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NWChem

General
NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources. NWChem has been developed by the Molecular Sciences Software group of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). See the official homepage for details.

The current release version is NWChem 4.5. It is presently available at Monolith together with the earlier version NWChem-4.1. To access 4.1 on Monolith you need to change the version number in the run script example below.

Policy
The EMSL Software Agreement is signed by NSC, and should be respected by all users accessing NWChem via NSC. The agreement stipulates that the use of NWChem will be acknowledged in any publications which use results obtained with NWChem. The acknowledgment should be of the form:

NWChem Version 4.5, as developed and distributed by Pacific Northwest National Laboratory, P. O. Box 999, Richland, Washington 99352 USA, and funded by the U. S. Department of Energy, was used to obtain some of these results.

Program citation

Please use the following citation when publishing results obtained with NWChem:

High Performance Computational Chemistry Group, NWChem, A Computational Chemistry Package for Parallel Computers, Version 4.5 (2003), Pacific Northwest National Laboratory, Richland, Washington 99352, USA.

If you use the DIRDYVTST portion of NWChem, please also use the additional citation:

DIRDYVTST, Yao-Yuan Chuang and Donald G. Truhlar, Department of Chemistry and Super Computer Institute, University of Minnesota; Ricky A. Kendall,Scalable Computing Laboratory, Ames Laboratory and Iowa State University; Bruce C. Garrett and Theresa L. Windus, Environmental Molecular Sciences Laboratory, Pacific Northwest Laboratory.

Manual
A manual is available on the official homepage .

Essentials
To run NWChem one has to provide it with one input file called xxxx.nw, where xxxx is an arbitrary string. The file contains molecular and wave function parameters as well as job a type specification. The program output is sent to standard output by default, but it may be re-directed. When executing NWChem one types:

nwchem xxxx > xxxx.out

A sample of input and output files is found here .

NWChem on Monolith
To run NWChem on Monolith with use of 4 processors (2 nodes with 2 processors each) for 1 hour, submit the shell script below to the queue (the submit command is: qsub scriptname). The input file xxxx.nw is assumed to be located in the submit directory. Temporary files created by the program are placed on the node local disk named /disk/local in order not to slow down the network file system (NFS), and the temporary files are removed after the calculation is completed.

#!/bin/bash
#PBS -l walltime=1:00:00
#PBS -l nodes=2:ppn=2

NProc=`wc -l < $PBS_NODEFILE`
export SCRATCH_DIR=/disk/local
NWCHEM=/usr/local/chem/nwchem/nwchem-4.5/bin/LINUX/nwchem

nwinp=xxxx

cd $PBS_O_WORKDIR
mpprun -Norder=block -np $NProc $NWCHEM $nwinp > $nwinp.out

#
# End of script
#





Page last modified: 2004-06-01 20:50
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