<html>
<head>
<title>MCCCS Towhee</title>
</head>
<body bgcolor="#FFFFFF" text="#000000">
<table width="800" border="0" cellspacing="0" cellpadding="0" height="590">
<tr>
<td colspan="2" height="29">
<div align="center"><font size="5"><b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS Towhee</font></b></font></div>
</td>
</tr>
<tr>
<A href="http://sourceforge.net">
<IMG src="http://sourceforge.net/sflogo.php?group_id=87039&type=5" width="210" height="62" border="0" alt="SourceForge.net Logo" align="right"/>
</A>
<tr>
<td colspan="2" height="108" valign="top">
<div align="center"><img src="canyon_towhee.jpg" align=center height=286 width="353">
<p></p>
<font face="Arial, Helvetica, sans-serif" size="2">
<dt><b>Photograph:</b> Canyon Towhee, July 1998, Albuquerque NM</dt>
<dt><b>Project Administrator:</b> <a href="http://www.photobirder.com/Simulation/cv.html">Marcus G. Martin</a></dt>
<dt>
<b>E-mail:</b> <a href="mailto:marcus_martin@users.sourceforge.net">marcus_martin@users.sourceforge.net</a>
</dt>
<dt><a href="http://www.usefulbias.com">Useful Bias Incorporated</a></dt>
<dt>88 Martinez Road</dt>
<dt>Edgewood, NM 87015</dt>
</font>
</div>
</td>
</tr>
<tr>
<td width="18" height="371" valign="top">
<p> </p>
<p> </p>
</td>
<td width="697" valign="top"> <b><font face="Arial, Helvetica, sans-serif" size="3" color="964CBD">Introduction to MCCCS Towhee</font></b>
<p></p>
<b>Towhee Project Executive Summary</b>
<ul>
Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields
and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been
extended to several ensembles, many different force fields, and solid (or at least porous) phases.
<p></p>
It is the hope of the developers that Towhee serves as a useful tool for the molecular simulation community and allows science to move forward more
quickly by eliminating the need for individual research groups to rewrite routines that already exist and instead allows them to focus on algorithm
advancement, force field development, and application to interesting systems.
</ul>
<p></p>
<b>A Brief History of MCCCS Towhee</b>
<ul>
The Monte Carlo for Complex Chemical Systems (MCCCS) program was first developed in 1994 in
<a href="http://www.chem.umn.edu/groups/siepmann">J. Ilja Siepmann's research group</a> at the University of Minnesota starting with software dating
back to the dawn of the configurational-bias Monte Carlo method. From 1994 to 1999 the code took shape as J. Ilja Siepmann, Marcus G. Martin,
Bin Chen, Collin D. Wick, Jeffrey J. Potoff, and John M. Stubbs all implemented (and developed) algorithms and force fields for predicting phase
coexistence using Monte Carlo. This research on MCCCS was supported by the National Science Foundation (Siepmann), and the Department of Energy (DoE)
<a href="http://www.krellinst.org/csgf/">Computational Science Graduate Fellowship</a> (Martin and Wick).
In 1999 the MCCCS program was placed under a <a href="code/gpl.html">GNU general public license</a>, but was not widely distributed.
<p></p>
In 2000 the DoE Office of Industrial Technologies, later renamed the <a href="http://www.eere.energy.gov/industry/">Industrial Technologies Program</a>,
funded Marcus G. Martin and some industrial collaborators to make MCCCS accessible to the broad molecular simulation community by creating a web manual,
improving the ease of use, and distributing the code via the web. This new version was called MCCCS Towhee, and is maintained by
<a href="mailto:marcus_martin@users.sourceforge.net">marcus_martin@users.sourceforge.net</a>.
<p></p>
In 2003 Towhee began migrating to the SourceForge site and it finished moving there completely in September of 2005. The user base has continued
to swell, and new developers are leaving their mark upon the code. Instructions for downloading, unpacking, and compiling the current Towhee
release are found on the <a href="code/download.html">Towhee download web page</a>.
</ul>
<p> </p>
<b><font face="Arial, Helvetica, sans-serif" size="3" color="964CBD">Site Map for MCCCS Towhee Web Manual</font></b>
<p></p>
<a href="citation_manual.html"><b>Citation Manual</b></a>
<ul>
The methods and force fields implemented into Towhee represent the ideas and efforts of a great many people. The Citation Manual explains
how users of Towhee can use the information provided in the towhee_citation output file as a convenient summary of the important works
to consider referencing based upon the algorithms and force fields utilized in their own simulations.
</ul>
<p></p>
<a href="towhee_capabilities.html"><b>Towhee Capabilities</b></a>
<ul>
Contains a list of all the Ensembles and Monte Carlo moves implemented into Towhee and summarizes all of the force fields included with the
distribution.
</ul>
<p></p>
<a href="usersmanual.html"><b>User Manual</b></a>
<ul>
Contains an overview of all of the files either input or output from the Towhee code. If you aren't sure where to start, look here
</ul>
<p></p>
<a href="examples/example_manual.html"><b>Example Manual</b></a>
<ul>
This section describes the examples included with the current download version of Towhee and gives some tips for getting started with these examples.
</ul>
<p></p>
<a href="utils/utility_summary.html"><b>Utility Summary</b></a>
<ul>
This section describes the utility programs that are included with the Towhee distribution. These utilities are designed to either make setting
up simulations easier, or to provide some post processing capability.
</ul>
<p></p>
<a href="code/download.html"><b>Download Towhee</b></a>
<ul>
This section describes the steps required to download a version of the MCCCS Towhee program.
</ul>
<p></p>
<a href="code/code_manual.html"><b>Code Manual</b></a>
<ul>
This section explains the general structure of the Towhee program and also includes instructions on compiling Towhee and submitting bug reports.
</ul>
<p></p>
<a href="developersmanual.html"><b>Developer Manual</b></a>
<ul>
The section contains information for Towhee developers, and for those who wish to become Towhee developers.
</ul>
<p></p>
<a href="algorithm/algorithm.html"><b>Algorithm Information</b></a>
<ul>
This section contains essays discussing various topics related to the Monte Carlo algorithms implemented into Towhee. Topics range from a quick
overview of the Monte Carlo method to detailed discussion about configurational-bias and the many faces of chemical potential.
</ul>
<p></p>
<a href="references.html"><b>References</b></a>
<ul>
This section contains references to papers and books that are either the source materials for the methods or force fields in Towhee, or are
helpful reviews of those subjects.
</ul>
<p></p>
<a href="towhee_pubs.html"><b>Towhee Publications</b></a>
<ul>
A list of user publications that have utilized the Towhee code.
</ul>
<p></p>
<a href="towhee_presentations.html"><b>Towhee Presentations</b></a>
<ul>
A list of user presentations that utilized the Towhee code.
</ul>
<p></p>
<a href="http://sourceforge.net/projects/towhee/"><b>MCCCS Towhee on SourceForge</b></a>
<ul>
The SourceForge home for Towhee. This is the place to come if you wish to submit bugs, request new features, or discuss general topics related
to Towhee on the <a href="http://sourceforge.net/forum/?group_id=87039">forums</a>. It also contains the CVS repository for Towhee and the
<a href="http://sourceforge.net/tracker/?atid=581786&group_id=87039&func=browse">Towhee Bug Tracker</a> utility.
</ul>
<p></p>
<a href="software.html"><b>Related Software</b></a>
<ul>
A list of software packages that are useful in combination with Towhee and also a list of other publicly available Monte Carlo molecular simulation
packages.
</ul>
<p> </p>
</td>
</tr>
</tr>
</table>
<p></p>
<font face="Arial, Helvetica, sans-serif" size="1">
<hr width="715" align="left"></hr>
<i><font size="2">Send comments to:</font></i>
<font size="2"><a href="mailto:marcus_martin@users.sourceforge.net">Marcus G. Martin</a>
<br></br>
<i>Last updated:</i> <!-- #BeginDate format:Am1 -->August 09, 2011<!-- #EndDate -->
</font>
<br></br>
</body>
</html>
distrib
>
Fedora
>
14
>
x86_64
>
media
>
updates
>
by-pkgid
>
2f8321c8e2a11ea8b160a642cfc9fd7f
>
files
>
232
