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<div class="section" id="fix-wall-lj93-command">
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<span id="index-0"></span><h1>fix wall/lj93 command<a class="headerlink" href="#fix-wall-lj93-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="fix-wall-lj126-command">
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<h1>fix wall/lj126 command<a class="headerlink" href="#fix-wall-lj126-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="fix-wall-lj1043-command">
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<h1>fix wall/lj1043 command<a class="headerlink" href="#fix-wall-lj1043-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="fix-wall-colloid-command">
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<h1>fix wall/colloid command<a class="headerlink" href="#fix-wall-colloid-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="fix-wall-harmonic-command">
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<h1>fix wall/harmonic command<a class="headerlink" href="#fix-wall-harmonic-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 style face args ... 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>style = <em>wall/lj93</em> or <em>wall/lj126</em> or <em>wall/lj1043</em> or <em>wall/colloid</em> or <em>wall/harmonic</em></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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args = coord epsilon sigma cutoff
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coord = position of wall = EDGE or constant or variable
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EDGE = current lo or hi 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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epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
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epsilon can be a variable (see below)
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sigma = size factor for wall-particle interaction (distance units)
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sigma can be a variable (see below)
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cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
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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> or <em>fld</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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<em>fld</em> value = <em>yes</em> or <em>no</em>
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<em>yes</em> = invoke the wall constraint to be compatible with implicit FLD
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<em>no</em> = invoke the wall constraint in the normal way
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<em>pbc</em> value = <em>yes</em> or <em>no</em>
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<em>yes</em> = allow periodic boundary in a wall dimension
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<em>no</em> = require non-perioidic boundaries in any wall dimension
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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 wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box
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fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5
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fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5
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fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858
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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 domain on one or more of its faces with a flat
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wall that interacts with the atoms in the group by generating a force
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on the atom in a direction perpendicular to the wall. The energy of
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wall-particle interactions depends on the style.</p>
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<p>For style <em>wall/lj93</em>, the energy E is given by the 9/3 potential:</p>
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<img alt="_images/fix_wall_lj93.jpg" class="align-center" src="_images/fix_wall_lj93.jpg" />
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<p>For style <em>wall/lj126</em>, the energy E is given by the 12/6 potential:</p>
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<img alt="_images/pair_lj.jpg" class="align-center" src="_images/pair_lj.jpg" />
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<p>For style <em>wall/lj1043</em>, the energy E is given by the 10/4/3 potential:</p>
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<img alt="_images/fix_wall_lj1043.jpg" class="align-center" src="_images/fix_wall_lj1043.jpg" />
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<p>For style <em>wall/colloid</em>, the energy E is given by an integrated form
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of the <a class="reference internal" href="pair_colloid.html"><em>pair_style colloid</em></a> potential:</p>
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<img alt="_images/fix_wall_colloid.jpg" class="align-center" src="_images/fix_wall_colloid.jpg" />
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<p>For style <em>wall/harmonic</em>, the energy E is given by a harmonic spring
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potential:</p>
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<img alt="_images/fix_wall_harmonic.jpg" class="align-center" src="_images/fix_wall_harmonic.jpg" />
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<p>In all cases, <em>r</em> is the distance from the particle to the wall at
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position <em>coord</em>, and Rc is the <em>cutoff</em> distance at which the
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particle and wall no longer interact. The energy of the wall
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potential is shifted so that the wall-particle interaction energy is
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0.0 at the cutoff distance.</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 interacts with
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particles near the lower side of the simulation box in that dimension.
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A <em>hi</em> face interacts with particles near the upper side of the
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simulation box in that dimension.</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. See examples below.</p>
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<p>For the <em>wall/lj93</em> and <em>wall/lj126</em> and <em>wall/lj1043</em> styles,
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<em>epsilon</em> and <em>sigma</em> are the usual Lennard-Jones parameters, which
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determine the strength and size of the particle as it interacts with
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the wall. Epsilon has energy units. Note that this <em>epsilon</em> and
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<em>sigma</em> may be different than any <em>epsilon</em> or <em>sigma</em> values defined
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for a pair style that computes particle-particle interactions.</p>
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<p>The <em>wall/lj93</em> interaction is derived by integrating over a 3d
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half-lattice of Lennard-Jones 12/6 particles. The <em>wall/lj126</em>
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interaction is effectively a harder, more repulsive wall interaction.
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The <em>wall/lj1043</em> interaction is yet a different form of wall
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interaction, described in Magda et al in <a class="reference internal" href="#magda"><span>(Magda)</span></a>.</p>
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<p>For the <em>wall/colloid</em> style, <em>R</em> is the radius of the colloid
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particle, <em>D</em> is the distance from the surface of the colloid particle
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to the wall (r-R), and <em>sigma</em> is the size of a constituent LJ
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particle inside the colloid particle and wall. Note that the cutoff
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distance Rc in this case is the distance from the colloid particle
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center to the wall. The prefactor <em>epsilon</em> can be thought of as an
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effective Hamaker constant with energy units for the strength of the
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colloid-wall interaction. More specifically, the <em>epsilon</em> pre-factor
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= 4 * pi^2 * rho_wall * rho_colloid * epsilon * sigma^6, where epsilon
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and sigma are the LJ parameters for the constituent LJ
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particles. Rho_wall and rho_colloid are the number density of the
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constituent particles, in the wall and colloid respectively, in units
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of 1/volume.</p>
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<p>The <em>wall/colloid</em> interaction is derived by integrating over
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constituent LJ particles of size <em>sigma</em> within the colloid particle
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and a 3d half-lattice of Lennard-Jones 12/6 particles of size <em>sigma</em>
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in the wall. As mentioned in the preceeding paragraph, the density of
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particles in the wall and colloid can be different, as specified by
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the <em>epsilon</em> pre-factor.</p>
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<p>For the <em>wall/harmonic</em> style, <em>epsilon</em> is effectively the spring
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constant K, and has units (energy/distance^2). The input parameter
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<em>sigma</em> is ignored. The minimum energy position of the harmonic
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spring is at the <em>cutoff</em>. This is a repulsive-only spring since the
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interaction is truncated at the <em>cutoff</em></p>
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<p>For any wall, the <em>epsilon</em> and/or <em>sigma</em> parameter can be specified
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as an <a class="reference internal" href="variable.html"><em>equal-style variable</em></a>, in which case it should be
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specified as v_name, where name is the variable name. As with a
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variable wall position, the variable is evaluated each timestep and
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the result becomes the current epsilon or sigma of the wall.
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Equal-style variables can specify formulas with various mathematical
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functions, and include <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command
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keywords for the simulation box parameters and timestep and elapsed
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time. Thus it is easy to specify a time-dependent wall interaction.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">For all of the styles, you must insure that r is always > 0 for
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all particles in the group, or LAMMPS will generate an error. This
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means you cannot start your simulation with particles at the wall
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position <em>coord</em> (r = 0) or with particles on the wrong side of the
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wall (r < 0). For the <em>wall/lj93</em> and <em>wall/lj126</em> styles, the energy
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of the wall/particle interaction (and hence the force on the particle)
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blows up as r -> 0. The <em>wall/colloid</em> style is even more
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restrictive, since the energy blows up as D = r-R -> 0. This means
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the finite-size particles of radius R must be a distance larger than R
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from the wall position <em>coord</em>. The <em>harmonic</em> style is a softer
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potential and does not blow up as r -> 0, but you must use a large
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enough <em>epsilon</em> that particles always reamin on the correct side of
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the wall (r > 0).</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 or
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variable is used. It is not relevant when EDGE is used to specify a
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face position. In the variable case, the variable is assumed to
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produce a value compatible with the <em>units</em> setting you specify.</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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<p>The <em>fld</em> keyword can be used with a <em>yes</em> setting to invoke the wall
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constraint before pairwise interactions are computed. This allows an
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implicit FLD model using <a class="reference internal" href="pair_lubricateU.html"><em>pair_style lubricateU</em></a>
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to include the wall force in its calculations. If the setting is
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<em>no</em>, wall forces are imposed after pairwise interactions, in the
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usual manner.</p>
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<p>The <em>pbc</em> keyword can be used with a <em>yes</em> setting to allow walls to
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be specified in a periodic dimension. See the
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<a class="reference internal" href="boundary.html"><em>boundary</em></a> command for options on simulation box
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boundaries. The default for <em>pbc</em> is <em>no</em>, which means the system
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must be non-periodic when using a wall. But you may wish to use a
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periodic box. E.g. to allow some particles to interact with the wall
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via the fix group-ID, and others to pass through it and wrap around a
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periodic box. In this case you should insure that the wall if
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sufficiently far enough away from the box boundary. If you do not,
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then particles may interact with both the wall and with periodic
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images on the other side of the box, which is probably not what you
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want.</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>. The wall interaction parameters (epsilon,
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sigma) could be varied with additional variable definitions.</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 xlo v_ramp 1.0 1.0 2.5
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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 xlo v_linear 1.0 1.0 2.5
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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 xlo v_wiggle 1.0 1.0 2.5
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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 xlo v_wiggle 1.0 1.0 2.5
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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 vdisplace(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>.</p>
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<p>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> option is supported by this
|
|
fix to add the energy of interaction between atoms and each wall to
|
|
the system’s potential energy as part of <a class="reference internal" href="thermo_style.html"><em>thermodynamic output</em></a>.</p>
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<p>This fix computes a global scalar energy and a global vector of
|
|
forces, which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. Note that the scalar energy is
|
|
the sum of interactions with all defined walls. If you want the
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|
energy on a per-wall basis, you need to use multiple fix wall
|
|
commands. The length of the vector is equal to the number of walls
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|
defined by the fix. Each vector value is the normal force on a
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|
specific wall. Note that an outward force on a wall will be a
|
|
negative value for <em>lo</em> walls and a positive value for <em>hi</em> walls.
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The scalar and vector values 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
|
|
the <a class="reference internal" href="run.html"><em>run</em></a> command.</p>
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<p>The forces due to this fix are imposed during an energy minimization,
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|
invoked by the <a class="reference internal" href="minimize.html"><em>minimize</em></a> command.</p>
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<div class="admonition note">
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|
<p class="first admonition-title">Note</p>
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|
<p class="last">If you want the atom/wall interaction energy to be included in
|
|
the total potential energy of the system (the quantity being
|
|
minimized), you MUST enable the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em>
|
|
option for this fix.</p>
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</div>
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</div>
|
|
<div class="section" id="restrictions">
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|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
|
<blockquote>
|
|
<div>none</div></blockquote>
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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_wall_reflect.html"><em>fix wall/reflect</em></a>,
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|
<a class="reference internal" href="fix_wall_gran.html"><em>fix wall/gran</em></a>,
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|
<a class="reference internal" href="fix_wall_region.html"><em>fix wall/region</em></a></p>
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</div>
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|
<div class="section" id="default">
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|
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
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|
<p>The option defaults units = lattice, fld = no, and pbc = no.</p>
|
|
<hr class="docutils" />
|
|
<p id="magda"><strong>(Magda)</strong> Magda, Tirrell, Davis, J Chem Phys, 83, 1888-1901 (1985);
|
|
erratum in JCP 84, 2901 (1986).</p>
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|
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