Difference between revisions of "Gaussian"
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Please note that Gaussian is restricted software. Users who intend to use it must sign the '''Gaussian Confidentiality Agreement'''. This form is available in NPB 2335,
Please note that Gaussian is restricted software. Users who intend to use it must sign the '''Gaussian Confidentiality Agreement'''. This form is available in NPB 2335, , or 2148. You may come by during office hours and sign the agreement. Once the form is signed, you will be added to the "gaussian" user group and will have access to the software.
See [[Gaussian License]].
See [[Gaussian License]].
Revision as of 15:30, 17 December 2018
Gaussian 09 is the latest in the Gaussian series of electronic structure programs. Gaussian 09 is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest. Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures.
Please note that Gaussian is restricted software. Users who intend to use it must sign the Gaussian Confidentiality Agreement. This form is available in NPB 2335, 2238, or 2148. You may come by during office hours and sign the agreement. Once the form is signed, you will be added to the "gaussian" user group and will have access to the software. See Gaussian License.
There are two mechanisms by which you can submit Gaussian Jobs.
- Command-line batch Job Submission: See the next section.
- Galaxy Framework: Galaxy can be accessed at: http://galaxy.rc.ufl.edu. Gaussian is listed in the "Tools" pane under "Chemistry". Please refer to Galaxy for more information on how to use this interface. For specific instructions concerning how to submit a Gaussian job using Galaxy, there is also a step-by-step procedure wiki entry: Gaussian Galaxy
Please see the Gaussian_galaxy-input page for a sample input file to run Gaussian using Galaxy.
Example Job Scripts
See the Gaussian Job Scripts page for sample Gaussian job submission scripts.
Please note that our version of Gaussian only supports shared-memory parallelism. This means that if you want to use more than one processor for a Gaussian job, you are limited to the number of processors in a single machine. You cannot run Gaussian across multiple machines on the Research Computing cluster.
This requires a resource request of the form
#SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=N
where N is constrained by the number of "cores" (i.e. processors) in a single machine. Most of the hipergator nodes have 32 cores per node.
Using Gaussview GUI
When starting gv via a SLURM GUI Session the following steps must be taken:
- Set gv to use MESAGL instead of OpenGL via '
export USE_MESAGL=1'. See http://csc.cnsi.ucsb.edu/docs/gaussview for reference.
- Start the session with both the module name and the executable name. E.g. for the default resource request:
- launch_gui_session --module gaussian -e gv
If you publish research that uses gaussian you have to cite it as follows:
Gaussian 09, Revision A.1, 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, Ö. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2009.