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<title>pair_style hbond/dreiding/lj command &mdash; LAMMPS 17 Dec 2015 documentation</title>
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<div class="section" id="pair-style-hbond-dreiding-lj-command">
<span id="index-0"></span><h1>pair_style hbond/dreiding/lj command<a class="headerlink" href="#pair-style-hbond-dreiding-lj-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-hbond-dreiding-lj-omp-command">
<h1>pair_style hbond/dreiding/lj/omp command<a class="headerlink" href="#pair-style-hbond-dreiding-lj-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-hbond-dreiding-morse-command">
<h1>pair_style hbond/dreiding/morse command<a class="headerlink" href="#pair-style-hbond-dreiding-morse-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-hbond-dreiding-morse-omp-command">
<h1>pair_style hbond/dreiding/morse/omp command<a class="headerlink" href="#pair-style-hbond-dreiding-morse-omp-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof
</pre></div>
</div>
<ul class="simple">
<li>style = <em>hbond/dreiding/lj</em> or <em>hbond/dreiding/morse</em></li>
<li>n = cosine angle periodicity</li>
<li>inner_distance_cutoff = global inner cutoff for Donor-Acceptor interactions (distance units)</li>
<li>outer_distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)</li>
<li>angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor</li>
<li>interactions (degrees)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90
pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90
pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>hbond/dreiding</em> styles compute the Acceptor-Hydrogen-Donor (AHD)
3-body hydrogen bond interaction for the
<a class="reference internal" href="Section_howto.html#howto-4"><span>DREIDING</span></a> force field, given by:</p>
<img alt="_images/pair_hbond_dreiding.jpg" class="align-center" src="_images/pair_hbond_dreiding.jpg" />
<p>where Rin is the inner spline distance cutoff, Rout is the outer
distance cutoff, theta_c is the angle cutoff, and n is the cosine
periodicity.</p>
<p>Here, <em>r</em> is the radial distance between the donor (D) and acceptor
(A) atoms and <em>theta</em> is the bond angle between the acceptor, the
hydrogen (H) and the donor atoms:</p>
<img alt="_images/dreiding_hbond.jpg" class="align-center" src="_images/dreiding_hbond.jpg" />
<p>These 3-body interactions can be defined for pairs of acceptor and
donor atoms, based on atom types. For each donor/acceptor atom pair,
the 3rd atom in the interaction is a hydrogen permanently bonded to
the donor atom, e.g. in a bond list read in from a data file via the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command. The atom types of possible
hydrogen atoms for each donor/acceptor type pair are specified by the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command (see below).</p>
<p>Style <em>hbond/dreiding/lj</em> is the original DREIDING potential of
<a class="reference internal" href="special_bonds.html#mayo"><span>(Mayo)</span></a>. It uses a LJ 12/10 functional for the Donor-Acceptor
interactions. To match the results in the original paper, use n = 4.</p>
<p>Style <em>hbond/dreiding/morse</em> is an improved version using a Morse
potential for the Donor-Acceptor interactions. <a class="reference internal" href="#liu"><span>(Liu)</span></a> showed
that the Morse form gives improved results for Dendrimer simulations,
when n = 2.</p>
<p>See this <a class="reference internal" href="Section_howto.html#howto-4"><span>howto section</span></a> of the manual for
more information on the DREIDING forcefield.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Because the Dreiding hydrogen bond potential is only one portion
of an overall force field which typically includes other pairwise
interactions, it is common to use it as a sub-style in a <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a> command, where another pair style
provides the repulsive core interaction between pairs of atoms, e.g. a
1/r^12 Lennard-Jones repulsion.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">When using the hbond/dreiding pair styles with <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a>, you should explicitly define pair
interactions between the donor atom and acceptor atoms, (as well as
between these atoms and ALL other atoms in your system). Whenever
<a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a> is used, ordinary mixing
rules are not applied to atoms like the donor and acceptor atoms
because they are typically referenced in multiple pair styles.
Neglecting to do this can cause difficult-to-detect physics problems.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">In the original Dreiding force field paper 1-4 non-bonded
interactions ARE allowed. If this is desired for your model, use the
special_bonds command (e.g. &#8220;special_bonds lj 0.0 0.0 1.0&#8221;) to turn
these interactions on.</p>
</div>
<hr class="docutils" />
<p>The following coefficients must be defined for pairs of eligible
donor/acceptor types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as
in the examples above.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Unlike other pair styles and their associated
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> commands, you do not need to specify
pair_coeff settings for all possible I,J type pairs. Only I,J type
pairs for atoms which act as joint donors/acceptors need to be
specified; all other type pairs are assumed to be inactive.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">A <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command can be speficied multiple
times for the same donor/acceptor type pair. This enables multiple
hydrogen types to be assigned to the same donor/acceptor type pair.
For other pair_styles, if the pair_coeff command is re-used for the
same I.J type pair, the settings for that type pair are overwritten.
For the hydrogen bond potentials this is not the case; the settings
are cummulative. This means the only way to turn off a previous
setting, is to re-use the pair_style command and start over.</p>
</div>
<p>For the <em>hbond/dreiding/lj</em> style the list of coefficients is as
follows:</p>
<ul class="simple">
<li>K = hydrogen atom type = 1 to Ntypes</li>
<li>donor flag = <em>i</em> or <em>j</em></li>
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>n = exponent in formula above</li>
<li>distance cutoff Rin (distance units)</li>
<li>distance cutoff Rout (distance units)</li>
<li>angle cutoff (degrees)</li>
</ul>
<p>For the <em>hbond/dreiding/morse</em> style the list of coefficients is as
follows:</p>
<ul class="simple">
<li>K = hydrogen atom type = 1 to Ntypes</li>
<li>donor flag = <em>i</em> or <em>j</em></li>
<li>D0 (energy units)</li>
<li>alpha (1/distance units)</li>
<li>r0 (distance units)</li>
<li>n = exponent in formula above</li>
<li>distance cutoff Rin (distance units)</li>
<li>distance cutoff Rout (distance units)</li>
<li>angle cutoff (degrees)</li>
</ul>
<p>A single hydrogen atom type K can be specified, or a wild-card
asterisk can be used in place of or in conjunction with the K
arguments to select multiple types as hydrogens. This takes the form
&#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;. See the <a class="reference external" href="pair_coeff">pair_coeff</a> command
doc page for details.</p>
<p>If the donor flag is <em>i</em>, then the atom of type I in the pair_coeff
command is treated as the donor, and J is the acceptor. If the donor
flag is <em>j</em>, then the atom of type J in the pair_coeff command is
treated as the donor and I is the donor. This option is required
because the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command requires that I &lt;= J.</p>
<p>Epsilon and sigma are settings for the hydrogen bond potential based
on a Lennard-Jones functional form. Note that sigma is defined as the
zero-crossing distance for the potential, not as the energy minimum at
2^(1/6) sigma.</p>
<p>D0 and alpha and r0 are settings for the hydrogen bond potential based
on a Morse functional form.</p>
<p>The last 3 coefficients for both styles are optional. If not
specified, the global n, distance cutoff, and angle cutoff specified
in the pair_style command are used. If you wish to only override the
2nd or 3rd optional parameter, you must also specify the preceding
optional parameters.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>These pair styles do not support mixing. You must explicitly identify
each donor/acceptor type pair.</p>
<p>These styles do not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the interactions.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant for
these pair styles.</p>
<p>These pair styles do not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
tail option for adding long-range tail corrections to energy and
pressure.</p>
<p>These pair styles do not write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands need to be
re-specified in an input script that reads a restart file.</p>
<p>These pair styles can only be used via the <em>pair</em> keyword of the
<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command. They do not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
<p>These pair styles tally a count of how many hydrogen bonding
interactions they calculate each timestep and the hbond energy. These
quantities can be accessed via the <a class="reference internal" href="compute_pair.html"><em>compute pair</em></a>
command as a vector of values of length 2.</p>
<p>To print these quantities to the log file (with a descriptive column
heading) the following commands could be included in an input script:</p>
<div class="highlight-python"><div class="highlight"><pre>compute hb all pair hbond/dreiding/lj
variable n_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
thermo_style custom step temp epair v_E_hbond
</pre></div>
</div>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="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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