sync w/ SVN

<ol class="arabic simple" start="4">

<li>Total force on each molecule and ave/max across all molecules:</li>

</ol>

<pre class="literal-block">

compute cc1 all chunk/atom molecule

fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out

variable xave equal ave(f_1<strong>2</strong>)

variable xmax equal max(f_1<strong>2</strong>)

thermo 1000

thermo_style custom step temp v_xave v_xmax

</pre>

<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>

<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">1000</span> <span class="mi">1</span> <span class="mi">1000</span> <span class="n">cc1</span> <span class="n">fx</span> <span class="n">fy</span> <span class="n">fz</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span>

<span class="n">variable</span> <span class="n">xave</span> <span class="n">equal</span> <span class="n">ave</span><span class="p">(</span><span class="n">f_1</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>

<span class="n">variable</span> <span class="n">xmax</span> <span class="n">equal</span> <span class="nb">max</span><span class="p">(</span><span class="n">f_1</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>

<span class="n">thermo</span> <span class="mi">1000</span>

<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">v_xave</span> <span class="n">v_xmax</span>

</pre></div>

</div>

<ol class="arabic simple" start="5">

<li>Histogram of cluster sizes:</li>

</ol>

<p>The simplest way to output the results of the compute omega/chunk

calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>

command, for example:</p>

<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>

<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">omega</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>

<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>

</pre></div>

</div>

<pre class="literal-block">

compute cc1 all chunk/atom molecule

compute myChunk all omega/chunk cc1

fix 1 all ave/time 100 1 100 c_myChunk<strong>*</strong> file tmp.out mode vector

</pre>

<p><strong>Output info:</strong></p>

<p>This compute calculates a global array where the number of rows = the

number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.  The number of columns =

<p>Perform constant NVE integration to update position and velocity for

atoms constrained to a curved surface (manifold) in the group each timestep. The constraint

is handled by RATTLE <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a> written out for the special case of

single-particle constraints as explained in <a class="reference internal" href="manifolds.html#paquay"><span class="std std-ref">(Paquay)</span></a>.

single-particle constraints as explained in <a class="reference internal" href="fix_nvt_manifold_rattle.html#paquay"><span class="std std-ref">(Paquay)</span></a>.

V is volume; E is energy. This way, the dynamics of particles constrained to

curved surfaces can be studied. If combined with <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, this generates

Brownian motion of particles constrained to a curved surface. For a list of currently supported

</div>

<div class="section" id="description">

<h2>Description</h2>

<p>This fix combines the RATTLE-based <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a> time integrator of <a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">fix nve/manifold/rattle</span></a> <a class="reference internal" href="manifolds.html#paquay"><span class="std std-ref">(Paquay)</span></a> with a Nose-Hoover-chain thermostat to sample the

<p>This fix combines the RATTLE-based <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a> time integrator of <a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">fix nve/manifold/rattle</span></a> <a class="reference internal" href="#paquay"><span class="std std-ref">(Paquay)</span></a> with a Nose-Hoover-chain thermostat to sample the

canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt).

For a list of currently supported manifolds and their parameters, see <a class="reference internal" href="manifolds.html"><span class="doc">manifolds</span></a></p>

</div>