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Supercomputing for Nanoscience

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Yang Wang

Pittsburgh Supercomputing Center

2006 SciTech Festival

- The type of fastest and most powerful computers available to us
- Designed for massive mathematical calculations
- Necessary for science and engineering applications

The calculation speed is measured by the number of Floating-point Operations per Second (FLOPS)

- Floating-point is the way that a real number is represented in terms of bits (“0”s and “1”s) in computer
- Typically, a single precision real number is represented by 32 bytes, and a double precision real number is represented by 64 bytes
1 FLOPS = 1 arithmetic operation (+, −, ×, or ÷) per second

- Human ~ 0.001 FLOPS
- Pocket Calculator ~ 10 FLOPS
- Typical home PC ~ few billions FLOPS
- CRAY-1 in 1976 ~ 136 millions FLOPS
- CRAY Y-MP in 1988 ~ 2.7 billions FLOPS

We are in the era of Teraflop (1 trillion floating-point operations per second) computing

- CRAY XT3 at PSC in July 2005 ~ 10 Teraflops
- IBM BlueGene/L (with 131,072 PowerPC 440 CPUs) at LLNL in November, 2005 ~ 280.6 Teraflops
An interesting comparison with game consoles (whose graphical processors are specially designed for rapid graphical image processing):

- Sony PlayStation 3 in 2006 ~ 2 Teraflops
- Microsoft Xbox 360 in Nov. 22, 2005 ~ 1 Teraflop

Match the quantity…

602,000,000,000,000,000,000,000

(602 billion trillion)

10,000,000,000,000 to

100,000,000,000,000 (10-100 trillion)

1,000,000,000,000

(one trillion)

6,446,131,400

(6.446 billion)

196,939,900

(197 million)

2,358,695

(2.4 million)

…with the item

Molecules in a mole (18g) of water

Cells in the human body

Stars in the Milky Way

Population of the Earth

Surface area of the earth

(in square miles)

Population of Pittsburgh Metropolitan Area

Credit: Laura F. McGinnis, Pittsburgh Supercomputing Center

Supercomputer Peak Speed

1 Teraflop

http://www.top500.org

- A household light bulb – 40 ~ 100 Watts
- Xbox 360 – 160 Watts
- A typical CPU – 60 ~ 100 Watts
- Human brain – 20 Watts
- Human body – 100 Watts
- IBM BlueGene/L at LLNL – 1.2 MegaWatts (~ lighting 3000 family houses)

- Aircraft design
- Automobile design
- Drug discovery
- Weather forecast
- Study of earth quakes
- Special effects in movies
- Much needed in many research areas in physics, chemistry, astronomy, materials science, biology, economics, etc.

What Makes Supercomputer Super Fast

Parallel Computing: make multiple CPUs working together to solve one problem

How to Get a Job Done Fast?

Goal: move 64 bowling balls from one place to another

= 2 hours and 8 minutes

One child: 2 minutes per ball

= 1 hours and 4 minutes

One adult: 1 minute per ball

Do the Job in Parallel

16 children= 4 minutes!

64 children= 1 minute!

http://www.psc.edu

- TCS (LeMieux), 6.0 TeraFLOPS
- 3000 Processors (1-GHz Alpha EV68)
- 4GB memory per node with 4 processors share the memory

- CRAY XT3 (BigBen), 10 TeraFLOPS
- 2068 Processors (2.4 GHz AMD Opteron )
- 1 GB memory per processor

- Petaflop (quadrillion floating-point operations per second) computing
- Fujitsu in 2010 ~ 3 Petaflop
- IBM BlueGene/P in 2007 ~ 1 Petaflop

- After Petaflop: Exaflop (quintillion floating-point operations per second)

Early Nanotechnology

Lycurgus cup (4th century AD)

The Lycurgus Cup is made of glass. It is Roman and dates to the fourth century AD. The Cup is surrounded by a frieze showing the myth of King Lycurgus. It belongs to a type of Roman glass called cage cups. One of the very unusual features of the Cup is its color. When viewed in reflected light, for example in daylight, it appears green. However, when a light is shone into the cup and transmitted through the glass, it appears red. Only a handful of ancient glasses showing this effect are known, all of them Roman.

This unusual feature is the effect of gold and silver nanoparticles in the glass

Individual Hair on Albert’s head

100,000 nm

Radius of a Hydrogen atom

~ 0.5 Å = 0.5 × 10−10meter = 0.05 nm

Subatomic Scale

?

?

Galactic Scale

“Micro”Scale

Atomic Scale

“Nano”Scale

“Macro” Scale

1020m

10−6m

1010m

101m

10−9m

10−15m

10−10m

- Nano means one billionth
10−9 = 0.000000001

- One nanometer = 0.000000001 meter

1 nm

Water (H20)

Nanometer Scale

25

n = 5

16

n = 4

Energy / (h2/8ml2)

9

n = 3

4

n = 2

1

n = 1

0

Small Size (1 nm ~ 100 nm) Can Make Big Difference

- Size and surface area effectsWhile fundamental materials properties remain the same, size, shape and large surface area alter some behaviors, e.g., work function, solubility, chemical potential, contaminate sorption
- Critical size and characteristic length scaleInteresting or unusual properties because the size of the system approaches some critical length (includesquantum effects). Many characteristics of material may have normal or nearly normal behavior
- Non-extensive propertiesNano-sized particles are not large enough to have extensive properties, and become effectively polymorphs of “bulk” materials and statistical homogeneity may not be valid.

- Super fast/small computers
- High density data storage
- Super strong materials
- Super slippery materials
- Tissue engineering
- Smart drug delivery
- Sensors
- Filters and membranes
- Adhesives, sealants, coatings, etc.

“Building Block”: Atom

“Glue” or the bonding “material”:Electron

Physical properties of matter, such as whether it is metal or non-metal, magnetic or non-magnetic, its mechanical strength, and so on, are determined by the behavior of the electrons (electronic states).

Buckyball Fullerene C60

Quantum Dot

Carbon Nanotube

1nm = 10−9m = 10Å, about 4 to 5 bonded atoms long

Electron:

Nucleus:

Many-electron problem

One-electron problem

Density Functional Theory

electron-electron interaction electron-nucleus interaction many-electron Schrödinger equation

non-interacting electrons move in an effective potential: Veff[r] one-electron Schrödinger equation

- Electron distribution
- Bonding, charge density, etc.

- Magnetic properties
- Ferromagnetic, anti-ferromagnetic, nonmagnetic, magneto-anisotropy, etc.

- Energetics
- Phase stability, crystal structure, etc.

- Electronics
- Conductivity, spintronics, magneto-electronic coupling, etc.

Fe nanoparticle (~ 5nm, 4,409 atoms) embedded in B2-FeAl compound. Total simulation size: 16,000 atoms

BCC Fe nanoparticle

B2-FeAl compound

Science of Disk Drives

Fe0.5Pt0.5 random alloy

L10-FePt nanoparticle

Ab initio calculation to determine the electronic and magnetic properties of ferromagnetic nano-structures: spherical L10-FePt nanoparticle (3.86 nm in diameter) embedded in FePt random alloy.

Total simulation size: 14,400 atoms.

The electronic and magnetic structure of the L10-FePt nanoparticle (a nano-structured material with potential applications in high density data storage: 1 particle/bit)

- There forms a screening region (~ 4 Å) below the surface of the nanoparticle that screens out the effect of the external random alloy from influencing the interior region
- The Fe (red balls) and Pt (silver balls) atoms in the interior region have the same electronic and magnetic properties as in the L10-FePt crystal

The locally self-consistent multiple scattering (LSMS) method (a Gordon-Bell Prize winner)

- A linear scaling ab initio electronic structure calculation method based on multiple scattering theory
- Achieves as high as 81% peak performance of CRAY-XT3
- It requires 1 petaflop machine to perform realistic simulations for nanostructures of ~ 50nm (~ 5,000,000 atoms) in size.

- With a Teraflop supercomputer, we can perform electronic structure calculations for nano-materials made of up to 100,000 atoms (~ 10 nm in dimensional size)
- It requires a Petaflop supercomputer to perform electronic structure calculations for nanoparticles of ~ 50nm (~ 5,000,000 atoms) in size, and other nanomaterials such as nanowire and nanotubes.

Will supercomputing help to build such nano-robot, a tiny machine for curing cancer in your body?