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<title>fix wall/srd command — LAMMPS 15 May 2015 version documentation</title>
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<div class="section" id="fix-wall-srd-command">
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<span id="index-0"></span><h1>fix wall/srd command<a class="headerlink" href="#fix-wall-srd-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID wall/srd face arg ... keyword value ...
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
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<li>wall/srd = style name of this fix command</li>
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<li>one or more face/arg pairs may be appended</li>
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<li>face = <em>xlo</em> or <em>xhi</em> or <em>ylo</em> or <em>yhi</em> or <em>zlo</em> or <em>zhi</em></li>
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</ul>
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<pre class="literal-block">
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<em>xlo</em>,*ylo*,*zlo* arg = EDGE or constant or variable
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EDGE = current lo edge of simulation box
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constant = number like 0.0 or -30.0 (distance units)
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variable = <a class="reference internal" href="variable.html"><em>equal-style variable</em></a> like v_x or v_wiggle
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<em>xhi</em>,*yhi*,*zhi* arg = EDGE or constant or variable
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EDGE = current hi edge of simulation box
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constant = number like 50.0 or 100.3 (distance units)
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variable = <a class="reference internal" href="variable.html"><em>equal-style variable</em></a> like v_x or v_wiggle
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</pre>
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<ul class="simple">
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<li>zero or more keyword/value pairs may be appended</li>
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<li>keyword = <em>units</em></li>
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</ul>
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<pre class="literal-block">
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<em>units</em> value = <em>lattice</em> or <em>box</em>
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<em>lattice</em> = the wall position is defined in lattice units
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<em>box</em> = the wall position is defined in simulation box units
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix xwalls all wall/srd xlo EDGE xhi EDGE
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fix walls all wall/srd xlo 0.0 ylo 10.0 units box
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fix top all wall/srd zhi v_pressdown
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Bound the simulation with one or more walls which interact with
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stochastic reaction dynamics (SRD) particles as slip (smooth) or
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no-slip (rough) flat surfaces. The wall interaction is actually
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invoked via the <a class="reference internal" href="fix_srd.html"><em>fix srd</em></a> command, only on the group of
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SRD particles it defines, so the group setting for the fix wall/srd
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command is ignored.</p>
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<p>A particle/wall collision occurs if an SRD particle moves outside the
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wall on a timestep. This alters the position and velocity of the SRD
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particle and imparts a force to the wall.</p>
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<p>The <em>collision</em> and <em>Tsrd</em> settings specified via the <a class="reference internal" href="fix_srd.html"><em>fix srd</em></a> command affect the SRD/wall collisions. A <em>slip</em>
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setting for the <em>collision</em> keyword means that the tangential
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component of the SRD particle momentum is preserved. Thus only a
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normal force is imparted to the wall. The normal component of the new
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SRD velocity is sampled from a Gaussian distribution at temperature
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<em>Tsrd</em>.</p>
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<p>For a <em>noslip</em> setting of the <em>collision</em> keyword, both the normal and
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tangential components of the new SRD velocity are sampled from a
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Gaussian distribution at temperature <em>Tsrd</em>. Additionally, a new
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tangential direction for the SRD velocity is chosen randomly. This
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collision style imparts both a normal and tangential force to the
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wall.</p>
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<p>Up to 6 walls or faces can be specified in a single command: <em>xlo</em>,
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<em>xhi</em>, <em>ylo</em>, <em>yhi</em>, <em>zlo</em>, <em>zhi</em>. A <em>lo</em> face reflects particles
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that move to a coordinate less than the wall position, back in the
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<em>hi</em> direction. A <em>hi</em> face reflects particles that move to a
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coordinate higher than the wall position, back in the <em>lo</em> direction.</p>
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<p>The position of each wall can be specified in one of 3 ways: as the
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EDGE of the simulation box, as a constant value, or as a variable. If
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EDGE is used, then the corresponding boundary of the current
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simulation box is used. If a numeric constant is specified then the
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wall is placed at that position in the appropriate dimension (x, y, or
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z). In both the EDGE and constant cases, the wall will never move.
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If the wall position is a variable, it should be specified as v_name,
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where name is an <a class="reference internal" href="variable.html"><em>equal-style variable</em></a> name. In this
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case the variable is evaluated each timestep and the result becomes
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the current position of the reflecting wall. Equal-style variables
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can specify formulas with various mathematical functions, and include
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<a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command keywords for the simulation
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box parameters and timestep and elapsed time. Thus it is easy to
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specify a time-dependent wall position.</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">Because the trajectory of the SRD particle is tracked
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as it collides with the wall, you must insure that r = distance of the
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particle from the wall, is always > 0 for SRD particles, or LAMMPS
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will generate an error. This means you cannot start your simulation
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with SRD particles at the wall position <em>coord</em> (r = 0) or with
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particles on the wrong side of the wall (r < 0).</p>
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</div>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">If you have 2 or more walls that come together at an
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edge or corner (e.g. walls in the x and y dimensions), then be sure to
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set the <em>overlap</em> keyword to <em>yes</em> in the <a class="reference internal" href="fix_srd.html"><em>fix srd</em></a>
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command, since the walls effectively overlap when SRD particles
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collide with them. LAMMPS will issue a warning if you do not do this.</p>
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</div>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">The walls of this fix only interact with SRD
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particles, as defined by the <a class="reference internal" href="fix_srd.html"><em>fix srd</em></a> command. If you
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are simulating a mixture containing other kinds of particles, then you
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should typically use <a class="reference internal" href="fix_wall.html"><em>another wall command</em></a> to act on
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the other particles. Since SRD particles will be colliding both with
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the walls and the other particles, it is important to insure that the
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other particle’s finite extent does not overlap an SRD wall. If you
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do not do this, you may generate errors when SRD particles end up
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“inside” another particle or a wall at the beginning of a collision
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step.</p>
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</div>
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<p>The <em>units</em> keyword determines the meaning of the distance units used
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to define a wall position, but only when a numeric constant is used.
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It is not relevant when EDGE or a variable is used to specify a face
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position.</p>
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<p>A <em>box</em> value selects standard distance units as defined by the
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<a class="reference internal" href="units.html"><em>units</em></a> command, e.g. Angstroms for units = real or metal.
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A <em>lattice</em> value means the distance units are in lattice spacings.
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The <a class="reference internal" href="lattice.html"><em>lattice</em></a> command must have been previously used to
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define the lattice spacings.</p>
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<hr class="docutils" />
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<p>Here are examples of variable definitions that move the wall position
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in a time-dependent fashion using equal-style
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<a class="reference internal" href="variable.html"><em>variables</em></a>.</p>
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<div class="highlight-python"><div class="highlight"><pre>variable ramp equal ramp(0,10)
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fix 1 all wall/srd xlo v_ramp
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>variable linear equal vdisplace(0,20)
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fix 1 all wall/srd xlo v_linear
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>variable wiggle equal swiggle(0.0,5.0,3.0)
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fix 1 all wall/srd xlo v_wiggle
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>variable wiggle equal cwiggle(0.0,5.0,3.0)
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fix 1 all wall/srd xlo v_wiggle
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</pre></div>
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</div>
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<p>The ramp(lo,hi) function adjusts the wall position linearly from lo to
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hi over the course of a run. The displace(c0,velocity) function does
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something similar using the equation position = c0 + velocity*delta,
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where delta is the elapsed time.</p>
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<p>The swiggle(c0,A,period) function causes the wall position to
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oscillate sinusoidally according to this equation, where omega = 2 PI
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/ period:</p>
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<div class="highlight-python"><div class="highlight"><pre>position = c0 + A sin(omega*delta)
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</pre></div>
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</div>
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<p>The cwiggle(c0,A,period) function causes the wall position to
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oscillate sinusoidally according to this equation, which will have an
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initial wall velocity of 0.0, and thus may impose a gentler
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perturbation on the particles:</p>
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<div class="highlight-python"><div class="highlight"><pre><span class="n">position</span> <span class="o">=</span> <span class="n">c0</span> <span class="o">+</span> <span class="n">A</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">cos</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">))</span>
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</pre></div>
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</div>
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</div>
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<hr class="docutils" />
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<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
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<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
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<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options
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are relevant to this fix.</p>
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<p>This fix computes a global array of values which can be accessed by
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various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The number of
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rows in the array is equal to the number of walls defined by the fix.
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The number of columns is 3, for the x,y,z components of force on each
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wall.</p>
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<p>Note that an outward normal force on a wall will be a negative value
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for <em>lo</em> walls and a positive value for <em>hi</em> walls. The array values
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calculated by this fix are “extensive”.</p>
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<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
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the <a class="reference internal" href="run.html"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<p>Any dimension (xyz) that has an SRD wall must be non-periodic.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="fix_srd.html"><em>fix srd</em></a></p>
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<p><strong>Default:</strong> none</p>
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</div>
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