Unverified Commit 223bfac2 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

remove ATC html files that are no longer needed

parent a6adf956

doc/src/USER/atc/man_add_molecule.html

deleted100644 → 0
+0 −57
Original line number Diff line number Diff line 
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">

<html xmlns="http://www.w3.org/1999/xhtml">

<head>

<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>

<title>ATC: fix_modify AtC add_molecule</title>

<link href="tabs.css" rel="stylesheet" type="text/css"/>

<link href="doxygen.css" rel="stylesheet" type="text/css"/>

</head>

<body>

<center>

  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;

  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;

  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;

  <a href="../../Commands_all.html">Commands</a>

</center>



<hr>





<!-- Generated by Doxygen 1.6.1 -->

<div class="contents">





<h3><a class="anchor" id="man_add_molecule">fix_modify AtC add_molecule </a></h3><h4><a class="anchor" id="syntax">

syntax</a></h4>

<p>fix_modify_AtC add_molecule &lt;small|large&gt; &lt;TAG&gt; &lt;GROUP_NAME&gt; <br/>

</p>

<ul>

<li>small|large = can be small if molecule size &lt; cutoff radius, must be large otherwise <br/>

</li>

<li>&lt;TAG&gt; = tag for tracking a species <br/>

</li>

<li>&lt;GROUP_NAME&gt; = name of group that tracking will be applied to <br/>

 </li>

</ul>

<h4><a class="anchor" id="examples">

examples</a></h4>

<p><code> group WATERGROUP type 1 2 </code> <br/>

 <code> fix_modify AtC add_molecule small water WATERGROUP </code> <br/>

 </p>

<h4><a class="anchor" id="description">

description</a></h4>

<p>Associates a tag with all molecules corresponding to a specified group. <br/>

 </p>

<h4><a class="anchor" id="restrictions">

restrictions</a></h4>

<h4><a class="anchor" id="related">

related</a></h4>

<h4><a class="anchor" id="default">

default</a></h4>

<p>No defaults for this command. </p>

</div>

<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

<a href="http://www.doxygen.org/index.html">

<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>

</body>

</html>

doc/src/USER/atc/man_add_species.html

deleted100644 → 0
+0 −57
Original line number Diff line number Diff line 
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">

<html xmlns="http://www.w3.org/1999/xhtml">

<head>

<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>

<title>ATC: fix_modify AtC add_species</title>

<link href="tabs.css" rel="stylesheet" type="text/css"/>

<link href="doxygen.css" rel="stylesheet" type="text/css"/>

</head>

<body>

<center>

  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;

  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;

  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;

  <a href="../../Commands_all.html">Commands</a>

</center>



<hr>





<!-- Generated by Doxygen 1.6.1 -->

<div class="contents">





<h3><a class="anchor" id="man_add_species">fix_modify AtC add_species </a></h3><h4><a class="anchor" id="syntax">

syntax</a></h4>

<p>fix_modify_AtC add_species &lt;TAG&gt; &lt;group|type&gt; &lt;ID&gt; <br/>

</p>

<ul>

<li>&lt;TAG&gt; = tag for tracking a species <br/>

</li>

<li>group|type = LAMMPS defined group or type of atoms <br/>

</li>

<li>&lt;ID&gt; = name of group or type number <br/>

 </li>

</ul>

<h4><a class="anchor" id="examples">

examples</a></h4>

<p><code> fix_modify AtC add_species gold type 1 </code> <br/>

 <code> group GOLDGROUP type 1 </code> <br/>

 <code> fix_modify AtC add_species gold group GOLDGROUP </code> </p>

<h4><a class="anchor" id="description">

description</a></h4>

<p>Associates a tag with all atoms of a specified type or within a specified group. <br/>

 </p>

<h4><a class="anchor" id="restrictions">

restrictions</a></h4>

<h4><a class="anchor" id="related">

related</a></h4>

<h4><a class="anchor" id="default">

default</a></h4>

<p>No defaults for this command. </p>

</div>

<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

<a href="http://www.doxygen.org/index.html">

<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>

</body>

</html>

doc/src/USER/atc/man_atom_element_map.html

deleted100644 → 0
+0 −50
Original line number Diff line number Diff line 
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">

<html xmlns="http://www.w3.org/1999/xhtml">

<head>

<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>

<title>ATC: fix_modify AtC atom_element_map</title>

<link href="tabs.css" rel="stylesheet" type="text/css"/>

<link href="doxygen.css" rel="stylesheet" type="text/css"/>

</head>

<body>

<center>

  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;

  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;

  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;

  <a href="../../Commands_all.html">Commands</a>

</center>



<hr>





<!-- Generated by Doxygen 1.6.1 -->

<div class="contents">





<h3><a class="anchor" id="man_atom_element_map">fix_modify AtC atom_element_map </a></h3><h4><a class="anchor" id="syntax">

syntax</a></h4>

<p>fix_modify AtC atom_element_map &lt;eulerian|lagrangian&gt; &lt;frequency&gt; <br/>

</p>

<ul>

<li>frequency (int) : frequency of updating atom-to-continuum maps based on the current configuration - only for eulerian </li>

</ul>

<h4><a class="anchor" id="examples">

examples</a></h4>

<p><code> fix_modify atc atom_element_map eulerian 100 </code> </p>

<h4><a class="anchor" id="description">

description</a></h4>

<p>Changes frame of reference from eulerian to lagrangian and sets the frequency for which the map from atoms to elements is reformed and all the attendant data is recalculated. </p>

<h4><a class="anchor" id="restrictions">

restrictions</a></h4>

<p>Cannot change map type after initialization. </p>

<h4><a class="anchor" id="related">

related</a></h4>

<h4><a class="anchor" id="default">

default</a></h4>

<p>lagrangian </p>

</div>

<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

<a href="http://www.doxygen.org/index.html">

<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>

</body>

</html>

doc/src/USER/atc/man_atom_weight.html

deleted100644 → 0
+0 −59
Original line number Diff line number Diff line 
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">

<html xmlns="http://www.w3.org/1999/xhtml">

<head>

<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>

<title>ATC: fix_modify AtC atom_weight</title>

<link href="tabs.css" rel="stylesheet" type="text/css"/>

<link href="doxygen.css" rel="stylesheet" type="text/css"/>

</head>

<body>

<center>

  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;

  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;

  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;

  <a href="../../Commands_all.html">Commands</a>

</center>



<hr>





<!-- Generated by Doxygen 1.6.1 -->

<div class="contents">





<h3><a class="anchor" id="man_atom_weight">fix_modify AtC atom_weight </a></h3><h4><a class="anchor" id="syntax">

syntax</a></h4>

<p>fix_modify AtC atom_weight &lt;method&gt; &lt;arguments&gt;</p>

<ul>

<li>&lt;method&gt; = <br/>

 value: atoms in specified group assigned constant value given <br/>

 lattice: volume per atom for specified lattice type (e.g. fcc) and parameter <br/>

 element: element volume divided among atoms within element <br/>

 region: volume per atom determined based on the atom count in the MD regions and their volumes. Note: meaningful only if atoms completely fill all the regions. <br/>

 group: volume per atom determined based on the atom count in a group and its volume<br/>

 read_in: list of values for atoms are read-in from specified file <br/>

 </li>

</ul>

<h4><a class="anchor" id="examples">

examples</a></h4>

<p><code> fix_modify atc atom_weight constant myatoms 11.8 </code> <br/>

 <code> fix_modify atc atom_weight lattice </code> <br/>

 <code> fix_modify atc atom_weight read-in atm_wt_file.txt </code> <br/>

 </p>

<h4><a class="anchor" id="description">

description</a></h4>

<p>Command for assigning the value of atomic weights used for atomic integration in atom-continuum coupled simulations. </p>

<h4><a class="anchor" id="restrictions">

restrictions</a></h4>

<p>Use of lattice option requires a lattice type and parameter is already specified. </p>

<h4><a class="anchor" id="related">

related</a></h4>

<h4><a class="anchor" id="default">

default</a></h4>

<p>lattice </p>

</div>

<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

<a href="http://www.doxygen.org/index.html">

<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>

</body>

</html>

doc/src/USER/atc/man_atomic_charge.html

deleted100644 → 0
+0 −49
Original line number Diff line number Diff line 
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">

<html xmlns="http://www.w3.org/1999/xhtml">

<head>

<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>

<title>ATC: fix_modify AtC atomic_charge</title>

<link href="tabs.css" rel="stylesheet" type="text/css"/>

<link href="doxygen.css" rel="stylesheet" type="text/css"/>

</head>

<body>

<center>

  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;

  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;

  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;

  <a href="../../Commands_all.html">Commands</a>

</center>



<hr>





<!-- Generated by Doxygen 1.6.1 -->

<div class="contents">





<h3><a class="anchor" id="man_atomic_charge">fix_modify AtC atomic_charge </a></h3><h4><a class="anchor" id="syntax">

syntax</a></h4>

<p>fix_modify AtC &lt;include | omit&gt; atomic_charge</p>

<ul>

<li>&lt;include | omit&gt; = switch to activiate/deactiviate inclusion of intrinsic atomic charge in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> </li>

</ul>

<h4><a class="anchor" id="examples">

examples</a></h4>

<p><code> fix_modify atc compute include atomic_charge </code> </p>

<h4><a class="anchor" id="description">

description</a></h4>

<p>Determines whether AtC tracks the total charge as a finite element field </p>

<h4><a class="anchor" id="restrictions">

restrictions</a></h4>

<p>Required for: electrostatics </p>

<h4><a class="anchor" id="related">

related</a></h4>

<h4><a class="anchor" id="default">

default</a></h4>

<p>if the atom charge is defined, default is on, otherwise default is off </p>

</div>

<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

<a href="http://www.doxygen.org/index.html">

<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>

</body>

</html>

CRA Git | Maintained and supported by SUSTech CRA and CCSE