Difference between revisions of "Gaussian"
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# Command-line batch Job Submission: See the next section. | # 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. | # 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. | ||
| + | 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 following form 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. | ||
| + | <pre> | ||
| + | #SBATCH --nodes=1 | ||
| + | #SBATCH --ntasks=1 | ||
| + | #SBATCH --cpus-per-task=N | ||
| + | </pre> | ||
|}} | |}} | ||
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g09 < $input > $output | g09 < $input > $output | ||
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Revision as of 14:55, 19 February 2023
Description
gaussian website
Gaussian 16 is the latest in the Gaussian series of electronic structure programs. Gaussian 16 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. Please submit a help ticket to request the license form. See Gaussian License.
Required Modules
Serial
- gaussian
- gaussian
System Variables
- HPC_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.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.
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 following form 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.
#SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=N
Example Job Scripts
Expand this section to view an example Gaussian script.
The following is a sample job submission script for Gaussian. It loads "gaussian" module, which detects the CPU type of the machine on which your job runs and chooses the appropriate version of Gaussian for best performance. If OMP_NUM_THREADS is set, Gaussian will use it for the number of processors unless %nproc or %nprocshared is set in your Gaussian input file.
The number of threads specified to Gaussian via either method above must be consistent with the number of processors in your resource request i.e (--cpus-per-task=N).
Automatic Processor Detection
#!/bin/bash
#SBATCH --job-name=gaussianjob
#SBATCH --output=gaussian.out
#SBATCH --error=gaussian.err
#SBATCH --mail-type=ALL
#SBATCH --mail-user=YOUR-EMAIL-ADDRESS
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4 # number of CPU core to use
#SBATCH --mem-per-cpu=4000
#SBATCH --account=YOUR-GRUOP-NAME
#SBATCH --qos=YOUR-GROUP-NAME
module load gaussian
which g09
input=YOUR_g09_input.com
output=YOUR_OUTPUT.log
g09 < $input > $output
Using Gaussview GUI
View instructions for GUI at Gaussian GUI
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.