some more smaller doc file cleanups. almost there...

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="#paquay"><span class="std std-ref">(Paquay)</span></a>.  V is volume; E is energy. This way,

explained in <a class="reference internal" href="#paquay2"><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

<p><strong>Default:</strong> every = 0, tchain = 3</p>

<hr class="docutils" />

<p id="andersen"><strong>(Andersen)</strong> Andersen, J. Comp. Phys. 52, 24, (1983).</p>

<p id="paquay"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, 6, (2016).

<p id="paquay2"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, 6, (2016).

preprint available at <a class="reference external" href="http://arxiv.org/abs/1411.3019/">arXiv:1411.3019</a>.</p>

</div>

</div>

</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="#paquay3"><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>

<hr class="docutils" />

<strong>Default:</strong> every = 0</p>

<hr class="docutils" />

<p id="andersen"><strong>(Andersen)</strong> Andersen, J. Comp. Phys. 52, 24, (1983).</p>

<p id="paquay"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, 6, (2016).

<p id="paquay3"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, 6, (2016).

preprint available at <a class="reference external" href="http://arxiv.org/abs/1411.3019/">arXiv:1411.3019</a>.</p>

</div>

</div>

</tr>

<tr class="row-odd"><td>cylinder_dent</td>

<td>R l a</td>

<td>x^2 + y^2 - r(z)^2 = 0, r(x) = R if <a href="#id1"><span class="problematic" id="id2">|z|</span></a> &gt; l, r(z) = R - a*(1 + cos(z/l))/2 otherwise</td>

<td>x^2 + y^2 - r(z)^2 = 0, r(x) = R if | z | &gt; l, r(z) = R - a*(1 + cos(z/l))/2 otherwise</td>

<td>A cylinder with a dent around z = 0</td>

<td>&nbsp;</td>

</tr>

</tr>

<tr class="row-odd"><td>supersphere</td>

<td>R q</td>

<td><a href="#id3"><span class="problematic" id="id4">|x|</span></a>^q + <a href="#id5"><span class="problematic" id="id6">|y|</span></a>^q + <a href="#id7"><span class="problematic" id="id8">|z|</span></a>^q - R^q = 0</td>

<td><div class="first last line-block">

<div class="line">x <a href="#id1"><span class="problematic" id="id2">|</span></a>^q + | y <a href="#id3"><span class="problematic" id="id4">|</span></a>^q + | z <a href="#id5"><span class="problematic" id="id6">|</span></a>^q - R^q = 0</div>

</div>

</td>

<td>A supersphere of hyperradius R</td>

<td>&nbsp;</td>

</tr>

</tr>

<tr class="row-even"><td>thylakoid</td>

<td>wB LB lB</td>

<td>Various, see <a class="reference internal" href="#paquay"><span class="std std-ref">(Paquay)</span></a></td>

<td>Various, see <a class="reference internal" href="#paquay1"><span class="std std-ref">(Paquay)</span></a></td>

<td>A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB</td>

<td>&nbsp;</td>

</tr>

</tr>

</tbody>

</table>

<p id="paquay"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,

<p id="paquay1"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, 6, (2016).

preprint available at <a class="reference external" href="http://arxiv.org/abs/1411.3019/">arXiv:1411.3019</a>.</p>

</div>

compute reax all pair reax/c

variable eb           equal c_reax[1]

variable ea           equal c_reax[2]

...

[...]

variable eqeq         equal c_reax[14]

thermo_style custom step temp epair v_eb v_ea ... v_eqeq

</pre>

atoms constrained to a curved surface (manifold) in the group each

timestep. The constraint is handled by RATTLE "(Andersen)"_#Andersen

written out for the special case of single-particle constraints as

explained in "(Paquay)"_#Paquay.  V is volume; E is energy. This way,

explained in "(Paquay)"_#Paquay2.  V is volume; E is energy. This way,

the dynamics of particles constrained to curved surfaces can be

studied. If combined with "fix langevin"_fix_langevin.html, this

generates Brownian motion of particles constrained to a curved

:link(Andersen)

[(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983).

:link(Paquay)

:link(Paquay2)

[(Paquay)] Paquay and Kusters, Biophys. J., 110, 6, (2016).

preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/.