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<div class="section" id="fix-manifoldforce-command">
<span id="index-0"></span><h1>fix manifoldforce command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">manifoldforce</span> <span class="n">manifold</span> <span class="n">manifold</span><span class="o">-</span><span class="n">args</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>manifold = name of the manifold</li>
<li>manifold-args = parameters for the manifold</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<p>fix constrain all manifoldforce sphere 5.0</p>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>This fix subtracts each time step from the force the component along the normal of the specified <a class="reference internal" href="manifolds.html"><span class="doc">manifold</span></a>.
This can be used in combination with <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> to remove overlap between particles while
keeping them (roughly) constrained to the given manifold, e.g. to set up a run with <a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">fix nve/manifold/rattle</span></a>.
I have found that only <em>hftn</em> and <em>quickmin</em> with a very small time step perform adequately though.</p>
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<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
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<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
section for more info.</p>
<p>Only use this with <em>min_style hftn</em> or <em>min_style quickmin</em>. If not, the constraints
will not be satisfied very well at all. A warning is generated if the <em>min_style</em> is
incompatible but no error.</p>
</div>
<hr class="docutils" />
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">fix nve/manifold/rattle</span></a>, <a class="reference internal" href="fix_nvt_manifold_rattle.html"><span class="doc">fix nvt/manifold/rattle</span></a></p>
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<div class="section" id="fix-nve-manifold-rattle-command">
<span id="index-0"></span><h1>fix nve/manifold/rattle command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">nve</span><span class="o">/</span><span class="n">manifold</span><span class="o">/</span><span class="n">rattle</span> <span class="n">tol</span> <span class="n">maxit</span> <span class="n">manifold</span> <span class="n">manifold</span><span class="o">-</span><span class="n">args</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>nve/manifold/rattle = style name of this fix command</li>
<li>tol = tolerance to which Newton iteration must converge</li>
<li>maxit = maximum number of iterations to perform</li>
<li>manifold = name of the manifold</li>
<li>manifold-args = parameters for the manifold</li>
<li>one or more keyword/value pairs may be appended</li>
</ul>
<pre class="literal-block">
keyword = <em>every</em>
<em>every</em> values = N
N = print info about iteration every N steps. N = 0 means no output
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">nve</span><span class="o">/</span><span class="n">manifold</span><span class="o">/</span><span class="n">rattle</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">4</span> <span class="mi">10</span> <span class="n">sphere</span> <span class="mf">5.0</span>
<span class="n">fix</span> <span class="n">step</span> <span class="nb">all</span> <span class="n">nve</span><span class="o">/</span><span class="n">manifold</span><span class="o">/</span><span class="n">rattle</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">8</span> <span class="mi">100</span> <span class="n">ellipsoid</span> <span class="mf">2.5</span> <span class="mf">2.5</span> <span class="mf">5.0</span> <span class="n">every</span> <span class="mi">25</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<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>.
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
manifolds and their parameters, see <a class="reference internal" href="manifolds.html"><span class="doc">manifolds</span></a>.</p>
<p>Note that the particles must initially be close to the manifold in question. If not, RATTLE will
not be able to iterate until the constraint is satisfied, and an error is generated. For simple
manifolds this can be achieved with <em>region</em> and <em>create_atoms</em> commands, but for more complex
surfaces it might be more useful to write a script.</p>
<p>The manifold args may be equal-style variables, like so:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">R</span> <span class="n">equal</span> <span class="s2">&quot;ramp(5.0,3.0)&quot;</span>
<span class="n">fix</span> <span class="n">shrink_sphere</span> <span class="nb">all</span> <span class="n">nve</span><span class="o">/</span><span class="n">manifold</span><span class="o">/</span><span class="n">rattle</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">4</span> <span class="mi">10</span> <span class="n">sphere</span> <span class="n">v_R</span>
</pre></div>
</div>
<p>In this case, the manifold parameter will change in time according to the variable.
This is not a problem for the time integrator as long as the change of the manifold is slow with respect to the dynamics of the particles.
Note that if the manifold has to exert work on the particles because of these changes, the total energy might not be conserved.</p>
</div>
<hr class="docutils" />
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<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.
This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
section for more info.</p>
<p>Only use this with <em>min_style hftn</em> or <em>min_style quickmin</em>. If not, the constraints
will not be satisfied very well at all. A warning is generated if the <em>min_style</em> is
incompatible but no error.</p>
</div>
<hr class="docutils" />
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_nvt_manifold_rattle.html"><span class="doc">fix nvt/manifold/rattle</span></a>, <a class="reference internal" href="fix_manifoldforce.html"><span class="doc">fix manifoldforce</span></a></p>
<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, ???, (2016), to be published,
preprint available at <a class="reference external" href="http://arxiv.org/abs/1411.3019/">arXiv:1411.3019</a>.</p>
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<div class="section" id="fix-nvt-manifold-rattle-command">
<span id="index-0"></span><h1>fix nvt/manifold/rattle command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">nvt</span><span class="o">/</span><span class="n">manifold</span><span class="o">/</span><span class="n">rattle</span> <span class="n">tol</span> <span class="n">maxit</span> <span class="n">manifold</span> <span class="n">manifold</span><span class="o">-</span><span class="n">args</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>nvt/manifold/rattle = style name of this fix command</li>
<li>tol = tolerance to which Newton iteration must converge</li>
<li>maxit = maximum number of iterations to perform</li>
<li>manifold = name of the manifold</li>
<li>manifold-args = parameters for the manifold</li>
<li>one or more keyword/value pairs may be appended</li>
</ul>
<pre class="literal-block">
keyword = <em>temp</em> or <em>tchain</em> or <em>every</em>
<em>temp</em> values = Tstart Tstop Tdamp
Tstart, Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units)
<em>tchain</em> value = N
N = length of thermostat chain (1 = single thermostat)
<em>every</em> value = N
N = print info about iteration every N steps. N = 0 means no output
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<p>fix 1 all nvt/manifold/rattle 1e-4 10 cylinder 3.0 temp 1.0 1.0 10.0</p>
</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
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>
<hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.
This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
section for more info.</p>
<p>Only use this with <em>min_style hftn</em> or <em>min_style quickmin</em>. If not, the constraints
will not be satisfied very well at all. A warning is generated if the <em>min_style</em> is
incompatible but no error.</p>
</div>
<hr class="docutils" />
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="#"><span class="doc">fix nve/manifold/rattle</span></a>, <a class="reference internal" href="fix_manifoldforce.html"><span class="doc">fix manifoldforce</span></a>
<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, ???, (2016), to be published,
preprint available at <a class="reference external" href="http://arxiv.org/abs/1411.3019/">arXiv:1411.3019</a>.</p>
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</dt>
<dt><a href="fix_manifoldforce.html#index-0">fix manifoldforce</a>
</dt>
<dt><a href="fix_meso.html#index-0">fix meso</a>
</dt>
@ -1236,6 +1240,10 @@
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<dt><a href="fix_nve_manifold_rattle.html#index-0">fix nve/manifold/rattle</a>
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<dt><a href="fix_nve_noforce.html#index-0">fix nve/noforce</a>
</dt>
@ -1264,6 +1272,10 @@
</dt>
<dt><a href="fix_nvt_manifold_rattle.html#index-0">fix nvt/manifold/rattle</a>
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<dt><a href="fix_nvt_sllod.html#index-0">fix nvt/sllod</a>
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<h1>Description</h1>
<p>Below is a list of currently supported manifolds, their parameters and a short description of them.
The parameters listed here are in the same order as they should be passed to the relevant fixes.</p>
<table border="1" class="docutils">
<colgroup>
<col width="5%" />
<col width="6%" />
<col width="43%" />
<col width="46%" />
<col width="1%" />
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<tbody valign="top">
<tr class="row-odd"><td><em>manifold</em></td>
<td><em>parameters</em></td>
<td><em>equation</em></td>
<td><em>description</em></td>
<td>&nbsp;</td>
</tr>
<tr class="row-even"><td>cylinder</td>
<td>R</td>
<td>x^2 + y^2 - R^2 = 0</td>
<td>Cylinder along z-axis, axis going through (0,0,0)</td>
<td>&nbsp;</td>
</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="#id7"><span class="problematic" id="id8">|z|</span></a> &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 class="row-even"><td>dumbbell</td>
<td>a A B c</td>
<td>-( x^2 + y^2 ) * (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0</td>
<td>A dumbbell</td>
<td>&nbsp;</td>
</tr>
<tr class="row-odd"><td>ellipsoid</td>
<td>a b c</td>
<td>(x/a)^2 + (y/b)^2 + (z/c)^2 = 0</td>
<td>An ellipsoid</td>
<td>&nbsp;</td>
</tr>
<tr class="row-even"><td>plane</td>
<td>a b c x0 y0 z0</td>
<td>a*(x-x0) + b*(y-y0) + c*(z-z0) = 0</td>
<td>A plane with normal (a,b,c) going through point (x0,y0,z0)</td>
<td>&nbsp;</td>
</tr>
<tr class="row-odd"><td>plane_wiggle</td>
<td>a w</td>
<td>z - a*sin(w*x) = 0</td>
<td>A plane with a sinusoidal modulation on z along x.</td>
<td>&nbsp;</td>
</tr>
<tr class="row-even"><td>sphere</td>
<td>R</td>
<td>x^2 + y^2 + z^2 - R^2 = 0</td>
<td>A sphere of radius R</td>
<td>&nbsp;</td>
</tr>
<tr class="row-odd"><td>supersphere</td>
<td>R q</td>
<td><a href="#id1"><span class="problematic" id="id2">|</span></a>x|^q + <a href="#id3"><span class="problematic" id="id4">|</span></a>y|^q + <a href="#id5"><span class="problematic" id="id6">|</span></a>z|^q - R^q = 0</td>
<td>A supersphere of hyperradius R</td>
<td>&nbsp;</td>
</tr>
<tr class="row-even"><td>spine</td>
<td>a, A, B, B2, c</td>
<td>-(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z &gt; 0, 1 otherwise; g(z) = B if z &gt; 0, B2 otherwise</td>
<td>An approximation to a dendtritic spine</td>
<td>&nbsp;</td>
</tr>
<tr class="row-odd"><td>spine_two</td>
<td>a, A, B, B2, c</td>
<td>-(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z &gt; 0, 1 otherwise; g(z) = B if z &gt; 0, B2 otherwise</td>
<td>Another approximation to a dendtritic spine</td>
<td>&nbsp;</td>
</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>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 class="row-odd"><td>torus</td>
<td>R r</td>
<td>(R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2</td>
<td>A torus with large radius R and small radius r, centered on (0,0,0)</td>
<td>&nbsp;</td>
</tr>
</tbody>
</table>
<p id="paquay"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
preprint available at <a class="reference external" href="http://arxiv.org/abs/1411.3019/">arXiv:1411.3019</a>.</p>
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