Difference between revisions of "Gaussian"

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__NOTOC__
 
 
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[[Category:Software]]
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[[Category:Software]][[Category:Chemistry]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|gaussian}}
 
|{{#vardefine:app|gaussian}}
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
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|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
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|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 
|{{#vardefine:pbs|1}}            <!--PBS SCRIPTS-->
 
|{{#vardefine:pbs|1}}            <!--PBS SCRIPTS-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
 
|{{#vardefine:testing|}}      <!--PROFILING-->
 
|{{#vardefine:testing|}}      <!--PROFILING-->
 
|{{#vardefine:faq|}}            <!--FAQ-->
 
|{{#vardefine:faq|}}            <!--FAQ-->
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|{{#vardefine:citation|}}      <!--CITATION-->
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|{{#vardefine:citation|1}}      <!--CITATION-->
 
|{{#vardefine:installation|}} <!--INSTALLATION-->
 
|{{#vardefine:installation|}} <!--INSTALLATION-->
 
|{{#vardefine:licensing|1}} <!--LICENSING-->
 
|{{#vardefine:licensing|1}} <!--LICENSING-->
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{{#if: {{#var: url}}|
 
{{#if: {{#var: url}}|
 
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
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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.
+
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. This article introduces several of its new and enhanced features.
+
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.
  
 
<!--LICENSING-->
 
<!--LICENSING-->
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==Gaussian License==
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===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 2238. 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.
+
Please note that Gaussian is restricted software. Users who intend to use it must sign the '''Gaussian Confidentiality Agreement'''. Please submit a [https://support.rc.ufl.edu help ticket] to request the license form.  
 
See [[Gaussian License]].
 
See [[Gaussian License]].
  
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[[Modules|modules documentation]]
 
[[Modules|modules documentation]]
 
===Serial===
 
===Serial===
 +
* {{#var:app}}
 +
 +
===Parallel (Shared memory with OpenMP)===
 
* {{#var:app}}
 
* {{#var:app}}
  
 
<!--
 
<!--
−
===Parallel (OpenMP)===
 
−
* intel
 
−
* {{#var:app}}
 
 
===Parallel (MPI)===
 
===Parallel (MPI)===
 
* intel
 
* intel
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-->
 
-->
 
==System Variables==
 
==System Variables==
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* HPC_{{#uppercase:{{#var:app}}}}_DIR
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* HPC_{{uc:{{#var:app}}}}_DIR
 
* GV_DIR
 
* GV_DIR
 
* g09root
 
* g09root
−
 
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* GAUSS_BSDDIR
 +
* GAUSS_EXEDIR
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* _DSM_BARRIER
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
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<!--Run-->
 
<!--Run-->
 
{{#if: {{#var: exe}}|==Additional Information==
 
{{#if: {{#var: exe}}|==Additional Information==
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WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+
 
 +
See [https://gaussian.com/gpu/ https://gaussian.com/gpu/] for information on using GPU(s) with Gaussian and [[GPU Access]] for information on how to set up a SLURM session with GPU(s).
 +
 
 +
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.
 +
<pre>
 +
#SBATCH --nodes=1
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#SBATCH --ntasks=1
 +
#SBATCH --cpus-per-task=N
 +
</pre>
 
|}}
 
|}}
 
<!--PBS scripts-->
 
<!--PBS scripts-->
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{{#if: {{#var: pbs}}|==PBS Script Examples==
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{{#if: {{#var: pbs}}|==Example Job Scripts==
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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 09 across multiple machines on the HPC Center cluster.
+
<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;">
 +
''Expand this section to view an example Gaussian script.''
 +
<div class="mw-collapsible-content" style="padding: 5px;">
 +
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.  
  
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This forces you to a resource request of the form
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'''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).'''
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<pre>
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==Automatic Processor Detection==
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#PBS -l nodes=1:ppn=<N> 
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<source lang=bash>
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</pre>
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#!/bin/bash
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where N is the number of processors and is constrained as follows:
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#SBATCH --job-name=gaussianjob
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<pre>
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#SBATCH --output=gaussian.out
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PhaseII:  N<=4
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#SBATCH --error=gaussian.err
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PhaseIII: N<=8
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#SBATCH --mail-type=ALL
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PhaseIV:  N<=12
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#SBATCH --mail-user=YOUR-EMAIL-ADDRESS
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PhaseV:  N<=16
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#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
  
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PhaseII through PhaseV refer to the set of machines we purchased during certain time period.  
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input=YOUR_g09_input.com
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The larger N you request, the more restricted your job will be in terms of resource availability.
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output=YOUR_OUTPUT.log
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</pre>
 
  
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
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g09 < $input > $output 
 +
</source></div></div>
 
|}}
 
|}}
 
<!--Policy-->
 
<!--Policy-->
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WRITE_PERFORMANCE_TESTING_RESULTS_HERE
 
WRITE_PERFORMANCE_TESTING_RESULTS_HERE
 
|}}
 
|}}
 +
==Using Gaussview GUI==
 +
View instructions for GUI at [[Gaussian GUI]]
 
<!--Faq-->
 
<!--Faq-->
 
{{#if: {{#var: faq}}|==FAQ==
 
{{#if: {{#var: faq}}|==FAQ==
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{{#if: {{#var: citation}}|==Citation==
 
{{#if: {{#var: citation}}|==Citation==
 
If you publish research that uses {{#var:app}} you have to cite it as follows:
 
If you publish research that uses {{#var:app}} you have to cite it as follows:
−
WRITE_CITATION_HERE
+
 
 +
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.
 
|}}
 
|}}
 
<!--Installation-->
 
<!--Installation-->

Latest revision as of 14:39, 8 March 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

modules documentation

Serial

  • gaussian

Parallel (Shared memory with OpenMP)

  • gaussian

System Variables

  • HPC_GAUSSIAN_DIR
  • GV_DIR
  • g09root
  • GAUSS_BSDDIR
  • GAUSS_EXEDIR
  • _DSM_BARRIER

Additional Information

See https://gaussian.com/gpu/ for information on using GPU(s) with Gaussian and GPU Access for information on how to set up a SLURM session with GPU(s).

There are two mechanisms by which you can submit Gaussian Jobs.

  1. Command-line batch Job Submission: See the next section.
  2. 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.


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