NWChem/doc/user/intro.tex

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\label{sec:intro}

NWChem is a computational chemistry package designed to run on
high-performance parallel supercomputers.
Code capabilities include the calculation of molecular electronic
energies and analytic gradients using Hartree-Fock self-consistent field (SCF) theory, Gaussian
density function theory (DFT), and second-order perturbation theory.
For all methods, geometry optimization is available to determine energy minima and transition states.
Classical molecular dynamics capabilities
provide for the simulation of macromolecules and solutions, including
the computation of free energies using a variety of force fields.

NWChem is scalable, both in its ability to treat large problems
efficiently, and in its utilization of available parallel computing
resources.  The code uses the parallel programming tools TCGMSG and
the Global Array (GA) library developed at PNNL for the High Performance
Computing and Communication (HPCC) grand-challenge
software program and the Environmental Molecular Sciences Laboratory
(EMSL) Project.  NWChem has been optimized to perform calculations on
large molecules using large parallel computers, and it is unique in
this regard.  

This document is intended as an aid to chemists using the code for
their own applications.  Users are not expected to have a detailed
understanding of the code internals, but some familiarity with the
overall structure of the code, how it handles information, and the
nature of the algorithms it contains will generally be helpful.  The
following sections describe the structure of the input file, and give
a brief overview of the code architecture.  All input directives
recognized by the code are described in detail, with options,
defaults, and recommended usages, where applicable.  The appendices
present additional information on the molecular geometry and basis
function libraries included in the code.

\section{Citation}

The EMSL Software 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:
\begin{quote}

  NWChem Version \nwchemversion, 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.
\end{quote}

The words ``A modified version of'' should be added at the beginning,
if appropriate.  {\em Note: Your EMSL Software Agreement contains the
complete specification of the required acknowledgment.}

Please use the following citation when publishing results obtained
with NWChem:
\begin{quote}
Straatsma, T.P.; Apr\`a, E.; Windus, T.L.; Bylaska, E.J.; de Jong, W.;
Hirata, S.; Valiev, M.; Hackler, M.; Pollack, L.; Harrison, R.;
Dupuis, M.; Smith, D.M.A; Nieplocha, J.; Tipparaju V.; Krishnan, M.;
Auer, A.A.; Brown, E.; Cisneros, G.; Fann, G.; Fr\"uchtl, H.; Garza, J.;
Hirao, K.; Kendall, R.; Nichols, J.; Tsemekhman, K.; Wolinski, K.;
Anchell, J.; Bernholdt, D.; Borowski, P.; Clark, T.; Clerc, D.;
Dachsel, H.; Deegan, M.; Dyall, K.; Elwood, D.; Glendening, E.;
Gutowski, M.; Hess, A.; Jaffe, J.; Johnson, B.; Ju, J.; Kobayashi, R.;
Kutteh, R.; Lin, Z.; Littlefield, R.; Long, X.; Meng, B.; Nakajima,
T.; Niu, S.; Rosing, M.; Sandrone, G.; Stave, M.; Taylor, H.; Thomas,
G.; van Lenthe, J.; Wong, A.; Zhang, Z.; {\em NWChem, A Computational
Chemistry Package for Parallel Computers, Version 4.6} (2004),
Pacific Northwest National Laboratory, Richland, Washington
99352-0999, USA. \\
{\em High Performance Computational Chemistry: an Overview of NWChem a
Distributed Parallel Application}, Kendall, R.A.; Apr\`a, E.;
Bernholdt, D.E.; Bylaska, E.J.; Dupuis, M.; Fann, G.I.; Harrison,
R.J.;  Ju, J.; Nichols, J.A.; Nieplocha, J.; Straatsma, T.P.; Windus,
T.L.; Wong, A.T. Computer Phys. Comm., 2000, {\bf 128}, 260--283 .
\end{quote}

If you use the DIRDYVTST portion of NWChem, please also use the additional
citation:
\begin{quote}
  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.
\end{quote}

\section{User Feedback}

This software comes without warranty or guarantee of support,
but we do try to meet the needs of our user community.  Please send bug
reports, requests for enhancement, or other comments to

\begin{verbatim}
 nwchem-users@emsl.pnl.gov
\end{verbatim}

When reporting problems, please provide as much information as possible, 
including:

\begin{itemize}
\item detailed description of problem
\item site name %(e.g., EMSL, NERSC, \ldots)
\item platform you are running on, including
\begin{itemize}
\item vendor name
\item computer model
\item operating system
\item compiler
\end{itemize}
\item input file
\item output file
%\item contact name and telephone number
\end{itemize}

Users can also subscribe to the {\tt nwchem-users@emsl.pnl.gov}
electronic mailing list itself.  
This is intended as a general forum through which code
users can contact one another and the developers, to share experience
with the code and discuss problems.  Announcements of new releases and
bug fixes will also be made to this list. 

To subscribe to the user list, send a message to 
\begin{verbatim}
  majordomo@emsl.pnl.gov
\end{verbatim}
The body of the message must contain the line 
\begin{verbatim}
  subscribe nwchem-users
\end{verbatim}

The automated list manager is capable of recognizing a number of
commands, including ; ``subscribe'', ``unsubscribe'', ``get'', ``index'',
``which'', ``who'', ``info'' and ``lists''.  The command ``end'' halts
processing of commands.  It will provide some help if the message
includes the line {\tt help} in the body.  

%Messages can be posted to
%the list by sending mail to {\tt nwchem-users@emsl.pnl.gov}.  Users
%are encouraged to report problems to the support address rather than the mailing list,
%since the support address (listed at the beginning of this section) interfaces to an automated
%bug tracking mechanism.