Running Gaussian 03Running Gaussian 03

Lim, Seok Ho

Byun, Jae Duk

OUT LineOUT Line

IntroductionIntroduction TaskTask Program StartProgram Start Input file exampleInput file example Basis setBasis set OutputOutput Method of executionMethod of execution paint a Orbital for using Gaussianpaint a Orbital for using Gaussian

IntroductionIntroduction

Exploring Chemistry with Electronic Structure Methods severs as an introduction to the capabilities of and procedures for this variety of computational chemistry.

This work was developed using the Gaussian This work was developed using the Gaussian series of computational chemistry programs for series of computational chemistry programs for all of its specific examples and exercises all of its specific examples and exercises (specifically Gaussain 94).(specifically Gaussain 94).

TaskTask

• Single point energy. • Geometry optimization. • Frequency and thermochemical analysis.• Reaction path following. • Find the maximum energy along a specific reaction path. • Potential energy surface scan.• Polarizabilities and hyperpolarizabilities. • Direct dynamics trajectory calculation. • Compute forces on the nuclei. • Test wavefunction stability. • Compute molecular volume. • Recompute population analysis only. • Print initial guess only; recompute population analysis. • Extract archive entry from checkpoint file only.

Program StartProgram Start

Input fileInput file

# HF/6-31G(d)

water energy 0 1 O -0.464 0.177 0.0 H -0.464 1.137 0.0 H 0.441 -0.143 0.0

MethodBasis set

Open H2O.gjf

%chk=water#p RHF/6-31G(d) opt

Water energy0 1O -0.464 0.177 0.0 H -0.464 1.137 0.0 H 0.441 -0.143 0.0

Single point energy

Geometry optimization.

Opt-method

Hartree-Fock, CIS, MP2, MP3, MP4(SDQ), CID, CISD, CCD, CCSD, QCISD, CASSCF, and all DFT and semi-empirical methods

Basis set

*.out file 을 자세하게 적을 것이다 .간단하게는 #t

모든 정보를 기록

Input fileInput file%chk=water#p RHF/6-31G(d) opt freq

Water energy, frequency0 1O -0.464 0.177 0.0 H -0.464 1.137 0.0 H 0.441 -0.143 0.0

Frequency

%mem=1Gb#p RHF/6-31G(d) opt freq

Water energy, frequency0 1O -0.464 0.177 0.0 H -0.464 1.137 0.0 H 0.441 -0.143 0.0

Memory

Input fileInput file%chk=water#p RHF/6-31G(d) opt freq

Water energy, frequency0 1O -0.464 0.177 0.0 H -0.464 1.137 0.0 H 0.441 -0.143 0.0

--link1-- %chk=water#p RHF/6-311G opt freq

Water energy, frequency0 1O -0.464 0.177 0.0 H -0.464 1.137 0.0 H 0.441 -0.143 0.0

Multi-Step Jobs

한 줄을 꼭 비워 두어야 한다 .!!!

Input fileInput file((Basis Set Supper position Error)

#P RMP2/6-31G(d) massage BSSE 0 1C 1.377177000 0.229823000 -0.156512000C 0.489309000 1.308302000 -0.154289000C 0.887121000 -1.078334000 -0.156030000C -0.490801000 -1.308014000 -0.153384000C -0.888615000 1.078620000 -0.151657000C -1.378670000 -0.229531000 -0.151192000H 2.449803000 0.408611000 -0.158527000H 0.870782000 2.326620000 -0.154584000H 1.578270000 -1.917862000 -0.157626000H -0.872282000 -2.326329000 -0.152865000H -1.579742000 1.918152000 -0.149885000H -2.451283000 -0.408342000 -0.149183000H 0.016414000 -0.003605000 3.599678000H 0.014910000 -0.002440000 2.861376000

13 Nuc 0.014 Nuc 0.0

13, 14 Atom 은 Basis function 만 갖는다 .

Input fileInput file((Basis Set Supper position Error)

#P RMP2/6-31G(d) counterpoise=2 BSSE 0 1C 1.377177000 0.229823000 -0.156512000 1C 0.489309000 1.308302000 -0.154289000 1C 0.887121000 -1.078334000 -0.156030000 1C -0.490801000 -1.308014000 -0.153384000 1C -0.888615000 1.078620000 -0.151657000 1C -1.378670000 -0.229531000 -0.151192000 1H 2.449803000 0.408611000 -0.158527000 1H 0.870782000 2.326620000 -0.154584000 1H 1.578270000 -1.917862000 -0.157626000 1H -0.872282000 -2.326329000 -0.152865000 1H -1.579742000 1.918152000 -0.149885000 1H -2.451283000 -0.408342000 -0.149183000 1H 0.016414000 -0.003605000 3.599678000 2H 0.014910000 -0.002440000 2.861376000 2

1. 전체 분자 계산2. 1 번 +2 번 (ghost)3. 1 번 (ghost)+2 번4. 1 번5. 2 번

Input fileInput file

#T RHF/6-31G(d) Opt=QST2 Test

Reactnts:

0 1SiX 1 1.0H 1 R1 2 A1H 1 R1 2 A1 3 180.0H 1 R2 2 A2 3 90.0H 1 R2 5 A3 2 180.0

R1=1.51A1=46.65R2=3.0A2=140.0A3=14.0

Products:

0 1SiX 1 1.0H 1 R 2 A1H 1 R 2 A1 3 180.0H 1 R 2 A2 3 90.0H 1 R 5 A3 2 180.0

R=1.48A1=54.75A2=125.2A3=109.5

처음의 coordinate 와 나중의 coordinate 사이의 saddle point 를 찾는다 .

Z-matrix 된 초기 좌표 Z-matrix 된 나중 좌표

Z-matrix 로 coordinate 를 표기하면 각 Atom 들을 고정하거나 임의의 값을 줄 수 있다

Input file Input file (batch file for linux)(batch file for linux)

#!/bin/ksh#@job_type = serial#@resources = ConsumableCpus(1) ConsumableMemory(31000mb)#@error = dhjung-test.err#@output = dhjung-test.out#@class = p_normal_1.7#@wall_clock_limit=90:00:00#@queue. ~/g03.ksh.login

rm -rf /gpfs2/Sukho27mkdir /gpfs2/Sukho27cd /gpfs2/Sukho27tmpd=/gpfs2/Sukho27

workd=/inst/r591pnj/Sukho2

cp $workd/1.gjf $tmpd/1.com

g03 1.com > 1.log

cp $tmpd/1.log $workd/

1 대의 computer 로 작업한다 .

Error massage 의 출력 file중요정보의 출력 file계산의 최대 시간

Scratch file 의 비움과 출력 file 의 work directory 로

copy 작업의 위치 지정

Scratch directory에서

작업 위치로의 복사

작업 위치에서 Scratch directory 로의

복사

Basis SetBasis Set

 Basis Set  Applies to Polarization Functions Diffuse Functions

STO-3G H-Xe *  

3-21G H-Xe * or ** +

6-21G H-Cl (d)  

4-31G H-Ne (d) or (d,p)  

6-31G H-Kr (3df,3pd) ++

6-311G H-Kr (3df,3pd) ++

D95 H-Cl except Na and Mg (3df,3pd) ++

D95V H-Ne (d) or (d,p) ++

SHC H-Cl *  

CEP-4G H-Rn * (Li-Ar only)  

CEP-31G H-Rn * (Li-Ar only)  

CEP-121G H-Rn * (Li-Ar only)  

Basis SetBasis Set

Atoms cc-pVDZ cc-pVTZ cc-pVQZ cc-pV5Z cc-pV6Z

H 2s,1p 3s,2p,1d 4s,3p,2d,1f 5s,4p,3d,2f,1g 6s,5p,4d,3f,2g,1h

He 2s,1p 3s,2p,1d 4s,3p,2d,1f 5s,4p,3d,2f,1g not available

B-Ne 3s,2p,1d4s,3p,2d,

1f5s,4p,3d,2f,1g 6s,5p,4d,3f,2g,1h 7s,6p,5d,4f,3g,2h,1i

Al-Ar 4s,3p,1d5s,4p,2d,

1f6s,5p,3d,2f,1g 7s,6p,4d,3f,2g,1h not available

Ga-Kr 5s,4p,1d6s,5p,3d,

1fnot available not available not available

Method of executionMethod of execution

Link 0 section

Route section

Title section

Molecule Specification section (charge and spin )

atomic coordinates …

# HF/6-31G(d)

water energy

0 1

O -0.464 0.177 0.0 H -0.464 1.137 0.0 H 0.441 -0.143 0.0

Output file Output file (RHF)(RHF)

Single Point Energy 로 RHF 에너지만 갖고 있다 .

Output file Output file (RMP2)(RMP2)

표시는 Single Point Energy이지만 RMP2 의 보정값도 갖고 있다 .

Output file Output file (Optimize)(Optimize)

각 Step 당 에너지를확인 할 수 있다 .

Output file Output file (Optimize)(Optimize)

Convergence 되는 과정을 볼 수 있다

Energy 단위 변환도 가능하다

Output file Output file (Frequency)(Frequency)

Job1 : OptimizeJob2 : Frequency

Output file Output file (Frequency)(Frequency)

진동모드의 확인

Output file Output file (BSSE)(BSSE)

1. 전체 분자 계산 결과2. 1 번 +2 번 (ghost) 결과3. 1 번 (ghost)+2 번 결과4. 1 번 결과5. 2 번 결과

Output file Output file (Saddle Point)(Saddle Point)

시작과 끝의 원자 좌표를 정해준 후 그사이의 각 Step Energy 를 확인 할 수 있다 .

Output file Output file (Saddle Point)(Saddle Point)

10 번째 Step 에서 Energy 가 가장 작은 것을 확인 할 수 있다 .

Utility Programs Included with Utility Programs Included with G03W G03W

c8603 Converts checkpoint files from previous program versions to Gaussian 03 format.

chkchk* Displays the route and title sections from a checkpoint file.

cubegen*

Standalone cube generation utility.

cubman*Manipulates Gaussian-produced cubes of electron density and electrostatic potential (allowing them to be added,

subtracted, and so on).

formchk*

Converts a binary checkpoint file into an ASCII form suitable for use with visualization programs and for moving checkpoint files between different types of computer systems.

freqchk*

Prints frequency and thermochemistry data from a checkpoint file. Alternate isotopes, temperature, pressure and scale factor can be specified for the thermochemistry analysis.

freqmem

Determines memory requirements for frequency calculations.

gauopt Performs optimizations of variables other than molecular coordinates.

ghelp On-line help for Gaussian.

mm Standalone molecular mechanics program.

newzmat*

Conversion between a variety of molecular geometry specification formats.

testrt* Route section syntax checker and non-standard route generation.

unfchk* Convert a formatted checkpoint file back to its binary form (e.g., after moving it from a different type of computer

system).

Benzene 의 17 state