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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<div class="section" id="fix-indent-command">
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<span id="index-0"></span><h1>fix indent command<a class="headerlink" href="#fix-indent-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 indent K keyword values ...
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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>indent = style name of this fix command</li>
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<li>K = force constant for indenter surface (force/distance^2 units)</li>
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<li>one or more keyword/value pairs may be appended</li>
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<li>keyword = <em>sphere</em> or <em>cylinder</em> or <em>plane</em> or <em>side</em> or <em>units</em></li>
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</ul>
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<pre class="literal-block">
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<em>sphere</em> args = x y z R
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x,y,z = initial position of center of indenter (distance units)
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R = sphere radius of indenter (distance units)
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any of x,y,z,R can be a variable (see below)
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<em>cylinder</em> args = dim c1 c2 R
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dim = <em>x</em> or <em>y</em> or <em>z</em> = axis of cylinder
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c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
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R = cylinder radius of indenter (distance units)
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any of c1,c2,R can be a variable (see below)
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<em>plane</em> args = dim pos side
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dim = <em>x</em> or <em>y</em> or <em>z</em> = plane perpendicular to this dimension
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pos = position of plane in dimension x, y, or z (distance units)
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pos can be a variable (see below)
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side = <em>lo</em> or <em>hi</em>
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<em>side</em> value = <em>in</em> or <em>out</em>
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<em>in</em> = the indenter acts on particles inside the sphere or cylinder
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<em>out</em> = the indenter acts on particles outside the sphere or cylinder
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<em>units</em> value = <em>lattice</em> or <em>box</em>
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lattice = the geometry is defined in lattice units
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box = the geometry 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 1 all indent 10.0 sphere 0.0 0.0 15.0 3.0
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fix 1 all indent 10.0 sphere v_x v_y 0.0 v_radius side in
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fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box
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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>Insert an indenter within a simulation box. The indenter repels all
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atoms in the group that touch it, so it can be used to push into a
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material or as an obstacle in a flow. Or it can be used as a
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constraining wall around a simulation; see the discussion of the
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<em>side</em> keyword below.</p>
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<p>The indenter can either be spherical or cylindrical or planar. You
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must set one of those 3 keywords.</p>
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<p>A spherical indenter exerts a force of magnitude</p>
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<div class="highlight-python"><div class="highlight"><pre><span class="n">F</span><span class="p">(</span><span class="n">r</span><span class="p">)</span> <span class="o">=</span> <span class="o">-</span> <span class="n">K</span> <span class="p">(</span><span class="n">r</span> <span class="o">-</span> <span class="n">R</span><span class="p">)</span><span class="o">^</span><span class="mi">2</span>
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</pre></div>
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</div>
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<p>on each atom where <em>K</em> is the specified force constant, <em>r</em> is the
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distance from the atom to the center of the indenter, and <em>R</em> is the
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radius of the indenter. The force is repulsive and F(r) = 0 for <em>r</em> >
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<em>R</em>.</p>
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<p>A cylindrical indenter exerts the same force, except that <em>r</em> is the
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distance from the atom to the center axis of the cylinder. The
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cylinder extends infinitely along its axis.</p>
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<p>Spherical and cylindrical indenters account for periodic boundaries in
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two ways. First, the center point of a spherical indenter (x,y,z) or
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axis of a cylindrical indenter (c1,c2) is remapped back into the
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simulation box, if the box is periodic in a particular dimension.
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This occurs every timestep if the indenter geometry is specified with
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a variable (see below), e.g. it is moving over time. Second, the
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calculation of distance to the indenter center or axis accounts for
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periodic boundaries. Both of these mean that an indenter can
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effectively move through and straddle one or more periodic boundaries.</p>
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<p>A planar indenter is really an axis-aligned infinite-extent wall
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exerting the same force on atoms in the system, where <em>R</em> is the
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position of the plane and <em>r-R</em> is the distance from the plane. If
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the <em>side</em> parameter of the plane is specified as <em>lo</em> then it will
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indent from the lo end of the simulation box, meaning that atoms with
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a coordinate less than the plane’s current position will be pushed
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towards the hi end of the box and atoms with a coordinate higher than
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the plane’s current position will feel no force. Vice versa if <em>side</em>
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is specified as <em>hi</em>.</p>
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<p>Any of the 4 quantities defining a spherical indenter’s geometry can
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be specified as an equal-style <a class="reference internal" href="variable.html"><em>variable</em></a>, namely <em>x</em>,
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<em>y</em>, <em>z</em>, or <em>R</em>. Similarly, for a cylindrical indenter, any of <em>c1</em>,
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<em>c2</em>, or <em>R</em>, can be a variable. For a planar indenter, <em>pos</em> can be
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a variable. If the value is a variable, it should be specified as
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v_name, where name is the variable name. In this case, the variable
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will be evaluated each timestep, and its value used to define the
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indenter geometry.</p>
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<p>Note that equal-style variables can specify formulas with various
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mathematical functions, and include <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a>
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command keywords for the simulation box parameters and timestep and
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elapsed time. Thus it is easy to specify indenter properties that
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change as a function of time or span consecutive runs in a continuous
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fashion. For the latter, see the <em>start</em> and <em>stop</em> keywords of the
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<a class="reference internal" href="run.html"><em>run</em></a> command and the <em>elaplong</em> keyword of <a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> for details.</p>
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<p>For example, if a spherical indenter’s x-position is specfied as v_x,
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then this variable definition will keep it’s center at a relative
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position in the simulation box, 1/4 of the way from the left edge to
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the right edge, even if the box size changes:</p>
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<div class="highlight-python"><div class="highlight"><pre>variable x equal "xlo + 0.25*lx"
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</pre></div>
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</div>
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<p>Similarly, either of these variable definitions will move the indenter
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from an initial position at 2.5 at a constant velocity of 5:</p>
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<div class="highlight-python"><div class="highlight"><pre>variable x equal "2.5 + 5*elaplong*dt"
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variable x equal vdisplace(2.5,5)
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</pre></div>
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</div>
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<p>If a spherical indenter’s radius is specified as v_r, then these
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variable definitions will grow the size of the indenter at a specfied
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rate.</p>
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<div class="highlight-python"><div class="highlight"><pre>variable r0 equal 0.0
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variable rate equal 1.0
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variable r equal "v_r0 + step*dt*v_rate"
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</pre></div>
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</div>
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<p>If the <em>side</em> keyword is specified as <em>out</em>, which is the default,
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then particles outside the indenter are pushded away from its outer
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surface, as described above. This only applies to spherical or
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cylindrical indenters. If the <em>side</em> keyword is specified as <em>in</em>,
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the action of the indenter is reversed. Particles inside the indenter
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are pushed away from its inner surface. In other words, the indenter
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is now a containing wall that traps the particles inside it. If the
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radius shrinks over time, it will squeeze the particles.</p>
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<p>The <em>units</em> keyword determines the meaning of the distance units used
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to define the indenter geometry. A <em>box</em> value selects standard
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distance units as defined by the <a class="reference internal" href="units.html"><em>units</em></a> command,
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e.g. Angstroms for units = real or metal. A <em>lattice</em> value means the
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distance units are in lattice spacings. The <a class="reference internal" href="lattice.html"><em>lattice</em></a>
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command must have been previously used to define the lattice spacing.
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The (x,y,z) coords of the indenter position are scaled by the x,y,z
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lattice spacings respectively. The radius of a spherical or
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cylindrical indenter is scaled by the x lattice spacing.</p>
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<p>Note that the units keyword only affects indenter geometry parameters
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specified directly with numbers, not those specified as variables. In
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the latter case, you should use the <em>xlat</em>, <em>ylat</em>, <em>zlat</em> keywords of
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the <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command if you want to include
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lattice spacings in a variable formula.</p>
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<p>The force constant <em>K</em> is not affected by the <em>units</em> keyword. It is
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always in force/distance^2 units where force and distance are defined
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by the <a class="reference internal" href="units.html"><em>units</em></a> command. If you wish K to be scaled by the
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lattice spacing, you can define K with a variable whose formula
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contains <em>xlat</em>, <em>ylat</em>, <em>zlat</em> keywords of the
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<a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command, e.g.</p>
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<div class="highlight-python"><div class="highlight"><pre>variable k equal 100.0/xlat/xlat
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fix 1 all indent $k sphere ...
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</pre></div>
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</div>
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</div>
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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
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fix to add the energy of interaction between atoms and the indenter to
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the system’s potential energy as part of <a class="reference internal" href="thermo_style.html"><em>thermodynamic output</em></a>. The energy of each particle interacting
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with the indenter is K/3 (r - R)^3.</p>
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<p>This fix computes a global scalar energy and a global 3-vector of
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forces (on the indenter), which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The scalar and vector values
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calculated by this fix are “extensive”.</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. Note that if you
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define the indenter geometry with a variable using a time-dependent
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formula, LAMMPS uses the iteration count in the minimizer as the
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timestep. But it is almost certainly a bad idea to have the indenter
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change its position or size during a minimization. LAMMPS does not
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check if you have done this.</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/indenter interaction energy to be included
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in the total potential energy of the system (the quantity being
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minimized), you must enable the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em>
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option for this fix.</p>
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</div>
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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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<blockquote>
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<div>none</div></blockquote>
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<p><strong>Related commands:</strong> none</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 are side = out and units = lattice.</p>
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