Massive Molecular Dynamics Simulation for Studying 100 Million Atoms System

1. Massive Molecular Dynamics Simulation for Studying 100 Million Atoms System 김상필, 이승협, 김경수, 이승철, 최정혜, 이규환, 이광렬 한국과학기술연구원, 미래기술연구본부 전산재료과학 심포지움, 2006. 10. 26-27, 제주 ICC

2. Deposition in Co-Al System Co on Al Al on Co

3. Simulation of Defects Materials science is all about the defects.

4. Cover Image of Nature Materials (2006. 10.) “Previous MD simulations have not seen the evolution of the strain from one- to three-dimensional compression that is observed in diffraction experiments. Our large-scale MD simulations of up to 352 million atoms resolve this important discrepancy through a detailed understanding of dislocation flow at high strain rates.” Nature Materials, 5, 805-809 (2006).

5. Nanoscience and Nanomaterials

6. Simulation in (sub) Atomic Scale First Principle Calculation Molecular Dynamic Simulation 10 nm : >1,000,000 atoms 100 nm : >1,000,000,000 atoms

7. 실질적 (공학적) 의미의 해석시스템 • 광범위하고 신뢰할만한 계산기법의 개발 • Advanced first principle approach • Reliable parameter DB의 구축 (TB parameters, force field) • 대규모 계산능력을 갖춘 hardware와 관련 software등 계산환경의 구축 • Multiscale simulation 기법 등 계산 algorithm 의 개발 • 가상현실 수준의 가시화 기술 및 Man-Machine-Interface 기술의 개발

8. 공정모사 나노 소자를 위한 차세대 TCAD • Atomic scale description of the devices • Electron transport in subatomic scale and via non-continuum media 소자 모사 소자구조 정의 소자 특성

9. 핵심역량 증진사업 (KIST) • 1 억 개 입자로 구성된 계의 거동을 해석하기 위한대규모 MD/MC 전산모사 기술 개발 • 나노 소자의 소자특성 해석을 위한Electron transport 해석 기술 개발 나노 CMOS FET 모사를 위한 차세대 TCAD의 prototype 구현

10. The present talk • Introduction to LAMMPS (parallel MD code) • Modification or improvement for materials science • Public release informations • 50M atoms system demo • Performance report at KIST grand supercomputer

11. LAMMPS • Large-scale Atomic/Molecular Massively Parallel Simulator • By Dr. S. Plimpton (http://www.cs.sandia.gov/~sjplimp) • Classical MD Code with • MPI parallelism (Suitable for PC cluster system) • Spatial-decomposition of simulation domain • Runs on a single processor or in parallel • Open-source distribution (C++) • atomic, polymeric, biological, metallic, granular, or hybrid systems • 유일하게 400억 개 원자 시스템에서의 MD 모사를 구현 L-J potential for 100 steps

12. Stress in Cu nanowires Entangled polymer chains Lipid membrane self-assembly LAMMPS • Implemented Potential • pairwise potentials: Lennard-Jones, Coulombic, Buckingham, Morse, Yukawa, frictional granular, tabulated, hybrid • molecular potentials: bond, angle, dihedral, improper, class 2 (COMPASS) • polymer potentials: all-atom, united-atom, bead-spring • long-range Coulombics: Ewald and PPPM (similar to particle-mesh Ewald) • CHARMM and AMBER force-field compatability

13. Stress in Cu nanowires Entangled polymer chains Lipid membrane self-assembly LAMMPS • Modification of LAMMPS  KIST-LAMMPS • Integration of Tersoff potentials for Si, Ge, C interactions • EAM potential data base for various transition metals • Implement of a powerful crystal builder for thin film process simulation

14. Public Release of KIST-LAMMPS

15. Public Release of KIST-LAMMPS

16. Crystal Builder Graphite Diamond Tetrahedral Carbon (4-ring) Lonsdaleit Zincblende β-tridymite

17. Diamond Surface (011) (111)

18. New crystal builder orient x i j k    orient y i j k    orient z i j k specify orientation tensor of the surface    lattice vector a             a : lattice parameter in Å    fill box xi xf yi yf zi zf specify box size : length in x axis =a*(xf-xi)    fill primitive x1 x2 x3 y1 y2 y3 z1 z2 z3 specify primitive vector of each axis    fill basis n {ni xi yi zi}             specify basis atom and its position n : number of basis atoms ni : index of atom specified in potential file xi yi zi : position of i atom w.r.t origin           {} : repeat for i=1..n New force field type (to be released) manybody [Tersoff | Brenner] Specify new potential category : manybody and specify the new potential : Tersoff or Brenner New Commands Si, Ge, C, N, O

19. Benchmark of LAMMPS • KIST-LAMMPS (Sep. 2006) • EAM (Au), Tersoff (Si) • 300K nvt ensemble • Δt = 1 fs, 1,000 steps • @ grand2.kist.re.kr • Intel Xeon 2.5GHz, 2Gbytes RAM • 1024 CPU, Myrinet • 3.07 TFlops

20. Elapsed Time EAM Tersoff

21. 50,000,000 Atoms System Demo • Scenario 2 Ar atoms of 10keV  Au (001) substrate of 50M atoms • Calculation condition • EAM+ZBL potential • Au substrate : 204 × 163.2 × 25.5 nm3 • Position output every 10,000 steps • Δt = 1 fs • 128 cpu @ grand2.kist.re.kr • Used memory : 28Gbytes in total

24. 9.8 hours per 104 MDs Elapsed Time

25. Visualization using AtomEye* Visualization by AtomEye* • Up to 4 M atoms: Serial Version • Beyond 4 M atom: Parallel Version • AtomEye is memory and I/O intensive program. 16 CPUs (Parallel version) 1 million atoms *http://164.107.79.177/Archive/Graphics/A3/A3.html

26. Public Release of KIST-LAMMPS http://diamond.kist.re.kr/SMS

27. 4th Conference of ACCMS (2007. 9. 13~16) 한국과학기술연구원, 국제협력관 컨벤션홀 http:// www-lab.imr.edu/~accms

28. Founded in Aug. 2000 @ Sendai • Prof. Y. Kawazoe (Tohoku Univ.)Prof. G. P. Das (IACS)Prof. B. L. Gu (Tsinghua Univ.) • To enhance corporation in Asian region on computational materials science. • Similar to Psi-k network or Pan American Consortium of Theorists (PACT) • Conferences of ACCMS • 1st Conference (Bangalore, India, Nov. 29 – Dec. 1, 2001.) • 2nd Conference (Novosibirsk, Russia, Jul. 14-16, 2004.) • 3rd Conference (Beijing, China, Sep. 8-11, 2005.) • WGM on Clusters and Nanomaterials (Sendai, Japan, Sep. 7-9, 2006.) • 4th Conference (Seoul, Korea, Sep. 13-16, 2007)

29. Scope • From ab-initio calc. to MD/MC simulation • From electron transport, materials process, property predition • From molecular devices to alloys Plenary lecture (45min) : 3 Invited (25min) : 21 Contributed Oral (15min) : 25 Contributed Poster : 77 Participant : ~150