Sophie

Sophie

distrib > Fedora > 14 > x86_64 > by-pkgid > 2f8321c8e2a11ea8b160a642cfc9fd7f > files > 152

towhee-doc-7.0.1-1.fc14.noarch.rpm

<html>
<head>
 <title>MCCCS Towhee (towhee_input Database Feature)</title>
</head>

<body bgcolor="#FFFFFF" text="#000000">
<table width="675" 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 (towhee_input Database Feature) </font></b> </font>
   </div>
  </td>
 </tr>
 <A href="http://sourceforge.net"> 
  <IMG src="http://sourceforge.net/sflogo.php?group_id=87039&amp;type=5" width="210" height="62" border="0" 
  alt="SourceForge.net Logo" align="right"/>
 </A>
 <tr> 
  <td width="18" height="371" valign="top"> 
   <p>&nbsp; </p>
   <p>&nbsp;</p>
  </td>
  <td width="697" valign="top"> <b>Overview</b> 
   <ul>
    This section covers the variables that are set in the towhee_input file when using the database feature.  This option is no longer valid and was 
    removed in the 6.1.4 relase of Towhee.
    Each variable is listed along with its type (logical, character, integer, or double precision).
    towhee_input is the main input file for Towhee and is generally the only file that needs to be edited on a regular basis. It has a regimented style
    to the input. The variables are described here in the order they appear in this file. 
   </ul>

   <b>Variable explanations for towhee_input</b> 
   <ul>
    <dt><a name="inputformat"><b>inputformat (character string)</b></a> 
     <ul>
      <li>'Database' : is the only valid option when utilizing the database features.</li>
     </ul>
    </dt>

    <dt><a name="minimum_vector_length"><b>minimum vector length (double precision)</b></a> 
     <ul>
      <li>The minimum length of any of the dimensions when creating the simulation box.</li>
     </ul>
    </dt>

    <dt><a name="classical_potential"><b>classical_potential (character*30)</b></a> 
     <ul>
      The setting for this variable controls the nonbonded potential type.  Depending on the setting there are a number of other variables that also must
      be listed.  Please see the <a href="../potentype/towhee_input_classical_potential.html">classical_potential</a> web page for more information.
     </ul>
    </dt>

    <dt><a name="energyfitstyle"><b>energyfitstyle (character*15)</b></a> 
     <ul>
      <li>'absolute': fits to the absolute energies specified in towhee_database.  This means the binding energy of the solid is explicitly in the fit.</li>
      <li>'relative': fits to the energies relative to the specified ground state.  The binding energy of the ground state is not included in the fit
        and is instead computed as part of the fit.
      </li>
     </ul>
    </dt>

    <dt><a name="loptimize"><b>loptimize (logical)</b></a> 
     <ul>
      <li> .true. if you want to use least squares to fit the optimal prefactors for the linear combination of the strictly pair-potential and the
       multi-body parts of the forcefield to the data set.
      </li>
      <li> .false. if you want the answers without any fitting of parameters.</li>
     </ul>
    </dt>

    <dt><a name="lprint"><b>lprint (logical)</b></a> 
     <ul>
      <li> .true. if you want to see the details of the energy output from engtotal for each of the data points in towhee_database.  Please note that
       this is a lot of output and should definitely not be used in combination with the Dakota fitting procedure.  It is intended for use when you 
       desire more information about a single parameter set.
      </li>
      <li> .false. if you do not want extra energy information.</li>
     </ul>
    </dt>

    <dt><a name="ffnumber"><b>ffnumber (integer)</b></a> 
     <ul>
      <li> 1 or more: reads the force field information from this number of file(s) listed in the <b>ff_filename</b>.</li>
     </ul>
    </dt>

    <dt><a name="ff_filename"><b>ff_filename (formatted character*70) [one line for each force field]</b></a> 
     <ul>
      <li>A list of the filenames (one per line) that contain the force field information.</li>
     </ul>
    </dt>

    <dt><a name="datapoints"><b>datapoints (integer)</b></a> 
     <ul>
      <li>The number of datapoints in the training set to read from towhee_database.</li>
     </ul>
    </dt>

    <dt><a name="scanstyle"><b>scanstyle (character string)</b></a> 
     <ul>
      <li>'dakota' reads dakota_input and adjusts some force field parameters accordingly.</li>
      <li>'none' no adjustment to the forcefield parameters.</li>
     </ul>
    </dt>

    <dt><font color="red">The following are only required if</font> <b>scanstyle</b> is 'dakota' <font color="red">and</font> 
     <b>classical_potential</b> is 'Embedded Atom Method'
    </dt>
    <dt><a name="nscale"><b>nscale (integer)</b></a> 
     <ul>
      <li>The number of interactions, involving pairs of atomtypes, that you wish to rescale.</li>
     </ul>
    </dt>
    <dt><a name="interaction"><b>interaction (character*5), atomone (character*2), atomtwo (character(2)</b></a> 
     <ul>
      <li>List on <b>nscale</b> lines where each line contains the name of the interaction (embed or pair),atom name #1, and atom name #2</li>
     </ul>
    </dt>
   </ul>
   <a href="../index.html">Return to the main towhee web page</a> 
   <p>&nbsp;</p>
  </td>
 </tr>
</table>
<hr width="715" align="left">
<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>
<i>Last updated:</i> 
<!-- #BeginDate format:Am1 -->December 7, 2008<!-- #EndDate -->
</font> <br>
</body>
</html>