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<div class="section" id="fix-shake-command">
<span id="index-0"></span><h1>fix shake command</h1>
</div>
<div class="section" id="fix-shake-cuda-command">
<h1>fix shake/cuda command</h1>
</div>
<div class="section" id="fix-rattle-command">
<h1>fix 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">style</span> <span class="n">tol</span> <span class="nb">iter</span> <span class="n">N</span> <span class="n">constraint</span> <span class="n">values</span> <span class="o">...</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>style = shake or rattle = style name of this fix command</li>
<li>tol = accuracy tolerance of SHAKE solution</li>
<li>iter = max # of iterations in each SHAKE solution</li>
<li>N = print SHAKE statistics every this many timesteps (0 = never)</li>
<li>one or more constraint/value pairs are appended</li>
<li>constraint = <em>b</em> or <em>a</em> or <em>t</em> or <em>m</em></li>
</ul>
<pre class="literal-block">
<em>b</em> values = one or more bond types
<em>a</em> values = one or more angle types
<em>t</em> values = one or more atom types
<em>m</em> value = one or more mass values
</pre>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>mol</em></li>
</ul>
<pre class="literal-block">
<em>mol</em> value = template-ID
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command
</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="n">sub</span> <span class="n">shake</span> <span class="mf">0.0001</span> <span class="mi">20</span> <span class="mi">10</span> <span class="n">b</span> <span class="mi">4</span> <span class="mi">19</span> <span class="n">a</span> <span class="mi">3</span> <span class="mi">5</span> <span class="mi">2</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="n">sub</span> <span class="n">shake</span> <span class="mf">0.0001</span> <span class="mi">20</span> <span class="mi">10</span> <span class="n">t</span> <span class="mi">5</span> <span class="mi">6</span> <span class="n">m</span> <span class="mf">1.0</span> <span class="n">a</span> <span class="mi">31</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="n">sub</span> <span class="n">shake</span> <span class="mf">0.0001</span> <span class="mi">20</span> <span class="mi">10</span> <span class="n">t</span> <span class="mi">5</span> <span class="mi">6</span> <span class="n">m</span> <span class="mf">1.0</span> <span class="n">a</span> <span class="mi">31</span> <span class="n">mol</span> <span class="n">myMol</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="n">sub</span> <span class="n">rattle</span> <span class="mf">0.0001</span> <span class="mi">20</span> <span class="mi">10</span> <span class="n">t</span> <span class="mi">5</span> <span class="mi">6</span> <span class="n">m</span> <span class="mf">1.0</span> <span class="n">a</span> <span class="mi">31</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="n">sub</span> <span class="n">rattle</span> <span class="mf">0.0001</span> <span class="mi">20</span> <span class="mi">10</span> <span class="n">t</span> <span class="mi">5</span> <span class="mi">6</span> <span class="n">m</span> <span class="mf">1.0</span> <span class="n">a</span> <span class="mi">31</span> <span class="n">mol</span> <span class="n">myMol</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Apply bond and angle constraints to specified bonds and angles in the
simulation by either the SHAKE or RATTLE algorithms. This typically
enables a longer timestep.</p>
<p><strong>SHAKE vs RATTLE:</strong></p>
<p>The SHAKE algorithm was invented for schemes such as standard Verlet
timesteppnig, where only the coordinates are integrated and the
velocities are approximated as finite differences to the trajectories
(<a class="reference internal" href="#ryckaert"><span class="std std-ref">Ryckaert et al. (1977)</span></a>). If the velocities are
integrated explicitly, as with velocity Verlet which is what LAMMPS
uses as an integration method, a second set of constraining forces is
required in order to eliminate velocity components along the bonds
(<a class="reference internal" href="#andersen"><span class="std std-ref">Andersen (1983)</span></a>).</p>
<p>In order to formulate individual constraints for SHAKE and RATTLE,
focus on a single molecule whose bonds are constrained. Let Ri and Vi
be the position and velocity of atom <em>i</em> at time <em>n</em>, for
<em>i</em>=1,...,<em>N</em>, where <em>N</em> is the number of sites of our reference
molecule. The distance vector between sites <em>i</em> and <em>j</em> is given by</p>
<img alt="_images/fix_rattle_rij.jpg" class="align-center" src="_images/fix_rattle_rij.jpg" />
<p>The constraints can then be formulated as</p>
<img alt="_images/fix_rattle_constraints.jpg" class="align-center" src="_images/fix_rattle_constraints.jpg" />
<p>The SHAKE algorithm satisfies the first condition, i.e. the sites at
time <em>n+1</em> will have the desired separations Dij immediately after the
coordinates are integrated. If we also enforce the second condition,
the velocity components along the bonds will vanish. RATTLE satisfies
both conditions. As implemented in LAMMPS, fix rattle uses fix shake
for satisfying the coordinate constraints. Therefore the settings and
optional keywords are the same for both fixes, and all the information
below about SHAKE is also relevant for RATTLE.</p>
<p><strong>SHAKE:</strong></p>
<p>Each timestep the specified bonds and angles are reset to their
equilibrium lengths and angular values via the SHAKE algorithm
(<a class="reference internal" href="#ryckaert"><span class="std std-ref">Ryckaert et al. (1977)</span></a>). This is done by applying an
additional constraint force so that the new positions preserve the
desired atom separations. The equations for the additional force are
solved via an iterative method that typically converges to an accurate
solution in a few iterations. The desired tolerance (e.g. 1.0e-4 = 1
part in 10000) and maximum # of iterations are specified as arguments.
Setting the N argument will print statistics to the screen and log
file about regarding the lengths of bonds and angles that are being
constrained. Small delta values mean SHAKE is doing a good job.</p>
<p>In LAMMPS, only small clusters of atoms can be constrained. This is
so the constraint calculation for a cluster can be performed by a
single processor, to enable good parallel performance. A cluster is
defined as a central atom connected to others in the cluster by
constrained bonds. LAMMPS allows for the following kinds of clusters
to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or
one central atom bonded to 2 others and the angle between the 3 atoms
also constrained. This means water molecules or CH2 or CH3 groups may
be constrained, but not all the C-C backbone bonds of a long polymer
chain.</p>
<p>The <em>b</em> constraint lists bond types that will be constrained. The <em>t</em>
constraint lists atom types. All bonds connected to an atom of the
specified type will be constrained. The <em>m</em> constraint lists atom
masses. All bonds connected to atoms of the specified masses will be
constrained (within a fudge factor of MASSDELTA specified in
fix_shake.cpp). The <em>a</em> constraint lists angle types. If both bonds
in the angle are constrained then the angle will also be constrained
if its type is in the list.</p>
<p>For all constraints, a particular bond is only constrained if both
atoms in the bond are in the group specified with the SHAKE fix.</p>
<p>The degrees-of-freedom removed by SHAKE bonds and angles are accounted
for in temperature and pressure computations. Similarly, the SHAKE
contribution to the pressure of the system (virial) is also accounted
for.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This command works by using the current forces on atoms to
caculate an additional constraint force which when added will leave
the atoms in positions that satisfy the SHAKE constraints (e.g. bond
length) after the next time integration step. If you define fixes
(e.g. <a class="reference internal" href="fix_efield.html"><span class="doc">fix efield</span></a>) that add additional force to the
atoms after fix shake operates, then this fix will not take them into
account and the time integration will typically not satisfy the SHAKE
constraints. The solution for this is to make sure that fix shake is
defined in your input script after any other fixes which add or change
forces (to atoms that fix shake operates on).</p>
</div>
<hr class="docutils" />
<p>The <em>mol</em> keyword should be used when other commands, such as <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a> or <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a>, add molecules
on-the-fly during a simulation, and you wish to contrain the new
molecules via SHAKE. You specify a <em>template-ID</em> previously defined
using the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command, which reads a file that
defines the molecule. You must use the same <em>template-ID</em> that the
command adding molecules uses. The coordinates, atom types, special
bond restrictions, and SHAKE info can be specified in the molecule
file. See the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command for details. The only
settings required to be in this file (by this command) are the SHAKE
info of atoms in the molecule.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.</p>
<p>These accelerated styles are part of the USER-CUDA package. They are
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>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<hr class="docutils" />
<p><strong>RATTLE:</strong></p>
<p>The velocity constraints lead to a linear system of equations which
can be solved analytically. The implementation of the algorithm in
LAMMPS closely follows (<a class="reference internal" href="#andersen"><span class="std std-ref">Andersen (1983)</span></a>).</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The fix rattle command modifies forces and velocities and thus
should be defined after all other integration fixes in your input
script. If you define other fixes that modify velocities or forces
after fix rattle operates, then fix rattle will not take them into
account and the overall time integration will typically not satisfy
the RATTLE constraints. You can check whether the constraints work
correctly by setting the value of RATTLE_DEBUG in src/fix_rattle.cpp
to 1 and recompiling LAMMPS.</p>
</div>
</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 these fixes 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 these fixes. No global or per-atom quantities are
stored by these fixes 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 these fixes
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. These fixes are not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>These fixes are part of the RIGID package. They are 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>For computational efficiency, there can only be one shake or rattle
fix defined in a simulation.</p>
<p>If you use a tolerance that is too large or a max-iteration count that
is too small, the constraints will not be enforced very strongly,
which can lead to poor energy conservation. You can test for this in
your system by running a constant NVE simulation with a particular set
of SHAKE parameters and monitoring the energy versus time.</p>
<p>SHAKE or RATTLE should not be used to contrain an angle at 180 degrees
(e.g. linear CO2 molecule). This causes numeric difficulties.</p>
<p><strong>Related commands:</strong> none</p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="ryckaert"><strong>(Ryckaert)</strong> J.-P. Ryckaert, G. Ciccotti and H. J. C. Berendsen,
J of Comp Phys, 23, 327-341 (1977).</p>
<p id="andersen"><strong>(Andersen)</strong> H. Andersen, J of Comp Phys, 52, 24-34 (1983).</p>
</div>
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