NBO/6.0...

Overview

This version of NBO program is available on Gadi as a binary distribution for RH/CentOS 6.x platform.

As such, it is still capable to run on Gadi as a stand-alone program or can be called from Gaussian, to which NBO/6.0 has the binary executable interface. Unfortunately, the NBO interface to GAMESS was provided as a static library built by the 4.x version of GNU compilers. This makes impossible to make any GAMESS-NBO6 version on Gadi running CentOS 8 due to compilers incompatibility.

Citation

When using NBO 6.0, the following citation is acceptable:

NBO 6.0. E. D. Glendening, J. K. Badenhoop, A. E. Reed, J. E. Carpenter, J. A. Bohmann, C. M. Morales, C. R. Landis, and F. Weinhold, Theoretical Chemistry Institute, University of Wisconsin, Madison (2013).

How to use

Manual

The NBO/6.0 can be downloaded from Gadi /apps/nbo/6.0/man/nbo6ab_man.pdf

Stand-alone program

Let us consider you have prepared an input file "somename.47^" to run the NBO/6.0 analysis using it as a stand-alone program. Note: the input file for NBO must bear extension ".47" but be fed to the program script without extension, see examples:

For bash:

# Load module, always specify version number.
$ module load nbo/6.0
 
$ INPUT=somename.47
$ gennbo.sh ${INPUT%.*}

For tcsh:

# Load module, always specify version number.
$ module load nbo/6.0
 
$ set INPUT = somename.47
$ gennbo $INPUT:r

Upon completion, output file should be produced with extension ".nbo", i.e., "somename.nbo" in our case above.

Using NBO/6.0 in Gaussian job

The appropriate modulefiles of both programs must be loaded before starting the job.

# Load modules, always specify version number.
$ module load gaussian[/version]
$ module load nbo/6.0

After that, a Gaussian job runs as usual. The NBO options are invoked via the G09/G16 Population keyword. Please refer to Gaussian and NBO manuals for all input syntax and details of Gaussian-NBO execution.

For more details on using Gaussian on Gadi, see our Gaussian software page.

Using NBO/6.0 in GAMESS job

On Gadi a GAMESS binary capable of NBO/6.0 calculation available via loading the raijin-image with the GAMESS version 2017-09-R2. It can be run on a single node only.

Example of a PBS script to run GAMESS-NBO6 calculation on Gadi:

#!/bin/bash
 
#PBS -P a99
#PBS -l walltime=30:00
#PBS -l ncpus=4
#PBS -l mem=4gb
#PBS -l jobfs=1gb
#PBS -l wd
#PBS -l image=raijin
 
# Load module, always specify version number.
module load gamess/2017-09-R2
 
# Must include `#PBS -l storage=scratch/ab12+gdata/yz98` if the job
# needs access to `/scratch/ab12/` and `/g/data/yz98/`
 
rungms input.inp $PBS_NCPUS nbo6 >& output.log

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