From efbee4a292d17e0c7fb0e0a3daf6e3af06487b37 Mon Sep 17 00:00:00 2001
From: Michael DeLyser <32076442+mdelyser@users.noreply.github.com>
Date: Wed, 2 May 2018 11:27:31 -0400
Subject: [PATCH] Delete man_fix_bocs.html
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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’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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