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CRD Method for Understanding Nanostructures Is a Gordon Bell Finalist

November 6, 2008

LS3DF.jpg

A test run of LS3DF, which took one hour on 17,000 processors of Franklin, performed electronic structure calculations for a 3500-atom ZnTeO alloy. Isosurface plots (yellow) show the electron wavefunction squares for the bottom of the conduction band (left) and the top of the oxygen-induced band (right). The small grey dots are Zn atoms, the blue dots are Te atoms, and the red dots are oxygen atoms.

The key to energy independence from petroleum, coal and other fossil fuels, could be tiny materials called nanostructures. At approximately 100,000 times finer than human hair, these structures may be microscopic individually, but in groups of thousands, they could revolutionize solar cell design by providing a cost-efficient resource for harvesting solar-energy.

To theoretically understand and simulate the energy harnessing potential of nanostructures, a team of researchers in the Berkeley Lab’s Computational Research Division (CRD) developed the Linear Scaling Three Dimensional Fragment (LS3DF) method. The computer algorithms in this method use a “divide-and-conquer” technique to efficiently gain insights into how nanostructures function in systems with 10,000 or more atoms.

A test run of LS3DF, which took one hour on 17,000 processors of Franklin, perfo

A test run of LS3DF, which took one hour on 17,000 processors of Franklin, performed electronic structure calculations for a 3500-atom ZnTeO alloy. Isosurface plots (yellow) show the electron wavefunction squares for the bottom of the conduction band (left) and the top of the oxygen-induced band (right). The small grey dots are Zn atoms, the blue dots are Te atoms, and the red dots are oxygen atoms.

“By incorporating the correct chemical formulas into efficient computer programs, scientists can learn a lot about the structures and properties of molecules and solids.… I like to think of computers as chemistry’s ‘third leg.’ In most cases, computer simulations complement information obtained by chemical experiments, but in some cases it can predict unobserved phenomena,” says Dr. Lin-Wang Wang, a CRD computational material scientist and leader of the LS3DF project.

The developers of LS3DF are finalists in the Association for Computing Machinery’s (ACM) Gordon Bell Prize Competition, which recognizes outstanding achievement in high-performance computing applications. The winners will be announced on November 20, 2008 at the SC08 Conference in Austin, Tex.

According to Wang, traditional methods for calculating the energy potential of nanostructure systems containing 10,000 or more atoms can be very time consuming and resource intensive. Because these techniques calculate the entire structure as a whole system, the compute time, disk space and memory required to determine the energy potential of these structures grows to the third power of the system’s size. That means calculating a 1000-atom system will be a thousand times more expensive than calculating a 100-atom system.

He notes that LS3DF offers a more efficient way for calculating energy potential because it is based on the observation that the total energy of a large nanostructure system can be broken down into small pieces, and each piece can be calculated separately. Wang refers to this technique as “divide-and-conquer.”

The total energy of the large system has two components: electrostatic energy and quantum mechanical energy. To determine the structure’s total quantum mechanical energy, the LS3DF method breaks the entire structure into small fragments, applies its algorithm to each individual piece, and then combines the results of the pieces to get a total for the whole system. Scientists say that under the traditional density functional theory methods, the quantum mechanical energy calculation typically requires the most compute time and resources. By breaking up the big problem into small pieces, LS3DF can solve it a lot more quickly and efficiently, making the computational cost proportional to the total number of the atoms in the system.

Meanwhile, the electrostatic energy of large-scale nanostructure systems is not as resource intensive to solve. Scientists calculate this classical energy by looking at the whole system, which may contain tens of thousands of atoms. This problem is solved separately from the quantum mechanical energy. In the end, both energy results are combined to get the structure’s total energy potential.

When team members tested the LS3DF method on supercomputers at the Department of Energy’s (DOE) National Energy Research Scientific Computing Center (NERSC) in Oakland, Calif., National Center for Computational Sciences (NCCS) at Oak Ridge National Laboratory in Oak Ridge, Tenn., and Argonne Leadership Computing Facility in Argonne, Ill., they found that the LS3DF method can work hundreds to thousands of times faster than traditional density functional theory calculations for systems with tens of thousands of atoms, and yielded essentially the same results.

“The core of LS3DF is a novel patching scheme that cancels out the artificial boundary effects caused by dividing the system into smaller fragments,” says Wang. “This cancellation is what gets us the same results as the traditional method.”

Because LS3DF scales almost perfectly with the number of compute cores, it is the first electronic structure code that runs efficiently on computer systems with tens to hundreds of thousands of cores. On 17,280 cores of the dual-core Cray XT4 (Franklin) at NERSC, LS3DF achieved 32 Tflop/s or 32% of the peak floating-point performance of the machine. On 30,720 cores of the quad-core Cray XT4 (Jaguar) at NCCS, LS3DF reached 60 Tflop/s or 23% of the theoretical peak. In a later run on the IBM BlueGene/P system (Intrepid) at Argonne, the code achieved 107.5 Tflop/s on 131,072 cores, or 24.2% of peak.

Energy Independence from Fossil Fuels     

Scientists agree that a fundamental understanding of nanostructure behaviors and properties could provide a solution for curbing our dependence on petroleum, coal, and other fossil fuels. 

According to Wang, nanostructure systems are cheaper to produce than the crystal thin films used in current solar cell designs, and offer the same material purity. In addition, nanostructures are extremely versatile. They can act as electrodes to carry electric currents, or active materials that absorb sunlight and convert it to electricity. 

One type of nanostructure, called quantum dots, actually changes color with size. Scientists say this color, or band gap, affects the type of light that the structure absorbs, which will be very useful for designing solar cells. 

“We still don't quite understand how the electron moves around in a nanostructure, and how such properties depend on the size, geometry, composition, and surface passivations.… Understanding such dependence  will allow us to design nanostructures for desired applications, and LS3DF can help us to understand and predict these properties with computers,” says Wang.

Other authors on the Gorden Bell paper include the Berkeley Lab’s Byounghak Lee, Hongzhang Shan, Zhengji Zhao, Juan Meza, Erich Strohmaier, and David Bailey.


About Computing Sciences at Berkeley Lab

The Lawrence Berkeley National Laboratory (Berkeley Lab) Computing Sciences organization provides the computing and networking resources and expertise critical to advancing the Department of Energy's research missions: developing new energy sources, improving energy efficiency, developing new materials and increasing our understanding of ourselves, our world and our universe.

ESnet, the Energy Sciences Network, provides the high-bandwidth, reliable connections that link scientists at 40 DOE research sites to each other and to experimental facilities and supercomputing centers around the country. The National Energy Research Scientific Computing Center (NERSC) powers the discoveries of 6,000 scientists at national laboratories and universities, including those at Berkeley Lab's Computational Research Division (CRD). CRD conducts research and development in mathematical modeling and simulation, algorithm design, data storage, management and analysis, computer system architecture and high-performance software implementation. NERSC and ESnet are DOE Office of Science User Facilities.

Lawrence Berkeley National Laboratory addresses the world's most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab's scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the DOE’s Office of Science.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.