sync with SVN

<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="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

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>

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="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 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>

<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" />

<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">

<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>

<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>

</div>

<hr class="docutils" />

<div class="section" id="related-commands">

<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,

<p id="paquay"><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>

<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">

<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,

<p id="paquay"><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>

keyword = {every}

  {every} values = N

    N = print info about iteration every N steps. N = 0 means no output :pre

:ule

[Examples:]

[Description:]

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 "(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, 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 surface. For a list of currently supported

manifolds and their parameters, see "manifolds"_manifolds.html.

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 {region} and {create_atoms} commands, but for more complex

surfaces it might be more useful to write a script.

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,

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

surface. For a list of currently supported manifolds and their

parameters, see "manifolds"_manifolds.html.

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 {region} and {create_atoms}

commands, but for more complex surfaces it might be more useful to

write a script.

The manifold args may be equal-style variables, like so:

variable R equal "ramp(5.0,3.0)"

fix shrink_sphere all nve/manifold/rattle 1e-4 10 sphere v_R :pre

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.

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.

:line

[Restrictions:]

This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS

was built with that package. See the "Making LAMMPS"_Section_start.html#start_3

section for more info.

This fix is part of the USER-MANIFOLD package. It is only enabled if

LAMMPS was built with that package. See the "Making

LAMMPS"_Section_start.html#start_3 section for more info.

:line

[Related commands:]

"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix manifoldforce"_fix_manifoldforce.html

"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix

manifoldforce"_fix_manifoldforce.html

[Default:] every = 0, tchain = 3

void ComputeOmegaChunk::compute_array()

{

  int i,j,index;

  int i,j,m,index;

  double dx,dy,dz,massone;

  double unwrap[3];