Working with Gaussian at CESCA

Working with Gaussian at CESCA

David Tur, PhD Scientific Applications expert [email protected]


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Introduction Capabilities & New features Renewed Maintenance: VIP customers Running Gaussian09 at CESCA

What is Gaussian?

Computational chemistry software package Starting from the basic laws of classical or quantum mechanics Gaussian predicts the energies, molecular structures, and vibrational frequencies of atomic or molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used by chemists, chemical engineers, biochemists, physicists and others scientist for research in established and emerging areas of chemical interest. It allows to perform virtual chemistry with a reasonable cost and saving much experimental time in the laboratory.

What is Gaussian?

Brief history of Gaussian: Gaussian70: Written by John Pople's group at Carnegie-Mellon University in the 1970s. John Pople was Nobel prize awarded in 1998 for his development of computational methods in quantum chemistry. Many versions (and revisions), all free till 1980s, became commercial and property of Gaussian, Inc. Most recent version Gaussian09 Rev. B.01 (Installed in cadi, obacs, prades and pirineus)

Gaussian09 at CESCA

Gaussian09, released in June 2009, is the latest in the Gaussian series of programs. Presented in Europe, in July, in a Workshop in the city of Ulm (Germany) CESCA was there…

Gaussian09 at CESCA

Gaussian Workshop in Ulm, July 2009 Speakers: Douglas Fox, Director of Gaussian Inc. Hrant Hratchian, Research Scientist of Gaussian Inc. George Petersson, Wesleyan University Mike Bearpark, Imperial College of London

Gaussian09 at CESCA

Gaussian Workshop in Ulm, July 2009

Gaussian available versions at CESCA Machine

Altix (Obacs)

CP4000 (Cadi)

NovaScale (Prades)

Altix UV (Pirineus)

Available Versions G09 Rev B.02 G09 Rev. A.02 G03 Rev. E.01 G03 Rev. D.02 G03 Rev. C.02 G09 Rev B.02 G09 Rev. A.02 G03 Rev. E.01 G03 Rev. D.02 G03 Rev. C.02 G09 Rev B.02 G09 Rev. A.02 G03 Rev. E.01 G03 Rev. D.02

Launch script g09b1 g09a2 g03e1 g03d2 G03c2 g09b1 g09a2 g03e1 g03d2 g03c2 g09b1 g09a2 g03e1 g03d2

G09 Rev B.02 G09 Rev. A.02

g09b1 g09a2


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Capabilities & New Features Quantum methods Classical methods Molecular Mechanics

Semi-empirical methods

GGA

DFT

Wavefunction based methods

HF&MCSCF

LDA LSDA SR

hybrid-GGA

MR

meta-GGA

Hybrid-meta-GGA

Post-HF MP2 Coupled Cluster FCI

CASPT2 MRCI

Capabilities & New Features

Gaussian 09: New Features, New Chemistry: Model Reactions of Very Large Systems with ONIOM Transition state optimizations. Much faster IRC calculations. Frequency calculations including electronic embedding. Calculations in solution. General performance enhancements. Fully customizable MM force fields. New implementations of AM1, PM3, PM3MM, PM6 and PDDG semi-empirical methods with true analytic gradients and frequencies (parameters also fully customizable).


Gaussian 09: New Features, New Chemistry: Model Reactions of Very Large Systems with ONIOM Transition state optimizations. Much faster IRC calculations. Frequency calculations including electronic embedding. Calculations in solution. General performance enhancements. Fully customizable MM force fields. New implementations of AM1, PM3, PM3MM, PM6 and PDDG semi-empirical methods with true analytic gradients and frequencies (parameters also fully customizable).


Gaussian 09: New Features, New Chemistry: Study Excited States in the Gas Phase and in Solution Analytic time-dependent DFT (TD-DFT) gradients. The EOM-CCSD method. State-specific solvation excitations and de-excitations. Franck-Condon and Herzberg-Teller analysis (and FCHT). Full support for CIS and TD-DFT calculations in solution (equilibrium and non-equilibrium).

Capabilities & New Features Gaussian 09: New Features, New Chemistry: Many More New Features Significantly enhanced solvation features Analytic gradients for the Brueckner Doubles (BD) method Additional spectra prediction Fragment-based initial guess and population analysis Many new DFT functionals Substantial performance improvements throughout the program, including optimizations for large molecules, frequency, calculations on large molecules (as much as 16x in parallel), IRC calculations (~3x faster), and optical rotations (~2x faster)

Capabilities & New Features Energies Molecular Mechanics: AMBER, DREIDING, UFF force field... Semi-emipirical: CNDO, INDO, MNDO, AM1, PM3, PM3MM, PM6 Hartree-Fock: RHF, ROHF, UHF... Post-HF methods: Møller Plesset (MP2, MP3...), CI (CIS, CISD), Coupled Cluster (CCS, CCSD, CCSD(T)...amplitudes can be saved now!!) DFT: LDA, GGA, Hybrid … new DFT functionals, including ones incorporating long range corrections, empirical dispersion, and double hybrids (B2PLYP, mPW2PLYP… with empirical dispersion “D”) Automated, high accurate methodologies: G1, G2, G3, CBS...Introduced recently developed Gn Compound Models.

Capabilities & New Features Gradients and Geometry Optimization Two and three-layer ONIOM (extended output) calculations for geometry optimizations: Modeling of very large molecules by defining two or three layers within the structure that are treated at different levels of accuracy.


Gradients and Geometry Optimization Two and three-layer ONIOM calculations for geometry optimizations. Automated geometry optimization to either minima or saddle points. Automated transition state searching using synchronous transit-guided quasi-Newton methods. Reaction path following using the intrinsic reaction coordinate (IRC). G09 offers news IRC and features on the Reaction paths Intersection optimization using state-averaged CASSCF. Classical trajectory calculation in which the classical equations of motion are integrated using analytical second derivatives [using either: Born Oppenheimer molecular dynamics (BOMD). Atom Centered Density Matrix Propagation molecular dynamics model.

Capabilities & New Features Frequencies and Second Derivatives Analytic computation of force constants, polarizabilities, hyperpolarizabilities, and dipole derivatives analytically for DFT and most of post-HF methods, and for excited states using CIS and CCSD using EOM-CCSD. Numerical differentiation of energies or gradients to produce force constants, polarizabilities, and dipole derivatives for the MP3, MP4(SDQ), CID, CISD, CCD, and QCISD methods. Frequencies: Determination of IR and Raman intensities (difference with polarizations/enantiomers) for vibrational transitions. Harmonic vibrational analysis and thermochemistry analysis using arbitrary isotopes, temperature, and pressure


Frequencies and Second Derivatives Thermochemistry analysis: Gaussian can predict various important thermodynamic quantities at the specified T and P, including thermal energy correction (TE, ZPE…), heat capacity, entropy and others

Capabilities & New Features Molecular Properties Evaluation of various one-electron properties using the SCF, DFT, MP2, CI, CCD and QCISD methods, including Mulliken population analysis, multipole moments, natural population analysis, electrostatic potentials, and electrostatic potential-derived charges

MEP of SiH3-C2H2-C4H4-COOH calculated at MP2/6-31+G*

HOMO of SiH3-C2H2-C4H4-COOH calculated at B97-1/aug-cc-pVDZ level

Capabilities & New Features Molecular Properties Evaluation of various one-electron properties using the SCF, DFT, MP2, CI, CCD and QCISD methods, including Mulliken population analysis, multipole moments, natural population analysis, electrostatic potentials, and electrostatic potential-derived charges. Polarizabilities and hyperpolarizabilities for Hartree-Fock and DFT methods. NMR shielding tensors and molecular susceptibilities using the SCF, DFT and MP2. Electron affinities and ionization potentials. Spectra and spectroscopic properties

Capabilities & New Features Molecular Properties Spectra and spectroscopic properties: IR and Raman Pre-resonance Raman UV-Visible NMR Vibrational circular dichroism (VCD) Electronic circular dichroism (ECD) Optical rotary dispersion (ORD) Harmonic vibration-rotation coupling Anharmonic vibration and vibration-rotation coupling g tensors and other hyperfine spectra tensors

Capabilities & New Features Periodic Boundary Conditions Gaussian expands the range of chemical systems that it can model to periodic systems such as polymers and crystals via its periodic boundary conditions (PBC) methods: Equilibrium geometries and transition structures of macromolecules Polymer reactivity Band gaps Surface Chemistry modeled with 2D PBC Bulk properties of crystals using 3D PBC Polarizabilities and hyperpolarizabilities for Hartree-Fock and DFT methods

Building a Graphite Sheet From Benzene, PBC/2D (Gaussian PBC Tutorial 2)

Capabilities & New Features Solvation Models (Enhanced in Gaussian09) Employing a self-consistent reaction field Gaussian can model systems in solution: Onsager model (dipole and sphere), including analytic first and second derivatives at the HF and DFT levels, and single-point energies at the MP2, MP3, MP4(SDQ), CI, CCD, and QCISD level Polarized Continuum (overlapping spheres) model (PCM) of Tomasi and coworkers analytic HF, DFT, MP2, MP3, MP4(SDQ), QCISD, CCD, CCSD, CID, and CISD energies and HF and DFT gradients and frequencies Large MM optimization in solution Highly increased the number of Solvents (Truhlar et al…>40)


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Renewed Maintenance program

CESCA has signed a New (and not cheap!) Maintenance Program that gives the following benefits: Priority telephone and/or email technical support for 2 designated users. All minor releases to the current product version Future major releases of software with no further licensing required Optional participation in major product release beta testing periods

Renewed Maintenance program Gaussian User (at CESCA of course!) with a problem/question on the program Send mail to [email protected]

Ingrid Barcena: Leader expert of Supercomputing and Drug Design Alfred Gil & David Tur, scientific applications experts

If necessary, scale the problem

Gaussian Technical Support Staff

Renewed Maintenance program

Gaussian Technical Support Staff

Dr. Fernando Clemente, technical support,

Dr. Douglas Fox Director of Gaussian, oversees technical support, addressing requests for technical assistance.


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Running Gaussian09 at CESCA

Script to run Gaussian 09: /usr/local/bin/g09b2 Example of file to submit jobs at /usr/local/examples/g09b2.lsf Installed at all machines: cadi, obacs, prades and pirineus See you on next talk!


Thank you for your attention!!! QUESTIONS????

David Tur, PhD Applications expert [email protected]

Working with Gaussian09: Hands On

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Introduction Preparing the input file Running the program via a batch queue (LSF) Examining and interpreting the output From Gaussian03 to Gaussian09 Optimizing performance

Introduction

Setting up the Gaussian environment (CESCA people did it for you ☺ ) Preparing the input file Running the program, either interactively or via a batch queue (LSF) Examining and interpreting the output Optimizing performance of Gaussian




Preparing the input file

Talking to Gaussian

Input syntax rules What do we want Gaussian to calculate? How? Information to be printed in the output

Preparing the input file Input syntax rules Input is free-format and case-Insensitive. Comments beginning with an exclamation point (!). Spaces, tabs, commas and forwards slashes can be used indistinctively to separate items within a line. Options to keywords in route section may be specified with ‘=‘ or in brackets: Keyword=option ; keyword(option1, option2…) In case options take values, the option is followed by ‘=‘ SCF(maxcycle=100) or SCF=maxcycle=100 All keywords and options may be shortened to their shortest unique abbreviation: Conventional can be shortened to Conven but not to Conv (due to the presence of Convergence keyword) External file may be included within the input file placing at the end of the file: @/home/whoever/filetobeplaced/N (/N is useful as it prevents the inclusion of the files content at the start of the output file)

Preparing the input file Scheme of the input: Water dimmer energy

Link 0 section (% lines) Route section (# line)

Title section

Molecule specification section

Extra information

Preparing the input file Scheme of the input

Link 0 section (% lines)

Link 0 section: Name and location of scratch directories, naming of checkpoint and read-write files, memory specifications, number of processors, etc…

Preparing the input file Link 0 section

%Mem=N Sets the amount of dynamic memory used to N words (8N bytes). N may be optionally followed by a units designation: KB, MB, GB, KW, MB or GW. %Chk=file Locates and names the checkpoint file. %RWF=file Locates and names a single, unified Read-Write file (old-style syntax). %Int=spec Locates and names the two-electron integral file(s). %D2E=spec Locates and names the two-electron integral derivative file(s). %Save Causes Link 0 to save scratch files at the end of the run.

Preparing the input file Scheme of the input Route section (# line): Specify desired calculation type, model chemistry and other options (blank line terminated)

Preparing the input file Route Section

This section specifies method, basis set, job type and additional keywords. # is required at the beginning of the line. p or n relates to the amount of output printed. Here we tell Gaussian what and how to computed, for available methods/basis sets, see next table: opt refers to an optimization. Other job types: sp (single point), freq (frequency) Note: for unrestricted calculations, add an "u" in front of the method: UHF/3-21G Additional typical keywords (added on the same line) include scf (to control scf cycles), scrf (for solvent calculations), guess (for reading/manipulation of wavefunction guess) etc ... The route section has to be followed by a blank line.

Preparing the input file Route Section: Job types

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. ReArchive Extract archive entry from checkpoint file only.

Preparing the input file Route Section: Method Availabilities in Gaussian 09

Preparing the input file Route Section: Basis Set stored internally in Gaussian09

LanL2MB LanL2DZ SDD SDDAll cc-pVDZ, cc-pVTZ, cc-pVQZ, ccpV5Z, cc-pV6Z SV, SVP, TZV, TZVP, QZVP MIDI! EPR-II and EPR-III UGBS: UGBSnP|V|O MTSmall DGDZVP, DGDZVP2 and DGTZVP CBSB7

CEP-4G CEP-31G CEP-121G STO-3G 3-21G 6-21G 4-31G 6-31G 6-31G† 6-311G D95V D95 SHC

Basis sets: Adding Polarization and Diffuse Functions 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)

LanL2MB

H-La, Hf-Bi

LanL2DZ

H, Li-La, Hf-Bi

SDD, SDDAll

all but Fr and Ra

cc-pV(DTQ5)Z

H-He, B-Ne, Al-Ar, Ga-Kr

included in definition

added via AUG- prefix

cc-pV6Z

H, B-Ne


added via AUG- prefix

SV

H-Kr

SVP

H-Kr


TZV and TZVP

H-Kr


MidiX

H, C-F, S-Cl, I, Br


EPR-II, EPR-III

H, B, C, N, O, F


UGBS

H-Lr

UGBS(1,2,3)P

+

Preparing the input file Route Section: From theoretical chemistry to ‘real’ chemistry Antiferromagnetic coupling: Guess=Fragment, Stability Atomic charges: Pop ∆G of solvation: SCRF=SMD Dipole moment: Pop Electron affinities: CBS-QB3, CCSD, EPT Electron density: cubegen Electronic circular dichroism: CIS, TD, EOM, SAC-CI Electrostatic potential: cubegen, Prop Electrostatic potential-derived charges: Pop=Chelp, ChelpG or MK Electronic transition band shape: Freq=FC, Freq=HT Polarizabilities/hyperpolarizabilities: Freq, Polar [CPHF=RdFreq], High accuracy energies: CBS-QB3, G2, G3, G4, W1U, W1BD Hyperfine coupling constants (anisotropic): Prop Hyperfine spectra tensors (including g tensors): Freq=(VCD, VibRot [, Anharmonic])

Preparing the input file Route Section: From theoretical chemistry to ‘real’ chemistry Ionization potentials: CBS-QB3, CCSD, EPT IR and Raman spectra: Freq[=Anharmonic] Pre-resonance Raman spectra: Freq CPHF=RdFreq Molecular orbitals: Pop=Regular Multipole moments: Pop NMR shielding and chemical shifts: NMR NMR spin-spin coupling constants: NMR=Mixed Optical rotations: Polar=OptRot Raman optical activity: Freq=ROA, CPHF=RdFreq Thermochemical analysis: Freq UV/Visible spectra: CIS, ZIndo, TD, EOM, SAC-CI Vibration-rotation coupling: Freq=VibRot Vibrational circular dichroism: Freq=VCD

Preparing the input file Title section

Title section (not required but useful). Followed by a blank line.

Preparing the input file Molecule specification section

Molecule specification section

Preparing the input file Molecule specification Section

This section starts with a line giving the overall molecular charge and multiplicity, directly followed by the coordinates Give charge and multiplicity separated by at least one space, e.g.: +1 1 Atoms can be written as symbols (H,C,O) or atomic numbers (1,6,8) The coordinate section has to be followed by a blank line Both Cartesian and z-matrix type coordinates are accepted.

Preparing the input file Molecule specification section

Cartesian Coordinates Z-matrix




Running Gaussian at CESCA

Available Gaussian versions at CESCA: Gaussian98: A.11 Gaussian03: B.02,C.02, D.02 and E.01 Gaussian09: A.02, B.01 Examples of input_file.dat and submitfile.lsf can be found at /usr/local/examples directory

Running Gaussian at CESCA As previosuly seen using LSF facilities, job is submitted as • bsub < submitfile.lsf Example of submitfile.lsf for Gaussian’s Jobs: • • • • • • • •

#!/usr/local/bin/bash #BSUB -J g09b1 #BSUB -o g09b1.log #BSUB -e g09b1.err #BSUB –N –u [email protected] #BSUB -R "select[(pirineus)] span[hosts=1]" cd $HOME/workdir g09b1 input_file.dat output_file.out

Running Gaussian at CESCA As previosuly seen using LSF facilities, job is submitted as • bsub < submitfile.lsf Example of submitfile.lsf for Gaussian’s Jobs: • • • • • • • •

#!/usr/local/bin/bash Important when using #BSUB -J g09b1 Gaussian in parallel! #BSUB -o g09b1.log #BSUB -e g09b1.err #BSUB –N –u [email protected] #BSUB -R "select[(pirineus)] span[hosts=1]" cd $HOME/workdir g09b1 input_file.dat output_file.out

Executing a Gaussian Job

Setting up the Gaussian environment (CESCA people did this for you :-) ) Preparing the input file Running the program, either interactively or via a batch queue (LSF) Examining and interpreting the output




Reading and interpreting the output

Output degree of information in Gaussian09 selected in the route section: #N Normal printing level (default) #T Output reduced to essential information and results #P HIGHLY RECOMMENDED!!!. Additional output is generated, including messages at the beginning and end of each link giving assorted machinedependent information. This includes execution timing data.

Reading and interpreting the output Gaussian is a collection of different programs or links, and the output file shows information about which of these links are in use, and its duration (in case #P present). Links of Gaussian09: L0 L1 L101 L102 L103 L105 L106

Initializes program and controls overlaying Processes route section, builds list of links to execute, and initializes scratch files Reads title and molecule specification Fletcher-Powell optimizations Berny optimizations to minima and TS, STQN transition state searches Murtaugh-Sargent optimizations Numerical differentiation of forces/dipoles to obtain polarizability/ hyperpolarizability

L107 L108 L109 L110 L111 L113 L114

Linear-synchronous-transit (LST) transition state search Unrelaxed potential energy surface scan Newton-Raphson optimization Double numerical differentiation of energies to produce frequencies Double numerical differentiation of energies to compute polarizabilities and hyperpolarizabilities EF optimization using analytic gradients EF numerical optimization (using only energies)

Reading and interpreting the output L115 L116 L117 L118 L120 L121 L122 L123 L124 L202 L301 L302 L303 L308 L310 L311 L314 L316 L319 L401 L402 L405

Follows reaction path using GS3 algorithm Numerical self-consistent reaction field (SCRF) Performs IPCM solvation calculations. BOMD calculations Controls ONIOM calculations ADMP calculations Counterpoise calculations Follows reaction path using the HPC algorithm (and others) Performs ONIOM with PCM and external-iteration PCM Reorients coordinates, calculates symmetry, and checks variables Generates basis set information Calculates overlap, kinetic, and potential integrals Calculates multipole integrals Computes dipole velocity and Rx∇integrals Computes spdf 2-electron integrals in a primitive fashion Computes sp 2-electron integrals Computes spdf 2-electron integrals Prints 2-electron integrals Computes 1-electron integrals for approximate spin orbital coupling Forms the initial MO guess Performs semi-empirical and molecular mechanics calculations Initializes an MCSCF calculation

Reading and interpreting the output L502 L503 L506 L508 L510 L601 L602 L604 L607 L608 L609 L610 L701 L702 L703 L716 L801 L802 L804 L811 L901 L902 L903 L904 L905

Iteratively solves the SCF equations (conven. UHF & ROHF, all direct methods, SCRF) Iteratively solves the SCF equations using direct minimization Performs an ROHF or GVB-PP calculation Quadratically convergent SCF program MC-SCF Population and related analyses (including multipole moments) 1-electron properties (potential, field, and field gradient) Evaluates MOs or density over a grid of points Performs NBO analyses Non-iterative DFT energies Atoms in Molecules properties Numerical integration (for testing integral codes) 1-electron integral first or second derivatives 2-electron integral first or second derivatives (sp) 2-electron integral first or second derivatives (spdf) Processes information for optimizations and frequencies Initializes transformation of 2-electron integrals Performs integral transformation (N3 in-core) Integral transformation Transforms integral derivatives & computes their contributions to MP2 2nd derivatives Anti-symmetrizes 2-electron integrals Determines the stability of the Hartree-Fock wavefunction Old in-core MP2 Complete basis set (CBS) extrapolation method of Petersson, et. al. Complex MP2

Reading and interpreting the output L905

Complex MP2

L906

Semi-direct MP2

L908

Electron Propagator Program

L913

Calculates post-SCF energies and gradient terms

L914

CI-Singles, RPA and ZIndo excited states; SCF stability

L915

Computes fifth order quantities (for MP5, QCISD(TQ) and BD(TQ))

L916

Old MP4 and CCSD

L918

Reoptimizes the wavefunction

L923

SAC-CI program

L1002 Iteratively solves the CPHF equations; computes various properties (including NMR) L1003 Iteratively solves the CP-MCSCF equations L1014 Computes analytic CI-Singles second derivatives L1101 Computes 1-electron integral derivatives L1102 Computes dipole derivative integrals L1110 2-electron integral derivative contribution to F(x) L1111 2 particle density matrix and post-SCF derivatives L1112 MP2 second derivatives L9999 Finalizes calculation and output

Reading and interpreting the output Dissecting the output file

This shows the version of Gaussian we are using

Entering Gaussian System, Link 0=/prod/G09/g09a2/g09 Initial command: /prod/G09/g09a2/l1.exe /tmp/dtur/560634.200910191401/Gau-7763.inp -scrdir=/tmp/dtur/560634.200910191401/ Entering Link 1 = /prod/G09/g09a2/l1.exe PID= 7764. Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009, Gaussian, Inc. All Rights Reserved. This is part of the Gaussian(R) 09 program. It is based on the Gaussian(R) 03 system (copyright 2003, Gaussian, Inc.), the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.), the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.), the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.), the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.), the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.), the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon University), and the Gaussian 82(TM) system (copyright 1983, Carnegie Mellon University). Gaussian is a federally registered trademark of Gaussian, Inc. This software contains proprietary and confidential information, including trade secrets, belonging to Gaussian, Inc. This software is provided under written license and may be used, copied, transmitted, or stored only in accord with that written license.

and the initial command (link 1) from the program: Gaussian has started!!

Reading and interpreting the output Dissecting the output file Cite this work as: Gaussian 09, Revision A.02, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2009. ****************************************** Gaussian 09: EM64L-G09RevA.02 11-Jun-2009 19-Oct-2009 ******************************************

The citation below is how the vendor wish to be cited in research papers or other reports

Information about the version of the program and the date of the output

Reading and interpreting the output Dissecting the output file ****************************************** The route section (that %nproc=4 we introduced in the Will use up to 4 processors via shared memory. %mem=3gb input file) --------------------------------------------------#p pbe1pbe counterpoise=2 aug-cc-pvtz maxdisk=150gb this part tells to the --------------------------------------------------1/38=1,62=2/1; programmer how the 2/12=2,17=6,18=5,40=1/2; calculation is being 1/38=1,53=5172,62=2/22; 3/5=16,6=1,7=10,11=2,16=1,25=1,30=1,74=-13/1,2,3; performed, IOPs and 99/5=1,9=1/99; other information (can Leave Link 1 at Mon Oct 19 17:54:53 2009, MaxMem= 402653184 cpu: 0.1 (Enter /prod/G09/g09a2/l101.exe) be useful when ---------------------------------------------------------------------troubleshooting) H2o dimer, single point energy calculation ----------------------------------------------------------------------

Title of the job as specified in the .dat file

Reading and interpreting the output Dissecting the output file -----------------------------------------H2o dimer, single point energy calculation -----------------------------------------Symbolic Z-matrix: Charge = 0 Multiplicity = 1 o o 1 oo2 h 1 ho3 2 hoo3 h 1 ho4 2 hoo4 3 dih4 h 2 ho5 1 hoo5 3 dih5 h 2 ho6 1 hoo6 3 dih6 Variables: oo2 2.87474 ho3 0.98886 hoo3 125.505 ho4 0.98864 hoo4 127.267 dih4 -145.704 ho5 0.9876 hoo5 98.226 dih5 -18.37 ho6 0.99242 hoo6 2.222 dih6 160.28

0 0 0

The Z-matrix represents how the software knows the molecular geometry (structure). Notice that the molecule has no charge and a multiplicity of 1 (all paired electrons).

Reading and interpreting the output Dissecting the output file Leave Link 101 at Sat Nov 29 19:15:37 2008, MaxMem= 851968000 cpu: (Enter /prod/G09/g09a2/l202.exe) Input orientation: --------------------------------------------------------------------Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------1 8 0 0.000000 0.000000 0.000000 2 8 0 0.000000 0.000000 2.874744 3 1 0 0.804995 0.000000 -0.574303 4 1 0 -0.649991 0.443327 -0.598652 5 1 0 0.927634 -0.308043 3.016048 6 1 0 -0.036221 0.012983 1.883073 --------------------------------------------------------------------Distance matrix (angstroms): 1 2 3 4 5 1 O 0.000000 2 O 2.874744 0.000000 3 H 0.988858 3.541743 0.000000 4 H 0.988641 3.561391 1.521221 0.000000 5 H 3.170480 0.987604 3.605628 4.014912 0.000000 6 H 1.883466 0.992417 2.597404 2.592464 1.521745 6 6 H 0.000000 Stoichiometry H4O2 Framework group C1[X(H4O2)]

0.2

The structure is also represented as a more standard X-Y-Z coordinate system.

The distance matrix shows the distance of each atom from the other, in units of angstroms.

Reading and interpreting the output Dissecting the output file Leave Link 101 at Sat Nov 29 19:15:37 2008, MaxMem= 851968000 cpu: 0.2 (Enter /prod/G09/g09a2/l202.exe) Input orientation: --------------------------------------------------------------------Center Atomic Atomic Coordinates (Angstroms) The structure is also Number Number Type X Y Z --------------------------------------------------------------------represented as a more 1 8 0 0.000000 0.000000 0.000000 standard X-Y-Z 2 8 0 0.000000 0.000000 2.874744 3 1 0 0.804995 0.000000 -0.574303 coordinate system. 4 1 0 -0.649991 0.443327 -0.598652 5 1 0 0.927634 -0.308043 3.016048 6 1 0 -0.036221 0.012983 1.883073 --------------------------------------------------------------------Distance matrix (angstroms): The distance matrix 1 2 3 4 5 1 O 0.000000 shows the distance of 2 O 2.874744 0.000000 each atom from the 3 H 0.988858 3.541743 0.000000 4 H 0.988641 3.561391 1.521221 0.000000 other, in units of 5 H 3.170480 0.987604 3.605628 4.014912 0.000000 angstroms 6 H 1.883466 0.992417 2.597404 2.592464 1.521745 6 6 H 0.000000 Stoichiometry of the compound and Stoichiometry H4O2 information about the symmetry Framework group C1[X(H4O2)]

Reading and interpreting the output Dissecting the output file --------------------------------------------------------------------Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------1 8 0 -1.336267 0.003540 -0.051160 2 8 0 1.535692 -0.106915 0.010523 Standard orientation. 3 1 0 -1.885532 0.794523 0.173551 4 1 0 -1.968208 -0.724440 0.168170 5 1 0 1.714869 0.864130 -0.007613 6 1 0 0.543468 -0.107220 -0.009016 --------------------------------------------------------------------Rotational constants (GHZ): 233.4754410 6.5562200 6.3922484 Leave Link 202 at Sat Nov 29 19:15:38 2008, MaxMem= 851968000 cpu: 0.3 Leave Link 202 at Sat Nov 29 19:15:38 2008, MaxMem= 851968000 cpu: 0.3 (Enter /prod/G09/g09a2/l301.exe) Standard basis: 6-31+G (6D, 7F) There are 34 symmetry adapted basis functions of A symmetry. Important information Integral buffers will be 131072 words long. about the number of Raffenetti 1 integral format. Two-electron integral symmetry is turned on. basis functions used in 34 basis functions, 68 primitive gaussians, 34 cartesian basis functions the calculation. 10 alpha electrons 10 beta electrons nuclear repulsion energy 36.2454414464 Hartrees. IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 ScaDFX= 1.000000 1.000000 1.000000 1.000000 IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 NAtoms= 6 NActive= 6 NUniq= 6 SFac= 7.50D-01 NAtFMM= 80 NAOKFM=F Big=F

Reading and interpreting the output Dissecting the output file (Enter /prod/G09/g09a2/l502.exe) Closed shell SCF: Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. Using DIIS extrapolation, IDIIS= 1040. Integral symmetry usage will be decided dynamically. Keep R1 integrals in memory in canonical form, NReq= 1020317. IEnd= 21573 IEndB= 21573 NGot= 851968000 MDV= 851786934 LenX= 851786934 Symmetry not used in FoFDir. MinBra= 0 MaxBra= 1 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. Cycle 1 Pass 1 IDiag 1: E= -151.836664298036 DIIS: error= 5.38D-02 at cycle 1 NSaved= 1. NSaved= 1 IEnMin= 1 EnMin= -151.836664298036 IErMin= 1 ErrMin= 5.38D-02 ErrMax= 5.38D-02 EMaxC= 1.00D-01 BMatC= 2.12D-01 BMatP= 2.12D-01 IDIUse=3 WtCom= 4.62D-01 WtEn= 5.38D-01 Coeff-Com: 0.100D+01 Coeff-En: 0.100D+01 Coeff: 0.100D+01 Gap= 0.487 Goal= None Shift= 0.000 GapD= 0.487 DampG=2.000 DampE=0.500 DampFc=1.0000 IDamp=-1. RMSDP=1.22D-02 MaxDP=1.25D-01 OVMax= 1.19D-01

The SCF starts, information about the requested converge criteria.

First Cycle of the SCF calculation.

Reading and interpreting the output Dissecting the output file

Cycle 11 Pass 1 IDiag 1: E= -151.985993274728 Delta-E= 0.000000000000 Rises=F Damp=F DIIS: error= 5.49D-09 at cycle 11 NSaved= 11. NSaved=11 IEnMin=11 EnMin= -151.985993274728 IErMin=11 ErrMin= 5.49D-09 ErrMax= 5.49D-09 EMaxC= 1.00D-01 BMatC= 1.71D-15 BMatP= 9.35D-14 IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 Coeff-Com: -0.150D-06-0.122D-07-0.321D-05 0.922D-04-0.142D-03-0.519D-03 Coeff-Com: 0.552D-02-0.286D-01 0.135D+00-0.460D+00 0.135D+01 Coeff: -0.150D-06-0.122D-07-0.321D-05 0.922D-04-0.142D-03-0.519D-03 Coeff: 0.552D-02-0.286D-01 0.135D+00-0.460D+00 0.135D+01 Gap= 0.580 Goal= None Shift= 0.000 RMSDP=4.10D-09 MaxDP=3.26D-08 DE=-3.41D-13 OVMax= 4.50D-08 SCF Done: E(RHF) = -151.985993275 A.U. after 11 cycles Convg = 0.4096D-08 -V/T = 2.0020 S**2 = 0.0000 KE= 1.516857342155D+02 PE=-4.332421091120D+02 EE= 9.332494017544D+01 Leave Link 502 at Sat Nov 29 19:15:44 2008, MaxMem= 851968000 cpu: 1.0

After 11 iterations the energy converged, and the energy is obtained and given in atomics units.

Reading and interpreting the output Dissecting the output file (Enter /prod/G09/g09a2/l9999.exe) 1\1\GINC-PRADES24\SP\RPBE1PBE\Aug-CC-pVTZ\C6H9N1\DTUR\19-Oct-2009\0\\# p pbe1pbe counterpoise=2 aug-cc-pvtz maxdisk=150gb\\Title Card Require d = mp2augdzb.dat resultat de optimitzat 631gdp, no pla\\0,1\C,0,-0.55 7432,-1.211151,0.757902\C,0,-0.736195,-1.226193,-0.639236\C,0,-0.82516 6,-0.014304,-1.351098\C,0,-0.73487,1.212627,-0.665718\C,0,-0.556059,1. 227723,0.731392\C,0,-0.467826,0.015842,1.443385\H,0,-0.481802,-2.15238 8,1.310137\H,0,-0.802958,-2.179602,-1.171776\H,0,-0.960287,-0.026025,2.436687\H,0,-0.800611,2.154311,-1.218854\H,0,-0.479654,2.180653,1.263 11\H,0,-0.316939,0.027512,2.526491\N,0,2.76361,-0.00394,-0.087468\H,0, 3.01991,-0.807712,-0.661928\H,0,2.99795,0.821976,-0.639439\H,0,1.74440 6,-0.018405,-0.018552\\Version=EM64L-G09RevA.02\State=1-A\HF=-56.51554 62\RMSD=1.884e-09\Dipole=-0.412894,0.0044153,-0.4840748\Quadrupole=-6. 3542218,3.8643851,2.4898367,0.0412819,-2.7318427,0.0127661\PG=C01 [X(C 6H9N1)]\\@

In the beginning the Universe was created. Gaussian’s This has made a lot of people very angry and been widely regarded as a bad move. -D.Adams Job cpu time: 0 days 0 hours 0 minutes 3.0 seconds. File lengths (MBytes): RWF= 13 Int= 0 D2E= 0 Chk= 10 Scr= 1 Normal termination of Gaussian 03 at Sat Nov 29 19:15:48 2008.

Summary of main results of the calculations.

“fortune cookie”.

The final message in the output file is a really good thing to see. It states that your job completed as requested, with no “failure to converge” or other problems.

Reading and interpreting the output Searching information within the output file: Using grep command in linux, or find or search within windows editors, we have to look for the previously seen sentences for the desired information e.g.: dtur@obacs:~/ws> grep Normal *.log h2o-sp.log: Normal termination of Gaussian 09 at Thu Nov 27 18:33:31 2008. dtur@obacs:~/ws> grep 'SCF D' *.log h2o-sp.log: SCF Done: E(RHF) = -151.985993275

A.U. after 11 cycles

Other important information that can be found in the output file, depending on the requested type of calculation e.g.: The Möller-Plesset energy: dtur@obacs:~/ws> grep EUMP2 h2o-sp.log.log E2 = -0.5450087887D+00 EUMP2 = -0.15266201365393D+03 The lower frequencies (freq keyword) to determinate what type of minima is found in the optimization dtur@obacs:~/ws> grep Low h2o-z-matrix-optedmp2tz.log Low frequencies --- -0.0005 0.0014 0.0019 23.5769 55.3398 198.4177 Low frequencies --- 505.7455 572.1785 589.8776

Working with Gaussian09

1. 2. 3. 4. 5. 6.


Working with Gaussian09

1. 2. 3. 4. 5. 6.


From Gaussian03 to Gaussian09

New Methods and Feature (previous talk) Efficiency Improvements Functional Differences Between Gaussian 09 and Gaussian 03

From Gaussian03 to Gaussian09 Efficiency Improvements HF and DFT frequencies on large molecules are much faster FMM and hence linear scaling Coulomb and Exchange are cluster-parallel ONIOM(MO:MM) frequencies on large systems are much faster, especially with electronic embedding Normal modes can be saved during large frequency calculations CC, BD and EOM-CCSD amplitudes can be saved on the checkpoint file Semi-empirical, HF, and DFT frequencies can be restarted CC and EOM-CC calculations can be restarted in mid-calculation. The initial guesses for individual steps within an ONIOM calculation can be taken from separate checkpoint files The density fitting sets corresponding to the SVP, TZVP, and QZV basis sets are included Density basis sets can be read in using coefficients of unnormalized primitives as though they were AOs

From Gaussian03 to Gaussian09 Functional Differences between G03 and G09 Single-point SCF calculations now default to full accuracy (SCF=Tight). The default for Freq=ROA is CPHF=RdFreq The default for post-SCF methods such as MP, BD and CC is Tran=IABC IRCs default to a new link, L123. Use IRC=Report to specify internal coordinates whose values should also be tabulated. Semi-empirical frequencies using CPHF=Separate Change on the assignment of atoms to fragments for Counterpoise and Guess=Fragment calculations: C(Fragment=3) 0.0 1.0 2.0 rather than C 0.0 1.0 2.0 3




Optimizing performance at CESCA Different tips, suggestions or tricks to optimally run Gaussian using CESCA facilities Ask Roberto Gomperts

Optimizing performance at CESCA Different tips, suggestions or tricks to optimally run Gaussian using CESCA facilities Ask Roberto Gomperts Type of calculation Hands-on Session: • Directories to be used • Cluster where the calculation is performed • Resources requested CESCA people is here to help you

Optimizing performance at CESCA Different tips, suggestions or tricks to optimally run Gaussian using CESCA facilities Ask Roberto Gomperts Type of calculation Hands-on Session: • Directories to be used • Cluster where the calculation is performed • Resources requested CESCA people is here to help you Ask Roberto again if necessary

Optimizing performance at CESCA

Take into account Performance and accuracy of the method: i.e. Hybrid Functionals Cost similar to HF for medium-large systems Accuracy better than HF Accuracy for MP2 except for weakly-bound systems No as accurate as CCSD(T), CBS-QB3, etc. If B3LYP and CBS-4 agree, good check

Optimizing performance at CESCA Take into account Performance and accuracy of the method: i.e. Møller-Plesset Theory Generally a good hierarchy of models MP2 cheap MP4 good for most systems Series tends to oscillate Converged problems If HF a poor starting point If serious spin contamination Not exact for two-electron system

Optimizing performance at CESCA Take into account Performance and accuracy of the method: i.e. Compound Model Chemistries for Thermochemistries Most accurate and expensive: W1U, CBS-APNO (~½ kcal error, 2 kcal worst case) Expensive but practical: CBS-QB3 (~½ kcal error, 6 kcal worst case) Usually less expensive than G2 and avoids big failures of G2, G3 (e.g. SF6) Cheapest: CBS-4M (only recommended for minima (~3 kcal error, 20 kcal worst case) (If CBS-4M and B3LYP agree can have confidence)


Initial Guess for Equilibrium Geometries GaussView, molden, molekel or other graphical interface Experiment Empirical force field calculations Semi-empirical MO calculations Lower level ab initio calculations Quantum chemical data bases

Optimizing performance at CESCA Testing Minima Compute the full Hessian (freq from converged opt) Check the number of negative eigenvalues: -1 of more indicates a transition state of higher order saddle point Totally symmetric: a transition structure Non-totally symmetric: wants to break symmetry to reach some minimum If there are any negative eigenvalues, follow the associated eigenvector to a lower energy structure

Optimizing performance at CESCA Things to try when optimizations fail Number of steps exceeded Check for very flexible coordinates and/or strongly coupled coordinates Restart from a reasonable step and use CalcFC Maximum step size exceeded If it happens too often, check for flexible and/or strongly coupled coordinates Change in point group during optimization Check structure and/or use NoSymm

Optimizing performance at CESCA Things to try when Transition State Searches fail Too many negative eigenvalues of the Hessian during TS optimization Follow the eigenvector with the negative eigenvalue Use Freq=Internal to see normal modes in internal coordinates No negative eigenvalues of the Hessian during a transition structure optimization Try QST2 or QST3 Relaxed scan along coordinate to loo k for highest energy (Opt=ModRedundant)

Optimizing performance at CESCA Selecting the machine and the number of processors depending on type of calculation. Example: Couterpoise Calculation of the NH3···Benzene dimer using CCSD(T)/cc-pVTZ method (5 energies, 220 basis functions)

Optimizing performance at CESCA Example: Couterpoise Calculation of the NH3···Benzene dimer using CCSD(T)/cc-pVTZ method (5 energies, 220 basis functions). Mem=3GB, maxdisk=150gb. Real Time of the calculation (min) OBACS

SCF

Int. Transf

CCSD(T)

N Procs.

Total

Link 502

Link 804

Link 913

1

10553

148

4488

5910

2

6098

77

2239

3772

4

4126

42

1215

2862

8

3493

25

861

2598

16

3312

17

497

2789

SCF

Int. Transf

CCSD(T)

Speed up OBACS N procs

Total

Link 502

Link 804

Link 913

1

1

1

1

1

2

1,7

1,9

2,0

1,6

4

2,6

3,5

3,7

2,1

8

3,0

5,9

5,2

2,3

16

3,2

8,7

9,0

2,1

Optimizing performance at CESCA Speed up of the links (CCSD(T)/cc-pVTZ method (5 energies, 220 basis functions) ): Speedup

18

Ideal

16 14 12 10

Link 804 Link 502

8 6 4

Total

2

Link 913

0 0

4

8

Number of processors

12

16

Optimizing performance at CESCA Example: Couterpoise Calculation of the NH3···Benzene dimer using CCSD(T)/ccpVTZ method (5 energies, 220 basis functions). Mem=3GB, maxdisk=150gb. Real Time of the calculation (min) OBACS

SCF

Int. Transf

CCSD(T)

N Procs.

Total

Link 502

Link 804

Link 913

1

10553

148

4488

5910

2

6098

77

2239

3772

4

4126

42

1215

2862

8

3493

25

861

2598

16

3312

17

497

2789

SCF

Int. Transf

CCSD(T)

CADI N procs

Total

Link 502

Link 804

Link 913

1

9537

261

1862

7375

2

5854

152

1275

4408

4

4116

90

1029

2979

Optimizing performance at CESCA Example: Couterpoise Calculation of the NH3···Benzene dimer using CCSD(T)/ccpVTZ method (5 energies, 220 basis functions). Mem=3GB, maxdisk=150gb. Real Time of the calculation (min) OBACS

SCF

Int. Transf

CCSD(T)

N Procs.

Total

Link 502

Link 804

Link 913

1

10553

148

4488

5910

2

6098

77

2239

3772

4

4126

42

1215

2862

8

3493

25

861

2598

16

3312

17

497

2789

SCF

Int. Transf

CCSD(T)

CADI N procs

Total

Link 502

Link 804

Link 913

1

9537

261

1862

7375

2

5854

152

1275

4408

4

4116

90

1029

2979

Optimizing performance at CESCA Type of calculation: Recommended number of processors Method

Energy

Opt. (Gradient) Freq (Hessian)

HF

4-32

4-32

4

DFT

4-32

4-32

4

MP2

2-4

2-4

2

MP3, MP4…

1

1

1

CCS,CCSDT…

1

1

1

CCSD(T)

1-4

1-4

1

CIS

2-4

2-4

1

CISD

1

1

1

Semi-empirical

1

1

1


Directories to be used Cluster where the calculation is performed Resources requested Type of calculation

CESCA people is here to help you


Thank you for your attention!!! QUESTIONS????

David Tur, PhD Scientific Applications expert [email protected]

Hands-on II: Running Gaussian09 at CESCA

Working directory: /cescascratch/handson/gaussian You can create your own directory inside /cescascratch/handson/users or work in your home Examples at: • /usr/local/examples (archive.lsf examples) • /prod/G09/g09b1/tests/com (tests from Gaussian Inc.) • /cescascratch/handson/gaussian (Hands-on II examples) Queu: curs Machines: obacs, cadi, prades and pirineus G03 versions: E.01,C.02, B.02 G09 version A.02, B01

Hands-on II: Running Gaussian09 Example 1: Creating the first input file, H20 SP energy calculation h2o-sphf.dat Input file can be created in two ways: • By hand: using local editor (VI, emacs, nedit...): • Coordenates file of H2O: h2o-zmatrix.dat and h2o-cartesianas.dat

Hands-on II: Running Gaussian09 Example 1: Creating the first input file, H20 SP energy calculation Input file can be created in two ways: • Using Molden:



Hands-on II: Running Gaussian09

/home and /cescascratch are NFS , better alternative running and writing at /tmp Hands-on II. Example 2. Water dimer optimization Running the job at /tmp, and when the job is finished copy log and chk files at /home/whereeveryouneed h2o-z-matrix-opthf-savechk.dat/lsf runs a hf/6-31+G* optimization, saving the chk h2o-z-matrix-spmp2-savedchk.dat/lsf reading the chk of the previous calculations, performs an mp2 single point calculation.


Hands-on III. Example 3. Water dimmer frequencies localizing an absolute minimum, and inspecting thermochemical data: h2o-dim-freq.dat This job is done writing output files in the tmp directory to be more efficient. h2o-dim-freq.lsf


Hands-on III. Example 4. Saving post-HF amplitudes Run a job with small basis set, and save the amplitudes: g09a2-ccsdt-1.dat (ccsd(t)/cc-pvdz) Reading amplitudes and run the job with a big basis set: G09a2-ccsdt-1.dat

Hands-on II: Running Gaussian09 Different tips, suggestions or tricks to optimally run Gaussian using CESCA facilities Error: Error termination via Lnk1e in /prod/G03/g03e1/g03/l906.exe Solution: You need more memory Error: Something like “IUnit=1 –“ or “ Error termination in NtrErr” Solution: You need more disk Error: “SCF failure” Solution 1: increase the number of steps “scf=(maxcyc=300)” Solution 2: try another algorithm “scf=qc”, much slower but more 'efficient'

Optimizing performance at CESCA Take into account Performance and accuracy of the method: i.e. Compound Model Chemistries for Thermochemistries Most accurate and expensive: W1U, CBS-APNO (~½ kcal error, 2 kcal worst case) Expensive but practical: CBS-QB3 (~½ kcal error, 6 kcal worst case) Usually less expensive than G2 and avoids big failures of G2, G3 (e.g. SF6) Cheapest: CBS-4M (only recommended for minima (~3 kcal error, 20 kcal worst case) (If CBS-4M and B3LYP agree can have confidence)


Initial Guess for Equilibrium Geometries GaussView, molden, molekel or other graphical interface Experiment Empirical force field calculations Semi-empirical MO calculations Lower level ab initio calculations Quantum chemical data bases

Optimizing performance at CESCA Testing Minima Compute the full Hessian (freq from converged opt) Check the number of negative eigenvalues: -1 of more indicates a transition state of higher order saddle point Totally symmetric: a transition structure Non-totally symmetric: wants to break symmetry to reach some minimum If there are any negative eigenvalues, follow the associated eigenvector to a lower energy structure

Optimizing performance at CESCA Things to try when optimizations fail Number of steps exceeded Check for very flexible coordinates and/or strongly coupled coordinates Restart from a reasonable step and use CalcFC Maximum step size exceeded If it happens too often, check for flexible and/or strongly coupled coordinates Change in point group during optimization Check structure and/or use NoSymm

Optimizing performance at CESCA Things to try when Transition State Searches fail Too many negative eigenvalues of the Hessian during TS optimization Follow the eigenvector with the negative eigenvalue Use Freq=Internal to see normal modes in internal coordinates No negative eigenvalues of the Hessian during a transition structure optimization Try QST2 or QST3 Relaxed scan along coordinate to loo k for highest energy (Opt=ModRedundant)

Working with Gaussian at CESCA

Working with Gaussian at CESCA

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