Difference between revisions of "Gaussian"
Moskalenko (talk | contribs) |
Moskalenko (talk | contribs) |
||
| Line 63: | Line 63: | ||
Please see the [[{{PAGENAME}}_galaxy-input]] page for a sample input file to run Gaussian using ''Galaxy''. | Please see the [[{{PAGENAME}}_galaxy-input]] page for a sample input file to run Gaussian using ''Galaxy''. | ||
| + | |||
| + | ==Running GaussView with Xpra== | ||
| + | When starting gv via a [[GUI Programs|SLURM GUI Session]] the following steps must be taken: | ||
| + | |||
| + | * Set gv to use MESAGL instead of OpenGL via '<code>export USE_MESAGL=1</code>'. See [http://csc.cnsi.ucsb.edu/docs/gaussview 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 | ||
|}} | |}} | ||
<!--PBS scripts--> | <!--PBS scripts--> | ||
| Line 87: | Line 94: | ||
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. | 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. | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
|}} | |}} | ||
<!--Policy--> | <!--Policy--> | ||
Revision as of 15:16, 20 January 2017
Description
gaussian website
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.
Gaussian License
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, 2240, 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.
Required Modules
Serial
- gaussian
- gaussian
System Variables
- HPC_{{#uppercase:gaussian}}_DIR
- GV_DIR
- g09root
- GAUSS_BSDDIR
- GAUSS_EXEDIR
- _DSM_BARRIER
Additional Information
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.hpc.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.
Running GaussView with Xpra
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
Gaussview
There is a separate Gaussview page for use of the Gaussview viewing software.
Citation
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.