Materials Simulations usingGaussian 09 Eunhwan Jung 1 INTRODUCTION 2 Information of Gaussian Gaussian website www.gaussian.com Gaussian Online Manual http://www.gaussian.com/g_tech/g_ur/g09help.htm Gaussian Program Error http://www.gaussianerrors.com/runtime-errors.html Gaussian has been designed with the needs of the user in mind. All of the standard input is free-format and mnemonic. Reasonable defaults for input data have been provided, and the output is intended to be self- explanatory. Mechanisms are available for the sophisticated user to override defaults or interface their own code to the Gaussian system. The authors hope that their efforts will allow users to concentrate their energies on the application of the methods to chemical problems and to the development of new methods, rather than on the mechanics of performing the calculations. 3 Capability in Gaussian 09 Fundamental Algorithms Energies Geometry Optimization Frequencies and Second derivatives Molecular Properties Solvation Models in gaussian manual 4 Method Availabilities in Gaussian 09 5 Abbreviation in Method Availabilities in Gaussian 09 SP Single point energy. Opt Geometry optimization. Freq Frequency and thermochemical analysis. IRC Reaction path following. IRCMax Find the maximum energy along a specific reaction path. Scan Potential energy surface scan. Polar Polarizabilities and hyperpolarizabilities. ADMP and BOMD Direct dynamics trajectory calculation. Force Compute forces on the nuclei. Stable Test wavefunction stability. Volume Compute molecular volume. Density=Checkpoint Recompute population analysis only. Guess=Only Print initial guess only; recompute population analysis. in gaussian manual 6 Cluster Gaussian 03, 09 Porion : 16 cpu, 32GB memory (09) Unist_smp1 : 32 cpu, 220GB memory Unist_smp2 : 32 cpu, 180GB memory Tusmp : 32 cpu, 200GB memory Cheetah : 8 cpu, 10GB memory (09) Pdaisy : 14 cpu, 16GB memory 7 RUNNING THE GAUSSIAN 09 8 Running and Scratch File in Gaussian 09 Running File • name.com Gaussian input describing the desired calculation • name.cmd Executable file • name.log output file Scratch File • The checkpoint file : name.chk • The Read-Write file : name.rwf • The Two-electron Integral file : name.int • The Two-Electron Integral Derivative file : name.d2e 9 com File in Gaussian 09 %Mem = Specifying resource requirements %NProc = Number of CPU %chk = Path of the Checkpoint file Porion, Unist_smp, Tusmp : /pwork01/$USER/G09_SCR/ or /work/$USER/G09_SCR/ Pdaisy : /Scratch2/$USER/name.chk Pgaia : /tmp/name.chk 10 com File in Gaussian 09 1. Calculation method or function • ex) MP2, HF, B3LYP, RHF / basis set 2. Calculation tool and Options • ex) SCF=QC, Freq=Raman, SP, Opt=(MaxCycle=N, TS) 1 2 11 com File in Gaussian 09 1. Title name 2. Charge Spin multiplicity *Spin multiplicity = 2S+1 S = electron spin 3. Molecule coordinate ex) neutral = 2*(1/2+(-1/2))+1=1 ex) radical = 2*(1/2)+1=2 4. Geometry connectivity 1 2 3 12 Running claculations with LoadLeveler Make running file => use vi editor Submit the running file => llsubmit name.cmd Confirm output file => vi name.log 13 cmd File in Gaussian 09 Job type; serial or parallel Load level class ; long or large User email Number of CPU Job-time 14 .cmd File in Gaussian 09 Running in Home directory 15 Important keyword in linux • vi name.file : editor • llsubmit name.cmd : key word to submit the job(.cmd file) • llq : key word to job status • llcancel job ID : keyword to cancel the submitted job • llstatus –X : keyword to show the computer node (usable cpu number and memory) 16 PRACTICE 17 GaussView on X manager enterprise #ssh porion01 #cd /applic/Applications/G09/gv #export GV_DIR=/applic/Applications/G09/gv #gview 18 GaussView on X manager enterprise 19 GaussView on X manager enterprise 20 GaussView on X manager enterprise 21 Water optimization + frequencies 22 GaussView Vibration Frequencies 23 GaussView Vibration Frequencies 24 GaussView Vibration Frequencies 25 GaussView MOs 26 GaussView MOs 27 GaussView Summary 28 GaussView Summary 29 Benzene calculation 30 Benzene calculation 31 Error message opt=(Cartesian) 32 Error message 33 chk file to fchk file ssh porion01 cd /applic/Applications/G09/g09 #formchk name.chk name.fchk 34