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<div class="section" id="fix-eos-table-rx-command">
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<span id="index-0"></span><h1>fix eos/table/rx 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">eos</span><span class="o">/</span><span class="n">table</span><span class="o">/</span><span class="n">rx</span> <span class="n">style</span> <span class="n">file1</span> <span class="n">N</span> <span class="n">keyword</span> <span class="n">file2</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>eos/table/rx = style name of this fix command</li>
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<li>style = <em>linear</em> = method of interpolation</li>
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<li>file1 = filename containing the tabulated equation of state</li>
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<li>N = use N values in <em>linear</em> tables</li>
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<li>keyword = name of table keyword correponding to table file</li>
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<li>file2 = filename containing the heats of formation of each species</li>
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</ul>
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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">eos</span><span class="o">/</span><span class="n">table</span><span class="o">/</span><span class="n">rx</span> <span class="n">linear</span> <span class="n">eos</span><span class="o">.</span><span class="n">table</span> <span class="mi">10000</span> <span class="n">KEYWORD</span> <span class="n">thermo</span><span class="o">.</span><span class="n">table</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>Fix <em>eos/table/rx</em> applies a tabulated mesoparticle equation
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of state to relate the concentration-dependent particle internal
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energy (u_i) to the particle internal temperature (dpdTheta_i).</p>
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<p>The concentration-dependent particle internal energy (u_i) is
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computed according to the following relation:</p>
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<img alt="_images/fix_eos_table_rx.jpg" class="align-center" src="_images/fix_eos_table_rx.jpg" />
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<p>where <em>m</em> is the number of species, <em>c_i,j</em> is the concentration of
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species <em>j</em> in particle <em>i</em>, <em>u_j</em> is the internal energy of species j,
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<em>DeltaH_f,j</em> is the heat of formation of species <em>j</em>, N is the number of
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molecules represented by the coarse-grained particle, kb is the
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Boltzmann constant, and T is the temperature of the system.</p>
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<p>Fix <em>eos/table/rx</em> creates interpolation tables of length <em>N</em> from <em>m</em>
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internal energy values of each species <em>u_j</em> listed in a file as a
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function of internal temperature. During a simulation, these tables
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are used to interpolate internal energy or temperature values as needed.
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The interpolation is done with the <em>linear</em> style. For the <em>linear</em> style,
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the internal temperature is used to find 2 surrounding table values from
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which an internal energy is computed by linear interpolation. A secant
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solver is used to determine the internal temperature from the internal energy.</p>
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<p>The first filename specifies a file containing tabulated internal
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temperature and <em>m</em> internal energy values for each species <em>u_j</em>.
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The keyword specifies a section of the file. The format of this
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file is described below.</p>
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<p>The second filename specifies a file containing heat of formation
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<em>DeltaH_f,j</em> for each species.</p>
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<hr class="docutils" />
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<p>The format of a tabulated file is as follows (without the
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parenthesized comments):</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># EOS TABLE (one or more comment or blank lines)</span>
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</pre></div>
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</div>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">KEYWORD</span> <span class="p">(</span><span class="n">keyword</span> <span class="ow">is</span> <span class="n">first</span> <span class="n">text</span> <span class="n">on</span> <span class="n">line</span><span class="p">)</span>
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<span class="n">N</span> <span class="mi">500</span> <span class="n">h2</span> <span class="n">no2</span> <span class="n">n2</span> <span class="o">...</span> <span class="n">no</span> <span class="p">(</span><span class="n">N</span> <span class="n">parameter</span> <span class="n">species1</span> <span class="n">species2</span> <span class="o">...</span> <span class="n">speciesN</span><span class="p">)</span>
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<span class="p">(</span><span class="n">blank</span><span class="p">)</span>
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<span class="mi">1</span> <span class="mf">1.00</span> <span class="mf">0.000</span> <span class="o">...</span> <span class="mf">0.0000</span> <span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">internal</span> <span class="n">temperature</span><span class="p">,</span> <span class="n">internal</span> <span class="n">energy</span> <span class="n">of</span> <span class="n">species</span> <span class="mi">1</span><span class="p">,</span> <span class="o">...</span><span class="p">,</span> <span class="n">internal</span> <span class="n">energy</span> <span class="n">of</span> <span class="n">species</span> <span class="n">m</span><span class="p">)</span>
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<span class="mi">2</span> <span class="mf">1.02</span> <span class="mf">0.001</span> <span class="o">...</span> <span class="mf">0.0002</span>
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<span class="o">...</span>
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<span class="mi">500</span> <span class="mf">10.0</span> <span class="mf">0.500</span> <span class="o">...</span> <span class="mf">1.0000</span>
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</pre></div>
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</div>
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<p>A section begins with a non-blank line whose 1st character is not a
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“#”; blank lines or lines starting with “#” can be used as comments
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between sections. The first line begins with a keyword which
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identifies the section. The line can contain additional text, but the
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initial text must match the argument specified in the fix command.</p>
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<p>The next line lists the number of table entries and the species names
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that correspond with all the species listed in the reaction equations
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through the <em>fix rx</em> command.
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The parameter “N” is required and its value is the number of table
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entries that follow. Let Nfile = “N” in the tabulated file.
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What LAMMPS does is a preliminary interpolation by creating splines
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using the Nfile tabulated values as nodal points.</p>
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<p>Following a blank line, the next N lines list the tabulated values.
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On each line, the 1st value is the index from 1 to N, the 2nd value is
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the internal temperature (in temperature units), the 3rd value until
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the <em>m+3</em> value are the internal energies of the m species (in energy units).</p>
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<p>Note that all internal temperature and internal energy values must
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increase from one line to the next.</p>
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<p>Note that one file can contain many sections, each with a tabulated
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potential. LAMMPS reads the file section by section until it finds
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one that matches the specified keyword.</p>
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<hr class="docutils" />
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<p>The format of a heat of formation file is as follows (without the
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parenthesized comments):</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># HEAT OF FORMATION TABLE (one or more comment or blank lines)</span>
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</pre></div>
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</div>
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<div class="highlight-default"><div class="highlight"><pre><span></span> <span class="p">(</span><span class="n">blank</span><span class="p">)</span>
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<span class="n">h2</span> <span class="mf">0.00</span> <span class="p">(</span><span class="n">species</span> <span class="n">name</span><span class="p">,</span> <span class="n">heat</span> <span class="n">of</span> <span class="n">formation</span><span class="p">)</span>
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<span class="n">no2</span> <span class="mf">0.34</span>
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<span class="n">n2</span> <span class="mf">0.00</span>
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<span class="o">...</span>
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<span class="n">no</span> <span class="mf">0.93</span>
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</pre></div>
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</div>
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<p>Note that the species can be listed in any order. The tag that is
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used as the species name must correspond with the tags used to define
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the reactions with the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command.</p>
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</div>
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<hr class="docutils" />
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<div class="section" id="restrictions">
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<h2>Restrictions</h2>
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<p>This command is part of the USER-DPD package. It is only enabled if
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LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
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<p>This command also requires use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a>
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command.</p>
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<p>The equation of state must be a monotonically increasing function.</p>
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<p>An error will occur if the internal temperature or internal energies
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are not within the table cutoffs.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands</h2>
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<p><a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a>,
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<span class="xref doc">pair dpd/fdt</span></p>
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<p><strong>Default:</strong> none</p>
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