Commit b76a42d3 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

making a few more in-page links unique. some more small corrections and clenups

parent 54d5a14f

doc/html/fix_balance.html

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@@ -241,7 +241,7 @@ applied.</p> 
               title=""

               data-title=""

               ><img src="_images/balance_uniform.jpg"

                     class="align-center"

                     class=""

                     width="25%"

                     height="auto"

                     alt=""/>
@@ -251,7 +251,7 @@ applied.</p> 
               title=""

               data-title=""

               ><img src="_images/balance_nonuniform.jpg"

                     class="align-center"

                     class=""

                     width="25%"

                     height="auto"

                     alt=""/>
@@ -261,7 +261,7 @@ applied.</p> 
               title=""

               data-title=""

               ><img src="_images/balance_rcb.jpg"

                     class="align-center"

                     class=""

                     width="25%"

                     height="auto"

                     alt=""/>

doc/html/fix_lb_rigid_pc_sphere.html

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@@ -170,7 +170,7 @@ 
created to be used in place of that fix, to integrate the equations of

motion of spherical rigid bodies when a lattice-Boltzmann fluid is

present with a user-specified value of the force-coupling constant.

The fix uses the integration algorithm described in <a class="reference internal" href="#mackay"><span class="std std-ref">Mackay et al.</span></a> to update the positions, velocities, and orientations of

The fix uses the integration algorithm described in <a class="reference internal" href="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a> to update the positions, velocities, and orientations of

a set of spherical rigid bodies experiencing velocity dependent

hydrodynamic forces.  The spherical bodies are assumed to rotate as

solid, uniform density spheres, with moments of inertia calculated

doc/html/fix_neb.html

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@@ -157,7 +157,7 @@ Atoms in the two end-point replicas do not experience these forces, 
but those in intermediate replicas do.  During the initial stage of

NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting

on the atoms of each intermediate replica I is altered, as described

in the <a class="reference internal" href="neb.html#henkelman1"><span class="std std-ref">(Henkelman1)</span></a> paper, to become:</p>

in the <a class="reference internal" href="#henkelman1"><span class="std std-ref">(Henkelman1)</span></a> paper, to become:</p>

<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Fi</span> <span class="o">=</span> <span class="o">-</span><span class="n">Grad</span><span class="p">(</span><span class="n">V</span><span class="p">)</span> <span class="o">+</span> <span class="p">(</span><span class="n">Grad</span><span class="p">(</span><span class="n">V</span><span class="p">)</span> <span class="n">dot</span> <span class="n">That</span><span class="p">)</span> <span class="n">That</span> <span class="o">+</span> <span class="n">Kspring</span> <span class="p">(</span><span class="o">|</span> <span class="n">Ri</span><span class="o">+</span><span class="n">i</span> <span class="o">-</span> <span class="n">Ri</span> <span class="o">|</span> <span class="o">-</span> <span class="o">|</span> <span class="n">Ri</span> <span class="o">-</span> <span class="n">Ri</span><span class="o">-</span><span class="mi">1</span> <span class="o">|</span><span class="p">)</span> <span class="n">That</span>

</pre></div>

</div>
@@ -166,7 +166,7 @@ coordinates of its neighbor replicas. That (t with a hat over it) is 
the unit &#8220;tangent&#8221; vector for replica I which is a function of Ri,

Ri-1, Ri+1, and the potential energy of the 3 replicas; it points

roughly in the direction of (Ri+i - Ri-1); see the

<a class="reference internal" href="neb.html#henkelman1"><span class="std std-ref">(Henkelman1)</span></a> paper for details.</p>

<a class="reference internal" href="#henkelman1"><span class="std std-ref">(Henkelman1)</span></a> paper for details.</p>

<p>The first two terms in the above equation are the component of the

interatomic forces perpendicular to the tangent vector.  The last term

is a spring force between replica I and its neighbors, parallel to the
@@ -184,7 +184,7 @@ states are equidistant from each other.</p> 
replica nearest the top of the energy barrier are altered so that it

climbs to the top of the barrier and finds the saddle point.  The

forces on atoms in this replica are described in the

<a class="reference internal" href="neb.html#henkelman2"><span class="std std-ref">(Henkelman2)</span></a> paper, and become:</p>

<a class="reference internal" href="#henkelman2"><span class="std std-ref">(Henkelman2)</span></a> paper, and become:</p>

<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Fi</span> <span class="o">=</span> <span class="o">-</span><span class="n">Grad</span><span class="p">(</span><span class="n">V</span><span class="p">)</span> <span class="o">+</span> <span class="mi">2</span> <span class="p">(</span><span class="n">Grad</span><span class="p">(</span><span class="n">V</span><span class="p">)</span> <span class="n">dot</span> <span class="n">That</span><span class="p">)</span> <span class="n">That</span>

</pre></div>

</div>
@@ -209,8 +209,8 @@ for more info on packages.</p> 
<h2>Related commands</h2>

<p><a class="reference internal" href="neb.html"><span class="doc">neb</span></a></p>

<p><strong>Default:</strong> none</p>

<p id="henkelman"><strong>(Henkelman1)</strong> Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).</p>

<p id="id3"><strong>(Henkelman2)</strong> Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,

<p id="henkelman1"><strong>(Henkelman1)</strong> Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).</p>

<p id="henkelman2"><strong>(Henkelman2)</strong> Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,

9901-9904 (2000).</p>

</div>

</div>

doc/html/fix_shardlow.html

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@@ -152,7 +152,7 @@ in conjunction with a deterministic integrator (e.g. <a class="reference interna 
integration of the dissipative and random forces is performed prior to

the deterministic integration of the conservative force. Further

details regarding the method are provided in <a class="reference internal" href="pair_dpd_fdt.html#lisal"><span class="std std-ref">(Lisal)</span></a> and

<a class="reference internal" href="fix_eos_cv.html#larentzos"><span class="std std-ref">(Larentzos)</span></a>.</p>

<a class="reference internal" href="#larentzos1"><span class="std std-ref">(Larentzos1)</span></a>.</p>

<p>The fix <em>shardlow</em> must be used with the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style dpd/fdt</span></a> or <a class="reference internal" href="pair_style.html"><span class="doc">pair_style dpd/fdt/energy</span></a> command to properly initialize the

fluctuation-dissipation theorem parameter(s) sigma (and kappa, if

necessary).</p>
@@ -190,11 +190,11 @@ requested.</p> 
particle dynamics as isothermal, isobaric, isoenergetic, and

isoenthalpic conditions using Shardlow-like splitting algorithms.&#8221;,

J. Chem. Phys., 135, 204105 (2011).</p>

<p id="larentzos"><strong>(Larentzos)</strong> J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and

<p id="larentzos1"><strong>(Larentzos1)</strong> J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and

W.D. Mattson, &#8220;Parallel Implementation of Isothermal and Isoenergetic

Dissipative Particle Dynamics Using Shardlow-Like Splitting

Algorithms&#8221;, Comput. Phys. Commun., 185, 1987-1998 (2014).</p>

<p id="id1"><strong>(Larentzos)</strong> J.P. Larentzos, J.K. Brennan, J.D. Moore, and

<p id="larentzos2"><strong>(Larentzos2)</strong> J.P. Larentzos, J.K. Brennan, J.D. Moore, and

W.D. Mattson, &#8220;LAMMPS Implementation of Constant Energy Dissipative

Particle Dynamics (DPD-E)&#8221;, ARL-TR-6863, U.S. Army Research

Laboratory, Aberdeen Proving Ground, MD (2014).</p>

doc/html/neb.html

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@@ -166,8 +166,8 @@ and last are the end points of the transition path.</p> 
of the energy barrier associated with a transition state, e.g. for an

atom to perform a diffusive hop from one energy basin to another in a

coordinated fashion with its neighbors.  The implementation in LAMMPS

follows the discussion in these 3 papers: <a class="reference internal" href="#henkelman1"><span class="std std-ref">(Henkelman1)</span></a>,

<a class="reference internal" href="#henkelman2"><span class="std std-ref">(Henkelman2)</span></a>, and <a class="reference internal" href="#nakano"><span class="std std-ref">(Nakano)</span></a>.</p>

follows the discussion in these 3 papers: <a class="reference internal" href="#henkelmana"><span class="std std-ref">(HenkelmanA)</span></a>,

<a class="reference internal" href="#henkelmanb"><span class="std std-ref">(HenkelmanB)</span></a>, and <a class="reference internal" href="#nakano"><span class="std std-ref">(Nakano)</span></a>.</p>

<p>Each replica runs on a partition of one or more processors.  Processor

partitions are defined at run-time using the -partition command-line

switch; see <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">Section 2.7</span></a> of the
@@ -346,7 +346,7 @@ due to the inter-replica spring force added by the <a class="reference internal" 
is selected and the inter-replica forces on it are converted to a

force that drives its atom coordinates to the top or saddle point of

the barrier, via the barrier-climbing calculation described in

<a class="reference internal" href="#henkelman2"><span class="std std-ref">(Henkelman2)</span></a>.  As before, the other replicas rearrange

<a class="reference internal" href="#henkelmanb"><span class="std std-ref">(HenkelmanB)</span></a>.  As before, the other replicas rearrange

themselves along the MEP so as to be roughly equally spaced.</p>

<p>When both stages are complete, if the NEB calculation was successful,

one of the replicas should be an atomic configuration at the top or
@@ -510,8 +510,8 @@ for more info on packages.</p> 
<p><a class="reference internal" href="prd.html"><span class="doc">prd</span></a>, <a class="reference internal" href="temper.html"><span class="doc">temper</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, <a class="reference internal" href="fix_viscous.html"><span class="doc">fix viscous</span></a></p>

<p><strong>Default:</strong> none</p>

<hr class="docutils" />

<p id="henkelman1"><strong>(Henkelman1)</strong> Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).</p>

<p id="henkelman2"><strong>(Henkelman2)</strong> Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,

<p id="henkelmana"><strong>(HenkelmanA)</strong> Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).</p>

<p id="henkelmanb"><strong>(HenkelmanB)</strong> Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,

9901-9904 (2000).</p>

<p id="nakano"><strong>(Nakano)</strong> Nakano, Comp Phys Comm, 178, 280-289 (2008).</p>

</div>

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