和佐田 裕昭P indd
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1 19 20 Gaussian 20 Gaussian 1998 J. A. Pople Gaussian Windows Macintosh Gaussian 12 [1] 21 HPC2500 Gaussian Gaussian 03 IT Gaussian
2 Gaussian Gaussian 94 5 [2-6] Gaussian 98 1 [7] Gaussian 03 Gaussian 03 [8] Gaussian 03 Gaussian B3LYP Gaussian 94 Gaussian Gaussian 03 Gaussian 03 [9] [10,11]
3 [12] Gaussian [13] b HF, KS-DFT (B3LYP ) M 2 M MP2 M CISD M CCSD M CCSD(T) M a b tert-
4 ONIOM Gaussian 03 Link 0 Gaussian 03 SCF 1 Z Z # [15] [16] #p rhf/sto-3g opt pop=full STO-3G RHF # p p 0 1
5 -1 1 xyz Z Z n N a 1 R a 2 T a 3 D N n R a 1 n Å T n a 1 a 2 D n a 1 a 2 a 3 Z z zx x Z N N a 1 R N a 1 R a 2 T Z Z Å H O H Gaussian Gaussian Link 0 1 %NPROC=4 4 CPU SCF Gaussian
6 Gaussian 03 HP2500 (hpc hpc Mac OS X telnet ssh Gaussian NQS Gaussian Gaussian CPU Gaussian ftp emacs 3a p8 g03p.err CPU 4 Gaussian example1.dat example1.out Gaussian p8 p16 CPU -lp
7 %NPROC= Hartree-Fock 8 12 CPU 16 CPU [17] CPU CPU CPU 1 CPU p64 CPU CPU CPU 10 2 CPU 5 CPU -lt 3b b NQS g03 cd bench large.dat large.out NQS g03.cmd qsub hpc% qsub g03.cmd Request 5877.sp0 submitted to queue: p8. qstat
8 hpc% qstat p8 type=batch; [ENABLED, RUNNING]; pri=31 0 exit; 6 run; 0 queued; 0 wait; 0 hold; 0 arrive; REQUEST NAME REQUEST ID USER PRI STATE PGRP 1: gauss sp0 w4900xa 31 RUNNING : g03.cmd 5877.sp0 w4900xa 31 RUNNING : TEST1.sh 5879.sp0 w4900xa 31 QUEUED STATE RUNNING QUEUED qstat -a REQUEST ID qstat ID 5877 hpc% qdel -k 5877 Request 5877.sp0 is running, and has been signalled. ID -k 4 Gaussian C qstat more b / hpc% more example1.out CS Chem Office MOLCAT moled hpc% moled < example1.out O H H
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10 moled example1.out Gaussian a.u. force grep hpc% grep 'E(' example1.out SCF Done: E(RHF) = A.U. after 7 cycles SCF Done: E(RHF) = A.U. after 7 cycles SCF Done: E(RHF) = A.U. after 6 cycles SCF Done: E(RHF) = A.U. after 6 cycles hpc% grep 'Maximum F' example1.out Maximum Force NO Maximum Force NO Maximum Force NO Maximum Force YES (1) (2)
11 (3) d 5d 6d (4) (4) ECP (effective core potential) ECP (5) (5) SCF 5 GradGrad...Grad Standard orientation z Input orientation Distance matrix (angstroms): Standard orientation symmetry-adapted 7 basis set 1s 2s 2p x 2p y 2p z 5 1 1s 5 alpha electrons 5 beta electrons 5 Closed shell SCF: SCF 6 SCF Done: SCF Done: E(RHF) = A.U. after 6 cycles a.u. atomic unit hartree 1 hartree kcal/mol ev cm kcal/mol 0 Axes restored to original set 30 Maximum Force Converged? YES Optimized Parameters Å RHF/STO-3G
12 180 名古屋大学情報連携基盤センターニュース Vol.５, No.２ 図 5 １ Gaussian 03 による水の RHF/STO-3G による構造最適化計算の出力ファイル
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15 6-31G* RHF/6-31G* B3LYP/6-31G* Derivative Info. 0 Mulliken Condensed to atoms moview[18] 5 Z Z 5 Normal termination of Gaussian 03 at Thu Mar 16 12:35: Error termination via Lnk1e in /opt/apl/sp/g03/l502.exe. Job cpu time: 0 days 10 hours 13 minutes 40.5 seconds. File lengths (MBytes): RWF= 114 Int= 0 D2E= 0 Chk= 9 Scr= 1 l502.exe qstat CPU root@sp0.cc.nagoya-u.ac.jp (Super-User) nucc -eo FORTRAN
16 IT nucc -me p8 -eo -o g03p.err -lt 100:00:00 -lp 8 -me Gaussian 03 Gaussian 03 HPC2500 Z (1) " 12" 2004 (2) " Gaussian94 " Vol. 29 No (1998) (3) " Gaussian94 " Vol. 29 No (1998) (4) " Gaussian94 " Vol. 29 No (1998) (5) " Gaussian94 " Vol. 29 No (1998)
17 (6) " Gaussian94 " 1999 Vol. 30 No (1998) (7) " Gaussian98 " Vol. 31 No (2000) (8) " 7 Gaussian03 " Vol. 3 No (2004) (9) P. Atkins, R. Friedman "Molecular Quantum Mechanics" Oxford University Press New York 2005 (10) 1990 (11) A. Szabo, N. S. Ostlund "Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory", Dover, 1996,, 1987 (12) M. Springborg "Methods of Electronic-Structure Calculations From Molecules to Solids" John Wiley & Sons New York 2000 (13) K. Raghavachari, J. B. Anderson J. Phys. Chem. 100, (1996) (14) M. Head-Gordon J. Phys. Chem. 100, (1996) (15) (16) Æ. Frisch, M. J. Frisch, G.W. Trucks "Gaussian 03 User's Reference" Gaussian, Inc. (2003) (17) " Gaussian98 " Vol. 32 No (2001) (18) " moplot moview " Vol. 29 No (1998)
和佐田P indd
B3LYP/6-31G* Hartree-Fock B3LYP Hartree-Fock 6-31G* Hartree-Fock LCAO Linear Combination of Atomic Orbitals Gauss Gaussian-Type Orbital: GTO Gaussian- Type Function: GTF 2 23 1 1 X, Y, Z x, y, z l m n
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2000 B3LYP/6-31G Gaussian 98 03 B3LYP/6-31G* Gaussian STO-3G RHF Gaussian RHF/STO-3G B3LYP RHF 6-31G* STO-3G Schrödinger Schrödinger s p d Schrödinger Schrödinger Hohenberg-Kohn Kohn-Sham Kohn-Sham [1-3]
P 和佐田.indd
B3LYP/6-31G* X HGS MOL-TALOU [1] 1 2-4 II CS Chem Office [2] Molecular Dynamics 1 ChemDraw 2 3 Chem 3D 4 Gaussian Input X 28 27 12 13 26 11 29 14 10 15 25 2 9 27 2 21 7 3 43 7 3 5 Cu 41 Cu 4 10 22 28 H
P 和佐田.indd
Gaussian 03 Q Gaussian 03 [1,2] Q U S 1 2 k B 1.38054 10 23 JK 1 T 1 2 Q el Q trans Q rot Q vib 3 Q Q el Q trans Q rot Q vib 1 24 5 U E el E trans E rot E vib S S el S trans S rot S vib 6 3 4 5 6 R R 1.987
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qstat -l ID (qstat -f) qscript ID BATCH REQUEST: 253443.batch1 Name: test.sh Owner: uid=32637, gid=30123 Priority: 63 State: 1(RUNNING) Created at: Tue Jun 30 05:36:24 2009 Started at: Tue Jun 30 05:36:27
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X Gaussian 03 POP Mulliken natural population analysis r Hartree-Fock 1 1 i n i n i 0, 1, 2 2 N 2 N N 3 3 spin spin Mulliken 1955 R. S. Mulliken [1-4] Gaussian 03 Mulliken Mulliken { (r)} 4 4 41 { (r)}
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force 0 m 1 m 2 k (1) (2) 1 2 R R e 0 4 (3) 3 dv/dx 0 x (3) (4) 4 (4) (1) k N 3N x y z 3N 6 3N 5 3N 3N 3N (Hessian) 0 1 (2) V 二次の鞍点 始状態 ( エネルギー極小点 ) 遷移状態 ( 鞍点 ) 遷移状態 終状態 ( エネルギー極小点 ) Gaussian FREQ 2 B3LYP/6-31G(d)
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