Running Gaussian 03
Byun, Jae Duk
Lim, Seok Ho
OUT Line
Introduction
Task
Program Start
Input file example
Basis set
Output
Method of execution
paint a Orbital for using Gaussian
Introduction
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 series
of computational chemistry programs for all of its
specific examples and exercises (specifically
Gaussain 94).
Task
• 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 Start
Input file
Open H2O.gjf
# HF/6-31G(d) Method
Basis set
water energy
01
O -0.464 0.177 0.0
H -0.464 1.137 0.0
H 0.441 -0.143 0.0
Opt-method
Hartree-Fock, CIS, MP2, MP3,
MP4(SDQ), CID, CISD, CCD,
CCSD, QCISD, CASSCF,
and all DFT
and semi-empirical methods
Single point energy
*.out file을 자세하게 적을 것이다.
간단하게는 #t
Basis set
모든 정보를 기록
%chk=water
#p RHF/6-31G(d) opt
Water energy
01
O -0.464 0.177 0.0
H -0.464 1.137 0.0
H 0.441 -0.143 0.0
Geometry
optimization.
Input file
%chk=water
#p RHF/6-31G(d) opt freq
Frequency
Water energy, frequency
01
O -0.464 0.177 0.0
H -0.464 1.137 0.0
H 0.441 -0.143 0.0
%mem=1Gb
#p RHF/6-31G(d) opt freq
Water energy, frequency
01
O -0.464 0.177 0.0
H -0.464 1.137 0.0
H 0.441 -0.143 0.0
Memory
Input file
%chk=water
#p RHF/6-31G(d) opt freq
Multi-Step Jobs
Water energy, frequency
01
O -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, frequency
01
O -0.464 0.177 0.0
H -0.464 1.137 0.0
H 0.441 -0.143 0.0
한 줄을 꼭 비워 두어야 한다.!!!
Input file(Basis Set Supper position Error)
#P RMP2/6-31G(d) massage
BSSE
01
C
C
C
C
C
C
H
H
H
H
H
H
H
H
13, 14 Atom은
Basis function만 갖는다.
1.377177000
0.489309000
0.887121000
-0.490801000
-0.888615000
-1.378670000
2.449803000
0.870782000
1.578270000
-0.872282000
-1.579742000
-2.451283000
0.016414000
0.014910000
13 Nuc 0.0
14 Nuc 0.0
0.229823000
1.308302000
-1.078334000
-1.308014000
1.078620000
-0.229531000
0.408611000
2.326620000
-1.917862000
-2.326329000
1.918152000
-0.408342000
-0.003605000
-0.002440000
-0.156512000
-0.154289000
-0.156030000
-0.153384000
-0.151657000
-0.151192000
-0.158527000
-0.154584000
-0.157626000
-0.152865000
-0.149885000
-0.149183000
3.599678000
2.861376000
Input file(Basis Set Supper position Error)
#P RMP2/6-31G(d) counterpoise=2
BSSE
1.
2.
3.
4.
5.
전체 분자 계산
1번+2번(ghost)
1번(ghost)+2번
1번
2번
01
C
C
C
C
C
C
H
H
H
H
H
H
H
H
1.377177000
0.489309000
0.887121000
-0.490801000
-0.888615000
-1.378670000
2.449803000
0.870782000
1.578270000
-0.872282000
-1.579742000
-2.451283000
0.016414000
0.014910000
0.229823000
1.308302000
-1.078334000
-1.308014000
1.078620000
-0.229531000
0.408611000
2.326620000
-1.917862000
-2.326329000
1.918152000
-0.408342000
-0.003605000
-0.002440000
-0.156512000
-0.154289000
-0.156030000
-0.153384000
-0.151657000
-0.151192000
-0.158527000
-0.154584000
-0.157626000
-0.152865000
-0.149885000
-0.149183000
3.599678000
2.861376000
1
1
1
1
1
1
1
1
1
1
1
1
2
2
Input file
Z-matrix로 coordinate를 표기하면 각
Atom들을 고정하거나 임의의 값을 줄 수 있다
#T RHF/6-31G(d) Opt=QST2 Test
Products:
Reactnts:
01
Si
X 1 1.0
H1R2
H1R2
H1R2
H1R5
01
Si
X 1 1.0
H 1 R1 2
H 1 R1 2
H 1 R2 2
H 1 R2 5
A1
A1 3 180.0
A2 3 90.0
A3 2 180.0
R1=1.51
A1=46.65
R2=3.0
A2=140.0
A3=14.0
Z-matrix된 초기 좌표
A1
A1 3 180.0
A2 3 90.0
A3 2 180.0
R=1.48
A1=54.75
A2=125.2
A3=109.5
Z-matrix된 나중 좌표
처음의 coordinate와 나중의 coordinate사이의 saddle point를 찾는다.
Input file
(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/Sukho27
mkdir /gpfs2/Sukho27
cd
/gpfs2/Sukho27
tmpd=/gpfs2/Sukho27
workd=/inst/r591pnj/Sukho2
cp
$workd/1.gjf
$tmpd/1.com
g03
1.com > 1.log
cp
$tmpd/1.log $workd/
1대의 computer로 작업한다.
Error massage의 출력 file
중요정보의 출력 file
계산의 최대 시간
Scratch file의 비움과 출력
file의 work directory로 copy
작업의 위치 지정
작업 위치에서
Scratch directory로의 복사
Scratch directory에서
작업 위치로의 복사
Basis 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 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,1d
4s,3p,2d,
1f
5s,4p,3d,2f,1g 6s,5p,4d,3f,2g,1h
7s,6p,5d,4f,3g,2h,1i
Al-Ar
4s,3p,1d
5s,4p,2d,
1f
6s,5p,3d,2f,1g 7s,6p,4d,3f,2g,1h
not available
Ga-Kr
5s,4p,1d
6s,5p,3d,
1f
not available
not available
not available
Method of execution
Link 0 section
# HF/6-31G(d)
Route section
water energy
Title section
01
O -0.464 0.177 0.0
H -0.464 1.137 0.0
H 0.441 -0.143 0.0
Molecule Specification section
(charge and spin )
atomic coordinates …
Output file
Single Point Energy로
RHF에너지만 갖고 있다.
(RHF)
Output file
표시는 Single Point Energy
이지만 RMP2의
보정값도 갖고 있다.
(RMP2)
Output file
각 Step당 에너지를
확인 할 수 있다.
(Optimize)
Output file
(Optimize)
Energy 단위
변환도 가능하다
Convergence 되는
과정을 볼 수 있다
Output file
Job1 : Optimize
Job2 : Frequency
(Frequency)
Output file
진동모드의 확인
(Frequency)
Output file
(BSSE)
1.
2.
3.
4.
5.
전체 분자 계산 결과
1번+2번(ghost) 결과
1번(ghost)+2번 결과
1번 결과
2번 결과
Output file
시작과 끝의 원자
좌표를 정해준 후
그사이의
각 Step Energy를
확인 할 수 있다.
(Saddle Point)
Output file
(Saddle Point)
10번째 Step에서 Energy가 가장 작은 것을 확인 할 수 있다.
Utility Programs Included with 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).
Benzene의 17 state