forked from lijiext/lammps
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<li>fix qeq/point command</li>
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<div class="section" id="fix-qeq-point-command">
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<span id="index-0"></span><h1>fix qeq/point command</h1>
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</div>
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<div class="section" id="fix-qeq-shielded-command">
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<h1>fix qeq/shielded command</h1>
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</div>
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<div class="section" id="fix-qeq-slater-command">
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<h1>fix qeq/slater command</h1>
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</div>
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<div class="section" id="fix-qeq-dynamic-command">
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<h1>fix qeq/dynamic command</h1>
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</div>
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<div class="section" id="fix-qeq-fire-command">
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<h1>fix qeq/fire 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">style</span> <span class="n">Nevery</span> <span class="n">cutoff</span> <span class="n">tolerance</span> <span class="n">maxiter</span> <span class="n">qfile</span> <span class="n">keyword</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>style = <em>qeq/point</em> or <em>qeq/shielded</em> or <em>qeq/slater</em> or <em>qeq/dynamic</em> or <em>qeq/fire</em></li>
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<li>Nevery = perform charge equilibration every this many steps</li>
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<li>cutoff = global cutoff for charge-charge interactions (distance unit)</li>
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<li>tolerance = precision to which charges will be equilibrated</li>
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<li>maxiter = maximum iterations to perform charge equilibration</li>
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<li>qfile = a filename with QEq parameters</li>
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<li>zero or more keyword/value pairs may be appended</li>
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<li>keyword = <em>alpha</em> or <em>qdamp</em> or <em>qstep</em></li>
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</ul>
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<pre class="literal-block">
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<em>alpha</em> value = Slater type orbital exponent (qeq/slater only)
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<em>qdamp</em> value = damping factor for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
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<em>qstep</em> value = time step size for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
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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">qeq</span><span class="o">/</span><span class="n">point</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mf">1.0e-6</span> <span class="mi">200</span> <span class="n">param</span><span class="o">.</span><span class="n">qeq1</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="n">qeq</span> <span class="n">qeq</span><span class="o">/</span><span class="n">shielded</span> <span class="mi">1</span> <span class="mi">8</span> <span class="mf">1.0e-6</span> <span class="mi">100</span> <span class="n">param</span><span class="o">.</span><span class="n">qeq2</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qeq</span><span class="o">/</span><span class="n">slater</span> <span class="mi">5</span> <span class="mi">10</span> <span class="mf">1.0e-6</span> <span class="mi">100</span> <span class="n">params</span> <span class="n">alpha</span> <span class="mf">0.2</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="n">qeq</span> <span class="n">qeq</span><span class="o">/</span><span class="n">dynamic</span> <span class="mi">1</span> <span class="mi">12</span> <span class="mf">1.0e-3</span> <span class="mi">100</span> <span class="n">my_qeq</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qeq</span><span class="o">/</span><span class="n">fire</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mf">1.0e-3</span> <span class="mi">100</span> <span class="n">my_qeq</span> <span class="n">qdamp</span> <span class="mf">0.2</span> <span class="n">qstep</span> <span class="mf">0.1</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>Perform the charge equilibration (QEq) method as described in <a class="reference internal" href="fix_qeq_reax.html#rappe"><span class="std std-ref">(Rappe and Goddard)</span></a> and formulated in <a class="reference internal" href="neb.html#nakano"><span class="std std-ref">(Nakano)</span></a> (also known
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as the matrix inversion method) and in <a class="reference internal" href="pair_smtbq.html#rick"><span class="std std-ref">(Rick and Stuart)</span></a> (also
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known as the extended Lagrangian method) based on the
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electronegativity equilization principle.</p>
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<p>These fixes can be used with any <a class="reference internal" href="pair_style.html"><span class="doc">pair style</span></a> in
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LAMMPS, so long as per-atom charges are defined. The most typical
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use-case is in conjunction with a <a class="reference internal" href="pair_style.html"><span class="doc">pair style</span></a> that
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performs charge equilibration periodically (e.g. every timestep), such
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as the ReaxFF or Streitz-Mintmire potential.
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But these fixes can also be used with
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potentials that normally assume per-atom charges are fixed, e.g. a
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<a class="reference internal" href="pair_buck.html"><span class="doc">Buckingham</span></a> or <a class="reference internal" href="pair_lj.html"><span class="doc">LJ/Coulombic</span></a> potential.</p>
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<p>Because the charge equilibration calculation is effectively
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independent of the pair style, these fixes can also be used to perform
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a one-time assignment of charges to atoms. For example, you could
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define the QEq fix, perform a zero-timestep run via the <a class="reference internal" href="run.html"><span class="doc">run</span></a>
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command without any pair style defined which would set per-atom
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charges (based on the current atom configuration), then remove the fix
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via the <a class="reference internal" href="unfix.html"><span class="doc">unfix</span></a> command before performing further dynamics.</p>
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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">Computing and using charge values different from published
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values defined for a fixed-charge potential like Buckingham or CHARMM
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or AMBER, can have a strong effect on energies and forces, and
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produces a different model than the published versions.</p>
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</div>
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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">The <a class="reference internal" href="fix_qeq_comb.html"><span class="doc">fix qeq/comb</span></a> command must still be used
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to perform charge equliibration with the <a class="reference internal" href="pair_comb.html"><span class="doc">COMB potential</span></a>. The <a class="reference internal" href="fix_qeq_reax.html"><span class="doc">fix qeq/reax</span></a>
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command can be used to perform charge equilibration with the <a class="reference internal" href="pair_reax_c.html"><span class="doc">ReaxFF force field</span></a>, although fix qeq/shielded yields the
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same results as fix qeq/reax if <em>Nevery</em>, <em>cutoff</em>, and <em>tolerance</em>
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are the same. Eventually the fix qeq/reax command will be deprecated.</p>
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</div>
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<p>The QEq method minimizes the electrostatic energy of the system (or
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equalizes the derivative of energy with respect to charge of all the
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atoms) by adjusting the partial charge on individual atoms based on
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interactions with their neighbors within <em>cutoff</em>. It reqires a few
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parameters, in <em>metal</em> units, for each atom type which provided in a
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file specified by <em>qfile</em>. The file has the following format</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">1</span> <span class="n">chi</span> <span class="n">eta</span> <span class="n">gamma</span> <span class="n">zeta</span> <span class="n">qcore</span>
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<span class="mi">2</span> <span class="n">chi</span> <span class="n">eta</span> <span class="n">gamma</span> <span class="n">zeta</span> <span class="n">qcore</span>
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<span class="o">...</span>
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<span class="n">Ntype</span> <span class="n">chi</span> <span class="n">eta</span> <span class="n">gamma</span> <span class="n">zeta</span> <span class="n">qcore</span>
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</pre></div>
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</div>
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<p>There is one line per atom type with the following parameters.
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Only a subset of the parameters is used by each QEq style as descibed
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below, thus the others can be set to 0.0 if desired.</p>
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<ul class="simple">
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<li><em>chi</em> = electronegativity in energy units</li>
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<li><em>eta</em> = self-Coulomb potential in energy units</li>
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<li><em>gamma</em> = shielded Coulomb constant defined by <a class="reference internal" href="#vanduin"><span class="std std-ref">ReaxFF force field</span></a> in distance units</li>
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<li><em>zeta</em> = Slater type orbital exponent defined by the <a class="reference internal" href="pair_coul.html#streitz"><span class="std std-ref">Streitz-Mintmire</span></a> potential in reverse distance units</li>
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<li><em>qcore</em> = charge of the nucleus defined by the <a class="reference internal" href="pair_coul.html#streitz"><span class="std std-ref">Streitz-Mintmire potential</span></a> potential in charge units</li>
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</ul>
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<p>The <em>qeq/point</em> style describes partial charges on atoms as point
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charges. Interaction between a pair of charged particles is 1/r,
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which is the simplest description of the interaction between charges.
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Only the <em>chi</em> and <em>eta</em> parameters from the <em>qfile</em> file are used.
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Note that Coulomb catastrophe can occur if repulsion between the pair
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of charged particles is too weak. This style solves partial charges
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on atoms via the matrix inversion method. A tolerance of 1.0e-6 is
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usually a good number.</p>
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<p>The <em>qeq/shielded</em> style describes partial charges on atoms also as
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point charges, but uses a shielded Coulomb potential to describe the
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interaction between a pair of charged particles. Interaction through
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the shielded Coulomb is given by equation (13) of the <a class="reference internal" href="#vanduin"><span class="std std-ref">ReaxFF force field</span></a> paper. The shielding accounts for charge overlap
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between charged particles at small separation. This style is the same
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as <a class="reference internal" href="fix_qeq_reax.html"><span class="doc">fix qeq/reax</span></a>, and can be used with <a class="reference internal" href="pair_reax_c.html"><span class="doc">pair_style reax/c</span></a>. Only the <em>chi</em>, <em>eta</em>, and <em>gamma</em>
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parameters from the <em>qfile</em> file are used. This style solves partial
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charges on atoms via the matrix inversion method. A tolerance of
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1.0e-6 is usually a good number.</p>
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<p>The <em>qeq/slater</em> style describes partial charges on atoms as spherical
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charge densities centered around atoms via the Slater 1<em>s</em> orbital, so
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that the interaction between a pair of charged particles is the
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product of two Slater 1<em>s</em> orbitals. The expression for the Slater
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1<em>s</em> orbital is given under equation (6) of the
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<a class="reference internal" href="pair_coul.html#streitz"><span class="std std-ref">Streitz-Mintmire</span></a> paper. Only the <em>chi</em>, <em>eta</em>, <em>zeta</em>, and
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<em>qcore</em> parameters from the <em>qfile</em> file are used. This style solves
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partial charges on atoms via the matrix inversion method. A tolerance
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of 1.0e-6 is usually a good number. Keyword <em>alpha</em> can be used to
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change the Slater type orbital exponent.</p>
|
||
|
|
<p>The <em>qeq/dynamic</em> style describes partial charges on atoms as point
|
||
|
|
charges that interact through 1/r, but the extended Lagrangian method
|
||
|
|
is used to solve partial charges on atoms. Only the <em>chi</em> and <em>eta</em>
|
||
|
|
parameters from the <em>qfile</em> file are used. Note that Coulomb
|
||
|
|
catastrophe can occur if repulsion between the pair of charged
|
||
|
|
particles is too weak. A tolerance of 1.0e-3 is usually a good
|
||
|
|
number. Keyword <em>qdamp</em> can be used to change the damping factor, while
|
||
|
|
keyword <em>qstep</em> can be used to change the time step size.</p>
|
||
|
|
<p>The <a class="reference internal" href="#shan"><span class="std std-ref">*qeq/fire*</span></a> style describes the same charge model and charge
|
||
|
|
solver as the <em>qeq/dynamic</em> style, but employs a FIRE minimization
|
||
|
|
algorithm to solve for equilibrium charges.
|
||
|
|
Keyword <em>qdamp</em> can be used to change the damping factor, while
|
||
|
|
keyword <em>qstep</em> can be used to change the time step size.</p>
|
||
|
|
<p>Note that <em>qeq/point</em>, <em>qeq/shielded</em>, and <em>qeq/slater</em> describe
|
||
|
|
different charge models, whereas the matrix inversion method and the
|
||
|
|
extended Lagrangian method (<em>qeq/dynamic</em> and <em>qeq/fire</em>) are
|
||
|
|
different solvers.</p>
|
||
|
|
<p>Note that <em>qeq/point</em>, <em>qeq/dynamic</em> and <em>qeq/fire</em> styles all describe
|
||
|
|
charges as point charges that interact through 1/r relationship, but
|
||
|
|
solve partial charges on atoms using different solvers. These three
|
||
|
|
styles should yield comparable results if
|
||
|
|
the QEq parameters and <em>Nevery</em>, <em>cutoff</em>, and <em>tolerance</em> are the
|
||
|
|
same. Style <em>qeq/point</em> is typically faster, <em>qeq/dynamic</em> scales
|
||
|
|
better on larger sizes, and <em>qeq/fire</em> is faster than <em>qeq/dynamic</em>.</p>
|
||
|
|
<div class="admonition note">
|
||
|
|
<p class="first admonition-title">Note</p>
|
||
|
|
<p class="last">To avoid the evaluation of the derivative of charge with respect
|
||
|
|
to position, which is typically ill-defined, the system should have a
|
||
|
|
zero net charge.</p>
|
||
|
|
</div>
|
||
|
|
<div class="admonition note">
|
||
|
|
<p class="first admonition-title">Note</p>
|
||
|
|
<p class="last">Developing QEq parameters (chi, eta, gamma, zeta, and qcore) is
|
||
|
|
non-trivial. Charges on atoms are not guaranteed to equilibrate with
|
||
|
|
arbitrary choices of these parameters. We do not develop these QEq
|
||
|
|
paramters. See the examples/qeq directory for some examples.</p>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
<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 these fixes is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. No global scalar or vector or per-atom
|
||
|
|
quantities are stored by these fixes 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 these fixes
|
||
|
|
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.</p>
|
||
|
|
<p>Thexe fixes are invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
|
||
|
|
</div>
|
||
|
|
<div class="section" id="restrictions">
|
||
|
|
<h2>Restrictions</h2>
|
||
|
|
<p>These fixes are part of the QEQ package. They are only enabled if
|
||
|
|
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>
|
||
|
|
</div>
|
||
|
|
<div class="section" id="related-commands">
|
||
|
|
<h2>Related commands</h2>
|
||
|
|
<p><a class="reference internal" href="fix_qeq_reax.html"><span class="doc">fix qeq/reax</span></a>, <a class="reference internal" href="fix_qeq_comb.html"><span class="doc">fix qeq/comb</span></a></p>
|
||
|
|
<p><strong>Default:</strong> none</p>
|
||
|
|
<hr class="docutils" />
|
||
|
|
<p id="rappe"><strong>(Rappe and Goddard)</strong> A. K. Rappe and W. A. Goddard III, J Physical
|
||
|
|
Chemistry, 95, 3358-3363 (1991).</p>
|
||
|
|
<p id="nakano"><strong>(Nakano)</strong> A. Nakano, Computer Physics Communications, 104, 59-69 (1997).</p>
|
||
|
|
<p id="rick"><strong>(Rick and Stuart)</strong> S. W. Rick, S. J. Stuart, B. J. Berne, J Chemical Physics
|
||
|
|
101, 16141 (1994).</p>
|
||
|
|
<p id="streitz"><strong>(Streitz-Mintmire)</strong> F. H. Streitz, J. W. Mintmire, Physical Review B, 50,
|
||
|
|
16, 11996 (1994)</p>
|
||
|
|
<p id="vanduin"><strong>(ReaxFF)</strong> A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J
|
||
|
|
Physical Chemistry, 105, 9396-9049 (2001)</p>
|
||
|
|
<p id="shan"><strong>(QEq/Fire)</strong> T.-R. Shan, A. P. Thompson, S. J. Plimpton, in preparation</p>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
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<p>
|
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</p>
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