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<div class="section" id="fix-bocs-command">
<span id="index-0"></span><h1>fix bocs command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix ID group-ID bocs keyword values ...
keyword = <em>temp</em> or <em>cgiso</em> or <em>analytic</em> or <em>linear_spline</em> or <em>cubic_spline</em>
<em>temp</em> values = Tstart Tstop Tdamp
<em>cgiso</em> values = Pstart Pstop Pdamp
<em>basis set</em>
<em>analytic</em> values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
<em>linear_spline</em> values = input_filename
<em>cubic_spline</em> values = input_filename
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<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">bocs</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">100.0</span> <span class="n">cgiso</span> <span class="mf">0.986</span> <span class="mf">0.986</span> <span class="mf">1000.0</span> <span class="n">analytic</span> <span class="mf">66476.015</span> <span class="mi">968</span> <span class="mi">2</span> <span class="mf">245030.10</span> <span class="mf">8962.20</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">bocs</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">100.0</span> <span class="n">cgiso</span> <span class="mf">0.986</span> <span class="mf">0.986</span> <span class="mf">1000.0</span> <span class="n">cubic_spline</span> <span class="n">input_Fv</span><span class="o">.</span><span class="n">dat</span>
<span class="n">compute</span> <span class="n">bocsPress</span> <span class="nb">all</span> <span class="n">pressureBocs</span> <span class="n">thermo_temp</span>
<span class="n">thermo_modify</span> <span class="n">press</span> <span class="n">bocsPress</span>
<span class="n">fix_modify</span> <span class="mi">1</span> <span class="n">press</span> <span class="n">bocsPress</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>These commands incorporate a pressure correction as described by
Dunn and Noid in <a class="reference internal" href="#bocs-dunn1"><span class="std std-ref">(Dunn1)</span></a> to the standard MTTK
barostat by Martyna et. al. in <a class="reference internal" href="#bocs-martyna"><span class="std std-ref">(Martyna)</span></a> .
The first half of the command mimics a standard fix npt command:</p>
<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">bocs</span> <span class="n">temp</span> <span class="n">Tstart</span> <span class="n">Tstop</span> <span class="n">Tcoupl</span> <span class="n">cgiso</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
</pre></div>
</div>
<p>The two differences are replacing <em>npt</em> with <em>bocs</em>, and replacing
<em>iso</em>/<em>aniso</em>/<em>etc</em> with <em>cgiso</em>.
The rest of the command details what form you would like to use for
the pressure correction equation. The choices are: <em>analytic</em>, <em>linear_spline</em>,
or <em>cubic_spline</em>.</p>
<p>With either spline method, the only argument that needs to follow it
is the name of a file that contains the desired pressure correction
as a function of volume. The file should be formatted so each line has:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Volume_i</span><span class="p">,</span> <span class="n">PressureCorrection_i</span>
</pre></div>
</div>
<p>Note both the COMMA and the SPACE separating the volume&#8217;s
value and its corresponding pressure correction. The volumes in the file
should be uniformly spaced. Both the volumes and the pressure corrections
should be provided in the proper units, e.g. if you are using <em>units real</em>,
the volumes should all be in cubic angstroms, and the pressure corrections
should all be in atomspheres. Furthermore, the table should start/end at a
volume considerably smaller/larger than you expect your system to sample
during the simulation. If the system ever reaches a volume outside of the
range provided, the simulation will stop.</p>
<p>With the <em>analytic</em> option, the arguments are as follows:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">...</span> <span class="n">analytic</span> <span class="n">V_avg</span> <span class="n">N_particles</span> <span class="n">N_coeff</span> <span class="n">Coeff_1</span> <span class="n">Coeff_2</span> <span class="o">...</span> <span class="n">Coeff_N</span>
</pre></div>
</div>
<p>Note that <em>V_avg</em> and <em>Coeff_i</em> should all be in the proper units, e.g. if you
are using <em>units real</em>, <em>V_avg</em> should be in cubic angstroms, and the
coefficients should all be in atmospheres * cubic angstroms.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>As this is computing a (modified) pressure, group-ID should be <em>all</em>.</p>
<p>The pressure correction has only been tested for use with an isotropic
pressure coupling in 3 dimensions.</p>
<p>There are three additional commands that must be supplied along with fix
bocs. They are given in the examples section. The name <em>bocsPress</em> can be
changed for any name of your choosing, provided it remains consistent across
all three commands. Additionally, the ID <em>1</em> in the <em>fix_modify</em> command must
match up with the <em>ID</em> specified in the original <em>fix bocs</em> command. Everything else
in those three commands must be unchanged. The first two commands can be
specified before the <em>fix bocs</em> command, but the <em>fix_modify</em> command must be
given after the original <em>fix bocs</em> command.</p>
<p>The <em>compute</em> command tells LAMMPS to compute the pressure using the modified
barostat.</p>
<p>The <em>thermo_modify</em> command tells LAMMPS to report the pressure from the modified
barostat instead of the default pressure, i.e. thermo_press.</p>
<p>The <em>fix_modify</em> command tells LAMMPS to use the pressure from the modified
barostat for the fix, instead of using the default presure, i.e. thermo_press.</p>
<p><strong>Related:</strong></p>
<p>For more details about the pressure correction and the entire BOCS software
package, visit the <a class="reference external" href="https://github.com/noid-group/BOCS">BOCS package on github</a> and read the release
paper by Dunn et. al. <a class="reference internal" href="#bocs-dunn2"><span class="std std-ref">(Dunn2)</span></a> .</p>
<hr class="docutils" />
<p id="bocs-dunn1"><strong>(Dunn1)</strong> Dunn and Noid, J Chem Phys, 143, 243148 (2015).</p>
<p id="bocs-martyna"><strong>(Martyna)</strong> Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).</p>
<p id="bocs-dunn2"><strong>(Dunn2)</strong> Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).</p>
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