stable crystals that can be regarded as new materials. They report on their findings in the scientific journal Physical Review Letters.

Elpasolite is a glassy, transparent, shiny and soft mineral with a cubic crystal structure. First discovered in El Paso County (Colorado, USA), it can also be...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Call for Paper – Panacea Green Infrastructure?

30.09.2016 | Event News

HLF: From an experiment to an establishment

29.09.2016 | Event News

European Health Forum Gastein 2016 kicks off today

28.09.2016 | Event News

 
Latest News

First-Ever 3D Printed Excavator Project Advances Large-Scale Additive Manufacturing R&D

30.09.2016 | Materials Sciences

New Technique for Finding Weakness in Earth’s Crust

30.09.2016 | Earth Sciences

Cells migrate collectively by intermittent bursts of activity

30.09.2016 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>