Software/Gaussian

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Contents

Version

Currently Phoenix is running Gaussian09.C.01.

Reference:

Gaussian 09, Revision C.01, 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, T. Keith, 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, 2010.

Basic Input File

%mem=1000MB
%NProcShared=2
#HF/STO-3G SP

Comment line

0,1
O   -0.0533920156     0.0000000000    -0.0413405155
H   -0.0502486311    -0.0000000000     0.9200071213
H    0.8781214711    -0.0000000000    -0.2789994805

Here we see the first line is the requested memory for the calculation. The second line is the number of processors used for the calculation. In general, Gaussian should use a maximum of 8 CPUS for a calculation. Based on the theoretical approach being used, some calculations cannot use multiple processors. Please check the Gaussian manual for more details.

    • If you are using WebMO to build your input files, it is important to specify the number of processors in the job setup screen. Do not edit this in the generate input screen. Due to how WebMO creates the pbs files, it will not submit the correct number of cores.

Next is the command line known as the route section. Here you input theoretical approach and any other key words. In this example, we are using Hartree-Fock method with the STO-3G basis set. We are performing a single energy point calculation.

Next is a blank line followed by a comment line. Here you put anything.

Following the comment line is another blank line. After the blank line is the charge and multiplicity. In this case, we have a neutral molecule with the multiplicity of 1.

Next is the geometry specification section. For examples on different types of inputs please see Molecule specification page on the Gaussian website.

Finally all Gaussian inputs must end with a blank line.


Types of Calculations

Energy Point

Epsmall.jpg

Geometry Optimization

Optbig.jpg

This keyword requests that a geometry optimization be performed. The geometry will be adjusted until a stationary point on the potential surface is found. Analytic gradients will be used if available. More information can be found on the gaussian website.

Frequency

Freqsmall.jpg

This calculation type keyword computes force constants and the resulting vibrational frequencies. Intensities are also computed. Here is a link to more info on the gaussian website for freq keyword.

Raman and IR info is also calculated with the FREQ keyword. If Raman results are not necessary the keyword FREQ(NORAMAN) should be used for bigger calculations to speed up the computation.

  • If you are having trouble finding a stationary point on a PES, try running a frequency calculation. You must specify a checkpoint file. Then, run a optimization on the same structure as in the frequency and use the force constants stored in the checkpoint to guide the optimization. In order for the optimization to use the force constants you must specify an option for the OPT key word:
OPT(READFC)

Bond Length Scan

Bondscan.jpg

Locating Transition States

There are many different ways to locate transition states with gaussian software. First a simple TS optimization is shown below.

TSopt2.jpg

Another way of finding a transition state is performing a QST2 calculation. Here we are going to include 2 geometries in the input file. The QST2 calculation will then attempt to find a transition state between the two inputed geometries. An example of a QST2 calculation is as followed.


Qst2.jpg

If you have a guess to the transition state structure, you may try the QST3 option. In addition to the QST2 calculation guess transition state structure is also included in the input (shown below).

Qst3.jpg

IRC

An IRC calculation allows one to map out a reaction pathway by integrating the intrinsic reaction coordinate. In the input the molecular geometry is of the transition state molecule. An IRC can go in the foward direction or in the reverse direction. By default BOTH reaction pathways are followed. An IRC calculation requires initial force constants. These can be calculated by computing a frequency on the transition state and saving the checkpoint file. Finally the same checkpoint is then used for the IRC calcation with the key word RCFC. If a frequency computation was not preformed, one can simply calculate the force constants before the IRC by using the keyword CALFC. More info about IRC calculations can be found here.

IRC.jpg


NMR

This properties keyword predicts NMR shielding tensors and magnetic susceptibilities using the Hartree-Fock method, all DFT methods and the MP2 method as stated on the NMR page on the Gaussian website.

Nmr.jpg


The Gaussian website also suggests that an NMR calculation be preformed on a high-quality structure. The NMR keyword can only be specified with HF, DFT and MP2 methods.


Natural Bond Orbital (NBO) Version 6.0

Request NBO6 analysis using the Gaussian keywords of the
following forms:

    pop=nbo6             -- default NBO6 analysis, no $NBO input
    pop=nbo6read         -- NBO6 analysis with $NBO input
    pop=nbo6del          -- NBO6 analysis with deletions
    pop=(nbo6,savenbos)  -- default NBO6 analysis, save NBOs on
       the checkpoint file
    pop=(nbo6,savenlmos) -- default NBO6 analysis, save NLMOs on
       the checkpoint file
    pop=(nbo6,savemixed) -- default NBO6 analysis, save sorted
       NLMOs on the checkpoint file

Note that these keywords are analogous to the pop=nbo, pop=nboread,
etc. keywords. Using the plain nbo keywords will invoke the old NBO 3.1 program.


Specialized Basis Sets

  • GEN keyword: Here we will show different ways to use specialized basis sets. First, if the basis set is not a defined basis set for gaussian on may use the key word GEN, as shown below.

GEN.jpg

Here we took the DZP+ basis set from the EMSL Basis Set Exchange website. With the EMSL website, you can specify your desired basis set, for each atom and then the format of the basis set. In this case Gaussian94 is the format. (The basis set input has not changed so the Gaussian94 version will work.) For more info visit the Gaussian page on the Gen keyword.


  • Extrabasis keyword: If you just want to include additional basis functions such as diffuse functions to a defined basis set one can do this by using the extrabasis keyword, shown below.

Extra.jpg


Submission Script for phoenix

qg09 -q [Queue name] -emailwhendone jobname

(the -q and -emailwhendone arguments are optional)

Tips

The purpose of this section is to put information about frequently asked questions and solutions to those problems. Please check back often. This page will be updated as issues are addressed.


Having problems with gaussview opening checkpoint files? Try these commands below:

formchk file.chk file.fchk

sed 's/independent/independant/' file.fchk > file-fixed.fchk

Then just open "file-fixed.fchk" with gaussview.

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