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<title>fix adapt/fep command — LAMMPS 15 May 2015 version documentation</title>
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<li>fix adapt/fep command</li>
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<div class="section" id="fix-adapt-fep-command">
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<span id="index-0"></span><h1>fix adapt/fep command<a class="headerlink" href="#fix-adapt-fep-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 adapt/fep N attribute 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>adapt/fep = 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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I = type(s) to set parameter for
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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> or <em>after</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
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of a run
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<em>after</em> value = <em>no</em> or <em>yes</em>
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<em>no</em> = parameters are adapted at timestep N
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<em>yes</em> = parameters are adapted one timestep after N
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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 adapt/fep 1 pair soft a 1 1 v_prefactor
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fix 1 all adapt/fep 1 pair soft a 2* 3 v_prefactor
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fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
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fix 1 all adapt/fep 10 atom diameter 1 v_size
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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>Change or adapt one or more specific simulation attributes or settings
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over time as a simulation runs.</p>
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<p>This is an enhanced version of the <a class="reference internal" href="fix_adapt.html"><em>fix_adapt</em></a> command
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with two differences,</p>
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<ul class="simple">
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<li>It is possible to modify the charges of chosen atom types only,
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instead of scaling all the charges in the system.</li>
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<li>There is a new option <em>after</em> for better compatibility with “fix
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ave/time”.</li>
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</ul>
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<p>This version is suited for free energy calculations using
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<a class="reference internal" href="compute_ti.html"><em>compute_ti</em></a> or <a class="reference internal" href="compute_fep.html"><em>compute_fep</em></a>.</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. Internally,
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the parameters themselves are actually altered; 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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<p>If the <em>after</em> keyword is set to <em>yes</em>, then the parameters are
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changed one timestep after the multiple of N. In this manner, if a fix
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such as “fix ave/time” is used to calculate averages at every N
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timesteps, all the contributions to the average will be obtained with
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the same values of the parameters.</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"><em>pair_style</em></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"><em>pair_style</em></a> and
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<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></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"><em>pair_style hybrid or hybrid/overlay</em></a> is used, <em>pstyle</em> should be
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a sub-style name. For example, <em>pstyle</em> could be specified as “soft”
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or “lubricate”. The <em>pparam</em> argument is the name of the parameter to
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change. This is the current list of pair styles and parameters that
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can be varied by this fix. See the doc pages for individual pair
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styles and their energy formulas for the 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="51%" />
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<col width="31%" />
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<col width="18%" />
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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"><em>born</em></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"><em>buck</em></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"><em>coul/cut</em></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"><em>coul/debye</em></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"><em>coul/long</em></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"><em>lj/cut</em></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"><em>lj/expand</em></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"><em>lubricate</em></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"><em>gauss</em></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_soft.html"><em>soft</em></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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</tbody>
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</table>
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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">It is easy to add new potentials and their parameters
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to this list. All it typically takes is adding an extract() method to
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the 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"><em>pair_style lubricate</em></a>.
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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"><em>pair_style soft</em></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"><em>coul/cut</em></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"><em>Buckingham potential</em></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"><em>pair_coeff command</em></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"><em>pair_style hybrid or hybrid/overlay</em></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"><em>pair_coeff</em></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"><em>equal-style variable</em></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"><em>thermo_style</em></a> command keywords for the
|
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simulation box parameters and timestep and elapsed time. Thus it is
|
|
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"><em>run</em></a> command and the
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|
<em>elaplong</em> keyword of <a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></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"><em>pair_style soft</em></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-python"><div class="highlight"><pre>variable prefactor equal ramp(10,30)
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fix 1 all adapt 1 pair soft a * * v_prefactor
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</pre></div>
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</div>
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<hr class="docutils" />
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<p>The <em>kspace</em> keyword used the specified variable as a scale factor on
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the energy, forces, virial calculated by whatever K-Space solver is
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defined by the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command. If the
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variable has a value of 1.0, then the solver is unaltered.</p>
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<p>The <em>kspace</em> keyword works this way whether the <em>scale</em> keyword
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is set to <em>no</em> or <em>yes</em>.</p>
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<hr class="docutils" />
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<p>The <em>atom</em> keyword enables various atom properties to be changed. The
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<em>aparam</em> argument is the name of the parameter to change. This is the
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current list of atom parameters that can be varied by this fix:</p>
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<ul class="simple">
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<li>charge = charge on particle</li>
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<li>diameter = diameter of particle</li>
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</ul>
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<p>The <em>I</em> argument indicates which atom types are affected. A wild-card
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asterisk can be used in place of or in conjunction with the I argument
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to set the coefficients for multiple atom types.</p>
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<p>The <em>v_name</em> argument of the <em>atom</em> keyword is the name of an
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<a class="reference internal" href="variable.html"><em>equal-style variable</em></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. See the
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discussion above describing the formulas associated with equal-style
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variables. The new value is assigned to the corresponding attribute
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for all atoms in the fix group.</p>
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<p>If the atom parameter is <em>diameter</em> and per-atom density and per-atom
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mass are defined for particles (e.g. <a class="reference internal" href="atom_style.html"><em>atom_style granular</em></a>), then the mass of each particle is also
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changed when the diameter changes (density is assumed to stay
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constant).</p>
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<p>For example, these commands would shrink the diameter of all granular
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particles in the “center” group from 1.0 to 0.1 in a linear fashion
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over the course of a 1000-step simulation:</p>
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<div class="highlight-python"><div class="highlight"><pre>variable size equal ramp(1.0,0.1)
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fix 1 center adapt 10 atom diameter * v_size
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</pre></div>
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</div>
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<p>For <a class="reference internal" href="run_style.html"><em>rRESPA time integration</em></a>, this fix changes
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parameters on the outermost rRESPA level.</p>
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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. No global or per-atom quantities are stored
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by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. No parameter of this fix can
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be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><em>run</em></a> command.
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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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<blockquote>
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<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="compute_fep.html"><em>compute fep</em></a>, <a class="reference internal" href="fix_adapt.html"><em>fix_adapt</em></a>, <a class="reference internal" href="compute_ti.html"><em>compute ti</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 are scale = no, reset = no, after = no.</p>
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