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 Single point energy Geometry optimization. Open H2O.gjf *.out file을 자세하게 적을 것이다. 간단하게는 #t # 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 Method Basis set Basis set 모든 정보를 기록 Geometry optimization. %chk=water #p RHF/6-31G(d) opt 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 Opt-method Hartree-Fock, CIS, MP2, MP3, MP4(SDQ), CID, CISD, CCD, CCSD, QCISD, CASSCF, and all DFT and semi-empirical methods

Input file Memory %chk=water #p RHF/6-31G(d) opt freq Water energy, frequency 0 1 O -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, frequency 0 1 O -0.464 0.177 0.0 H -0.464 1.137 0.0 H 0.441 -0.143 0.0 Memory

Input file Multi-Step Jobs %chk=water #p RHF/6-31G(d) opt freq Water energy, frequency 0 1 O -0.464 0.177 0.0 H -0.464 1.137 0.0 H 0.441 -0.143 0.0 --link1-- #p RHF/6-311G opt freq Multi-Step Jobs 한 줄을 꼭 비워 두어야 한다.!!!

Input file(Basis Set Supper position Error) #P RMP2/6-31G(d) massage BSSE 0 1 C 1.377177000 0.229823000 -0.156512000 C 0.489309000 1.308302000 -0.154289000 C 0.887121000 -1.078334000 -0.156030000 C -0.490801000 -1.308014000 -0.153384000 C -0.888615000 1.078620000 -0.151657000 C -1.378670000 -0.229531000 -0.151192000 H 2.449803000 0.408611000 -0.158527000 H 0.870782000 2.326620000 -0.154584000 H 1.578270000 -1.917862000 -0.157626000 H -0.872282000 -2.326329000 -0.152865000 H -1.579742000 1.918152000 -0.149885000 H -2.451283000 -0.408342000 -0.149183000 H 0.016414000 -0.003605000 3.599678000 H 0.014910000 -0.002440000 2.861376000 13 Nuc 0.0 14 Nuc 0.0 13, 14 Atom은 Basis function만 갖는다.

Input file(Basis Set Supper position Error) #P RMP2/6-31G(d) counterpoise=2 BSSE 0 1 C 1.377177000 0.229823000 -0.156512000 1 C 0.489309000 1.308302000 -0.154289000 1 C 0.887121000 -1.078334000 -0.156030000 1 C -0.490801000 -1.308014000 -0.153384000 1 C -0.888615000 1.078620000 -0.151657000 1 C -1.378670000 -0.229531000 -0.151192000 1 H 2.449803000 0.408611000 -0.158527000 1 H 0.870782000 2.326620000 -0.154584000 1 H 1.578270000 -1.917862000 -0.157626000 1 H -0.872282000 -2.326329000 -0.152865000 1 H -1.579742000 1.918152000 -0.149885000 1 H -2.451283000 -0.408342000 -0.149183000 1 H 0.016414000 -0.003605000 3.599678000 2 H 0.014910000 -0.002440000 2.861376000 2 1. 전체 분자 계산 2. 1번+2번(ghost) 3. 1번(ghost)+2번 4. 1번 5. 2번

Input file Z-matrix로 coordinate를 표기하면 각 Atom들을 고정하거나 임의의 값을 줄 수 있다 #T RHF/6-31G(d) Opt=QST2 Test Reactnts: 0 1 Si X 1 1.0 H 1 R1 2 A1 H 1 R1 2 A1 3 180.0 H 1 R2 2 A2 3 90.0 H 1 R2 5 A3 2 180.0 R1=1.51 A1=46.65 R2=3.0 A2=140.0 A3=14.0 Products: 0 1 Si X 1 1.0 H 1 R 2 A1 H 1 R 2 A1 3 180.0 H 1 R 2 A2 3 90.0 H 1 R 5 A3 2 180.0 R=1.48 A1=54.75 A2=125.2 A3=109.5 Z-matrix된 초기 좌표 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 * or ** + 6-21G H-Cl (d) 4-31G H-Ne (d) or (d,p) 6-31G H-Kr (3df,3pd) ++ 6-311G D95 H-Cl except Na and Mg D95V SHC CEP-4G H-Rn * (Li-Ar only) CEP-31G CEP-121G

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 not available B-Ne 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 Ga-Kr 5s,4p,1d 6s,5p,3d,1f

Method of execution Link 0 section Route section Title section # HF/6-31G(d) Route section Title section water energy 0 1 Molecule Specification section (charge and spin ) atomic coordinates … O -0.464 0.177 0.0 H -0.464 1.137 0.0 H 0.441 -0.143 0.0

Output file (RHF) Single Point Energy로 RHF에너지만 갖고 있다.

Output file (RMP2) 표시는 Single Point Energy 이지만 RMP2의 보정값도 갖고 있다.

Output file (Optimize) 각 Step당 에너지를 확인 할 수 있다.

Output file (Optimize) Energy 단위 변환도 가능하다 Convergence 되는 과정을 볼 수 있다

Output file (Frequency) Job1 : Optimize Job2 : Frequency

Output file (Frequency) 진동모드의 확인

Output file (BSSE) 1. 전체 분자 계산 결과 2. 1번+2번(ghost) 결과 1. 전체 분자 계산 결과 2. 1번+2번(ghost) 결과 3. 1번(ghost)+2번 결과 4. 1번 결과 5. 2번 결과

Output file (Saddle Point) 시작과 끝의 원자 좌표를 정해준 후 그사이의 각 Step Energy를 확인 할 수 있다.

Output file (Saddle Point) 10번째 Step에서 Energy가 가장 작은 것을 확인 할 수 있다.

Utility Programs Included with G03W 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