The Art of Molecular Dynamics Simulation
                ========================================


Introduction
============

This software is intended to accompany the book `The Art of Molecular Dynamics
Simulation', 2nd edition, by D. C. Rapaport, published by Cambridge University
Press (2004). The material is being supplied in computer-readable form to
enable readers to follow the case studies described in the book.


Copyright and permission to use
===============================

This software is copyrighted material reproduced from the book and its use
is subject to the GNU General Public License (Version 3).

Disclaimer
==========

The reader planning to use the software should note that, from the legal point
of view, there is no warranty, expressed or implied, that the programs are free
of error or will prove suitable for a particular application; by using the
software the reader accepts full responsibility for the results produced, and
the author and publisher disclaim all liability from any consequences arising
from use of the software.


Mode of use together with book
==============================

Since the programs are meant to accompany the book, where full descriptions of
the computational algorithms, data, and other details are to be found, no
documentation is included in the program listings.


Getting started
===============

All the software is supplied in a single compressed Unix archive file
`artmdsim2.tar.gz'. Readers should unpack this archive with the tar utility to
produce a directory `artmdsim2' containing all the material.

Contents of subdirectories:

 `src':  program files referenced in the book
 `data': sample data files for the case studies

The (52) MD program files are named `pr_xx_y.c', as in the book, where `xx' is
the chapter number; the other (11) program files also have the prefix `pr_'.
Each is a complete program, apart from a few (7) common include files prefixed
by `in_'. 

The results produced by each of these programs should be similar to those shown
in the book. Numerically identical results may not always be obtained due to
different hardware and compilers, but any differences should not be
statistically significant.


Compilation
===========

Run the `compile.sh' script to check that all programs compile successfully;
compiled programs are deleted by this script. Two of the programs will not
compile because they require either an MPI package or the pthreads library; if
available edit the script accordingly. For production work, compilation should
use the highest level of optimization that proves effective. The `crun.sh'
script can be used to carry out test runs.

Compilation has been tested on the following platform(s) and operating system(s)
(possible minor system incompatibilities may be encountered with other
environments):
- Redhat Linux version 9 for 32-bit Intel processors
- Fedora version 14 for 64-bit Intel processors

Please notify the author of errors or any other problems. Suggestions for
enhancing the collection, as well as reports on how this material is used, will
be greatly appreciated. The author's e-mail address is:
rapaport@mail.biu.ac.il.


Errors
======

As errors come to light (as they surely will), the program files will be
updated and the changes noted.


Software version
================

This is the original release (version 2.0) of the software.


(March 31, 2004)

(Revised May 1, 2011)