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<li>pair_style hbond/dreiding/lj command</li>
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<div class="section" id="pair-style-hbond-dreiding-lj-command">
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<span id="index-0"></span><h1>pair_style hbond/dreiding/lj command</h1>
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</div>
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<div class="section" id="pair-style-hbond-dreiding-lj-omp-command">
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<h1>pair_style hbond/dreiding/lj/omp command</h1>
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</div>
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<div class="section" id="pair-style-hbond-dreiding-morse-command">
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<h1>pair_style hbond/dreiding/morse command</h1>
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</div>
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<div class="section" id="pair-style-hbond-dreiding-morse-omp-command">
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<h1>pair_style hbond/dreiding/morse/omp 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">pair_style</span> <span class="n">style</span> <span class="n">N</span> <span class="n">inner_distance_cutoff</span> <span class="n">outer_distance_cutoff</span> <span class="n">angle_cutof</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li>style = <em>hbond/dreiding/lj</em> or <em>hbond/dreiding/morse</em></li>
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<li>n = cosine angle periodicity</li>
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<li>inner_distance_cutoff = global inner cutoff for Donor-Acceptor interactions (distance units)</li>
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<li>outer_distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)</li>
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<li>angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor</li>
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<li>interactions (degrees)</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">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span> <span class="n">hbond</span><span class="o">/</span><span class="n">dreiding</span><span class="o">/</span><span class="n">lj</span> <span class="mi">4</span> <span class="mf">9.0</span> <span class="mf">11.0</span> <span class="mi">90</span>
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<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">hbond</span><span class="o">/</span><span class="n">dreiding</span><span class="o">/</span><span class="n">lj</span> <span class="mi">3</span> <span class="n">i</span> <span class="mf">9.5</span> <span class="mf">2.75</span> <span class="mi">4</span> <span class="mf">9.0</span> <span class="mf">11.0</span> <span class="mf">90.0</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">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span> <span class="n">hbond</span><span class="o">/</span><span class="n">dreiding</span><span class="o">/</span><span class="n">morse</span> <span class="mi">2</span> <span class="mf">9.0</span> <span class="mf">11.0</span> <span class="mi">90</span>
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<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">hbond</span><span class="o">/</span><span class="n">dreiding</span><span class="o">/</span><span class="n">morse</span> <span class="mi">3</span> <span class="n">i</span> <span class="mf">3.88</span> <span class="mf">1.7241379</span> <span class="mf">2.9</span> <span class="mi">2</span> <span class="mi">9</span> <span class="mi">11</span> <span class="mi">90</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>The <em>hbond/dreiding</em> styles compute the Acceptor-Hydrogen-Donor (AHD)
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3-body hydrogen bond interaction for the
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<a class="reference internal" href="Section_howto.html#howto-4"><span class="std std-ref">DREIDING</span></a> force field, given by:</p>
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<img alt="_images/pair_hbond_dreiding.jpg" class="align-center" src="_images/pair_hbond_dreiding.jpg" />
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<p>where Rin is the inner spline distance cutoff, Rout is the outer
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distance cutoff, theta_c is the angle cutoff, and n is the cosine
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periodicity.</p>
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<p>Here, <em>r</em> is the radial distance between the donor (D) and acceptor
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(A) atoms and <em>theta</em> is the bond angle between the acceptor, the
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hydrogen (H) and the donor atoms:</p>
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<img alt="_images/dreiding_hbond.jpg" class="align-center" src="_images/dreiding_hbond.jpg" />
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<p>These 3-body interactions can be defined for pairs of acceptor and
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donor atoms, based on atom types. For each donor/acceptor atom pair,
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the 3rd atom in the interaction is a hydrogen permanently bonded to
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the donor atom, e.g. in a bond list read in from a data file via the
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<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command. The atom types of possible
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hydrogen atoms for each donor/acceptor type pair are specified by the
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<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command (see below).</p>
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<p>Style <em>hbond/dreiding/lj</em> is the original DREIDING potential of
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<a class="reference internal" href="#pair-mayo"><span class="std std-ref">(Mayo)</span></a>. It uses a LJ 12/10 functional for the Donor-Acceptor
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interactions. To match the results in the original paper, use n = 4.</p>
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<p>Style <em>hbond/dreiding/morse</em> is an improved version using a Morse
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potential for the Donor-Acceptor interactions. <a class="reference internal" href="#liu"><span class="std std-ref">(Liu)</span></a> showed
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that the Morse form gives improved results for Dendrimer simulations,
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when n = 2.</p>
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<p>See this <a class="reference internal" href="Section_howto.html#howto-4"><span class="std std-ref">howto section</span></a> of the manual for
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more information on the DREIDING forcefield.</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">Because the Dreiding hydrogen bond potential is only one portion
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of an overall force field which typically includes other pairwise
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interactions, it is common to use it as a sub-style in a <a class="reference internal" href="pair_hybrid.html"><span class="doc">pair_style hybrid/overlay</span></a> command, where another pair style
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provides the repulsive core interaction between pairs of atoms, e.g. a
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1/r^12 Lennard-Jones repulsion.</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">When using the hbond/dreiding pair styles with <a class="reference internal" href="pair_hybrid.html"><span class="doc">pair_style hybrid/overlay</span></a>, you should explicitly define pair
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interactions between the donor atom and acceptor atoms, (as well as
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between these atoms and ALL other atoms in your system). Whenever
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<a class="reference internal" href="pair_hybrid.html"><span class="doc">pair_style hybrid/overlay</span></a> is used, ordinary mixing
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rules are not applied to atoms like the donor and acceptor atoms
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because they are typically referenced in multiple pair styles.
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Neglecting to do this can cause difficult-to-detect physics problems.</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">In the original Dreiding force field paper 1-4 non-bonded
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interactions ARE allowed. If this is desired for your model, use the
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special_bonds command (e.g. “special_bonds lj 0.0 0.0 1.0”) to turn
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these interactions on.</p>
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</div>
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<hr class="docutils" />
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<p>The following coefficients must be defined for pairs of eligible
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donor/acceptor types via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as
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in the examples above.</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">Unlike other pair styles and their associated
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<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> commands, you do not need to specify
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pair_coeff settings for all possible I,J type pairs. Only I,J type
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pairs for atoms which act as joint donors/acceptors need to be
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specified; all other type pairs are assumed to be inactive.</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">A <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command can be speficied multiple
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times for the same donor/acceptor type pair. This enables multiple
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hydrogen types to be assigned to the same donor/acceptor type pair.
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For other pair_styles, if the pair_coeff command is re-used for the
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same I.J type pair, the settings for that type pair are overwritten.
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For the hydrogen bond potentials this is not the case; the settings
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are cummulative. This means the only way to turn off a previous
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setting, is to re-use the pair_style command and start over.</p>
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</div>
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<p>For the <em>hbond/dreiding/lj</em> style the list of coefficients is as
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follows:</p>
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<ul class="simple">
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<li>K = hydrogen atom type = 1 to Ntypes</li>
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<li>donor flag = <em>i</em> or <em>j</em></li>
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<li>epsilon (energy units)</li>
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<li>sigma (distance units)</li>
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<li>n = exponent in formula above</li>
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<li>distance cutoff Rin (distance units)</li>
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<li>distance cutoff Rout (distance units)</li>
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<li>angle cutoff (degrees)</li>
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</ul>
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<p>For the <em>hbond/dreiding/morse</em> style the list of coefficients is as
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follows:</p>
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<ul class="simple">
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<li>K = hydrogen atom type = 1 to Ntypes</li>
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<li>donor flag = <em>i</em> or <em>j</em></li>
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<li>D0 (energy units)</li>
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<li>alpha (1/distance units)</li>
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<li>r0 (distance units)</li>
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<li>n = exponent in formula above</li>
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<li>distance cutoff Rin (distance units)</li>
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<li>distance cutoff Rout (distance units)</li>
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<li>angle cutoff (degrees)</li>
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</ul>
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<p>A single hydrogen atom type K can be specified, or a wild-card
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asterisk can be used in place of or in conjunction with the K
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arguments to select multiple types as hydrogens. This takes the form
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“*” or “<em>n” or “n</em>” or “m*n”. See the <a class="reference external" href="pair_coeff">pair_coeff</a> command
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doc page for details.</p>
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<p>If the donor flag is <em>i</em>, then the atom of type I in the pair_coeff
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command is treated as the donor, and J is the acceptor. If the donor
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flag is <em>j</em>, then the atom of type J in the pair_coeff command is
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treated as the donor and I is the donor. This option is required
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because the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command requires that I <= J.</p>
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<p>Epsilon and sigma are settings for the hydrogen bond potential based
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on a Lennard-Jones functional form. Note that sigma is defined as the
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zero-crossing distance for the potential, not as the energy minimum at
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2^(1/6) sigma.</p>
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<p>D0 and alpha and r0 are settings for the hydrogen bond potential based
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on a Morse functional form.</p>
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<p>The last 3 coefficients for both styles are optional. If not
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specified, the global n, distance cutoff, and angle cutoff specified
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in the pair_style command are used. If you wish to only override the
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2nd or 3rd optional parameter, you must also specify the preceding
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optional parameters.</p>
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<hr class="docutils" />
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<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a>
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.</p>
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<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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USER-OMP and OPT packages, respectively. They are only enabled if
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LAMMPS was built with those packages. 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>You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
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use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
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<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
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more instructions on how to use the accelerated styles effectively.</p>
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<hr class="docutils" />
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<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
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<p>These pair styles do not support mixing. You must explicitly identify
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each donor/acceptor type pair.</p>
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<p>These styles do not support the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> shift
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option for the energy of the interactions.</p>
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<p>The <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> table option is not relevant for
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these pair styles.</p>
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<p>These pair styles do not support the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a>
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tail option for adding long-range tail corrections to energy and
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pressure.</p>
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<p>These pair styles do not write their information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so pair_style and pair_coeff commands need to be
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re-specified in an input script that reads a restart file.</p>
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<p>These pair styles can only be used via the <em>pair</em> keyword of the
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<a class="reference internal" href="run_style.html"><span class="doc">run_style respa</span></a> command. They do not support the
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<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
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<p>These pair styles tally a count of how many hydrogen bonding
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interactions they calculate each timestep and the hbond energy. These
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quantities can be accessed via the <a class="reference internal" href="compute_pair.html"><span class="doc">compute pair</span></a>
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command as a vector of values of length 2.</p>
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<p>To print these quantities to the log file (with a descriptive column
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heading) the following commands could be included in an input script:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">hb</span> <span class="nb">all</span> <span class="n">pair</span> <span class="n">hbond</span><span class="o">/</span><span class="n">dreiding</span><span class="o">/</span><span class="n">lj</span>
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<span class="n">variable</span> <span class="n">n_hbond</span> <span class="n">equal</span> <span class="n">c_hb</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="c1">#number hbonds</span>
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<span class="n">variable</span> <span class="n">E_hbond</span> <span class="n">equal</span> <span class="n">c_hb</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="c1">#hbond energy</span>
|
|
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">epair</span> <span class="n">v_E_hbond</span>
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|
</pre></div>
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</div>
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</div>
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<hr class="docutils" />
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
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<blockquote>
|
|
<div>none</div></blockquote>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
|
|
<p><strong>Default:</strong> none</p>
|
|
<hr class="docutils" />
|
|
<p id="pair-mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
|
|
(1990).</p>
|
|
<p id="liu"><strong>(Liu)</strong> Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8)
|
|
2798 (2009)</p>
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