胡維平 國立中正大學化學暨生物化學系 Aug. 30, 2017

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1 胡維平 國立中正大學化學暨生物化學系 Aug. 30, 2017
計算機發展史與 分子模擬程式簡介 胡維平 國立中正大學化學暨生物化學系 Aug. 30, 2017

2 An Early Computer ENIAC, 1947 US Army 27 ton 63 m2 5 kHz ~400 FLOP
150 kW

3 Computers in Early Space Programs
IBM 7090 1960 Transistor Based ~100 K FLOPs 50000 transistors

4 Cray-2 Computer 1985 Cray-2 250 MHz 1.9 GFLOP 256 MW 1.5 m X 2.0 m

5 PC Evolution Year CPU Clock Memory HD 1986 IBM XT 4.77 MHz 640 KB
20 MB 1988 IBM AT 12 MHz 2 MB 40 MB 1989 80386 16 MHz 4 MB 80 MB 1991 80486 33 MHz 8 MB 1997 Pentium 100 MHz 64 MB 20 GB

6 PC Evolution Year CPU Clock Memory HD 1998 Pentium II 400 MHz 512 MB
80 GB 2000 Pentium III 733 MHz 1 GB 120 GB 2002 Pentium 4 2.4 GHz 2 GB 200 GB 2006 Core 2 Quad 2.8 GHz 8 GB 500 GB 2009 i7-920 3.8 GHz 12 GB 1 TB 2015 i K 3.6 GHz 64 GB 3 TB 2017 i X 4.3 GHz 128 GB 6 TB

7 14 nm 22 nm 32 nm 45 nm 250 nm (Pentium) "Moore's law" is the observation that the number of transistors in a dense integrated circuit has doubled approximately every two years.

8 Sunway TaihuLight -神威·太湖之光 93 Peta 10,649,600 cores
FLOPS (double precision) Intel 8088/8087: 1 M Cray 2: 2G G = 109; T = 1012; P = 1015 From TOP500 (June 2017): Sunway TaihuLight -神威·太湖之光 93 Peta 10,649,600 cores NUDT Tianhe-2: P (2nd) Cray XC50: 20 P (3rd) ALPS (NCHC 御風者): cores, 177 TFlop (> 500th) (was 445 th at 2015) (was 370th at 2014) (was 42nd at 2011)

9 國家高速網路與計算中心 NCHC 御風者 ALPS — Acer AR585 F1 Cluster US$ 10,000,000
25,600 compute cores 177 TFlops Processors: AMD Opteron 6174, 12 cores, 2.2GHz (compute nodes) AMD Opteron 6136, 8 cores, 2.4GHz (fat nodes) Main Memory (per node): 128 GB (compute nodes) 256 GB (fat nodes) US$ 10,000,000

10 中國國家超級計算廣州中心 Tianhe-2 US$ 100,000,000
16,000 compute nodes (3,120,000 cores) 33.9 PFlops Processors (per node) Two Intel Xeon E5, 12 cores, 2.2 GHz Three Intel Phi, 57 cores, 1.1 GHz Main Memory (per node) 88 GB (compute nodes) US$ 100,000,000

11 中國國家超級計算無錫中心 US$ 100,000,000 Sunway TaihuLight
10,649,600 cores 33.9 Pflops $232 millions Processors : Sunway SW C 1.45GHz 260-core, 64-bit RISC chip that exceeds 3 teraflops Main Memory 1,310,720 GB

12 System Architecture Est. Rmax：> 1700 TF
Intel Omni-Path (100Gb/s) for both Comm/IO System Architecture NCHC 新 Peta 級主機 Internet Storage Island CPU Island GPU Utility Island BigMem 2.2PB 250TB 1PB 6TB NCHC TC Gateway Thin node 192GB 502 nodes Fat node 384GB 128 nodes Shared Ethernet LAN for control and mgmt 10G Eth 40Gb/s EF: CPU:0.8 GPU:0.7 1 nodes 80 cores 6 TB Mem. 3TF 630 nodes 25,200 cores 1051 TF 20 nodes 64 nodes 256 GPUs 684TF Top500 June 2017 排名 66 Est. Rmax：> 1700 TF 開放服務 NCHC tiered storage

13 Programs for Molecular Modeling
Gaussian Molpro Gamess Spartan (Q-Chem) ADF CASTEP VASP

14 分子結構模擬 模擬什麼？ Structure  Properties  Chemistry 化學式  結構式  三度空間結構
C6H6O   　 結構  熱力學性質 電荷分布 光譜性質 分子間作用力及反應性

15 Methods for Molecular Modeling
Force Field Methods (Functional form + Parameter Sets  Properties) Amber, Charmm, MMFF, Sybyl, MM2 Density Functional Theory (Density  Properties) BLYP, B3LYP, B98, MPW1PW91, M06-2X, BMK, DSD-BLYP Ab Initio Theory (Latin, “from the beginning”) (Wavefunction  Properties) HF  MP2  QCISD(T), CCSD(T), BD(T) CIS  TD-DFT  EOM-CCSD, CCn CASSCF  CASPT2  MRCI  MRCI-PT2 Semiempirical (Wavefunction and parameter set  Properties) ZINDO, CNDO, INDO/S, MNDO, AM1, PM3, PM6

16 Spartan 軟體簡介 Wavefunction Inc. 1991 創立，提供化學研究學者及教師方便使用的分子模擬工具。
Spartan 16 結合了完整的分子模擬圖形介面以及功能強大的量子化學計算軟體 (Q-Chem)。 國家高速網路與計算中心 (NCHC) 已購置42個浮動使用授權，下載安裝後只要曾向NCHC登記過網址的研究單位都可隨時於個人電腦上使用，於校外亦可藉由VPN連線授權使用。 Spartan 16 for Window 安裝及使用請參閱：