curs09 dtur working with gaussian09

WorkingWorking withwith Gaussian09Gaussian09

David Tur, PhDScientific Applications expert

[email protected]

1. Introduction2. Preparing the input file3. Running the program via a batch queue (LSF)4. Examining and interpreting the output5. From Gaussian03 to Gaussian096. Optimizing performance

Working with Gaussian09Working with Gaussian09

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

IntroductionIntroduction

Talking to Gaussian

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

Preparing the input filePreparing 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)


Link 0 section (% lines)

Route section (# line)

Title section

Molecule

specification section

Scheme of the input: Water dimmer energy

Extra information


Scheme of the input

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


Link 0 section (% lines)

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.


Scheme of the input

Route section (# line): Specify desired Route section (# line): Specify desired Route section (# line): Specify desired Route section (# line): Specify desired

calculation type, model chemistry and calculation type, model chemistry and calculation type, model chemistry and calculation type, model chemistry and

other options (blank line terminated)other options (blank line terminated)other options (blank line terminated)other options (blank line terminated)


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.


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.


Route Section: Method Availabilities in Gaussian 09



Route Section: Basis Set stored internally in Gaussian09

CEP-4GCEP-31GCEP-121GSTO-3G 3-21G 6-21G 4-31G 6-31G 6-31G6-311GD95VD95SHC

LanL2MBLanL2DZSDDSDDAllcc-pVDZ, cc-pVTZ, cc-pVQZ, cc-pV5Z, cc-pV6ZSV, SVP, TZV, TZVP, QZVP MIDI! EPR-II and EPR-IIIUGBS: UGBSnP|V|OMTSmall DGDZVP, DGDZVP2 and DGTZVPCBSB7

Basis sets: Adding Polarization and Diffuse Functions

UGBS(1,2,3)P H-LrUGBS included in definition H, B, C, N, O, F EPR-II, EPR-III

included in definition H, C-F, S-Cl, I, Br MidiX

included in definition H-Kr TZV and TZVP

included in definition H-Kr SVP

H-Kr SV

added via AUG- prefixincluded in definition H, B-Ne cc-pV6Z

added via AUG- prefixincluded in definition H-He, B-Ne, Al-Ar, Ga-Kr cc-pV(DTQ5)Z all but Fr and Ra SDD, SDDAll

H, Li-La, Hf-Bi LanL2DZ

H-La, Hf-Bi LanL2MB

* (Li-Ar only) H-RnCEP-121G * (Li-Ar only) H-RnCEP-31G * (Li-Ar only) H-RnCEP-4G * H-ClSHC

++(d) or (d,p) H-Ne D95V ++(3df,3pd) H-Cl except Na and Mg D95 ++(3df,3pd) H-Kr 6-311G ++(3df,3pd) H-Kr 6-31G

(d) or (d,p) H-Ne 4-31G (d) H-Cl6-21G

+* or ** H-Xe3-21G

* H-XeSTO-3G

Diffuse FunctionsPolarization Functions Applies to Basis Set

Route Section: From theoretical chemistry to real

chemistry

Antiferromagnetic coupling: Guess=Fragment, StabilityAtomic charges: PopG of solvation: SCRF=SMDDipole moment: PopElectron affinities: CBS-QB3, CCSD, EPTElectron density: cubegenElectronic circular dichroism: CIS, TD, EOM, SAC-CIElectrostatic potential: cubegen, PropElectrostatic potential-derived charges: Pop=Chelp, ChelpG or MKElectronic transition band shape: Freq=FC, Freq=HTPolarizabilities/hyperpolarizabilities: Freq, Polar [CPHF=RdFreq], Highaccuracy energies: CBS-QB3, G2, G3, G4, W1U, W1BDHyperfine coupling constants (anisotropic): PropHyperfine spectra tensors (including g tensors): Freq=(VCD, VibRot [, Anharmonic])


Route Section: From theoretical chemistry to real

chemistry

Ionization potentials: CBS-QB3, CCSD, EPTIR and Raman spectra: Freq[=Anharmonic]Pre-resonance Raman spectra: Freq CPHF=RdFreqMolecular orbitals: Pop=RegularMultipole moments: PopNMR shielding and chemical shifts: NMRNMR spin-spin coupling constants: NMR=MixedOptical rotations: Polar=OptRotRaman optical activity: Freq=ROA, CPHF=RdFreqThermochemical analysis: FreqUV/Visible spectra: CIS, ZIndo, TD, EOM, SAC-CIVibration-rotation coupling: Freq=VibRotVibrational circular dichroism: Freq=VCD


Title section (not

required but useful).

Followed by a blank

line.

Title section


Molecule specification

section

Molecule specification section


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.


Molecule specification section

Cartesian Coordinates

Z-matrix



Working with Working with Gaussian09Gaussian09

Running Gaussian at CESCARunning Gaussian at CESCA

Available Gaussian versions at CESCA:Gaussian98: A.11 Gaussian03: B.02,C.02, D.02 and E.01Gaussian09: A.02

Examples of input_file.dat and submitfile.lsfcan be found at /usr/local/examples directory


As previosuly seen using LSF facilities, job is submitted as bsub < submitfile.lsf

Example of submitfile.lsf for Gaussians Jobs:

#!/usr/local/bin/bash #BSUB -J g09a2 #BSUB -o g09a2.log #BSUB -e g09a2.err #BSUB N u [email protected] #BSUB -R "select[(prades)] span[hosts=1]" cd $HOME/workdir g09a2 input_file.dat output_file.out


As previosuly seen using LSF facilities, job is submitted as bsub < submitfile.lsf

Example of submitfile.lsf for Gaussians Jobs:

#!/usr/local/bin/bash #BSUB -J g09a2 #BSUB -o g09a2.log #BSUB -e g09a2.err #BSUB N u [email protected] #BSUB -R "select[(prades)] span[hosts=1]" cd $HOME/workdir g09a2 input_file.dat output_file.out

Important when using Important when using Gaussian in parallel!Gaussian in parallel!

Executing a Gaussian JobExecuting 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

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 machine-dependent information. This includes execution timing data.

Reading and interpreting the outputReading 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:


EF numerical optimization (using only energies)L114EF optimization using analytic gradientsL113Double numerical differentiation of energies to compute polarizabilities and hyperpolarizabilitiesL111Double numerical differentiation of energies to produce frequenciesL110Newton-Raphson optimizationL109Unrelaxed potential energy surface scanL108Linear-synchronous-transit (LST) transition state searchL107Numerical differentiation of forces/dipoles to obtain polarizability/ hyperpolarizabilityL106Murtaugh-Sargent optimizationsL105Berny optimizations to minima and TS, STQN transition state searchesL103Fletcher-Powell optimizationsL102Reads title and molecule specificationL101Processes route section, builds list of links to execute, and initializes scratch filesL1Initializes program and controls overlayingL0


Initializes an MCSCF calculationL405Performs semi-empirical and molecular mechanics calculationsL402Forms the initial MO guessL401Computes 1-electron integrals for approximate spin orbital couplingL319Prints 2-electron integralsL316Computes spdf 2-electron integralsL314Computes sp 2-electron integralsL311Computes spdf 2-electron integrals in a primitive fashionL310Computes dipole velocity and RxintegralsL308Calculates multipole integralsL303Calculates overlap, kinetic, and potential integralsL302Generates basis set informationL301Reorients coordinates, calculates symmetry, and checks variablesL202Performs ONIOM with PCM and external-iteration PCML124Follows reaction path using the HPC algorithm (and others)L123Counterpoise calculationsL122ADMP calculationsL121Controls ONIOM calculationsL120BOMD calculationsL118Performs IPCM solvation calculations.L117Numerical self-consistent reaction field (SCRF)L116Follows reaction path using GS3 algorithmL115


Complex MP2L905Complete basis set (CBS) extrapolation method of Petersson, et. al.L904Old in-core MP2L903Determines the stability of the Hartree-Fock wavefunctionL902Anti-symmetrizes 2-electron integralsL901Transforms integral derivatives & computes their contributions to MP2 2nd derivativesL811Integral transformationL804Performs integral transformation (N3 in-core)L802Initializes transformation of 2-electron integralsL801Processes information for optimizations and frequenciesL7162-electron integral first or second derivatives (spdf)L7032-electron integral first or second derivatives (sp)L7021-electron integral first or second derivativesL701Numerical integration (for testing integral codes)L610Atoms in Molecules propertiesL609Non-iterative DFT energiesL608Performs NBO analysesL607Evaluates MOs or density over a grid of pointsL6041-electron properties (potential, field, and field gradient)L602Population and related analyses (including multipole moments)L601MC-SCFL510Quadratically convergent SCF programL508Performs an ROHF or GVB-PP calculationL506Iteratively solves the SCF equations using direct minimizationL503Iteratively solves the SCF equations (conven. UHF & ROHF, all direct methods, SCRF)L502


Finalizes calculation and outputL9999MP2 second derivativesL11122 particle density matrix and post-SCF derivativesL11112-electron integral derivative contribution to F(x)L1110Computes dipole derivative integralsL1102Computes 1-electron integral derivativesL1101Computes analytic CI-Singles second derivativesL1014Iteratively solves the CP-MCSCF equationsL1003Iteratively solves the CPHF equations; computes various properties (including NMR)L1002SAC-CI programL923Reoptimizes the wavefunctionL918Old MP4 and CCSDL916Computes fifth order quantities (for MP5, QCISD(TQ) and BD(TQ))L915CI-Singles, RPA and ZIndo excited states; SCF stabilityL914Calculates post-SCF energies and gradient termsL913Electron Propagator ProgramL908Semi-direct MP2L906Complex MP2L905

Entering Gaussian System, Link 0=/prod/G09/g09a2/g09Initial 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 onthe 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 MellonUniversity), and the Gaussian 82(TM) system (copyright 1983,Carnegie Mellon University). Gaussian is a federally registeredtrademark 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 beused, copied, transmitted, or stored only in accord with thatwritten license.

Dissecting the output file This shows the version of Gaussian we are using

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


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-200919-Oct-2009

******************************************

Dissecting the output fileThe 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


******************************************

%nproc=4Will use up to 4 processors via shared memory.%mem=3gb---------------------------------------------------

#p pbe1pbe counterpoise=2 aug-cc-pvtz maxdisk=150gb---------------------------------------------------

1/38=1,62=2/1;2/12=2,17=6,18=5,40=1/2;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;99/5=1,9=1/99;Leave Link 1 at Mon Oct 19 17:54:53 2009, MaxMem= 402653184 cpu: 0.1(Enter /prod/G09/g09a2/l101.exe)----------------------------------------------------------------------

H2o dimer, single point energy calculation ----------------------------------------------------------------------

Dissecting the output file

The route section (that we introduced in the input file)

this part tells to the programmer how the calculation is being performed, IOPs and other information (can be useful when troubleshooting)

Title of the job as specified in the .dat file


------------------------------------------

H2o dimer, single point energy calculation------------------------------------------

Symbolic Z-matrix:Charge = 0 Multiplicity = 1oo 1 oo2h 1 ho3 2 hoo3h 1 ho4 2 hoo4 3 dih4 0h 2 ho5 1 hoo5 3 dih5 0h 2 ho6 1 hoo6 3 dih6 0

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


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


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)Number Number Type X Y Z---------------------------------------------------------------------

1 8 0 0.000000 0.000000 0.0000002 8 0 0.000000 0.000000 2.8747443 1 0 0.804995 0.000000 -0.5743034 1 0 -0.649991 0.443327 -0.5986525 1 0 0.927634 -0.308043 3.0160486 1 0 -0.036221 0.012983 1.883073

---------------------------------------------------------------------

Distance matrix (angstroms):1 2 3 4 5

1 O 0.0000002 O 2.874744 0.0000003 H 0.988858 3.541743 0.0000004 H 0.988641 3.561391 1.521221 0.0000005 H 3.170480 0.987604 3.605628 4.014912 0.0000006 H 1.883466 0.992417 2.597404 2.592464 1.521745

66 H 0.000000

Stoichiometry H4O2Framework group C1[X(H4O2)]


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.


Leave Link 101 at Sat Nov 29 19:15:37 2008, MaxMem= 851968000 cpu: 0.2(Enter /prod/G09/g09a2/l202.exe)

Input orientation: ---------------------------------------------------------------------


1 8 0 0.000000 0.000000 0.0000002 8 0 0.000000 0.000000 2.8747443 1 0 0.804995 0.000000 -0.5743034 1 0 -0.649991 0.443327 -0.5986525 1 0 0.927634 -0.308043 3.0160486 1 0 -0.036221 0.012983 1.883073

---------------------------------------------------------------------

Distance matrix (angstroms):1 2 3 4 5

1 O 0.0000002 O 2.874744 0.0000003 H 0.988858 3.541743 0.0000004 H 0.988641 3.561391 1.521221 0.0000005 H 3.170480 0.987604 3.605628 4.014912 0.0000006 H 1.883466 0.992417 2.597404 2.592464 1.521745

66 H 0.000000

Stoichiometry H4O2Framework group C1[X(H4O2)]


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

Stoichiometry of the compound and information about the symmetry


---------------------------------------------------------------------


1 8 0 -1.336267 0.003540 -0.0511602 8 0 1.535692 -0.106915 0.0105233 1 0 -1.885532 0.794523 0.1735514 1 0 -1.968208 -0.724440 0.1681705 1 0 1.714869 0.864130 -0.0076136 1 0 0.543468 -0.107220 -0.009016

---------------------------------------------------------------------

Rotational constants (GHZ): 233.4754410 6.5562200 6.3922484Leave 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.Integral buffers will be 131072 words long.Raffenetti 1 integral format.Two-electron integral symmetry is turned on.

34 basis functions, 68 primitive gaussians, 34 cartesian basis functions10 alpha electrons 10 beta electrons

nuclear repulsion energy 36.2454414464 Hartrees.IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000ScaDFX= 1.000000 1.000000 1.000000 1.000000IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0NAtoms= 6 NActive= 6 NUniq= 6 SFac= 7.50D-01 NAtFMM= 80 NAOKFM=F Big=F


Standard orientation.

Important information about the number of basis functions used in the calculation.


(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= 851786934LenX= 851786934Symmetry 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-02ErrMax= 5.38D-02 EMaxC= 1.00D-01 BMatC= 2.12D-01 BMatP= 2.12D-01IDIUse=3 WtCom= 4.62D-01 WtEn= 5.38D-01Coeff-Com: 0.100D+01Coeff-En: 0.100D+01Coeff: 0.100D+01Gap= 0.487 Goal= None Shift= 0.000GapD= 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.


Cycle 11 Pass 1 IDiag 1:E= -151.985993274728 Delta-E= 0.000000000000 Rises=F Damp=FDIIS: error= 5.49D-09 at cycle 11 NSaved= 11.NSaved=11 IEnMin=11 EnMin= -151.985993274728 IErMin=11 ErrMin= 5.49D-09ErrMax= 5.49D-09 EMaxC= 1.00D-01 BMatC= 1.71D-15 BMatP= 9.35D-14IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00Coeff-Com: -0.150D-06-0.122D-07-0.321D-05 0.922D-04-0.142D-03-0.519D-03Coeff-Com: 0.552D-02-0.286D-01 0.135D+00-0.460D+00 0.135D+01Coeff: -0.150D-06-0.122D-07-0.321D-05 0.922D-04-0.142D-03-0.519D-03Coeff: 0.552D-02-0.286D-01 0.135D+00-0.460D+00 0.135D+01Gap= 0.580 Goal= None Shift= 0.000RMSDP=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 cyclesConvg = 0.4096D-08 -V/T = 2.0020S**2 = 0.0000

KE= 1.516857342155D+02 PE=-4.332421091120D+02 EE= 9.332494017544D+01Leave 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.


(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 Required = mp2augdzb.dat resultat de optimitzat 631gdp, no pla\\0,1\C,0,-0.557432,-1.211151,0.757902\C,0,-0.736195,-1.226193,-0.639236\C,0,-0.825166,-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,-2.152388,1.310137\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,-0.479654,2.180653,1.26311\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,0,1.744406,-0.018405,-0.018552\\Version=EM64L-G09RevA.02\State=1-A\HF=-56.5155462\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(C6H9N1)]\\@

In the beginning the Universe was created.This has made a lot of people very angryand been widely regarded as a bad move.

-D.AdamsJob cpu time: 0 days 0 hours 0 minutes 3.0 seconds.File lengths (MBytes): RWF= 13 Int= 0 D2E= 0 Chk= 10 Scr= 1Normal termination of Gaussian 03 at Sat Nov 29 19:15:48 2008.


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.

Gaussians fortune cookie.

Summary of main results of the calculations.


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 *.logh2o-sp.log: Normal termination of Gaussian 09 at Thu Nov 27 18:33:31 2008.

dtur@obacs:~/ws> grep 'SCF D' *.logh2o-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 Mller-Plesset energy: dtur@obacs:~/ws> grep EUMP2 h2o-sp.log.logE2 = -0.5450087887D+00 EUMP2 = -0.15266201365393D+03

The lower frequencies (freq keyword) to determinate what type of minima is found in the optimizationdtur@obacs:~/ws> grep Low h2o-z-matrix-optedmp2tz.logLow frequencies --- -0.0005 0.0014 0.0019 23.5769 55.3398 198.4177Low frequencies --- 505.7455 572.1785 589.8776

(Other examples will be seen in the Hands-on section)


New Methods and Feature (previous talk)

Efficiency Improvements

Functional Differences Between Gaussian 09 and Gaussian 03

From Gaussian03 to Gaussian09From 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


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


Different tips, suggestions or tricks to optimally run Gaussian using CESCA facilities

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 CESCAOptimizing performance at CESCA

Take into account Performance and accuracy of the method: i.e. Hybrid Functionals

Cost similar to HF for medium-large systemsAccuracy better than HFAccuracy for MP2 except for weakly-bound systemsNo as accurate as CCSD(T), CBS-QB3, etc.If B3LYP and CBS-4 agree, good check


Take into account Performance and accuracy of the method: i.e. Mller-Plesset Theory

Generally a good hierarchy of modelsMP2 cheapMP4 good for most systemsSeries tends to oscillate

Converged problems If HF a poor starting point If serious spin contamination

Not exact for two-electron system


Take into account Performance and accuracy of the method: i.e. Compound Model Chemistries for Thermochemistries

Most accurate and expensive: W1U, CBS-APNO(~ kcal error, 2 kcal worst case)

Expensive but practical: CBS-QB3(~ 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


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 structureNon-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


Things to try when optimizations fail

Number of steps exceeded Check for very flexible coordinates and/or strongly

coupled coordinatesRestart from a reasonable step and use CalcFC

Maximum step size exceeded If it happens too often, check for flexible and/or strongly

coupled coordinatesChange in point group during optimizationCheck structure and/or use NoSymm


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 QST3Relaxed scan along coordinate to loo k for highest

energy (Opt=ModRedundant)


Selecting the machine and the number of processors depending on type of calculation. Example: Couterpoise Calculation of the NH3Benzene dimer using CCSD(T)/cc-pVTZ method (5 energies, 220 basis functions)


Example: Couterpoise Calculation of the NH3Benzene dimer using CCSD(T)/cc-pVTZmethod (5 energies, 220 basis functions). Mem=3GB, maxdisk=150gb.

2789497173312162598861253493828621215424126437722239776098259104488148105531

Link 913Link 804Link 502Total N Procs.CCSD(T)Int. TransfSCFOBACS

Real Time of the calculation (min)

2,19,08,73,2162,35,25,93,082,13,73,52,641,62,01,91,7211111

Link 913Link 804Link 502Total N procsCCSD(T)Int. TransfSCFOBACS

Speed up


02

4

6

8

10

12

14

16

18

0 4 8 12 16

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

Number of processors

Ideal

Link 913Total

Link 502Link 804

Speedup


2789497173312162598861253493828621215424126437722239776098259104488148105531

Link 913Link 804Link 502Total N Procs.CCSD(T)Int. TransfSCFOBACS

Real Time of the calculation (min)

29791029904116444081275152585427375186226195371

Link 913Link 804Link 502Total N procsCCSD(T)Int. TransfSCFCADI

Example: Couterpoise Calculation of the NH3Benzene dimer using CCSD(T)/cc-pVTZ method (5 energies, 220 basis functions). Mem=3GB, maxdisk=150gb.


Type of calculation: Recommended number of processors

111CISD111Semi-empirical

12-42-4CIS11-41-4CCSD(T)111CCS,CCSDT111MP3, MP422-42-4MP244-164-16DFT44-164-16HF

Freq (Hessian)Opt. (Gradient)EnergyMethod


Directories to be usedCluster where the calculation is performedResources requestedType of calculation

CESCA people is here to help you


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

David Tur, PhDScientific Applications expert

[email protected]


curs09 dtur working with gaussian09

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