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 The PPT format of this presentation is available here: http://its2.unc.edu/divisions/rc/training/scientific/ /afs/isis/depts/its/public_html/divisions/rc/training/scientific/short_courses/
Course Goal • What Gaussian/GaussView packages are • How to prepare input files via GaussView • How to run G03/G09 jobs on UNC-CH servers • How to view G03/G09 results • Learn selected advanced topics • Hands-on experiments
Pre-requisites • Basic UNIX knowledge • Introduction to Scientific Computing • An account on Emerald
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Research Computing Center Where and who are we and what do we do? ITS Manning: 211 Manning Drive Website http://its.unc.edu/research-computing.html Groups Infrastructure -- Hardware User Support -- Software Engagement -- Collaboration
About Myself Ph.D. from Chemistry, UNC-CH Currently Senior Computational Scientist @ Research Computing Center, UNC-CH Responsibilities: 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 Development of DFT theory and concept tools Applications in biological and material science systems
About You • Name, department, group, interest? • Any experience before with Gaussian or GaussView? • What do you expect to use them? What kind of systems?
Gaussian & GaussView • Gaussian is a general purpose electronic structure package for use in computational chemistry. Current default version 03 E01 • Most widely used computational chemistry package. The latest release is Gaussian 09A02. • GaussView is a graphical user interface (GUI) designed to be used with Gaussian to make calculation preparation and output analysis easier, quicker and more efficient. Current default version 4.1.2. The latest release is 5.0.9. • Vendor’s website: http://www.gaussian.com
Gaussian 03/09 Functionality • Energies • MM: AMBER, Dreiding, UFF force field • Semiempirical: CNDO, INDO, MINDO/3, MNDO, AM1, PM3 • HF: closed-shell, restricted/unrestricted open-shell • DFT: many local/nonlocal functionals to choose • MP: 2nd-5th order; direct and semi-direct methods • CI: single and double • CC: single, double, triples contribution • High accuracy methods: G1, G2, CBS, etc. • MCSCF: including CASSCF • GVB
Gaussian 03/09 Functionality • Gradients/Geometry optimizations • Frequencies (IR/Raman, NMR, etc.) • Other properties • Populations analyses • Electrostatic potentials • NMR tensors • Several solvation models (PCM, COSMOS) • Two and three layer ONIOM – E, grad, freq • Transition state search • IRC for reaction path
New in Gaussian 03/09 • Molecular Dynamics • BOMD – Born-Oppenheimer MD • ADMP – Atom-Centered Density Matrix Propagation • Periodic Boundary Conditions (PBC) – HF and DFT energies and gradients • Properties with ONIOM models • Spin-spin coupling and other additions to spectroscopic properties • Also – improved algorithms for initial guesses in DFT and faster SCF convergence • Many new DFT functionals! • DFTB (tight-binding DFT)
Gaussian Input File Structure • .com,.inp, or .gjf (Windows version) • Free format, case insensitive • Spaces, commas, tabs, forward slash as delimiters between keywords • ! as comment line/section • Divided into sections (in order) • Link 0 commands (%) • Route section – what calculation is to do • Title • Molecular specification • Optional additional sections
Input File – Example 1 # HF/6-31G(d) !Route section !Blank line water energy !Title section !Blank line 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
Input File – Example 2 %nproc=2 !Link 0 section %chk=water.chk #b3lyp/6-311+G(3df,2p) opt freq !Route/Keywords !Blank line Calcn Title: test !Title !Ban line 0 1 !Charge & multiplicity O !Geometry in Z-matrix h 1 r h 1 r 2 a variables r=0.98 a=109. !Blank line at the end
Input File – Link 0 Commands • First “Link 0” options (Examples) • %chk • %chk=myjob.chk • %mem • %mem=12MW • %nproc • $nproc=4 • %rwf • %rwf=1,1999mb,b,1999mb • %scr • %sc=e,1999mb,f,1999mb
Input File – Keyword Specification • Keyword line(s) – specify calculation type and other job options • Start with # symbol • Can be multiple lines • Terminate with a blank line • Format • keyword=option • keyword(option) • keyword(option1,option2,…) • keyword=(option1,option2,…) • User’s guide provides list of keywords, options, and basis set notion http://www.gaussian.com/g_ur/keywords.htm
Basis Set • Why are basis sets required: MO-LCAO! • Basis sets are atomic orbitals (AOs). • Minimal basis set (e.g., STO-3G) • Double zeta basis set (DZ) • Split valence basis Set (e.g., 6-31G) • Polarization and diffuse functions (6-31+G*) • Correlation-consistent basis functions (e.g., aug-cc-pvTZ) • Pseudopotentials, effective core potentials
Input File – Title Specification • Brief description of calculation – for users benefit • Terminate with a blank line
Input File – Molecular Geometry • 1st line charge and multiplicity • Element label and location • Cartesian coordinate • Label x y z • Z-matrix • Label atoms bond length atom2 angle atm3 dihedral • If parameters used instead of numerical values then variables section follows • Again end in blank line
A More Complicated Example %chk=/scr/APPS_SCRDIR/f33em5p77c.chk %mem=4096MB %NProc=4 #B3LYP/6-31G* opt geom=Checkpoint Guess=read nosymm scf=tight Geometry optimization of a sample molecule 1 1 --Link1-- %chk=/scr/APPS_SCRDIR/f33em5p77c.chk %mem=4096MB %NProc=2 # 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. 0 2
Other Gaussian Utilities • formchk – formats checkpoint file so it can be used by other programs • cubgen – generate cube file to look at MOs, densities, gradients, NMR in GaussView • freqchk – retrieves frequency/thermochemsitry data from chk file • newzmat – converting molecular specs between formats (zmat, cart, chk, cache, frac coord, MOPAC, pdb, and others)
GaussView GaussView 4.1.2 makes using Gaussian 03 simple and straightforward: • Sketch in molecules using its advanced 3D Structure Builder, or load in molecules from standard files. • Set up and submit Gaussian 03 jobs right from the interface, and monitor their progress as they run. • Examine calculation results graphically via state-of-the-art visualization features: display molecular orbitals and other surfaces, view spectra, animate normal modes, geometry optimizations and reaction paths. • Online help: http://www.gaussian.com/g_gv/gvtop.htm
GaussView Availability • Support platforms: – IBM RS6000 (AIX 5.1) (Happy/yatta/p575) – LINUX 32-bit OS (Emeraldtest) – LINUX 64-bit OS (Emerald, Topsail, Kure)
GaussView: Build • Build structures by atom, functional group, ring, amino acid (central fragment, amino-terminated and carboxyl-terminated forms) or nucleoside (central fragment, C3’-terminated, C5’-terminated and free nucleoside forms). • Show or hide as many builder panels as desired. • Define custom fragment libraries. • Open PDB files and other standard molecule file formats. • Optionally add hydrogen atoms to structures automatically, with excellent accuracy. • Graphically examine & modify all structural parameters. • Rotate even large molecules in 3 dimension: translation, 3D rotation and zooming are all accomplished via simple mouse operations. • Move multiple molecules in the same window individually or as a group. • Adjust the orientation of any molecule display. • View molecules in several display modes: wire frame, tubes, ball and stick or space fill style. • Display multiple views of the same structure. • Customize element colors and window backgrounds. • Use the advanced Clean function to rationalize sketched-in structures • Constrain molecular structure to a specific symmetry (point group). • Recompute bonding on demand. • Build unit cells for 1, 2 and 3 dimensional periodic boundary conditions calculations (including constraining to a specific space group symmetry). • Specify ONIOM layer assignments in several simple, intuitive ways: by clicking on the desired atoms, by bond attachment proximity to a specified atom, by absolute distance from a specified atom, and by PDB file residue.
GuassView: Setup • Molecule specification input is set up automatically. • Specify additional redundant internal coordinates by clicking on the appropriate atoms and optionally setting the value. • Specify the input for any Gaussian 03 calculation type. • Select the job from a pop-up menu. Related options automatically appear in the dialog. • Select any method and basis set from pop-up menus. • Set up calculations for systems in solution. Select the desired solvent from a pop-up menu. • Set up calculations for solids using the periodic boundary conditions method. GaussView specifies the translation vectors automatically. • Set up molecule specifications for QST2 and QST3 transition state searches using the Builder’s molecule group feature to transform one structure into the reactants, products and/or transition state guess. • Select orbitals for CASSCF calculations using a graphical MO editor, rearranging the order and occupations with the mouse. • Start and monitor local Gaussian jobs. • Start remote jobs via a custom script.
GuassView: Showing Results • Show calculation results summary. • Examine atomic changes: display numerical values or color atoms by charge (optionally selecting custom colors). • Create surfaces for molecular orbitals, electron density, electrostatic potential, spin density, or NMR shielding density from Gaussian job results. • Display as solid, translucent or wire mesh. • Color surfaces by a separate property. • Load and display any cube created by Gaussian 03. • Animate normal modes associated with vibrational frequencies (or indicate the motion with vectors). • Display spectra: IR, Raman, NMR, VCD. • Display absolute NMR results or results with respect to an available reference compound. • Animate geometry optimizations, IRC reaction path following, potential energy surface scans, and BOMD and ADMP trajectories. • Produce web graphics and publication quality graphics files and printouts. • Save/print images at arbitrary size and resolution. • Create TIFF, JPEG, PNG, BMP and vector graphics EPS files. • Customize element, surface, charge and background colors, or select high quality gray scale output.
Reflection-Absorption Infrared Spectrum of AlQ3 Wavenumbers (cm-1) 1473 752 1386 1338 1116 1580 1605 800 1000 1200 1400 1600
GaussView: VCD (Vibrational Circular Dichroism) Spectra 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).
GaussView: ONIOM 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).
Gaussian/GaussView @ UNC • Installed in AFS ISIS package space /afs/isis/pkg/gaussian • Package name: gaussian • Versions: 09A02, 03E01 (default version) • Type “ipm add gaussian” to subscribe the service • Availability • Linux Cluster, kure.isis.unc.edu • LINUX cluster, emerald.isis.unc.edu • LINUX Cluster, topsail.unc.edu • Package information available at: http://help.unc.edu/6082
Access GaussView • From UNIX workstation • Login to emerald, kure, topsail ssh -X emerlad.isis.unc.edu • Invoke gaussview or gview via LSF interactive queue • From PC desktop via X-Win32 or SecureCRT • Detailed document available at: http://its2.unc.edu/divisions/rc/training/scientific/g03_gv_instructions.doc
Submit G03 Jobs to Servers • To submit single-CPU G03 jobs to computing servers via LSF: 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. For example: bsub -q idle -R blade g03 input.inp
Submit G03 Jobs to Servers • To submit multiple-CPU G03 jobs via LSF: -- 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. For example 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
Default Settings • Temporary files • Emerald: /largefs/gausswork • Memory • Emerald: 512MB • MAXDISK • Emerald: 2GB
Advanced Topics • Potential energy surfaces • Transition state optimization • Thermochemistry • NMR, VCD, IR/Raman spectra • NBO analysis • Excited states (UV/visible spectra) • Solvent effect • PBC • ONIOM model • ABMD, BOMD, etc.
Potential Energy Surfaces • Many aspects of chemistry can be reduced to questions about potential energy surfaces (PES) • A PES displays the energy of a molecule as a function of its geometry • Energy is plotted on the vertical axis, geometric coordinates (e.g bond lengths, valence angles, etc.) are plotted on the horizontal axes • A PES can be thought of it as a hilly landscape, with valleys, mountain passes and peaks • Real PES have many dimensions, but key feature can be represented by a 3 dimensional PES
Calculating PES in Gaussian/GaussView • Use the keyword “scan” • Then change input file properly