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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li>fix adapt command</li>
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<div class="section" id="fix-adapt-command">
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<span id="index-0"></span><h1>fix adapt command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<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">adapt</span> <span class="n">N</span> <span class="n">attribute</span> <span class="n">args</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
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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"><span class="doc">fix</span></a> command</li>
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<li>adapt = style name of this fix command</li>
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<li>N = adapt simulation settings every this many timesteps</li>
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<li>one or more attribute/arg pairs may be appended</li>
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<li>attribute = <em>pair</em> or <em>kspace</em> or <em>atom</em></li>
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</ul>
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<pre class="literal-block">
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<em>pair</em> args = pstyle pparam I J v_name
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pstyle = pair style name, e.g. lj/cut
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pparam = parameter to adapt over time
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I,J = type pair(s) to set parameter for
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v_name = variable with name that calculates value of pparam
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<em>kspace</em> arg = v_name
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v_name = variable with name that calculates scale factor on K-space terms
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<em>atom</em> args = aparam v_name
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aparam = parameter to adapt over time
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v_name = variable with name that calculates value of aparam
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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>scale</em> or <em>reset</em></li>
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</ul>
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<pre class="literal-block">
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<em>scale</em> value = <em>no</em> or <em>yes</em>
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<em>no</em> = the variable value is the new setting
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<em>yes</em> = the variable value multiplies the original setting
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<em>reset</em> value = <em>no</em> or <em>yes</em>
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<em>no</em> = values will remain altered at the end of a run
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<em>yes</em> = reset altered values to their original values at the end of a run
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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</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">soft</span> <span class="n">a</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">v_prefactor</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">soft</span> <span class="n">a</span> <span class="mi">2</span><span class="o">*</span> <span class="mi">3</span> <span class="n">v_prefactor</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="n">epsilon</span> <span class="o">*</span> <span class="o">*</span> <span class="n">v_scale1</span> <span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="n">scale</span> <span class="mi">3</span> <span class="mi">3</span> <span class="n">v_scale2</span> <span class="n">scale</span> <span class="n">yes</span> <span class="n">reset</span> <span class="n">yes</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span> <span class="mi">10</span> <span class="n">atom</span> <span class="n">diameter</span> <span class="n">v_size</span>
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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</h2>
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<p>Change or adapt one or more specific simulation attributes or settings
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over time as a simulation runs. Pair potential and K-space and atom
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attributes which can be varied by this fix are discussed below. Many
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other fixes can also be used to time-vary simulation parameters,
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e.g. the “fix deform” command will change the simulation box
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size/shape and the “fix move” command will change atom positions and
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velocities in a prescribed manner. Also note that many commands allow
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variables as arguments for specific parameters, if described in that
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manner on their doc pages. An equal-style variable can calculate a
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time-dependent quantity, so this is another way to vary a simulation
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parameter over time.</p>
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<p>If <em>N</em> is specified as 0, the specified attributes are only changed
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once, before the simulation begins. This is all that is needed if the
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associated variables are not time-dependent. If <em>N</em> > 0, then changes
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are made every <em>N</em> steps during the simulation, presumably with a
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variable that is time-dependent.</p>
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<p>Depending on the value of the <em>reset</em> keyword, attributes changed by
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this fix will or will not be reset back to their original values at
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the end of a simulation. Even if <em>reset</em> is specified as <em>yes</em>, a
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restart file written during a simulation will contain the modified
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settings.</p>
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<p>If the <em>scale</em> keyword is set to <em>no</em>, then the value the parameter is
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set to will be whatever the variable generates. If the <em>scale</em>
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keyword is set to <em>yes</em>, then the value of the altered parameter will
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be the initial value of that parameter multiplied by whatever the
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variable generates. I.e. the variable is now a “scale factor” applied
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in (presumably) a time-varying fashion to the parameter.</p>
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<p>Note that whether scale is <em>no</em> or <em>yes</em>, internally, the parameters
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themselves are actually altered by this fix. Make sure you use the
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<em>reset yes</em> option if you want the parameters to be restored to their
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initial values after the run.</p>
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<hr class="docutils" />
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<p>The <em>pair</em> keyword enables various parameters of potentials defined by
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the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> command to be changed, if the pair
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style supports it. Note that the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> and
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<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> commands must be used in the usual manner
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to specify these parameters initially; the fix adapt command simply
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overrides the parameters.</p>
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<p>The <em>pstyle</em> argument is the name of the pair style. If <a class="reference internal" href="pair_hybrid.html"><span class="doc">pair_style hybrid or hybrid/overlay</span></a> is used, <em>pstyle</em> should be
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a sub-style name. If there are multiple sub-styles using the same
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pair style, then <em>pstyle</em> should be specified as “style:N” where N is
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which instance of the pair style you wish to adapt, e.g. the first,
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second, etc. For example, <em>pstyle</em> could be specified as “soft” or
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“lubricate” or “lj/cut:1” or “lj/cut:2”. The <em>pparam</em> argument is the
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name of the parameter to change. This is the current list of pair
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styles and parameters that can be varied by this fix. See the doc
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pages for individual pair styles and their energy formulas for the
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meaning of these parameters:</p>
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<table border="1" class="docutils">
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<colgroup>
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<col width="49%" />
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<col width="35%" />
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<col width="17%" />
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td><a class="reference internal" href="pair_born.html"><span class="doc">born</span></a></td>
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<td>a,b,c</td>
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<td>type pairs</td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="pair_buck.html"><span class="doc">buck</span></a></td>
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<td>a,c</td>
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<td>type pairs</td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><span class="doc">coul/cut</span></a></td>
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<td>scale</td>
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<td>type pairs</td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="pair_coul.html"><span class="doc">coul/debye</span></a></td>
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<td>scale</td>
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<td>type pairs</td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><span class="doc">coul/long</span></a></td>
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<td>scale</td>
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<td>type pairs</td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="pair_lj.html"><span class="doc">lj/cut</span></a></td>
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<td>epsilon,sigma</td>
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<td>type pairs</td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="pair_lj_expand.html"><span class="doc">lj/expand</span></a></td>
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<td>epsilon,sigma,delta</td>
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<td>type pairs</td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="pair_lubricate.html"><span class="doc">lubricate</span></a></td>
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<td>mu</td>
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<td>global</td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="pair_gauss.html"><span class="doc">gauss</span></a></td>
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<td>a</td>
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<td>type pairs</td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="pair_morse.html"><span class="doc">morse</span></a></td>
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<td>d0,r0,alpha</td>
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<td>type pairs</td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="pair_soft.html"><span class="doc">soft</span></a></td>
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<td>a</td>
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<td>type pairs</td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="pair_kim.html"><span class="doc">kim</span></a></td>
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<td>PARAM_FREE_*&#58i,j,...</td>
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<td>global</td>
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</tr>
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</tbody>
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</table>
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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">It is easy to add new potentials and their parameters to this
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list. All it typically takes is adding an extract() method to the
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pair_*.cpp file associated with the potential.</p>
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</div>
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<p>Some parameters are global settings for the pair style, e.g. the
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viscosity setting “mu” for <a class="reference internal" href="pair_lubricate.html"><span class="doc">pair_style lubricate</span></a>.
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For <a class="reference internal" href="pair_kim.html"><span class="doc">pair_kim</span></a>, all free parameters supported by the
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KIM Model are available (e.g., PARAM_FREE_sigmas provided by the
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LennardJones612_Universal__MO_826355984548_001 Model). If the free
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parameter corresponds to an array, then the particular array element
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to be adapted must be specified (e.g., “PARAM_FREE_sigmas:10”, to
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adapt the tenth entry of the sigmas array).
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Other parameters apply to atom type pairs within the pair style,
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e.g. the prefactor “a” for <a class="reference internal" href="pair_soft.html"><span class="doc">pair_style soft</span></a>.</p>
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<p>Note that for many of the potentials, the parameter that can be varied
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is effectively a prefactor on the entire energy expression for the
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potential, e.g. the lj/cut epsilon. The parameters listed as “scale”
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are exactly that, since the energy expression for the
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<a class="reference internal" href="pair_coul.html"><span class="doc">coul/cut</span></a> potential (for example) has no labeled
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prefactor in its formula. To apply an effective prefactor to some
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potentials, multiple parameters need to be altered. For example, the
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<a class="reference internal" href="pair_buck.html"><span class="doc">Buckingham potential</span></a> needs both the A and C terms
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altered together. To scale the Buckingham potential, you should thus
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list the pair style twice, once for A and once for C.</p>
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<p>If a type pair parameter is specified, the <em>I</em> and <em>J</em> settings should
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be specified to indicate which type pairs to apply it to. If a global
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parameter is specified, the <em>I</em> and <em>J</em> settings still need to be
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specified, but are ignored.</p>
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<p>Similar to the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff command</span></a>, I and J can be
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specified in one of two ways. Explicit numeric values can be used for
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each, as in the 1st example above. I <= J is required. LAMMPS sets
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the coefficients for the symmetric J,I interaction to the same values.</p>
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<p>A wild-card asterisk can be used in place of or in conjunction with
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the I,J arguments to set the coefficients for multiple pairs of atom
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types. This takes the form “*” or “<em>n” or “n</em>” or “m*n”. If N = the
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number of atom types, then an asterisk with no numeric values means
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all types from 1 to N. A leading asterisk means all types from 1 to n
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(inclusive). A trailing asterisk means all types from n to N
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(inclusive). A middle asterisk means all types from m to n
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(inclusive). Note that only type pairs with I <= J are considered; if
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asterisks imply type pairs where J < I, they are ignored.</p>
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<p>IMPROTANT NOTE: If <a class="reference internal" href="pair_hybrid.html"><span class="doc">pair_style hybrid or hybrid/overlay</span></a> is being used, then the <em>pstyle</em> will
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be a sub-style name. You must specify I,J arguments that correspond
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to type pair values defined (via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a>
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command) for that sub-style.</p>
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<p>The <em>v_name</em> argument for keyword <em>pair</em> is the name of an
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<a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> which will be evaluated each time
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this fix is invoked to set the parameter to a new value. It should be
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specified as v_name, where name is the variable name. Equal-style
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variables can specify formulas with various mathematical functions,
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and include <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command keywords for the
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simulation box parameters and timestep and elapsed time. Thus it is
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easy to specify parameters that change as a function of time or span
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consecutive runs in a continuous fashion. For the latter, see the
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<em>start</em> and <em>stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command and the
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<em>elaplong</em> keyword of <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> for
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details.</p>
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<p>For example, these commands would change the prefactor coefficient of
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the <a class="reference internal" href="pair_soft.html"><span class="doc">pair_style soft</span></a> potential from 10.0 to 30.0 in a
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linear fashion over the course of a simulation:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">prefactor</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span><span class="mi">30</span><span class="p">)</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">soft</span> <span class="n">a</span> <span class="o">*</span> <span class="o">*</span> <span class="n">v_prefactor</span>
|
|
</pre></div>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p>The <em>kspace</em> keyword used the specified variable as a scale factor on
|
|
the energy, forces, virial calculated by whatever K-Space solver is
|
|
defined by the <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> command. If the
|
|
variable has a value of 1.0, then the solver is unaltered.</p>
|
|
<p>The <em>kspace</em> keyword works this way whether the <em>scale</em> keyword
|
|
is set to <em>no</em> or <em>yes</em>.</p>
|
|
<hr class="docutils" />
|
|
<p>The <em>atom</em> keyword enables various atom properties to be changed. The
|
|
<em>aparam</em> argument is the name of the parameter to change. This is the
|
|
current list of atom parameters that can be varied by this fix:</p>
|
|
<ul class="simple">
|
|
<li>charge = charge on particle</li>
|
|
<li>diameter = diameter of particle</li>
|
|
</ul>
|
|
<p>The <em>v_name</em> argument of the <em>atom</em> keyword is the name of an
|
|
<a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> which will be evaluated each time
|
|
this fix is invoked to set the parameter to a new value. It should be
|
|
specified as v_name, where name is the variable name. See the
|
|
discussion above describing the formulas associated with equal-style
|
|
variables. The new value is assigned to the corresponding attribute
|
|
for all atoms in the fix group.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">The <em>atom</em> keyword works this way whether the <em>scale</em> keyword is
|
|
set to <em>no</em> or <em>yes</em>. I.e. the use of scale yes is not yet supported
|
|
by the <em>atom</em> keyword.</p>
|
|
</div>
|
|
<p>If the atom parameter is <em>diameter</em> and per-atom density and per-atom
|
|
mass are defined for particles (e.g. <a class="reference internal" href="atom_style.html"><span class="doc">atom_style granular</span></a>), then the mass of each particle is also
|
|
changed when the diameter changes (density is assumed to stay
|
|
constant).</p>
|
|
<p>For example, these commands would shrink the diameter of all granular
|
|
particles in the “center” group from 1.0 to 0.1 in a linear fashion
|
|
over the course of a 1000-step simulation:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">size</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mf">1.0</span><span class="p">,</span><span class="mf">0.1</span><span class="p">)</span>
|
|
<span class="n">fix</span> <span class="mi">1</span> <span class="n">center</span> <span class="n">adapt</span> <span class="mi">10</span> <span class="n">atom</span> <span class="n">diameter</span> <span class="n">v_size</span>
|
|
</pre></div>
|
|
</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 this fix 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 this fix. No global or per-atom quantities are stored
|
|
by this fix 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 this fix 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.
|
|
This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
|
|
<p>For <a class="reference internal" href="run_style.html"><span class="doc">rRESPA time integration</span></a>, this fix changes
|
|
parameters on the outermost rRESPA level.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<blockquote>
|
|
<div>none</div></blockquote>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="compute_ti.html"><span class="doc">compute ti</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The option defaults are scale = no, reset = no.</p>
|
|
</div>
|
|
</div>
|
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