Gaussian & GaussView. Shubin Liu, Ph.D. Research Computing Center, ITS University of North Carolina at Chapel Hill. Agenda. Introduction Capabilities Input File Preparation Gaussian GUI – GaussView Run G03/G09 Jobs @ UNC-CH Some Advanced Topics Hands-on Experiments – next hour.
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Gaussian & GaussView
Shubin Liu, Ph.D.
Research Computing Center, ITS
University of North Carolina at Chapel Hill
The PPT format of this presentation is available here:
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Ph.D. from Chemistry, UNC-CH
Currently Senior Computational Scientist @ Research Computing Center, UNC-CH
Support Computational Chemistry/Physics/Material Science software
Support Programming (FORTRAN/C/C++) tools, code porting, parallel computing, etc.
Training, Workshops/Short Courses – currently 4, one more to come soon
Conduct research and engagement projects in Computational Chemistry
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Applications in biological and material science systems
# HF/6-31G(d)!Route section
water energy !Title section
0 1 !Charge & multiplicity
O -0.464 0.177 0.0 !Geometry in Cartesian Coordinate
H -0.464 1.137 0.0
H 0.441 -0.143 0.0
!Blank line at the end
%nproc=2 !Link 0 section
#b3lyp/6-311+G(3df,2p) opt freq !Route/Keywords !Blank line
Calcn Title: test !Title
0 1 !Charge & multiplicity
O!Geometry in Z-matrix
h 1 r
h 1 r 2 a
!Blank line at the end
#B3LYP/6-31G* opt geom=Checkpoint Guess=read nosymm scf=tight
Geometry optimization of a sample molecule
# B3LYP/6-311++G** sp pop=nbo nosymm guess=read geom=checkpoint
Single Point Energy for the "reference state" of molecule with one more electron.
GaussView 4.1.2 makes using Gaussian 03 simple and straightforward:
– IBM RS6000 (AIX 5.1) (Happy/yatta/p575)
– LINUX 32-bit OS (Emeraldtest)
– LINUX 64-bit OS (Emerald, Topsail, Kure)
GaussView can display a variety of computed spectra, including IR, Raman, NMR and VCD. Here we see the VCD spectra for two conformations of spiropentyl acetate, a chiral derivative of spiropentane. See F. J. Devlin, P. J. Stephens, C. Österle, K. B. Wiberg, J. R. Cheeseman, and M. J. Frisch, J. Org. Chem. 67, 8090 (2002).
Bacteriorhodopsin, set up for an ONIOM calculation (stylized). See T. Vreven and K. Morokuma, “Investigation of the S0->S1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method,” Theor. Chem. Acc. (2003).
ssh -X emerlad.isis.unc.edu
bsub -q qname -m mname g03 input.inp
where “qname” stands for a queue name, e.g., week, month, etc., “mname” represents a machine name, e.g., cypress,yatta, etc., and “input.inp” denotes the input file prepared manually or via GaussView.
bsub -q idle -R blade g03 input.inp
-- G03 is parallelized via OpenMP
bsub -q qname -n ncpu -m mname g03 input.inp
where “qname” stands for a queue name, e.g., week, idle, etc., “ncpu” is the number of CPUs requested, e.g., 2 or 4 or 8, “mname” represents a machine name, e.g., yatta, cypress, etc., and “input.inp” denotes the input file prepared manually or via GaussView.
bsub -q week -n 4 -m cypress g03 input.inp
To submit multiple CPU g03 jobs on Emerald, make sure only all CPUs are from the same node because G03 is parallelized via OpenMP (for share-memory SMP machines)
bsub -q week -n 4 -R “blade span[ptile=4]” g03 input.inp
input file properly
TS Search inGaussian/GaussView
frequency corresponds to
the TS you search for.
StepSize=N Step size along the reaction path, in units of 0.01 amu-1/2-Bohr. The default is 10.
RCFC Specifies that the computed force constants in Cartesian coordinates from a frequency calculation are to be read from the checkpoint file. ReadCartesianFC is a synonym for RCFC.
Solvent Effect: Menshutkin Model Reaction Transition State
#p hf/6-311+g(2d,p) nmr
From GaussView menu: Edit -> Select Layer
From GaussView menu: Calculate->Gaussian->Method
#rhf/3-21g pop=nbo RHF/3-21G for formamide (H2NCHO) 0 1 H -1.908544 0.420906 0.000111 H -1.188060 -1.161135 0.000063 N -1.084526 -0.157315 0.000032 C 0.163001 0.386691 -0.000154 O 1.196265 -0.246372 0.000051 H 0.140159 1.492269 0.000126
NPA Output Sample
bsub –R blade –q now g03 input.com
The WORD .doc format of this hands-on exercises is available here: