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<div class="section" id="pair-style-bop-command">
<span id="index-0"></span><h1>pair_style bop command<a class="headerlink" href="#pair-style-bop-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 bop keyword ...
</pre></div>
</div>
<ul class="simple">
<li>zero or more keywords may be appended</li>
<li>keyword = <em>save</em></li>
</ul>
<div class="highlight-python"><div class="highlight"><pre>save = pre-compute and save some values
</pre></div>
</div>
</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 bop
pair_coeff * * ../potentials/CdTe_bop Cd Te
pair_style bop save
pair_coeff * * ../potentials/CdTe.bop.table Cd Te Te
comm_modify cutoff 14.70
</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>bop</em> pair style computes Bond-Order Potentials (BOP) based on
quantum mechanical theory incorporating both sigma and pi bondings.
By analytically deriving the BOP from quantum mechanical theory its
transferability to different phases can approach that of quantum
mechanical methods. This potential is similar to the original BOP
developed by Pettifor (<span class="xref std std-ref">Pettifor_1</span>,
<span class="xref std std-ref">Pettifor_2</span>, <span class="xref std std-ref">Pettifor_3</span>) and later updated
by Murdick, Zhou, and Ward (<a class="reference internal" href="#murdick"><span>Murdick</span></a>, <a class="reference internal" href="#ward"><span>Ward</span></a>).
Currently, BOP potential files for these systems are provided with
LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A sysstem with
only a subset of these elements, including a single element (e.g. C or
Cu or Al or Ga or Zn or CdZn), can also be modeled by using the
appropriate alloy file and assigning all atom types to the
singleelement or subset of elements via the pair_coeff command, as
discussed below.</p>
<p>The BOP potential consists of three terms:</p>
<img alt="_images/pair_bop.jpg" class="align-center" src="_images/pair_bop.jpg" />
<p>where phi_ij(r_ij) is a short-range two-body function representing the
repulsion between a pair of ion cores, beta_(sigma,ij)(r_ij) and
beta_(sigma,ij)(r_ij) are respectively sigma and pi bond ingtegrals,
THETA_(sigma,ij) and THETA_(pi,ij) are sigma and pi bond-orders, and
U_prom is the promotion energy for sp-valent systems.</p>
<p>The detailed formulas for this potential are given in Ward
(<a class="reference internal" href="#ward"><span>Ward</span></a>); here we provide only a brief description.</p>
<p>The repulsive energy phi_ij(r_ij) and the bond integrals
beta_(sigma,ij)(r_ij) and beta_(phi,ij)(r_ij) are functions of the
interatomic distance r_ij between atom i and j. Each of these
potentials has a smooth cutoff at a radius of r_(cut,ij). These
smooth cutoffs ensure stable behavior at situations with high sampling
near the cutoff such as melts and surfaces.</p>
<p>The bond-orders can be viewed as environment-dependent local variables
that are ij bond specific. The maximum value of the sigma bond-order
(THETA_sigma) is 1, while that of the pi bond-order (THETA_pi) is 2,
attributing to a maximum value of the total bond-order
(THETA_sigma+THETA_pi) of 3. The sigma and pi bond-orders reflect the
ubiquitous single-, double-, and triple- bond behavior of
chemistry. Their analytical expressions can be derived from tight-
binding theory by recursively expanding an inter-site Green&#8217;s function
as a continued fraction. To accurately represent the bonding with a
computationally efficient potential formulation suitable for MD
simulations, the derived BOP only takes (and retains) the first two
levels of the recursive representations for both the sigma and the pi
bond-orders. Bond-order terms can be understood in terms of molecular
orbital hopping paths based upon the Cyrot-Lackmann theorem
(<span class="xref std std-ref">Pettifor_1</span>). The sigma bond-order with a half-full
valence shell is used to interpolate the bond-order expressiont that
incorporated explicite valance band filling. This pi bond-order
expression also contains also contains a three-member ring term that
allows implementation of an asymmetric density of states, which helps
to either stabilize or destabilize close-packed structures. The pi
bond-order includes hopping paths of length 4. This enables the
incorporation of dihedral angles effects.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Note that unlike for other potentials, cutoffs for BOP
potentials are not set in the pair_style or pair_coeff command; they
are specified in the BOP potential files themselves. Likewise, the
BOP potential files list atomic masses; thus you do not need to use
the <a class="reference internal" href="mass.html"><em>mass</em></a> command to specify them. Note that for BOP
potentials with hydrogen, you will likely want to set the mass of H
atoms to be 10x or 20x larger to avoid having to use a tiny timestep.
You can do this by using the <a class="reference internal" href="mass.html"><em>mass</em></a> command after using the
<code class="xref doc docutils literal"><span class="pre">pair_coeff</span></code> command to read the BOP potential
file.</p>
</div>
<p>One option can be specified as a keyword with the pair_style command.</p>
<p>The <em>save</em> keyword gives you the option to calculate in advance and
store a set of distances, angles, and derivatives of angles. The
default is to not do this, but to calculate them on-the-fly each time
they are needed. The former may be faster, but takes more memory.
The latter requires less memory, but may be slower. It is best to
test this option to optimize the speed of BOP for your particular
system configuration.</p>
<hr class="docutils" />
<p>Only a single pair_coeff command is used with the <em>bop</em> style which
specifies a BOP potential file, with parameters for all needed
elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N element names = mapping of BOP elements to atom types</li>
</ul>
<p>As an example, imagine the CdTe.bop file has BOP values for Cd
and Te. If your LAMMPS simulation has 4 atoms types and you want the
1st 3 to be Cd, and the 4th to be Te, you would use the following
pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * CdTe Cd Cd Cd Te
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Cd arguments map LAMMPS atom types 1,2,3 to the Cd
element in the BOP file. The final Te argument maps LAMMPS atom type
4 to the Te element in the BOP file.</p>
<p>BOP files in the <em>potentials</em> directory of the LAMMPS distribution
have a &#8221;.bop&#8221; suffix. The potentials are in tabulated form containing
pre-tabulated pair functions for phi_ij(r_ij), beta_(sigma,ij)(r_ij),
and beta_pi,ij)(r_ij).</p>
<p>The parameters/coefficients format for the different kinds of BOP
files are given below with variables matching the formulation of Ward
(<a class="reference internal" href="#ward"><span>Ward</span></a>) and Zhou (<a class="reference internal" href="pair_polymorphic.html#zhou"><span>Zhou</span></a>). Each header line containing a
&#8221;:&#8221; is preceded by a blank line.</p>
<hr class="docutils" />
<p><strong>No angular table file format</strong>:</p>
<p>The parameters/coefficients format for the BOP potentials input file
containing pre-tabulated functions of g is given below with variables
matching the formulation of Ward (<a class="reference internal" href="#ward"><span>Ward</span></a>). This format also
assumes the angular functions have the formulation of (<a class="reference internal" href="#ward"><span>Ward</span></a>).</p>
<ul class="simple">
<li>Line 1: # elements N</li>
</ul>
<p>The first line is followed by N lines containing the atomic
number, mass, and element symbol of each element.</p>
<p>Following the definition of the elements several global variables for
the tabulated functions are given.</p>
<ul class="simple">
<li>Line 1: nr, nBOt (nr is the number of divisions the radius is broken
into for function tables and MUST be a factor of 5; nBOt is the number
of divisions for the tabulated values of THETA_(S,ij)</li>
<li>Line 2: delta_1-delta_7 (if all are not used in the particular</li>
<li>formulation, set unused values to 0.0)</li>
</ul>
<p>Following this N lines for e_1-e_N containing p_pi.</p>
<ul class="simple">
<li>Line 3: p_pi (for e_1)</li>
<li>Line 4: p_pi (for e_2 and continues to e_N)</li>
</ul>
<p>The next section contains several pair constants for the number of
interaction types e_i-e_j, with i=1-&gt;N, j=i-&gt;N</p>
<ul class="simple">
<li>Line 1: r_cut (for e_1-e_1 interactions)</li>
<li>Line 2: c_sigma, a_sigma, c_pi, a_pi</li>
<li>Line 3: delta_sigma, delta_pi</li>
<li>Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of
the previous section but is interaction type dependent)</li>
</ul>
<p>The next section contains a line for each three body interaction type
e_j-e_i-e_k with i=0-&gt;N, j=0-&gt;N, k=j-&gt;N</p>
<ul class="simple">
<li>Line 1: g_(sigma0), g_(sigma1), g_(sigma2) (These are coefficients for
g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. <a class="reference internal" href="#ward"><span>Ward</span></a>
contains the full expressions for the constants as functions of
b_(sigma,ijk), p_(sigma,ijk), u_(sigma,ijk))</li>
<li>Line 2: g_(sigma0), g_(sigma1), g_(sigma2) (for e_1-e_1-e_2)</li>
</ul>
<p>The next section contains a block for each interaction type for the
phi_ij(r_ij). Each block has nr entries with 5 entries per line.</p>
<ul class="simple">
<li>Line 1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5) (for the e_1-e_1
interaction type)</li>
<li>Line 2: phi(r6), phi(r7), phi(r8), phi(r9), phi(r10) (this continues
until nr)</li>
<li>...</li>
<li>Line nr/5_1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5), (for the
e_1-e_1 interaction type)</li>
</ul>
<p>The next section contains a block for each interaction type for the
beta_(sigma,ij)(r_ij). Each block has nr entries with 5 entries per
line.</p>
<ul class="simple">
<li>Line 1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3), beta_sigma(r4),
beta_sigma(r5) (for the e_1-e_1 interaction type)</li>
<li>Line 2: beta_sigma(r6), beta_sigma(r7), beta_sigma(r8), beta_sigma(r9),
beta_sigma(r10) (this continues until nr)</li>
<li>...</li>
<li>Line nr/5+1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3),
beta_sigma(r4), beta_sigma(r5) (for the e_1-e_2 interaction type)</li>
</ul>
<p>The next section contains a block for each interaction type for
beta_(pi,ij)(r_ij). Each block has nr entries with 5 entries per line.</p>
<ul class="simple">
<li>Line 1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4), beta_pi(r5)
(for the e_1-e_1 interaction type)</li>
<li>Line 2: beta_pi(r6), beta_pi(r7), beta_pi(r8), beta_pi(r9),
beta_pi(r10) (this continues until nr)</li>
<li>...</li>
<li>Line nr/5+1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4),
beta_pi(r5) (for the e_1-e_2 interaction type)</li>
</ul>
<p>The next section contains a block for each interaction type for the
THETA_(S,ij)((THETA_(sigma,ij))^(1/2), f_(sigma,ij)). Each block has
nBOt entries with 5 entries per line.</p>
<ul class="simple">
<li>Line 1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3),
THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type)</li>
<li>Line 2: THETA_(S,ij)(r6), THETA_(S,ij)(r7), THETA_(S,ij)(r8),
THETA_(S,ij)(r9), THETA_(S,ij)(r10) (this continues until nBOt)</li>
<li>...</li>
<li>Line nBOt/5+1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3),
THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type)</li>
</ul>
<p>The next section contains a block of N lines for e_1-e_N</p>
<ul class="simple">
<li>Line 1: delta^mu (for e_1)</li>
<li>Line 2: delta^mu (for e_2 and repeats to e_N)</li>
</ul>
<p>The last section contains more constants for e_i-e_j interactions with
i=0-&gt;N, j=i-&gt;N</p>
<ul class="simple">
<li>Line 1: (A_ij)^(mu*nu) (for e1-e1)</li>
<li>Line 2: (A_ij)^(mu*nu) (for e1-e2 and repeats as above)</li>
</ul>
<hr class="docutils" />
<p><strong>Angular spline table file format</strong>:</p>
<p>The parameters/coefficients format for the BOP potentials input file
containing pre-tabulated functions of g is given below with variables
matching the formulation of Ward (<a class="reference internal" href="#ward"><span>Ward</span></a>). This format also
assumes the angular functions have the formulation of (<a class="reference internal" href="pair_polymorphic.html#zhou"><span>Zhou</span></a>).</p>
<ul class="simple">
<li>Line 1: # elements N</li>
</ul>
<p>The first line is followed by N lines containing the atomic
number, mass, and element symbol of each element.</p>
<p>Following the definition of the elements several global variables for
the tabulated functions are given.</p>
<ul class="simple">
<li>Line 1: nr, ntheta, nBOt (nr is the number of divisions the radius is broken
into for function tables and MUST be a factor of 5; ntheta is the power of the
power of the spline used to fit the angular function; nBOt is the number
of divisions for the tabulated values of THETA_(S,ij)</li>
<li>Line 2: delta_1-delta_7 (if all are not used in the particular</li>
<li>formulation, set unused values to 0.0)</li>
</ul>
<p>Following this N lines for e_1-e_N containing p_pi.</p>
<ul class="simple">
<li>Line 3: p_pi (for e_1)</li>
<li>Line 4: p_pi (for e_2 and continues to e_N)</li>
</ul>
<p>The next section contains several pair constants for the number of
interaction types e_i-e_j, with i=1-&gt;N, j=i-&gt;N</p>
<ul class="simple">
<li>Line 1: r_cut (for e_1-e_1 interactions)</li>
<li>Line 2: c_sigma, a_sigma, c_pi, a_pi</li>
<li>Line 3: delta_sigma, delta_pi</li>
<li>Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of
the previous section but is interaction type dependent)</li>
</ul>
<p>The next section contains a line for each three body interaction type
e_j-e_i-e_k with i=0-&gt;N, j=0-&gt;N, k=j-&gt;N</p>
<ul class="simple">
<li>Line 1: g0, g1, g2... (These are coefficients for the angular spline
of the g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. The
function can contain up to 10 term thus 10 constants. The first line
can contain up to five constants. If the spline has more than five
terms the second line will contain the remaining constants The
following lines will then contain the constants for the remainaing g0,
g1, g2... (for e_1-e_1-e_2) and the other three body
interactions</li>
</ul>
<p>The rest of the table has the same structure as the previous section
(see above).</p>
<hr class="docutils" />
<p><strong>Angular no-spline table file format</strong>:</p>
<p>The parameters/coefficients format for the BOP potentials input file
containing pre-tabulated functions of g is given below with variables
matching the formulation of Ward (<a class="reference internal" href="#ward"><span>Ward</span></a>). This format also
assumes the angular functions have the formulation of (<a class="reference internal" href="pair_polymorphic.html#zhou"><span>Zhou</span></a>).</p>
<ul class="simple">
<li>Line 1: # elements N</li>
</ul>
<p>The first two lines are followed by N lines containing the atomic
number, mass, and element symbol of each element.</p>
<p>Following the definition of the elements several global variables for
the tabulated functions are given.</p>
<ul class="simple">
<li>Line 1: nr, ntheta, nBOt (nr is the number of divisions the radius is broken
into for function tables and MUST be a factor of 5; ntheta is the number of
divisions for the tabulated values of the g angular function; nBOt is the number
of divisions for the tabulated values of THETA_(S,ij)</li>
<li>Line 2: delta_1-delta_7 (if all are not used in the particular</li>
<li>formulation, set unused values to 0.0)</li>
</ul>
<p>Following this N lines for e_1-e_N containing p_pi.</p>
<ul class="simple">
<li>Line 3: p_pi (for e_1)</li>
<li>Line 4: p_pi (for e_2 and continues to e_N)</li>
</ul>
<p>The next section contains several pair constants for the number of
interaction types e_i-e_j, with i=1-&gt;N, j=i-&gt;N</p>
<ul class="simple">
<li>Line 1: r_cut (for e_1-e_1 interactions)</li>
<li>Line 2: c_sigma, a_sigma, c_pi, a_pi</li>
<li>Line 3: delta_sigma, delta_pi</li>
<li>Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of
the previous section but is interaction type dependent)</li>
</ul>
<p>The next section contains a line for each three body interaction type
e_j-e_i-e_k with i=0-&gt;N, j=0-&gt;N, k=j-&gt;N</p>
<ul class="simple">
<li>Line 1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5) (for the e_1-e_1-e_1
interaction type)</li>
<li>Line 2: g(theta6), g(theta7), g(theta8), g(theta9), g(theta10) (this continues
until ntheta)</li>
<li>...</li>
<li>Line ntheta/5+1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5), (for the
e_1-e_1-e_2 interaction type)</li>
</ul>
<p>The rest of the table has the same structure as the previous section (see above).</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table tail correction, restart</strong>:</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
mix, shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>These pair styles are part of the MANYBODY package. They are only
enabled if LAMMPS was built with that package (which it is by default).
See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more
info.</p>
<p>These pair potentials require the <a class="reference internal" href="newton.html"><em>newtion</em></a> setting to be
&#8220;on&#8221; for pair interactions.</p>
<p>The CdTe.bop and GaAs.bop potential files provided with LAMMPS (see the
potentials directory) are parameterized for metal <a class="reference internal" href="units.html"><em>units</em></a>.
You can use the BOP potential with any LAMMPS units, but you would need
to create your own BOP potential file with coefficients listed in the
appropriate units if your simulation does not use &#8220;metal&#8221; units.</p>
</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>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>non-tabulated potential file, a_0 is non-zero.</p>
<hr class="docutils" />
<p id="pettofor-1"><strong>(Pettifor_1)</strong> D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487
(1999).</p>
<p id="pettofor-2"><strong>(Pettifor_2)</strong> D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84,
4124 (2000).</p>
<p id="pettofor-3"><strong>(Pettifor_3)</strong> D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103
(2002).</p>
<p id="murdick"><strong>(Murdick)</strong> D.A. Murdick, X.W. Zhou, H.N.G. Wadley, D. Nguyen-Manh, R.
Drautz, and D.G. Pettifor, Phys. Rev. B, 73, 45206 (2006).</p>
<p id="ward"><strong>(Ward)</strong> D.K. Ward, X.W. Zhou, B.M. Wong, F.P. Doty, and J.A.
Zimmerman, Phys. Rev. B, 85,115206 (2012).</p>
<p id="zhou"><strong>(Zhou)</strong> X.W. Zhou, D.K. Ward, M. Foster (TBP).</p>
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<div class="section" id="pair-style-born-command">
<span id="index-0"></span><h1>pair_style born command<a class="headerlink" href="#pair-style-born-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-born-omp-command">
<h1>pair_style born/omp command<a class="headerlink" href="#pair-style-born-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-born-gpu-command">
<h1>pair_style born/gpu command<a class="headerlink" href="#pair-style-born-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-born-coul-long-command">
<h1>pair_style born/coul/long command<a class="headerlink" href="#pair-style-born-coul-long-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-born-coul-long-cs-command">
<h1>pair_style born/coul/long/cs command<a class="headerlink" href="#pair-style-born-coul-long-cs-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-born-coul-long-cuda-command">
<h1>pair_style born/coul/long/cuda command<a class="headerlink" href="#pair-style-born-coul-long-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-born-coul-long-gpu-command">
<h1>pair_style born/coul/long/gpu command<a class="headerlink" href="#pair-style-born-coul-long-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-born-coul-long-omp-command">
<h1>pair_style born/coul/long/omp command<a class="headerlink" href="#pair-style-born-coul-long-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-born-coul-msm-command">
<h1>pair_style born/coul/msm command<a class="headerlink" href="#pair-style-born-coul-msm-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-born-coul-msm-omp-command">
<h1>pair_style born/coul/msm/omp command<a class="headerlink" href="#pair-style-born-coul-msm-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-born-coul-wolf-command">
<h1>pair_style born/coul/wolf command<a class="headerlink" href="#pair-style-born-coul-wolf-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-born-coul-wolf-gpu-command">
<h1>pair_style born/coul/wolf/gpu command<a class="headerlink" href="#pair-style-born-coul-wolf-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-born-coul-wolf-omp-command">
<h1>pair_style born/coul/wolf/omp command<a class="headerlink" href="#pair-style-born-coul-wolf-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 args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>born</em> or <em>born/coul/long</em> or <em>born/coul/long/cs</em> or <em>born/coul/msm</em> or <em>born/coul/wolf</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>born</em> args = cutoff
cutoff = global cutoff for non-Coulombic interactions (distance units)
<em>born/coul/long</em> or <em>born/coul/long/cs</em> args = cutoff (cutoff2)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>born/coul/msm</em> args = cutoff (cutoff2)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>born/coul/wolf</em> args = alpha cutoff (cutoff2)
alpha = damping parameter (inverse distance units)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</pre>
</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 born 10.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style born/coul/long 10.0
pair_style born/coul/long/cs 10.0
pair_style born/coul/long 10.0 8.0
pair_style born/coul/long/cs 10.0 8.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style born/coul/msm 10.0
pair_style born/coul/msm 10.0 8.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style born/coul/wolf 0.25 10.0
pair_style born/coul/wolf 0.25 10.0 9.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
</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>born</em> style computes the Born-Mayer-Huggins or Tosi/Fumi
potential described in <a class="reference internal" href="#fumitosi"><span>(Fumi and Tosi)</span></a>, given by</p>
<img alt="_images/pair_born.jpg" class="align-center" src="_images/pair_born.jpg" />
<p>where sigma is an interaction-dependent length parameter, rho is an
ionic-pair dependent length parameter, and Rc is the cutoff.</p>
<p>The styles with <em>coul/long</em> or <em>coul/msm</em> add a Coulombic term as
described for the <a class="reference internal" href="pair_lj.html"><em>lj/cut</em></a> pair styles. An additional
damping factor is applied to the Coulombic term so it can be used in
conjunction with the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command and its
<em>ewald</em> or <em>pppm</em> of <em>msm</em> option. The Coulombic cutoff specified for
this style means that pairwise interactions within this distance are
computed directly; interactions outside that distance are computed in
reciprocal space.</p>
<p>If one cutoff is specified for the <em>born/coul/long</em> and
<em>born/coul/msm</em> style, it is used for both the A,C,D and Coulombic
terms. If two cutoffs are specified, the first is used as the cutoff
for the A,C,D terms, and the second is the cutoff for the Coulombic
term.</p>
<p>The <em>born/coul/wolf</em> style adds a Coulombic term as described for the
Wolf potential in the <a class="reference internal" href="pair_coul.html"><em>coul/wolf</em></a> pair style.</p>
<p>Style <em>born/coul/long/cs</em> is identical to <em>born/coul/long</em> except that
a term is added for the <a class="reference internal" href="Section_howto.html#howto-25"><span>core/shell model</span></a>
to allow charges on core and shell particles to be separated by r =
0.0.</p>
<p>Note that these potentials are related to the <a class="reference internal" href="pair_buck.html"><em>Buckingham potential</em></a>.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>A (energy units)</li>
<li>rho (distance units)</li>
<li>sigma (distance units)</li>
<li>C (energy units * distance units^6)</li>
<li>D (energy units * distance units^8)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The second coefficient, rho, must be greater than zero.</p>
<p>The last coefficient is optional. If not specified, the global A,C,D
cutoff specified in the pair_style command is used.</p>
<p>For <em>born/coul/long</em> and <em>born/coul/wolf</em> no Coulombic cutoff can be
specified for an individual I,J type pair. All type pairs use the
same global Coulombic cutoff specified in the pair_style command.</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. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>These styles support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option
for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair
interaction.</p>
<p>The <em>born/coul/long</em> pair style supports the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option ti tabulate the
short-range portion of the long-range Coulombic interaction.</p>
<p>These styles support the pair_modify tail option for adding long-range
tail corrections to energy and pressure.</p>
<p>Thess styles writes thei information to binary <a class="reference internal" href="restart.html"><em>restart</em></a>
files, so pair_style and pair_coeff commands do not need to be
specified in an input script that reads a restart file.</p>
<p>These 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>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The <em>born/coul/long</em> style is part of the KSPACE package. It is only
enabled if LAMMPS was built with that package (which it is by
default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
for more info.</p>
</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>, <a class="reference internal" href="pair_buck.html"><em>pair_style buck</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="fumitosi">Fumi and Tosi, J Phys Chem Solids, 25, 31 (1964),
Fumi and Tosi, J Phys Chem Solids, 25, 45 (1964).</p>
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<div class="section" id="pair-style-brownian-command">
<span id="index-0"></span><h1>pair_style brownian command<a class="headerlink" href="#pair-style-brownian-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-brownian-omp-command">
<h1>pair_style brownian/omp command<a class="headerlink" href="#pair-style-brownian-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-brownian-poly-command">
<h1>pair_style brownian/poly command<a class="headerlink" href="#pair-style-brownian-poly-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-brownian-poly-omp-command">
<h1>pair_style brownian/poly/omp command<a class="headerlink" href="#pair-style-brownian-poly-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 mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF
</pre></div>
</div>
<ul class="simple">
<li>style = <em>brownian</em> or <em>brownian/poly</em></li>
<li>mu = dynamic viscosity (dynamic viscosity units)</li>
<li>flaglog = 0/1 log terms in the lubrication approximation on/off</li>
<li>flagfld = 0/1 to include/exclude Fast Lubrication Dynamics effects</li>
<li>cutinner = inner cutoff distance (distance units)</li>
<li>cutoff = outer cutoff for interactions (distance units)</li>
<li>t_target = target temp of the system (temperature units)</li>
<li>seed = seed for the random number generator (positive integer)</li>
<li>flagHI (optional) = 0/1 to include/exclude 1/r hydrodynamic interactions</li>
<li>flagVF (optional) = 0/1 to include/exclude volume fraction corrections in the long-range isotropic terms</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 brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1)
pair_coeff 1 1 2.05 2.8
pair_coeff * *
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Styles <em>brownian</em> and <em>brownain/poly</em> compute Brownian forces and
torques on finite-size spherical particles. The former requires
monodisperse spherical particles; the latter allows for polydisperse
spherical particles.</p>
<p>These pair styles are designed to be used with either the <a class="reference internal" href="pair_lubricate.html"><em>pair_style lubricate</em></a> or <a class="reference internal" href="pair_lubricateU.html"><em>pair_style lubricateU</em></a> commands to provide thermostatting
when dissipative lubrication forces are acting. Thus the parameters
<em>mu</em>, <em>flaglog</em>, <em>flagfld</em>, <em>cutinner</em>, and <em>cutoff</em> should be
specified consistent with the settings in the lubrication pair styles.
For details, refer to either of the lubrication pair styles.</p>
<p>The <em>t_target</em> setting is used to specify the target temperature of
the system. The random number <em>seed</em> is used to generate random
numbers for the thermostatting procedure.</p>
<p>The <em>flagHI</em> and <em>flagVF</em> settings are optional. Neither should be
used, or both must be defined.</p>
<hr class="docutils" />
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>cutinner (distance units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The two coefficients are optional. If neither is specified, the two
cutoffs specified in the pair_style command are used. Otherwise both
must be specified.</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>this section</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>this section</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>For atom type pairs I,J and I != J, the two cutoff distances for this
pair style can be mixed. The default mix value is <em>geometric</em>. See
the &#8220;pair_modify&#8221; command for details.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option for the energy of the pair interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>This pair style does 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>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>These styles are part of the COLLOID package. They are only enabled
if LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
<p>Only spherical monodisperse particles are allowed for pair_style
brownian.</p>
<p>Only spherical particles are allowed for pair_style brownian/poly.</p>
</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>, <a class="reference internal" href="pair_lubricate.html"><em>pair_style lubricate</em></a>, <a class="reference internal" href="pair_lubricateU.html"><em>pair_style lubricateU</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The default settings for the optional args are flagHI = 1 and flagVF =
1.</p>
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<div class="section" id="pair-style-buck-command">
<span id="index-0"></span><h1>pair_style buck command<a class="headerlink" href="#pair-style-buck-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-cuda-command">
<h1>pair_style buck/cuda command<a class="headerlink" href="#pair-style-buck-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-gpu-command">
<h1>pair_style buck/gpu command<a class="headerlink" href="#pair-style-buck-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-intel-command">
<h1>pair_style buck/intel command<a class="headerlink" href="#pair-style-buck-intel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-kk-command">
<h1>pair_style buck/kk command<a class="headerlink" href="#pair-style-buck-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-omp-command">
<h1>pair_style buck/omp command<a class="headerlink" href="#pair-style-buck-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-coul-cut-command">
<h1>pair_style buck/coul/cut command<a class="headerlink" href="#pair-style-buck-coul-cut-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-coul-cut-cuda-command">
<h1>pair_style buck/coul/cut/cuda command<a class="headerlink" href="#pair-style-buck-coul-cut-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-coul-cut-gpu-command">
<h1>pair_style buck/coul/cut/gpu command<a class="headerlink" href="#pair-style-buck-coul-cut-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-coul-cut-intel-command">
<h1>pair_style buck/coul/cut/intel command<a class="headerlink" href="#pair-style-buck-coul-cut-intel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-coul-cut-kk-command">
<h1>pair_style buck/coul/cut/kk command<a class="headerlink" href="#pair-style-buck-coul-cut-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-coul-cut-omp-command">
<h1>pair_style buck/coul/cut/omp command<a class="headerlink" href="#pair-style-buck-coul-cut-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-coul-long-command">
<h1>pair_style buck/coul/long command<a class="headerlink" href="#pair-style-buck-coul-long-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-coul-long-cs-command">
<h1>pair_style buck/coul/long/cs command<a class="headerlink" href="#pair-style-buck-coul-long-cs-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-coul-long-cuda-command">
<h1>pair_style buck/coul/long/cuda command<a class="headerlink" href="#pair-style-buck-coul-long-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-coul-long-gpu-command">
<h1>pair_style buck/coul/long/gpu command<a class="headerlink" href="#pair-style-buck-coul-long-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-coul-long-intel-command">
<h1>pair_style buck/coul/long/intel command<a class="headerlink" href="#pair-style-buck-coul-long-intel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-coul-long-kk-command">
<h1>pair_style buck/coul/long/kk command<a class="headerlink" href="#pair-style-buck-coul-long-kk-command" title="Permalink to this headline"></a></h1>
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<div class="section" id="pair-style-buck-coul-long-omp-command">
<h1>pair_style buck/coul/long/omp command<a class="headerlink" href="#pair-style-buck-coul-long-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-coul-msm-command">
<h1>pair_style buck/coul/msm command<a class="headerlink" href="#pair-style-buck-coul-msm-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-coul-msm-omp-command">
<h1>pair_style buck/coul/msm/omp command<a class="headerlink" href="#pair-style-buck-coul-msm-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 args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>buck</em> or <em>buck/coul/cut</em> or <em>buck/coul/long</em> or <em>buck/coul/long/cs</em> or <em>buck/coul/msm</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>buck</em> args = cutoff
cutoff = global cutoff for Buckingham interactions (distance units)
<em>buck/coul/cut</em> args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>buck/coul/long</em> or <em>buck/coul/long/cs</em> args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>buck/coul/msm</em> args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</pre>
</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 buck 2.5
pair_coeff * * 100.0 1.5 200.0
pair_coeff * * 100.0 1.5 200.0 3.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style buck/coul/cut 10.0
pair_style buck/coul/cut 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0
pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style buck/coul/long 10.0
pair_style buck/coul/long/cs 10.0
pair_style buck/coul/long 10.0 8.0
pair_style buck/coul/long/cs 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style buck/coul/msm 10.0
pair_style buck/coul/msm 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0
</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>buck</em> style computes a Buckingham potential (exp/6 instead of
Lennard-Jones 12/6) given by</p>
<img alt="_images/pair_buck.jpg" class="align-center" src="_images/pair_buck.jpg" />
<p>where rho is an ionic-pair dependent length parameter, and Rc is the
cutoff on both terms.</p>
<p>The styles with <em>coul/cut</em> or <em>coul/long</em> or <em>coul/msm</em> add a
Coulombic term as described for the <a class="reference internal" href="pair_lj.html"><em>lj/cut</em></a> pair styles.
For <em>buck/coul/long</em> and <em>buc/coul/msm</em>, an additional damping factor
is applied to the Coulombic term so it can be used in conjunction with
the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command and its <em>ewald</em> or <em>pppm</em>
or <em>msm</em> option. The Coulombic cutoff specified for this style means
that pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.</p>
<p>If one cutoff is specified for the <em>born/coul/cut</em> and
<em>born/coul/long</em> and <em>born/coul/msm</em> styles, it is used for both the
A,C and Coulombic terms. If two cutoffs are specified, the first is
used as the cutoff for the A,C terms, and the second is the cutoff for
the Coulombic term.</p>
<p>Style <em>buck/coul/long/cs</em> is identical to <em>buck/coul/long</em> except that
a term is added for the <a class="reference internal" href="Section_howto.html#howto-25"><span>core/shell model</span></a>
to allow charges on core and shell particles to be separated by r =
0.0.</p>
<p>Note that these potentials are related to the <a class="reference internal" href="pair_born.html"><em>Born-Mayer-Huggins potential</em></a>.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">For all these pair styles, the terms with A and C are always
cutoff. The additional Coulombic term can be cutoff or long-range (no
cutoff) depending on whether the style name includes coul/cut or
coul/long or coul/msm. If you wish the C/r^6 term to be long-range
(no cutoff), then see the <a class="reference internal" href="pair_buck_long.html"><em>pair_style buck/long/coul/long</em></a> command.</p>
</div>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>A (energy units)</li>
<li>rho (distance units)</li>
<li>C (energy-distance^6 units)</li>
<li>cutoff (distance units)</li>
<li>cutoff2 (distance units)</li>
</ul>
<p>The second coefficient, rho, must be greater than zero.</p>
<p>The latter 2 coefficients are optional. If not specified, the global
A,C and Coulombic cutoffs are used. If only one cutoff is specified,
it is used as the cutoff for both A,C and Coulombic interactions for
this type pair. If both coefficients are specified, they are used as
the A,C and Coulombic cutoffs for this type pair. You cannot specify
2 cutoffs for style <em>buck</em>, since it has no Coulombic terms.</p>
<p>For <em>buck/coul/long</em> only the LJ cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.</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. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>These styles support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option
for the energy of the exp() and 1/r^6 portion of the pair interaction.</p>
<p>The <em>buck/coul/long</em> pair style supports the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option to tabulate the
short-range portion of the long-range Coulombic interaction.</p>
<p>These styles support the pair_modify tail option for adding long-range
tail corrections to energy and pressure for the A,C terms in the
pair interaction.</p>
<p>These styles write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>These 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>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The <em>buck/coul/long</em> style is part of the KSPACE package. The
<em>buck/coul/long/cs</em> style is part of the CORESHELL package. They are
only enabled if LAMMPS was built with that package (which it is by
default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
for more info.</p>
</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>, <a class="reference internal" href="pair_born.html"><em>pair_style born</em></a></p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="pair-style-buck-long-coul-long-command">
<span id="index-0"></span><h1>pair_style buck/long/coul/long command<a class="headerlink" href="#pair-style-buck-long-coul-long-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-long-coul-long-omp-command">
<h1>pair_style buck/long/coul/long/omp command<a class="headerlink" href="#pair-style-buck-long-coul-long-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 buck/long/coul/long flag_buck flag_coul cutoff (cutoff2)
</pre></div>
</div>
<ul class="simple">
<li>flag_buck = <em>long</em> or <em>cut</em></li>
</ul>
<pre class="literal-block">
<em>long</em> = use Kspace long-range summation for the dispersion term 1/r^6
<em>cut</em> = use a cutoff
</pre>
<ul class="simple">
<li>flag_coul = <em>long</em> or <em>off</em></li>
</ul>
<pre class="literal-block">
<em>long</em> = use Kspace long-range summation for the Coulombic term 1/r
<em>off</em> = omit the Coulombic term
</pre>
<ul class="simple">
<li>cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units)</li>
<li>cutoff2 = global cutoff for Coulombic (optional) (distance units)</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 buck/long/coul/long cut off 2.5
pair_style buck/long/coul/long cut long 2.5 4.0
pair_style buck/long/coul/long long long 4.0
pair_coeff * * 1 1
pair_coeff 1 1 1 3 4
</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>buck/long/coul/long</em> style computes a Buckingham potential (exp/6
instead of Lennard-Jones 12/6) and Coulombic potential, given by</p>
<img alt="_images/pair_buck.jpg" class="align-center" src="_images/pair_buck.jpg" />
<img alt="_images/pair_coulomb.jpg" class="align-center" src="_images/pair_coulomb.jpg" />
<p>Rc is the cutoff. If one cutoff is specified in the pair_style
command, it is used for both the Buckingham and Coulombic terms. If
two cutoffs are specified, they are used as cutoffs for the Buckingham
and Coulombic terms respectively.</p>
<p>The purpose of this pair style is to capture long-range interactions
resulting from both attractive 1/r^6 Buckingham and Coulombic 1/r
interactions. This is done by use of the <em>flag_buck</em> and <em>flag_coul</em>
settings. The &#8220;<a class="reference internal" href="#ismail"><span>Ismail</span></a> paper has more details on when it is
appropriate to include long-range 1/r^6 interactions, using this
potential.</p>
<p>If <em>flag_buck</em> is set to <em>long</em>, no cutoff is used on the Buckingham
1/r^6 dispersion term. The long-range portion can be calculated by
using the <a class="reference internal" href="kspace_style.html"><em>kspace_style ewald/disp or pppm/disp</em></a>
commands. The specified Buckingham cutoff then determines which
portion of the Buckingham interactions are computed directly by the
pair potential versus which part is computed in reciprocal space via
the Kspace style. If <em>flag_buck</em> is set to <em>cut</em>, the Buckingham
interactions are simply cutoff, as with <a class="reference internal" href="pair_buck.html"><em>pair_style buck</em></a>.</p>
<p>If <em>flag_coul</em> is set to <em>long</em>, no cutoff is used on the Coulombic
interactions. The long-range portion can calculated by using any of
several <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command options such as
<em>pppm</em> or <em>ewald</em>. Note that if <em>flag_buck</em> is also set to long, then
the <em>ewald/disp</em> or <em>pppm/disp</em> Kspace style needs to be used to
perform the long-range calculations for both the Buckingham and
Coulombic interactions. If <em>flag_coul</em> is set to <em>off</em>, Coulombic
interactions are not computed.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>A (energy units)</li>
<li>rho (distance units)</li>
<li>C (energy-distance^6 units)</li>
<li>cutoff (distance units)</li>
<li>cutoff2 (distance units)</li>
</ul>
<p>The second coefficient, rho, must be greater than zero.</p>
<p>The latter 2 coefficients are optional. If not specified, the global
Buckingham and Coulombic cutoffs specified in the pair_style command
are used. If only one cutoff is specified, it is used as the cutoff
for both Buckingham and Coulombic interactions for this type pair. If
both coefficients are specified, they are used as the Buckingham and
Coulombic cutoffs for this type pair. Note that if you are using
<em>flag_buck</em> set to <em>long</em>, you cannot specify a Buckingham cutoff for
an atom type pair, since only one global Buckingham cutoff is allowed.
Similarly, if you are using <em>flag_coul</em> set to <em>long</em>, you cannot
specify a Coulombic cutoff for an atom type pair, since only one
global Coulombic cutoff is allowed.</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>This pair styles does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>This pair style supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the exp() and 1/r^6 portion of the pair
interaction, assuming <em>flag_buck</em> is <em>cut</em>.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option for the energy of the Buckingham portion of the pair
interaction.</p>
<p>This pair style supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table and
table/disp options since they can tabulate the short-range portion of
the long-range Coulombic and dispersion interactions.</p>
<p>This pair style write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style supports the use of the <em>inner</em>, <em>middle</em>, and <em>outer</em>
keywords of the <a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command, meaning the
pairwise forces can be partitioned by distance at different levels of
the rRESPA hierarchy. See the <a class="reference internal" href="run_style.html"><em>run_style</em></a> command for
details.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This style is part of the KSPACE package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info. Note that
the KSPACE package is installed by default.</p>
</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="ismail"><strong>(Ismail)</strong> Ismail, Tsige, In &#8216;t Veld, Grest, Molecular Physics
(accepted) (2007).</p>
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<div class="section" id="pair-style-lj-charmm-coul-charmm-command">
<span id="index-0"></span><h1>pair_style lj/charmm/coul/charmm command<a class="headerlink" href="#pair-style-lj-charmm-coul-charmm-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-charmm-cuda-command">
<h1>pair_style lj/charmm/coul/charmm/cuda command<a class="headerlink" href="#pair-style-lj-charmm-coul-charmm-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-charmm-omp-command">
<h1>pair_style lj/charmm/coul/charmm/omp command<a class="headerlink" href="#pair-style-lj-charmm-coul-charmm-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-charmm-implicit-command">
<h1>pair_style lj/charmm/coul/charmm/implicit command<a class="headerlink" href="#pair-style-lj-charmm-coul-charmm-implicit-command" title="Permalink to this headline"></a></h1>
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<div class="section" id="pair-style-lj-charmm-coul-charmm-implicit-cuda-command">
<h1>pair_style lj/charmm/coul/charmm/implicit/cuda command<a class="headerlink" href="#pair-style-lj-charmm-coul-charmm-implicit-cuda-command" title="Permalink to this headline"></a></h1>
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<div class="section" id="pair-style-lj-charmm-coul-charmm-implicit-omp-command">
<h1>pair_style lj/charmm/coul/charmm/implicit/omp command<a class="headerlink" href="#pair-style-lj-charmm-coul-charmm-implicit-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-long-command">
<h1>pair_style lj/charmm/coul/long command<a class="headerlink" href="#pair-style-lj-charmm-coul-long-command" title="Permalink to this headline"></a></h1>
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<div class="section" id="pair-style-lj-charmm-coul-long-cuda-command">
<h1>pair_style lj/charmm/coul/long/cuda command<a class="headerlink" href="#pair-style-lj-charmm-coul-long-cuda-command" title="Permalink to this headline"></a></h1>
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<div class="section" id="pair-style-lj-charmm-coul-long-gpu-command">
<h1>pair_style lj/charmm/coul/long/gpu command<a class="headerlink" href="#pair-style-lj-charmm-coul-long-gpu-command" title="Permalink to this headline"></a></h1>
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<div class="section" id="pair-style-lj-charmm-coul-long-intel-command">
<h1>pair_style lj/charmm/coul/long/intel command<a class="headerlink" href="#pair-style-lj-charmm-coul-long-intel-command" title="Permalink to this headline"></a></h1>
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<div class="section" id="pair-style-lj-charmm-coul-long-opt-command">
<h1>pair_style lj/charmm/coul/long/opt command<a class="headerlink" href="#pair-style-lj-charmm-coul-long-opt-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-long-omp-command">
<h1>pair_style lj/charmm/coul/long/omp command<a class="headerlink" href="#pair-style-lj-charmm-coul-long-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-msm-command">
<h1>pair_style lj/charmm/coul/msm command<a class="headerlink" href="#pair-style-lj-charmm-coul-msm-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-msm-omp-command">
<h1>pair_style lj/charmm/coul/msm/omp command<a class="headerlink" href="#pair-style-lj-charmm-coul-msm-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 args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lj/charmm/coul/charmm</em> or <em>lj/charmm/coul/charmm/implicit</em> or <em>lj/charmm/coul/long</em> or <em>lj/charmm/coul/msm</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>lj/charmm/coul/charmm</em> args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional)
<em>lj/charmm/coul/charmm/implicit</em> args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional)
<em>lj/charmm/coul/long</em> args = inner outer (cutoff)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
<em>lj/charmm/coul/msm</em> args = inner outer (cutoff)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
</pre>
</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 lj/charmm/coul/charmm 8.0 10.0
pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/charmm/coul/long 8.0 10.0
pair_style lj/charmm/coul/long 8.0 10.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/charmm/coul/msm 8.0 10.0
pair_style lj/charmm/coul/msm 8.0 10.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
</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>lj/charmm</em> styles compute LJ and Coulombic interactions with an
additional switching function S(r) that ramps the energy and force
smoothly to zero between an inner and outer cutoff. It is a widely
used potential in the <a class="reference external" href="http://www.scripps.edu/brooks">CHARMM</a> MD code.
See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
field.</p>
<img alt="_images/pair_charmm.jpg" class="align-center" src="_images/pair_charmm.jpg" />
<p>Both the LJ and Coulombic terms require an inner and outer cutoff.
They can be the same for both formulas or different depending on
whether 2 or 4 arguments are used in the pair_style command. In each
case, the inner cutoff distance must be less than the outer cutoff.
It it typical to make the difference between the 2 cutoffs about 1.0
Angstrom.</p>
<p>Style <em>lj/charmm/coul/charmm/implicit</em> computes the same formulas as
style <em>lj/charmm/coul/charmm</em> except that an additional 1/r term is
included in the Coulombic formula. The Coulombic energy thus varies
as 1/r^2. This is effectively a distance-dependent dielectric term
which is a simple model for an implicit solvent with additional
screening. It is designed for use in a simulation of an unsolvated
biomolecule (no explicit water molecules).</p>
<p>Styles <em>lj/charmm/coul/long</em> and <em>lj/charmm/coul/msm</em> compute the same
formulas as style <em>lj/charmm/coul/charmm</em> except that an additional
damping factor is applied to the Coulombic term, as described for the
<a class="reference internal" href="pair_lj.html"><em>lj/cut</em></a> pair styles. Only one Coulombic cutoff is
specified for <em>lj/charmm/coul/long</em> and <em>lj/charmm/coul/msm</em>; if only
2 arguments are used in the pair_style command, then the outer LJ
cutoff is used as the single Coulombic cutoff.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>epsilon_14 (energy units)</li>
<li>sigma_14 (distance units)</li>
</ul>
<p>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at 2^(1/6)
sigma.</p>
<p>The latter 2 coefficients are optional. If they are specified, they
are used in the LJ formula between 2 atoms of these types which are
also first and fourth atoms in any dihedral. No cutoffs are specified
because this CHARMM force field does not allow varying cutoffs for
individual atom pairs; all pairs use the global cutoff(s) specified in
the pair_style command.</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>For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14,
and sigma_14 coefficients for all of the lj/charmm pair styles can be
mixed. The default mix value is <em>arithmetic</em> to coincide with the
usual settings for the CHARMM force field. See the &#8220;pair_modify&#8221;
command for details.</p>
<p>None of the lj/charmm pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option, since the Lennard-Jones
portion of the pair interaction is smoothed to 0.0 at the cutoff.</p>
<p>The <em>lj/charmm/coul/long</em> style supports the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option since it can tabulate the
short-range portion of the long-range Coulombic interaction.</p>
<p>None of the lj/charmm pair styles 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, since the Lennard-Jones portion of
the pair interaction is smoothed to 0.0 at the cutoff.</p>
<p>All of the lj/charmm pair styles write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.</p>
<p>The lj/charmm/coul/long pair style supports the use of the <em>inner</em>,
<em>middle</em>, and <em>outer</em> keywords of the <a class="reference internal" href="run_style.html"><em>run_style respa</em></a>
command, meaning the pairwise forces can be partitioned by distance at
different levels of the rRESPA hierarchy. The other styles only
support the <em>pair</em> keyword of run_style respa. See the
<a class="reference internal" href="run_style.html"><em>run_style</em></a> command for details.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The <em>lj/charmm/coul/charmm</em> and <em>lj/charmm/coul/charmm/implicit</em>
styles are part of the MOLECULE package. The <em>lj/charmm/coul/long</em>
style is part of the KSPACE package. 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. Note that
the MOLECULE and KSPACE packages are installed by default.</p>
</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="mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</p>
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<div class="section" id="pair-style-lj-class2-command">
<span id="index-0"></span><h1>pair_style lj/class2 command<a class="headerlink" href="#pair-style-lj-class2-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-class2-cuda-command">
<h1>pair_style lj/class2/cuda command<a class="headerlink" href="#pair-style-lj-class2-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-class2-gpu-command">
<h1>pair_style lj/class2/gpu command<a class="headerlink" href="#pair-style-lj-class2-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-class2-kk-command">
<h1>pair_style lj/class2/kk command<a class="headerlink" href="#pair-style-lj-class2-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-class2-omp-command">
<h1>pair_style lj/class2/omp command<a class="headerlink" href="#pair-style-lj-class2-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-class2-coul-cut-command">
<h1>pair_style lj/class2/coul/cut command<a class="headerlink" href="#pair-style-lj-class2-coul-cut-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-class2-coul-cut-cuda-command">
<h1>pair_style lj/class2/coul/cut/cuda command<a class="headerlink" href="#pair-style-lj-class2-coul-cut-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-class2-coul-cut-kk-command">
<h1>pair_style lj/class2/coul/cut/kk command<a class="headerlink" href="#pair-style-lj-class2-coul-cut-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-class2-coul-cut-omp-command">
<h1>pair_style lj/class2/coul/cut/omp command<a class="headerlink" href="#pair-style-lj-class2-coul-cut-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-class2-coul-long-command">
<h1>pair_style lj/class2/coul/long command<a class="headerlink" href="#pair-style-lj-class2-coul-long-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-class2-coul-long-cuda-command">
<h1>pair_style lj/class2/coul/long/cuda command<a class="headerlink" href="#pair-style-lj-class2-coul-long-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-class2-coul-long-gpu-command">
<h1>pair_style lj/class2/coul/long/gpu command<a class="headerlink" href="#pair-style-lj-class2-coul-long-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-class2-coul-long-kk-command">
<h1>pair_style lj/class2/coul/long/kk command<a class="headerlink" href="#pair-style-lj-class2-coul-long-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-class2-coul-long-omp-command">
<h1>pair_style lj/class2/coul/long/omp command<a class="headerlink" href="#pair-style-lj-class2-coul-long-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 args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lj/class2</em> or <em>lj/class2/coul/cut</em> or <em>lj/class2/coul/long</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>lj/class2</em> args = cutoff
cutoff = global cutoff for class 2 interactions (distance units)
<em>lj/class2/coul/cut</em> args = cutoff (cutoff2)
cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>lj/class2/coul/long</em> args = cutoff (cutoff2)
cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</pre>
</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 lj/class2 10.0
pair_coeff * * 100.0 2.5
pair_coeff 1 2* 100.0 2.5 9.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/class2/coul/cut 10.0
pair_style lj/class2/coul/cut 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_coeff 1 1 100.0 3.5 9.0 9.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/class2/coul/long 10.0
pair_style lj/class2/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
</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>lj/class2</em> styles compute a 6/9 Lennard-Jones potential given by</p>
<img alt="_images/pair_class2.jpg" class="align-center" src="_images/pair_class2.jpg" />
<p>Rc is the cutoff.</p>
<p>The <em>lj/class2/coul/cut</em> and <em>lj/class2/coul/long</em> styles add a
Coulombic term as described for the <a class="reference internal" href="pair_lj.html"><em>lj/cut</em></a> pair styles.</p>
<p>See <a class="reference internal" href="pair_modify.html#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>cutoff1 (distance units)</li>
<li>cutoff2 (distance units)</li>
</ul>
<p>The latter 2 coefficients are optional. If not specified, the global
class 2 and Coulombic cutoffs are used. If only one cutoff is
specified, it is used as the cutoff for both class 2 and Coulombic
interactions for this type pair. If both coefficients are specified,
they are used as the class 2 and Coulombic cutoffs for this type pair.
You cannot specify 2 cutoffs for style <em>lj/class2</em>, since it has no
Coulombic terms.</p>
<p>For <em>lj/class2/coul/long</em> only the class 2 cutoff can be specified
since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.</p>
<hr class="docutils" />
<p>If the pair_coeff command is not used to define coefficients for a
particular I != J type pair, the mixing rule for epsilon and sigma for
all class2 potentials is to use the <em>sixthpower</em> formulas documented
by the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> command. The <a class="reference internal" href="pair_modify.html"><em>pair_modify mix</em></a> setting is thus ignored for class2 potentials
for epsilon and sigma. However it is still followed for mixing the
cutoff distance.</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>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/class2 pair styles can be mixed.
Epsilon and sigma are always mixed with the value <em>sixthpower</em>. The
cutoff distance is mixed by whatever option is set by the pair_modify
command (default = geometric). See the &#8220;pair_modify&#8221; command for
details.</p>
<p>All of the lj/class2 pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option for the energy of the
Lennard-Jones portion of the pair interaction.</p>
<p>The <em>lj/class2/coul/long</em> pair style does not support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option since a tabulation
capability has not yet been added to this potential.</p>
<p>All of the lj/class2 pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> tail option for adding a long-range
tail correction to the energy and pressure of the Lennard-Jones
portion of the pair interaction.</p>
<p>All of the lj/class2 pair styles write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.</p>
<p>All of the lj/class2 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>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>These styles are part of the CLASS2 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>Making LAMMPS</span></a> section for more info.</p>
</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="sun"><strong>(Sun)</strong> Sun, J Phys Chem B 102, 7338-7364 (1998).</p>
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<div class="section" id="pair-coeff-command">
<span id="index-0"></span><h1>pair_coeff command<a class="headerlink" href="#pair-coeff-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_coeff I J args
</pre></div>
</div>
<ul class="simple">
<li>I,J = atom types (see asterisk form below)</li>
<li>args = coefficients for one or more pairs of atom types</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_coeff 1 2 1.0 1.0 2.5
pair_coeff 2 * 1.0 1.0
pair_coeff 3* 1*2 1.0 1.0 2.5
pair_coeff * * 1.0 1.0
pair_coeff * * nialhjea 1 1 2
pair_coeff * 3 morse.table ENTRY1
pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid)
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Specify the pairwise force field coefficients for one or more pairs of
atom types. The number and meaning of the coefficients depends on the
pair style. Pair coefficients can also be set in the data file read
by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command or in a restart file.</p>
<p>I and J can be specified in one of two ways. Explicit numeric values
can be used for each, as in the 1st example above. I &lt;= J is
required. LAMMPS sets the coefficients for the symmetric J,I
interaction to the same values.</p>
<p>A wildcard asterisk can be used in place of or in conjunction with the
I,J arguments to set the coefficients for multiple pairs of atom
types. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;. If N = the
number of atom types, then an asterisk with no numeric values means all
types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive). Note that only type pairs with I &lt;= J are considered; if
asterisks imply type pairs where J &lt; I, they are ignored.</p>
<p>Note that a pair_coeff command can override a previous setting for the
same I,J pair. For example, these commands set the coeffs for all I,J
pairs, then overwrite the coeffs for just the I,J = 2,3 pair:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * 1.0 1.0 2.5
pair_coeff 2 3 2.0 1.0 1.12
</pre></div>
</div>
<p>A line in a data file that specifies pair coefficients uses the exact
same format as the arguments of the pair_coeff command in an input
script, with the exception of the I,J type arguments. In each line of
the &#8220;Pair Coeffs&#8221; section of a data file, only a single type I is
specified, which sets the coefficients for type I interacting with
type I. This is because the section has exactly N lines, where N =
the number of atom types. For this reason, the wild-card asterisk
should also not be used as part of the I argument. Thus in a data
file, the line corresponding to the 1st example above would be listed
as</p>
<div class="highlight-python"><div class="highlight"><pre>2 1.0 1.0 2.5
</pre></div>
</div>
<p>For many potentials, if coefficients for type pairs with I != J are
not set explicitly by a pair_coeff command, the values are inferred
from the I,I and J,J settings by mixing rules; see the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> command for a discussion. Details on
this option as it pertains to individual potentials are described on
the doc page for the potential.</p>
<p>Many pair styles, typically for many-body potentials, use tabulated
potential files as input, when specifying the pair_coeff command.
Potential files provided with LAMMPS are in the potentials directory
of the distribution. For some potentials, such as EAM, other archives
of suitable files can be found on the Web. They can be used with
LAMMPS so long as they are in the format LAMMPS expects, as discussed
on the individual doc pages.</p>
<p>When a pair_coeff command using a potential file is specified, LAMMPS
looks for the potential file in 2 places. First it looks in the
location specified. E.g. if the file is specified as &#8220;niu3.eam&#8221;, it
is looked for in the current working directory. If it is specified as
&#8221;../potentials/niu3.eam&#8221;, then it is looked for in the potentials
directory, assuming it is a sister directory of the current working
directory. If the file is not found, it is then looked for in the
directory specified by the LAMMPS_POTENTIALS environment variable.
Thus if this is set to the potentials directory in the LAMMPS distro,
then you can use those files from anywhere on your system, without
copying them into your working directory. Environment variables are
set in different ways for different shells. Here are example settings
for</p>
<p>csh, tcsh:</p>
<div class="highlight-python"><div class="highlight"><pre>% setenv LAMMPS_POTENTIALS /path/to/lammps/potentials
</pre></div>
</div>
<p>bash:</p>
<div class="highlight-python"><div class="highlight"><pre>% export LAMMPS_POTENTIALS=/path/to/lammps/potentials
</pre></div>
</div>
<p>Windows:</p>
<pre class="literal-block">
% set LAMMPS_POTENTIALS=&quot;C:Path to LAMMPSPotentials&quot;
</pre>
<hr class="docutils" />
<p>The alphabetic list of pair styles defined in LAMMPS is given on the
<a class="reference internal" href="pair_style.html"><em>pair_style</em></a> doc page. They are also given in more
compact form in the pair section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<p>Click on the style to display the formula it computes, arguments
specified in the pair_style command, and coefficients specified by the
associated <a class="reference internal" href=""><em>pair_coeff</em></a> command.</p>
<p>Note that there are also additional pair styles (not listed on the
<a class="reference internal" href="pair_style.html"><em>pair_style</em></a> doc page) submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the pair section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<p>There are also additional accelerated pair styles (not listed on the
<a class="reference internal" href="pair_style.html"><em>pair_style</em></a> doc page) included in the LAMMPS
distribution for faster performance on CPUs and GPUs. The list of
these with links to the individual styles are given in the pair
section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This command must come after the simulation box is defined by a
<a class="reference internal" href="read_data.html"><em>read_data</em></a>, <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>, or
<a class="reference internal" href="create_box.html"><em>create_box</em></a> command.</p>
</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_style.html"><em>pair_style</em></a>, <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>,
<a class="reference internal" href="read_data.html"><em>read_data</em></a>, <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>,
<a class="reference internal" href="pair_write.html"><em>pair_write</em></a></p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="pair-style-colloid-command">
<span id="index-0"></span><h1>pair_style colloid command<a class="headerlink" href="#pair-style-colloid-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-colloid-gpu-command">
<h1>pair_style colloid/gpu command<a class="headerlink" href="#pair-style-colloid-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-colloid-omp-command">
<h1>pair_style colloid/omp command<a class="headerlink" href="#pair-style-colloid-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 colloid cutoff
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for colloidal interactions (distance units)</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 colloid 10.0
pair_coeff * * 25 1.0 10.0 10.0
pair_coeff 1 1 144 1.0 0.0 0.0 3.0
pair_coeff 1 2 75.398 1.0 0.0 10.0 9.0
pair_coeff 2 2 39.478 1.0 10.0 10.0 25.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>colloid</em> computes pairwise interactions between large colloidal
particles and small solvent particles using 3 formulas. A colloidal
particle has a size &gt; sigma; a solvent particle is the usual
Lennard-Jones particle of size sigma.</p>
<p>The colloid-colloid interaction energy is given by</p>
<img alt="_images/pair_colloid_cc.jpg" class="align-center" src="_images/pair_colloid_cc.jpg" />
<p>where A_cc is the Hamaker constant, a1 and a2 are the radii of the two
colloidal particles, and Rc is the cutoff. This equation results from
describing each colloidal particle as an integrated collection of
Lennard-Jones particles of size sigma and is derived in
<a class="reference internal" href="pair_resquared.html#everaers"><span>(Everaers)</span></a>.</p>
<p>The colloid-solvent interaction energy is given by</p>
<img alt="_images/pair_colloid_cs.jpg" class="align-center" src="_images/pair_colloid_cs.jpg" />
<p>where A_cs is the Hamaker constant, a is the radius of the colloidal
particle, and Rc is the cutoff. This formula is derived from the
colloid-colloid interaction, letting one of the particle sizes go to
zero.</p>
<p>The solvent-solvent interaction energy is given by the usual
Lennard-Jones formula</p>
<img alt="_images/pair_colloid_ss.jpg" class="align-center" src="_images/pair_colloid_ss.jpg" />
<p>with A_ss set appropriately, which results from letting both particle
sizes go to zero.</p>
<p>When used in combination with <a class="reference internal" href=""><em>pair_style yukawa/colloid</em></a>, the two terms become the so-called
DLVO potential, which combines electrostatic repulsion and van der
Waals attraction.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>A (energy units)</li>
<li>sigma (distance units)</li>
<li>d1 (distance units)</li>
<li>d2 (distance units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>A is the Hamaker energy prefactor and should typically be set as
follows:</p>
<ul class="simple">
<li>A_cc = colloid/colloid = 4 pi^2 = 39.5</li>
<li>A_cs = colloid/solvent = sqrt(A_cc*A_ss)</li>
<li>A_ss = solvent/solvent = 144 (assuming epsilon = 1, so that 144/36 = 4)</li>
</ul>
<p>Sigma is the size of the solvent particle or the constituent particles
integrated over in the colloidal particle and should typically be set
as follows:</p>
<ul class="simple">
<li>Sigma_cc = colloid/colloid = 1.0</li>
<li>Sigma_cs = colloid/solvent = arithmetic mixing between colloid sigma and solvent sigma</li>
<li>Sigma_ss = solvent/solvent = 1.0 or whatever size the solvent particle is</li>
</ul>
<p>Thus typically Sigma_cs = 1.0, unless the solvent particle&#8217;s size !=
1.0.</p>
<p>D1 and d2 are particle diameters, so that d1 = 2*a1 and d2 = 2*a2 in
the formulas above. Both d1 and d2 must be values &gt;= 0. If d1 &gt; 0
and d2 &gt; 0, then the pair interacts via the colloid-colloid formula
above. If d1 = 0 and d2 = 0, then the pair interacts via the
solvent-solvent formula. I.e. a d value of 0 is a Lennard-Jones
particle of size sigma. If either d1 = 0 or d2 = 0 and the other is
larger, then the pair interacts via the colloid-solvent formula.</p>
<p>Note that the diameter of a particular particle type may appear in
multiple pair_coeff commands, as it interacts with other particle
types. You should insure the particle diameter is specified
consistently each time it appears.</p>
<p>The last coefficient is optional. If not specified, the global cutoff
specified in the pair_style command is used. However, you typically
want different cutoffs for interactions between different particle
sizes. E.g. if colloidal particles of diameter 10 are used with
solvent particles of diameter 1, then a solvent-solvent cutoff of 2.5
would correspond to a colloid-colloid cutoff of 25. A good
rule-of-thumb is to use a colloid-solvent cutoff that is half the big
diameter + 4 times the small diameter. I.e. 9 = 5 + 4 for the
colloid-solvent cutoff in this case.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">When using pair_style colloid for a mixture with 2 (or more)
widely different particles sizes (e.g. sigma=10 colloids in a
background sigma=1 LJ fluid), you will likely want to use these
commands for efficiency: <a class="reference internal" href="neighbor.html"><em>neighbor multi</em></a> and
<a class="reference internal" href="comm_modify.html"><em>comm_modify multi</em></a>.</p>
</div>
<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>For atom type pairs I,J and I != J, the A, sigma, d1, and d2
coefficients and cutoff distance for this pair style can be mixed. A
is an energy value mixed like a LJ epsilon. D1 and d2 are distance
values and are mixed like sigma. The default mix value is
<em>geometric</em>. See the &#8220;pair_modify&#8221; command for details.</p>
<p>This pair style supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the pair interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>This pair style does 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>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This style is part of the COLLOID package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>Normally, this pair style should be used with finite-size particles
which have a diameter, e.g. see the <a class="reference internal" href="atom_style.html"><em>atom_style sphere</em></a> command. However, this is not a requirement,
since the only definition of particle size is via the pair_coeff
parameters for each type. In other words, the physical radius of the
particle is ignored. Thus you should insure that the d1,d2 parameters
you specify are consistent with the physical size of the particles of
that type.</p>
<p>Per-particle polydispersity is not yet supported by this pair style;
only per-type polydispersity is enabled via the pair_coeff parameters.</p>
</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="everaers"><strong>(Everaers)</strong> Everaers, Ejtehadi, Phys Rev E, 67, 041710 (2003).</p>
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<div class="section" id="pair-style-comb-command">
<span id="index-0"></span><h1>pair_style comb command<a class="headerlink" href="#pair-style-comb-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-comb-omp-command">
<h1>pair_style comb/omp command<a class="headerlink" href="#pair-style-comb-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-comb3-command">
<h1>pair_style comb3 command<a class="headerlink" href="#pair-style-comb3-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 comb
pair_style comb3 keyword
</pre></div>
</div>
<pre class="literal-block">
keyword = <em>polar</em>
<em>polar</em> value = <em>polar_on</em> or <em>polar_off</em> = whether or not to include atomic polarization
</pre>
</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 comb
pair_coeff * * ../potentials/ffield.comb Si
pair_coeff * * ../potentials/ffield.comb Hf Si O
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style comb3 polar_off
pair_coeff * * ../potentials/ffield.comb3 O Cu N C O
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>comb</em> computes the second-generation variable charge COMB
(Charge-Optimized Many-Body) potential. Style <em>comb3</em> computes the
third-generation COMB potential. These COMB potentials are described
in <a class="reference internal" href="#comb"><span>(COMB)</span></a> and <a class="reference internal" href="#comb3"><span>(COMB3)</span></a>. Briefly, the total energy
<em>E&lt;sub&gt;T&lt;/sub&gt;</em> of a system of atoms is given by</p>
<img alt="_images/pair_comb1.jpg" class="align-center" src="_images/pair_comb1.jpg" />
<p>where <em>E&lt;sub&gt;i&lt;/sub&gt;&lt;sup&gt;self&lt;/sup&gt;</em> is the self-energy of atom <em>i</em>
(including atomic ionization energies and electron affinities),
<em>E&lt;sub&gt;ij&lt;/sub&gt;&lt;sup&gt;short&lt;/sup&gt;</em> is the bond-order potential between
atoms <em>i</em> and <em>j</em>,
<em>E&lt;sub&gt;ij&lt;/sub&gt;&lt;sup&gt;Coul&lt;/sup&gt;</em> is the Coulomb interactions,
<em>E&lt;sup&gt;polar&lt;/sup&gt;</em> is the polarization term for organic systems
(style <em>comb3</em> only),
<em>E&lt;sup&gt;vdW&lt;/sup&gt;</em> is the van der Waals energy (style <em>comb3</em> only),
<em>E&lt;sup&gt;barr&lt;/sup&gt;</em> is a charge barrier function, and
<em>E&lt;sup&gt;corr&lt;/sup&gt;</em> are angular correction terms.</p>
<p>The COMB potentials (styles <em>comb</em> and <em>comb3</em>) are variable charge
potentials. The equilibrium charge on each atom is calculated by the
electronegativity equalization (QEq) method. See <a class="reference internal" href="pair_smtbq.html#rick"><span>Rick</span></a> for
further details. This is implemented by the <a class="reference internal" href="fix_qeq_comb.html"><em>fix qeq/comb</em></a> command, which should normally be
specified in the input script when running a model with the COMB
potential. The <a class="reference internal" href="fix_qeq_comb.html"><em>fix qeq/comb</em></a> command has options
that determine how often charge equilibration is performed, its
convergence criterion, and which atoms are included in the
calculation.</p>
<p>Only a single pair_coeff command is used with the <em>comb</em> and <em>comb3</em>
styles which specifies the COMB potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the potential file in the pair_coeff
command, where N is the number of LAMMPS atom types.</p>
<p>For example, if your LAMMPS simulation of a Si/SiO&lt;sub&gt;2&lt;/sub&gt;/
HfO&lt;sub&gt;2&lt;/sub&gt; interface has 4 atom types, and you want the 1st and
last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
use the following pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * ../potentials/ffield.comb Si Hf O Si
</pre></div>
</div>
<p>The first two arguments must be * * so as to span all LAMMPS atom
types. The first and last Si arguments map LAMMPS atom types 1 and 4
to the Si element in the <em>ffield.comb</em> file. The second Hf argument
maps LAMMPS atom type 2 to the Hf element, and the third O argument
maps LAMMPS atom type 3 to the O element in the potential file. If a
mapping value is specified as NULL, the mapping is not performed.
This can be used when a <em>comb</em> potential is used as part of the
<em>hybrid</em> pair style. The NULL values are placeholders for atom types
that will be used with other potentials.</p>
<p>For style <em>comb</em>, the provided potential file <em>ffield.comb</em> contains
all currently-available 2nd generation COMB parameterizations: for Si,
Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style
<em>comb3</em>, the potential file <em>ffield.comb3</em> contains all
currently-available 3rd generation COMB paramterizations: O, Cu, N, C,
H, Ti, Zn and Zr. The status of the optimization of the compounds, for
example Cu&lt;sub&gt;2&lt;/sub&gt;O, TiN and hydrocarbons, are given in the
following table:</p>
<img alt="_images/pair_comb2.jpg" class="align-center" src="_images/pair_comb2.jpg" />
<p>For style <em>comb3</em>, in addition to ffield.comb3, a special parameter
file, <em>lib.comb3</em>, that is exclusively used for C/O/H systems, will be
automatically loaded if carbon atom is detected in LAMMPS input
structure. This file must be in your working directory or in the
directory pointed to by the environment variable LAMMPS_POTENTIALS, as
described on the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command doc page.</p>
<p>Keyword <em>polar</em> indicates whether the force field includes
the atomic polarization. Since the equilibration of the polarization
has not yet been implemented, it can only set polar_off at present.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">You can not use potential file <em>ffield.comb</em> with style <em>comb3</em>,
nor file <em>ffield.comb3</em> with style <em>comb</em>.</p>
</div>
<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>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.</p>
<p>These pair styles does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>These pair styles do not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style, pair_coeff, and <a class="reference internal" href="fix_qeq_comb.html"><em>fix qeq/comb</em></a> commands 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>These pair styles are part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>These pair styles requires the <a class="reference internal" href="newton.html"><em>newton</em></a> setting to be &#8220;on&#8221;
for pair interactions.</p>
<p>The COMB potentials in the <em>ffield.comb</em> and <em>ffield.comb3</em> files provided
with LAMMPS (see the potentials directory) are parameterized for metal
<a class="reference internal" href="units.html"><em>units</em></a>. You can use the COMB potential with any LAMMPS
units, but you would need to create your own COMB potential file with
coefficients listed in the appropriate units if your simulation
doesn&#8217;t use &#8220;metal&#8221; units.</p>
</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_style.html"><em>pair_style</em></a>, <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>,
<a class="reference internal" href="fix_qeq_comb.html"><em>fix qeq/comb</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="comb"><strong>(COMB)</strong> T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and
S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)</p>
<p id="comb3"><strong>(COMB3)</strong> T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek,
Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. &amp; Eng: R 74,
255-279 (2013).</p>
<p id="rick"><strong>(Rick)</strong> S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
(1994).</p>
</div>
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<div class="section" id="pair-style-coul-cut-command">
<span id="index-0"></span><h1>pair_style coul/cut command<a class="headerlink" href="#pair-style-coul-cut-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-cut-gpu-command">
<h1>pair_style coul/cut/gpu command<a class="headerlink" href="#pair-style-coul-cut-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-cut-kk-command">
<h1>pair_style coul/cut/kk command<a class="headerlink" href="#pair-style-coul-cut-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-cut-omp-command">
<h1>pair_style coul/cut/omp command<a class="headerlink" href="#pair-style-coul-cut-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-debye-command">
<h1>pair_style coul/debye command<a class="headerlink" href="#pair-style-coul-debye-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-debye-gpu-command">
<h1>pair_style coul/debye/gpu command<a class="headerlink" href="#pair-style-coul-debye-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-debye-kk-command">
<h1>pair_style coul/debye/kk command<a class="headerlink" href="#pair-style-coul-debye-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-debye-omp-command">
<h1>pair_style coul/debye/omp command<a class="headerlink" href="#pair-style-coul-debye-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-dsf-command">
<h1>pair_style coul/dsf command<a class="headerlink" href="#pair-style-coul-dsf-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-dsf-gpu-command">
<h1>pair_style coul/dsf/gpu command<a class="headerlink" href="#pair-style-coul-dsf-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-dsf-kk-command">
<h1>pair_style coul/dsf/kk command<a class="headerlink" href="#pair-style-coul-dsf-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-dsf-omp-command">
<h1>pair_style coul/dsf/omp command<a class="headerlink" href="#pair-style-coul-dsf-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-long-command">
<h1>pair_style coul/long command<a class="headerlink" href="#pair-style-coul-long-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-long-cs-command">
<h1>pair_style coul/long/cs command<a class="headerlink" href="#pair-style-coul-long-cs-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-long-omp-command">
<h1>pair_style coul/long/omp command<a class="headerlink" href="#pair-style-coul-long-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-long-gpu-command">
<h1>pair_style coul/long/gpu command<a class="headerlink" href="#pair-style-coul-long-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-long-kk-command">
<h1>pair_style coul/long/kk command<a class="headerlink" href="#pair-style-coul-long-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-msm-command">
<h1>pair_style coul/msm command<a class="headerlink" href="#pair-style-coul-msm-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-msm-omp-command">
<h1>pair_style coul/msm/omp command<a class="headerlink" href="#pair-style-coul-msm-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-streitz-command">
<h1>pair_style coul/streitz command<a class="headerlink" href="#pair-style-coul-streitz-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-wolf-command">
<h1>pair_style coul/wolf command<a class="headerlink" href="#pair-style-coul-wolf-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-wolf-kk-command">
<h1>pair_style coul/wolf/kk command<a class="headerlink" href="#pair-style-coul-wolf-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-wolf-omp-command">
<h1>pair_style coul/wolf/omp command<a class="headerlink" href="#pair-style-coul-wolf-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tip4p-cut-command">
<h1>pair_style tip4p/cut command<a class="headerlink" href="#pair-style-tip4p-cut-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tip4p-long-command">
<h1>pair_style tip4p/long command<a class="headerlink" href="#pair-style-tip4p-long-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tip4p-cut-omp-command">
<h1>pair_style tip4p/cut/omp command<a class="headerlink" href="#pair-style-tip4p-cut-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tip4p-long-omp-command">
<h1>pair_style tip4p/long/omp command<a class="headerlink" href="#pair-style-tip4p-long-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 coul/cut cutoff
pair_style coul/debye kappa cutoff
pair_style coul/dsf alpha cutoff
pair_style coul/long cutoff
pair_style coul/long/cs cutoff
pair_style coul/long/gpu cutoff
pair_style coul/wolf alpha cutoff
pair_style coul/streitz cutoff keyword alpha
pair_style tip4p/cut otype htype btype atype qdist cutoff
pair_style tip4p/long otype htype btype atype qdist cutoff
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for Coulombic interactions</li>
<li>kappa = Debye length (inverse distance units)</li>
<li>alpha = damping parameter (inverse distance units)</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 coul/cut 2.5
pair_coeff * *
pair_coeff 2 2 3.5
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style coul/debye 1.4 3.0
pair_coeff * *
pair_coeff 2 2 3.5
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style coul/dsf 0.05 10.0
pair_coeff * *
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style coul/long 10.0
pair_style coul/long/cs 10.0
pair_coeff * *
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style coul/msm 10.0
pair_coeff * *
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style coul/wolf 0.2 9.0
pair_coeff * *
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style coul/streitz 12.0 ewald
pair_style coul/streitz 12.0 wolf 0.30
pair_coeff * * AlO.streitz Al O
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style tip4p/cut 1 2 7 8 0.15 12.0
pair_coeff * *
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style tip4p/long 1 2 7 8 0.15 10.0
pair_coeff * *
</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>coul/cut</em> style computes the standard Coulombic interaction
potential given by</p>
<img alt="_images/pair_coulomb.jpg" class="align-center" src="_images/pair_coulomb.jpg" />
<p>where C is an energy-conversion constant, Qi and Qj are the charges on
the 2 atoms, and epsilon is the dielectric constant which can be set
by the <a class="reference internal" href="dielectric.html"><em>dielectric</em></a> command. The cutoff Rc truncates
the interaction distance.</p>
<hr class="docutils" />
<p>Style <em>coul/debye</em> adds an additional exp() damping factor to the
Coulombic term, given by</p>
<img alt="_images/pair_debye.jpg" class="align-center" src="_images/pair_debye.jpg" />
<p>where kappa is the Debye length. This potential is another way to
mimic the screening effect of a polar solvent.</p>
<hr class="docutils" />
<p>Style <em>coul/dsf</em> computes Coulombic interactions via the damped
shifted force model described in <a class="reference internal" href="pair_lj.html#fennell"><span>Fennell</span></a>, given by:</p>
<img alt="_images/pair_coul_dsf.jpg" class="align-center" src="_images/pair_coul_dsf.jpg" />
<p>where <em>alpha</em> is the damping parameter and erfc() is the
complementary error-function. The potential corrects issues in the
Wolf model (described below) to provide consistent forces and energies
(the Wolf potential is not differentiable at the cutoff) and smooth
decay to zero.</p>
<hr class="docutils" />
<p>Style <em>coul/wolf</em> computes Coulombic interactions via the Wolf
summation method, described in <a class="reference internal" href="pair_smtbq.html#wolf"><span>Wolf</span></a>, given by:</p>
<img alt="_images/pair_coul_wolf.jpg" class="align-center" src="_images/pair_coul_wolf.jpg" />
<p>where <em>alpha</em> is the damping parameter, and erc() and erfc() are
error-fuction and complementary error-function terms. This potential
is essentially a short-range, spherically-truncated,
charge-neutralized, shifted, pairwise <em>1/r</em> summation. With a
manipulation of adding and substracting a self term (for i = j) to the
first and second term on the right-hand-side, respectively, and a
small enough <em>alpha</em> damping parameter, the second term shrinks and
the potential becomes a rapidly-converging real-space summation. With
a long enough cutoff and small enough alpha parameter, the energy and
forces calcluated by the Wolf summation method approach those of the
Ewald sum. So it is a means of getting effective long-range
interactions with a short-range potential.</p>
<hr class="docutils" />
<p>Style <em>coul/streitz</em> is the Coulomb pair interaction defined as part
of the Streitz-Mintmire potential, as described in <a class="reference internal" href="#streitz"><span>this paper</span></a>, in which charge distribution about an atom is modeled
as a Slater 1*s* orbital. More details can be found in the referenced
paper. To fully reproduce the published Streitz-Mintmire potential,
which is a variable charge potential, style <em>coul/streitz</em> must be
used with <a class="reference internal" href="pair_eam.html"><em>pair_style eam/alloy</em></a> (or some other
short-range potential that has been parameterized appropriately) via
the <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a> command. Likewise,
charge equilibration must be performed via the <a class="reference internal" href="fix_qeq.html"><em>fix qeq/slater</em></a> command. For example:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy
pair_coeff * * coul/streitz AlO.streitz Al O
pair_coeff * * eam/alloy AlO.eam.alloy Al O
fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz
</pre></div>
</div>
<p>The keyword <em>wolf</em> in the coul/streitz command denotes computing
Coulombic interactions via Wolf summation. An additional damping
parameter is required for the Wolf summation, as described for the
coul/wolf potential above. Alternatively, Coulombic interactions can
be computed via an Ewald summation. For example:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy
kspace_style ewald 1e-6
</pre></div>
</div>
<p>Keyword <em>ewald</em> does not need a damping parameter, but a
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> must be defined, which can be style
<em>ewald</em> or <em>pppm</em>. The Ewald method was used in Streitz and
Mintmire&#8217;s original paper, but a Wolf summation offers a speed-up in
some cases.</p>
<p>For the fix qeq/slater command, the <em>qfile</em> can be a filename that
contains QEq parameters as discussed on the <a class="reference internal" href="fix_qeq.html"><em>fix qeq</em></a>
command doc page. Alternatively <em>qfile</em> can be replaced by
&#8220;coul/streitz&#8221;, in which case the fix will extract QEq parameters from
the coul/streitz pair style itself.</p>
<p>See the examples/strietz directory for an example input script that
uses the Streitz-Mintmire potential. The potentials directory has the
AlO.eam.alloy and AlO.streitz potential files used by the example.</p>
<p>Note that the Streiz-Mintmire potential is generally used for oxides,
but there is no conceptual problem with extending it to nitrides and
carbides (such as SiC, TiN). Pair coul/strietz used by itself or with
any other pair style such as EAM, MEAM, Tersoff, or LJ in
hybrid/overlay mode. To do this, you would need to provide a
Streitz-Mintmire parameterizaion for the material being modeled.</p>
<hr class="docutils" />
<p>Styles <em>coul/long</em> and <em>coul/msm</em> compute the same Coulombic
interactions as style <em>coul/cut</em> except that an additional damping
factor is applied so it can be used in conjunction with the
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command and its <em>ewald</em> or <em>pppm</em>
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.</p>
<p>Style <em>coul/long/cs</em> is identical to <em>coul/long</em> except that a term is
added for the <a class="reference internal" href="Section_howto.html#howto-25"><span>core/shell model</span></a> to allow
charges on core and shell particles to be separated by r = 0.0.</p>
<p>Styles <em>tip4p/cut</em> and <em>tip4p/long</em> implement the coulomb part of
the TIP4P water model of <a class="reference internal" href="pair_lj.html#jorgensen"><span>(Jorgensen)</span></a>, which introduces
a massless site located a short distance away from the oxygen atom
along the bisector of the HOH angle. The atomic types of the oxygen and
hydrogen atoms, the bond and angle types for OH and HOH interactions,
and the distance to the massless charge site are specified as
pair_style arguments. Style <em>tip4p/cut</em> uses a global cutoff for
Coulomb interactions; style <em>tip4p/long</em> is for use with a long-range
Coulombic solver (Ewald or PPPM).</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">For each TIP4P water molecule in your system, the atom IDs for
the O and 2 H atoms must be consecutive, with the O atom first. This
is to enable LAMMPS to &#8220;find&#8221; the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.</p>
</div>
<p>See the <a class="reference internal" href="Section_howto.html#howto-8"><span>howto section</span></a> for more
information on how to use the TIP4P pair styles and lists of
parameters to set. Note that the neighobr list cutoff for Coulomb
interactions is effectively extended by a distance 2*qdist when using
the TIP4P pair style, to account for the offset distance of the
fictitious charges on O atoms in water molecules. Thus it is
typically best in an efficiency sense to use a LJ cutoff &gt;= Coulomb
cutoff + 2*qdist, to shrink the size of the neighbor list. This leads
to slightly larger cost for the long-range calculation, so you can
test the trade-off for your model.</p>
<hr class="docutils" />
<p>Note that these potentials are designed to be combined with other pair
potentials via the <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a>
command. This is because they have no repulsive core. Hence if they
are used by themselves, there will be no repulsion to keep two
oppositely charged particles from moving arbitrarily close to each
other.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>cutoff (distance units)</li>
</ul>
<p>For <em>coul/cut</em> and <em>coul/debye</em>, the cutoff coefficient is optional.
If it is not used (as in some of the examples above), the default
global value specified in the pair_style command is used.</p>
<p>For <em>coul/long</em> and <em>coul/msm</em> no cutoff can be specified for an
individual I,J type pair via the pair_coeff command. All type pairs
use the same global Coulombic cutoff specified in the pair_style
command.</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>For atom type pairs I,J and I != J, the cutoff distance for the
<em>coul/cut</em> style can be mixed. The default mix value is <em>geometric</em>.
See the &#8220;pair_modify&#8221; command for details.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option is not relevant
for these pair styles.</p>
<p>The <em>coul/long</em> style supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
table option for tabulation of the short-range portion of the
long-range Coulombic interaction.</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 write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The <em>coul/long</em>, <em>coul/msm</em> and <em>tip4p/long</em> styles are part of the
KSPACE package. The <em>coul/long/cs</em> style is part of the CORESHELL
package. They are only enabled if LAMMPS was built with that package
(which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</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>, <a class="reference internal" href="pair_hybrid.html"><em>pair_style, hybrid/overlay</em></a>, <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="wolf"><strong>(Wolf)</strong> D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
Phys, 110, 8254 (1999).</p>
<p id="fennell"><strong>(Fennell)</strong> C. J. Fennell, J. D. Gezelter, J Chem Phys, 124,
234104 (2006).</p>
<p id="streitz"><strong>(Streitz)</strong> F. H. Streitz, J. W. Mintmire, Phys Rev B, 50, 11996-12003
(1994).</p>
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<div class="section" id="pair-style-coul-diel-command">
<span id="index-0"></span><h1>pair_style coul/diel command<a class="headerlink" href="#pair-style-coul-diel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-coul-diel-omp-command">
<h1>pair_style coul/diel/omp command<a class="headerlink" href="#pair-style-coul-diel-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 coul/diel cutoff
</pre></div>
</div>
<p>cutoff = global cutoff (distance units)</p>
</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 coul/diel 3.5
pair_coeff 1 4 78. 1.375 0.112
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>coul/diel</em> computes a Coulomb correction for implict solvent
ion interactions in which the dielectric perimittivity is distance dependent.
The dielectric permittivity epsilon_D(r) connects to limiting regimes:
One limit is defined by a small dielectric permittivity (close to vacuum)
at or close to contact seperation between the ions. At larger separations
the dielectric permittivity reaches a bulk value used in the regular Coulomb
interaction coul/long or coul/cut.
The transition is modeled by a hyperbolic function which is incorporated
in the Coulomb correction term for small ion separations as follows</p>
<img alt="_images/pair_coul_diel.jpg" class="align-center" src="_images/pair_coul_diel.jpg" />
<p>where r_me is the inflection point of epsilon_D(r) and sigma_e is a slope
defining length scale. C is the same Coulomb conversion factor as in the
pair_styles coul/cut, coul/long, and coul/debye. In this way the Coulomb
interaction between ions is corrected at small distances r. The lower
limit of epsilon_D(r-&gt;0)=5.2 due to dielectric saturation <a class="reference internal" href="#stiles"><span>(Stiles)</span></a>
while the Coulomb interaction reaches its bulk limit by setting
epsilon_D(r-&gt;infty)=epsilon, the bulk value of the solvent which is 78
for water at 298K.</p>
<p>Examples of the use of this type of Coulomb interaction include implicit
solvent simulations of salt ions
<a class="reference internal" href="pair_gauss.html#lenart"><span>(Lenart)</span></a> and of ionic surfactants <a class="reference internal" href="pair_gauss.html#jusufi"><span>(Jusufi)</span></a>.
Note that this potential is only reasonable for implicit solvent simulations
and in combiantion with coul/cut or coul/long. It is also usually combined
with gauss/cut, see <a class="reference internal" href="pair_gauss.html#lenart"><span>(Lenart)</span></a> or <a class="reference internal" href="pair_gauss.html#jusufi"><span>(Jusufi)</span></a>.</p>
<p>The following coefficients must be defined for each pair of atom
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the example
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>epsilon (no units)</li>
<li>r_me (distance units)</li>
<li>sigma_e (distance units)</li>
</ul>
<p>The global cutoff (r_c) specified in the pair_style command is used.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support parameter mixing. Coefficients must be given explicitly for each type of particle pairs.</p>
<p>This pair style supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the Gauss-potential portion of the pair
interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>This pair style does 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>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This style is part of the &#8220;user-misc&#8221; package. It is only enabled
if LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
</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>
<a class="reference internal" href="pair_gauss.html"><em>pair_style gauss/cut</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="stiles"><strong>(Stiles)</strong> Stiles , Hubbard, and Kayser, J Chem Phys, 77,
6189 (1982).</p>
<p id="lenart"><strong>(Lenart)</strong> Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126,
044509 (2007).</p>
<p id="jusufi"><strong>(Jusufi)</strong> Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112,
13783 (2008).</p>
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<div class="section" id="pair-style-born-coul-long-cs-command">
<span id="index-0"></span><h1>pair_style born/coul/long/cs command<a class="headerlink" href="#pair-style-born-coul-long-cs-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-coul-long-cs-command">
<h1>pair_style buck/coul/long/cs command<a class="headerlink" href="#pair-style-buck-coul-long-cs-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 args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>born/coul/long/cs</em> or <em>buck/coul/long/cs</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>born/coul/long/cs</em> args = cutoff (cutoff2)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>buck/coul/long/cs</em> args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</pre>
</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 born/coul/long/cs 10.0 8.0
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style buck/coul/long/cs 10.0
pair_style buck/coul/long/cs 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>These pair styles are designed to be used with the adiabatic
core/shell model of <a class="reference internal" href="#mitchellfinchham"><span>(Mitchell and Finchham)</span></a>. See
<a class="reference internal" href="Section_howto.html#howto-25"><span>Section_howto 25</span></a> of the manual for an
overview of the model as implemented in LAMMPS.</p>
<p>These pair styles are identical to the <a class="reference internal" href="pair_born.html"><em>pair_style born/coul/long</em></a> and <a class="reference internal" href="pair_buck.html"><em>pair_style buck/coul/long</em></a> styles, except they correctly treat the
special case where the distance between two charged core and shell
atoms in the same core/shell pair approach r = 0.0. This needs
special treatment when a long-range solver for Coulombic interactions
is also used, i.e. via the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command.</p>
<p>More specifically, the short-range Coulomb interaction between a core
and its shell should be turned off using the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command by setting the 1-2 weight
to 0.0, which works because the core and shell atoms are bonded to
each other. This induces a long-range correction approximation which
fails at small distances (~&lt; 10e-8). Therefore, the Coulomb term which
is used to calculate the correction factor is extended by a minimal
distance (r_min = 1.0-6) when the interaction between a core/shell
pair is treated, as follows</p>
<img alt="_images/pair_cs.jpg" class="align-center" src="_images/pair_cs.jpg" />
<p>where C is an energy-conversion constant, Qi and Qj are the charges on
the core and shell, epsilon is the dielectric constant and r_min is the
minimal distance.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>These pair styles are part of the CORESHELL 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>Making LAMMPS</span></a> section for more info.</p>
</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>, <a class="reference internal" href="pair_born.html"><em>pair_style born</em></a>,
<a class="reference internal" href="pair_buck.html"><em>pair_style buck</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="mitchellfinchham"><strong>(Mitchell and Finchham)</strong> Mitchell, Finchham, J Phys Condensed Matter,
5, 1031-1038 (1993).</p>
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<div class="section" id="pair-style-lj-cut-dipole-cut-command">
<span id="index-0"></span><h1>pair_style lj/cut/dipole/cut command<a class="headerlink" href="#pair-style-lj-cut-dipole-cut-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-dipole-cut-gpu-command">
<h1>pair_style lj/cut/dipole/cut/gpu command<a class="headerlink" href="#pair-style-lj-cut-dipole-cut-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-dipole-cut-omp-command">
<h1>pair_style lj/cut/dipole/cut/omp command<a class="headerlink" href="#pair-style-lj-cut-dipole-cut-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-sf-dipole-sf-command">
<h1>pair_style lj/sf/dipole/sf command<a class="headerlink" href="#pair-style-lj-sf-dipole-sf-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-sf-dipole-sf-gpu-command">
<h1>pair_style lj/sf/dipole/sf/gpu command<a class="headerlink" href="#pair-style-lj-sf-dipole-sf-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-sf-dipole-sf-omp-command">
<h1>pair_style lj/sf/dipole/sf/omp command<a class="headerlink" href="#pair-style-lj-sf-dipole-sf-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-dipole-long-command">
<h1>pair_style lj/cut/dipole/long command<a class="headerlink" href="#pair-style-lj-cut-dipole-long-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-long-dipole-long-command">
<h1>pair_style lj/long/dipole/long command<a class="headerlink" href="#pair-style-lj-long-dipole-long-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 lj/cut/dipole/cut cutoff (cutoff2)
pair_style lj/sf/dipole/sf cutoff (cutoff2)
pair_style lj/cut/dipole/long cutoff (cutoff2)
pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2)
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units)</li>
<li>cutoff2 = global cutoff for Coulombic and dipole (optional) (distance units)</li>
<li>flag_lj = <em>long</em> or <em>cut</em> or <em>off</em></li>
</ul>
<pre class="literal-block">
<em>long</em> = use long-range damping on dispersion 1/r^6 term
<em>cut</em> = use a cutoff on dispersion 1/r^6 term
<em>off</em> = omit disperion 1/r^6 term entirely
</pre>
<ul class="simple">
<li>flag_coul = <em>long</em> or <em>off</em></li>
</ul>
<pre class="literal-block">
<em>long</em> = use long-range damping on Coulombic 1/r and point-dipole terms
<em>off</em> = omit Coulombic and point-dipole terms entirely
</pre>
</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 lj/cut/dipole/cut 10.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/sf/dipole/sf 9.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/dipole/long 10.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/long/dipole/long long long 3.5 10.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>lj/cut/dipole/cut</em> computes interactions between pairs of particles
that each have a charge and/or a point dipole moment. In addition to
the usual Lennard-Jones interaction between the particles (Elj) the
charge-charge (Eqq), charge-dipole (Eqp), and dipole-dipole (Epp)
interactions are computed by these formulas for the energy (E), force
(F), and torque (T) between particles I and J.</p>
<img alt="_images/pair_dipole.jpg" class="align-center" src="_images/pair_dipole.jpg" />
<p>where qi and qj are the charges on the two particles, pi and pj are
the dipole moment vectors of the two particles, r is their separation
distance, and the vector r = Ri - Rj is the separation vector between
the two particles. Note that Eqq and Fqq are simply Coulombic energy
and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
torques do not act symmetrically. These formulas are discussed in
<a class="reference internal" href="pair_gayberne.html#allen"><span>(Allen)</span></a> and in <a class="reference internal" href="#toukmaji"><span>(Toukmaji)</span></a>.</p>
<p>Style <em>lj/sf/dipole/sf</em> computes &#8220;shifted-force&#8221; interactions between
pairs of particles that each have a charge and/or a point dipole
moment. In general, a shifted-force potential is a (sligthly) modified
potential containing extra terms that make both the energy and its
derivative go to zero at the cutoff distance; this removes
(cutoff-related) problems in energy conservation and any numerical
instability in the equations of motion <a class="reference internal" href="pair_gayberne.html#allen"><span>(Allen)</span></a>. Shifted-force
interactions for the Lennard-Jones (E_LJ), charge-charge (Eqq),
charge-dipole (Eqp), dipole-charge (Epq) and dipole-dipole (Epp)
potentials are computed by these formulas for the energy (E), force
(F), and torque (T) between particles I and J:</p>
<img alt="_images/pair_dipole_sf.jpg" class="align-center" src="_images/pair_dipole_sf.jpg" />
<img alt="_images/pair_dipole_sf2.jpg" class="align-center" src="_images/pair_dipole_sf2.jpg" />
<p>where epsilon and sigma are the standard LJ parameters, r_c is the
cutoff, qi and qj are the charges on the two particles, pi and pj are
the dipole moment vectors of the two particles, r is their separation
distance, and the vector r = Ri - Rj is the separation vector between
the two particles. Note that Eqq and Fqq are simply Coulombic energy
and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
torques do not act symmetrically. The shifted-force formula for the
Lennard-Jones potential is reported in <a class="reference internal" href="#stoddard"><span>(Stoddard)</span></a>. The
original (unshifted) formulas for the electrostatic potentials, forces
and torques can be found in <a class="reference internal" href="#price"><span>(Price)</span></a>. The shifted-force
electrostatic potentials have been obtained by applying equation 5.13
of <a class="reference internal" href="pair_gayberne.html#allen"><span>(Allen)</span></a>. The formulas for the corresponding forces and
torques have been obtained by applying the &#8216;chain rule&#8217; as in appendix
C.3 of <a class="reference internal" href="pair_gayberne.html#allen"><span>(Allen)</span></a>.</p>
<p>If one cutoff is specified in the pair_style command, it is used for
both the LJ and Coulombic (q,p) terms. If two cutoffs are specified,
they are used as cutoffs for the LJ and Coulombic (q,p) terms
respectively.</p>
<p>Style <em>lj/cut/dipole/long</em> computes long-range point-dipole
interactions as discussed in <a class="reference internal" href="#toukmaji"><span>(Toukmaji)</span></a>. Dipole-dipole,
dipole-charge, and charge-charge interactions are all supported, along
with the standard 12/6 Lennard-Jones interactions, which are computed
with a cutoff. A <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> must be defined to
use this pair style. Currently, only <a class="reference internal" href="kspace_style.html"><em>kspace_style ewald/disp</em></a> support long-range point-dipole
interactions.</p>
<p>Style <em>lj/long/dipole/long</em> also computes point-dipole interactions as
discussed in <a class="reference internal" href="#toukmaji"><span>(Toukmaji)</span></a>. Long-range dipole-dipole,
dipole-charge, and charge-charge interactions are all supported, along
with the standard 12/6 Lennard-Jones interactions. LJ interactions
can be cutoff or long-ranged.</p>
<p>For style <em>lj/long/dipole/long</em>, if <em>flag_lj</em> is set to <em>long</em>, no
cutoff is used on the LJ 1/r^6 dispersion term. The long-range
portion is calculated by using the <a class="reference internal" href="kspace_style.html"><em>kspace_style ewald_disp</em></a> command. The specified LJ cutoff then
determines which portion of the LJ interactions are computed directly
by the pair potential versus which part is computed in reciprocal
space via the Kspace style. If <em>flag_lj</em> is set to <em>cut</em>, the LJ
interactions are simply cutoff, as with <a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut</em></a>. If <em>flag_lj</em> is set to <em>off</em>, LJ interactions
are not computed at all.</p>
<p>If <em>flag_coul</em> is set to <em>long</em>, no cutoff is used on the Coulombic or
dipole interactions. The long-range portion is calculated by using
<em>ewald_disp</em> of the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command. If
<em>flag_coul</em> is set to <em>off</em>, Coulombic and dipole interactions are not
computed at all.</p>
<p>Atoms with dipole moments should be integrated using the <a class="reference internal" href="fix_nve_sphere.html"><em>fix nve/sphere update dipole</em></a> command to rotate the
dipole moments. The <em>omega</em> option on the <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a> command can be used to thermostat the
rotational motion. The <a class="reference internal" href="compute_temp_sphere.html"><em>compute temp/sphere</em></a>
command can be used to monitor the temperature, since it includes
rotational degrees of freedom. The <a class="reference internal" href="atom_style.html"><em>atom_style dipole</em></a> command should be used since it defines the
point dipoles and their rotational state. The magnitude of the dipole
moment for each type of particle can be defined by the
<code class="xref doc docutils literal"><span class="pre">dipole</span></code> command or in the &#8220;Dipoles&#8221; section of the data
file read in by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command. Their initial
orientation can be defined by the <a class="reference internal" href="set.html"><em>set dipole</em></a> command or in
the &#8220;Atoms&#8221; section of the data file.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>cutoff1 (distance units)</li>
<li>cutoff2 (distance units)</li>
</ul>
<p>The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.</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>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distances for this pair style can be mixed. The default
mix value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command for details.</p>
<p>For atom type pairs I,J and I != J, the A, sigma, d1, and d2
coefficients and cutoff distance for this pair style can be mixed. A
is an energy value mixed like a LJ epsilon. D1 and d2 are distance
values and are mixed like sigma. The default mix value is
<em>geometric</em>. See the &#8220;pair_modify&#8221; command for details.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option for the energy of the Lennard-Jones portion of the pair
interaction; such energy goes to zero at the cutoff by construction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>This pair style does 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>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The <em>lj/cut/dipole/cut</em>, <em>lj/cut/dipole/long</em>, and
<em>lj/long/dipole/long</em> styles are part of the DIPOLE 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>Making LAMMPS</span></a> section for more info.</p>
<p>The <em>lj/sf/dipole/sf</em> style is part of the USER-MISC package. It is
only enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>Using dipole pair styles with <em>electron</em> <a class="reference internal" href="units.html"><em>units</em></a> is not
currently supported.</p>
</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="allen"><strong>(Allen)</strong> Allen and Tildesley, Computer Simulation of Liquids,
Clarendon Press, Oxford, 1987.</p>
<p id="toukmaji"><strong>(Toukmaji)</strong> Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
10913 (2000).</p>
<p id="stoddard"><strong>(Stoddard)</strong> Stoddard and Ford, Phys Rev A, 8, 1504 (1973).</p>
<p id="price"><strong>(Price)</strong> Price, Stone and Alderton, Mol Phys, 52, 987 (1984).</p>
</div>
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<div class="section" id="pair-style-dpd-command">
<span id="index-0"></span><h1>pair_style dpd command<a class="headerlink" href="#pair-style-dpd-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-dpd-gpu-command">
<h1>pair_style dpd/gpu command<a class="headerlink" href="#pair-style-dpd-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-dpd-omp-command">
<h1>pair_style dpd/omp command<a class="headerlink" href="#pair-style-dpd-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-dpd-tstat-command">
<h1>pair_style dpd/tstat command<a class="headerlink" href="#pair-style-dpd-tstat-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-dpd-tstat-gpu-command">
<h1>pair_style dpd/tstat/gpu command<a class="headerlink" href="#pair-style-dpd-tstat-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-dpd-tstat-omp-command">
<h1>pair_style dpd/tstat/omp command<a class="headerlink" href="#pair-style-dpd-tstat-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 dpd T cutoff seed
pair_style dpd/tstat Tstart Tstop cutoff seed
</pre></div>
</div>
<ul class="simple">
<li>T = temperature (temperature units)</li>
<li>Tstart,Tstop = desired temperature at start/end of run (temperature units)</li>
<li>cutoff = global cutoff for DPD interactions (distance units)</li>
<li>seed = random # seed (positive integer)</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 dpd 1.0 2.5 34387
pair_coeff * * 3.0 1.0
pair_coeff 1 1 3.0 1.0 1.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style dpd/tstat 1.0 1.0 2.5 34387
pair_coeff * * 1.0
pair_coeff 1 1 1.0 1.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>dpd</em> computes a force field for dissipative particle dynamics
(DPD) following the exposition in <a class="reference internal" href="#groot"><span>(Groot)</span></a>.</p>
<p>Style <em>dpd/tstat</em> invokes a DPD thermostat on pairwise interactions,
which is equivalent to the non-conservative portion of the DPD force
field. This pair-wise thermostat can be used in conjunction with any
<a class="reference internal" href="pair_style.html"><em>pair style</em></a>, and in leiu of per-particle thermostats
like <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a> or ensemble thermostats like
Nose Hoover as implemented by <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>. To use
<em>dpd/tstat</em> as a thermostat for another pair style, use the <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a> command to compute both the desired
pair interaction and the thermostat for each pair of particles.</p>
<p>For style <em>dpd</em>, the force on atom I due to atom J is given as a sum
of 3 terms</p>
<img alt="_images/pair_dpd.jpg" class="align-center" src="_images/pair_dpd.jpg" />
<p>where Fc is a conservative force, Fd is a dissipative force, and Fr is
a random force. Rij is a unit vector in the direction Ri - Rj, Vij is
the vector difference in velocities of the two atoms = Vi - Vj, alpha
is a Gaussian random number with zero mean and unit variance, dt is
the timestep size, and w(r) is a weighting factor that varies between
0 and 1. Rc is the cutoff. Sigma is set equal to sqrt(2 Kb T gamma),
where Kb is the Boltzmann constant and T is the temperature parameter
in the pair_style command.</p>
<p>For style <em>dpd/tstat</em>, the force on atom I due to atom J is the same
as the above equation, except that the conservative Fc term is
dropped. Also, during the run, T is set each timestep to a ramped
value from Tstart to Tstop.</p>
<p>For style <em>dpd</em>, the pairwise energy associated with style <em>dpd</em> is
only due to the conservative force term Fc, and is shifted to be zero
at the cutoff distance Rc. The pairwise virial is calculated using
all 3 terms. For style <em>dpd/tstat</em> there is no pairwise energy, but
the last two terms of the formula make a contribution to the virial.</p>
<p>For style <em>dpd</em>, the following coefficients must be defined for each
pair of atoms types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in
the examples above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>A (force units)</li>
<li>gamma (force/velocity units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global DPD
cutoff is used. Note that sigma is set equal to sqrt(2 T gamma),
where T is the temperature set by the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a>
command so it does not need to be specified.</p>
<p>For style <em>dpd/tstat</em>, the coefficiencts defined for each pair of
atoms types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command is the same,
except that A is not included.</p>
<p>The GPU-accelerated versions of these styles are implemented based on
the work of <a class="reference internal" href="#afshar"><span>(Afshar)</span></a> and <a class="reference internal" href="#phillips"><span>(Phillips)</span></a>.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you are modeling DPD polymer chains, you may want to use the
<a class="reference internal" href="pair_srp.html"><em>pair_style srp</em></a> command in conjuction with these pair
styles. It is a soft segmental repulsive potential (SRP) that can
prevent DPD polymer chains from crossing each other.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The virial calculation for pressure when using this pair style
includes all the components of force listed above, including the
random force.</p>
</div>
<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. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>These pair 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 pair interaction. Note that as
discussed above, the energy due to the conservative Fc term is already
shifted to be 0.0 at the cutoff distance Rc.</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 style 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 writes their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file. Note
that the user-specified random number seed is stored in the restart
file, so when a simulation is restarted, each processor will
re-initialize its random number generator the same way it did
initially. This means the random forces will be random, but will not
be the same as they would have been if the original simulation had
continued past the restart time.</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>The <em>dpd/tstat</em> style can ramp its target temperature over multiple
runs, using the <em>start</em> and <em>stop</em> keywords of the <a class="reference internal" href="run.html"><em>run</em></a>
command. See the <a class="reference internal" href="run.html"><em>run</em></a> command for details of how to do
this.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The default frequency for rebuilding neighbor lists is every 10 steps
(see the <a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a> command). This may be too
infrequent for style <em>dpd</em> simulations since particles move rapidly
and can overlap by large amounts. If this setting yields a non-zero
number of &#8220;dangerous&#8221; reneighborings (printed at the end of a
simulation), you should experiment with forcing reneighboring more
often and see if system energies/trajectories change.</p>
<p>These pair styles requires you to use the <a class="reference internal" href="comm_modify.html"><em>comm_modify vel yes</em></a> command so that velocites are stored by ghost
atoms.</p>
<p>These pair styles will not restart exactly when using the
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command, though they should provide
statistically similar results. This is because the forces they
compute depend on atom velocities. See the
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command for more details.</p>
</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>, <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a>, <a class="reference internal" href="pair_srp.html"><em>pair_style srp</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="groot"><strong>(Groot)</strong> Groot and Warren, J Chem Phys, 107, 4423-35 (1997).</p>
<p id="afshar"><strong>(Afshar)</strong> Afshar, F. Schmid, A. Pishevar, S. Worley, Comput Phys
Comm, 184, 1119-1128 (2013).</p>
<p id="phillips"><strong>(Phillips)</strong> C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput
Phys Comm, 230, 7191-7201 (2011).</p>
</div>
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<div class="section" id="pair-style-dpd-conservative-command">
<span id="index-0"></span><h1>pair_style dpd/conservative command<a class="headerlink" href="#pair-style-dpd-conservative-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 dpd/conservative cutoff
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for DPD interactions (distance units)</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 dpd/conservative 2.5
pair_coeff * * 3.0 2.5
pair_coeff 1 1 3.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>dpd/conservative</em> computes the conservative force for
dissipative particle dynamics (DPD). The conservative force on atom I
due to atom J is given by</p>
<img alt="_images/pair_dpd_conservative.jpg" class="align-center" src="_images/pair_dpd_conservative.jpg" />
<p>where the weighting factor, omega_ij, varies between 0 and 1, and is
chosen to have the following functional form:</p>
<img alt="_images/pair_dpd_omega.jpg" class="align-center" src="_images/pair_dpd_omega.jpg" />
<p>where Rij is a unit vector in the direction Ri - Rj, and Rc is the
cutoff. Note that alternative definitions of the weighting function
exist, but would have to be implemented as a separate pair style
command.</p>
<p>Style <em>dpd/conservative</em> differs from the other dpd styles in that the
dissipative and random forces are not computed within the pair style.</p>
<p>For style <em>dpd/conservative</em>, the pairwise energy is due only to the
conservative force term Fc, and is shifted to be zero at the cutoff
distance Rc. The pairwise virial is calculated using only the
conservative term.</p>
<p>Style <em>dpd/conservative</em> requires the following coefficients to be
defined for each pair of atoms types via the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li>A (force units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global DPD
cutoff is used.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The pair style <em>dpd/conservative</em> is only available if LAMMPS is built
with the USER-DPD package.</p>
</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>, <a class="reference internal" href="pair_dpd.html"><em>pair_dpd</em></a></p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="pair-style-dpd-fdt-command">
<span id="index-0"></span><h1>pair_style dpd/fdt command<a class="headerlink" href="#pair-style-dpd-fdt-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-dpd-fdt-energy-command">
<h1>pair_style dpd/fdt/energy command<a class="headerlink" href="#pair-style-dpd-fdt-energy-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 args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>dpd/fdt</em> or <em>dpd/fdt/energy</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>dpd/fdt</em> args = T cutoff seed
T = temperature (temperature units)
cutoff = global cutoff for DPD interactions (distance units)
seed = random # seed (positive integer)
<em>dpd/fdt/energy</em> args = cutoff seed
cutoff = global cutoff for DPD interactions (distance units)
seed = random # seed (positive integer)
</pre>
</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 dpd/fdt 300.0 2.5 34387
pair_coeff * * 3.0 1.0 2.5
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style dpd/fdt/energy 2.5 34387
pair_coeff * * 3.0 1.0 0.1 2.5
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Styles <em>dpd/fdt</em> and <em>dpd/fdt/energy</em> set the fluctuation-dissipation
theorem parameters and compute the conservative force for dissipative
particle dynamics (DPD). The conservative force on atom I due to atom
J is given by</p>
<img alt="_images/pair_dpd_conservative.jpg" class="align-center" src="_images/pair_dpd_conservative.jpg" />
<p>where the weighting factor, omega_ij, varies between 0 and 1, and is
chosen to have the following functional form:</p>
<img alt="_images/pair_dpd_omega.jpg" class="align-center" src="_images/pair_dpd_omega.jpg" />
<p>where Rij is a unit vector in the direction Ri - Rj, and Rc is the
cutoff. Note that alternative definitions of the weighting function
exist, but would have to be implemented as a separate pair style
command.</p>
<p>These pair style differ from the other dpd styles in that the
dissipative and random forces are not computed within the pair style.
This style can be combined with the <a class="reference internal" href="fix_shardlow.html"><em>fix shardlow</em></a>
to perform the stochastic integration of the dissipative and random
forces through the Shardlow splitting algorithm approach.</p>
<p>The pairwise energy associated with styles <em>dpd/fdt</em> and
<em>dpd/fdt/energy</em> is only due to the conservative force term Fc, and is
shifted to be zero at the cutoff distance Rc. The pairwise virial is
calculated using only the conservative term.</p>
<p>For style <em>dpd/fdt</em>, the fluctuation-dissipation theorem defines gamma
to be set equal to sigma*sigma/(2 T), where T is the set point
temperature specified as a pair style parameter in the above examples.
This style can be combined with <a class="reference internal" href="fix_shardlow.html"><em>fix shardlow</em></a> to
perform DPD simulations under isothermal and isobaric conditions (see
<a class="reference internal" href="#lisal"><span>(Lisal)</span></a>). The following coefficients must be defined for
each pair of atoms types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command
as in the examples above, or in the data file or restart files read by
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>A (force units)</li>
<li>sigma (force*time^(1/2) units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global DPD
cutoff is used.</p>
<p>For style <em>dpd/fdt/energy</em>, the fluctuation-dissipation theorem
defines gamma to be set equal to sigma*sigma/(2 dpdTheta), where
dpdTheta is the average internal temperature for the pair.
Furthermore, the fluctuation-dissipation defines alpha*alpha to be set
equal to 2*kB*kappa, where kappa is the mesoparticle thermal
conductivity parameter. This style can be combined with <a class="reference internal" href="fix_shardlow.html"><em>fix shardlow</em></a> to perform DPD simulations under
isoenergetic and isoenthalpic conditions (see <a class="reference internal" href="#lisal"><span>(Lisal)</span></a>). The
following coefficients must be defined for each pair of atoms types
via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above,
or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>A (force units)</li>
<li>sigma (force*time^(1/2) units)</li>
<li>kappa (1/time units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global DPD
cutoff is used.</p>
<p>For style <em>dpd/fdt/energy</em>, the particle internal temperature is
related to the particle internal energy through a mesoparticle
equation of state. Thus, an an additional <a class="reference internal" href="fix.html"><em>fix eos</em></a> must be
specified.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>Pair styles <em>dpd/fdt</em> and <em>dpd/fdt/energy</em> are only available if
LAMMPS is built with the USER-DPD package.</p>
<p>Pair styles <em>dpd/fdt</em> and <em>dpd/fdt/energy</em> require use of the
<code class="xref doc docutils literal"><span class="pre">communicate</span> <span class="pre">vel</span> <span class="pre">yes</span></code> option so that velocites are
stored by ghost atoms.</p>
<p>Pair style <em>dpd/fdt/energy</em> requires <a class="reference internal" href="atom_style.html"><em>atom_style dpd</em></a>
to be used in order to properly account for the particle internal
energies and temperatures.</p>
</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>, <a class="reference internal" href="fix_shardlow.html"><em>fix shardlow</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="lisal"><strong>(Lisal)</strong> M. Lisal, J.K. Brennan, J. Bonet Avalos, &#8220;Dissipative
particle dynamics as isothermal, isobaric, isoenergetic, and
isoenthalpic conditions using Shardlow-like splitting algorithms.&#8221;,
J. Chem. Phys., 135, 204105 (2011).</p>
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<div class="section" id="pair-style-dsmc-command">
<span id="index-0"></span><h1>pair_style dsmc command<a class="headerlink" href="#pair-style-dsmc-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 dsmc max_cell_size seed weighting Tref Nrecompute Nsample
</pre></div>
</div>
<ul class="simple">
<li>max_cell_size = global maximum cell size for DSMC interactions (distance units)</li>
<li>seed = random # seed (positive integer)</li>
<li>weighting = macroparticle weighting</li>
<li>Tref = reference temperature (temperature units)</li>
<li>Nrecompute = recompute v*sigma_max every this many timesteps (timesteps)</li>
<li>Nsample = sample this many times in recomputing v*sigma_max</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 dsmc 2.5 34387 10 1.0 100 20
pair_coeff * * 1.0
pair_coeff 1 1 1.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>dsmc</em> computes collisions between pairs of particles for a
direct simulation Monte Carlo (DSMC) model following the exposition in
<a class="reference internal" href="#bird"><span>(Bird)</span></a>. Each collision resets the velocities of the two
particles involved. The number of pairwise collisions for each pair
or particle types and the length scale within which they occur are
determined by the parameters of the pair_style and pair_coeff
commands.</p>
<p>Stochastic collisions are performed using the variable hard sphere
(VHS) approach, with the user-defined <em>max_cell_size</em> value used as
the maximum DSMC cell size, and reference cross-sections for
collisions given using the pair_coeff command.</p>
<p>There is no pairwise energy or virial contributions associated with
this pair style.</p>
<p>The following coefficient must be defined for each pair of atoms types
via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above,
or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>sigma (area units, i.e. distance-squared)</li>
</ul>
<p>The global DSMC <em>max_cell_size</em> determines the maximum cell length
used in the DSMC calculation. A structured mesh is overlayed on the
simulation box such that an integer number of cells are created in
each direction for each processor&#8217;s sub-domain. Cell lengths are
adjusted up to the user-specified maximum cell size.</p>
<hr class="docutils" />
<p>To perform a DSMC simulation with LAMMPS, several additional options
should be set in your input script, though LAMMPS does not check for
these settings.</p>
<p>Since this pair style does not compute particle forces, you should use
the &#8220;fix nve/noforce&#8221; time integration fix for the DSMC particles,
e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>fix 1 all nve/noforce
</pre></div>
</div>
<p>This pair style assumes that all particles will communicated to
neighboring processors every timestep as they move. This makes it
possible to perform all collisions between pairs of particles that are
on the same processor. To ensure this occurs, you should use
these commands:</p>
<div class="highlight-python"><div class="highlight"><pre>neighbor 0.0 bin
neigh_modify every 1 delay 0 check no
atom_modify sort 0 0.0
communicate single cutoff 0.0
</pre></div>
</div>
<p>These commands ensure that LAMMPS communicates particles to
neighboring processors every timestep and that no ghost atoms are
created. The output statistics for a simulation run should indicate
there are no ghost particles or neighbors.</p>
<p>In order to get correct DSMC collision statistics, users should
specify a Gaussian velocity distribution when populating the
simulation domain. Note that the default velocity distribution is
uniform, which will not give good DSMC collision rates. Specify
&#8220;dist gaussian&#8221; when using the <a class="reference internal" href="velocity.html"><em>velocity</em></a> command
as in the following:</p>
<div class="highlight-python"><div class="highlight"><pre>velocity all create 594.6 87287 loop geom dist gaussian
</pre></div>
</div>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option for the energy of the pair interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>This pair style does 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>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file. Note
that the user-specified random number seed is stored in the restart
file, so when a simulation is restarted, each processor will
re-initialize its random number generator the same way it did
initially. This means the random forces will be random, but will not
be the same as they would have been if the original simulation had
continued past the restart time.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This style is part of the MC package. It is only enabled if LAMMPS
was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</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>, <a class="reference internal" href="fix_nve_noforce.html"><em>fix nve/noforce</em></a>,
<a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a>, <a class="reference internal" href="neighbor.html"><em>neighbor</em></a>,
<a class="reference internal" href="comm_modify.html"><em>comm_modify</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="bird"><strong>(Bird)</strong> G. A. Bird, &#8220;Molecular Gas Dynamics and the Direct Simulation
of Gas Flows&#8221; (1994).</p>
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<div class="section" id="pair-style-eam-command">
<span id="index-0"></span><h1>pair_style eam command<a class="headerlink" href="#pair-style-eam-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-cuda-command">
<h1>pair_style eam/cuda command<a class="headerlink" href="#pair-style-eam-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-gpu-command">
<h1>pair_style eam/gpu command<a class="headerlink" href="#pair-style-eam-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-kk-command">
<h1>pair_style eam/kk command<a class="headerlink" href="#pair-style-eam-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-omp-command">
<h1>pair_style eam/omp command<a class="headerlink" href="#pair-style-eam-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-opt-command">
<h1>pair_style eam/opt command<a class="headerlink" href="#pair-style-eam-opt-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-alloy-command">
<h1>pair_style eam/alloy command<a class="headerlink" href="#pair-style-eam-alloy-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-alloy-cuda-command">
<h1>pair_style eam/alloy/cuda command<a class="headerlink" href="#pair-style-eam-alloy-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-alloy-gpu-command">
<h1>pair_style eam/alloy/gpu command<a class="headerlink" href="#pair-style-eam-alloy-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-alloy-kk-command">
<h1>pair_style eam/alloy/kk command<a class="headerlink" href="#pair-style-eam-alloy-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-alloy-omp-command">
<h1>pair_style eam/alloy/omp command<a class="headerlink" href="#pair-style-eam-alloy-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-alloy-opt-command">
<h1>pair_style eam/alloy/opt command<a class="headerlink" href="#pair-style-eam-alloy-opt-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-cd-command">
<h1>pair_style eam/cd command<a class="headerlink" href="#pair-style-eam-cd-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-cd-omp-command">
<h1>pair_style eam/cd/omp command<a class="headerlink" href="#pair-style-eam-cd-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-fs-command">
<h1>pair_style eam/fs command<a class="headerlink" href="#pair-style-eam-fs-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-fs-cuda-command">
<h1>pair_style eam/fs/cuda command<a class="headerlink" href="#pair-style-eam-fs-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-fs-gpu-command">
<h1>pair_style eam/fs/gpu command<a class="headerlink" href="#pair-style-eam-fs-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-fs-kk-command">
<h1>pair_style eam/fs/kk command<a class="headerlink" href="#pair-style-eam-fs-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-fs-omp-command">
<h1>pair_style eam/fs/omp command<a class="headerlink" href="#pair-style-eam-fs-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eam-fs-opt-command">
<h1>pair_style eam/fs/opt command<a class="headerlink" href="#pair-style-eam-fs-opt-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
</pre></div>
</div>
<ul class="simple">
<li>style = <em>eam</em> or <em>eam/alloy</em> or <em>eam/cd</em> or <em>eam/fs</em></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 eam
pair_coeff * * cuu3
pair_coeff 1*3 1*3 niu3.eam
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style eam/alloy
pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style eam/cd
pair_coeff * * ../potentials/FeCr.cdeam Fe Cr
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style eam/fs
pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>eam</em> computes pairwise interactions for metals and metal alloys
using embedded-atom method (EAM) potentials <a class="reference internal" href="pair_polymorphic.html#daw"><span>(Daw)</span></a>. The total
energy Ei of an atom I is given by</p>
<img alt="_images/pair_eam.jpg" class="align-center" src="_images/pair_eam.jpg" />
<p>where F is the embedding energy which is a function of the atomic
electron density rho, phi is a pair potential interaction, and alpha
and beta are the element types of atoms I and J. The multi-body
nature of the EAM potential is a result of the embedding energy term.
Both summations in the formula are over all neighbors J of atom I
within the cutoff distance.</p>
<p>The cutoff distance and the tabulated values of the functionals F,
rho, and phi are listed in one or more files which are specified by
the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command. These are ASCII text files
in a DYNAMO-style format which is described below. DYNAMO was the
original serial EAM MD code, written by the EAM originators. Several
DYNAMO potential files for different metals are included in the
&#8220;potentials&#8221; directory of the LAMMPS distribution. All of these files
are parameterized in terms of LAMMPS <a class="reference internal" href="units.html"><em>metal units</em></a>.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The <em>eam</em> style reads single-element EAM potentials in the
DYNAMO <em>funcfl</em> format. Either single element or alloy systems can be
modeled using multiple <em>funcfl</em> files and style <em>eam</em>. For the alloy
case LAMMPS mixes the single-element potentials to produce alloy
potentials, the same way that DYNAMO does. Alternatively, a single
DYNAMO <em>setfl</em> file or Finnis/Sinclair EAM file can be used by LAMMPS
to model alloy systems by invoking the <em>eam/alloy</em> or <em>eam/cd</em> or
<em>eam/fs</em> styles as described below. These files require no mixing
since they specify alloy interactions explicitly.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Note that unlike for other potentials, cutoffs for EAM
potentials are not set in the pair_style or pair_coeff command; they
are specified in the EAM potential files themselves. Likewise, the
EAM potential files list atomic masses; thus you do not need to use
the <a class="reference internal" href="mass.html"><em>mass</em></a> command to specify them.</p>
</div>
<p>There are several WWW sites that distribute and document EAM
potentials stored in DYNAMO or other formats:</p>
<div class="highlight-python"><div class="highlight"><pre>http://www.ctcms.nist.gov/potentials
http://cst-www.nrl.navy.mil/ccm6/ap
http://enpub.fulton.asu.edu/cms/potentials/main/main.htm
</pre></div>
</div>
<p>These potentials should be usable with LAMMPS, though the alternate
formats would need to be converted to the DYNAMO format used by LAMMPS
and described on this page. The NIST site is maintained by Chandler
Becker (cbecker at nist.gov) who is good resource for info on
interatomic potentials and file formats.</p>
<hr class="docutils" />
<p>For style <em>eam</em>, potential values are read from a file that is in the
DYNAMO single-element <em>funcfl</em> format. If the DYNAMO file was created
by a Fortran program, it cannot have &#8220;D&#8221; values in it for exponents.
C only recognizes &#8220;e&#8221; or &#8220;E&#8221; for scientific notation.</p>
<p>Note that unlike for other potentials, cutoffs for EAM potentials are
not set in the pair_style or pair_coeff command; they are specified in
the EAM potential files themselves.</p>
<p>For style <em>eam</em> a potential file must be assigned to each I,I pair of
atom types by using one or more pair_coeff commands, each with a
single argument:</p>
<ul class="simple">
<li>filename</li>
</ul>
<p>Thus the following command</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff *2 1*2 cuu3.eam
</pre></div>
</div>
<p>will read the cuu3 potential file and use the tabulated Cu values for
F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
1,2 and 2,1 are ignored). See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc
page for alternate ways to specify the path for the potential file.
In effect, this makes atom types 1 and 2 in LAMMPS be Cu atoms.
Different single-element files can be assigned to different atom types
to model an alloy system. The mixing to create alloy potentials for
type pairs with I != J is done automatically the same way that the
serial DYNAMO code originally did it; you do not need to specify
coefficients for these type pairs.</p>
<p><em>Funcfl</em> files in the <em>potentials</em> directory of the LAMMPS
distribution have an &#8221;.eam&#8221; suffix. A DYNAMO single-element <em>funcfl</em>
file is formatted as follows:</p>
<ul class="simple">
<li>line 1: comment (ignored)</li>
<li>line 2: atomic number, mass, lattice constant, lattice type (e.g. FCC)</li>
<li>line 3: Nrho, drho, Nr, dr, cutoff</li>
</ul>
<p>On line 2, all values but the mass are ignored by LAMMPS. The mass is
in mass <a class="reference internal" href="units.html"><em>units</em></a>, e.g. mass number or grams/mole for metal
units. The cubic lattice constant is in Angstroms. On line 3, Nrho
and Nr are the number of tabulated values in the subsequent arrays,
drho and dr are the spacing in density and distance space for the
values in those arrays, and the specified cutoff becomes the pairwise
cutoff used by LAMMPS for the potential. The units of dr are
Angstroms; I&#8217;m not sure of the units for drho - some measure of
electron density.</p>
<p>Following the three header lines are three arrays of tabulated values:</p>
<ul class="simple">
<li>embedding function F(rho) (Nrho values)</li>
<li>effective charge function Z(r) (Nr values)</li>
<li>density function rho(r) (Nr values)</li>
</ul>
<p>The values for each array can be listed as multiple values per line,
so long as each array starts on a new line. For example, the
individual Z(r) values are for r = 0,dr,2*dr, ... (Nr-1)*dr.</p>
<p>The units for the embedding function F are eV. The units for the
density function rho are the same as for drho (see above, electron
density). The units for the effective charge Z are &#8220;atomic charge&#8221; or
sqrt(Hartree * Bohr-radii). For two interacting atoms i,j this is used
by LAMMPS to compute the pair potential term in the EAM energy
expression as r*phi, in units of eV-Angstroms, via the formula</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">r</span><span class="o">*</span><span class="n">phi</span> <span class="o">=</span> <span class="mf">27.2</span> <span class="o">*</span> <span class="mf">0.529</span> <span class="o">*</span> <span class="n">Zi</span> <span class="o">*</span> <span class="n">Zj</span>
</pre></div>
</div>
<p>where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms.</p>
<hr class="docutils" />
<p>Style <em>eam/alloy</em> computes pairwise interactions using the same
formula as style <em>eam</em>. However the associated
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command reads a DYNAMO <em>setfl</em> file
instead of a <em>funcfl</em> file. <em>Setfl</em> files can be used to model a
single-element or alloy system. In the alloy case, as explained
above, <em>setfl</em> files contain explicit tabulated values for alloy
interactions. Thus they allow more generality than <em>funcfl</em> files for
modeling alloys.</p>
<p>For style <em>eam/alloy</em>, potential values are read from a file that is
in the DYNAMO multi-element <em>setfl</em> format, except that element names
(Ni, Cu, etc) are added to one of the lines in the file. If the
DYNAMO file was created by a Fortran program, it cannot have &#8220;D&#8221;
values in it for exponents. C only recognizes &#8220;e&#8221; or &#8220;E&#8221; for
scientific notation.</p>
<p>Only a single pair_coeff command is used with the <em>eam/alloy</em> style
which specifies a DYNAMO <em>setfl</em> file, which contains information for
M elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N element names = mapping of <em>setfl</em> elements to atom types</li>
</ul>
<p>As an example, the potentials/NiAlH_jea.eam.alloy file is a <em>setfl</em>
file which has tabulated EAM values for 3 elements and their alloy
interactions: Ni, Al, and H. See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc
page for alternate ways to specify the path for the potential file.
If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to
be Ni, and the 4th to be Al, you would use the following pair_coeff
command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni
element in the <em>setfl</em> file. The final Al argument maps LAMMPS atom
type 4 to the Al element in the <em>setfl</em> file. Note that there is no
requirement that your simulation use all the elements specified by the
<em>setfl</em> file.</p>
<p>If a mapping value is specified as NULL, the mapping is not performed.
This can be used when an <em>eam/alloy</em> potential is used as part of the
<em>hybrid</em> pair style. The NULL values are placeholders for atom types
that will be used with other potentials.</p>
<p><em>Setfl</em> files in the <em>potentials</em> directory of the LAMMPS distribution
have an &#8221;.eam.alloy&#8221; suffix. A DYNAMO multi-element <em>setfl</em> file is
formatted as follows:</p>
<ul class="simple">
<li>lines 1,2,3 = comments (ignored)</li>
<li>line 4: Nelements Element1 Element2 ... ElementN</li>
<li>line 5: Nrho, drho, Nr, dr, cutoff</li>
</ul>
<p>In a DYNAMO <em>setfl</em> file, line 4 only lists Nelements = the # of
elements in the <em>setfl</em> file. For LAMMPS, the element name (Ni, Cu,
etc) of each element must be added to the line, in the order the
elements appear in the file.</p>
<p>The meaning and units of the values in line 5 is the same as for the
<em>funcfl</em> file described above. Note that the cutoff (in Angstroms) is
a global value, valid for all pairwise interactions for all element
pairings.</p>
<p>Following the 5 header lines are Nelements sections, one for each
element, each with the following format:</p>
<ul class="simple">
<li>line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)</li>
<li>embedding function F(rho) (Nrho values)</li>
<li>density function rho(r) (Nr values)</li>
</ul>
<p>As with the <em>funcfl</em> files, only the mass (in mass <a class="reference internal" href="units.html"><em>units</em></a>,
e.g. mass number or grams/mole for metal units) is used by LAMMPS from
the 1st line. The cubic lattice constant is in Angstroms. The F and
rho arrays are unique to a single element and have the same format and
units as in a <em>funcfl</em> file.</p>
<p>Following the Nelements sections, Nr values for each pair potential
phi(r) array are listed for all i,j element pairs in the same format
as other arrays. Since these interactions are symmetric (i,j = j,i)
only phi arrays with i &gt;= j are listed, in the following order: i,j =
(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements,
Nelements). Unlike the effective charge array Z(r) in <em>funcfl</em> files,
the tabulated values for each phi function are listed in <em>setfl</em> files
directly as r*phi (in units of eV-Angstroms), since they are for atom
pairs.</p>
<hr class="docutils" />
<p>Style <em>eam/cd</em> is similar to the <em>eam/alloy</em> style, except that it
computes alloy pairwise interactions using the concentration-dependent
embedded-atom method (CD-EAM). This model can reproduce the enthalpy
of mixing of alloys over the full composition range, as described in
<a class="reference internal" href="#stukowski"><span>(Stukowski)</span></a>.</p>
<p>The pair_coeff command is specified the same as for the <em>eam/alloy</em>
style. However the DYNAMO <em>setfl</em> file must has two
lines added to it, at the end of the file:</p>
<ul class="simple">
<li>line 1: Comment line (ignored)</li>
<li>line 2: N Coefficient0 Coefficient1 ... CoeffincientN</li>
</ul>
<p>The last line begins with the degree <em>N</em> of the polynomial function
<em>h(x)</em> that modifies the cross interaction between A and B elements.
Then <em>N+1</em> coefficients for the terms of the polynomial are then
listed.</p>
<p>Modified EAM <em>setfl</em> files used with the <em>eam/cd</em> style must contain
exactly two elements, i.e. in the current implementation the <em>eam/cd</em>
style only supports binary alloys. The first and second elements in
the input EAM file are always taken as the <em>A</em> and <em>B</em> species.</p>
<p><em>CD-EAM</em> files in the <em>potentials</em> directory of the LAMMPS
distribution have a &#8221;.cdeam&#8221; suffix.</p>
<hr class="docutils" />
<p>Style <em>eam/fs</em> computes pairwise interactions for metals and metal
alloys using a generalized form of EAM potentials due to Finnis and
Sinclair <a class="reference internal" href="#finnis"><span>(Finnis)</span></a>. The total energy Ei of an atom I is
given by</p>
<img alt="_images/pair_eam_fs.jpg" class="align-center" src="_images/pair_eam_fs.jpg" />
<p>This has the same form as the EAM formula above, except that rho is
now a functional specific to the atomic types of both atoms I and J,
so that different elements can contribute differently to the total
electron density at an atomic site depending on the identity of the
element at that atomic site.</p>
<p>The associated <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command for style <em>eam/fs</em>
reads a DYNAMO <em>setfl</em> file that has been extended to include
additional rho_alpha_beta arrays of tabulated values. A discussion of
how FS EAM differs from conventional EAM alloy potentials is given in
<a class="reference internal" href="#ackland1"><span>(Ackland1)</span></a>. An example of such a potential is the same
author&#8217;s Fe-P FS potential <a class="reference internal" href="#ackland2"><span>(Ackland2)</span></a>. Note that while FS
potentials always specify the embedding energy with a square root
dependence on the total density, the implementation in LAMMPS does not
require that; the user can tabulate any functional form desired in the
FS potential files.</p>
<p>For style <em>eam/fs</em>, the form of the pair_coeff command is exactly the
same as for style <em>eam/alloy</em>, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al
</pre></div>
</div>
<p>where there are N additional arguments after the filename, where N is
the number of LAMMPS atom types. See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>
doc page for alternate ways to specify the path for the potential
file. The N values determine the mapping of LAMMPS atom types to EAM
elements in the file, as described above for style <em>eam/alloy</em>. As
with <em>eam/alloy</em>, if a mapping value is NULL, the mapping is not
performed. This can be used when an <em>eam/fs</em> potential is used as
part of the <em>hybrid</em> pair style. The NULL values are used as
placeholders for atom types that will be used with other potentials.</p>
<p>FS EAM files include more information than the DYNAMO <em>setfl</em> format
files read by <em>eam/alloy</em>, in that i,j density functionals for all
pairs of elements are included as needed by the Finnis/Sinclair
formulation of the EAM.</p>
<p>FS EAM files in the <em>potentials</em> directory of the LAMMPS distribution
have an &#8221;.eam.fs&#8221; suffix. They are formatted as follows:</p>
<ul class="simple">
<li>lines 1,2,3 = comments (ignored)</li>
<li>line 4: Nelements Element1 Element2 ... ElementN</li>
<li>line 5: Nrho, drho, Nr, dr, cutoff</li>
</ul>
<p>The 5-line header section is identical to an EAM <em>setfl</em> file.</p>
<p>Following the header are Nelements sections, one for each element I,
each with the following format:</p>
<ul class="simple">
<li>line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)</li>
<li>embedding function F(rho) (Nrho values)</li>
<li>density function rho(r) for element I at element 1 (Nr values)</li>
<li>density function rho(r) for element I at element 2</li>
<li>...</li>
<li>density function rho(r) for element I at element Nelement</li>
</ul>
<p>The units of these quantities in line 1 are the same as for <em>setfl</em>
files. Note that the rho(r) arrays in Finnis/Sinclair can be
asymmetric (i,j != j,i) so there are Nelements^2 of them listed in the
file.</p>
<p>Following the Nelements sections, Nr values for each pair potential
phi(r) array are listed in the same manner (r*phi, units of
eV-Angstroms) as in EAM <em>setfl</em> files. Note that in Finnis/Sinclair,
the phi(r) arrays are still symmetric, so only phi arrays for i &gt;= j
are listed.</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_accerlate</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>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above with the individual styles. You never need to specify
a pair_coeff command with I != J arguments for the eam styles.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>The eam pair styles do not write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in tabulated potential files.
Thus, you need to re-specify the pair_style and pair_coeff commands in
an input script that reads a restart file.</p>
<p>The eam 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>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>All of these styles except the <em>eam/cd</em> style are part of the MANYBODY
package. They are only enabled if LAMMPS was built with that package
(which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>The <em>eam/cd</em> style is part of the USER-MISC package and also requires
the MANYBODY package. It is 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>
</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="ackland1"><strong>(Ackland1)</strong> Ackland, Condensed Matter (2005).</p>
<p id="ackland2"><strong>(Ackland2)</strong> Ackland, Mendelev, Srolovitz, Han and Barashev, Journal
of Physics: Condensed Matter, 16, S2629 (2004).</p>
<p id="daw"><strong>(Daw)</strong> Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
Daw, Baskes, Phys Rev B, 29, 6443 (1984).</p>
<p id="finnis"><strong>(Finnis)</strong> Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).</p>
<p id="stukowski"><strong>(Stukowski)</strong> Stukowski, Sadigh, Erhart, Caro; Modeling Simulation
Materials Science &amp; Engineering, 7, 075005 (2009).</p>
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<div class="section" id="pair-style-edip-command">
<span id="index-0"></span><h1>pair_style edip command<a class="headerlink" href="#pair-style-edip-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 edip
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style edip/omp
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<p>pair_style edip
pair_coeff * * Si.edip Si</p>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>edip</em> style computes a 3-body <a class="reference internal" href="#edip"><span>EDIP</span></a> potential which is
popular for modeling silicon materials where it can have advantages
over other models such as the <a class="reference internal" href="pair_sw.html"><em>Stillinger-Weber</em></a> or
<a class="reference internal" href="pair_tersoff.html"><em>Tersoff</em></a> potentials. In EDIP, the energy E of a
system of atoms is</p>
<img alt="_images/pair_edip.jpg" class="align-center" src="_images/pair_edip.jpg" />
<p>where phi2 is a two-body term and phi3 is a three-body term. The
summations in the formula are over all neighbors J and K of atom I
within a cutoff distance = a.
Both terms depend on the local environment of atom I through its
effective coordination number defined by Z, which is unity for a
cutoff distance &lt; c and gently goes to 0 at distance = a.</p>
<p>Only a single pair_coeff command is used with the <em>edip</em> style which
specifies a EDIP potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N element names = mapping of EDIP elements to atom types</li>
</ul>
<p>See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc page for alternate ways
to specify the path for the potential file.</p>
<p>As an example, imagine a file Si.edip has EDIP values for Si.</p>
<p>EDIP files in the <em>potentials</em> directory of the LAMMPS
distribution have a &#8221;.edip&#8221; suffix. Lines that are not blank or
comments (starting with #) define parameters for a triplet of
elements. The parameters in a single entry correspond to the two-body
and three-body coefficients in the formula above:</p>
<ul class="simple">
<li>element 1 (the center atom in a 3-body interaction)</li>
<li>element 2</li>
<li>element 3</li>
<li>A (energy units)</li>
<li>B (distance units)</li>
<li>cutoffA (distance units)</li>
<li>cutoffC (distance units)</li>
<li>alpha</li>
<li>beta</li>
<li>eta</li>
<li>gamma (distance units)</li>
<li>lambda (energy units)</li>
<li>mu</li>
<li>tho</li>
<li>sigma (distance units)</li>
<li>Q0</li>
<li>u1</li>
<li>u2</li>
<li>u3</li>
<li>u4</li>
</ul>
<p>The A, B, beta, sigma parameters are used only for two-body interactions.
The eta, gamma, lambda, mu, Q0 and all u1 to u4 parameters are used only
for three-body interactions. The alpha and cutoffC parameters are used
for the coordination environment function only.</p>
<p>The EDIP potential file must contain entries for all the
elements listed in the pair_coeff command. It can also contain
entries for additional elements not being used in a particular
simulation; LAMMPS ignores those entries.</p>
<p>For a single-element simulation, only a single entry is required
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
specify EDIP parameters for all permutations of the two elements
interacting in three-body configurations. Thus for 3 elements, 27
entries would be required, etc.</p>
<p>At the moment, only a single element parametrization is
implemented. However, the author is not aware of other
multi-element EDIP parametrizations. If you know any and
you are interest in that, please contact the author of
the EDIP package.</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>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info on packages.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><em>newton</em></a> setting to be &#8220;on&#8221;
for pair interactions.</p>
<p>The EDIP potential files provided with LAMMPS (see the potentials directory)
are parameterized for metal <a class="reference internal" href="units.html"><em>units</em></a>.
You can use the SW potential with any LAMMPS units, but you would need
to create your own EDIP potential file with coefficients listed in the
appropriate units if your simulation doesn&#8217;t use &#8220;metal&#8221; units.</p>
</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="edip"><strong>(EDIP)</strong> J. F. Justo et al., Phys. Rev. B 58, 2539 (1998).</p>
</div>
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<div class="section" id="pair-style-eff-cut-command">
<span id="index-0"></span><h1>pair_style eff/cut command<a class="headerlink" href="#pair-style-eff-cut-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 eff/cut cutoff keyword args ...
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for Coulombic interactions</li>
<li>zero or more keyword/value pairs may be appended</li>
</ul>
<pre class="literal-block">
keyword = <em>limit/eradius</em> or <em>pressure/evirials</em> or <em>ecp</em>
<em>limit/eradius</em> args = none
<em>pressure/evirials</em> args = none
<em>ecp</em> args = type element type element ...
type = LAMMPS atom type (1 to Ntypes)
element = element symbol (e.g. H, Si)
</pre>
</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 eff/cut 39.7
pair_style eff/cut 40.0 limit/eradius
pair_style eff/cut 40.0 limit/eradius pressure/evirials
pair_style eff/cut 40.0 ecp 1 Si 3 C
pair_coeff * *
pair_coeff 2 2 20.0
pair_coeff 1 s 0.320852 2.283269 0.814857
pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>This pair style contains a LAMMPS implementation of the electron Force
Field (eFF) potential currently under development at Caltech, as
described in <a class="reference internal" href="#jaramillo-botero"><span>(Jaramillo-Botero)</span></a>. The eFF for Z&lt;6
was first introduced by <a class="reference internal" href="#su"><span>(Su)</span></a> in 2007. It has been extended to
higher Zs by using effective core potentials (ECPs) that now cover up
to 2nd and 3rd row p-block elements of the periodic table.</p>
<p>eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
structure methods to describe atomic structure, bonding, and chemistry
in materials, and of plasma methods to describe nonequilibrium
dynamics of large systems with a large number of highly excited
electrons. Yet, eFF relies on a simplification of the electronic
wavefunction in which electrons are described as floating Gaussian
wave packets whose position and size respond to the various dynamic
forces between interacting classical nuclear particles and spherical
Gaussian electron wavepackets. The wavefunction is taken to be a
Hartree product of the wave packets. To compensate for the lack of
explicit antisymmetry in the resulting wavefunction, a spin-dependent
Pauli potential is included in the Hamiltonian. Substituting this
wavefunction into the time-dependent Schrodinger equation produces
equations of motion that correspond - to second order - to classical
Hamiltonian relations between electron position and size, and their
conjugate momenta. The N-electron wavefunction is described as a
product of one-electron Gaussian functions, whose size is a dynamical
variable and whose position is not constrained to a nuclear
center. This form allows for straightforward propagation of the
wavefunction, with time, using a simple formulation from which the
equations of motion are then integrated with conventional MD
algorithms. In addition to this spin-dependent Pauli repulsion
potential term between Gaussians, eFF includes the electron kinetic
energy from the Gaussians. These two terms are based on
first-principles quantum mechanics. On the other hand, nuclei are
described as point charges, which interact with other nuclei and
electrons through standard electrostatic potential forms.</p>
<p>The full Hamiltonian (shown below), contains then a standard
description for electrostatic interactions between a set of
delocalized point and Gaussian charges which include, nuclei-nuclei
(NN), electron-electron (ee), and nuclei-electron (Ne). Thus, eFF is a
mixed QM-classical mechanics method rather than a conventional force
field method (in which electron motions are averaged out into ground
state nuclear motions, i.e a single electronic state, and particle
interactions are described via empirically parameterized interatomic
potential functions). This makes eFF uniquely suited to simulate
materials over a wide range of temperatures and pressures where
electronically excited and ionized states of matter can occur and
coexist. Furthermore, the interactions between particles -nuclei and
electrons- reduce to the sum of a set of effective pairwise potentials
in the eFF formulation. The <em>eff/cut</em> style computes the pairwise
Coulomb interactions between nuclei and electrons (E_NN,E_Ne,E_ee),
and the quantum-derived Pauli (E_PR) and Kinetic energy interactions
potentials between electrons (E_KE) for a total energy expression
given as,</p>
<img alt="_images/eff_energy_expression.jpg" class="align-center" src="_images/eff_energy_expression.jpg" />
<p>The individual terms are defined as follows:</p>
<img alt="_images/eff_KE.jpg" class="align-center" src="_images/eff_KE.jpg" />
<img alt="_images/eff_NN.jpg" class="align-center" src="_images/eff_NN.jpg" />
<img alt="_images/eff_Ne.jpg" class="align-center" src="_images/eff_Ne.jpg" />
<img alt="_images/eff_ee.jpg" class="align-center" src="_images/eff_ee.jpg" />
<img alt="_images/eff_Pauli.jpg" class="align-center" src="_images/eff_Pauli.jpg" />
<p>where, s_i correspond to the electron sizes, the sigmas i&#8217;s to the
fixed spins of the electrons, Z_i to the charges on the nuclei, R_ij
to the distances between the nuclei or the nuclei and electrons, and
r_ij to the distances between electrons. For additional details see
<a class="reference internal" href="#jaramillo-botero"><span>(Jaramillo-Botero)</span></a>.</p>
<p>The overall electrostatics energy is given in Hartree units of energy
by default and can be modified by an energy-conversion constant,
according to the units chosen (see <a class="reference internal" href="units.html"><em>electron_units</em></a>). The
cutoff Rc, given in Bohrs (by default), truncates the interaction
distance. The recommended cutoff for this pair style should follow
the minimum image criterion, i.e. half of the minimum unit cell
length.</p>
<p>Style <em>eff/long</em> (not yet available) computes the same interactions as
style <em>eff/cut</em> except that an additional damping factor is applied so
it can be used in conjunction with the
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command and its <em>ewald</em> or <em>pppm</em>
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.</p>
<p>This potential is designed to be used with <a class="reference internal" href="atom_style.html"><em>atom_style electron</em></a> definitions, in order to handle the
description of systems with interacting nuclei and explicit electrons.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>cutoff (distance units)</li>
</ul>
<p>For <em>eff/cut</em>, the cutoff coefficient is optional. If it is not used
(as in some of the examples above), the default global value specified
in the pair_style command is used.</p>
<p>For <em>eff/long</em> (not yet available) no cutoff will be specified for an
individual I,J type pair via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command.
All type pairs use the same global cutoff specified in the pair_style
command.</p>
<hr class="docutils" />
<p>The <em>limit/eradius</em> and <em>pressure/evirials</em> keywrods are optional.
Neither or both must be specified. If not specified they are unset.</p>
<p>The <em>limit/eradius</em> keyword is used to restrain electron size from
becoming excessively diffuse at very high temperatures were the
Gaussian wave packet representation breaks down, and from expanding as
free particles to infinite size. If unset, electron radius is free to
increase without bounds. If set, a restraining harmonic potential of
the form E = 1/2k_ss^2 for s &gt; L_box/2, where k_s = 1 Hartrees/Bohr^2,
is applied on the electron radius.</p>
<p>The <em>pressure/evirials</em> keyword is used to control between two types
of pressure computation: if unset, the computed pressure does not
include the electronic radial virials contributions to the total
pressure (scalar or tensor). If set, the computed pressure will
include the electronic radial virial contributions to the total
pressure (scalar and tensor).</p>
<p>The <em>ecp</em> keyword is used to associate an ECP representation for a
particular atom type. The ECP captures the orbital overlap between a
core pseudo particle and valence electrons within the Pauli repulsion.
A list of type:element-symbol pairs may be provided for all ECP
representations, after the &#8220;ecp&#8221; keyword.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Default ECP parameters are provided for C, N, O, Al, and Si.
Users can modify these using the pair_coeff command as exemplified
above. For this, the User must distinguish between two different
functional forms supported, one that captures the orbital overlap
assuming the s-type core interacts with an s-like valence electron
(s-s) and another that assumes the interaction is s-p. For systems
that exhibit significant p-character (e.g. C, N, O) the s-p form is
recommended. The &#8220;s&#8221; ECP form requires 3 parameters and the &#8220;p&#8221; 5
parameters.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">there are two different pressures that can be reported for eFF
when defining this pair_style, one (default) that considers electrons
do not contribute radial virial components (i.e. electrons treated as
incompressible &#8216;rigid&#8217; spheres) and one that does. The radial
electronic contributions to the virials are only tallied if the
flexible pressure option is set, and this will affect both global and
per-atom quantities. In principle, the true pressure of a system is
somewhere in between the rigid and the flexible eFF pressures, but,
for most cases, the difference between these two pressures will not be
significant over long-term averaged runs (i.e. even though the energy
partitioning changes, the total energy remains similar).</p>
</div>
<hr class="docutils" />
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This implemention of eFF gives a reasonably accurate description
for systems containing nuclei from Z = 1-6 in &#8220;all electron&#8221;
representations. For systems with increasingly non-spherical
electrons, Users should use the ECP representations. ECPs are now
supported and validated for most of the 2nd and 3rd row elements of
the p-block. Predefined parameters are provided for C, N, O, Al, and
Si. The ECP captures the orbital overlap between the core and valence
electrons (i.e. Pauli repulsion) with one of the functional forms:</p>
</div>
<img alt="_images/eff_ECP1.jpg" class="align-center" src="_images/eff_ECP1.jpg" />
<img alt="_images/eff_ECP2.jpg" class="align-center" src="_images/eff_ECP2.jpg" />
<p>Where the 1st form correspond to core interactions with s-type valence
electrons and the 2nd to core interactions with p-type valence
electrons.</p>
<p>The current version adds full support for models with fixed-core and
ECP definitions. to enable larger timesteps (i.e. by avoiding the
high frequency vibrational modes -translational and radial- of the 2 s
electrons), and in the ECP case to reduce the increased orbital
complexity in higher Z elements (up to Z&lt;18). A fixed-core should be
defined with a mass that includes the corresponding nuclear mass plus
the 2 s electrons in atomic mass units (2x5.4857990943e-4), and a
radius equivalent to that of minimized 1s electrons (see examples
under /examples/USER/eff/fixed-core). An pseudo-core should be
described with a mass that includes the corresponding nuclear mass,
plus all the core electrons (i.e no outer shell electrons), and a
radius equivalent to that of a corresponding minimized full-electron
system. The charge for a pseudo-core atom should be given by the
number of outer shell electrons.</p>
<p>In general, eFF excels at computing the properties of materials in
extreme conditions and tracing the system dynamics over multi-picosend
timescales; this is particularly relevant where electron excitations
can change significantly the nature of bonding in the system. It can
capture with surprising accuracy the behavior of such systems because
it describes consistently and in an unbiased manner many different
kinds of bonds, including covalent, ionic, multicenter, ionic, and
plasma, and how they interconvert and/or change when they become
excited. eFF also excels in computing the relative thermochemistry of
isodemic reactions and conformational changes, where the bonds of the
reactants are of the same type as the bonds of the products. eFF
assumes that kinetic energy differences dominate the overall exchange
energy, which is true when the electrons present are nearly spherical
and nodeless and valid for covalent compounds such as dense hydrogen,
hydrocarbons, and diamond; alkali metals (e.g. lithium), alkali earth
metals (e.g. beryllium) and semimetals such as boron; and various
compounds containing ionic and/or multicenter bonds, such as boron
dihydride.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, the cutoff distance for the
<em>eff/cut</em> style can be mixed. The default mix value is <em>geometric</em>.
See the &#8220;pair_modify&#8221; command for details.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option is not relevant for
these pair styles.</p>
<p>The <em>eff/long</em> (not yet available) style supports the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option for tabulation of the
short-range portion of the long-range Coulombic interaction.</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 write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be 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>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>These pair styles will only be enabled if LAMMPS is built with the
USER-EFF package. It will only be enabled if LAMMPS was built with
that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info.</p>
<p>These pair styles require that particles store electron attributes
such as radius, radial velocity, and radital force, as defined by the
<a class="reference internal" href="atom_style.html"><em>atom_style</em></a>. The <em>electron</em> atom style does all of
this.</p>
<p>Thes pair styles require you to use the <a class="reference internal" href="comm_modify.html"><em>comm_modify vel yes</em></a> command so that velocites are stored by ghost
atoms.</p>
</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>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>If not specified, limit_eradius = 0 and pressure_with_evirials = 0.</p>
<hr class="docutils" />
<p id="su"><strong>(Su)</strong> Su and Goddard, Excited Electron Dynamics Modeling of Warm
Dense Matter, Phys Rev Lett, 99:185003 (2007).</p>
<p id="jaramillo-botero"><strong>(Jaramillo-Botero)</strong> Jaramillo-Botero, Su, Qi, Goddard, Large-scale,
Long-term Non-adiabatic Electron Molecular Dynamics for Describing
Material Properties and Phenomena in Extreme Environments, J Comp
Chem, 32, 497-512 (2011).</p>
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<div class="section" id="pair-style-eim-command">
<span id="index-0"></span><h1>pair_style eim command<a class="headerlink" href="#pair-style-eim-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-eim-omp-command">
<h1>pair_style eim/omp command<a class="headerlink" href="#pair-style-eim-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
</pre></div>
</div>
<ul class="simple">
<li>style = <em>eim</em></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 eim
pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl
pair_coeff * * Na Cl ffield.eim Na Na Na Cl
pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>eim</em> computes pairwise interactions for ionic compounds
using embedded-ion method (EIM) potentials <a class="reference internal" href="pair_polymorphic.html#zhou"><span>(Zhou)</span></a>. The
energy of the system E is given by</p>
<img alt="_images/pair_eim1.jpg" class="align-center" src="_images/pair_eim1.jpg" />
<p>The first term is a double pairwise sum over the J neighbors of all I
atoms, where phi_ij is a pair potential. The second term sums over
the embedding energy E_i of atom I, which is a function of its charge
q_i and the electrical potential sigma_i at its location. E_i, q_i,
and sigma_i are calculated as</p>
<img alt="_images/pair_eim2.jpg" class="align-center" src="_images/pair_eim2.jpg" />
<p>where eta_ji is a pairwise function describing electron flow from atom
I to atom J, and psi_ij is another pairwise function. The multi-body
nature of the EIM potential is a result of the embedding energy term.
A complete list of all the pair functions used in EIM is summarized
below</p>
<img alt="_images/pair_eim3.jpg" class="align-center" src="_images/pair_eim3.jpg" />
<p>Here E_b, r_e, r_(c,phi), alpha, beta, A_(psi), zeta, r_(s,psi),
r_(c,psi), A_(eta), r_(s,eta), r_(c,eta), chi, and pair function type
p are parameters, with subscripts ij indicating the two species of
atoms in the atomic pair.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Even though the EIM potential is treating atoms as charged ions,
you should not use a LAMMPS <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> that stores a
charge on each atom and thus requires you to assign a charge to each
atom, e.g. the <em>charge</em> or <em>full</em> atom styles. This is because the
EIM potential infers the charge on an atom from the equation above for
q_i; you do not assign charges explicitly.</p>
</div>
<hr class="docutils" />
<p>All the EIM parameters are listed in a potential file which is
specified by the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command. This is an
ASCII text file in a format described below. The &#8220;ffield.eim&#8221; file
included in the &#8220;potentials&#8221; directory of the LAMMPS distribution
currently includes nine elements Li, Na, K, Rb, Cs, F, Cl, Br, and I.
A system with any combination of these elements can be modeled. This
file is parameterized in terms of LAMMPS <a class="reference internal" href="units.html"><em>metal units</em></a>.</p>
<p>Note that unlike other potentials, cutoffs for EIM potentials are not
set in the pair_style or pair_coeff command; they are specified in the
EIM potential file itself. Likewise, the EIM potential file lists
atomic masses; thus you do not need to use the <a class="reference internal" href="mass.html"><em>mass</em></a>
command to specify them.</p>
<p>Only a single pair_coeff command is used with the <em>eim</em> style which
specifies an EIM potential file and the element(s) to extract
information for. The EIM elements are mapped to LAMMPS atom types by
specifying N additional arguments after the filename in the pair_coeff
command, where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>Elem1, Elem2, ...</li>
<li>EIM potential file</li>
<li>N element names = mapping of EIM elements to atom types</li>
</ul>
<p>See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc page for alternate ways
to specify the path for the potential file.</p>
<p>As an example like one of those above, suppose you want to model a
system with Na and Cl atoms. If your LAMMPS simulation has 4 atoms
types and you want the 1st 3 to be Na, and the 4th to be Cl, you would
use the following pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * Na Cl ffield.eim Na Na Na Cl
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The filename is the EIM potential file. The Na and Cl arguments
(before the file name) are the two elements for which info will be
extracted from the potentail file. The first three trailing Na
arguments map LAMMPS atom types 1,2,3 to the EIM Na element. The
final Cl argument maps LAMMPS atom type 4 to the EIM Cl element.</p>
<p>If a mapping value is specified as NULL, the mapping is not performed.
This can be used when an <em>eim</em> potential is used as part of the
<em>hybrid</em> pair style. The NULL values are placeholders for atom types
that will be used with other potentials.</p>
<p>The ffield.eim file in the <em>potentials</em> directory of the LAMMPS
distribution is formated as follows:</p>
<p>Lines starting with # are comments and are ignored by LAMMPS. Lines
starting with &#8220;global:&#8221; include three global values. The first value
divides the cations from anions, i.e., any elements with
electronegativity above this value are viewed as anions, and any
elements with electronegativity below this value are viewed as
cations. The second and third values are related to the cutoff
function - i.e. the 0.510204, 1.64498, and 0.010204 shown in the above
equation can be derived from these values.</p>
<p>Lines starting with &#8220;element:&#8221; are formatted as follows: name of
element, atomic number, atomic mass, electronic negativity, atomic
radius (LAMMPS ignores it), ionic radius (LAMMPS ignores it), cohesive
energy (LAMMPS ignores it), and q0 (must be 0).</p>
<p>Lines starting with &#8220;pair:&#8221; are entered as: element 1, element 2,
r_(c,phi), r_(c,phi) (redundant for historical reasons), E_b, r_e,
alpha, beta, r_(c,eta), A_(eta), r_(s,eta), r_(c,psi), A_(psi), zeta,
r_(s,psi), and p.</p>
<p>The lines in the file can be in any order; LAMMPS extracts the info it
needs.</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>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This style is part of the MANYBODY package. It is only enabled if
LAMMPS was built with that package (which it is by default).</p>
</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="zhou"><strong>(Zhou)</strong> Zhou, submitted for publication (2010). Please contact
Xiaowang Zhou (Sandia) for details via email at xzhou at sandia.gov.</p>
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<div class="section" id="pair-style-gauss-command">
<span id="index-0"></span><h1>pair_style gauss command<a class="headerlink" href="#pair-style-gauss-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-gauss-gpu-command">
<h1>pair_style gauss/gpu command<a class="headerlink" href="#pair-style-gauss-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-gauss-omp-command">
<h1>pair_style gauss/omp command<a class="headerlink" href="#pair-style-gauss-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-gauss-cut-command">
<h1>pair_style gauss/cut command<a class="headerlink" href="#pair-style-gauss-cut-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-gauss-cut-omp-command">
<h1>pair_style gauss/cut/omp command<a class="headerlink" href="#pair-style-gauss-cut-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 gauss cutoff
pair_style gauss/cut cutoff
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for Gauss interactions (distance units)</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 gauss 12.0
pair_coeff * * 1.0 0.9
pair_coeff 1 4 1.0 0.9 10.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style gauss/cut 3.5
pair_coeff 1 4 0.2805 1.45 0.112
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>gauss</em> computes a tethering potential of the form</p>
<img alt="_images/pair_gauss.jpg" class="align-center" src="_images/pair_gauss.jpg" />
<p>between an atom and its corresponding tether site which will typically
be a frozen atom in the simulation. Rc is the cutoff.</p>
<p>The following coefficients must be defined for each pair of atom types
via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above,
or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>A (energy units)</li>
<li>B (1/distance^2 units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global cutoff
is used.</p>
<p>Style <em>gauss/cut</em> computes a generalized Gaussian interaction potential
between pairs of particles:</p>
<img alt="_images/pair_gauss_cut.jpg" class="align-center" src="_images/pair_gauss_cut.jpg" />
<p>where H determines together with the standard deviation sigma_h the
peak height of the Gaussian function, and r_mh the peak position.
Examples of the use of the Gaussian potentials include implicit
solvent simulations of salt ions <a class="reference internal" href="#lenart"><span>(Lenart)</span></a> and of surfactants
<a class="reference internal" href="#jusufi"><span>(Jusufi)</span></a>. In these instances the Gaussian potential mimics
the hydration barrier between a pair of particles. The hydration
barrier is located at r_mh and has a width of sigma_h. The prefactor
determines the hight of the potential barrier.</p>
<p>The following coefficients must be defined for each pair of atom types
via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the example above,
or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>H (energy * distance units)</li>
<li>r_mh (distance units)</li>
<li>sigma_h (distance units)</li>
</ul>
<p>The global cutoff (r_c) specified in the pair_style command is used.</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 &#8220;-suffix command-line
switch7_Section_start.html#start_6 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. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>The <em>gauss</em> style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option. There is no effect due to the Gaussian well beyond the
cutoff; hence reasonable cutoffs need to be specified.</p>
<p>The <em>gauss/cut</em> style supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the Gauss-potential portion of the pair
interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table and tail options are not
relevant for these pair styles.</p>
<p>These pair styles write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be 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>The <em>gauss</em> pair style tallies an &#8220;occupancy&#8221; count of how many Gaussian-well
sites have an atom within the distance at which the force is a maximum
= sqrt(0.5/b). This quantity 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 1.</p>
<p>To print this quantity 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 gauss all pair gauss
variable occ equal c_gauss[1]
thermo_style custom step temp epair v_occ
</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>
<p>The <em>gauss/cut</em> style is part of the &#8220;user-misc&#8221; package. It is only
enabled if LAMMPS is build with that package. See the <span class="xref std std-ref">Making of LAMMPS</span> section for more info.</p>
</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>,
<a class="reference internal" href="pair_coul_diel.html"><em>pair_style coul/diel</em></a></p>
<p><strong>Default:</strong> none</p>
<p id="lenart"><strong>(Lenart)</strong> Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126,
044509 (2007).</p>
<p id="jusufi"><strong>(Jusufi)</strong> Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112,
13783 (2008).</p>
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<div class="section" id="pair-style-gayberne-command">
<span id="index-0"></span><h1>pair_style gayberne command<a class="headerlink" href="#pair-style-gayberne-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-gayberne-gpu-command">
<h1>pair_style gayberne/gpu command<a class="headerlink" href="#pair-style-gayberne-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-gayberne-intel-command">
<h1>pair_style gayberne/intel command<a class="headerlink" href="#pair-style-gayberne-intel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-gayberne-omp-command">
<h1>pair_style gayberne/omp command<a class="headerlink" href="#pair-style-gayberne-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 gayberne gamma upsilon mu cutoff
</pre></div>
</div>
<ul class="simple">
<li>gamma = shift for potential minimum (typically 1)</li>
<li>upsilon = exponent for eta orientation-dependent energy function</li>
<li>mu = exponent for chi orientation-dependent energy function</li>
<li>cutoff = global cutoff for interactions (distance units)</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 gayberne 1.0 1.0 1.0 10.0
pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
</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>gayberne</em> styles compute a Gay-Berne anisotropic LJ interaction
<a class="reference internal" href="#berardi"><span>(Berardi)</span></a> between pairs of ellipsoidal particles or an
ellipsoidal and spherical particle via the formulas</p>
<img alt="_images/pair_gayberne.jpg" class="align-center" src="_images/pair_gayberne.jpg" />
<p>where A1 and A2 are the transformation matrices from the simulation
box frame to the body frame and r12 is the center to center vector
between the particles. Ur controls the shifted distance dependent
interaction based on the distance of closest approach of the two
particles (h12) and the user-specified shift parameter gamma. When
both particles are spherical, the formula reduces to the usual
Lennard-Jones interaction (see details below for when Gay-Berne treats
a particle as &#8220;spherical&#8221;).</p>
<p>For large uniform molecules it has been shown that the energy
parameters are approximately representable in terms of local contact
curvatures <a class="reference internal" href="pair_resquared.html#everaers"><span>(Everaers)</span></a>:</p>
<img alt="_images/pair_gayberne2.jpg" class="align-center" src="_images/pair_gayberne2.jpg" />
<p>The variable names utilized as potential parameters are for the most
part taken from <a class="reference internal" href="pair_resquared.html#everaers"><span>(Everaers)</span></a> in order to be consistent with
the <a class="reference internal" href="pair_resquared.html"><em>RE-squared pair potential</em></a>. Details on the
upsilon and mu parameters are given
<a class="reference external" href="PDF/pair_resquared_extra.pdf">here</a>.</p>
<p>More details of the Gay-Berne formulation are given in the references
listed below and in <a class="reference external" href="PDF/pair_gayberne_extra.pdf">this supplementary document</a>.</p>
<p>Use of this pair style requires the NVE, NVT, or NPT fixes with the
<em>asphere</em> extension (e.g. <a class="reference internal" href="fix_nve_asphere.html"><em>fix nve/asphere</em></a>) in
order to integrate particle rotation. Additionally, <a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> should be used since it defines the
rotational state and the size and shape of each ellipsoidal particle.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>epsilon = well depth (energy units)</li>
<li>sigma = minimum effective particle radii (distance units)</li>
<li>epsilon_i_a = relative well depth of type I for side-to-side interactions</li>
<li>epsilon_i_b = relative well depth of type I for face-to-face interactions</li>
<li>epsilon_i_c = relative well depth of type I for end-to-end interactions</li>
<li>epsilon_j_a = relative well depth of type J for side-to-side interactions</li>
<li>epsilon_j_b = relative well depth of type J for face-to-face interactions</li>
<li>epsilon_j_c = relative well depth of type J for end-to-end interactions</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used.</p>
<p>It is typical with the Gay-Berne potential to define <em>sigma</em> as the
minimum of the 3 shape diameters of the particles involved in an I,I
interaction, though this is not required. Note that this is a
different meaning for <em>sigma</em> than the <a class="reference internal" href="pair_resquared.html"><em>pair_style resquared</em></a> potential uses.</p>
<p>The epsilon_i and epsilon_j coefficients are actually defined for atom
types, not for pairs of atom types. Thus, in a series of pair_coeff
commands, they only need to be specified once for each atom type.</p>
<p>Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are
non-zero, the three values are assigned to atom type I. If all the
epsilon_i values are zero, they are ignored. If any of epsilon_j_a,
epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned
to atom type J. If all three epsilon_j values are zero, they are
ignored. Thus the typical way to define the epsilon_i and epsilon_j
coefficients is to list their values in &#8220;pair_coeff I J&#8221; commands when
I = J, but set them to 0.0 when I != J. If you do list them when I !=
J, you should insure they are consistent with their values in other
pair_coeff commands, since only the last setting will be in effect.</p>
<p>Note that if this potential is being used as a sub-style of
<a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a>, and there is no &#8220;pair_coeff I I&#8221;
setting made for Gay-Berne for a particular type I (because I-I
interactions are computed by another hybrid pair potential), then you
still need to insure the epsilon a,b,c coefficients are assigned to
that type. e.g. in a &#8220;pair_coeff I J&#8221; command.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If the epsilon a = b = c for an atom type, and if the shape of
the particle itself is spherical, meaning its 3 shape parameters are
all the same, then the particle is treated as an LJ sphere by the
Gay-Berne potential. This is significant because if two LJ spheres
interact, then the simple Lennard-Jones formula is used to compute
their interaction energy/force using the specified epsilon and sigma
as the standard LJ parameters. This is much cheaper to compute than
the full Gay-Berne formula. To treat the particle as a LJ sphere with
sigma = D, you should normally set epsilon a = b = c = 1.0, set the
pair_coeff sigma = D, and also set the 3 shape parameters for the
particle to D. The one exception is that if the 3 shape parameters
are set to 0.0, which is a valid way in LAMMPS to specify a point
particle, then the Gay-Berne potential will treat that as shape
parameters of 1.0 (i.e. a LJ particle with sigma = 1), since it
requires finite-size particles. In this case you should still set the
pair_coeff sigma to 1.0 as well.</p>
</div>
<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>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for this pair style can be mixed. The default mix
value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command for details.</p>
<p>This pair styles supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the Lennard-Jones portion of the pair
interaction, but only for sphere-sphere interactions. There is no
shifting performed for ellipsoidal interactions due to the anisotropic
dependence of the interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>This pair style does 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>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The <em>gayberne</em> style is part of the ASPHERE package. It is only
enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>These pair style require that atoms store torque and a quaternion to
represent their orientation, as defined by the
<a class="reference internal" href="atom_style.html"><em>atom_style</em></a>. It also require they store a per-type
<code class="xref doc docutils literal"><span class="pre">shape</span></code>. The particles cannot store a per-particle
diameter.</p>
<p>This pair style requires that atoms be ellipsoids as defined by the
<a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> command.</p>
<p>Particles acted on by the potential can be finite-size aspherical or
spherical particles, or point particles. Spherical particles have all
3 of their shape parameters equal to each other. Point particles have
all 3 of their shape parameters equal to 0.0.</p>
<p>The Gay-Berne potential does not become isotropic as r increases
<a class="reference internal" href="pair_resquared.html#everaers"><span>(Everaers)</span></a>. The distance-of-closest-approach
approximation used by LAMMPS becomes less accurate when high-aspect
ratio ellipsoids are used.</p>
</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>, <a class="reference internal" href="fix_nve_asphere.html"><em>fix nve/asphere</em></a>,
<a class="reference internal" href="compute_temp_asphere.html"><em>compute temp/asphere</em></a>, <a class="reference internal" href="pair_resquared.html"><em>pair_style resquared</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="everaers"><strong>(Everaers)</strong> Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).</p>
<p id="berardi"><strong>(Berardi)</strong> Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998).
Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).</p>
<p id="perram"><strong>(Perram)</strong> Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).</p>
<p id="allen"><strong>(Allen)</strong> Allen and Germano, Mol Phys 104, 3225-3235 (2006).</p>
</div>
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<div class="section" id="pair-style-gran-hooke-command">
<span id="index-0"></span><h1>pair_style gran/hooke command<a class="headerlink" href="#pair-style-gran-hooke-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-gran-cuda-command">
<h1>pair_style gran/cuda command<a class="headerlink" href="#pair-style-gran-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-gran-omp-command">
<h1>pair_style gran/omp command<a class="headerlink" href="#pair-style-gran-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-gran-hooke-history-command">
<h1>pair_style gran/hooke/history command<a class="headerlink" href="#pair-style-gran-hooke-history-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-gran-hooke-history-omp-command">
<h1>pair_style gran/hooke/history/omp command<a class="headerlink" href="#pair-style-gran-hooke-history-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-gran-hertz-history-command">
<h1>pair_style gran/hertz/history command<a class="headerlink" href="#pair-style-gran-hertz-history-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-gran-hertz-history-omp-command">
<h1>pair_style gran/hertz/history/omp command<a class="headerlink" href="#pair-style-gran-hertz-history-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 Kn Kt gamma_n gamma_t xmu dampflag
</pre></div>
</div>
<ul class="simple">
<li>style = <em>gran/hooke</em> or <em>gran/hooke/history</em> or <em>gran/hertz/history</em></li>
<li>Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)</li>
<li>Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)</li>
<li>gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)</li>
<li>gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)</li>
<li>xmu = static yield criterion (unitless value between 0.0 and 1.0e4)</li>
<li>dampflag = 0 or 1 if tangential damping force is excluded or included</li>
</ul>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Versions of LAMMPS before 9Jan09 had different style names for
granular force fields. This is to emphasize the fact that the
Hertzian equation has changed to model polydispersity more accurately.
A side effect of the change is that the Kn, Kt, gamma_n, and gamma_t
coefficients in the pair_style command must be specified with
different values in order to reproduce calculations made with earlier
versions of LAMMPS, even for monodisperse systems. See the NOTE below
for details.</p>
</div>
</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 gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1
pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0
</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>gran</em> styles use the following formulas for the frictional force
between two granular particles, as described in
<a class="reference internal" href="#brilliantov"><span>(Brilliantov)</span></a>, <a class="reference internal" href="#silbert"><span>(Silbert)</span></a>, and
<a class="reference internal" href="#zhang"><span>(Zhang)</span></a>, when the distance r between two particles of radii
Ri and Rj is less than their contact distance d = Ri + Rj. There is
no force between the particles when r &gt; d.</p>
<p>The two Hookean styles use this formula:</p>
<img alt="_images/pair_gran_hooke.jpg" class="align-center" src="_images/pair_gran_hooke.jpg" />
<p>The Hertzian style uses this formula:</p>
<img alt="_images/pair_gran_hertz.jpg" class="align-center" src="_images/pair_gran_hertz.jpg" />
<p>In both equations the first parenthesized term is the normal force
between the two particles and the second parenthesized term is the
tangential force. The normal force has 2 terms, a contact force and a
damping force. The tangential force also has 2 terms: a shear force
and a damping force. The shear force is a &#8220;history&#8221; effect that
accounts for the tangential displacement between the particles for the
duration of the time they are in contact. This term is included in
pair styles <em>hooke/history</em> and <em>hertz/history</em>, but is not included
in pair style <em>hooke</em>. The tangential damping force term is included
in all three pair styles if <em>dampflag</em> is set to 1; it is not included
if <em>dampflag</em> is set to 0.</p>
<p>The other quantities in the equations are as follows:</p>
<ul class="simple">
<li>delta = d - r = overlap distance of 2 particles</li>
<li>Kn = elastic constant for normal contact</li>
<li>Kt = elastic constant for tangential contact</li>
<li>gamma_n = viscoelastic damping constant for normal contact</li>
<li>gamma_t = viscoelastic damping constant for tangential contact</li>
<li>m_eff = Mi Mj / (Mi + Mj) = effective mass of 2 particles of mass Mi and Mj</li>
<li>Delta St = tangential displacement vector between 2 spherical particles which is truncated to satisfy a frictional yield criterion</li>
<li>n_ij = unit vector along the line connecting the centers of the 2 particles</li>
<li>Vn = normal component of the relative velocity of the 2 particles</li>
<li>Vt = tangential component of the relative velocity of the 2 particles</li>
</ul>
<p>The Kn, Kt, gamma_n, and gamma_t coefficients are specified as
parameters to the pair_style command. If a NULL is used for Kt, then
a default value is used where Kt = 2/7 Kn. If a NULL is used for
gamma_t, then a default value is used where gamma_t = 1/2 gamma_n.</p>
<p>The interpretation and units for these 4 coefficients are different in
the Hookean versus Hertzian equations.</p>
<p>The Hookean model is one where the normal push-back force for two
overlapping particles is a linear function of the overlap distance.
Thus the specified Kn is in units of (force/distance). Note that this
push-back force is independent of absolute particle size (in the
monodisperse case) and of the relative sizes of the two particles (in
the polydisperse case). This model also applies to the other terms in
the force equation so that the specified gamma_n is in units of
(1/time), Kt is in units of (force/distance), and gamma_t is in units
of (1/time).</p>
<p>The Hertzian model is one where the normal push-back force for two
overlapping particles is proportional to the area of overlap of the
two particles, and is thus a non-linear function of overlap distance.
Thus Kn has units of force per area and is thus specified in units of
(pressure). The effects of absolute particle size (monodispersity)
and relative size (polydispersity) are captured in the radii-dependent
pre-factors. When these pre-factors are carried through to the other
terms in the force equation it means that the specified gamma_n is in
units of (1/(time*distance)), Kt is in units of (pressure), and
gamma_t is in units of (1/(time*distance)).</p>
<p>Note that in the Hookean case, Kn can be thought of as a linear spring
constant with units of force/distance. In the Hertzian case, Kn is
like a non-linear spring constant with units of force/area or
pressure, and as shown in the <a class="reference internal" href="#zhang"><span>(Zhang)</span></a> paper, Kn = 4G /
(3(1-nu)) where nu = the Poisson ratio, G = shear modulus = E /
(2(1+nu)), and E = Young&#8217;s modulus. Similarly, Kt = 4G / (2-nu).
(NOTE: in an earlier version of the manual, we incorrectly stated that
Kt = 8G / (2-nu).)</p>
<p>Thus in the Hertzian case Kn and Kt can be set to values that
corresponds to properties of the material being modeled. This is also
true in the Hookean case, except that a spring constant must be chosen
that is appropriate for the absolute size of particles in the model.
Since relative particle sizes are not accounted for, the Hookean
styles may not be a suitable model for polydisperse systems.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">In versions of LAMMPS before 9Jan09, the equation for Hertzian
interactions did not include the sqrt(RiRj/Ri+Rj) term and thus was
not as accurate for polydisperse systems. For monodisperse systems,
sqrt(RiRj/Ri+Rj) is a constant factor that effectively scales all 4
coefficients: Kn, Kt, gamma_n, gamma_t. Thus you can set the values
of these 4 coefficients appropriately in the current code to reproduce
the results of a previous Hertzian monodisperse calculation. For
example, for the common case of a monodisperse system with particles
of diameter 1, all 4 of these coefficients should now be set 2x larger
than they were previously.</p>
</div>
<p>Xmu is also specified in the pair_style command and is the upper limit
of the tangential force through the Coulomb criterion Ft = xmu*Fn,
where Ft and Fn are the total tangential and normal force components
in the formulas above. Thus in the Hookean case, the tangential force
between 2 particles grows according to a tangential spring and
dash-pot model until Ft/Fn = xmu and is then held at Ft = Fn*xmu until
the particles lose contact. In the Hertzian case, a similar analogy
holds, though the spring is no longer linear.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Normally, xmu should be specified as a fractional value between
0.0 and 1.0, however LAMMPS allows large values (up to 1.0e4) to allow
for modeling of systems which can sustain very large tangential
forces.</p>
</div>
<p>For granular styles there are no additional coefficients to set for
each pair of atom types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command.
All settings are global and are made via the pair_style command.
However you must still use the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> for all
pairs of granular atom types. For example the command</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * *
</pre></div>
</div>
<p>should be used if all atoms in the simulation interact via a granular
potential (i.e. one of the pair styles above is used). If a granular
potential is used as a sub-style of <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a>, then specific atom types can be used in the
pair_coeff command to determine which atoms interact via a granular
potential.</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>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> mix, shift, table, and tail options
are not relevant for granular pair styles.</p>
<p>These pair styles write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so a pair_style command does not need to be
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>The single() function of these pair styles returns 0.0 for the energy
of a pairwise interaction, since energy is not conserved in these
dissipative potentials. It also returns only the normal component of
the pairwise interaction force. However, the single() function also
calculates 4 extra pairwise quantities. The first 3 are the
components of the tangential force between particles I and J, acting
on particle I. <em>P4</em> is the magnitude of this tangential force. These
extra quantites can be accessed by the <a class="reference internal" href="compute_pair_local.html"><em>compute pair/local</em></a> command, as <em>p1</em>, <em>p2</em>, <em>p3</em>,
<em>p4</em>.</p>
</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>
<p>All the granular pair styles are part of the GRANULAR package. It is
only enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>These pair styles require that atoms store torque and angular velocity
(omega) as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style</em></a>. They also
require a per-particle radius is stored. The <em>sphere</em> atom style does
all of this.</p>
<p>This pair style requires you to use the <a class="reference internal" href="comm_modify.html"><em>comm_modify vel yes</em></a> command so that velocites are stored by ghost
atoms.</p>
<p>These pair styles will not restart exactly when using the
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command, though they should provide
statistically similar results. This is because the forces they
compute depend on atom velocities. See the
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command for more details.</p>
</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="brilliantov"><strong>(Brilliantov)</strong> Brilliantov, Spahn, Hertzsch, Poschel, Phys Rev E, 53,
p 5382-5392 (1996).</p>
<p id="silbert"><strong>(Silbert)</strong> Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev
E, 64, p 051302 (2001).</p>
<p id="zhang"><strong>(Zhang)</strong> Zhang and Makse, Phys Rev E, 72, p 011301 (2005).</p>
</div>
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<div class="section" id="pair-style-lj-gromacs-command">
<span id="index-0"></span><h1>pair_style lj/gromacs command<a class="headerlink" href="#pair-style-lj-gromacs-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-gromacs-cuda-command">
<h1>pair_style lj/gromacs/cuda command<a class="headerlink" href="#pair-style-lj-gromacs-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-gromacs-gpu-command">
<h1>pair_style lj/gromacs/gpu command<a class="headerlink" href="#pair-style-lj-gromacs-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-gromacs-omp-command">
<h1>pair_style lj/gromacs/omp command<a class="headerlink" href="#pair-style-lj-gromacs-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-gromacs-coul-gromacs-command">
<h1>pair_style lj/gromacs/coul/gromacs command<a class="headerlink" href="#pair-style-lj-gromacs-coul-gromacs-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-gromacs-coul-gromacs-cuda-command">
<h1>pair_style lj/gromacs/coul/gromacs/cuda command<a class="headerlink" href="#pair-style-lj-gromacs-coul-gromacs-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-gromacs-coul-gromacs-omp-command">
<h1>pair_style lj/gromacs/coul/gromacs/omp command<a class="headerlink" href="#pair-style-lj-gromacs-coul-gromacs-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 args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lj/gromacs</em> or <em>lj/gromacs/coul/gromacs</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>lj/gromacs</em> args = inner outer
inner, outer = global switching cutoffs for Lennard Jones
<em>lj/gromacs/coul/gromacs</em> args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional)
</pre>
</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 lj/gromacs 9.0 12.0
pair_coeff * * 100.0 2.0
pair_coeff 2 2 100.0 2.0 8.0 10.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/gromacs/coul/gromacs 9.0 12.0
pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
pair_coeff * * 100.0 2.0
</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>lj/gromacs</em> styles compute shifted LJ and Coulombic interactions
with an additional switching function S(r) that ramps the energy and force
smoothly to zero between an inner and outer cutoff. It is a commonly
used potential in the <a class="reference external" href="http://www.gromacs.org">GROMACS</a> MD code and for
the coarse-grained models of <a class="reference internal" href="#marrink"><span>(Marrink)</span></a>.</p>
<img alt="_images/pair_gromacs.jpg" class="align-center" src="_images/pair_gromacs.jpg" />
<p>r1 is the inner cutoff; rc is the outer cutoff. The coefficients A, B,
and C are computed by LAMMPS to perform the shifting and smoothing.
The function
S(r) is actually applied once to each term of the LJ formula and once
to the Coulombic formula, so there are 2 or 3 sets of A,B,C coefficients
depending on which pair_style is used. The boundary conditions
applied to the smoothing function are as follows: S&#8217;(r1) = S&#8217;&#8216;(r1) = 0,
S(rc) = -E(rc), S&#8217;(rc) = -E&#8217;(rc), and S&#8217;&#8216;(rc) = -E&#8217;&#8216;(rc),
where E(r) is the corresponding term
in the LJ or Coulombic potential energy function.
Single and double primes denote first and second
derivatives with respect to r, respectively.</p>
<p>The inner and outer cutoff for the LJ and Coulombic terms can be the
same or different depending on whether 2 or 4 arguments are used in
the pair_style command. The inner LJ cutoff must be &gt; 0, but the
inner Coulombic cutoff can be &gt;= 0.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>inner (distance units)</li>
<li>outer (distance units)</li>
</ul>
<p>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at 2^(1/6)
sigma.</p>
<p>The last 2 coefficients are optional inner and outer cutoffs for style
<em>lj/gromacs</em>. If not specified, the global <em>inner</em> and <em>outer</em> values
are used.</p>
<p>The last 2 coefficients cannot be used with style
<em>lj/gromacs/coul/gromacs</em> because this force field does not allow
varying cutoffs for individual atom pairs; all pairs use the global
cutoff(s) specified in the pair_style command.</p>
<hr class="docutils" />
<p>Styles <em>intel</em>, <em>kk</em>, with a <em>cuda</em>, <em>gpu</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>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command
for details.</p>
<p>None of the GROMACS pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option, since the Lennard-Jones
portion of the pair interaction is already smoothed to 0.0 at the
cutoff.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>None of the GROMACS pair styles 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, since there are no corrections for
a potential that goes to 0.0 at the cutoff.</p>
<p>All of the GROMACS pair styles write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.</p>
<p>All of the GROMACS 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>
</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="marrink"><strong>(Marrink)</strong> Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004).</p>
</div>
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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>
</div>
</div>
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<div class="section" id="pair-style-hybrid-command">
<span id="index-0"></span><h1>pair_style hybrid command<a class="headerlink" href="#pair-style-hybrid-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-hybrid-omp-command">
<h1>pair_style hybrid/omp command<a class="headerlink" href="#pair-style-hybrid-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-hybrid-overlay-command">
<h1>pair_style hybrid/overlay command<a class="headerlink" href="#pair-style-hybrid-overlay-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-hybrid-overlay-omp-command">
<h1>pair_style hybrid/overlay/omp command<a class="headerlink" href="#pair-style-hybrid-overlay-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 hybrid style1 args style2 args ...
pair_style hybrid/overlay style1 args style2 args ...
</pre></div>
</div>
<ul class="simple">
<li>style1,style2 = list of one or more pair styles and their arguments</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 lj/cut/coul/cut 10.0 eam lj/cut 5.0
pair_coeff 1*2 1*2 eam niu3
pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
pair_coeff 1*2 3 lj/cut 0.5 1.2
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0
pair_coeff * * lj/cut 1.0 1.0
pair_coeff * * coul/long
</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>hybrid</em> and <em>hybrid/overlay</em> styles enable the use of multiple
pair styles in one simulation. With the <em>hybrid</em> style, exactly one
pair style is assigned to each pair of atom types. With the
<em>hybrid/overlay</em> style, one or more pair styles can be assigned to
each pair of atom types. The assignment of pair styles to type pairs
is made via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command.</p>
<p>Here are two examples of hybrid simulations. The <em>hybrid</em> style could
be used for a simulation of a metal droplet on a LJ surface. The
metal atoms interact with each other via an <em>eam</em> potential, the
surface atoms interact with each other via a <em>lj/cut</em> potential, and
the metal/surface interaction is also computed via a <em>lj/cut</em>
potential. The <em>hybrid/overlay</em> style could be used as in the 2nd
example above, where multiple potentials are superposed in an additive
fashion to compute the interaction between atoms. In this example,
using <em>lj/cut</em> and <em>coul/long</em> together gives the same result as if
the <em>lj/cut/coul/long</em> potential were used by itself. In this case,
it would be more efficient to use the single combined potential, but
in general any combination of pair potentials can be used together in
to produce an interaction that is not encoded in any single pair_style
file, e.g. adding Coulombic forces between granular particles.</p>
<p>All pair styles that will be used are listed as &#8220;sub-styles&#8221; following
the <em>hybrid</em> or <em>hybrid/overlay</em> keyword, in any order. Each
sub-style&#8217;s name is followed by its usual arguments, as illustrated in
the example above. See the doc pages of individual pair styles for a
listing and explanation of the appropriate arguments.</p>
<p>Note that an individual pair style can be used multiple times as a
sub-style. For efficiency this should only be done if your model
requires it. E.g. if you have different regions of Si and C atoms and
wish to use a Tersoff potential for pure Si for one set of atoms, and
a Tersoff potetnial for pure C for the other set (presumably with some
3rd potential for Si-C interactions), then the sub-style <em>tersoff</em>
could be listed twice. But if you just want to use a Lennard-Jones or
other pairwise potential for several different atom type pairs in your
model, then you should just list the sub-style once and use the
pair_coeff command to assign parameters for the different type pairs.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">There are two exceptions to this option to list an individual
pair style multiple times. The first is for pair styles implemented
as Fortran libraries: <a class="reference internal" href="pair_meam.html"><em>pair_style meam</em></a> and <a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a> (<a class="reference internal" href="pair_reax_c.html"><em>pair_style reax/c</em></a> is OK).
This is because unlike a C++ class, they can not be instantiated
multiple times, due to the manner in which they were coded in Fortran.
The second is for GPU-enabled pair styles in the GPU package. This is
b/c the GPU package also currently assumes that only one instance of a
pair style is being used.</p>
</div>
<p>In the pair_coeff commands, the name of a pair style must be added
after the I,J type specification, with the remaining coefficients
being those appropriate to that style. If the pair style is used
multiple times in the pair_style command, then an additional numeric
argument must also be specified which is a number from 1 to M where M
is the number of times the sub-style was listed in the pair style
command. The extra number indicates which instance of the sub-style
these coefficients apply to.</p>
<p>For example, consider a simulation with 3 atom types: types 1 and 2
are Ni atoms, type 3 are LJ atoms with charges. The following
commands would set up a hybrid simulation:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
pair_coeff * * eam/alloy nialhjea Ni Ni NULL
pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
pair_coeff 1*2 3 lj/cut 0.8 1.3
</pre></div>
</div>
<p>As an example of using the same pair style multiple times, consider a
simulation with 2 atom types. Type 1 is Si, type 2 is C. The
following commands would model the Si atoms with Tersoff, the C atoms
with Tersoff, and the cross-interactions with Lennard-Jones:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid lj/cut 2.5 tersoff tersoff
pair_coeff * * tersoff 1 Si.tersoff Si NULL
pair_coeff * * tersoff 2 C.tersoff NULL C
pair_coeff 1 2 lj/cut 1.0 1.5
</pre></div>
</div>
<p>If pair coefficients are specified in the data file read via the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command, then the same rule applies.
E.g. &#8220;eam/alloy&#8221; or &#8220;lj/cut&#8221; must be added after the atom type, for
each line in the &#8220;Pair Coeffs&#8221; section, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>Pair Coeffs
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>1 lj/cut/coul/cut 1.0 1.0
...
</pre></div>
</div>
<p>Note that the pair_coeff command for some potentials such as
<a class="reference internal" href="pair_eam.html"><em>pair_style eam/alloy</em></a> includes a mapping specification
of elements to all atom types, which in the hybrid case, can include
atom types not assigned to the <em>eam/alloy</em> potential. The NULL
keyword is used by many such potentials (eam/alloy, Tersoff, AIREBO,
etc), to denote an atom type that will be assigned to a different
sub-style.</p>
<p>For the <em>hybrid</em> style, each atom type pair I,J is assigned to exactly
one sub-style. Just as with a simulation using a single pair style,
if you specify the same atom type pair in a second pair_coeff command,
the previous assignment will be overwritten.</p>
<p>For the <em>hybrid/overlay</em> style, each atom type pair I,J can be
assigned to one or more sub-styles. If you specify the same atom type
pair in a second pair_coeff command with a new sub-style, then the
second sub-style is added to the list of potentials that will be
calculated for two interacting atoms of those types. If you specify
the same atom type pair in a second pair_coeff command with a
sub-style that has already been defined for that pair of atoms, then
the new pair coefficients simply override the previous ones, as in the
normal usage of the pair_coeff command. E.g. these two sets of
commands are the same:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 2 2 1.5 0.8
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid/overlay lj/cut 2.5
pair_coeff * * lj/cut 1.0 1.0
pair_coeff 2 2 lj/cut 1.5 0.8
</pre></div>
</div>
<p>Coefficients must be defined for each pair of atoms types via the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as described above, or in the
data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> or
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands, or by mixing as described
below.</p>
<p>For both the <em>hybrid</em> and <em>hybrid/overlay</em> styles, every atom type
pair I,J (where I &lt;= J) must be assigned to at least one sub-style via
the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above, or
in the data file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>, or by mixing
as described below.</p>
<p>If you want there to be no interactions between a particular pair of
atom types, you have 3 choices. You can assign the type pair to some
sub-style and use the <a class="reference internal" href="neigh_modify.html"><em>neigh_modify exclude type</em></a>
command. You can assign it to some sub-style and set the coefficients
so that there is effectively no interaction (e.g. epsilon = 0.0 in a
LJ potential). Or, for <em>hybrid</em> and <em>hybrid/overlay</em> simulations, you
can use this form of the pair_coeff command in your input script:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff 2 3 none
</pre></div>
</div>
<p>or this form in the &#8220;Pair Coeffs&#8221; section of the data file:</p>
<div class="highlight-python"><div class="highlight"><pre>3 none
</pre></div>
</div>
<p>If an assignment to <em>none</em> is made in a simulation with the
<em>hybrid/overlay</em> pair style, it wipes out all previous assignments of
that atom type pair to sub-styles.</p>
<p>Note that you may need to use an <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> hybrid
command in your input script, if atoms in the simulation will need
attributes from several atom styles, due to using multiple pair
potentials.</p>
<hr class="docutils" />
<p>Different force fields (e.g. CHARMM vs AMBER) may have different rules
for applying weightings that change the strength of pairwise
interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4
neighbors in the molecular bond topology, as normally set by the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command. Different weights can be
assigned to different pair hybrid sub-styles via the <a class="reference internal" href="pair_modify.html"><em>pair_modify special</em></a> command. This allows multiple force fields
to be used in a model of a hybrid system, however, there is no consistent
approach to determine parameters automatically for the interactions
between the two force fields, this is only recommended when particles
described by the different force fields do not mix.</p>
<p>Here is an example for mixing CHARMM and AMBER: The global <em>amber</em>
setting sets the 1-4 interactions to non-zero scaling factors and
then overrides them with 0.0 only for CHARMM:</p>
<div class="highlight-python"><div class="highlight"><pre>special_bonds amber
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
</pre></div>
</div>
<p>The this input achieves the same effect:</p>
<div class="highlight-python"><div class="highlight"><pre>special_bonds 0.0 0.0 0.1
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
</pre></div>
</div>
<p>Here is an example for mixing Tersoff with OPLS/AA based on
a data file that defines bonds for all atoms where for the
Tersoff part of the system the force constants for the bonded
interactions have been set to 0. Note the global settings are
effectively <em>lj/coul 0.0 0.0 0.5</em> as required for OPLS/AA:</p>
<div class="highlight-python"><div class="highlight"><pre>special_bonds lj/coul 1e-20 1e-20 0.5
pair_hybrid tersoff lj/cut/coul/long 12.0
pair_modify pair tersoff special lj/coul 1.0 1.0 1.0
</pre></div>
</div>
<p>See the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> doc page for details on
the specific syntax, requirements and restrictions.</p>
<hr class="docutils" />
<p>The potential energy contribution to the overall system due to an
individual sub-style can be accessed and output via the <a class="reference internal" href="compute_pair.html"><em>compute pair</em></a> command.</p>
<hr class="docutils" />
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Several of the potentials defined via the pair_style command in
LAMMPS are really many-body potentials, such as Tersoff, AIREBO, MEAM,
ReaxFF, etc. The way to think about using these potentials in a
hybrid setting is as follows.</p>
</div>
<p>A subset of atom types is assigned to the many-body potential with a
single <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command, using &#8220;* <a href="#id1"><span class="problematic" id="id2">*</span></a>&#8221; to include
all types and the NULL keywords described above to exclude specific
types not assigned to that potential. If types 1,3,4 were assigned in
that way (but not type 2), this means that all many-body interactions
between all atoms of types 1,3,4 will be computed by that potential.
Pair_style hybrid allows interactions between type pairs 2-2, 1-2,
2-3, 2-4 to be specified for computation by other pair styles. You
could even add a second interaction for 1-1 to be computed by another
pair style, assuming pair_style hybrid/overlay is used.</p>
<p>But you should not, as a general rule, attempt to exclude the
many-body interactions for some subset of the type pairs within the
set of 1,3,4 interactions, e.g. exclude 1-1 or 1-3 interactions. That
is not conceptually well-defined for many-body interactions, since the
potential will typically calculate energies and foces for small groups
of atoms, e.g. 3 or 4 atoms, using the neighbor lists of the atoms to
find the additional atoms in the group. It is typically non-physical
to think of excluding an interaction between a particular pair of
atoms when the potential computes 3-body or 4-body interactions.</p>
<p>However, you can still use the pair_coeff none setting or the
<a class="reference internal" href="neigh_modify.html"><em>neigh_modify exclude</em></a> command to exclude certain
type pairs from the neighbor list that will be passed to a manybody
sub-style. This will alter the calculations made by a many-body
potential, since it builds its list of 3-body, 4-body, etc
interactions from the pair list. You will need to think carefully as
to whether it produces a physically meaningful result for your model.</p>
<p>For example, imagine you have two atom types in your model, type 1 for
atoms in one surface, and type 2 for atoms in the other, and you wish
to use a Tersoff potential to compute interactions within each
surface, but not between surfaces. Then either of these two command
sequences would implement that model:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid tersoff
pair_coeff * * tersoff SiC.tersoff C C
pair_coeff 1 2 none
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style tersoff
pair_coeff * * SiC.tersoff C C
neigh_modify exclude type 1 2
</pre></div>
</div>
<p>Either way, only neighbor lists with 1-1 or 2-2 interactions would be
passed to the Tersoff potential, which means it would compute no
3-body interactions containing both type 1 and 2 atoms.</p>
<p>Here is another example, using hybrid/overlay, to use 2 many-body
potentials together, in an overlapping manner. Imagine you have CNT
(C atoms) on a Si surface. You want to use Tersoff for Si/Si and Si/C
interactions, and AIREBO for C/C interactions. Si atoms are type 1; C
atoms are type 2. Something like this will work:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid/overlay tersoff airebo 3.0
pair_coeff * * tersoff SiC.tersoff.custom Si C
pair_coeff * * airebo CH.airebo NULL C
</pre></div>
</div>
<p>Note that to prevent the Tersoff potential from computing C/C
interactions, you would need to modify the SiC.tersoff file to turn
off C/C interaction, i.e. by setting the appropriate coefficients to
0.0.</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.</p>
<p>Since the <em>hybrid</em> and <em>hybrid/overlay</em> styles delegate computation
to the individual sub-styles, the suffix versions of the <em>hybrid</em>
and <em>hybrid/overlay</em> styles are used to propagate the corresponding
suffix to all sub-styles, if those versions exist. Otherwise the
non-accelerated version will be used.</p>
<p>The individual accelerated sub-styles are part of the USER-CUDA, GPU,
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>Any pair potential settings made via the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> command are passed along to all
sub-styles of the hybrid potential.</p>
<p>For atom type pairs I,J and I != J, if the sub-style assigned to I,I
and J,J is the same, and if the sub-style allows for mixing, then the
coefficients for I,J can be mixed. This means you do not have to
specify a pair_coeff command for I,J since the I,J type pair will be
assigned automatically to the sub-style defined for both I,I and J,J
and its coefficients generated by the mixing rule used by that
sub-style. For the <em>hybrid/overlay</em> style, there is an additional
requirement that both the I,I and J,J pairs are assigned to a single
sub-style. See the &#8220;pair_modify&#8221; command for details of mixing rules.
See the See the doc page for the sub-style to see if allows for
mixing.</p>
<p>The hybrid pair styles supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options for an I,J pair interaction, if the
associated sub-style supports it.</p>
<p>For the hybrid pair styles, the list of sub-styles and their
respective settings are written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so a <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command does
not need to specified in an input script that reads a restart file.
However, the coefficient information is not stored in the restart
file. Thus, pair_coeff commands need to be re-specified in the
restart input script.</p>
<p>These pair styles support the use of the <em>inner</em>, <em>middle</em>, and
<em>outer</em> keywords of the <a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command, if
their sub-styles do.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>When using a long-range Coulombic solver (via the
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command) with a hybrid pair_style,
one or more sub-styles will be of the &#8220;long&#8221; variety,
e.g. <em>lj/cut/coul/long</em> or <em>buck/coul/long</em>. You must insure that the
short-range Coulombic cutoff used by each of these long pair styles is
the same or else LAMMPS will generate an error.</p>
</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>
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<div class="section" id="pair-style-kim-command">
<span id="index-0"></span><h1>pair_style kim command<a class="headerlink" href="#pair-style-kim-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 kim virialmode model printflag
</pre></div>
</div>
<ul class="simple">
<li>virialmode = KIMvirial or LAMMPSvirial</li>
<li>model = name of KIM model (potential)</li>
<li>printflag = 1/0 do or do not print KIM descriptor file, optional</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 kim KIMvirial model_Ar_P_Morse
pair_coeff * * Ar Ar
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style kim KIMvirial model_Ar_P_Morse 1
pair_coeff * * Ar Ar
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>This pair style is a wrapper on the <a class="reference external" href="https://openkim.org">Knowledge Base for Interatomic Models (KIM)</a> repository of interatomic potentials,
so that they can be used by LAMMPS scripts.</p>
<p>In KIM lingo, a potential is a &#8220;model&#8221; and a model contains both the
analytic formulas that define the potential as well as the parameters
needed to run it for one or more materials, including coefficients and
cutoffs.</p>
<p>The argument <em>virialmode</em> determines how the global virial is
calculated. If <em>KIMvirial</em> is specified, the KIM model performs the
global virial calculation (if it knows how). If <em>LAMMPSvirial</em> is
specified, LAMMPS computes the global virial using its fdotr mechanism.</p>
<p>The argument <em>model</em> is the name of the KIM model for a specific
potential as KIM defines it. In principle, LAMMPS can invoke any KIM
model. You should get an error or warning message from either LAMMPS
or KIM if there is an incompatibility.</p>
<p>The argument <em>printflag</em> is optional. If it is set to a non-zero
value then a KIM dsecriptor file is printed when KIM is invoked. This
can be useful for debugging. The default is to not print this file.</p>
<p>Only a single pair_coeff command is used with the <em>kim</em> style which
specifies the mapping of LAMMPS atom types to KIM elements. This is
done by specifying N additional arguments after the * * in the
pair_coeff command, where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>N element names = mapping of KIM elements to atom types</li>
</ul>
<p>As an example, imagine the KIM model supports Si and C atoms. If your
LAMMPS simulation has 4 atom types and you want the 1st 3 to be Si,
and the 4th to be C, you would use the following pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * Si Si Si C
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to Si as
defined within KIM. The final C argument maps LAMMPS atom type 4 to C
as defined within KIM. If a mapping value is specified as NULL, the
mapping is not performed. This can only be used when a <em>kim</em>
potential is used as part of the <em>hybrid</em> pair style. The NULL values
are placeholders for atom types that will be used with other
potentials.</p>
<hr class="docutils" />
<p>In addition to the usual LAMMPS error messages, the KIM library itself
may generate errors, which should be printed to the screen. In this
case it is also useful to check the kim.log file for additional error
information. This file kim.log should be generated in the same
directory where LAMMPS is running.</p>
<p>To download, build, and install the KIM library on your system, see
the lib/kim/README file. Once you have done this and built LAMMPS
with the KIM package installed you can run the example input scripts
in examples/kim.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
mix, shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since KIM stores the potential parameters.
Thus, you need to re-specify the pair_style and pair_coeff commands in
an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style is part of the KIM package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>This current version of pair_style kim is compatible with the
kim-api package version 1.6.0 and higher.</p>
</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>
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<div class="section" id="pair-style-lcbop-command">
<span id="index-0"></span><h1>pair_style lcbop command<a class="headerlink" href="#pair-style-lcbop-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 lcbop
</pre></div>
</div>
</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 lcbop
pair_coeff * * ../potentials/C.lcbop C
</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>lcbop</em> pair style computes the long-range bond-order potential
for carbon (LCBOP) of <a class="reference internal" href="#los"><span>(Los and Fasolino)</span></a>. See section II in
that paper for the analytic equations associated with the potential.</p>
<p>Only a single pair_coeff command is used with the <em>lcbop</em> style which
specifies an LCBOP potential file with parameters for specific
elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N element names = mapping of LCBOP elements to atom types</li>
</ul>
<p>See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc page for alternate ways
to specify the path for the potential file.</p>
<p>As an example, if your LAMMPS simulation has 4 atom types and you want
the 1st 3 to be C you would use the following pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * C.lcbop C C C NULL
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first C argument maps LAMMPS atom type 1 to the C element in the
LCBOP file. If a mapping value is specified as NULL, the mapping is
not performed. This can be used when a <em>lcbop</em> potential is used as
part of the <em>hybrid</em> pair style. The NULL values are placeholders for
atom types that will be used with other potentials.</p>
<p>The parameters/coefficients for the LCBOP potential as applied to C
are listed in the C.lcbop file to agree with the original <a class="reference internal" href="#los"><span>(Los and Fasolino)</span></a> paper. Thus the parameters are specific to this
potential and the way it was fit, so modifying the file should be done
carefully.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
mix, shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair styles is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>This pair potential requires the <a class="reference internal" href="newton.html"><em>newton</em></a> setting to be
&#8220;on&#8221; for pair interactions.</p>
<p>The C.lcbop potential file provided with LAMMPS (see the potentials
directory) is parameterized for metal <a class="reference internal" href="units.html"><em>units</em></a>. You can use
the LCBOP potential with any LAMMPS units, but you would need to
create your own LCBOP potential file with coefficients listed in the
appropriate units if your simulation doesn&#8217;t use &#8220;metal&#8221; units.</p>
</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_airebo.html"><em>pair_airebo</em></a>, <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="los"><strong>(Los and Fasolino)</strong> J. H. Los and A. Fasolino, Phys. Rev. B 68, 024107
(2003).</p>
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<div class="section" id="pair-style-line-lj-command">
<span id="index-0"></span><h1>pair_style line/lj command<a class="headerlink" href="#pair-style-line-lj-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 line/lj cutoff
</pre></div>
</div>
<p>cutoff = global cutoff for interactions (distance units)</p>
</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 line/lj 3.0
pair_coeff * * 1.0 1.0 1.0 0.8 1.12
pair_coeff 1 2 1.0 2.0 1.0 1.5 1.12 5.0
pair_coeff 1 2 1.0 0.0 1.0 1.0 2.5
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>line/lj</em> treats particles which are line segments as a set of
small spherical particles that tile the line segment length as
explained below. Interactions between two line segments, each with N1
and N2 spherical particles, are calculated as the pairwise sum of
N1*N2 Lennard-Jones interactions. Interactions between a line segment
with N spherical particles and a point particle are treated as the
pairwise sum of N Lennard-Jones interactions. See the <a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut</em></a> doc page for the definition of Lennard-Jones
interactions.</p>
<p>The set of non-overlapping spherical sub-particles that represent a
line segment are generated in the following manner. Their size is a
function of the line segment length and the specified sub-particle
size for that particle type. If a line segment has a length L and is
of type I, then the number of spheres N that represent the segment is
calculated as N = L/sizeI, rounded up to an integer value. Thus if L
is not evenly divisibly by sizeI, N is incremented to include one
extra sphere. The centers of the spheres are spaced equally along the
line segment. Imagine N+1 equally-space points, which include the 2
end points of the segment. The sphere centers are halfway between
each pair of points.</p>
<p>The LJ interaction between 2 spheres on different line segments (or a
sphere on a line segment and a point particles) is computed with
sub-particle epsilon, sigma, and cutoff values that are set by the
pair_coeff command, as described below. If the distance bewteen the 2
spheres is greater than the sub-particle cutoff, there is no
interaction. This means that some pairs of sub-particles on 2 line
segments may interact, but others may not.</p>
<p>For purposes of creating the neighbor list for pairs of interacting
line segments or lines/point particles, a regular particle-particle
cutoff is used, as defined by the <em>cutoff</em> setting above in the
pair_style command or overridden with an optional argument in the
pair_coeff command for a type pair as discussed below. The distance
between the centers of 2 line segments, or the center of a line
segment and a point particle, must be less than this distance (plus
the neighbor skin; see the <a class="reference external" href="neighbor">neighbor</a> command), for the pair
of particles to be included in the neighbor list.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This means that a too-short value for the <em>cutoff</em> setting can
exclude a pair of particles from the neighbor list even if pairs of
their sub-particle spheres would interact, based on the sub-particle
cutoff specified in the pair_coeff command. E.g. sub-particles at the
ends of the line segments that are close to each other. Which may not
be what you want, since it means the ends of 2 line segments could
pass through each other. It is up to you to specify a <em>cutoff</em>
setting that is consistent with the length of the line segments you
are using and the sub-particle cutoff settings.</p>
</div>
<p>For style <em>line/lj</em>, the following coefficients must be defined for
each pair of atom types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command
as in the examples above, or in the data file or restart files read by
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>sizeI (distance units)</li>
<li>sizeJ (distance units)</li>
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>subcutoff (distance units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The <em>sizeI</em> and <em>sizeJ</em> coefficients are the sub-particle sizes for
line particles of type I and type J. They are used to define the N
sub-particles per segment as described above. These coefficients are
actually stored on a per-type basis. Thus if there are multiple
pair_coeff commmands that involve type I, as either the first or
second atom type, you should use consistent values for sizeI or sizeJ
in all of them. If you do not do this, the last value specified for
sizeI will apply to all segments of type I. If typeI or typeJ refers
to point particles, the corresponding sizeI or sizeJ is ignored; it
can be set to 0.0.</p>
<p>The <em>epsilon</em>, <em>sigma</em>, and <em>subcutoff</em> coefficients are used to
compute an LJ interactions between a pair of sub-particles on 2 line
segments (of type I and J), or between a sub particle/point particle
pair. As discussed above, the <em>subcutoff</em> and <em>cutoff</em> params are
different. The latter is only used for building the neighbor list
when the distance between centers of two line segments or one segment
and a point particle is calculated.</p>
<p>The <em>cutoff</em> coefficient is optional. If not specified, the global
cutoff is used.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, coeffiecients must be specified.
No default mixing rules are used.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This style is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
<p>Defining particles to be line segments so they participate in
line/line or line/particle interactions requires the use the
<a class="reference internal" href="atom_style.html"><em>atom_style line</em></a> command.</p>
</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>, <a class="reference internal" href="pair_tri_lj.html"><em>pair_style tri/lj</em></a></p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="pair-style-list-command">
<span id="index-0"></span><h1>pair_style list command<a class="headerlink" href="#pair-style-list-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 list listfile cutoff keyword
</pre></div>
</div>
<ul class="simple">
<li>listfile = name of file with list of pairwise interactions</li>
<li>cutoff = global cutoff (distance units)</li>
<li>keyword = optional flag <em>nocheck</em> or <em>check</em> (default is <em>check</em>)</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 list restraints.txt 200.0
pair_coeff * *
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
pair_coeff * * lj/cut 1.0 1.0
pair_coeff 3* 3* list
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>list</em> computes interactions between explicitly listed pairs of
atoms with the option to select functional form and parameters for
each individual pair. Because the parameters are set in the list
file, the pair_coeff command has no parameters (but still needs to be
provided). The <em>check</em> and <em>nocheck</em> keywords enable/disable a test
that checks whether all listed bonds were present and computed.</p>
<p>This pair style can be thought of as a hybrid between bonded,
non-bonded, and restraint interactions. It will typically be used as
an additional interaction within the <em>hybrid/overlay</em> pair style. It
currently supports three interaction styles: a 12-6 Lennard-Jones, a
Morse and a harmonic potential.</p>
<p>The format of the list file is as follows:</p>
<ul class="simple">
<li>one line per pair of atoms</li>
<li>empty lines will be ignored</li>
<li>comment text starts with a &#8216;#&#8217; character</li>
<li>line syntax: <em>ID1 ID2 style coeffs cutoff</em></li>
</ul>
<div class="highlight-python"><div class="highlight"><pre>ID1 = atom ID of first atom
ID2 = atom ID of second atom
style = style of interaction
coeffs = list of coeffs
cutoff = cutoff for interaction (optional)
</pre></div>
</div>
<p>The cutoff parameter is optional. If not specified, the global cutoff
is used.</p>
<p>Here is an example file:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># this is a comment</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>15 259 lj126 1.0 1.0 50.0
15 603 morse 10.0 1.2 2.0 10.0 # and another comment
18 470 harmonic 50.0 1.2 5.0
</pre></div>
</div>
<p>The style <em>lj126</em> computes pairwise interactions with the formula</p>
<img alt="_images/pair_lj.jpg" class="align-center" src="_images/pair_lj.jpg" />
<p>and the coefficients:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
</ul>
<p>The style <em>morse</em> computes pairwise interactions with the formula</p>
<img alt="_images/pair_morse.jpg" class="align-center" src="_images/pair_morse.jpg" />
<p>and the coefficients:</p>
<ul class="simple">
<li>D0 (energy units)</li>
<li>alpha (1/distance units)</li>
<li>r0 (distance units)</li>
</ul>
<p>The style <em>harmonic</em> computes pairwise interactions with the formula</p>
<img alt="_images/bond_harmonic.jpg" class="align-center" src="_images/bond_harmonic.jpg" />
<p>and the coefficients:</p>
<ul class="simple">
<li>K (energy units)</li>
<li>r0 (distance units)</li>
</ul>
<p>Note that the usual 1/2 factor is included in K.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support mixing since all parameters are
explicit for each pair.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option is supported by this
pair style.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table and tail options are not
relevant for this pair style.</p>
<p>This pair style does not write its 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 specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style does not use a neighbor list and instead identifies
atoms by their IDs. This has two consequences: 1) The cutoff has to be
chosen sufficiently large, so that the second atom of a pair has to be
a ghost atom on the same node on which the first atom is local;
otherwise the interaction will be skipped. You can use the <em>check</em>
option to detect, if interactions are missing. 2) Unlike other pair
styles in LAMMPS, an atom I will not interact with multiple images of
atom J (assuming the images are within the cutoff distance), but only
with the nearest image.</p>
<p>This style is part of the USER-MISC package. It is only enabled if
LAMMPS is build with that package. See the <span class="xref std std-ref">Making of LAMMPS</span> section for more info.</p>
</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>,
<a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a>,
<a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut</em></a>,
<a class="reference internal" href="pair_morse.html"><em>pair_style morse</em></a>,
<a class="reference internal" href="bond_harmonic.html"><em>bond_style harmonic</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
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<div class="section" id="pair-style-lj-cut-command">
<span id="index-0"></span><h1>pair_style lj/cut command<a class="headerlink" href="#pair-style-lj-cut-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-cuda-command">
<h1>pair_style lj/cut/cuda command<a class="headerlink" href="#pair-style-lj-cut-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-gpu-command">
<h1>pair_style lj/cut/gpu command<a class="headerlink" href="#pair-style-lj-cut-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-intel-command">
<h1>pair_style lj/cut/intel command<a class="headerlink" href="#pair-style-lj-cut-intel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-kk-command">
<h1>pair_style lj/cut/kk command<a class="headerlink" href="#pair-style-lj-cut-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-opt-command">
<h1>pair_style lj/cut/opt command<a class="headerlink" href="#pair-style-lj-cut-opt-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-omp-command">
<h1>pair_style lj/cut/omp command<a class="headerlink" href="#pair-style-lj-cut-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-cut-command">
<h1>pair_style lj/cut/coul/cut command<a class="headerlink" href="#pair-style-lj-cut-coul-cut-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-cut-cuda-command">
<h1>pair_style lj/cut/coul/cut/cuda command<a class="headerlink" href="#pair-style-lj-cut-coul-cut-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-cut-gpu-command">
<h1>pair_style lj/cut/coul/cut/gpu command<a class="headerlink" href="#pair-style-lj-cut-coul-cut-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-cut-omp-command">
<h1>pair_style lj/cut/coul/cut/omp command<a class="headerlink" href="#pair-style-lj-cut-coul-cut-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-debye-command">
<h1>pair_style lj/cut/coul/debye command<a class="headerlink" href="#pair-style-lj-cut-coul-debye-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-debye-cuda-command">
<h1>pair_style lj/cut/coul/debye/cuda command<a class="headerlink" href="#pair-style-lj-cut-coul-debye-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-debye-gpu-command">
<h1>pair_style lj/cut/coul/debye/gpu command<a class="headerlink" href="#pair-style-lj-cut-coul-debye-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-debye-kk-command">
<h1>pair_style lj/cut/coul/debye/kk command<a class="headerlink" href="#pair-style-lj-cut-coul-debye-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-debye-omp-command">
<h1>pair_style lj/cut/coul/debye/omp command<a class="headerlink" href="#pair-style-lj-cut-coul-debye-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-dsf-command">
<h1>pair_style lj/cut/coul/dsf command<a class="headerlink" href="#pair-style-lj-cut-coul-dsf-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-dsf-gpu-command">
<h1>pair_style lj/cut/coul/dsf/gpu command<a class="headerlink" href="#pair-style-lj-cut-coul-dsf-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-dsf-kk-command">
<h1>pair_style lj/cut/coul/dsf/kk command<a class="headerlink" href="#pair-style-lj-cut-coul-dsf-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-dsf-omp-command">
<h1>pair_style lj/cut/coul/dsf/omp command<a class="headerlink" href="#pair-style-lj-cut-coul-dsf-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-long-command">
<h1>pair_style lj/cut/coul/long command<a class="headerlink" href="#pair-style-lj-cut-coul-long-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-long-cs-command">
<h1>pair_style lj/cut/coul/long/cs command<a class="headerlink" href="#pair-style-lj-cut-coul-long-cs-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-long-cuda-command">
<h1>pair_style lj/cut/coul/long/cuda command<a class="headerlink" href="#pair-style-lj-cut-coul-long-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-long-gpu-command">
<h1>pair_style lj/cut/coul/long/gpu command<a class="headerlink" href="#pair-style-lj-cut-coul-long-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-long-intel-command">
<h1>pair_style lj/cut/coul/long/intel command<a class="headerlink" href="#pair-style-lj-cut-coul-long-intel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-long-opt-command">
<h1>pair_style lj/cut/coul/long/opt command<a class="headerlink" href="#pair-style-lj-cut-coul-long-opt-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-long-omp-command">
<h1>pair_style lj/cut/coul/long/omp command<a class="headerlink" href="#pair-style-lj-cut-coul-long-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-msm-command">
<h1>pair_style lj/cut/coul/msm command<a class="headerlink" href="#pair-style-lj-cut-coul-msm-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-msm-gpu-command">
<h1>pair_style lj/cut/coul/msm/gpu command<a class="headerlink" href="#pair-style-lj-cut-coul-msm-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-msm-omp-command">
<h1>pair_style lj/cut/coul/msm/omp command<a class="headerlink" href="#pair-style-lj-cut-coul-msm-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-tip4p-cut-command">
<h1>pair_style lj/cut/tip4p/cut command<a class="headerlink" href="#pair-style-lj-cut-tip4p-cut-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-tip4p-cut-omp-command">
<h1>pair_style lj/cut/tip4p/cut/omp command<a class="headerlink" href="#pair-style-lj-cut-tip4p-cut-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-tip4p-long-command">
<h1>pair_style lj/cut/tip4p/long command<a class="headerlink" href="#pair-style-lj-cut-tip4p-long-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-tip4p-long-omp-command">
<h1>pair_style lj/cut/tip4p/long/omp command<a class="headerlink" href="#pair-style-lj-cut-tip4p-long-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-tip4p-long-opt-command">
<h1>pair_style lj/cut/tip4p/long/opt command<a class="headerlink" href="#pair-style-lj-cut-tip4p-long-opt-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 args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lj/cut</em> or <em>lj/cut/coul/cut</em> or <em>lj/cut/coul/debye</em> or <em>lj/cut/coul/dsf</em> or <em>lj/cut/coul/long</em> or <em>lj/cut/coul/long/cs</em> or <em>lj/cut/coul/msm</em> or <em>lj/cut/tip4p/long</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>lj/cut</em> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<em>lj/cut/coul/cut</em> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>lj/cut/coul/debye</em> args = kappa cutoff (cutoff2)
kappa = inverse of the Debye length (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>lj/cut/coul/dsf</em> args = alpha cutoff (cutoff2)
alpha = damping parameter (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (distance units)
<em>lj/cut/coul/long</em> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>lj/cut/coul/msm</em> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>lj/cut/tip4p/cut</em> args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>lj/cut/tip4p/long</em> args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</pre>
</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 lj/cut 2.5
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/coul/cut 10.0
pair_style lj/cut/coul/cut 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_coeff 1 1 100.0 3.5 9.0 9.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/coul/debye 1.5 3.0
pair_style lj/cut/coul/debye 1.5 2.5 5.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.5 2.5
pair_coeff 1 1 1.0 1.5 2.5 5.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/coul/dsf 0.05 2.5 10.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.0 2.5
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/coul/long 10.0
pair_style lj/cut/coul/long/cs 10.0
pair_style lj/cut/coul/long 10.0 8.0
pair_style lj/cut/coul/long/cs 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/coul/msm 10.0
pair_style lj/cut/coul/msm 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0
pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
</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>lj/cut</em> styles compute the standard 12/6 Lennard-Jones potential,
given by</p>
<img alt="_images/pair_lj.jpg" class="align-center" src="_images/pair_lj.jpg" />
<p>Rc is the cutoff.</p>
<p>Style <em>lj/cut/coul/cut</em> adds a Coulombic pairwise interaction given by</p>
<img alt="_images/pair_coulomb.jpg" class="align-center" src="_images/pair_coulomb.jpg" />
<p>where C is an energy-conversion constant, Qi and Qj are the charges on
the 2 atoms, and epsilon is the dielectric constant which can be set
by the <a class="reference internal" href="dielectric.html"><em>dielectric</em></a> command. If one cutoff is
specified in the pair_style command, it is used for both the LJ and
Coulombic terms. If two cutoffs are specified, they are used as
cutoffs for the LJ and Coulombic terms respectively.</p>
<p>Style <em>lj/cut/coul/debye</em> adds an additional exp() damping factor
to the Coulombic term, given by</p>
<img alt="_images/pair_debye.jpg" class="align-center" src="_images/pair_debye.jpg" />
<p>where kappa is the inverse of the Debye length. This potential is
another way to mimic the screening effect of a polar solvent.</p>
<p>Style <em>lj/cut/coul/dsf</em> computes the Coulombic term via the damped
shifted force model described in <a class="reference internal" href="#fennell"><span>Fennell</span></a>, given by:</p>
<img alt="_images/pair_coul_dsf.jpg" class="align-center" src="_images/pair_coul_dsf.jpg" />
<p>where <em>alpha</em> is the damping parameter and erfc() is the complementary
error-function. This potential is essentially a short-range,
spherically-truncated, charge-neutralized, shifted, pairwise <em>1/r</em>
summation. The potential is based on Wolf summation, proposed as an
alternative to Ewald summation for condensed phase systems where
charge screening causes electrostatic interactions to become
effectively short-ranged. In order for the electrostatic sum to be
absolutely convergent, charge neutralization within the cutoff radius
is enforced by shifting the potential through placement of image
charges on the cutoff sphere. Convergence can often be improved by
setting <em>alpha</em> to a small non-zero value.</p>
<p>Styles <em>lj/cut/coul/long</em> and <em>lj/cut/coul/msm</em> compute the same
Coulombic interactions as style <em>lj/cut/coul/cut</em> except that an
additional damping factor is applied to the Coulombic term so it can
be used in conjunction with the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a>
command and its <em>ewald</em> or <em>pppm</em> option. The Coulombic cutoff
specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.</p>
<p>Style <em>lj/cut/coul/long/cs</em> is identical to <em>lj/cut/coul/long</em> except
that a term is added for the <a class="reference internal" href="Section_howto.html#howto-25"><span>core/shell model</span></a> to allow charges on core and shell
particles to be separated by r = 0.0.</p>
<p>Styles <em>lj/cut/tip4p/cut</em> and <em>lj/cut/tip4p/long</em> implement the TIP4P
water model of <a class="reference internal" href="#jorgensen"><span>(Jorgensen)</span></a>, which introduces a massless
site located a short distance away from the oxygen atom along the
bisector of the HOH angle. The atomic types of the oxygen and
hydrogen atoms, the bond and angle types for OH and HOH interactions,
and the distance to the massless charge site are specified as
pair_style arguments. Style <em>lj/cut/tip4p/cut</em> uses a cutoff for
Coulomb interactions; style <em>lj/cut/tip4p/long</em> is for use with a
long-range Coulombic solver (Ewald or PPPM).</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">For each TIP4P water molecule in your system, the atom IDs for
the O and 2 H atoms must be consecutive, with the O atom first. This
is to enable LAMMPS to &#8220;find&#8221; the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.</p>
</div>
<p>See the <a class="reference internal" href="Section_howto.html#howto-8"><span>howto section</span></a> for more
information on how to use the TIP4P pair styles and lists of
parameters to set. Note that the neighobr list cutoff for Coulomb
interactions is effectively extended by a distance 2*qdist when using
the TIP4P pair style, to account for the offset distance of the
fictitious charges on O atoms in water molecules. Thus it is
typically best in an efficiency sense to use a LJ cutoff &gt;= Coulomb
cutoff + 2*qdist, to shrink the size of the neighbor list. This leads
to slightly larger cost for the long-range calculation, so you can
test the trade-off for your model.</p>
<p>For all of the <em>lj/cut</em> pair styles, the following coefficients must
be defined for each pair of atoms types via the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands, or by mixing as
described below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>cutoff1 (distance units)</li>
<li>cutoff2 (distance units)</li>
</ul>
<p>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at 2^(1/6)
sigma.</p>
<p>The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair. You cannot specify 2 cutoffs for style <em>lj/cut</em>, since it
has no Coulombic terms.</p>
<p>For <em>lj/cut/coul/long</em> and <em>lj/cut/coul/msm</em> and <em>lj/cut/tip4p/cut</em>
and <em>lj/cut/tip4p/long</em> only the LJ cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.</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>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command
for details.</p>
<p>All of the <em>lj/cut</em> pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option for the energy of the
Lennard-Jones portion of the pair interaction.</p>
<p>The <em>lj/cut/coul/long</em> and <em>lj/cut/tip4p/long</em> pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.</p>
<p>All of the <em>lj/cut</em> pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> tail option for adding a long-range
tail correction to the energy and pressure for the Lennard-Jones
portion of the pair interaction.</p>
<p>All of the <em>lj/cut</em> pair styles write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.</p>
<p>The <em>lj/cut</em> and <em>lj/cut/coul/long</em> pair styles support the use of the
<em>inner</em>, <em>middle</em>, and <em>outer</em> keywords of the <a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
The other styles only support the <em>pair</em> keyword of run_style respa.
See the <a class="reference internal" href="run_style.html"><em>run_style</em></a> command for details.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The <em>lj/cut/coul/long</em> and <em>lj/cut/tip4p/long</em> styles are part of the
KSPACE package. The <em>lj/cut/tip4p/cut</em> style is part of the MOLECULE
package. These styles 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. Note that the KSPACE and MOLECULE packages are
installed by default.</p>
</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="jorgensen"><strong>(Jorgensen)</strong> Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).</p>
<p id="fennell"><strong>(Fennell)</strong> C. J. Fennell, J. D. Gezelter, J Chem Phys, 124,
234104 (2006).</p>
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<div class="section" id="pair-style-lj96-cut-command">
<span id="index-0"></span><h1>pair_style lj96/cut command<a class="headerlink" href="#pair-style-lj96-cut-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj96-cut-cuda-command">
<h1>pair_style lj96/cut/cuda command<a class="headerlink" href="#pair-style-lj96-cut-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj96-cut-gpu-command">
<h1>pair_style lj96/cut/gpu command<a class="headerlink" href="#pair-style-lj96-cut-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj96-cut-omp-command">
<h1>pair_style lj96/cut/omp command<a class="headerlink" href="#pair-style-lj96-cut-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 lj96/cut cutoff
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for lj96/cut interactions (distance units)</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 lj96/cut 2.5
pair_coeff * * 1.0 1.0 4.0
pair_coeff 1 1 1.0 1.0
</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>lj96/cut</em> style compute a 9/6 Lennard-Jones potential, instead
of the standard 12/6 potential, given by</p>
<img alt="_images/pair_lj96.jpg" class="align-center" src="_images/pair_lj96.jpg" />
<p>Rc is the cutoff.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global LJ
cutoff specified in the pair_style command is used.</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>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command
for details.</p>
<p>This pair style supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the pair interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>This pair style supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> tail
option for adding a long-range tail correction to the energy and
pressure of the pair interaction.</p>
<p>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style supports the use of the <em>inner</em>, <em>middle</em>, and <em>outer</em>
keywords of the <a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command, meaning the
pairwise forces can be partitioned by distance at different levels of
the rRESPA hierarchy. See the <a class="reference internal" href="run_style.html"><em>run_style</em></a> command for
details.</p>
</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>
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<div class="section" id="pair-style-lj-cubic-command">
<span id="index-0"></span><h1>pair_style lj/cubic command<a class="headerlink" href="#pair-style-lj-cubic-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cubic-gpu-command">
<h1>pair_style lj/cubic/gpu command<a class="headerlink" href="#pair-style-lj-cubic-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cubic-omp-command">
<h1>pair_style lj/cubic/omp command<a class="headerlink" href="#pair-style-lj-cubic-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 lj/cubic
</pre></div>
</div>
</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 lj/cubic
pair_coeff * * 1.0 0.8908987
</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>lj/cubic</em> style computes a truncated LJ interaction potential
whose energy and force are continuous everywhere. Inside the
inflection point the interaction is identical to the standard 12/6
<a class="reference internal" href="pair_lj.html"><em>Lennard-Jones</em></a> potential. The LJ function outside the
inflection point is replaced with a cubic function of distance. The
energy, force, and second derivative are continuous at the inflection
point. The cubic coefficient A3 is chosen so that both energy and
force go to zero at the cutoff distance. Outside the cutoff distance
the energy and force are zero.</p>
<img alt="_images/pair_lj_cubic.jpg" class="align-center" src="_images/pair_lj_cubic.jpg" />
<p>The location of the inflection point rs is defined
by the LJ diameter, rs/sigma = (26/7)^1/6. The cutoff distance
is defined by rc/rs = 67/48 or rc/sigma = 1.737....
The analytic expression for the
the cubic coefficient
A3*rmin^3/epsilon = 27.93... is given in the paper by
Holian and Ravelo <a class="reference internal" href="#holian"><span>(Holian)</span></a>.</p>
<p>This potential is commonly used to study the shock mechanics of FCC
solids, as in Ravelo et al. <a class="reference internal" href="#ravelo"><span>(Ravelo)</span></a>.</p>
<p>The following coefficients must be defined for each pair of atom types
via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the example above,
or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
</ul>
<p>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum, which is
located at rmin = 2^(1/6)*sigma. In the above example, sigma =
0.8908987, so rmin = 1.</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>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command
for details.</p>
<p>The lj/cubic pair style does not support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option,
since pair interaction is already smoothed to 0.0 at the
cutoff.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>The lj/cubic pair style does 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, since there are no corrections for
a potential that goes to 0.0 at the cutoff.</p>
<p>The lj/cubic pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.</p>
<p>The lj/cubic pair style 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. It does not
support the <em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</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="ravelo"><span id="holian"></span><strong>(Holian)</strong> Holian and Ravelo, Phys Rev B, 51, 11275 (1995).</p>
<p><strong>(Ravelo)</strong> Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004).</p>
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<HR>
<H3>pair_style lj/cut/smooth command
</H3>
<H3>pair_style lj/cut/smooth/cuda command
</H3>
<H3>pair_style lj/cut/smooth/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style lj/cut/smooth Rc
</PRE>
<UL><LI>Rc = cutoff for lj/cut/smooth interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/cut/smooth 5.456108274435118
pair_coeff * * 0.7242785984051078 2.598146797350056
pair_coeff 1 1 20.0 1.3 9.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>lj/cut/smooth</I> computes a LJ interaction that combines the standard
12/6 Lennard-Jones function and subtracts a linear term that includes a
cutoff distance Rc.
</P>
<CENTER><IMG SRC = "Eqs/pair_lj_cut_smooth.jpg">
</CENTER>
<P>At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>cutoff (distance units)
</UL>
<P>If not specified, the global value for Rc is used.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> 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 HREF = "Section_accelerate.html">Section_accelerate</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-OMP and OPT
packages, respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</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 HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients and
cutoff distance can be mixed. The default mix value is geometric.
See the "pair_modify" command for details.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A> shift
option for the energy of the pair interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
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<div class="section" id="pair-style-lj-expand-command">
<span id="index-0"></span><h1>pair_style lj/expand command<a class="headerlink" href="#pair-style-lj-expand-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-expand-cuda-command">
<h1>pair_style lj/expand/cuda command<a class="headerlink" href="#pair-style-lj-expand-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-expand-gpu-command">
<h1>pair_style lj/expand/gpu command<a class="headerlink" href="#pair-style-lj-expand-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-expand-omp-command">
<h1>pair_style lj/expand/omp command<a class="headerlink" href="#pair-style-lj-expand-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 lj/expand cutoff
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for lj/expand interactions (distance units)</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 lj/expand 2.5
pair_coeff * * 1.0 1.0 0.5
pair_coeff 1 1 1.0 1.0 -0.2 2.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>lj/expand</em> computes a LJ interaction with a distance shifted by
delta which can be useful when particles are of different sizes, since
it is different that using different sigma values in a standard LJ
formula:</p>
<img alt="_images/pair_lj_expand.jpg" class="align-center" src="_images/pair_lj_expand.jpg" />
<p>Rc is the cutoff which does not include the delta distance. I.e. the
actual force cutoff is the sum of cutoff + delta.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>delta (distance units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The delta values can be positive or negative. The last coefficient is
optional. If not specified, the global LJ cutoff is used.</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>For atom type pairs I,J and I != J, the epsilon, sigma, and shift
coefficients and cutoff distance for this pair style can be mixed.
Shift is always mixed via an <em>arithmetic</em> rule. The other
coefficients are mixed according to the pair_modify mix value. The
default mix value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command for
details.</p>
<p>This pair style supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the pair interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>This pair style supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> tail
option for adding a long-range tail correction to the energy and
pressure of the pair interaction.</p>
<p>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</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>
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<div class="section" id="pair-style-lj-long-coul-long-command">
<span id="index-0"></span><h1>pair_style lj/long/coul/long command<a class="headerlink" href="#pair-style-lj-long-coul-long-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-long-coul-long-omp-command">
<h1>pair_style lj/long/coul/long/omp command<a class="headerlink" href="#pair-style-lj-long-coul-long-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-long-coul-long-opt-command">
<h1>pair_style lj/long/coul/long/opt command<a class="headerlink" href="#pair-style-lj-long-coul-long-opt-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-long-tip4p-long-command">
<h1>pair_style lj/long/tip4p/long command<a class="headerlink" href="#pair-style-lj-long-tip4p-long-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 args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lj/long/coul/long</em> or <em>lj/long/tip4p/long</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>lj/long/coul/long</em> args = flag_lj flag_coul cutoff (cutoff2)
flag_lj = <em>long</em> or <em>cut</em> or <em>off</em>
<em>long</em> = use Kspace long-range summation for dispersion 1/r^6 term
<em>cut</em> = use a cutoff on dispersion 1/r^6 term
<em>off</em> = omit disperion 1/r^6 term entirely
flag_coul = <em>long</em> or <em>off</em>
<em>long</em> = use Kspace long-range summation for Coulombic 1/r term
<em>off</em> = omit Coulombic term
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>lj/long/tip4p/long</em> args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
flag_lj = <em>long</em> or <em>cut</em>
<em>long</em> = use Kspace long-range summation for dispersion 1/r^6 term
<em>cut</em> = use a cutoff
flag_coul = <em>long</em> or <em>off</em>
<em>long</em> = use Kspace long-range summation for Coulombic 1/r term
<em>off</em> = omit Coulombic term
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</pre>
</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 lj/long/coul/long cut off 2.5
pair_style lj/long/coul/long cut long 2.5 4.0
pair_style lj/long/coul/long long long 2.5 4.0
pair_coeff * * 1 1
pair_coeff 1 1 1 3 4
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0
pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>lj/long/coul/long</em> computes the standard 12/6 Lennard-Jones and
Coulombic potentials, given by</p>
<img alt="_images/pair_lj.jpg" class="align-center" src="_images/pair_lj.jpg" />
<img alt="_images/pair_coulomb.jpg" class="align-center" src="_images/pair_coulomb.jpg" />
<p>where C is an energy-conversion constant, Qi and Qj are the charges on
the 2 atoms, epsilon is the dielectric constant which can be set by
the <a class="reference internal" href="dielectric.html"><em>dielectric</em></a> command, and Rc is the cutoff. If
one cutoff is specified in the pair_style command, it is used for both
the LJ and Coulombic terms. If two cutoffs are specified, they are
used as cutoffs for the LJ and Coulombic terms respectively.</p>
<p>The purpose of this pair style is to capture long-range interactions
resulting from both attractive 1/r^6 Lennard-Jones and Coulombic 1/r
interactions. This is done by use of the <em>flag_lj</em> and <em>flag_coul</em>
settings. The <a class="reference internal" href="#veld"><span>In &#8216;t Veld</span></a> paper has more details on when it is
appropriate to include long-range 1/r^6 interactions, using this
potential.</p>
<p>Style <em>lj/long/tip4p/long</em> implements the TIP4P water model of
<a class="reference internal" href="pair_lj.html#jorgensen"><span>(Jorgensen)</span></a>, which introduces a massless site located a
short distance away from the oxygen atom along the bisector of the HOH
angle. The atomic types of the oxygen and hydrogen atoms, the bond
and angle types for OH and HOH interactions, and the distance to the
massless charge site are specified as pair_style arguments.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">For each TIP4P water molecule in your system, the atom IDs for
the O and 2 H atoms must be consecutive, with the O atom first. This
is to enable LAMMPS to &#8220;find&#8221; the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.</p>
</div>
<p>See the <a class="reference internal" href="Section_howto.html#howto-8"><span>howto section</span></a> for more
information on how to use the TIP4P pair style. Note that the
neighobr list cutoff for Coulomb interactions is effectively extended
by a distance 2*qdist when using the TIP4P pair style, to account for
the offset distance of the fictitious charges on O atoms in water
molecules. Thus it is typically best in an efficiency sense to use a
LJ cutoff &gt;= Coulomb cutoff + 2*qdist, to shrink the size of the
neighbor list. This leads to slightly larger cost for the long-range
calculation, so you can test the trade-off for your model.</p>
<p>If <em>flag_lj</em> is set to <em>long</em>, no cutoff is used on the LJ 1/r^6
dispersion term. The long-range portion can be calculated by using
the <a class="reference internal" href="kspace_style.html"><em>kspace_style ewald/disp or pppm/disp</em></a> commands.
The specified LJ cutoff then determines which portion of the LJ
interactions are computed directly by the pair potential versus which
part is computed in reciprocal space via the Kspace style. If
<em>flag_lj</em> is set to <em>cut</em>, the LJ interactions are simply cutoff, as
with <a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut</em></a>.</p>
<p>If <em>flag_coul</em> is set to <em>long</em>, no cutoff is used on the Coulombic
interactions. The long-range portion can calculated by using any of
several <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command options such as
<em>pppm</em> or <em>ewald</em>. Note that if <em>flag_lj</em> is also set to long, then
the <em>ewald/disp</em> or <em>pppm/disp</em> Kspace style needs to be used to
perform the long-range calculations for both the LJ and Coulombic
interactions. If <em>flag_coul</em> is set to <em>off</em>, Coulombic interactions
are not computed.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>cutoff1 (distance units)</li>
<li>cutoff2 (distance units)</li>
</ul>
<p>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at 2^(1/6)
sigma.</p>
<p>The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.</p>
<p>Note that if you are using <em>flag_lj</em> set to <em>long</em>, you
cannot specify a LJ cutoff for an atom type pair, since only one
global LJ cutoff is allowed. Similarly, if you are using <em>flag_coul</em>
set to <em>long</em>, you cannot specify a Coulombic cutoff for an atom type
pair, since only one global Coulombic cutoff is allowed.</p>
<p>For <em>lj/long/tip4p/long</em> only the LJ cutoff can be specified
since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.</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>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/long pair styles can be mixed.
The default mix value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command
for details.</p>
<p>These pair styles support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the Lennard-Jones portion of the pair
interaction, assuming <em>flag_lj</em> is <em>cut</em>.</p>
<p>These pair styles support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table and
table/disp options since they can tabulate the short-range portion of
the long-range Coulombic and dispersion interactions.</p>
<p>Thes pair styles do not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
tail option for adding a long-range tail correction to the
Lennard-Jones portion of the energy and pressure.</p>
<p>These pair styles write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>The pair lj/long/coul/long styles support the use of the <em>inner</em>,
<em>middle</em>, and <em>outer</em> keywords of the <a class="reference internal" href="run_style.html"><em>run_style respa</em></a>
command, meaning the pairwise forces can be partitioned by distance at
different levels of the rRESPA hierarchy. See the
<a class="reference internal" href="run_style.html"><em>run_style</em></a> command for details.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>These styles are part of the KSPACE 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>Making LAMMPS</span></a> section for more info. Note that
the KSPACE package is installed by default.</p>
</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="veld"><strong>(In &#8216;t Veld)</strong> In &#8216;t Veld, Ismail, Grest, J Chem Phys (accepted) (2007).</p>
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<div class="section" id="pair-style-lj-sf-command">
<span id="index-0"></span><h1>pair_style lj/sf command<a class="headerlink" href="#pair-style-lj-sf-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-sf-omp-command">
<h1>pair_style lj/sf/omp command<a class="headerlink" href="#pair-style-lj-sf-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 lj/sf cutoff
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for Lennard-Jones interactions (distance units)</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 lj/sf 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.0 3.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>lj/sf</em> computes a truncated and force-shifted LJ interaction
(Shifted Force Lennard-Jones), so that both the potential and the
force go continuously to zero at the cutoff <a class="reference internal" href="#toxvaerd"><span>(Toxvaerd)</span></a>:</p>
<img alt="_images/pair_lj_sf.jpg" class="align-center" src="_images/pair_lj_sf.jpg" />
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global
LJ cutoff specified in the pair_style command is used.</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>For atom type pairs I,J and I != J, the epsilon and sigma
coefficients and cutoff distance for this pair style can be mixed.
Rin is a cutoff value and is mixed like the cutoff. The
default mix value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command for
details.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option is not relevant for
this pair style, since the pair interaction goes to 0.0 at the cutoff.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>This pair style does 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, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.</p>
<p>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style is part of the USER-MISC package. It is only enabled
if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</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="toxvaerd"><strong>(Toxvaerd)</strong> Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011).</p>
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<div class="section" id="pair-style-lj-smooth-command">
<span id="index-0"></span><h1>pair_style lj/smooth command<a class="headerlink" href="#pair-style-lj-smooth-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-smooth-cuda-command">
<h1>pair_style lj/smooth/cuda command<a class="headerlink" href="#pair-style-lj-smooth-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-smooth-omp-command">
<h1>pair_style lj/smooth/omp command<a class="headerlink" href="#pair-style-lj-smooth-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 lj/smooth Rin Rc
</pre></div>
</div>
<ul class="simple">
<li>Rin = inner cutoff beyond which force smoothing will be applied (distance units)</li>
<li>Rc = outer cutoff for lj/smooth interactions (distance units)</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 lj/smooth 8.0 10.0
pair_coeff * * 10.0 1.5
pair_coeff 1 1 20.0 1.3 7.0 9.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>lj/smooth</em> computes a LJ interaction with a force smoothing
applied between the inner and outer cutoff.</p>
<img alt="_images/pair_lj_smooth.jpg" class="align-center" src="_images/pair_lj_smooth.jpg" />
<p>The polynomial coefficients C1, C2, C3, C4 are computed by LAMMPS to
cause the force to vary smoothly from the inner cutoff Rin to the
outer cutoff Rc.</p>
<p>At the inner cutoff the force and its 1st derivative
will match the unsmoothed LJ formula. At the outer cutoff the force
and its 1st derivative will be 0.0. The inner cutoff cannot be 0.0.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">this force smoothing causes the energy to be discontinuous both
in its values and 1st derivative. This can lead to poor energy
conservation and may require the use of a thermostat. Plot the energy
and force resulting from this formula via the
<a class="reference internal" href="pair_write.html"><em>pair_write</em></a> command to see the effect.</p>
</div>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>innner (distance units)</li>
<li>outer (distance units)</li>
</ul>
<p>The last 2 coefficients are optional inner and outer cutoffs. If not
specified, the global values for Rin and Rc are used.</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>For atom type pairs I,J and I != J, the epsilon, sigma, Rin
coefficients and the cutoff distance for this pair style can be mixed.
Rin is a cutoff value and is mixed like the cutoff. The other
coefficients are mixed according to the pair_modify mix option. The
default mix value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command for
details.</p>
<p>This pair style supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the pair interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>This pair style does 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, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.</p>
<p>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</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>, <a class="reference internal" href="pair_lj_smooth_linear.html"><em>pair lj/smooth/linear</em></a></p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="pair-style-lj-smooth-linear-command">
<span id="index-0"></span><h1>pair_style lj/smooth/linear command<a class="headerlink" href="#pair-style-lj-smooth-linear-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-smooth-linear-omp-command">
<h1>pair_style lj/smooth/linear/omp command<a class="headerlink" href="#pair-style-lj-smooth-linear-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 lj/smooth/linear Rc
</pre></div>
</div>
<ul class="simple">
<li>Rc = cutoff for lj/smooth/linear interactions (distance units)</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 lj/smooth/linear 5.456108274435118
pair_coeff * * 0.7242785984051078 2.598146797350056
pair_coeff 1 1 20.0 1.3 9.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>lj/smooth/linear</em> computes a LJ interaction that combines the
standard 12/6 Lennard-Jones function and subtracts a linear term that
includes the cutoff distance Rc, as in this formula:</p>
<img alt="_images/pair_lj_smooth_linear.jpg" class="align-center" src="_images/pair_lj_smooth_linear.jpg" />
<p>At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global value
for Rc is used.</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>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance can be mixed. The default mix value is geometric.
See the &#8220;pair_modify&#8221; command for details.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option for the energy of the pair interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant for
this pair style.</p>
<p>This pair style does 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, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.</p>
<p>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</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>, <a class="reference internal" href="pair_lj_smooth.html"><em>pair lj/smooth</em></a></p>
<p><strong>Default:</strong> none</p>
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<span id="index-0"></span><h1>pair_style lj/cut/soft command<a class="headerlink" href="#pair-style-lj-cut-soft-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-soft-omp-command">
<h1>pair_style lj/cut/soft/omp command<a class="headerlink" href="#pair-style-lj-cut-soft-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-cut-soft-command">
<h1>pair_style lj/cut/coul/cut/soft command<a class="headerlink" href="#pair-style-lj-cut-coul-cut-soft-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-cut-soft-omp-command">
<h1>pair_style lj/cut/coul/cut/soft/omp command<a class="headerlink" href="#pair-style-lj-cut-coul-cut-soft-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-coul-long-soft-command">
<h1>pair_style lj/cut/coul/long/soft command<a class="headerlink" href="#pair-style-lj-cut-coul-long-soft-command" title="Permalink to this headline"></a></h1>
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<div class="section" id="pair-style-lj-cut-coul-long-soft-omp-command">
<h1>pair_style lj/cut/coul/long/soft/omp command<a class="headerlink" href="#pair-style-lj-cut-coul-long-soft-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-tip4p-long-soft-command">
<h1>pair_style lj/cut/tip4p/long/soft command<a class="headerlink" href="#pair-style-lj-cut-tip4p-long-soft-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-tip4p-long-soft-omp-command">
<h1>pair_style lj/cut/tip4p/long/soft/omp command<a class="headerlink" href="#pair-style-lj-cut-tip4p-long-soft-omp-command" title="Permalink to this headline"></a></h1>
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<div class="section" id="pair-style-lj-charmm-coul-long-soft-command">
<h1>pair_style lj/charmm/coul/long/soft command<a class="headerlink" href="#pair-style-lj-charmm-coul-long-soft-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-charmm-coul-long-soft-omp-command">
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</div>
<div class="section" id="pair-style-coul-cut-soft-command">
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<div class="section" id="pair-style-coul-cut-soft-omp-command">
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<div class="section" id="pair-style-coul-long-soft-command">
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<div class="section" id="pair-style-coul-long-soft-omp-command">
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</div>
<div class="section" id="pair-style-tip4p-long-soft-command">
<h1>pair_style tip4p/long/soft command<a class="headerlink" href="#pair-style-tip4p-long-soft-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tip4p-long-soft-omp-command">
<h1>pair_style tip4p/long/soft/omp command<a class="headerlink" href="#pair-style-tip4p-long-soft-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 args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lj/cut/soft</em> or <em>lj/cut/coul/cut/soft</em> or <em>lj/cut/coul/long/soft</em> or <em>lj/cut/tip4p/long/soft</em> or <em>lj/charmm/coul/long/soft</em> or <em>coul/cut/soft</em> or <em>coul/long/soft</em> or <em>tip4p/long/soft</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>lj/cut/soft</em> args = n alpha_lj cutoff
n, alpha_LJ = parameters of soft-core potential
cutoff = global cutoff for Lennard-Jones interactions (distance units)
<em>lj/cut/coul/cut/soft</em> args = n alpha_LJ alpha_C cutoff (cutoff2)
n, alpha_LJ, alpha_C = parameters of soft-core potential
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>lj/cut/coul/long/soft</em> args = n alpha_LJ alpha_C cutoff
n, alpha_LJ, alpha_C = parameters of the soft-core potential
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>lj/cut/tip4p/long/soft</em> args = otype htype btype atype qdist n alpha_LJ alpha_C cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
n, alpha_LJ, alpha_C = parameters of the soft-core potential
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>lj/charmm/coul/long/soft</em> args = n alpha_LJ alpha_C inner outer (cutoff)
n, alpha_LJ, alpha_C = parameters of the soft-core potential
inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args)
cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args)
<em>coul/cut/soft</em> args = n alpha_C cutoff
n, alpha_C = parameters of the soft-core potential
cutoff = global cutoff for Coulomb interactions (distance units)
<em>coul/long/soft</em> args = n alpha_C cutoff
n, alpha_C = parameters of the soft-core potential
cutoff = global cutoff for Coulomb interactions (distance units)
<em>tip4p/long/soft</em> args = otype htype btype atype qdist n alpha_C cutoff
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
n, alpha_C = parameters of the soft-core potential
cutoff = global cutoff for Coulomb interactions (distance units)
</pre>
</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 lj/cut/soft 2.0 0.5 9.5
pair_coeff * * 0.28 3.1 1.0
pair_coeff 1 1 0.28 3.1 1.0 9.5
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5
pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5
pair_coeff * * 0.28 3.1 1.0
pair_coeff 1 1 0.28 3.1 0.5 10.0
pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5
pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5
pair_coeff * * 0.28 3.1 1.0
pair_coeff 1 1 0.28 3.1 0.0 10.0
pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5
pair_coeff * * 0.155 3.1536 1.0
pair_coeff 1 1 0.155 3.1536 1.0 9.5
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0
pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0
pair_coeff * * 0.28 3.1 1.0
pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style coul/long/soft 1.0 10.0 9.5
pair_coeff * * 1.0
pair_coeff 1 1 1.0 9.5
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
pair_coeff * * 1.0
pair_coeff 1 1 1.0 9.5
</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>lj/cut/soft</em> style and substyles compute the 12/6 Lennard-Jones
and Coulomb potential modified by a soft core, in order to avoid
singularities during free energy calculations when sites are created
or anihilated <a class="reference internal" href="#beutler"><span>(Beutler)</span></a>,</p>
<img alt="_images/pair_lj_soft.jpg" class="align-center" src="_images/pair_lj_soft.jpg" />
<p>Coulomb interactions are also damped with a soft core at short
distance,</p>
<img alt="_images/pair_coul_soft.jpg" class="align-center" src="_images/pair_coul_soft.jpg" />
<p>In the Coulomb part C is an energy-conversion constant, q_i and q_j
are the charges on the 2 atoms, and epsilon is the dielectric constant
which can be set by the <a class="reference internal" href="dielectric.html"><em>dielectric</em></a> command.</p>
<p>The coefficient lambda is an activation parameter. When lambda = 1 the
pair potentiel is identical to a Lennard-Jones term or a Coulomb term
or a combination of both. When lambda = 0 the interactions are
deactivated. The transition between these two extrema is smoothed by a
soft repulsive core in order to avoid singularities in potential
energy and forces when sites are created or anihilated and can overlap
<a class="reference internal" href="#beutler"><span>(Beutler)</span></a>.</p>
<p>The paratemers n, alpha_LJ and alpha_C are set in the
<a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command, before the cutoffs. Usual
choices for the exponent are n = 2 or n = 1. For the remaining
coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are
appropriate choices. Plots of the LJ and Coulomb terms are shown
below, for lambda ranging from 1 to 0 every 0.1.</p>
<img alt="_images/lj_soft.jpg" class="align-center" src="_images/lj_soft.jpg" />
<img alt="_images/coul_soft.jpg" class="align-center" src="_images/coul_soft.jpg" />
<p>For the <em>lj/cut/coul/cut/soft</em> or <em>lj/cut/coul/long/soft</em> pair styles,
the following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>lambda (activation parameter between 0 and 1)</li>
<li>cutoff1 (distance units)</li>
<li>cutoff2 (distance units)</li>
</ul>
<p>The latter two coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair. You cannot specify 2 cutoffs for style <em>lj/cut/soft</em>,
since it has no Coulombic terms. For the <em>coul/cut/soft</em> and
<em>coul/long/soft</em> only lambda and the optional cutoff2 are to be
specified.</p>
<p>Style <em>lj/cut/tip4p/long/soft</em> implements a soft-core version of the
TIP4P water model. The usage of this pair style is documented in the
<a class="reference internal" href="pair_lj.html"><em>pair_lj</em></a> styles. The soft-core version introduces the
lambda parameter to the list of arguments, after epsilon and sigma in
the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command. The paratemers n, alpha_LJ
and alpha_C are set in the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command,
before the cutoffs.</p>
<p>Style <em>lj/charmm/coul/long/soft</em> implements a soft-core version of the
CHARMM version of LJ interactions with an additional switching
function S(r) that ramps the energy and force smoothly to zero between
an inner and outer cutoff. The usage of this pair style is documented
in the <a class="reference internal" href="pair_charmm.html"><em>pair_charmm</em></a> styles. The soft-core version
introduces the lambda parameter to the list of arguments, after
epsilon and sigma in the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command (and
before the optional eps14 and sigma14). The paratemers n,
alpha_LJ and alpha_C are set in the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a>
command, before the cutoffs.</p>
<p>The <em>coul/cut/soft</em>, <em>coul/long/soft</em> and <em>tip4p/long/soft</em> substyles
are designed to be combined with other pair potentials via the
<a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a> command. This is because
they have no repulsive core. Hence, if used by themselves, there will
be no repulsion to keep two oppositely charged particles from
overlapping each other. In this case, if lambda = 1, a singularity may
occur. These substyles are suitable to represent charges embedded in
the Lennard-Jones radius of another site (for example hydrogen atoms
in several water models).</p>
<p>NOTES: When using the core-softed Coulomb potentials with long-range
solvers (<em>coul/long/soft</em>, <em>lj/cut/coul/long/soft</em>, etc.) in a free
energy calculation in which sites holding electrostatic charges are
being created or anihilated (using <a class="reference internal" href="fix_adapt_fep.html"><em>fix adapt/fep</em></a>
and <a class="reference internal" href="compute_fep.html"><em>compute fep</em></a>) it is important to adapt both the
lambda activation parameter (from 0 to 1, or the reverse) and the
value of the charge (from 0 to its final value, or the reverse). This
ensures that long-range electrostatic terms (kspace) are correct. It
is not necessary to use core-softed Coulomb potentials if the van der
Waals site is present during the free-energy route, thus avoiding
overlap of the charges. Examples are provided in the LAMMPS source
directory tree, under examples/USER/fep.</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, tail correction, restart info</strong>:</p>
<p>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for this pair style can be mixed.
The default mix value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command
for details.</p>
<p>These pair styles support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the Lennard-Jones portion of the pair
interaction.</p>
<p>These pair styles support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> tail
option for adding a long-range tail correction to the energy and
pressure for the Lennard-Jones portion of the pair interaction.</p>
<p>These pair styles write information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>To avoid division by zero do not set sigma = 0; use the lambda
parameter instead to activate/deactivate interactions, or use
epsilon = 0 and sigma = 1. Alternatively, when sites do not
interact though the Lennard-Jones term the <em>coul/long/soft</em> or
similar substyle can be used via the
<a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a> command.</p>
<hr class="docutils" />
<p>All of the plain <em>soft</em> pair styles are part of the USER-FEP package.
The <em>long</em> styles also requires the KSPACE package to be installed.
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>
</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>, <a class="reference internal" href="fix_adapt.html"><em>fix adapt</em></a>,
<a class="reference internal" href="fix_adapt_fep.html"><em>fix adapt/fep</em></a>, <a class="reference internal" href="compute_fep.html"><em>compute fep</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="beutler"><strong>(Beutler)</strong> Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem
Phys Lett, 222, 529 (1994).</p>
</div>
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<div class="section" id="pair-style-lubricate-command">
<span id="index-0"></span><h1>pair_style lubricate command<a class="headerlink" href="#pair-style-lubricate-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lubricate-omp-command">
<h1>pair_style lubricate/omp command<a class="headerlink" href="#pair-style-lubricate-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lubricate-poly-command">
<h1>pair_style lubricate/poly command<a class="headerlink" href="#pair-style-lubricate-poly-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lubricate-poly-omp-command">
<h1>pair_style lubricate/poly/omp command<a class="headerlink" href="#pair-style-lubricate-poly-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 mu flaglog flagfld cutinner cutoff flagHI flagVF
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lubricate</em> or <em>lubricate/poly</em></li>
<li>mu = dynamic viscosity (dynamic viscosity units)</li>
<li>flaglog = 0/1 to exclude/include log terms in the lubrication approximation</li>
<li>flagfld = 0/1 to exclude/include Fast Lubrication Dynamics (FLD) effects</li>
<li>cutinner = inner cutoff distance (distance units)</li>
<li>cutoff = outer cutoff for interactions (distance units)</li>
<li>flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions</li>
<li>flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms</li>
</ul>
<p><strong>Examples:</strong> (all assume radius = 1)</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style lubricate 1.5 1 1 2.01 2.5
pair_coeff 1 1 2.05 2.8
pair_coeff * *
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lubricate 1.5 1 1 2.01 2.5
pair_coeff * *
variable mu equal ramp(1,2)
fix 1 all adapt 1 pair lubricate mu * * v_mu
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Styles <em>lubricate</em> and <em>lubricate/poly</em> compute hydrodynamic
interactions between mono-disperse finite-size spherical particles in
a pairwise fashion. The interactions have 2 components. The first is
Ball-Melrose lubrication terms via the formulas in <a class="reference internal" href="pair_lubricateU.html#ball"><span>(Ball and Melrose)</span></a></p>
<img alt="_images/pair_lubricate.jpg" class="align-center" src="_images/pair_lubricate.jpg" />
<p>which represents the dissipation W between two nearby particles due to
their relative velocities in the presence of a background solvent with
viscosity <em>mu</em>. Note that this is dynamic viscosity which has units of
mass/distance/time, not kinematic viscosity.</p>
<p>The Asq (squeeze) term is the strongest and is included if <em>flagHI</em> is
set to 1 (default). It scales as 1/gap where gap is the separation
between the surfaces of the 2 particles. The Ash (shear) and Apu
(pump) terms are only included if <em>flaglog</em> is set to 1. They are the
next strongest interactions, and the only other singular interaction,
and scale as log(gap). Note that <em>flaglog</em> = 1 and <em>flagHI</em> = 0 is
invalid, and will result in a warning message, after which <em>flagHI</em> will
be set to 1. The Atw (twist) term is currently not included. It is
typically a very small contribution to the lubrication forces.</p>
<p>The <em>flagHI</em> and <em>flagVF</em> settings are optional. Neither should be
used, or both must be defined.</p>
<p><em>Cutinner</em> sets the minimum center-to-center separation that will be
used in calculations irrespective of the actual separation. <em>Cutoff</em>
is the maximum center-to-center separation at which an interaction is
computed. Using a <em>cutoff</em> less than 3 radii is recommended if
<em>flaglog</em> is set to 1.</p>
<p>The other component is due to the Fast Lubrication Dynamics (FLD)
approximation, described in <a class="reference internal" href="pair_lubricateU.html#kumar"><span>(Kumar)</span></a>, which can be
represented by the following equation</p>
<img alt="_images/fld.jpg" class="align-center" src="_images/fld.jpg" />
<p>where U represents the velocities and angular velocities of the
particles, U^*infty* represents the velocity and the angular velocity
of the undisturbed fluid, and E^*infty* represents the rate of strain
tensor of the undisturbed fluid with viscosity <em>mu</em>. Again, note that
this is dynamic viscosity which has units of mass/distance/time, not
kinematic viscosity. Volume fraction corrections to R_FU are included
as long as <em>flagVF</em> is set to 1 (default).</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">When using the FLD terms, these pair styles are designed to be
used with explicit time integration and a correspondingly small
timestep. Thus either <a class="reference internal" href="fix_nve_sphere.html"><em>fix nve/sphere</em></a> or <a class="reference internal" href="fix_nve_asphere.html"><em>fix nve/asphere</em></a> should be used for time integration.
To perform implicit FLD, see the <a class="reference internal" href="pair_lubricateU.html"><em>pair_style lubricateU</em></a> command.</p>
</div>
<p>Style <em>lubricate</em> requires monodisperse spherical particles; style
<em>lubricate/poly</em> allows for polydisperse spherical particles.</p>
<p>The viscosity <em>mu</em> can be varied in a time-dependent manner over the
course of a simluation, in which case in which case the pair_style
setting for <em>mu</em> will be overridden. See the <a class="reference internal" href="fix_adapt.html"><em>fix adapt</em></a>
command for details.</p>
<p>If the suspension is sheared via the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a>
command then the pair style uses the shear rate to adjust the
hydrodynamic interactions accordingly. Volume changes due to fix
deform are accounted for when computing the volume fraction
corrections to R_FU.</p>
<p>When computing the volume fraction corrections to R_FU, the presence
of walls (whether moving or stationary) will affect the volume
fraction available to colloidal particles. This is currently accounted
for with the following types of walls: <a class="reference internal" href="fix_wall.html"><em>wall/lj93</em></a>,
<a class="reference internal" href="fix_wall.html"><em>wall/lj126</em></a>, <a class="reference internal" href="fix_wall.html"><em>wall/colloid</em></a>, and
<a class="reference internal" href="fix_wall.html"><em>wall/harmonic</em></a>. For these wall styles, the correct
volume fraction will be used when walls do not coincide with the box
boundary, as well as when walls move and thereby cause a change in the
volume fraction. Other wall styles will still work, but they will
result in the volume fraction being computed based on the box
boundaries.</p>
<p>Since lubrication forces are dissipative, it is usually desirable to
thermostat the system at a constant temperature. If Brownian motion
(at a constant temperature) is desired, it can be set using the
<a class="reference internal" href="pair_brownian.html"><em>pair_style brownian</em></a> command. These pair styles
and the brownian style should use consistent parameters for <em>mu</em>,
<em>flaglog</em>, <em>flagfld</em>, <em>cutinner</em>, <em>cutoff</em>, <em>flagHI</em> and <em>flagVF</em>.</p>
<hr class="docutils" />
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>cutinner (distance units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The two coefficients are optional. If neither is specified, the two
cutoffs specified in the pair_style command are used. Otherwise both
must be specified.</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>this section</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>this section</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>For atom type pairs I,J and I != J, the two cutoff distances for this
pair style can be mixed. The default mix value is <em>geometric</em>. See
the &#8220;pair_modify&#8221; command for details.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option for the energy of the pair interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>This pair style does 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>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>These styles are part of the COLLOID package. They are only enabled
if LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
<p>Only spherical monodisperse particles are allowed for pair_style
lubricate.</p>
<p>Only spherical particles are allowed for pair_style lubricate/poly.</p>
<p>These pair styles will not restart exactly when using the
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command, though they should provide
statistically similar results. This is because the forces they
compute depend on atom velocities. See the
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command for more details.</p>
</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>, <a class="reference internal" href="pair_lubricateU.html"><em>pair_style lubricateU</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The default settings for the optional args are flagHI = 1 and flagVF =
1.</p>
<hr class="docutils" />
<p id="ball"><strong>(Ball)</strong> Ball and Melrose, Physica A, 247, 444-472 (1997).</p>
<p id="kumar"><strong>(Kumar)</strong> Kumar and Higdon, Phys Rev E, 82, 051401 (2010). See also
his thesis for more details: A. Kumar, &#8220;Microscale Dynamics in
Suspensions of Non-spherical Particles&#8221;, Thesis, University of
Illinois Urbana-Champaign,
(2010). (<a class="reference external" href="https://www.ideals.illinois.edu/handle/2142/16032">https://www.ideals.illinois.edu/handle/2142/16032</a>)</p>
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<div class="section" id="pair-style-lubricateu-command">
<span id="index-0"></span><h1>pair_style lubricateU command<a class="headerlink" href="#pair-style-lubricateu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lubricateu-poly-command">
<h1>pair_style lubricateU/poly command<a class="headerlink" href="#pair-style-lubricateu-poly-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 mu flaglog cutinner cutoff gdot flagHI flagVF
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lubricateU</em> or <em>lubricateU/poly</em></li>
<li>mu = dynamic viscosity (dynamic viscosity units)</li>
<li>flaglog = 0/1 to exclude/include log terms in the lubrication approximation</li>
<li>cutinner = inner cut off distance (distance units)</li>
<li>cutoff = outer cutoff for interactions (distance units)</li>
<li>gdot = shear rate (1/time units)</li>
<li>flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions</li>
<li>flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms</li>
</ul>
<p><strong>Examples:</strong> (all assume radius = 1)</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1
pair_coeff 1 1 2.05 2.8
pair_coeff * *
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Styles <em>lubricateU</em> and <em>lubricateU/poly</em> compute velocities and
angular velocities for finite-size spherical particles such that the
hydrodynamic interaction balances the force and torque due to all
other types of interactions.</p>
<p>The interactions have 2 components. The first is
Ball-Melrose lubrication terms via the formulas in <a class="reference internal" href="#ball"><span>(Ball and Melrose)</span></a></p>
<img alt="_images/pair_lubricate.jpg" class="align-center" src="_images/pair_lubricate.jpg" />
<p>which represents the dissipation W between two nearby particles due to
their relative velocities in the presence of a background solvent with
viscosity <em>mu</em>. Note that this is dynamic viscosity which has units of
mass/distance/time, not kinematic viscosity.</p>
<p>The Asq (squeeze) term is the strongest and is included as long as
<em>flagHI</em> is set to 1 (default). It scales as 1/gap where gap is the
separation between the surfaces of the 2 particles. The Ash (shear)
and Apu (pump) terms are only included if <em>flaglog</em> is set to 1. They
are the next strongest interactions, and the only other singular
interaction, and scale as log(gap). Note that <em>flaglog</em> = 1 and
<em>flagHI</em> = 0 is invalid, and will result in a warning message, after
which <em>flagHI</em> will be set to 1. The Atw (twist) term is currently not
included. It is typically a very small contribution to the lubrication
forces.</p>
<p>The <em>flagHI</em> and <em>flagVF</em> settings are optional. Neither should be
used, or both must be defined.</p>
<p><em>Cutinner</em> sets the minimum center-to-center separation that will be
used in calculations irrespective of the actual separation. <em>Cutoff</em>
is the maximum center-to-center separation at which an interaction is
computed. Using a <em>cutoff</em> less than 3 radii is recommended if
<em>flaglog</em> is set to 1.</p>
<p>The other component is due to the Fast Lubrication Dynamics (FLD)
approximation, described in <a class="reference internal" href="#kumar"><span>(Kumar)</span></a>. The equation being
solved to balance the forces and torques is</p>
<img alt="_images/fld2.jpg" class="align-center" src="_images/fld2.jpg" />
<p>where U represents the velocities and angular velocities of the
particles, U^*infty* represents the velocities and the angular
velocities of the undisturbed fluid, and E^*infty* represents the rate
of strain tensor of the undisturbed fluid flow with viscosity
<em>mu</em>. Again, note that this is dynamic viscosity which has units of
mass/distance/time, not kinematic viscosity. Volume fraction
corrections to R_FU are included if <em>flagVF</em> is set to 1 (default).</p>
<p>F*rest* represents the forces and torques due to all other types of
interactions, e.g. Brownian, electrostatic etc. Note that this
algorithm neglects the inertial terms, thereby removing the
restriction of resolving the small interial time scale, which may not
be of interest for colloidal particles. This pair style solves for
the velocity such that the hydrodynamic force balances all other types
of forces, thereby resulting in a net zero force (zero inertia limit).
When defining this pair style, it must be defined last so that when
this style is invoked all other types of forces have already been
computed. For the same reason, it won&#8217;t work if additional non-pair
styles are defined (such as bond or Kspace forces) as they are
calculated in LAMMPS after the pairwise interactions have been
computed.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">When using these styles, the these pair styles are designed to
be used with implicit time integration and a correspondingly larger
timestep. Thus either <a class="reference internal" href="fix_nve_noforce.html"><em>fix nve/noforce</em></a> should
be used for spherical particles defined via <a class="reference internal" href="atom_style.html"><em>atom_style sphere</em></a> or <a class="reference internal" href="fix_nve_asphere_noforce.html"><em>fix nve/asphere/noforce</em></a> should be used for
spherical particles defined via <a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a>. This is because the velocity and angular
momentum of each particle is set by the pair style, and should not be
reset by the time integration fix.</p>
</div>
<p>Style <em>lubricateU</em> requires monodisperse spherical particles; style
<em>lubricateU/poly</em> allows for polydisperse spherical particles.</p>
<p>If the suspension is sheared via the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a>
command then the pair style uses the shear rate to adjust the
hydrodynamic interactions accordingly. Volume changes due to fix
deform are accounted for when computing the volume fraction
corrections to R_FU.</p>
<p>When computing the volume fraction corrections to R_FU, the presence
of walls (whether moving or stationary) will affect the volume
fraction available to colloidal particles. This is currently accounted
for with the following types of walls: <a class="reference internal" href="fix_wall.html"><em>wall/lj93</em></a>,
<a class="reference internal" href="fix_wall.html"><em>wall/lj126</em></a>, <a class="reference internal" href="fix_wall.html"><em>wall/colloid</em></a>, and
&#8220;wall/harmonic_fix_wall.html&#8221;. For these wall styles, the correct
volume fraction will be used when walls do not coincide with the box
boundary, as well as when walls move and thereby cause a change in the
volume fraction. To use these wall styles with pair_style <em>lubricateU</em>
or <em>lubricateU/poly</em>, the <em>fld yes</em> option must be specified in the
fix wall command.</p>
<p>Since lubrication forces are dissipative, it is usually desirable to
thermostat the system at a constant temperature. If Brownian motion
(at a constant temperature) is desired, it can be set using the
<a class="reference internal" href="pair_brownian.html"><em>pair_style brownian</em></a> command. These pair styles
and the brownian style should use consistent parameters for <em>mu</em>,
<em>flaglog</em>, <em>flagfld</em>, <em>cutinner</em>, <em>cutoff</em>, <em>flagHI</em> and <em>flagVF</em>.</p>
<hr class="docutils" />
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>cutinner (distance units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The two coefficients are optional. If neither is specified, the two
cutoffs specified in the pair_style command are used. Otherwise both
must be specified.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, the two cutoff distances for this
pair style can be mixed. The default mix value is <em>geometric</em>. See
the &#8220;pair_modify&#8221; command for details.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option for the energy of the pair interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>This pair style does 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>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>These styles are part of the COLLOID package. They are only enabled
if LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
<p>Currently, these pair styles assume that all other types of
forces/torques on the particles have been already been computed when
it is invoked. This requires this style to be defined as the last of
the pair styles, and that no fixes apply additional constraint forces.
One exception is the <a class="reference internal" href="fix_wall.html"><em>fix wall/colloid</em></a> commands, which
has an &#8220;fld&#8221; option to apply their wall forces correctly.</p>
<p>Only spherical monodisperse particles are allowed for pair_style
lubricateU.</p>
<p>Only spherical particles are allowed for pair_style lubricateU/poly.</p>
<p>For sheared suspensions, it is assumed that the shearing is done in
the xy plane, with x being the velocity direction and y being the
velocity-gradient direction. In this case, one must use <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> with the same rate of shear (erate).</p>
</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>, <a class="reference internal" href="pair_lubricate.html"><em>pair_style lubricate</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The default settings for the optional args are flagHI = 1 and flagVF =
1.</p>
<hr class="docutils" />
<p id="ball"><strong>(Ball)</strong> Ball and Melrose, Physica A, 247, 444-472 (1997).</p>
<p id="kumar"><strong>(Kumar)</strong> Kumar and Higdon, Phys Rev E, 82, 051401 (2010).</p>
</div>
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<div class="section" id="pair-style-lj-mdf-command">
<span id="index-0"></span><h1>pair_style lj/mdf command<a class="headerlink" href="#pair-style-lj-mdf-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-mdf-command">
<h1>pair_style buck/mdf command<a class="headerlink" href="#pair-style-buck-mdf-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lennard-mdf-command">
<h1>pair_style lennard/mdf command<a class="headerlink" href="#pair-style-lennard-mdf-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 args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lj/mdf</em> or <em>buck/mdf</em> or <em>lennard/mdf</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>lj/mdf</em> args = cutoff1 cutoff2
cutoff1 = inner cutoff for the start of the tapering function
cutoff1 = out cutoff for the end of the tapering function
<em>buck/mdf</em> args = cutoff1 cutoff2
cutoff1 = inner cutoff for the start of the tapering function
cutoff1 = out cutoff for the end of the tapering function
<em>lennard/mdf</em> args = cutoff1 cutoff2
cutoff1 = inner cutoff for the start of the tapering function
cutoff1 = out cutoff for the end of the tapering function
</pre>
</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 lj/mdf 2.5 3.0
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8 3.0 3.2
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style buck 2.5 3.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff * * 100.0 1.5 200.0 3.0 3.5
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lennard/mdf 2.5 3.0
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8 3.0 3.2
</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>lj/mdf</em>, <em>buck/mdf</em> and <em>lennard/mdf</em> compute the standard 12-6
Lennard-Jones and Buckingham potential with the addition of a taper
function that ramps the energy and force smoothly to zero between an
inner and outer cutoff.</p>
<img alt="_images/pair_mdf-1.jpg" class="align-center" src="_images/pair_mdf-1.jpg" />
<p>The tapering, <em>f(r)</em>, is done by using the Mei, Davenport, Fernando
function <a class="reference internal" href="#mei"><span>(Mei)</span></a>.</p>
<img alt="_images/pair_mdf-2.jpg" class="align-center" src="_images/pair_mdf-2.jpg" />
<p>where</p>
<img alt="_images/pair_mdf-3.jpg" class="align-center" src="_images/pair_mdf-3.jpg" />
<p>Here <em>r_m</em> is the inner cutoff radius and <em>r_cut</em> is the outer cutoff
radius.</p>
<hr class="docutils" />
<p>For the <em>lj/mdf</em> pair_style, the potential energy, <em>E(r)</em>, is the
standard 12-6 Lennard-Jones written in the epsilon/sigma form:</p>
<img alt="_images/pair_mdf-4.jpg" class="align-center" src="_images/pair_mdf-4.jpg" />
<p>The following coefficients must be defined for each pair of atoms
types via the pair_coeff command as in the examples above, or in the
data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> or
<a class="reference internal" href="read_restart.html"><em>read_restart commands</em></a>, or by mixing as described
below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>r_m (distance units)</li>
<li>r_*cut* (distance units)</li>
</ul>
<hr class="docutils" />
<p>For the <em>buck/mdf</em> pair_style, the potential energy, <em>E(r)</em>, is the
standard Buckingham potential:</p>
<img alt="_images/pair_mdf-5.jpg" class="align-center" src="_images/pair_mdf-5.jpg" />
<ul class="simple">
<li>A (energy units)</li>
<li>rho (distance units)</li>
<li>C (energy-distance^6 units)</li>
<li>r_m (distance units)</li>
<li>r_*cut*$ (distance units)</li>
</ul>
<hr class="docutils" />
<p>For the <em>lennard/mdf</em> pair_style, the potential energy, <em>E(r)</em>, is the
standard 12-6 Lennard-Jones written in the $A/B$ form:</p>
<img alt="_images/pair_mdf-6.jpg" class="align-center" src="_images/pair_mdf-6.jpg" />
<p>The following coefficients must be defined for each pair of atoms
types via the pair_coeff command as in the examples above, or in the
data file or restart files read by the read_data or read_restart
commands, or by mixing as described below:</p>
<ul class="simple">
<li>A (energy-distance^12 units)</li>
<li>B (energy-distance^6 units)</li>
<li>r_m (distance units)</li>
<li>r_*cut* (distance units)</li>
</ul>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command
for details.</p>
<p>All of the <em>lj/cut</em> pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option for the energy of the
Lennard-Jones portion of the pair interaction.</p>
<p>The <em>lj/cut/coul/long</em> and <em>lj/cut/tip4p/long</em> pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.</p>
<p>All of the <em>lj/cut</em> pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> tail option for adding a long-range
tail correction to the energy and pressure for the Lennard-Jones
portion of the pair interaction.</p>
<p>All of the <em>lj/cut</em> pair styles write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.</p>
<p>The <em>lj/cut</em> and <em>lj/cut/coul/long</em> pair styles support the use of the
<em>inner</em>, <em>middle</em>, and <em>outer</em> keywords of the <a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
The other styles only support the <em>pair</em> keyword of run_style respa.
See the <a class="reference internal" href="run_style.html"><em>run_style</em></a> command for details.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>These pair styles can only be used if LAMMPS was built with the
USER-MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info on packages.</p>
</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="mei"><strong>(Mei)</strong> Mei, Davenport, Fernando, Phys Rev B, 43 4653 (1991)</p>
</div>
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<div class="section" id="pair-style-meam-command">
<span id="index-0"></span><h1>pair_style meam command<a class="headerlink" href="#pair-style-meam-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 meam
</pre></div>
</div>
</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 meam
pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The behavior of the MEAM potential for alloy systems has changed
as of November 2010; see description below of the mixture_ref_t
parameter</p>
</div>
<p>Style <em>meam</em> computes pairwise interactions for a variety of materials
using modified embedded-atom method (MEAM) potentials
<a class="reference internal" href="#baskes"><span>(Baskes)</span></a>. Conceptually, it is an extension to the original
<a class="reference internal" href="pair_eam.html"><em>EAM potentials</em></a> which adds angular forces. It is
thus suitable for modeling metals and alloys with fcc, bcc, hcp and
diamond cubic structures, as well as covalently bonded materials like
silicon and carbon.</p>
<p>In the MEAM formulation, the total energy E of a system of atoms is
given by:</p>
<img alt="_images/pair_meam.jpg" class="align-center" src="_images/pair_meam.jpg" />
<p>where F is the embedding energy which is a function of the atomic
electron density rho, and phi is a pair potential interaction. The
pair interaction is summed over all neighbors J of atom I within the
cutoff distance. As with EAM, the multi-body nature of the MEAM
potential is a result of the embedding energy term. Details of the
computation of the embedding and pair energies, as implemented in
LAMMPS, are given in <a class="reference internal" href="#gullet"><span>(Gullet)</span></a> and references therein.</p>
<p>The various parameters in the MEAM formulas are listed in two files
which are specified by the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command.
These are ASCII text files in a format consistent with other MD codes
that implement MEAM potentials, such as the serial DYNAMO code and
Warp. Several MEAM potential files with parameters for different
materials are included in the &#8220;potentials&#8221; directory of the LAMMPS
distribution with a &#8221;.meam&#8221; suffix. All of these are parameterized in
terms of LAMMPS <a class="reference internal" href="units.html"><em>metal units</em></a>.</p>
<p>Note that unlike for other potentials, cutoffs for MEAM potentials are
not set in the pair_style or pair_coeff command; they are specified in
the MEAM potential files themselves.</p>
<p>Only a single pair_coeff command is used with the <em>meam</em> style which
specifies two MEAM files and the element(s) to extract information
for. The MEAM elements are mapped to LAMMPS atom types by specifying
N additional arguments after the 2nd filename in the pair_coeff
command, where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>MEAM library file</li>
<li>Elem1, Elem2, ...</li>
<li>MEAM parameter file</li>
<li>N element names = mapping of MEAM elements to atom types</li>
</ul>
<p>See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc page for alternate ways
to specify the path for the potential files.</p>
<p>As an example, the potentials/library.meam file has generic MEAM
settings for a variety of elements. The potentials/sic.meam file has
specific parameter settings for a Si and C alloy system. If your
LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si,
and the 4th to be C, you would use the following pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * library.meam Si C sic.meam Si Si Si C
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The two filenames are for the library and parameter file respectively.
The Si and C arguments (between the file names) are the two elements
for which info will be extracted from the library file. The first
three trailing Si arguments map LAMMPS atom types 1,2,3 to the MEAM Si
element. The final C argument maps LAMMPS atom type 4 to the MEAM C
element.</p>
<p>If the 2nd filename is specified as NULL, no parameter file is read,
which simply means the generic parameters in the library file are
used. Use of the NULL specification for the parameter file is
discouraged for systems with more than a single element type
(e.g. alloys), since the parameter file is expected to set element
interaction terms that are not captured by the information in the
library file.</p>
<p>If a mapping value is specified as NULL, the mapping is not performed.
This can be used when a <em>meam</em> potential is used as part of the
<em>hybrid</em> pair style. The NULL values are placeholders for atom types
that will be used with other potentials.</p>
<p>The MEAM library file provided with LAMMPS has the name
potentials/library.meam. It is the &#8220;meamf&#8221; file used by other MD
codes. Aside from blank and comment lines (start with #) which can
appear anywhere, it is formatted as a series of entries, each of which
has 19 parameters and can span multiple lines:</p>
<p>elt, lat, z, ielement, atwt, alpha, b0, b1, b2, b3, alat, esub, asub,
t0, t1, t2, t3, rozero, ibar</p>
<p>The &#8220;elt&#8221; and &#8220;lat&#8221; parameters are text strings, such as elt = Si or
Cu and lat = dia or fcc. Because the library file is used by Fortran
MD codes, these strings may be enclosed in single quotes, but this is
not required. The other numeric parameters match values in the
formulas above. The value of the &#8220;elt&#8221; string is what is used in the
pair_coeff command to identify which settings from the library file
you wish to read in. There can be multiple entries in the library
file with the same &#8220;elt&#8221; value; LAMMPS reads the 1st matching entry it
finds and ignores the rest.</p>
<p>Other parameters in the MEAM library file correspond to single-element
potential parameters:</p>
<pre class="literal-block">
lat = lattice structure of reference configuration
z = number of nearest neighbors in the reference structure
ielement = atomic number
atwt = atomic weight
alat = lattice constant of reference structure
esub = energy per atom (eV) in the reference structure at equilibrium
asub = &quot;A&quot; parameter for MEAM (see e.g. <a class="reference internal" href="#baskes"><span>(Baskes)</span></a>)
</pre>
<p>The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the
standard MEAM parameters in the literature <a class="reference internal" href="#baskes"><span>(Baskes)</span></a> (the b
parameters are the standard beta parameters). The rozero parameter is
an element-dependent density scaling that weights the reference
background density (see e.g. equation 4.5 in <a class="reference internal" href="#gullet"><span>(Gullet)</span></a>) and
is typically 1.0 for single-element systems. The ibar parameter
selects the form of the function G(Gamma) used to compute the electron
density; options are</p>
<div class="highlight-python"><div class="highlight"><pre> 0 =&gt; G = sqrt(1+Gamma)
1 =&gt; G = exp(Gamma/2)
2 =&gt; not implemented
3 =&gt; G = 2/(1+exp(-Gamma))
4 =&gt; G = sqrt(1+Gamma)
-5 =&gt; G = +-sqrt(abs(1+Gamma))
</pre></div>
</div>
<p>If used, the MEAM parameter file contains settings that override or
complement the library file settings. Examples of such parameter
files are in the potentials directory with a &#8221;.meam&#8221; suffix. Their
format is the same as is read by other Fortran MD codes. Aside from
blank and comment lines (start with #) which can appear anywhere, each
line has one of the following forms. Each line can also have a
trailing comment (starting with #) which is ignored.</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">keyword</span> <span class="o">=</span> <span class="n">value</span>
<span class="n">keyword</span><span class="p">(</span><span class="n">I</span><span class="p">)</span> <span class="o">=</span> <span class="n">value</span>
<span class="n">keyword</span><span class="p">(</span><span class="n">I</span><span class="p">,</span><span class="n">J</span><span class="p">)</span> <span class="o">=</span> <span class="n">value</span>
<span class="n">keyword</span><span class="p">(</span><span class="n">I</span><span class="p">,</span><span class="n">J</span><span class="p">,</span><span class="n">K</span><span class="p">)</span> <span class="o">=</span> <span class="n">value</span>
</pre></div>
</div>
<p>The recognized keywords are as follows:</p>
<p>Ec, alpha, rho0, delta, lattce, attrac, repuls, nn2, Cmin, Cmax, rc, delr,
augt1, gsmooth_factor, re</p>
<p>where</p>
<pre class="literal-block">
rc = cutoff radius for cutoff function; default = 4.0
delr = length of smoothing distance for cutoff function; default = 0.1
rho0(I) = relative density for element I (overwrites value
read from meamf file)
Ec(I,J) = cohesive energy of reference structure for I-J mixture
delta(I,J) = heat of formation for I-J alloy; if Ec_IJ is input as
zero, then LAMMPS sets Ec_IJ = (Ec_II + Ec_JJ)/2 - delta_IJ
alpha(I,J) = alpha parameter for pair potential between I and J (can
be computed from bulk modulus of reference structure
re(I,J) = equilibrium distance between I and J in the reference
structure
Cmax(I,J,K) = Cmax screening parameter when I-J pair is screened
by K (I&lt;=J); default = 2.8
Cmin(I,J,K) = Cmin screening parameter when I-J pair is screened
by K (I&lt;=J); default = 2.0
lattce(I,J) = lattice structure of I-J reference structure:
dia = diamond (interlaced fcc for alloy)
fcc = face centered cubic
bcc = body centered cubic
dim = dimer
b1 = rock salt (NaCl structure)
hcp = hexagonal close-packed
c11 = MoSi2 structure
l12 = Cu3Au structure (lower case L, followed by 12)
b2 = CsCl structure (interpenetrating simple cubic)
nn2(I,J) = turn on second-nearest neighbor MEAM formulation for
I-J pair (see for example <a class="reference internal" href="#lee"><span>(Lee)</span></a>).
0 = second-nearest neighbor formulation off
1 = second-nearest neighbor formulation on
default = 0
attrac(I,J) = additional cubic attraction term in Rose energy I-J pair potential
default = 0
repuls(I,J) = additional cubic repulsive term in Rose energy I-J pair potential
default = 0
zbl(I,J) = blend the MEAM I-J pair potential with the ZBL potential for small
atom separations <a class="reference internal" href="pair_tersoff_zbl.html#zbl"><span>(ZBL)</span></a>
default = 1
gsmooth_factor = factor determining the length of the G-function smoothing
region; only significant for ibar=0 or ibar=4.
99.0 = short smoothing region, sharp step
0.5 = long smoothing region, smooth step
default = 99.0
augt1 = integer flag for whether to augment t1 parameter by
3/5*t3 to account for old vs. new meam formulations;
0 = don't augment t1
1 = augment t1
default = 1
ialloy = integer flag to use alternative averaging rule for t parameters,
for comparison with the DYNAMO MEAM code
0 = standard averaging (matches ialloy=0 in DYNAMO)
1 = alternative averaging (matches ialloy=1 in DYNAMO)
2 = no averaging of t (use single-element values)
default = 0
mixture_ref_t = integer flag to use mixture average of t to compute the background
reference density for alloys, instead of the single-element values
(see description and warning elsewhere in this doc page)
0 = do not use mixture averaging for t in the reference density
1 = use mixture averaging for t in the reference density
default = 0
erose_form = integer value to select the form of the Rose energy function
(see description below).
default = 0
emb_lin_neg = integer value to select embedding function for negative densities
0 = F(rho)=0
1 = F(rho) = -asub*esub*rho (linear in rho, matches DYNAMO)
default = 0
bkgd_dyn = integer value to select background density formula
0 = rho_bkgd = rho_ref_meam(a) (as in the reference structure)
1 = rho_bkgd = rho0_meam(a)*Z_meam(a) (matches DYNAMO)
default = 0
</pre>
<p>Rc, delr, re are in distance units (Angstroms in the case of metal
units). Ec and delta are in energy units (eV in the case of metal
units).</p>
<p>Each keyword represents a quantity which is either a scalar, vector,
2d array, or 3d array and must be specified with the correct
corresponding array syntax. The indices I,J,K each run from 1 to N
where N is the number of MEAM elements being used.</p>
<p>Thus these lines</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">rho0</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span> <span class="o">=</span> <span class="mf">2.25</span>
<span class="n">alpha</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">)</span> <span class="o">=</span> <span class="mf">4.37</span>
</pre></div>
</div>
<p>set rho0 for the 2nd element to the value 2.25 and set alpha for the
alloy interaction between elements 1 and 2 to 4.37.</p>
<p>The augt1 parameter is related to modifications in the MEAM
formulation of the partial electron density function. In recent
literature, an extra term is included in the expression for the
third-order density in order to make the densities orthogonal (see for
example <a class="reference internal" href="pair_polymorphic.html#wang"><span>(Wang)</span></a>, equation 3d); this term is included in the
MEAM implementation in lammps. However, in earlier published work
this term was not included when deriving parameters, including most of
those provided in the library.meam file included with lammps, and to
account for this difference the parameter t1 must be augmented by
3/5*t3. If augt1=1, the default, this augmentation is done
automatically. When parameter values are fit using the modified
density function, as in more recent literature, augt1 should be set to
0.</p>
<p>The mixture_ref_t parameter is available to match results with those
of previous versions of lammps (before January 2011). Newer versions
of lammps, by default, use the single-element values of the t
parameters to compute the background reference density. This is the
proper way to compute these parameters. Earlier versions of lammps
used an alloy mixture averaged value of t to compute the background
reference density. Setting mixture_ref_t=1 gives the old behavior.
WARNING: using mixture_ref_t=1 will give results that are demonstrably
incorrect for second-neighbor MEAM, and non-standard for
first-neighbor MEAM; this option is included only for matching with
previous versions of lammps and should be avoided if possible.</p>
<p>The parameters attrac and repuls, along with the integer selection
parameter erose_form, can be used to modify the Rose energy function
used to compute the pair potential. This function gives the energy of
the reference state as a function of interatomic spacing. The form of
this function is:</p>
<div class="highlight-python"><div class="highlight"><pre>astar = alpha * (r/re - 1.d0)
if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar)
if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar)
if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar)
a3 = repuls, astar &lt; 0
a3 = attrac, astar &gt;= 0
</pre></div>
</div>
<p>Most published MEAM parameter sets use the default values attrac=repulse=0.
Setting repuls=attrac=delta corresponds to the form used in several
recent published MEAM parameter sets, such as <span class="xref std std-ref">(Vallone)</span></p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The default form of the erose expression in LAMMPS was corrected
in March 2009. The current version is correct, but may show different
behavior compared with earlier versions of lammps with the attrac
and/or repuls parameters are non-zero. To obtain the previous default
form, use erose_form = 1 (this form does not seem to appear in the
literature). An alternative form (see e.g. <a class="reference internal" href="#lee2"><span>(Lee2)</span></a>) is
available using erose_form = 2.</p>
</div>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS with
user-specifiable parameters as described above. You never need to
specify a pair_coeff command with I != J arguments for this style.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This style is part of the MEAM package. It is only enabled if LAMMPS
was built with that package, which also requires the MEAM library be
built and linked with LAMMPS. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</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>, <a class="reference internal" href="pair_eam.html"><em>pair_style eam</em></a>,
<a class="reference internal" href="pair_meam_spline.html"><em>pair_style meam/spline</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="baskes"><strong>(Baskes)</strong> Baskes, Phys Rev B, 46, 2727-2742 (1992).</p>
<p id="gullet"><strong>(Gullet)</strong> Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
This report may be accessed on-line via <a class="reference external" href="http://infoserve.sandia.gov/sand_doc/2003/038782.pdf">this link</a>.</p>
<p id="lee"><strong>(Lee)</strong> Lee, Baskes, Phys. Rev. B, 62, 8564-8567 (2000).</p>
<p id="lee2"><strong>(Lee2)</strong> Lee, Baskes, Kim, Cho. Phys. Rev. B, 64, 184102 (2001).</p>
<p id="valone"><strong>(Valone)</strong> Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006).</p>
<p id="wang"><strong>(Wang)</strong> Wang, Van Hove, Ross, Baskes, J. Chem. Phys., 121, 5410 (2004).</p>
<p id="zbl"><strong>(ZBL)</strong> J.F. Ziegler, J.P. Biersack, U. Littmark, &#8220;Stopping and Ranges
of Ions in Matter&#8221;, Vol 1, 1985, Pergamon Press.</p>
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<div class="section" id="pair-style-meam-spline">
<h1>pair_style meam/spline<a class="headerlink" href="#pair-style-meam-spline" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-meam-spline-omp">
<h1>pair_style meam/spline/omp<a class="headerlink" href="#pair-style-meam-spline-omp" 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 meam/spline
</pre></div>
</div>
</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 meam/spline
pair_coeff * * Ti.meam.spline Ti
pair_coeff * * Ti.meam.spline Ti Ti Ti
</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>meam/spline</em> style computes pairwise interactions for metals
using a variant of modified embedded-atom method (MEAM) potentials
<a class="reference internal" href="pair_meam_sw_spline.html#lenosky"><span>(Lenosky)</span></a>. The total energy E is given by</p>
<img alt="_images/pair_meam_spline.jpg" class="align-center" src="_images/pair_meam_spline.jpg" />
<p>where rho_i is the density at atom I, theta_jik is the angle between
atoms J, I, and K centered on atom I. The five functions Phi, U, rho,
f, and g are represented by cubic splines.</p>
<p>The cutoffs and the coefficients for these spline functions are listed
in a parameter file which is specified by the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command. Parameter files for different
elements are included in the &#8220;potentials&#8221; directory of the LAMMPS
distribution and have a &#8221;.meam.spline&#8221; file suffix. All of these
files are parameterized in terms of LAMMPS <a class="reference internal" href="units.html"><em>metal units</em></a>.</p>
<p>Note that unlike for other potentials, cutoffs for spline-based MEAM
potentials are not set in the pair_style or pair_coeff command; they
are specified in the potential files themselves.</p>
<p>Unlike the EAM pair style, which retrieves the atomic mass from the
potential file, the spline-based MEAM potentials do not include mass
information; thus you need to use the <a class="reference internal" href="mass.html"><em>mass</em></a> command to
specify it.</p>
<p>Only a single pair_coeff command is used with the <em>meam/spline</em> style
which specifies a potential file with parameters for all needed
elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N element names = mapping of spline-based MEAM elements to atom types</li>
</ul>
<p>See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc page for alternate ways
to specify the path for the potential file.</p>
<p>As an example, imagine the Ti.meam.spline file has values for Ti. If
your LAMMPS simulation has 3 atoms types and they are all to be
treated with this potentials, you would use the following pair_coeff
command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * Ti.meam.spline Ti Ti Ti
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element
in the potential file. If a mapping value is specified as NULL, the
mapping is not performed. This can be used when a <em>meam/spline</em>
potential is used as part of the <em>hybrid</em> pair style. The NULL values
are placeholders for atom types that will be used with other
potentials.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The <em>meam/spline</em> style currently supports only single-element
MEAM potentials. It may be extended for alloy systems in the future.</p>
</div>
<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>The current version of this pair style does not support multiple
element types or mixing. It has been designed for pure elements only.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>The <em>meam/spline</em> pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in an external
potential parameter file. Thus, you need to re-specify the pair_style
and pair_coeff commands in an input script that reads a restart file.</p>
<p>The <em>meam/spline</em> pair style 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>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style requires the <a class="reference internal" href="newton.html"><em>newton</em></a> setting to be &#8220;on&#8221;
for pair interactions.</p>
<p>This pair style is only enabled if LAMMPS was built with the USER-MISC
package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
for more info.</p>
</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>, <a class="reference internal" href="pair_meam.html"><em>pair_style meam</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="lenosky"><strong>(Lenosky)</strong> Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter,
Kress, Modelling Simulation Materials Science Enginerring, 8, 825
(2000).</p>
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<div class="section" id="pair-style-meam-sw-spline">
<h1>pair_style meam/sw/spline<a class="headerlink" href="#pair-style-meam-sw-spline" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-meam-sw-spline-omp">
<h1>pair_style meam/sw/spline/omp<a class="headerlink" href="#pair-style-meam-sw-spline-omp" 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 meam/sw/spline
</pre></div>
</div>
</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 meam/sw/spline
pair_coeff * * Ti.meam.sw.spline Ti
pair_coeff * * Ti.meam.sw.spline Ti Ti Ti
</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>meam/sw/spline</em> style computes pairwise interactions for metals
using a variant of modified embedded-atom method (MEAM) potentials
<a class="reference internal" href="#lenosky"><span>(Lenosky)</span></a> with an additional Stillinger-Weber (SW) term
<a class="reference internal" href="pair_sw.html#stillinger"><span>(Stillinger)</span></a> in the energy. This form of the potential
was first proposed by Nicklas, Fellinger, and Park
<a class="reference internal" href="#nicklas"><span>(Nicklas)</span></a>. We refer to it as MEAM+SW. The total energy E
is given by</p>
<img alt="_images/pair_meam_sw_spline.jpg" class="align-center" src="_images/pair_meam_sw_spline.jpg" />
<p>where rho_I is the density at atom I, theta_JIK is the angle between
atoms J, I, and K centered on atom I. The seven functions
Phi, F, G, U, rho, f, and g are represented by cubic splines.</p>
<p>The cutoffs and the coefficients for these spline functions are listed
in a parameter file which is specified by the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command. Parameter files for different
elements are included in the &#8220;potentials&#8221; directory of the LAMMPS
distribution and have a &#8221;.meam.sw.spline&#8221; file suffix. All of these
files are parameterized in terms of LAMMPS <a class="reference internal" href="units.html"><em>metal units</em></a>.</p>
<p>Note that unlike for other potentials, cutoffs for spline-based
MEAM+SW potentials are not set in the pair_style or pair_coeff
command; they are specified in the potential files themselves.</p>
<p>Unlike the EAM pair style, which retrieves the atomic mass from the
potential file, the spline-based MEAM+SW potentials do not include
mass information; thus you need to use the <a class="reference internal" href="mass.html"><em>mass</em></a> command to
specify it.</p>
<p>Only a single pair_coeff command is used with the meam/sw/spline style
which specifies a potential file with parameters for all needed
elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N element names = mapping of spline-based MEAM+SW elements to atom types</li>
</ul>
<p>See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc page for alternate ways
to specify the path for the potential file.</p>
<p>As an example, imagine the Ti.meam.sw.spline file has values for Ti.
If your LAMMPS simulation has 3 atoms types and they are all to be
treated with this potential, you would use the following pair_coeff
command:</p>
<p>pair_coeff * * Ti.meam.sw.spline Ti Ti Ti</p>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element
in the potential file. If a mapping value is specified as NULL, the
mapping is not performed. This can be used when a <em>meam/sw/spline</em>
potential is used as part of the hybrid pair style. The NULL values
are placeholders for atom types that will be used with other
potentials.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The <em>meam/sw/spline</em> style currently supports only
single-element MEAM+SW potentials. It may be extended for alloy
systems in the future.</p>
</div>
<p>Example input scripts that use this pair style are provided
in the examples/USER/misc/meam_sw_spline directory.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>The pair style does not support multiple element types or mixing.
It has been designed for pure elements only.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>The <em>meam/sw/spline</em> pair style does not write its information to
<a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in an external
potential parameter file. Thus, you need to re-specify the pair_style
and pair_coeff commands in an input script that reads a restart file.</p>
<p>The <em>meam/sw/spline</em> pair style 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>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style requires the <a class="reference internal" href="newton.html"><em>newton</em></a> setting to be &#8220;on&#8221;
for pair interactions.</p>
<p>This pair style is only enabled if LAMMPS was built with the USER-MISC package.
See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</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>, <a class="reference internal" href="pair_meam.html"><em>pair_style meam</em></a>,
<a class="reference internal" href="pair_meam_spline.html"><em>pair_style meam/spline</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="lenosky"><strong>(Lenosky)</strong> Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter,
Kress, Modell. Simul. Mater. Sci. Eng. 8, 825 (2000).</p>
<p id="stillinger"><strong>(Stillinger)</strong> Stillinger, Weber, Phys. Rev. B 31, 5262 (1985).</p>
<p id="nicklas"><strong>(Nicklas)</strong>
The spline-based MEAM+SW format was first devised and used to develop
potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger,
and Hyoungki Park at The Ohio State University.</p>
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<div class="section" id="pair-style-mgpt-command">
<span id="index-0"></span><h1>pair_style mgpt command<a class="headerlink" href="#pair-style-mgpt-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 mgpt
</pre></div>
</div>
</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 mgpt
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega
cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin
cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin
pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double
pair_coeff * * parmin potin Omega volpress yes nbody 12
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Within DFT quantum mechanics, generalized pseudopotential theory (GPT)
(<a class="reference internal" href="#moriarty1"><span>Moriarty1</span></a>) provides a first-principles approach to
multi-ion interatomic potentials in d-band transition metals, with a
volume-dependent, real-space total-energy functional for the N-ion
elemental bulk material in the form</p>
<img alt="_images/pair_mgpt.jpg" class="align-center" src="_images/pair_mgpt.jpg" />
<p>where the prime on each summation sign indicates the exclusion of all
self-interaction terms from the summation. The leading volume term
E_vol as well as the two-ion central-force pair potential v_2 and the
three- and four-ion angular-force potentials, v_3 and v_4, depend
explicitly on the atomic volume Omega, but are structure independent
and transferable to all bulk ion configurations, either ordered or
disordered, and with of without the presence of point and line
defects. The simplified model GPT or MGPT (<a class="reference internal" href="#moriarty2"><span>Moriarty2</span></a>,
<a class="reference internal" href="#moriarty3"><span>Moriarty3</span></a>), which retains the form of E_tot and permits
more efficient large-scale atomistic simulations, derives from the GPT
through a series of systematic approximations applied to E_vol and the
potentials v_n that are valid for mid-period transition metals with
nearly half-filled d bands.</p>
<p>Both analytic (<a class="reference internal" href="#moriarty2"><span>Moriarty2</span></a>) and matrix
(<a class="reference internal" href="#moriarty3"><span>Moriarty3</span></a>) representations of MGPT have been developed.
In the more general matrix representation, which can also be applied
to f-band actinide metals and permits both canonical and non-canonical
d/f bands, the multi-ion potentials are evaluated on the fly during a
simulation through d- or f-state matrix multiplication, and the forces
that move the ions are determined analytically. Fast matrix-MGPT
algorithms have been developed independently by Glosli
(<a class="reference internal" href="#glosli"><span>Glosli</span></a>, <a class="reference internal" href="#moriarty3"><span>Moriarty3</span></a>) and by Oppelstrup
(<a class="reference internal" href="#oppelstrup"><span>Oppelstrup</span></a>)</p>
<p>The <em>mgpt</em> pair style calculates forces, energies, and the total
energy per atom, E_tot/N, using the Oppelstrup matrix-MGPT algorithm.
Input potential and control data are entered through the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command. Each material treated requires
input parmin and potin potential files, as shown in the above
examples, as well as specification by the user of the initial atomic
volume Omega through pair_coeff. At the beginning of a time step in
any simulation, the total volume of the simulation cell V should
always be equal to Omega*N, where N is the number of metal ions
present, taking into account the presence of any vacancies and/or
interstitials in the case of a solid. In a constant-volume
simulation, which is the normal mode of operation for the <em>mgpt</em> pair
style, Omega, V and N all remain constant throughout the simulation
and thus are equal to their initial values. In a constant-stress
simulation, the cell volume V will change (slowly) as the simulation
proceeds. After each time step, the atomic volume should be updated
by the code as Omega = V/N. In addition, the volume term E_vol and
the potentials v_2, v_3 and v_4 have to be removed at the end of the
time step, and then respecified at the new value of Omega. In all
smulations, Omega must remain within the defined volume range for
E_vol and the potentials for the given material.</p>
<p>The default option volpress yes in the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>
command includes all volume derivatives of E_tot required to calculate
the stress tensor and pressure correctly. The option volpress no
disregards the pressure contribution resulting from the volume term
E_vol, and can be used for testing and analysis purposes. The
additional optional variable nbody controls the specific terms in
E_tot that are calculated. The default option and the normal option
for mid-period transition and actinide metals is nbody 1234 for which
all four terms in E_tot are retained. The option nbody 12, for
example, retains only the volume term and the two-ion pair potential
term and can be used for GPT series-end transition metals that can be
well described without v_3 and v_4. The nbody option can also be used
to test or analyze the contribution of any of the four terms in E_tot
to a given calculated property.</p>
<p>The <em>mgpt</em> pair style makes extensive use of matrix algebra and
includes optimized kernels for the BlueGene/Q architecture and the
Intel/AMD (x86) architectures. When compiled with the appropriate
compiler and compiler switches (-msse3 on x86, and using the IBM XL
compiler on BG/Q), these optimized routines are used automatically.
For BG/Q machines, building with the default Makefile for that
architecture (e.g., &#8220;make bgq&#8221;) should enable the optimized algebra
routines. For x-86 machines, the here provided Makefile.mpi_fastmgpt
(build with &#8220;make mpi_fastmgpt&#8221;) enables the fast algebra routines.
The user will be informed in the output files of the matrix kernels in
use. To further improve speed, on x86 the option precision single can
be added to the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command line, which
improves speed (up to a factor of two) at the cost of doing matrix
calculations with 7 digit precision instead of the default 16. For
consistency the default option can be specified explicitly by the
option precision double.</p>
<p>All remaining potential and control data are contained with the parmin
and potin files, including cutoffs, atomic mass, and other basic MGPT
variables. Specific MGPT potential data for the transition metals
tantalum (Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials),
and vanadium (V6.1 potentials) are contained in the LAMMPS potentials
directory. The stored files are, respectively, Ta4.mgpt.parmin,
Ta4.mgpt.potin, Ta6.8x.mgpt.parmin, Ta6.8x.mgpt.potin,
Mo5.2.mgpt.parmin, Mo5.2.mgpt.potin, V6.1.mgpt.parmin, and
V6.1.mgpt.potin . Useful corresponding informational &#8220;README&#8221; files
on the Ta4, Ta6.8x, Mo5.2 and V6.1 potentials are also included in the
potentials directory. These latter files indicate the volume mesh and
range for each potential and give appropriate references for the
potentials. It is expected that MGPT potentials for additional
materials will be added over time.</p>
<p>Useful example MGPT scripts are given in the examples/USER/mgpt
directory. These scripts show the necessary steps to perform
constant-volume calculations and simulations. It is strongly
recommended that the user work through and understand these examples
before proceeding to more complex simulations.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">For good performance, LAMMPS should be built with the compiler
flags &#8220;-O3 -msse3 -funroll-loops&#8221; when including this pair style. The
src/MAKE/OPTIONS/Makefile.mpi_fastmgpt is an example machine Makefile
with these options included as part of a standard MPI build. Note
that as-is it will build with whatever low-level compiler (g++, icc,
etc) is the default for your MPI installation.</p>
</div>
<hr class="docutils" />
<p><strong>Mixing, shift, table tail correction, restart</strong>:</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
mix, shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
needs to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style is part of the USER-MGPT package and is only enabled
if LAMMPS is built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>The MGPT potentials require the <a class="reference internal" href="newton.html"><em>newtion</em></a> setting to be
&#8220;on&#8221; for pair style interactions.</p>
<p>The stored parmin and potin potential files provided with LAMMPS in
the &#8220;potentials&#8221; directory are written in Rydberg atomic units, with
energies in Rydbergs and distances in Bohr radii. The <em>mgpt</em> pair
style converts Rydbergs to Hartrees to make the potential files
compatible with LAMMPS electron <a class="reference internal" href="units.html"><em>units</em></a>.</p>
<p>The form of E_tot used in the <em>mgpt</em> pair style is only appropriate
for elemental bulk solids and liquids. This includes solids with
point and extended defects such as vacancies, interstitials, grain
boundaries and dislocations. Alloys and free surfaces, however,
require significant modifications, which are not included in the
<em>mgpt</em> pair style. Likewise, the <em>hybrid</em> pair style is not allowed,
where MGPT would be used for some atoms but not for others.</p>
<p>Electron-thermal effects are not included in the standard MGPT
potentials provided in the &#8220;potentials&#8221; directory, where the
potentials have been constructed at zero electron temperature.
Physically, electron-thermal effects may be important in 3d (e.g., V)
and 4d (e.g., Mo) transition metals at high temperatures near melt and
above. It is expected that temperature-dependent MGPT potentials for
such cases will be added over time.</p>
</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>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The options defaults for the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command are
volpress yes, nbody 1234, and precision double.</p>
<hr class="docutils" />
<p id="moriarty1"><strong>(Moriarty1)</strong> Moriarty, Physical Review B, 38, 3199 (1988).</p>
<p id="moriarty2"><strong>(Moriarty2)</strong> Moriarty, Physical Review B, 42, 1609 (1990).
Moriarty, Physical Review B 49, 12431 (1994).</p>
<p id="moriarty3"><strong>(Moriarty3)</strong> Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang,
Journal of Materials Research, 21, 563 (2006).</p>
<p id="glosli"><strong>(Glosli)</strong> Glosli, unpublished, 2005.
Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference
Series, 46, 254 (2006).</p>
<p id="oppelstrup"><strong>(Oppelstrup)</strong> Oppelstrup, unpublished, 2015.
Oppelstrup and Moriarty, to be published.</p>
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<div class="section" id="pair-style-mie-cut-command">
<span id="index-0"></span><h1>pair_style mie/cut command<a class="headerlink" href="#pair-style-mie-cut-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-mie-cut-gpu-command">
<h1>pair_style mie/cut/gpu command<a class="headerlink" href="#pair-style-mie-cut-gpu-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 mie/cut cutoff
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for mie/cut interactions (distance units)</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 mie/cut 10.0
pair_coeff 1 1 0.72 3.40 23.00 6.66
pair_coeff 2 2 0.30 3.55 12.65 6.00
pair_coeff 1 2 0.46 3.32 16.90 6.31
</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>mie/cut</em> style computes the Mie potential, given by</p>
<img alt="_images/pair_mie.jpg" class="align-center" src="_images/pair_mie.jpg" />
<p>Rc is the cutoff and C is a function that depends on the repulsive and
attractive exponents, given by:</p>
<img alt="_images/pair_mie2.jpg" class="align-center" src="_images/pair_mie2.jpg" />
<p>Note that for 12/6 exponents, C is equal to 4 and the formula is the
same as the standard Lennard-Jones potential.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>gammaR</li>
<li>gammaA</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the mie/cut pair styles can be mixed.
If not explicity defined, both the repulsive and attractive gamma
exponents for different atoms will be calculated following the same
mixing rule defined for distances. The default mix value is
<em>geometric</em>. See the &#8220;pair_modify&#8221; command for details.</p>
<p>This pair style supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the pair interaction.</p>
<p>This pair style supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> tail
option for adding a long-range tail correction to the energy and
pressure of the pair interaction.</p>
<p>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style supports the use of the <em>inner</em>, <em>middle</em>, and <em>outer</em>
keywords of the <a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command, meaning the
pairwise forces can be partitioned by distance at different levels of
the rRESPA hierarchy. See the <a class="reference internal" href="run_style.html"><em>run_style</em></a> command for
details.</p>
</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="mie"><strong>(Mie)</strong> G. Mie, Ann Phys, 316, 657 (1903).</p>
<p id="avendano"><strong>(Avendano)</strong> C. Avendano, T. Lafitte, A. Galindo, C. S. Adjiman,
G. Jackson, E. Muller, J Phys Chem B, 115, 11154 (2011).</p>
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<div class="section" id="pair-modify-command">
<span id="index-0"></span><h1>pair_modify command<a class="headerlink" href="#pair-modify-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_modify keyword values ...
</pre></div>
</div>
<ul class="simple">
<li>one or more keyword/value pairs may be listed</li>
<li>keyword = <em>pair</em> or <em>shift</em> or <em>mix</em> or <em>table</em> or <em>table/disp</em> or <em>tabinner</em> or <em>tabinner/disp</em> or <em>tail</em> or <em>compute</em></li>
</ul>
<pre class="literal-block">
<em>pair</em> values = sub-style N <em>special</em> which wt1 wt2 wt3
sub-style = sub-style of <a class="reference internal" href="pair_hybrid.html"><em>pair hybrid</em></a>
N = which instance of sub-style (only if sub-style is used multiple times)
<em>special</em> which wt1 wt2 wt3 = override <em>special_bonds</em> settings (optional)
which = <em>lj/coul</em> or <em>lj</em> or <em>coul</em>
w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
<em>mix</em> value = <em>geometric</em> or <em>arithmetic</em> or <em>sixthpower</em>
<em>shift</em> value = <em>yes</em> or <em>no</em>
<em>table</em> value = N
2^N = # of values in table
<em>table/disp</em> value = N
2^N = # of values in table
<em>tabinner</em> value = cutoff
cutoff = inner cutoff at which to begin table (distance units)
<em>tabinner/disp</em> value = cutoff
cutoff = inner cutoff at which to begin table (distance units)
<em>tail</em> value = <em>yes</em> or <em>no</em>
<em>compute</em> value = <em>yes</em> or <em>no</em>
</pre>
</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_modify shift yes mix geometric
pair_modify tail yes
pair_modify table 12
pair_modify pair lj/cut compute no
pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Modify the parameters of the currently defined pair style. Not all
parameters are relevant to all pair styles.</p>
<p>If used, the <em>pair</em> keyword must appear first in the list of keywords.
It can only be used with the <a class="reference internal" href="pair_hybrid.html"><em>hybrid and hybrid/overlay</em></a> pair styles. It means that all the
following parameters will only be modified for the specified
sub-style. If the sub-style is defined multiple times, then an
additional numeric argument <em>N</em> must also be specified, which is a
number from 1 to M where M is the number of times the sub-style was
listed in the <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> command. The extra
number indicates which instance of the sub-style the remaining
keywords will be applied to. Note that if the <em>pair</em> keyword is not
used, and the pair style is <em>hybrid</em> or <em>hybrid/overlay</em>, then all the
specified keywords will be applied to all sub-styles.</p>
<p>The <em>special</em> keyword can only be used in conjunction with the <em>pair</em>
keyword and must directly follow it. It allows to override the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> settings for the specified sub-style.
More details are given below.</p>
<p>The <em>mix</em> keyword affects pair coefficients for interactions between
atoms of type I and J, when I != J and the coefficients are not
explicitly set in the input script. Note that coefficients for I = J
must be set explicitly, either in the input script via the
&#8220;pair_coeff&#8221; command or in the &#8220;Pair Coeffs&#8221; section of the <a class="reference internal" href="read_data.html"><em>data file</em></a>. For some pair styles it is not necessary to
specify coefficients when I != J, since a &#8220;mixing&#8221; rule will create
them from the I,I and J,J settings. The pair_modify <em>mix</em> value
determines what formulas are used to compute the mixed coefficients.
In each case, the cutoff distance is mixed the same way as sigma.</p>
<p>Note that not all pair styles support mixing. Also, some mix options
are not available for certain pair styles. See the doc page for
individual pair styles for those restrictions. Note also that the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command also can be to directly set
coefficients for a specific I != J pairing, in which case no mixing is
performed.</p>
<p>mix <em>geometric</em></p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">epsilon_ij</span> <span class="o">=</span> <span class="n">sqrt</span><span class="p">(</span><span class="n">epsilon_i</span> <span class="o">*</span> <span class="n">epsilon_j</span><span class="p">)</span>
<span class="n">sigma_ij</span> <span class="o">=</span> <span class="n">sqrt</span><span class="p">(</span><span class="n">sigma_i</span> <span class="o">*</span> <span class="n">sigma_j</span><span class="p">)</span>
</pre></div>
</div>
<p>mix <em>arithmetic</em></p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">epsilon_ij</span> <span class="o">=</span> <span class="n">sqrt</span><span class="p">(</span><span class="n">epsilon_i</span> <span class="o">*</span> <span class="n">epsilon_j</span><span class="p">)</span>
<span class="n">sigma_ij</span> <span class="o">=</span> <span class="p">(</span><span class="n">sigma_i</span> <span class="o">+</span> <span class="n">sigma_j</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span>
</pre></div>
</div>
<p>mix <em>sixthpower</em></p>
<div class="highlight-python"><div class="highlight"><pre>epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
(sigma_i^6 + sigma_j^6)
sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
</pre></div>
</div>
<p>The <em>shift</em> keyword determines whether a Lennard-Jones potential is
shifted at its cutoff to 0.0. If so, this adds an energy term to each
pairwise interaction which will be included in the thermodynamic
output, but does not affect pair forces or atom trajectories. See the
doc page for individual pair styles to see which ones support this
option.</p>
<p>The <em>table</em> and <em>table/disp</em> keywords apply to pair styles with a
long-range Coulombic term or long-range dispersion term respectively;
see the doc page for individual styles to see which potentials support
these options. If N is non-zero, a table of length 2^N is
pre-computed for forces and energies, which can shrink their
computational cost by up to a factor of 2. The table is indexed via a
bit-mapping technique <a class="reference internal" href="pair_table.html#wolff"><span>(Wolff)</span></a> and a linear interpolation is
performed between adjacent table values. In our experiments with
different table styles (lookup, linear, spline), this method typically
gave the best performance in terms of speed and accuracy.</p>
<p>The choice of table length is a tradeoff in accuracy versus speed. A
larger N yields more accurate force computations, but requires more
memory which can slow down the computation due to cache misses. A
reasonable value of N is between 8 and 16. The default value of 12
(table of length 4096) gives approximately the same accuracy as the
no-table (N = 0) option. For N = 0, forces and energies are computed
directly, using a polynomial fit for the needed erfc() function
evaluation, which is what earlier versions of LAMMPS did. Values
greater than 16 typically slow down the simulation and will not
improve accuracy; values from 1 to 8 give unreliable results.</p>
<p>The <em>tabinner</em> and <em>tabinner/disp</em> keywords set an inner cutoff above
which the pairwise computation is done by table lookup (if tables are
invoked), for the corresponding Coulombic and dispersion tables
discussed with the <em>table</em> and <em>table/disp</em> keywords. The smaller the
cutoff is set, the less accurate the table becomes (for a given number
of table values), which can require use of larger tables. The default
cutoff value is sqrt(2.0) distance units which means nearly all
pairwise interactions are computed via table lookup for simulations
with &#8220;real&#8221; units, but some close pairs may be computed directly
(non-table) for simulations with &#8220;lj&#8221; units.</p>
<p>When the <em>tail</em> keyword is set to <em>yes</em>, certain pair styles will add
a long-range VanderWaals tail &#8220;correction&#8221; to the energy and pressure.
These corrections are bookkeeping terms which do not affect dynamics,
unless a constant-pressure simulation is being performed. See the doc
page for individual styles to see which support this option. These
corrections are included in the calculation and printing of
thermodynamic quantities (see the <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a>
command). Their effect will also be included in constant NPT or NPH
simulations where the pressure influences the simulation box
dimensions (e.g. the <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> and <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a>
commands). The formulas used for the long-range corrections come from
equation 5 of <a class="reference internal" href="#sun"><span>(Sun)</span></a>.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The tail correction terms are computed at the beginning of each
run, using the current atom counts of each atom type. If atoms are
deleted (or lost) or created during a simulation, e.g. via the <a class="reference internal" href="fix_gcmc.html"><em>fix gcmc</em></a> command, the correction factors are not
re-computed. If you expect the counts to change dramatically, you can
break a run into a series of shorter runs so that the correction
factors are re-computed more frequently.</p>
</div>
<p>Several additional assumptions are inherent in using tail corrections,
including the following:</p>
<ul class="simple">
<li>The simulated system is a 3d bulk homogeneous liquid. This option
should not be used for systems that are non-liquid, 2d, have a slab
geometry (only 2d periodic), or inhomogeneous.</li>
<li>G(r), the radial distribution function (rdf), is unity beyond the
cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an
LJ fluid), and it is probably a good idea to verify this assumption by
checking the rdf. The rdf is not exactly unity beyond the cutoff for
each pair of interaction types, so the tail correction is necessarily
an approximation.</li>
</ul>
<p>The tail corrections are computed at the beginning of each simulation
run. If the number of atoms changes during the run, e.g. due to atoms
leaving the simulation domain, or use of the <a class="reference internal" href="fix_gcmc.html"><em>fix gcmc</em></a>
command, then the corrections are not updates to relect the changed
atom count. If this is a large effect in your simulation, you should
break the long run into several short runs, so that the correction
factors are re-computed multiple times.</p>
<ul class="simple">
<li>Thermophysical properties obtained from calculations with this option
enabled will not be thermodynamically consistent with the truncated
force-field that was used. In other words, atoms do not feel any LJ
pair interactions beyond the cutoff, but the energy and pressure
reported by the simulation include an estimated contribution from
those interactions.</li>
</ul>
<p>The <em>compute</em> keyword allows pairwise computations to be turned off,
even though a <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> is defined. This is not
useful for running a real simulation, but can be useful for debugging
purposes or for performing a <a class="reference internal" href="rerun.html"><em>rerun</em></a> simulation, when you
only wish to compute partial forces that do not include the pairwise
contribution.</p>
<p>Two examples are as follows. First, this option allows you to perform
a simulation with <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> with only a
subset of the hybrid sub-styles enabled. Second, this option allows
you to perform a simulation with only long-range interactions but no
short-range pairwise interactions. Doing this by simply not defining
a pair style will not work, because the
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command requires a Kspace-compatible
pair style be defined.</p>
<hr class="docutils" />
<div class="section" id="use-of-special-keyword">
<h3>Use of <em>special</em> keyword<a class="headerlink" href="#use-of-special-keyword" title="Permalink to this headline"></a></h3>
<p>The <em>special</em> keyword allows to override the 1-2, 1-3, and 1-4
exclusion settings for individual sub-styles of a
<a class="reference internal" href="pair_hybrid.html"><em>hybrid pair style</em></a>. It requires 4 arguments similar
to the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command, <em>which</em> and
wt1,wt2,wt3. The <em>which</em> argument can be <em>lj</em> to change the
Lennard-Jones settings, <em>coul</em> to change the Coulombic settings,
or <em>lj/coul</em> to change both to the same set of 3 values. The wt1,wt2,wt3
values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
1-3, and 1-4 bond topology neighbors, respectively. The <em>special</em>
keyword can only be used in conjunction with the <em>pair</em> keyword
and has to directly follow it.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The global settings specified by the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command affect the construction of
neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
exclude those pairs from the neighbor list entirely. Weights of 1.0
store the neighbor with no weighting applied. Thus only global values
different from exactly 0.0 or 1.0 can be overridden and an error is
generated if the requested setting is not compatible with the global
setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is
usually a sufficient workaround in this case without causing a
significant error.</p>
</div>
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<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>
<p>You cannot use <em>shift</em> yes with <em>tail</em> yes, since those are
conflicting options. You cannot use <em>tail</em> yes with 2d simulations.</p>
</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_style.html"><em>pair_style</em></a>, <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>,
<a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option defaults are mix = geometric, shift = no, table = 12,
tabinner = sqrt(2.0), tail = no, and compute = yes.</p>
<p>Note that some pair styles perform mixing, but only a certain style of
mixing. See the doc pages for individual pair styles for details.</p>
<hr class="docutils" />
<p id="wolff"><strong>(Wolff)</strong> Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).</p>
<p id="sun"><strong>(Sun)</strong> Sun, J Phys Chem B, 102, 7338-7364 (1998).</p>
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<div class="section" id="pair-style-morse-command">
<span id="index-0"></span><h1>pair_style morse command<a class="headerlink" href="#pair-style-morse-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-morse-cuda-command">
<h1>pair_style morse/cuda command<a class="headerlink" href="#pair-style-morse-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-morse-gpu-command">
<h1>pair_style morse/gpu command<a class="headerlink" href="#pair-style-morse-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-morse-omp-command">
<h1>pair_style morse/omp command<a class="headerlink" href="#pair-style-morse-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-morse-opt-command">
<h1>pair_style morse/opt command<a class="headerlink" href="#pair-style-morse-opt-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-morse-smooth-linear-command">
<h1>pair_style morse/smooth/linear command<a class="headerlink" href="#pair-style-morse-smooth-linear-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-morse-smooth-linear-omp-command">
<h1>pair_style morse/smooth/linear/omp command<a class="headerlink" href="#pair-style-morse-smooth-linear-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 morse cutoff
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for Morse interactions (distance units)</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 morse 2.5
pair_style morse/smooth/linear 2.5
pair_coeff * * 100.0 2.0 1.5
pair_coeff 1 1 100.0 2.0 1.5 3.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>morse</em> computes pairwise interactions with the formula</p>
<img alt="_images/pair_morse.jpg" class="align-center" src="_images/pair_morse.jpg" />
<p>Rc is the cutoff.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>D0 (energy units)</li>
<li>alpha (1/distance units)</li>
<li>r0 (distance units)</li>
<li>cutoff (distance units)</li>
<li>The last coefficient is optional. If not specified, the global morse</li>
<li>cutoff is used.</li>
</ul>
<hr class="docutils" />
<p>The <em>smooth/linear</em> variant is similar to the lj/smooth/linear variant
in that it adds to the potential a shift and a linear term to make both
the potential energy and force go to zero at the cut-off:</p>
<img alt="_images/pair_morse_smooth_linear.jpg" class="align-center" src="_images/pair_morse_smooth_linear.jpg" />
<p>The syntax of the pair_style and pair_coeff commands are the same for
the <em>morse</em> and <em>morse/smooth/linear</em> styles.</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>None of these pair styles support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>All of these pair styles support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option for the energy of the pair interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table options is not relevant for
the Morse pair styles.</p>
<p>None of these pair styles 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>All of these pair styles write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be 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>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The <em>morse/smooth/linear</em> pair style is only enabled if LAMMPS was
built with the USER-MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</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>
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<div class="section" id="pair-style-nb3b-harmonic-command">
<span id="index-0"></span><h1>pair_style nb3b/harmonic command<a class="headerlink" href="#pair-style-nb3b-harmonic-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-nb3b-harmonic-omp-command">
<h1>pair_style nb3b/harmonic/omp command<a class="headerlink" href="#pair-style-nb3b-harmonic-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 nb3b/harmonic
</pre></div>
</div>
</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 nb3b/harmonic
pair_coeff * * MgOH.nb3bharmonic Mg O H
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>This pair style computes a nonbonded 3-body harmonic potential for the
energy E of a system of atoms as</p>
<img alt="_images/pair_nb3b_harmonic.jpg" class="align-center" src="_images/pair_nb3b_harmonic.jpg" />
<p>where <em>theta_0</em> is the equilibrium value of the angle and <em>K</em> is a
prefactor. Note that the usual 1/2 factor is included in <em>K</em>. The form
of the potential is identical to that used in angle_style <em>harmonic</em>,
but in this case, the atoms do not need to be explicitly bonded.</p>
<p>Only a single pair_coeff command is used with this style which
specifies a potential file with parameters for specified elements.
These are mapped to LAMMPS atom types by specifying N additional
arguments after the filename in the pair_coeff command, where N is the
number of LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N element names = mapping of elements to atom types</li>
</ul>
<p>See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc page for alternate ways
to specify the path for the potential file.</p>
<p>As an example, imagine a file SiC.nb3b.harmonic has potential values
for Si and C. If your LAMMPS simulation has 4 atoms types and you
want the 1st 3 to be Si, and the 4th to be C, you would use the
following pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * SiC.nb3b.harmonic Si Si Si C
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
element in the potential file. The final C argument maps LAMMPS atom
type 4 to the C element in the potential file. If a mapping value is
specified as NULL, the mapping is not performed. This can be used
when the potential is used as part of the <em>hybrid</em> pair style. The
NULL values are placeholders for atom types that will be used with
other potentials. An example of a pair_coeff command for use with the
<em>hybrid</em> pair style is:</p>
<p>pair_coeff * * nb3b/harmonic MgOH.nb3b.harmonic Mg O H</p>
<p>Three-body nonbonded harmonic files in the <em>potentials</em> directory of
the LAMMPS distribution have a &#8221;.nb3b.harmonic&#8221; suffix. Lines that
are not blank or comments (starting with #) define parameters for a
triplet of elements.</p>
<p>Each entry has six arguments. The first three are atom types as
referenced in the LAMMPS input file. The first argument specifies the
central atom. The fourth argument indicates the <em>K</em> parameter. The
fifth argument indicates <em>theta_0</em>. The sixth argument indicates a
separation cutoff in Angstroms.</p>
<p>For a given entry, if the second and third arguments are identical,
then the entry is for a cutoff for the distance between types 1 and 2
(values for <em>K</em> and <em>theta_0</em> are irrelevant in this case).</p>
<p>For a given entry, if the first three arguments are all different,
then the entry is for the <em>K</em> and <em>theta_0</em> parameters (the cutoff in
this case is irrelevant).</p>
<p>It is <em>not</em> required that the potential file contain entries for all
of the elements listed in the pair_coeff command. It can also contain
entries for additional elements not being used in a particular
simulation; LAMMPS ignores those entries.</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>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style can only be used if LAMMPS was built with the MANYBODY
package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</p>
</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>
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<div class="section" id="pair-style-nm-cut-command">
<span id="index-0"></span><h1>pair_style nm/cut command<a class="headerlink" href="#pair-style-nm-cut-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-nm-cut-coul-cut-command">
<h1>pair_style nm/cut/coul/cut command<a class="headerlink" href="#pair-style-nm-cut-coul-cut-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-nm-cut-coul-long-command">
<h1>pair_style nm/cut/coul/long command<a class="headerlink" href="#pair-style-nm-cut-coul-long-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-nm-cut-omp-command">
<h1>pair_style nm/cut/omp command<a class="headerlink" href="#pair-style-nm-cut-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-nm-cut-coul-cut-omp-command">
<h1>pair_style nm/cut/coul/cut/omp command<a class="headerlink" href="#pair-style-nm-cut-coul-cut-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-nm-cut-coul-long-omp-command">
<h1>pair_style nm/cut/coul/long/omp command<a class="headerlink" href="#pair-style-nm-cut-coul-long-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 args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>nm/cut</em> or <em>nm/cut/coul/cut</em> or <em>nm/cut/coul/long</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>nm/cut</em> args = cutoff
cutoff = global cutoff for Pair interactions (distance units)
<em>nm/cut/coul/cut</em> args = cutoff (cutoff2)
cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>nm/cut/coul/long</em> args = cutoff (cutoff2)
cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</pre>
</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 nm/cut 12.0
pair_coeff * * 0.01 5.4 8.0 7.0
pair_coeff 1 1 0.01 4.4 7.0 6.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style nm/cut/coul/cut 12.0 15.0
pair_coeff * * 0.01 5.4 8.0 7.0
pair_coeff 1 1 0.01 4.4 7.0 6.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style nm/cut/coul/long 12.0 15.0
pair_coeff * * 0.01 5.4 8.0 7.0
pair_coeff 1 1 0.01 4.4 7.0 6.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>nm</em> computes site-site interactions based on the N-M potential
by <a class="reference internal" href="#clarke"><span>Clarke</span></a>, mainly used for ionic liquids. A site can
represent a single atom or a united-atom site. The energy of an
interaction has the following form:</p>
<img alt="_images/pair_nm.jpg" class="align-center" src="_images/pair_nm.jpg" />
<p>Rc is the cutoff.</p>
<p>Style <em>nm/cut/coul/cut</em> adds a Coulombic pairwise interaction given by</p>
<img alt="_images/pair_coulomb.jpg" class="align-center" src="_images/pair_coulomb.jpg" />
<p>where C is an energy-conversion constant, Qi and Qj are the charges on
the 2 atoms, and epsilon is the dielectric constant which can be set
by the <a class="reference internal" href="dielectric.html"><em>dielectric</em></a> command. If one cutoff is
specified in the pair_style command, it is used for both the NM and
Coulombic terms. If two cutoffs are specified, they are used as
cutoffs for the NM and Coulombic terms respectively.</p>
<p>Styles <em>nm/cut/coul/long</em> compute the same
Coulombic interactions as style <em>nm/cut/coul/cut</em> except that an
additional damping factor is applied to the Coulombic term so it can
be used in conjunction with the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a>
command and its <em>ewald</em> or <em>pppm</em> option. The Coulombic cutoff
specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.</p>
<p>For all of the <em>nm</em> pair styles, the following coefficients must
be defined for each pair of atoms types
via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the
examples above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands.</p>
<ul class="simple">
<li>E0 (energy units)</li>
<li>r0 (distance units)</li>
<li>n (unitless)</li>
<li>m (unitless)</li>
<li>cutoff1 (distance units)</li>
<li>cutoff2 (distance units)</li>
</ul>
<p>The latter 2 coefficients are optional. If not specified, the global
NM and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both NM
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the NM and Coulombic cutoffs for this
type pair. You cannot specify 2 cutoffs for style <em>nm</em>, since it
has no Coulombic terms.</p>
<p>For <em>nm/cut/coul/long</em> only the NM cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>All of the <em>nm</em> pair styles supports the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option for the energy of the pair
interaction.</p>
<p>The <em>nm/cut/coul/long</em> pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.</p>
<p>All of the <em>nm</em> pair styles support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
tail option for adding a long-range tail correction to the energy and
pressure for the NM portion of the pair interaction.</p>
<p>All of the <em>nm</em> pair styles write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>All of the <em>nm</em> 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>
<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>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>These pair styles are part of the MISC package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</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="clarke"><strong>(Clarke)</strong> Clarke and Smith, J Chem Phys, 84, 2290 (1986).</p>
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<div class="section" id="pair-style-none-command">
<span id="index-0"></span><h1>pair_style none command<a class="headerlink" href="#pair-style-none-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 none
</pre></div>
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<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 none
</pre></div>
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<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Using a pair style of none means pair forces and energies are not
computed.</p>
<p>With this choice, the force cutoff is 0.0, which means that only atoms
within the neighbor skin distance (see the <a class="reference internal" href="neighbor.html"><em>neighbor</em></a>
command) are communicated between processors. You must insure the
skin distance is large enough to acquire atoms needed for computing
bonds, angles, etc.</p>
<p>A pair style of <em>none</em> will also prevent pairwise neighbor lists from
being built. However if the <a class="reference internal" href="neighbor.html"><em>neighbor</em></a> style is <em>bin</em>,
data structures for binning are still allocated. If the neighbor skin
distance is small, then these data structures can consume a large
amount of memory. So you should either set the neighbor style to
<em>nsq</em> or set the skin distance to a larger value.</p>
<p>See the <a class="reference internal" href="pair_zero.html"><em>pair_style zero</em></a> for a way to trigger the
building of a neighbor lists, but compute no pairwise interactions.</p>
</div>
<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_zero.html"><em>pair_style zero</em></a></p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="pair-style-peri-pmb-command">
<span id="index-0"></span><h1>pair_style peri/pmb command<a class="headerlink" href="#pair-style-peri-pmb-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-peri-pmb-omp-command">
<h1>pair_style peri/pmb/omp command<a class="headerlink" href="#pair-style-peri-pmb-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-peri-lps-command">
<h1>pair_style peri/lps command<a class="headerlink" href="#pair-style-peri-lps-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-peri-lps-omp-command">
<h1>pair_style peri/lps/omp command<a class="headerlink" href="#pair-style-peri-lps-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-peri-ves-command">
<h1>pair_style peri/ves command<a class="headerlink" href="#pair-style-peri-ves-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-peri-eps-command">
<h1>pair_style peri/eps command<a class="headerlink" href="#pair-style-peri-eps-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
</pre></div>
</div>
<ul class="simple">
<li>style = <em>peri/pmb</em> or <em>peri/lps</em> or <em>peri/ves</em> or <em>peri/eps</em></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 peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style peri/lps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style peri/ves
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style peri/eps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43
</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 peridynamic pair styles implement material models that can be used
at the mescscopic and macroscopic scales. See <a class="reference external" href="PDF/PDLammps_overview.pdf">this document</a> for an overview of LAMMPS commands
for Peridynamics modeling.</p>
<p>Style <em>peri/pmb</em> implements the Peridynamic bond-based prototype
microelastic brittle (PMB) model.</p>
<p>Style <em>peri/lps</em> implements the Peridynamic state-based linear
peridynamic solid (LPS) model.</p>
<p>Style <em>peri/ves</em> implements the Peridynamic state-based linear
peridynamic viscoelastic solid (VES) model.</p>
<p>Style <em>peri/eps</em> implements the Peridynamic state-based elastic-plastic
solid (EPS) model.</p>
<p>The canonical papers on Peridynamics are <a class="reference internal" href="#silling2000"><span>(Silling 2000)</span></a>
and <a class="reference internal" href="#silling2007"><span>(Silling 2007)</span></a>. The implementation of Peridynamics
in LAMMPS is described in <a class="reference internal" href="#parks"><span>(Parks)</span></a>. Also see the <a class="reference external" href="http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS user guide</a> for
more details about its implementation.</p>
<p>The peridynamic VES and EPS models in PDLAMMPS were implemented by
R. Rahman and J. T. Foster at University of Texas at San Antonio. The
original VES formulation is described in &#8220;(Mitchell2011)&#8221; and the
original EPS formulation is in &#8220;(Mitchell2011a)&#8221;. Additional PDF docs
that describe the VES and EPS implementations are include in the
LAMMPS distro in <a class="reference external" href="PDF/PDLammps_VES.pdf">doc/PDF/PDLammps_VES.pdf</a> and
<a class="reference external" href="PDF/PDLammps_EPS.pdf">doc/PDF/PDLammps_EPS.pdf</a>. For questions
regarding the VES and EPS models in LAMMPS you can contact R. Rahman
(rezwanur.rahman at utsa.edu).</p>
<p>The following coefficients must be defined for each pair of atom types
via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above,
or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below.</p>
<p>For the <em>peri/pmb</em> style:</p>
<ul class="simple">
<li>c (energy/distance/volume^2 units)</li>
<li>horizon (distance units)</li>
<li>s00 (unitless)</li>
<li>alpha (unitless)</li>
</ul>
<p>C is the effectively a spring constant for Peridynamic bonds, the
horizon is a cutoff distance for truncating interactions, and s00 and
alpha are used as a bond breaking criteria. The units of c are such
that c/distance = stiffness/volume^2, where stiffness is
energy/distance^2 and volume is distance^3. See the users guide for
more details.</p>
<p>For the <em>peri/lps</em> style:</p>
<ul class="simple">
<li>K (force/area units)</li>
<li>G (force/area units)</li>
<li>horizon (distance units)</li>
<li>s00 (unitless)</li>
<li>alpha (unitless)</li>
</ul>
<p>K is the bulk modulus and G is the shear modulus. The horizon is a
cutoff distance for truncating interactions, and s00 and alpha are
used as a bond breaking criteria. See the users guide for more
details.</p>
<p>For the <em>peri/ves</em> style:</p>
<ul class="simple">
<li>K (force/area units)</li>
<li>G (force/area units)</li>
<li>horizon (distance units)</li>
<li>s00 (unitless)</li>
<li>alpha (unitless)</li>
<li>m_lambdai (unitless)</li>
<li>m_taubi (unitless)</li>
</ul>
<p>K is the bulk modulus and G is the shear modulus. The horizon is a
cutoff distance for truncating interactions, and s00 and alpha are
used as a bond breaking criteria. m_lambdai and m_taubi are the
viscoelastic relaxation parameter and time constant,
respectively. m_lambdai varies within zero to one. For very small
values of m_lambdai the viscoelsatic model responds very similar to a
linear elastic model. For details please see the description in
&#8220;(Mtchell2011)&#8221;.</p>
<p>For the <em>peri/eps</em> style:</p>
<p>K (force/area units)
G (force/area units)
horizon (distance units)
s00 (unitless)
alpha (unitless)
m_yield_stress (force/area units)</p>
<p>K is the bulk modulus and G is the shear modulus. The horizon is a
cutoff distance and s00 and alpha are used as a bond breaking
criteria. m_yield_stress is the yield stress of the material. For
details please see the description in &#8220;(Mtchell2011a)&#8221;.</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. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>These pair styles do not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table and tail options are not
relevant for these pair styles.</p>
<p>These pair styles write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be 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>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>All of these styles are part of the PERI 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>Making LAMMPS</span></a> section for more info.</p>
</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="parks"><strong>(Parks)</strong> Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11),
777-783 (2008).</p>
<p id="silling2000"><strong>(Silling 2000)</strong> Silling, J Mech Phys Solids, 48, 175-209 (2000).</p>
<p id="silling2007"><strong>(Silling 2007)</strong> Silling, Epton, Weckner, Xu, Askari, J Elasticity,
88, 151-184 (2007).</p>
<p id="mitchell2011"><strong>(Mitchell2011)</strong> Mitchell. A non-local, ordinary-state-based
viscoelasticity model for peridynamics. Sandia National Lab Report,
8064:1-28 (2011).</p>
<p id="mitchell2011a"><strong>(Mitchell2011a)</strong> Mitchell. A Nonlocal, Ordinary, State-Based
Plasticity Model for Peridynamics. Sandia National Lab Report,
3166:1-34 (2011).</p>
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<div class="section" id="pair-style-polymorphic-command">
<span id="index-0"></span><h1>pair_style polymorphic command<a class="headerlink" href="#pair-style-polymorphic-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 polymorphic
</pre></div>
</div>
<p>style = <em>polymorphic</em></p>
</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 polymorphic
pair_coeff * * TlBr_msw.polymorphic Tl Br
pair_coeff * * AlCu_eam.polymorphic Al Cu
pair_coeff * * GaN_tersoff.polymorphic Ga N
pair_coeff * * GaN_sw.polymorphic GaN
</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>polymorphic</em> pair style computes a 3-body free-form potential
(<a class="reference internal" href="#zhou"><span>Zhou</span></a>) for the energy E of a system of atoms as</p>
<img alt="_images/polymorphic1.jpg" class="align-center" src="_images/polymorphic1.jpg" />
<img alt="_images/polymorphic2.jpg" class="align-center" src="_images/polymorphic2.jpg" />
<img alt="_images/polymorphic3.jpg" class="align-center" src="_images/polymorphic3.jpg" />
<p>where I, J, K represent species of atoms i, j, and k, i_1, ..., i_N
represents a list of i&#8217;s neighbors, delta_ij is a Direc constant
(i.e., delta_ij = 1 when i = j, and delta_ij = 0 otherwise), eta_ij is
similar constant that can be set either to eta_ij = delta_ij or eta_ij
= 1 - delta_ij depending on the potential type, U_IJ(r_ij),
V_IJ(r_ij), W_IK(r_ik) are pair functions, G_JIK(cos(theta)) is an
angular function, P_IK(delta r_jik) is a function of atomic spacing
differential delta r_jik = r_ij - xi_IJ*r_ik with xi_IJ being a
pair-dependent parameter, and F_IJ(X_ij) is a function of the local
environment variable X_ij. This generic potential is fully defined
once the constants eta_ij and xi_IJ, and the six functions U_IJ(r_ij),
V_IJ(r_ij), W_IK(r_ik), G_JIK(cos(theta)), P_IK(delta r_jik), and
F_IJ(X_ij) are given. Note that these six functions are all one
dimensional, and hence can be provided in an analytic or tabular
form. This allows users to design different potentials solely based on
a manipulation of these functions. For instance, the potential reduces
to Stillinger-Weber potential (<a class="reference internal" href="#sw"><span>SW</span></a>) if we set</p>
<img alt="_images/polymorphic4.jpg" class="align-center" src="_images/polymorphic4.jpg" />
<p>The potential reduces to Tersoff types of potential
(<a class="reference internal" href="#tersoff"><span>Tersoff</span></a> or <a class="reference internal" href="pair_tersoff_zbl.html#albe"><span>Albe</span></a>) if we set</p>
<img alt="_images/polymorphic5.jpg" class="align-center" src="_images/polymorphic5.jpg" />
<img alt="_images/polymorphic6.jpg" class="align-center" src="_images/polymorphic6.jpg" />
<p>The potential reduces to Rockett-Tersoff (<a class="reference internal" href="#wang"><span>Wang</span></a>) type if we set</p>
<img alt="_images/polymorphic7.jpg" class="align-center" src="_images/polymorphic7.jpg" />
<img alt="_images/polymorphic6.jpg" class="align-center" src="_images/polymorphic6.jpg" />
<img alt="_images/polymorphic8.jpg" class="align-center" src="_images/polymorphic8.jpg" />
<p>The potential becomes embedded atom method (<a class="reference internal" href="#daw"><span>Daw</span></a>) if we set</p>
<img alt="_images/polymorphic9.jpg" class="align-center" src="_images/polymorphic9.jpg" />
<p>In the embedded atom method case, phi_IJ(r_ij) is the pair energy,
F_I(X) is the embedding energy, X is the local electron density, and
f_K(r) is the atomic electron density function.</p>
<p>If the tabulated functions are created using the parameters of sw,
tersoff, and eam potentials, the polymorphic pair style will produce
the same global properties (energies and stresses) and the same forces
as the sw, tersoff, and eam pair styles. The polymorphic pair style
also produces the same atom properties (energies and stresses) as the
corresponding tersoff and eam pair styles. However, due to a different
partition of global properties to atom properties, the polymorphic
pair style will produce different atom properties (energies and
stresses) as the sw pair style. This does not mean that polymorphic
pair style is different from the sw pair style in this case. It just
means that the definitions of the atom energies and atom stresses are
different.</p>
<p>Only a single pair_coeff command is used with the polymorphic style
which specifies an potential file for all needed elements. These are
mapped to LAMMPS atom types by specifying N additional arguments after
the filename in the pair_coeff command, where N is the number of
LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N element names = mapping of Tersoff elements to atom types</li>
</ul>
<p>See the pair_coeff doc page for alternate ways to specify the path for
the potential file. Several files for polymorphic potentials are
included in the potentials dir of the LAMMPS distro. They have a
&#8220;poly&#8221; suffix.</p>
<p>As an example, imagine the SiC_tersoff.polymorphic file has tabulated
functions for Si-C tersoff potential. If your LAMMPS simulation has 4
atoms types and you want the 1st 3 to be Si, and the 4th to be C, you
would use the following pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * SiC_tersoff.polymorphic Si Si Si C
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom
types. The first three Si arguments map LAMMPS atom types 1,2,3 to the
Si element in the polymorphic file. The final C argument maps LAMMPS
atom type 4 to the C element in the polymorphic file. If a mapping
value is specified as NULL, the mapping is not performed. This can be
used when an polymorphic potential is used as part of the hybrid pair
style. The NULL values are placeholders for atom types that will be
used with other potentials.</p>
<p>Potential files in the potentials directory of the LAMMPS distribution
have a &#8221;.poly&#8221; suffix. At the beginning of the files, an unlimited
number of lines starting with &#8216;#&#8217; are used to describe the potential
and are ignored by LAMMPS. The next line lists two numbers:</p>
<div class="highlight-python"><div class="highlight"><pre>ntypes eta
</pre></div>
</div>
<p>Here ntypes represent total number of species defined in the potential
file, and eta = 0 or 1. The number ntypes must equal the total number
of different species defined in the pair_coeff command. When eta = 1,
eta_ij defined in the potential functions above is set to 1 -
delta_ij, otherwise eta_ij is set to delta_ij. The next ntypes lines
each lists two numbers and a character string representing atomic
number, atomic mass, and name of the species of the ntypes elements:</p>
<div class="highlight-python"><div class="highlight"><pre>atomic_number atomic-mass element (1)
atomic_number atomic-mass element (2)
...
atomic_number atomic-mass element (ntypes)
</pre></div>
</div>
<p>The next ntypes*(ntypes+1)/2 lines contain two numbers:</p>
<div class="highlight-python"><div class="highlight"><pre>cut xi (1)
cut xi (2)
...
cut xi (ntypes*(ntypes+1)/2)
</pre></div>
</div>
<p>Here cut means the cutoff distance of the pair functions, xi is the
same as defined in the potential functions above. The
ntypes*(ntypes+1)/2 lines are related to the pairs according to the
sequence of first ii (self) pairs, i = 1, 2, ..., ntypes, and then
then ij (cross) pairs, i = 1, 2, ..., ntypes-1, and j = i+1, i+2, ...,
ntypes (i.e., the sequence of the ij pairs follows 11, 22, ..., 12,
13, 14, ..., 23, 24, ...).</p>
<p>The final blocks of the potential file are the U, V, W, P, G, and F
functions are listed sequentially. First, U functions are given for
each of the ntypes*(ntypes+1)/2 pairs according to the sequence
described above. For each of the pairs, nr values are listed. Next,
similar arrays are given for V, W, and P functions. Then G functions
are given for all the ntypes*ntypes*ntypes ijk triplets in a natural
sequence i from 1 to ntypes, j from 1 to ntypes, and k from 1 to
ntypes (i.e., ijk = 111, 112, 113, ..., 121, 122, 123 ..., 211, 212,
...). Each of the ijk functions contains ng values. Finally, the F
functions are listed for all ntypes*(ntypes+1)/2 pairs, each
containing nx values. Either analytic or tabulated functions can be
specified. Currently, constant, exponential, sine and cosine analytic
functions are available which are specified with: constant c1 , where
f(x) = c1 exponential c1 c2 , where f(x) = c1 exp(c2*x) sine c1 c2 ,
where f(x) = c1 sin(c2*x) cos c1 c2 , where f(x) = c1 cos(c2*x)
Tabulated functions are specified by spline n x1 x2, where n=number of
point, (x1,x2)=range and then followed by n values evaluated uniformly
over these argument ranges. The valid argument ranges of the
functions are between 0 &lt;= r &lt;= cut for the U(r), V(r), W(r)
functions, -cutmax &lt;= delta_r &lt;= cutmax for the P(delta_r) functions,
-1 &lt;= costheta &lt;= 1 for the G(costheta) functions, and 0 &lt;= X &lt;= maxX
for the F(X) functions.</p>
<p><strong>Mixing, shift, table tail correction, restart</strong>:</p>
<p>This pair styles does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This pair style does not write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>If using create_atoms command, atomic masses must be defined in the
input script. If using read_data, atomic masses must be defined in the
atomic structure data file.</p>
<p>This pair style is part of the MANYBODY package. It is only enabled if
LAMMPS was built with that package (which it is by default). See the
<a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>This pair potential requires the <a class="reference internal" href="newton.html"><em>newtion</em></a> setting to be
&#8220;on&#8221; for pair interactions.</p>
<p>The potential files provided with LAMMPS (see the potentials
directory) are parameterized for metal <a class="reference internal" href="units.html"><em>units</em></a>. You can use
any LAMMPS units, but you would need to create your own potential
files.</p>
</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>
<hr class="docutils" />
<p id="zhou"><strong>(Zhou)</strong> X. W. Zhou, M. E. Foster, R. E. Jones, P. Yang, H. Fan, and
F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015).</p>
<p id="sw"><strong>(SW)</strong> F. H. Stillinger-Weber, and T. A. Weber, Phys. Rev. B, 31, 5262 (1985).</p>
<p id="tersoff"><strong>(Tersoff)</strong> J. Tersoff, Phys. Rev. B, 39, 5566 (1989).</p>
<p id="albe"><strong>(Albe)</strong> K. Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B,
66, 035205 (2002).</p>
<p id="wang"><strong>(Wang)</strong> J. Wang, and A. Rockett, Phys. Rev. B, 43, 12571 (1991).</p>
<p id="daw"><strong>(Daw)</strong> M. S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984).</p>
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<div class="section" id="pair-style-quip-command">
<span id="index-0"></span><h1>pair_style quip command<a class="headerlink" href="#pair-style-quip-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 quip
</pre></div>
</div>
</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 quip
pair_coeff * * gap_example.xml &quot;Potential xml_label=GAP_2014_5_8_60_17_10_38_466&quot; 14
pair_coeff * * sw_example.xml &quot;IP SW&quot; 14
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>quip</em> provides an interface for calling potential routines from
the QUIP package. QUIP is built separately, and then linked to
LAMMPS. The most recent version of the QUIP package can be downloaded
from GitHub:
<a class="reference external" href="https://github.com/libAtoms/QUIP">https://github.com/libAtoms/QUIP</a>. The
interface is chiefly intended to be used to run Gaussian Approximation
Potentials (GAP), which are described in the following publications:
<a class="reference internal" href="#bartok-2010"><span>(Bartok et al)</span></a> and <a class="reference internal" href="#bartok-phd"><span>(PhD thesis of Bartok)</span></a>.</p>
<p>Only a single pair_coeff command is used with the <em>quip</em> style that
specifies a QUIP potential file containing the parameters of the
potential for all needed elements in XML format. This is followed by a
QUIP initialization string. Finally, the QUIP elements are mapped to
LAMMPS atom types by specifying N atomic numbers, where N is the
number of LAMMPS atom types:</p>
<ul class="simple">
<li>QUIP filename</li>
<li>QUIP initialization string</li>
<li>N atomic numbers = mapping of QUIP elements to atom types</li>
</ul>
<p>See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc page for alternate ways
to specify the path for the potential file.</p>
<p>A QUIP potential is fully specified by the filename which contains the
parameters of the potential in XML format, the initialisation string,
and the map of atomic numbers.</p>
<p>GAP potentials can be obtained from the Data repository section of
<a class="reference external" href="http://www.libatoms.org">http://www.libatoms.org</a>, where the
appropriate initialisation strings are also advised. The list of
atomic numbers must be matched to the LAMMPS atom types specified in
the LAMMPS data file or elsewhere.</p>
<p>Two examples input scripts are provided in the examples/USER/quip
directory.</p>
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
mix, shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style is part of the USER-QUIP package. It is only enabled
if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>QUIP potentials are parametrized in electron-volts and Angstroms and
therefore should be used with LAMMPS metal <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</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>
<hr class="docutils" />
<p id="bartok-2010"><strong>(Bartok_2010)</strong> AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical
Review Letters 104, 136403 (2010).</p>
<p id="bartok-phd"><strong>(Bartok_PhD)</strong> A Bartok-Partay, PhD Thesis, University of Cambridge,
(2010).</p>
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<div class="section" id="pair-style-reax-command">
<span id="index-0"></span><h1>pair_style reax command<a class="headerlink" href="#pair-style-reax-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 reax hbcut hbnewflag tripflag precision
</pre></div>
</div>
<ul class="simple">
<li>hbcut = hydrogen-bond cutoff (optional) (distance units)</li>
<li>hbnewflag = use old or new hbond function style (0 or 1) (optional)</li>
<li>tripflag = apply stabilization to all triple bonds (0 or 1) (optional)</li>
<li>precision = precision for charge equilibration (optional)</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 reax
pair_style reax 10.0 0 1 1.0e-5
pair_coeff * * ffield.reax 3 1 2 2
pair_coeff * * ffield.reax 3 NULL NULL 3
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>reax</em> computes the ReaxFF potential of van Duin, Goddard and
co-workers. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. There is more than one version of ReaxFF. The version
implemented in LAMMPS uses the functional forms documented in the
supplemental information of the following paper:
<a class="reference internal" href="pair_reax_c.html#chenoweth-2008"><span>(Chenoweth)</span></a>. The version integrated into LAMMPS matches
the most up-to-date version of ReaxFF as of summer 2010.</p>
<p>WARNING: pair style reax is now deprecated and will soon be retired. Users
should switch to <a class="reference internal" href="pair_reax_c.html"><em>pair_style reax/c</em></a>. The <em>reax</em> style
differs from the <em>reax/c</em> style in the lo-level implementation details.
The <em>reax</em> style is a
Fortran library, linked to LAMMPS. The <em>reax/c</em> style was initially
implemented as stand-alone C code and is now integrated into LAMMPS as
a package.</p>
<p>LAMMPS requires that a file called ffield.reax be provided, containing
the ReaxFF parameters for each atom type, bond type, etc. The format
is identical to the ffield file used by van Duin and co-workers. The
filename is required as an argument in the pair_coeff command. Any
value other than &#8220;ffield.reax&#8221; will be rejected (see below).</p>
<p>LAMMPS provides several different versions of ffield.reax in its
potentials dir, each called potentials/ffield.reax.label. These are
documented in potentials/README.reax. The default ffield.reax
contains parameterizations for the following elements: C, H, O, N.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">We do not distribute a wide variety of ReaxFF force field files
with LAMMPS. Adri van Duin&#8217;s group at PSU is the central repository
for this kind of data as they are continuously deriving and updating
parameterizations for different classes of materials. You can submit
a contact request at the Materials Computation Center (MCC) website
<a class="reference external" href="https://www.mri.psu.edu/materials-computation-center/connect-mcc">https://www.mri.psu.edu/materials-computation-center/connect-mcc</a>,
describing the material(s) you are interested in modeling with ReaxFF.
They can tell
you what is currently available or what it would take to create a
suitable ReaxFF parameterization.</p>
</div>
<p>The format of these files is identical to that used originally by van
Duin. We have tested the accuracy of <em>pair_style reax</em> potential
against the original ReaxFF code for the systems mentioned above. You
can use other ffield files for specific chemical systems that may be
available elsewhere (but note that their accuracy may not have been
tested).</p>
<p>The <em>hbcut</em>, <em>hbnewflag</em>, <em>tripflag</em>, and <em>precision</em> settings are
optional arguments. If none are provided, default settings are used:
<em>hbcut</em> = 6 (which is Angstroms in real units), <em>hbnewflag</em> = 1 (use
new hbond function style), <em>tripflag</em> = 1 (apply stabilization to all
triple bonds), and <em>precision</em> = 1.0e-6 (one part in 10^6). If you
wish to override any of these defaults, then all of the settings must
be specified.</p>
<p>Two examples using <em>pair_style reax</em> are provided in the examples/reax
sub-directory, along with corresponding examples for
<a class="reference internal" href="pair_reax_c.html"><em>pair_style reax/c</em></a>. Note that while the energy and force
calculated by both of these pair styles match very closely, the
contributions due to the valence angles differ slightly due to
the fact that with <em>pair_style reax/c</em> the default value of <em>thb_cutoff_sq</em>
is 0.00001, while for <em>pair_style reax</em> it is hard-coded to be 0.001.</p>
<p>Use of this pair style requires that a charge be defined for every
atom since the <em>reax</em> pair style performs a charge equilibration (QEq)
calculation. See the <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> and
<a class="reference internal" href="read_data.html"><em>read_data</em></a> commands for details on how to specify
charges.</p>
<p>The thermo variable <em>evdwl</em> stores the sum of all the ReaxFF potential
energy contributions, with the exception of the Coulombic and charge
equilibration contributions which are stored in the thermo variable
<em>ecoul</em>. The output of these quantities is controlled by the
<a class="reference internal" href="thermo.html"><em>thermo</em></a> command.</p>
<p>This pair style tallies a breakdown of the total ReaxFF potential
energy into sub-categories, which 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 14.
The 14 values correspond to the following sub-categories (the variable
names in italics match those used in the ReaxFF FORTRAN library):</p>
<ol class="arabic simple">
<li><em>eb</em> = bond energy</li>
<li><em>ea</em> = atom energy</li>
<li><em>elp</em> = lone-pair energy</li>
<li><em>emol</em> = molecule energy (always 0.0)</li>
<li><em>ev</em> = valence angle energy</li>
<li><em>epen</em> = double-bond valence angle penalty</li>
<li><em>ecoa</em> = valence angle conjugation energy</li>
<li><em>ehb</em> = hydrogen bond energy</li>
<li><em>et</em> = torsion energy</li>
<li><em>eco</em> = conjugation energy</li>
<li><em>ew</em> = van der Waals energy</li>
<li><em>ep</em> = Coulomb energy</li>
<li><em>efi</em> = electric field energy (always 0.0)</li>
<li><em>eqeq</em> = charge equilibration energy</li>
</ol>
<p>To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:</p>
<div class="highlight-python"><div class="highlight"><pre>compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
...
variable eqeq equal c_reax[14]
thermo_style custom step temp epair v_eb v_ea ... v_eqeq
</pre></div>
</div>
<p>Only a single pair_coeff command is used with the <em>reax</em> style which
specifies a ReaxFF potential file with parameters for all needed
elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N indices = mapping of ReaxFF elements to atom types</li>
</ul>
<p>The specification of the filename and the mapping of LAMMPS atom types
recognized by the ReaxFF is done differently than for other LAMMPS
potentials, due to the non-portable difficulty of passing character
strings (e.g. filename, element names) between C++ and Fortran.</p>
<p>The filename has to be &#8220;ffield.reax&#8221; and it has to exist in the
directory you are running LAMMPS in. This means you cannot prepend a
path to the file in the potentials dir. Rather, you should copy that
file into the directory you are running from. If you wish to use
another ReaxFF potential file, then name it &#8220;ffield.reax&#8221; and put it
in the directory you run from.</p>
<p>In the ReaxFF potential file, near the top, after the general
parameters, is the atomic parameters section that contains element
names, each with a couple dozen numeric parameters. If there are M
elements specified in the <em>ffield</em> file, think of these as numbered 1
to M. Each of the N indices you specify for the N atom types of LAMMPS
atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
be mapped to whatever element you specify as the first index value,
etc. If a mapping value is specified as NULL, the mapping is not
performed. This can be used when a ReaxFF potential is used as part
of the <em>hybrid</em> pair style. The NULL values are placeholders for atom
types that will be used with other potentials.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Currently the reax pair style cannot be used as part of the
<em>hybrid</em> pair style. Some additional changes still need to be made to
enable this.</p>
</div>
<p>As an example, say your LAMMPS simulation has 4 atom types and the
elements are ordered as C, H, O, N in the <em>ffield</em> file. If you want
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
H, you would use the following pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * ffield.reax 1 1 4 2
</pre></div>
</div>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
mix, shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The ReaxFF potential files provided with LAMMPS in the potentials
directory are parameterized for real <a class="reference internal" href="units.html"><em>units</em></a>. You can use
the ReaxFF potential with any LAMMPS units, but you would need to
create your own potential file with coefficients listed in the
appropriate units if your simulation doesn&#8217;t use &#8220;real&#8221; units.</p>
</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>, <a class="reference internal" href="pair_reax_c.html"><em>pair_style reax/c</em></a>,
<a class="reference internal" href="fix_reax_bonds.html"><em>fix_reax_bonds</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The keyword defaults are <em>hbcut</em> = 6, <em>hbnewflag</em> = 1, <em>tripflag</em> = 1,
<em>precision</em> = 1.0e-6.</p>
<hr class="docutils" />
<p id="chenoweth-2008"><strong>(Chenoweth_2008)</strong> Chenoweth, van Duin and Goddard,
Journal of Physical Chemistry A, 112, 1040-1053 (2008).</p>
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<div class="section" id="pair-style-reax-c-command">
<span id="index-0"></span><h1>pair_style reax/c command<a class="headerlink" href="#pair-style-reax-c-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 reax/c cfile keyword value
</pre></div>
</div>
<ul class="simple">
<li>cfile = NULL or name of a control file</li>
<li>zero or more keyword/value pairs may be appended</li>
</ul>
<pre class="literal-block">
keyword = <em>checkqeq</em> or <em>lgvdw</em> or <em>safezone</em> or <em>mincap</em>
<em>checkqeq</em> value = <em>yes</em> or <em>no</em> = whether or not to require qeq/reax fix
<em>lgvdw</em> value = <em>yes</em> or <em>no</em> = whether or not to use a low gradient vdW correction
<em>safezone</em> = factor used for array allocation
<em>mincap</em> = minimum size for array allocation
</pre>
</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 reax/c NULL
pair_style reax/c controlfile checkqeq no
pair_style reax/c NULL lgvdw yes
pair_style reax/c NULL safezone 1.6 mincap 100
pair_coeff * * ffield.reax C H O N
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>reax/c</em> computes the ReaxFF potential of van Duin, Goddard and
co-workers. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. There is more than one version of ReaxFF. The version
implemented in LAMMPS uses the functional forms documented in the
supplemental information of the following paper: <a class="reference internal" href="#chenoweth-2008"><span>(Chenoweth et al., 2008)</span></a>. The version integrated into LAMMPS matches
the most up-to-date version of ReaxFF as of summer 2010. For more
technical details about the pair reax/c implementation of ReaxFF, see
the <a class="reference internal" href="#aktulga"><span>(Aktulga)</span></a> paper.</p>
<p>The <em>reax/c</em> style differs from the <a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a>
command in the lo-level implementation details. The <em>reax</em> style is a
Fortran library, linked to LAMMPS. The <em>reax/c</em> style was initially
implemented as stand-alone C code and is now integrated into LAMMPS as
a package.</p>
<p>LAMMPS provides several different versions of ffield.reax in its
potentials dir, each called potentials/ffield.reax.label. These are
documented in potentials/README.reax. The default ffield.reax
contains parameterizations for the following elements: C, H, O, N.</p>
<p>The format of these files is identical to that used originally by van
Duin. We have tested the accuracy of <em>pair_style reax/c</em> potential
against the original ReaxFF code for the systems mentioned above. You
can use other ffield files for specific chemical systems that may be
available elsewhere (but note that their accuracy may not have been
tested).</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">We do not distribute a wide variety of ReaxFF force field files
with LAMMPS. Adri van Duin&#8217;s group at PSU is the central repository
for this kind of data as they are continuously deriving and updating
parameterizations for different classes of materials. You can submit
a contact request at the Materials Computation Center (MCC) website
<a class="reference external" href="https://www.mri.psu.edu/materials-computation-center/connect-mcc">https://www.mri.psu.edu/materials-computation-center/connect-mcc</a>,
describing the material(s) you are interested in modeling with ReaxFF.
They can tell
you what is currently available or what it would take to create a
suitable ReaxFF parameterization.</p>
</div>
<p>The <em>cfile</em> setting can be specified as NULL, in which case default
settings are used. A control file can be specified which defines
values of control variables. Some control variables are
global parameters for the ReaxFF potential. Others define certain
performance and output settings.
Each line in the control file specifies the value for
a control variable. The format of the control file is described
below.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The LAMMPS default values for the ReaxFF global parameters
correspond to those used by Adri van Duin&#8217;s stand-alone serial
code. If these are changed by setting control variables in the control
file, the results from LAMMPS and the serial code will not agree.</p>
</div>
<p>Two examples using <em>pair_style reax/c</em> are provided in the examples/reax
sub-directory, along with corresponding examples for
<a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a>.</p>
<p>Use of this pair style requires that a charge be defined for every
atom. See the <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> and
<a class="reference internal" href="read_data.html"><em>read_data</em></a> commands for details on how to specify
charges.</p>
<p>The ReaxFF parameter files provided were created using a charge
equilibration (QEq) model for handling the electrostatic interactions.
Therefore, by default, LAMMPS requires that the <a class="reference internal" href="fix_qeq_reax.html"><em>fix qeq/reax</em></a> command be used with <em>pair_style reax/c</em>
when simulating a ReaxFF model, to equilibrate charge each timestep.
Using the keyword <em>checkqeq</em> with the value <em>no</em>
turns off the check for <em>fix qeq/reax</em>,
allowing a simulation to be run without charge equilibration.
In this case, the static charges you
assign to each atom will be used for computing the electrostatic
interactions in the system.
See the <a class="reference internal" href="fix_qeq_reax.html"><em>fix qeq/reax</em></a> command for details.</p>
<p>Using the optional keyword <em>lgvdw</em> with the value <em>yes</em> turns on
the low-gradient correction of the ReaxFF/C for long-range
London Dispersion, as described in the <a class="reference internal" href="#liu-2011"><span>(Liu)</span></a> paper. Force field
file <em>ffield.reax.lg</em> is designed for this correction, and is trained
for several energetic materials (see &#8220;Liu&#8221;). When using lg-correction,
recommended value for parameter <em>thb</em> is 0.01, which can be set in the
control file. Note: Force field files are different for the original
or lg corrected pair styles, using wrong ffield file generates an error message.</p>
<p>Optional keywords <em>safezone</em> and <em>mincap</em> are used for allocating
reax/c arrays. Increase these values can avoid memory problems, such
as segmentation faults and bondchk failed errors, that could occur under
certain conditions.</p>
<p>The thermo variable <em>evdwl</em> stores the sum of all the ReaxFF potential
energy contributions, with the exception of the Coulombic and charge
equilibration contributions which are stored in the thermo variable
<em>ecoul</em>. The output of these quantities is controlled by the
<a class="reference internal" href="thermo.html"><em>thermo</em></a> command.</p>
<p>This pair style tallies a breakdown of the total ReaxFF potential
energy into sub-categories, which 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 14.
The 14 values correspond to the following sub-categories (the variable
names in italics match those used in the original FORTRAN ReaxFF code):</p>
<ol class="arabic simple">
<li><em>eb</em> = bond energy</li>
<li><em>ea</em> = atom energy</li>
<li><em>elp</em> = lone-pair energy</li>
<li><em>emol</em> = molecule energy (always 0.0)</li>
<li><em>ev</em> = valence angle energy</li>
<li><em>epen</em> = double-bond valence angle penalty</li>
<li><em>ecoa</em> = valence angle conjugation energy</li>
<li><em>ehb</em> = hydrogen bond energy</li>
<li><em>et</em> = torsion energy</li>
<li><em>eco</em> = conjugation energy</li>
<li><em>ew</em> = van der Waals energy</li>
<li><em>ep</em> = Coulomb energy</li>
<li><em>efi</em> = electric field energy (always 0.0)</li>
<li><em>eqeq</em> = charge equilibration energy</li>
</ol>
<p>To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:</p>
<div class="highlight-python"><div class="highlight"><pre>compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
...
variable eqeq equal c_reax[14]
thermo_style custom step temp epair v_eb v_ea ... v_eqeq
</pre></div>
</div>
<p>Only a single pair_coeff command is used with the <em>reax/c</em> style which
specifies a ReaxFF potential file with parameters for all needed
elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N indices = ReaxFF elements</li>
</ul>
<p>The filename is the ReaxFF potential file. Unlike for the <em>reax</em>
pair style, any filename can be used.</p>
<p>In the ReaxFF potential file, near the top, after the general
parameters, is the atomic parameters section that contains element
names, each with a couple dozen numeric parameters. If there are M
elements specified in the <em>ffield</em> file, think of these as numbered 1
to M. Each of the N indices you specify for the N atom types of LAMMPS
atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
be mapped to whatever element you specify as the first index value,
etc. If a mapping value is specified as NULL, the mapping is not
performed. This can be used when the <em>reax/c</em> style is used as part
of the <em>hybrid</em> pair style. The NULL values are placeholders for atom
types that will be used with other potentials.</p>
<p>As an example, say your LAMMPS simulation has 4 atom types and the
elements are ordered as C, H, O, N in the <em>ffield</em> file. If you want
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
H, you would use the following pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * ffield.reax C C N H
</pre></div>
</div>
<hr class="docutils" />
<p>The format of a line in the control file is as follows:</p>
<div class="highlight-python"><div class="highlight"><pre>variable_name value
</pre></div>
</div>
<p>and it may be followed by an &#8221;!&#8221; character and a trailing comment.</p>
<p>If the value of a control variable is not specified, then default
values are used. What follows is the list of variables along with a
brief description of their use and default values.</p>
<p>simulation_name: Output files produced by <em>pair_style reax/c</em> carry
this name + extensions specific to their contents. Partial energies
are reported with a &#8221;.pot&#8221; extension, while the trajectory file has
&#8221;.trj&#8221; extension.</p>
<p>tabulate_long_range: To improve performance, long range interactions
can optionally be tabulated (0 means no tabulation). Value of this
variable denotes the size of the long range interaction table. The
range from 0 to long range cutoff (defined in the <em>ffield</em> file) is
divided into <em>tabulate_long_range</em> points. Then at the start of
simulation, we fill in the entries of the long range interaction table
by computing the energies and forces resulting from van der Waals and
Coulomb interactions between every possible atom type pairs present in
the input system. During the simulation we consult to the long range
interaction table to estimate the energy and forces between a pair of
atoms. Linear interpolation is used for estimation. (default value =
0)</p>
<p>energy_update_freq: Denotes the frequency (in number of steps) of
writes into the partial energies file. (default value = 0)</p>
<p>nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms)
regarding the bonded interactions. (default value = 5.0)</p>
<p>hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen
bond interactions.(default value = 7.5. Value of 0.0 turns off hydrogen</p>
<blockquote>
<div>bonds)</div></blockquote>
<p>bond_graph_cutoff: is the threshold used in determining what is a
physical bond, what is not. Bonds and angles reported in the
trajectory file rely on this cutoff. (default value = 0.3)</p>
<p>thb_cutoff: cutoff value for the strength of bonds to be considered in
three body interactions. (default value = 0.001)</p>
<p>thb_cutoff_sq: cutoff value for the strength of bond order products
to be considered in three body interactions. (default value = 0.00001)</p>
<p>write_freq: Frequency of writes into the trajectory file. (default
value = 0)</p>
<p>traj_title: Title of the trajectory - not the name of the trajectory
file.</p>
<p>atom_info: 1 means print only atomic positions + charge (default = 0)</p>
<p>atom_forces: 1 adds net forces to atom lines in the trajectory file
(default = 0)</p>
<p>atom_velocities: 1 adds atomic velocities to atoms line (default = 0)</p>
<p>bond_info: 1 prints bonds in the trajectory file (default = 0)</p>
<p>angle_info: 1 prints angles in the trajectory file (default = 0)</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
mix, shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style is part of the USER-REAXC package. It is only enabled
if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>The ReaxFF potential files provided with LAMMPS in the potentials
directory are parameterized for real <a class="reference internal" href="units.html"><em>units</em></a>. You can use
the ReaxFF potential with any LAMMPS units, but you would need to
create your own potential file with coefficients listed in the
appropriate units if your simulation doesn&#8217;t use &#8220;real&#8221; units.</p>
</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>, <a class="reference internal" href="fix_qeq_reax.html"><em>fix qeq/reax</em></a>, <a class="reference internal" href="fix_reax_bonds.html"><em>fix reax/c/bonds</em></a>, <a class="reference internal" href="fix_reaxc_species.html"><em>fix reax/c/species</em></a>, <a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The keyword defaults are checkqeq = yes, lgvdw = no, safezone = 1.2,
mincap = 50.</p>
<hr class="docutils" />
<p id="chenoweth-2008"><strong>(Chenoweth_2008)</strong> Chenoweth, van Duin and Goddard,
Journal of Physical Chemistry A, 112, 1040-1053 (2008).</p>
<p id="aktulga">(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
245-259 (2012).</p>
<p id="liu-2011"><strong>(Liu)</strong> L. Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal
of Physical Chemistry A, 115, 11016-11022 (2011).</p>
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<div class="section" id="pair-style-resquared-command">
<span id="index-0"></span><h1>pair_style resquared command<a class="headerlink" href="#pair-style-resquared-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-resquared-gpu-command">
<h1>pair_style resquared/gpu command<a class="headerlink" href="#pair-style-resquared-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-resquared-omp-command">
<h1>pair_style resquared/omp command<a class="headerlink" href="#pair-style-resquared-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 resquared cutoff
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for interactions (distance units)</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 resquared 10.0
pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>resquared</em> computes the RE-squared anisotropic interaction
<a class="reference internal" href="#everaers"><span>(Everaers)</span></a>, <a class="reference internal" href="#babadi"><span>(Babadi)</span></a> between pairs of
ellipsoidal and/or spherical Lennard-Jones particles. For ellipsoidal
interactions, the potential considers the ellipsoid as being comprised
of small spheres of size sigma. LJ particles are a single sphere of
size sigma. The distinction is made to allow the pair style to make
efficient calculations of ellipsoid/solvent interactions.</p>
<p>Details for the equations used are given in the references below and
in <a class="reference external" href="PDF/pair_resquared_extra.pdf">this supplementary document</a>.</p>
<p>Use of this pair style requires the NVE, NVT, or NPT fixes with the
<em>asphere</em> extension (e.g. <a class="reference internal" href="fix_nve_asphere.html"><em>fix nve/asphere</em></a>) in
order to integrate particle rotation. Additionally, <a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> should be used since it defines the
rotational state and the size and shape of each ellipsoidal particle.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>A12 = Energy Prefactor/Hamaker constant (energy units)</li>
<li>sigma = atomic interaction diameter (distance units)</li>
<li>epsilon_i_a = relative well depth of type I for side-to-side interactions</li>
<li>epsilon_i_b = relative well depth of type I for face-to-face interactions</li>
<li>epsilon_i_c = relative well depth of type I for end-to-end interactions</li>
<li>epsilon_j_a = relative well depth of type J for side-to-side interactions</li>
<li>epsilon_j_b = relative well depth of type J for face-to-face interactions</li>
<li>epsilon_j_c = relative well depth of type J for end-to-end interactions</li>
<li>cutoff (distance units)</li>
</ul>
<p>The parameters used depend on the type of the interacting particles,
i.e. ellipsoids or LJ spheres. The type of a particle is determined
by the diameters specified for its 3 shape paramters. If all 3 shape
parameters = 0.0, then the particle is treated as an LJ sphere. The
epsilon_i_* or epsilon_j_* parameters are ignored for LJ spheres. If
the 3 shape paraemters are &gt; 0.0, then the particle is treated as an
ellipsoid (even if the 3 parameters are equal to each other).</p>
<p>A12 specifies the energy prefactor which depends on the types of the
two interacting particles.</p>
<p>For ellipsoid/ellipsoid interactions, the interaction is computed by
the formulas in the supplementary docuement referenced above. A12 is
the Hamaker constant as described in <a class="reference internal" href="#everaers"><span>(Everaers)</span></a>. In LJ
units:</p>
<img alt="_images/pair_resquared.jpg" class="align-center" src="_images/pair_resquared.jpg" />
<p>where rho gives the number density of the spherical particles
composing the ellipsoids and epsilon_LJ determines the interaction
strength of the spherical particles.</p>
<p>For ellipsoid/LJ sphere interactions, the interaction is also computed
by the formulas in the supplementary docuement referenced above. A12
has a modifed form (see <a class="reference external" href="PDF/pair_resquared_extra.pdf">here</a> for
details):</p>
<img alt="_images/pair_resquared2.jpg" class="align-center" src="_images/pair_resquared2.jpg" />
<p>For ellipsoid/LJ sphere interactions, a correction to the distance-
of-closest approach equation has been implemented to reduce the error
from two particles of disparate sizes; see <a class="reference external" href="PDF/pair_resquared_extra.pdf">this supplementary document</a>.</p>
<p>For LJ sphere/LJ sphere interactions, the interaction is computed
using the standard Lennard-Jones formula, which is much cheaper to
compute than the ellipsoidal formulas. A12 is used as epsilon in the
standard LJ formula:</p>
<img alt="_images/pair_resquared3.jpg" class="align-center" src="_images/pair_resquared3.jpg" />
<p>and the specified <em>sigma</em> is used as the sigma in the standard LJ
formula.</p>
<p>When one of both of the interacting particles are ellipsoids, then
<em>sigma</em> specifies the diameter of the continuous distribution of
constituent particles within each ellipsoid used to model the
RE-squared potential. Note that this is a different meaning for
<em>sigma</em> than the <a class="reference internal" href="pair_gayberne.html"><em>pair_style gayberne</em></a> potential
uses.</p>
<p>The epsilon_i and epsilon_j coefficients are defined for atom types,
not for pairs of atom types. Thus, in a series of pair_coeff
commands, they only need to be specified once for each atom type.</p>
<p>Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are
non-zero, the three values are assigned to atom type I. If all the
epsilon_i values are zero, they are ignored. If any of epsilon_j_a,
epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned
to atom type J. If all three epsilon_i values are zero, they are
ignored. Thus the typical way to define the epsilon_i and epsilon_j
coefficients is to list their values in &#8220;pair_coeff I J&#8221; commands when
I = J, but set them to 0.0 when I != J. If you do list them when I !=
J, you should insure they are consistent with their values in other
pair_coeff commands.</p>
<p>Note that if this potential is being used as a sub-style of
<a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a>, and there is no &#8220;pair_coeff I I&#8221;
setting made for RE-squared for a particular type I (because I-I
interactions are computed by another hybrid pair potential), then you
still need to insure the epsilon a,b,c coefficients are assigned to
that type in a &#8220;pair_coeff I J&#8221; command.</p>
<p>For large uniform molecules it has been shown that the epsilon_*_*
energy parameters are approximately representable in terms of local
contact curvatures <a class="reference internal" href="#everaers"><span>(Everaers)</span></a>:</p>
<img alt="_images/pair_resquared4.jpg" class="align-center" src="_images/pair_resquared4.jpg" />
<p>where a, b, and c give the particle diameters.</p>
<p>The last coefficient is optional. If not specified, the global cutoff
specified in the pair_style command is used.</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>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance can be mixed, but only for sphere pairs. The
default mix value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command for
details. Other type pairs cannot be mixed, due to the different
meanings of the energy prefactors used to calculate the interactions
and the implicit dependence of the ellipsoid-sphere interaction on the
equation for the Hamaker constant presented here. Mixing of sigma and
epsilon followed by calculation of the energy prefactors using the
equations above is recommended.</p>
<p>This pair styles supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the Lennard-Jones portion of the pair
interaction, but only for sphere-sphere interactions. There is no
shifting performed for ellipsoidal interactions due to the anisotropic
dependence of the interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>This pair style does 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>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords of the <a class="reference internal" href="run_style.html"><em>run_style command</em></a>.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This style is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>This pair style requires that atoms be ellipsoids as defined by the
<a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> command.</p>
<p>Particles acted on by the potential can be finite-size aspherical or
spherical particles, or point particles. Spherical particles have all
3 of their shape parameters equal to each other. Point particles have
all 3 of their shape parameters equal to 0.0.</p>
<p>The distance-of-closest-approach approximation used by LAMMPS becomes
less accurate when high-aspect ratio ellipsoids are used.</p>
</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>, <a class="reference internal" href="fix_nve_asphere.html"><em>fix nve/asphere</em></a>,
<a class="reference internal" href="compute_temp_asphere.html"><em>compute temp/asphere</em></a>, <a class="reference internal" href="pair_gayberne.html"><em>pair_style gayberne</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="everaers"><strong>(Everaers)</strong> Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).</p>
<p id="babadi"><strong>(Berardi)</strong> Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).</p>
</div>
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<div class="section" id="pair-style-lj-sdk-command">
<span id="index-0"></span><h1>pair_style lj/sdk command<a class="headerlink" href="#pair-style-lj-sdk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-sdk-gpu-command">
<h1>pair_style lj/sdk/gpu command<a class="headerlink" href="#pair-style-lj-sdk-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-sdk-kk-command">
<h1>pair_style lj/sdk/kk command<a class="headerlink" href="#pair-style-lj-sdk-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-sdk-omp-command">
<h1>pair_style lj/sdk/omp command<a class="headerlink" href="#pair-style-lj-sdk-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-sdk-coul-long-command">
<h1>pair_style lj/sdk/coul/long command<a class="headerlink" href="#pair-style-lj-sdk-coul-long-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-sdk-coul-long-gpu-command">
<h1>pair_style lj/sdk/coul/long/gpu command<a class="headerlink" href="#pair-style-lj-sdk-coul-long-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-sdk-coul-long-omp-command">
<h1>pair_style lj/sdk/coul/long/omp command<a class="headerlink" href="#pair-style-lj-sdk-coul-long-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 args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lj/sdk</em> or <em>lj/sdk/coul/long</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>lj/sdk</em> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<em>lj/sdk/coul/long</em> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</pre>
</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 lj/sdk 2.5
pair_coeff 1 1 lj12_6 1 1.1 2.8
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/sdk/coul/long 10.0
pair_style lj/sdk/coul/long 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 12.0
</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>lj/sdk</em> styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
given by</p>
<img alt="_images/pair_cmm.jpg" class="align-center" src="_images/pair_cmm.jpg" />
<p>as required for the SDK Coarse-grained MD parametrization discussed in
<a class="reference internal" href="#shinoda"><span>(Shinoda)</span></a> and <a class="reference internal" href="#devane"><span>(DeVane)</span></a>. Rc is the cutoff.</p>
<p>Style <em>lj/sdk/coul/long</em> computes the adds Coulombic interactions
with an additional damping factor applied so it can be used in
conjunction with the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command and
its <em>ewald</em> or <em>pppm</em> or <em>pppm/cg</em> option. The Coulombic cutoff
specified for this style means that pairwise interactions within
this distance are computed directly; interactions outside that
distance are computed in reciprocal space.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>cg_type (lj9_6, lj12_4, or lj12_6)</li>
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>cutoff1 (distance units)</li>
</ul>
<p>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum. The prefactors
are chosen so that the potential minimum is at -epsilon.</p>
<p>The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.</p>
<p>For <em>lj/sdk/coul/long</em> only the LJ cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.</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, and rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/sdk pair styles <em>cannot</em> be mixed,
since different pairs may have different exponents. So all parameters
for all pairs have to be specified explicitly through the &#8220;pair_coeff&#8221;
command. Defining then in a data file is also not supported, due to
limitations of that file format.</p>
<p>All of the lj/sdk pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option for the energy of the
Lennard-Jones portion of the pair interaction.</p>
<p>The <em>lj/sdk/coul/long</em> pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.</p>
<p>All of the lj/sdk pair styles write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.</p>
<p>The lj/sdk and lj/cut/coul/long pair styles do not support
the use of the <em>inner</em>, <em>middle</em>, and <em>outer</em> keywords of the <a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command.</p>
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<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>All of the lj/sdk pair styles are part of the USER-CG-CMM package.
The <em>lj/sdk/coul/long</em> style also requires the KSPACE package to be
built (which is enabled by default). They are only enabled if LAMMPS
was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</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>, <a class="reference internal" href="angle_sdk.html"><em>angle_style sdk</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="shinoda"><strong>(Shinoda)</strong> Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).</p>
<p id="devane"><strong>(DeVane)</strong> Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).</p>
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<div class="section" id="pair-style-smd-hertz-command">
<span id="index-0"></span><h1>pair_style smd/hertz command<a class="headerlink" href="#pair-style-smd-hertz-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 smd/hertz scale_factor
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<p>pair_style smd/hertz 1.0
pair_coeff 1 1 &lt;contact_stiffness&gt;</p>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>smd/hertz</em> style calculates contact forces between SPH particles belonging to different physical bodies.</p>
<p>The contact forces are calculated using a Hertz potential, which evaluates the overlap between two particles
(whose spatial extents are defined via its contact radius).
The effect is that a particles cannot penetrate into each other.
The parameter &lt;contact_stiffness&gt; has units of pressure and should equal roughly one half
of the Young&#8217;s modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles.</p>
<p>The parameter <em>scale_factor</em> can be used to scale the particles&#8217; contact radii. This can be useful to control how close
particles can approach each other. Usually, <a href="#id1"><span class="problematic" id="id2">*</span></a>scale_factor*=1.0.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>No mixing is performed automatically.
Currently, no part of USER-SMD supports restarting nor minimization.
rRESPA does not apply to this pair style.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This fix is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info.</p>
</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>
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<div class="section" id="pair-style-smd-tlsph-command">
<span id="index-0"></span><h1>pair_style smd/tlsph command<a class="headerlink" href="#pair-style-smd-tlsph-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 smd/tlsph args
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<p>pair_style smd/tlsph</p>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>smd/tlsph</em> style computes particle interactions according to continuum mechanics constitutive laws and a Total-Lagrangian Smooth-Particle Hydrodynamics algorithm.</p>
<p>This pair style is invoked with the following command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style smd/tlsph
pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp &amp;
*END
</pre></div>
</div>
<p>Here, <em>i</em> and <em>j</em> denote the <em>LAMMPS</em> particle types for which this pair style is
defined. Note that <em>i</em> and <em>j</em> must be equal, i.e., no <em>tlsph</em> cross interactions
between different particle types are allowed.
In contrast to the usual <em>LAMMPS</em> <em>pair coeff</em> definitions, which are given solely a
number of floats and integers, the <em>tlsph</em> <em>pair coeff</em> definition is organised using
keywords. These keywords mark the beginning of different sets of parameters for particle properties,
material constitutive models, and damage models. The <em>pair coeff</em> line must be terminated with
the <a href="#id5"><span class="problematic" id="id6">**</span></a>END* keyword. The use the line continuation operator <em>&amp;</em> is recommended. A typical
invocation of the <em>tlsph</em> for a solid body would consist of an equation of state for computing
the pressure (the diagonal components of the stress tensor), and a material model to compute shear
stresses (the off-diagonal components of the stress tensor). Damage and failure models can also be added.</p>
<p>Please see the <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">SMD user guide</a> for a complete listing of the possible keywords and material models.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>No mixing is performed automatically.
Currently, no part of USER-SMD supports restarting nor minimization.
rRESPA does not apply to this pair style.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This fix is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info.</p>
</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>
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<div class="section" id="pair-style-smd-tri-surface-command">
<span id="index-0"></span><h1>pair_style smd/tri_surface command<a class="headerlink" href="#pair-style-smd-tri-surface-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 smd/tri_surface scale_factor
</pre></div>
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<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<p>pair_style smd/tri_surface 1.0
pair_coeff 1 1 &lt;contact_stiffness&gt;</p>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>smd/tri_surface</em> style calculates contact forces between SPH particles and a rigid wall boundary defined via the
<a class="reference internal" href="fix_smd_wall_surface.html"><em>smd/wall_surface</em></a> fix.</p>
<p>The contact forces are calculated using a Hertz potential, which evaluates the overlap between a particle
(whose spatial extents are defined via its contact radius) and the triangle.
The effect is that a particle cannot penetrate into the triangular surface.
The parameter &lt;contact_stiffness&gt; has units of pressure and should equal roughly one half
of the Young&#8217;s modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle</p>
<p>The parameter <em>scale_factor</em> can be used to scale the particles&#8217; contact radii. This can be useful to control how close
particles can approach the triangulated surface. Usually, <a href="#id1"><span class="problematic" id="id2">*</span></a>scale_factor*=1.0.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>No mixing is performed automatically.
Currently, no part of USER-SMD supports restarting nor minimization.
rRESPA does not apply to this pair style.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This fix is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info.</p>
</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>
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<div class="section" id="pair-style-smd-ulsph-command">
<span id="index-0"></span><h1>pair_style smd/ulsph command<a class="headerlink" href="#pair-style-smd-ulsph-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 smd/ulsph args
</pre></div>
</div>
<ul class="simple">
<li>these keywords must be given</li>
</ul>
<p>keyword = <a href="#id1"><span class="problematic" id="id2">**</span></a>DENSITY_SUMMATION* or <a href="#id3"><span class="problematic" id="id4">**</span></a>DENSITY_CONTINUITY* and <a href="#id5"><span class="problematic" id="id6">**</span></a>VELOCITY_GRADIENT* or <a href="#id7"><span class="problematic" id="id8">**</span></a>NO_VELOCITY_GRADIENT* and <a href="#id9"><span class="problematic" id="id10">**</span></a>GRADIENT_CORRECTION* or <a href="#id11"><span class="problematic" id="id12">**</span></a>NO_GRADIENT_CORRECTION*</p>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<p>pair_style smd/ulsph <a href="#id13"><span class="problematic" id="id14">*</span></a>DENSITY_CONTINUITY <a href="#id15"><span class="problematic" id="id16">*</span></a>VELOCITY_GRADIENT <a href="#id17"><span class="problematic" id="id18">*</span></a>NO_GRADIENT_CORRECTION</p>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>smd/ulsph</em> style computes particle interactions according to continuum mechanics constitutive laws and an updated Lagrangian Smooth-Particle Hydrodynamics algorithm.</p>
<p>This pair style is invoked similar to the following command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION
pair_coeff i j *COMMON rho0 c0 Q1 Cp hg &amp;
*END
</pre></div>
</div>
<p>Here, <em>i</em> and <em>j</em> denote the <em>LAMMPS</em> particle types for which this pair style is
defined. Note that <em>i</em> and <em>j</em> can be different, i.e., <em>ulsph</em> cross interactions
between different particle types are allowed. However, <em>i</em>&#8211;<em>i</em> respectively <em>j</em>&#8211;<em>j</em> pair_coeff lines have to preceed a cross interaction.
In contrast to the usual <em>LAMMPS</em> <em>pair coeff</em> definitions, which are given solely a
number of floats and integers, the <em>ulsph</em> <em>pair coeff</em> definition is organised using
keywords. These keywords mark the beginning of different sets of parameters for particle properties,
material constitutive models, and damage models. The <em>pair coeff</em> line must be terminated with
the <a href="#id29"><span class="problematic" id="id30">**</span></a>END* keyword. The use the line continuation operator <em>&amp;</em> is recommended. A typical
invocation of the <em>ulsph</em> for a solid body would consist of an equation of state for computing
the pressure (the diagonal components of the stress tensor), and a material model to compute shear
stresses (the off-diagonal components of the stress tensor).</p>
<p>Note that the use of <a href="#id31"><span class="problematic" id="id32">*</span></a>GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, <a href="#id33"><span class="problematic" id="id34">*</span></a>NO_GRADIENT_CORRECTION is recommended.</p>
<p>Please see the <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">SMD user guide</a> for a complete listing of the possible keywords and material models.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>No mixing is performed automatically.
Currently, no part of USER-SMD supports restarting nor minimization.
rRESPA does not apply to this pair style.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This fix is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info.</p>
</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>
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<div class="section" id="pair-style-smtbq-command">
<span id="index-0"></span><h1>pair_style smtbq command<a class="headerlink" href="#pair-style-smtbq-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 smtbq
</pre></div>
</div>
</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 smtbq
pair_coeff * * ffield.smtbq.Al2O3 O Al
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>This pair stylecomputes a variable charge SMTB-Q (Second-Moment
tight-Binding QEq) potential as described in <a class="reference internal" href="#smtb-q-1"><span>SMTB-Q_1</span></a> and
<a class="reference internal" href="#smtb-q-2"><span>SMTB-Q_2</span></a>. Briefly, the energy of metallic-oxygen systems
is given by three contributions:</p>
<img alt="_images/pair_smtbq1.jpg" class="align-center" src="_images/pair_smtbq1.jpg" />
<p>where <em>E&lt;sub&gt;tot&lt;/sub&gt;</em> is the total potential energy of the system,
<em>E&lt;sub&gt;ES&lt;/sub&gt;</em> is the electrostatic part of the total energy,
<em>E&lt;sub&gt;OO&lt;/sub&gt;</em> is the interaction between oxygens and
<em>E&lt;sub&gt;MO&lt;/sub&gt;</em> is a short-range interaction between metal and oxygen
atoms. This interactions depend on interatomic distance
<em>r&lt;sub&gt;ij&lt;/sub&gt;</em> and/or the charge <em>Q&lt;sub&gt;i&lt;/sub&gt;</em> of atoms
<em>i</em>. Cut-off function enables smooth convergence to zero interaction.</p>
<p>The parameters appearing in the upper expressions are set in the
ffield.SMTBQ.Syst file where Syst corresponds to the selected system
(e.g. field.SMTBQ.Al2O3). Exemples for TiO&lt;sub&gt;2&lt;/sub&gt;,
Al&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3&lt;/sub&gt; are provided. A single pair_coeff command
is used with the SMTBQ styles which provides the path to the potential
file with parameters for needed elements. These are mapped to LAMMPS
atom types by specifying additional arguments after the potential
filename in the pair_coeff command. Note that atom type 1 must always
correspond to oxygen atoms. As an example, to simulate a TiO2 system,
atom type 1 has to be oxygen and atom type 2 Ti. The following
pair_coeff command should then be used:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti
</pre></div>
</div>
<p>The electrostatic part of the energy consists of two components</p>
<p>self-energy of atom <em>i</em> in the form of a second order charge dependent
polynomial and a long-range Coulombic electrostatic interaction. The
latter uses the wolf summation method described in <a class="reference internal" href="#wolf"><span>Wolf</span></a>,
spherically truncated at a longer cutoff, <em>R&lt;sub&gt;coul&lt;/sub&gt;</em>. The
charge of each ion is modeled by an orbital Slater which depends on
the principal quantum number (<em>n</em>) of the outer orbital shared by the
ion.</p>
<p>Interaction between oxygen, <em>E&lt;sub&gt;OO&lt;/sub&gt;</em>, consists of two parts,
an attractive and a repulsive part. The attractive part is effective
only at short range (&lt; r&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;OO&lt;/sup&gt;). The attractive
contribution was optimized to study surfaces reconstruction
(e.g. <a class="reference internal" href="#smtb-q-2"><span>SMTB-Q_2</span></a> in TiO&lt;sub&gt;2&lt;/sub&gt;) and is not necessary
for oxide bulk modeling. The repulsive part is the Pauli interaction
between the electron clouds of oxygen. The Pauli repulsion and the
coulombic electrostatic interaction have same cut off value. In the
ffield.SMTBQ.Syst, the keyword <em>&#8216;buck&#8217;</em> allows to consider only the
repulsive O-O interactions. The keyword <em>&#8216;buckPlusAttr&#8217;</em> allows to
consider the repulsive and the attractive O-O interactions.</p>
<p>The short-range interaction between metal-oxygen, <em>E&lt;sub&gt;MO&lt;/sub&gt;</em> is
based on the second moment approximation of the density of states with
a N-body potential for the band energy term,
<em>E&lt;sup&gt;i&lt;/sup&gt;&lt;sub&gt;cov&lt;/sub&gt;</em>, and a Born-Mayer type repulsive terms
as indicated by the keyword <em>&#8216;second_moment&#8217;</em> in the
ffield.SMTBQ.Syst. The energy band term is given by:</p>
<img alt="_images/pair_smtbq2.jpg" class="align-center" src="_images/pair_smtbq2.jpg" />
<p>where <em>&amp;#951&lt;sub&gt;i&lt;/sub&gt;</em> is the stoichiometry of atom <em>i</em>,
<em>&amp;#948Q&lt;sub&gt;i&lt;/sub&gt;</em> is the charge delocalization of atom <em>i</em>,
compared to its formal charge
<em>Q&lt;sup&gt;F&lt;/sup&gt;&lt;sub&gt;i&lt;/sub&gt;</em>. n&lt;sub&gt;0&lt;/sub&gt;, the number of hybridized
orbitals, is calculated with to the atomic orbitals shared
<em>d&lt;sub&gt;i&lt;/sub&gt;</em> and the stoichiometry
<em>&amp;#951&lt;sub&gt;i&lt;/sub&gt;</em>. <em>r&lt;sub&gt;c1&lt;/sub&gt;</em> and <em>r&lt;sub&gt;c2&lt;/sub&gt;</em> are the two
cutoff radius around the fourth neighbors in the cutoff function.</p>
<p>In the formalism used here, <em>&amp;#958&lt;sup&gt;0&lt;/sup&gt;</em> is the energy
parameter. <em>&amp;#958&lt;sup&gt;0&lt;/sup&gt;</em> is in tight-binding approximation the
hopping integral between the hybridized orbitals of the cation and the
anion. In the literature we find many ways to write the hopping
integral depending on whether one takes the point of view of the anion
or cation. These are equivalent vision. The correspondence between the
two visions is explained in appendix A of the article in the
SrTiO&lt;sub&gt;3&lt;/sub&gt; <a class="reference internal" href="#smtb-q-3"><span>SMTB-Q_3</span></a> (parameter <em>&amp;#946</em> shown in
this article is in fact the <em>&amp;#946&lt;sub&gt;O&lt;/sub&gt;</em>). To summarize the
relationship between the hopping integral <em>&amp;#958&lt;sup&gt;0&lt;/sup&gt;</em> and the
others, we have in an oxide C&lt;sub&gt;n&lt;/sub&gt;O&lt;sub&gt;m&lt;/sub&gt; the following
relationship:</p>
<img alt="_images/pair_smtbq3.jpg" class="align-center" src="_images/pair_smtbq3.jpg" />
<p>Thus parameter &amp;#956, indicated above, is given by : &amp;#956 = (&amp;#8730n
+ &amp;#8730m) &amp;#8260 2</p>
<p>The potential offers the possibility to consider the polarizability of
the electron clouds of oxygen by changing the slater radius of the
charge density around the oxygens through the parameters <em>rBB, rB and
rS</em> in the ffield.SMTBQ.Syst. This change in radius is performed
according to the method developed by E. Maras
<a class="reference internal" href="#smtb-q-2"><span>SMTB-Q_2</span></a>. This method needs to determine the number of
nearest neighbors around the oxygen. This calculation is based on
first (<em>r&lt;sub&gt;1n&lt;/sub&gt;</em>) and second (<em>r&lt;sub&gt;2n&lt;/sub&gt;</em>) distances
neighbors.</p>
<p>The SMTB-Q potential is a variable charge potential. The equilibrium
charge on each atom is calculated by the electronegativity
equalization (QEq) method. See <a class="reference internal" href="#rick"><span>Rick</span></a> for further detail. One
can adjust the frequency, the maximum number of iterative loop and the
convergence of the equilibrium charge calculation. To obtain the
energy conservation in NVE thermodynamic ensemble, we recommend to use
a convergence parameter in the interval 10&lt;sup&gt;-5&lt;/sup&gt; -
10&lt;sup&gt;-6&lt;/sup&gt; eV.</p>
<p>The ffield.SMTBQ.Syst files are provided for few systems. They consist
of nine parts and the lines beginning with &#8216;#&#8217; are comments (note that
the number of comment lines matter). The first sections are on the
potential parameters and others are on the simulation options and
might be modified. Keywords are character type and must be enclosed in
quotation marks (&#8216;&#8217;).</p>
<ol class="arabic simple">
<li>Number of different element in the oxide:</li>
</ol>
<ul class="simple">
<li>N&lt;sub&gt;elem&lt;/sub&gt;= 2 or 3</li>
<li>Divided line</li>
</ul>
<ol class="arabic simple" start="2">
<li>Atomic parameters</li>
</ol>
<p>For the anion (oxygen)</p>
<ul class="simple">
<li>Name of element (char) and stoichiometry in oxide</li>
<li>Formal charge and mass of element</li>
<li>Principal quantic number of outer orbital (<em>n</em>), electronegativity (<em>&amp;#967&lt;sup&gt;0&lt;/sup&gt;&lt;sub&gt;i&lt;/simulationub&gt;</em>) and hardness (<em>J&lt;sup&gt;0&lt;/sup&gt;&lt;sub&gt;i&lt;/sub&gt;</em>)</li>
<li>Ionic radius parameters : max coordination number (<em>coordBB</em> = 6 by default), bulk coordination number <em>(coordB)</em>, surface coordination number <em>(coordS)</em> and <em>rBB, rB and rS</em> the slater radius for each coordination number. (&lt;b&gt;note : If you don&#8217;t want to change the slater radius, use three identical radius values&lt;/b&gt;)</li>
<li>Number of orbital shared by the element in the oxide (<em>d&lt;sub&gt;i&lt;/sub&gt;</em>)</li>
<li>Divided line</li>
</ul>
<p>For each cations (metal):</p>
<ul class="simple">
<li>Name of element (char) and stoichiometry in oxide</li>
<li>Formal charge and mass of element</li>
<li>Number of electron in outer orbital <em>(ne)</em>, electronegativity (<em>&amp;#967&lt;sup&gt;0&lt;/sup&gt;&lt;sub&gt;i&lt;/simulationub&gt;</em>), hardness (<em>J&lt;sup&gt;0&lt;/sup&gt;&lt;sub&gt;i&lt;/sub&gt;</em>) and <em>r&lt;sub&gt;Salter&lt;/sub&gt;</em> the slater radius for the cation.</li>
<li>Number of orbitals shared by the elements in the oxide (<em>d&lt;sub&gt;i&lt;/sub&gt;</em>)</li>
<li>Divided line</li>
</ul>
<ol class="arabic simple" start="3">
<li>Potential parameters:</li>
</ol>
<ul class="simple">
<li>Keyword for element1, element2 and interaction potential (&#8216;second_moment&#8217; or &#8216;buck&#8217; or &#8216;buckPlusAttr&#8217;) between element 1 and 2. If the potential is &#8216;second_moment&#8217;, specify &#8216;oxide&#8217; or &#8216;metal&#8217; for metal-oxygen or metal-metal interactions respectively.</li>
<li>Potential parameter: &lt;pre&gt;&lt;br/&gt; If type of potential is &#8216;second_moment&#8217; : <em>A (eV)</em>, <em>p</em>, <em>&amp;#958&lt;sup&gt;0&lt;/sup&gt;</em> (eV) and <em>q</em> &lt;br/&gt; <em>r&lt;sub&gt;c1&lt;/sub&gt;</em> (&amp;#197), <em>r&lt;sub&gt;c2&lt;/sub&gt;</em> (&amp;#197) and <em>r&lt;sub&gt;0&lt;/sub&gt;</em> (&amp;#197) &lt;br/&gt; If type of potential is &#8216;buck&#8217; : <em>C</em> (eV) and <em>&amp;#961</em> (&amp;#197) &lt;br/&gt; If type of potential is &#8216;buckPlusAttr&#8217; : <em>C</em> (eV) and <em>&amp;#961</em> (&amp;#197) &lt;br/&gt; <em>D</em> (eV), <em>B</em> (&amp;#197&lt;sup&gt;-1&lt;/sup&gt;), <em>r&lt;sub&gt;1&lt;/sub&gt;&lt;sup&gt;OO&lt;/sup&gt;</em> (&amp;#197) and <em>r&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;OO&lt;/sup&gt;</em> (&amp;#197) &lt;/pre&gt;</li>
<li>Divided line</li>
</ul>
<ol class="arabic simple" start="4">
<li>Tables parameters:</li>
</ol>
<ul class="simple">
<li>Cutoff radius for the Coulomb interaction (<em>R&lt;sub&gt;coul&lt;/sub&gt;</em>)</li>
<li>Starting radius (<em>r&lt;sub&gt;min&lt;/sub&gt;</em> = 1,18845 &amp;#197) and increments (<em>dr</em> = 0,001 &amp;#197) for creating the potential table.</li>
<li>Divided line</li>
</ul>
<ol class="arabic simple" start="5">
<li>Rick model parameter:</li>
</ol>
<ul class="simple">
<li><em>Nevery</em> : parameter to set the frequency (<em>1/Nevery</em>) of the charge resolution. The charges are evaluated each <em>Nevery</em> time steps.</li>
<li>Max number of iterative loop (<em>loopmax</em>) and precision criterion (<em>prec</em>) in eV of the charge resolution</li>
<li>Divided line</li>
</ul>
<ol class="arabic simple" start="6">
<li>Coordination parameter:</li>
</ol>
<ul class="simple">
<li>First (<em>r&lt;sub&gt;1n&lt;/sub&gt;</em>) and second (<em>r&lt;sub&gt;2n&lt;/sub&gt;</em>) neighbor distances in &amp;#197</li>
<li>Divided line</li>
</ul>
<ol class="arabic simple" start="7">
<li>Charge initialization mode:</li>
</ol>
<ul class="simple">
<li>Keyword (<em>QInitMode</em>) and initial oxygen charge (<em>Q&lt;sub&gt;init&lt;/sub&gt;</em>). If keyword = &#8216;true&#8217;, all oxygen charges are initially set equal to <em>Q&lt;sub&gt;init&lt;/sub&gt;</em>. The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = &#8216;false&#8217;, all atom charges are initially set equal to 0 if you use &#8220;create_atom&#8221;#create_atom command or the charge specified in the file structure using <span class="xref std std-ref">read_data</span> command.</li>
<li>Divided line</li>
</ul>
<ol class="arabic simple" start="8">
<li>Mode for the electronegativity equalization (Qeq)</li>
</ol>
<ul class="simple">
<li>Keyword mode: &lt;pre&gt; &lt;br/&gt; QEqAll (one QEq group) | no parameters &lt;br/&gt; QEqAllParallel (several QEq groups) | no parameters &lt;br/&gt; Surface | zlim (QEq only for z&gt;zlim) &lt;/pre&gt;</li>
<li>Parameter if necessary</li>
<li>Divided line</li>
</ul>
<ol class="arabic simple" start="9">
<li>Verbose</li>
</ol>
<ul class="simple">
<li>If you want the code to work in verbose mode or not : &#8216;true&#8217; or &#8216;false&#8217;</li>
<li>If you want to print or not in file &#8216;Energy_component.txt&#8217; the three main contributions to the energy of the system according to the description presented above : &#8216;true&#8217; or &#8216;false&#8217; and <em>N&lt;sub&gt;Energy&lt;/sub&gt;</em>. This option writes in file every <em>N&lt;sub&gt;Energy&lt;/sub&gt;</em> time step. If the value is &#8216;false&#8217; then <em>N&lt;sub&gt;Energy&lt;/sub&gt;</em> = 0. The file take into account the possibility to have several QEq group <em>g</em> then it writes: time step, number of atoms in group <em>g</em>, electrostatic part of energy, <em>E&lt;sub&gt;ES&lt;/sub&gt;</em>, the interaction between oxygen, <em>E&lt;sub&gt;OO&lt;/sub&gt;</em>, and short range metal-oxygen interaction, <em>E&lt;sub&gt;MO&lt;/sub&gt;</em>.</li>
<li>If you want to print in file &#8216;Electroneg_component.txt&#8217; the electronegativity component (<em>&amp;#8706E&lt;sub&gt;tot&lt;/sub&gt; &amp;#8260&amp;#8706Q&lt;sub&gt;i&lt;/sub&gt;</em>) or not: &#8216;true&#8217; or &#8216;false&#8217; and <em>N&lt;sub&gt;Electroneg&lt;/sub&gt;</em>.This option writes in file every <em>N&lt;sub&gt;Electroneg&lt;/sub&gt;</em> time step. If the value is &#8216;false&#8217; then <em>N&lt;sub&gt;Electroneg&lt;/sub&gt;</em> = 0. The file consist in atom number <em>i</em>, atom type (1 for oxygen and # higher than 1 for metal), atom position: <em>x</em>, <em>y</em> and <em>z</em>, atomic charge of atom <em>i</em>, electrostatic part of atom <em>i</em> electronegativity, covalent part of atom <em>i</em> electronegativity, the hopping integral of atom <em>i</em> <em>(Z&amp;#946&lt;sup&gt;2&lt;/sup&gt;)&lt;sub&gt;i&lt;sub&gt;</em> and box electronegativity.</li>
</ul>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This last option slows down the calculation dramatically. Use
only with a single processor simulation.</p>
</div>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info:</strong></p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
mix, shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
needs to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
<hr class="docutils" />
<p><strong>Restriction:</strong></p>
<p>This pair style is part of the USER-SMTBQ package and is only enabled
if LAMMPS is built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>This potential requires using atom type 1 for oxygen and atom type
higher than 1 for metal atoms.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><em>newton</em></a> setting to be &#8220;on&#8221;
for pair interactions.</p>
<p>The SMTB-Q potential files provided with LAMMPS (see the potentials
directory) are parameterized for metal <code class="xref doc docutils literal"><span class="pre">units</span></code>.</p>
<hr class="docutils" />
<p><strong>Citing this work:</strong></p>
<p>Please cite related publication: N. Salles, O. Politano, E. Amzallag
and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189</p>
<hr class="docutils" />
<p id="smtb-q-1"><strong>(SMTB-Q_1)</strong> N. Salles, O. Politano, E. Amzallag, R. Tetot,
Comput. Mater. Sci. 111 (2016) 181-189</p>
<p id="smtb-q-2"><strong>(SMTB-Q_2)</strong> E. Maras, N. Salles, R. Tetot, T. Ala-Nissila,
H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399</p>
<p id="smtb-q-3"><strong>(SMTB-Q_3)</strong> R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface
Science 616, 19-8722 28 (2013)</p>
<p id="wolf"><strong>(Wolf)</strong> D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
Phys, 110, 8254 (1999).</p>
<p id="rick"><strong>(Rick)</strong> S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
(1994).</p>
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<div class="section" id="pair-style-snap-command">
<span id="index-0"></span><h1>pair_style snap command<a class="headerlink" href="#pair-style-snap-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 snap
</pre></div>
</div>
</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 snap
pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>snap</em> computes interactions
using the spectral neighbor analysis potential (SNAP)
<a class="reference internal" href="#thompson2014"><span>(Thompson)</span></a>. Like the GAP framework of Bartok et al.
<a class="reference internal" href="#bartok2010"><span>(Bartok2010)</span></a>, <a class="reference internal" href="#bartok2013"><span>(Bartok2013)</span></a>
it uses bispectrum components
to characterize the local neighborhood of each atom
in a very general way. The mathematical definition of the
bispectrum calculation used by SNAP is identical
to that used of <a class="reference internal" href="compute_sna_atom.html"><em>compute sna/atom</em></a>.
In SNAP, the total energy is decomposed into a sum over
atom energies. The energy of atom <em>i</em> is
expressed as a weighted sum over bispectrum components.</p>
<img alt="_images/pair_snap.jpg" class="align-center" src="_images/pair_snap.jpg" />
<p>where <em>B_k^i</em> is the <em>k</em>-th bispectrum component of atom <em>i</em>,
and <em>beta_k^alpha_i</em> is the corresponding linear coefficient
that depends on <em>alpha_i</em>, the SNAP element of atom <em>i</em>. The
number of bispectrum components used and their definitions
depend on the values of <em>twojmax</em> and <em>diagonalstyle</em>
defined in the SNAP parameter file described below.
The bispectrum calculation is described in more detail
in <a class="reference internal" href="compute_sna_atom.html"><em>compute sna/atom</em></a>.</p>
<p>Note that unlike for other potentials, cutoffs for SNAP potentials are
not set in the pair_style or pair_coeff command; they are specified in
the SNAP potential files themselves.</p>
<p>Only a single pair_coeff command is used with the <em>snap</em> style which
specifies two SNAP files and the list SNAP element(s) to be
extracted.
The SNAP elements are mapped to LAMMPS atom types by specifying
N additional arguments after the 2nd filename in the pair_coeff
command, where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>SNAP element file</li>
<li>Elem1, Elem2, ...</li>
<li>SNAP parameter file</li>
<li>N element names = mapping of SNAP elements to atom types</li>
</ul>
<p>As an example, if a LAMMPS indium phosphide simulation has 4 atoms
types, with the first two being indium and the 3rd and 4th being
phophorous, the pair_coeff command would look like this:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The two filenames are for the element and parameter files, respectively.
The &#8216;In&#8217; and &#8216;P&#8217; arguments (between the file names) are the two elements
which will be extracted from the element file. The
two trailing &#8216;In&#8217; arguments map LAMMPS atom types 1 and 2 to the
SNAP &#8216;In&#8217; element. The two trailing &#8216;P&#8217; arguments map LAMMPS atom types
3 and 4 to the SNAP &#8216;P&#8217; element.</p>
<p>If a SNAP mapping value is
specified as NULL, the mapping is not performed.
This can be used when a <em>snap</em> potential is used as part of the
<em>hybrid</em> pair style. The NULL values are placeholders for atom types
that will be used with other potentials.</p>
<p>The name of the SNAP element file usually ends in the
&#8221;.snapcoeff&#8221; extension. It may contain coefficients
for many SNAP elements.
Only those elements listed in the pair_coeff command are extracted.
The name of the SNAP parameter file usually ends in the &#8221;.snapparam&#8221;
extension. It contains a small number
of parameters that define the overall form of the SNAP potential.
See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc page for alternate ways
to specify the path for these files.</p>
<p>Quite commonly,
SNAP potentials are combined with one or more other LAMMPS pair styles
using the <em>hybrid/overlay</em> pair style. As an example, the SNAP
tantalum potential provided in the LAMMPS potentials directory
combines the <em>snap</em> and <em>zbl</em> pair styles. It is invoked
by the following commands:</p>
<div class="highlight-python"><div class="highlight"><pre>variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 73
pair_style hybrid/overlay &amp;
zbl ${zblcutinner} ${zblcutouter} snap
pair_coeff * * zbl 0.0
pair_coeff 1 1 zbl ${zblz}
pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &amp;
../potentials/Ta06A.snapparam Ta
</pre></div>
</div>
<p>It is convenient to keep these commands in a separate file that can
be inserted in any LAMMPS input script using the <a class="reference internal" href="include.html"><em>include</em></a>
command.</p>
<p>The top of the SNAP element file can contain any number of blank and comment
lines (start with #), but follows a strict
format after that. The first non-blank non-comment
line must contain two integers:</p>
<ul class="simple">
<li>nelem = Number of elements</li>
<li>ncoeff = Number of coefficients</li>
</ul>
<p>This is followed by one block for each of the <em>nelem</em> elements.
The first line of each block contains three entries:</p>
<ul class="simple">
<li>Element symbol (text string)</li>
<li>R = Element radius (distance units)</li>
<li>w = Element weight (dimensionless)</li>
</ul>
<p>This line is followed by <em>ncoeff</em> coefficients, one per line.</p>
<p>The SNAP parameter file can contain blank and comment lines (start
with #) anywhere. Each non-blank non-comment line must contain one
keyword/value pair. The required keywords are <em>rcutfac</em> and
<em>twojmax</em>. Optional keywords are <em>rfac0</em>, <em>rmin0</em>, <em>diagonalstyle</em>,
and <em>switchflag</em>.</p>
<p>The default values for these keywords are</p>
<ul class="simple">
<li><em>rfac0</em> = 0.99363</li>
<li><em>rmin0</em> = 0.0</li>
<li><em>diagonalstyle</em> = 3</li>
<li><em>switchflag</em> = 0</li>
</ul>
<p>Detailed definitions of these keywords are given on the <a class="reference internal" href="compute_sna_atom.html"><em>compute sna/atom</em></a> doc page.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS with
user-specifiable parameters as described above. You never need to
specify a pair_coeff command with I != J arguments for this style.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This style is part of the SNAP package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</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="compute_sna_atom.html"><em>compute sna/atom</em></a>,
<a class="reference internal" href="compute_sna_atom.html"><em>compute snad/atom</em></a>,
<a class="reference internal" href="compute_sna_atom.html"><em>compute snav/atom</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="thompson2014"><strong>(Thompson)</strong> Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
available at <a class="reference external" href="http://arxiv.org/abs/1409.3880">arXiv:1409.3880</a></p>
<p id="bartok2010"><strong>(Bartok2010)</strong> Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).</p>
<p id="bartok2013"><strong>(Bartok2013)</strong> Bartok, Gillan, Manby, Csanyi, Phys Rev B 87, 184115 (2013).</p>
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<div class="section" id="pair-style-soft-command">
<span id="index-0"></span><h1>pair_style soft command<a class="headerlink" href="#pair-style-soft-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-soft-gpu-command">
<h1>pair_style soft/gpu command<a class="headerlink" href="#pair-style-soft-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-soft-omp-command">
<h1>pair_style soft/omp command<a class="headerlink" href="#pair-style-soft-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 soft cutoff
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for soft interactions (distance units)</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 soft 1.0
pair_coeff * * 10.0
pair_coeff 1 1 10.0 3.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style soft 1.0
pair_coeff * * 0.0
variable prefactor equal ramp(0,30)
fix 1 all adapt 1 pair soft a * * v_prefactor
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>soft</em> computes pairwise interactions with the formula</p>
<img alt="_images/pair_soft.jpg" class="align-center" src="_images/pair_soft.jpg" />
<p>It is useful for pushing apart overlapping atoms, since it does not
blow up as r goes to 0. A is a pre-factor that can be made to vary in
time from the start to the end of the run (see discussion below),
e.g. to start with a very soft potential and slowly harden the
interactions over time. Rc is the cutoff. See the <a class="reference internal" href="fix_nve_limit.html"><em>fix nve/limit</em></a> command for another way to push apart
overlapping atoms.</p>
<p>The following coefficients must be defined for each pair of atom types
via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above,
or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>A (energy units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global soft
cutoff is used.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The syntax for <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> with a single A
coeff is different in the current version of LAMMPS than in older
versions which took two values, Astart and Astop, to ramp between
them. This functionality is now available in a more general form
through the <a class="reference internal" href="fix_adapt.html"><em>fix adapt</em></a> command, as explained below.
Note that if you use an old input script and specify Astart and Astop
without a cutoff, then LAMMPS will interpret that as A and a cutoff,
which is probabably not what you want.</p>
</div>
<p>The <a class="reference internal" href="fix_adapt.html"><em>fix adapt</em></a> command can be used to vary A for one
or more pair types over the course of a simulation, in which case
pair_coeff settings for A must still be specified, but will be
overridden. For example these commands will vary the prefactor A for
all pairwise interactions from 0.0 at the beginning to 30.0 at the end
of a run:</p>
<div class="highlight-python"><div class="highlight"><pre>variable prefactor equal ramp(0,30)
fix 1 all adapt 1 pair soft a * * v_prefactor
</pre></div>
</div>
<p>Note that a formula defined by an <a class="reference internal" href="variable.html"><em>equal-style variable</em></a>
can use the current timestep, elapsed time in the current run, elapsed
time since the beginning of a series of runs, as well as access other
variables.</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>For atom type pairs I,J and I != J, the A coefficient and cutoff
distance for this pair style can be mixed. A is always mixed via a
<em>geometric</em> rule. The cutoff is mixed according to the pair_modify
mix value. The default mix value is <em>geometric</em>. See the
&#8220;pair_modify&#8221; command for details.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option, since the pair interaction goes to 0.0 at the cutoff.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table and tail options are not
relevant for this pair style.</p>
<p>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</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>, <a class="reference internal" href="fix_nve_limit.html"><em>fix nve/limit</em></a>, <a class="reference internal" href="fix_adapt.html"><em>fix adapt</em></a></p>
<p><strong>Default:</strong> none</p>
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<span id="index-0"></span><h1>pair_style sph/heatconduction command<a class="headerlink" href="#pair-style-sph-heatconduction-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 sph/heatconduction
</pre></div>
</div>
</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 sph/heatconduction
pair_coeff * * 1.0 2.4
</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 sph/heatconduction style computes heat transport between SPH particles.
The transport model is the diffusion euqation for the internal energy.</p>
<p>See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to using SPH in
LAMMPS.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above.</p>
<ul class="simple">
<li>D diffusion coefficient (length^2/time units)</li>
<li>h kernel function cutoff (distance units)</li>
</ul>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>This style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This style does not write information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. Thus, you need to re-specify the pair_style and
pair_coeff commands in an input script that reads a restart file.</p>
<p>This style 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. It does not support the <em>inner</em>,
<em>middle</em>, <em>outer</em> keywords.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style is part of the USER-SPH package. It is only enabled
if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</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>, pair_sph/rhosum</p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="pair-style-sph-idealgas-command">
<span id="index-0"></span><h1>pair_style sph/idealgas command<a class="headerlink" href="#pair-style-sph-idealgas-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 sph/idealgas
</pre></div>
</div>
</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 sph/idealgas
pair_coeff * * 1.0 2.4
</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 sph/idealgas style computes pressure forces between particles
according to the ideal gas equation of state:</p>
<img alt="_images/pair_sph_ideal.jpg" class="align-center" src="_images/pair_sph_ideal.jpg" />
<p>where gamma = 1.4 is the heat capacity ratio, rho is the local
density, and e is the internal energy per unit mass. This pair style
also computes Monaghan&#8217;s artificial viscosity to prevent particles
from interpentrating <a class="reference internal" href="pair_sph_taitwater.html#monoghan"><span>(Monaghan)</span></a>.</p>
<p>See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to using SPH in
LAMMPS.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above.</p>
<ul class="simple">
<li>nu artificial viscosity (no units)</li>
<li>h kernel function cutoff (distance units)</li>
</ul>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>This style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This style does not write information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. Thus, you need to re-specify the pair_style and
pair_coeff commands in an input script that reads a restart file.</p>
<p>This style 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. It does not support the <em>inner</em>,
<em>middle</em>, <em>outer</em> keywords.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style is part of the USER-SPH package. It is only enabled
if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</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>, pair_sph/rhosum</p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="monoghan"><strong>(Monaghan)</strong> Monaghan and Gingold, Journal of Computational Physics,
52, 374-389 (1983).</p>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<div class="section" id="pair-style-sph-lj-command">
<span id="index-0"></span><h1>pair_style sph/lj command<a class="headerlink" href="#pair-style-sph-lj-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 sph/lj
</pre></div>
</div>
</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 sph/lj
pair_coeff * * 1.0 2.4
</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 sph/lj style computes pressure forces between particles according
to the Lennard-Jones equation of state, which is computed according to
Ree&#8217;s 1980 polynomial fit <a class="reference internal" href="#ree"><span>(Ree)</span></a>. The Lennard-Jones parameters
epsilon and sigma are set to unity. This pair style also computes
Monaghan&#8217;s artificial viscosity to prevent particles from
interpentrating <a class="reference internal" href="pair_sph_taitwater.html#monoghan"><span>(Monaghan)</span></a>.</p>
<p>See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to using SPH in
LAMMPS.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above.</p>
<ul class="simple">
<li>nu artificial viscosity (no units)</li>
<li>h kernel function cutoff (distance units)</li>
</ul>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>This style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This style does not write information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. Thus, you need to re-specify the pair_style and
pair_coeff commands in an input script that reads a restart file.</p>
<p>This style 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. It does not support the <em>inner</em>,
<em>middle</em>, <em>outer</em> keywords.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>As noted above, the Lennard-Jones parameters epsilon and sigma are set
to unity.</p>
<p>This pair style is part of the USER-SPH package. It is only enabled
if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</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>, pair_sph/rhosum</p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="ree"><strong>(Ree)</strong> Ree, Journal of Chemical Physics, 73, 5401 (1980).</p>
<p id="monoghan"><strong>(Monaghan)</strong> Monaghan and Gingold, Journal of Computational Physics,
52, 374-389 (1983).</p>
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<div class="section" id="pair-style-sph-rhosum-command">
<span id="index-0"></span><h1>pair_style sph/rhosum command<a class="headerlink" href="#pair-style-sph-rhosum-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 sph/rhosum Nstep
</pre></div>
</div>
<ul class="simple">
<li>Nstep = timestep interval</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 sph/rhosum 10
pair_coeff * * 2.4
</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 sph/rhosum style computes the local particle mass density rho for
SPH particles by kernel function interpolation, every Nstep timesteps.</p>
<p>See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to using SPH in
LAMMPS.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above.</p>
<ul class="simple">
<li>h (distance units)</li>
</ul>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>This style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This style does not write information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. Thus, you need to re-specify the pair_style and
pair_coeff commands in an input script that reads a restart file.</p>
<p>This style 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. It does not support the <em>inner</em>,
<em>middle</em>, <em>outer</em> keywords.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style is part of the USER-SPH package. It is only enabled
if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</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>, pair_sph/taitwater</p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="pair-style-sph-taitwater-command">
<span id="index-0"></span><h1>pair_style sph/taitwater command<a class="headerlink" href="#pair-style-sph-taitwater-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 sph/taitwater
</pre></div>
</div>
</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 sph/taitwater
pair_coeff * * 1000.0 1430.0 1.0 2.4
</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 sph/taitwater style computes pressure forces between SPH particles
according to Tait&#8217;s equation of state:</p>
<img alt="_images/pair_sph_tait.jpg" class="align-center" src="_images/pair_sph_tait.jpg" />
<p>where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the
reference density and c_0 the reference speed of sound.</p>
<p>This pair style also computes Monaghan&#8217;s artificial viscosity to
prevent particles from interpentrating <span class="xref std std-ref">(Monaghan)</span>.</p>
<p>See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to using SPH in
LAMMPS.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above.</p>
<ul class="simple">
<li>rho0 reference density (mass/volume units)</li>
<li>c0 reference soundspeed (distance/time units)</li>
<li>nu artificial viscosity (no units)</li>
<li>h kernel function cutoff (distance units)</li>
</ul>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>This style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This style does not write information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. Thus, you need to re-specify the pair_style and
pair_coeff commands in an input script that reads a restart file.</p>
<p>This style 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. It does not support the <em>inner</em>,
<em>middle</em>, <em>outer</em> keywords.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style is part of the USER-SPH package. It is only enabled
if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</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>, pair_sph/rhosum</p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="monoghan"><strong>(Monaghan)</strong> Monaghan and Gingold, Journal of Computational Physics,
52, 374-389 (1983).</p>
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<div class="section" id="pair-style-sph-taitwater-morris-command">
<span id="index-0"></span><h1>pair_style sph/taitwater/morris command<a class="headerlink" href="#pair-style-sph-taitwater-morris-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 sph/taitwater/morris
</pre></div>
</div>
</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 sph/taitwater/morris
pair_coeff * * 1000.0 1430.0 1.0 2.4
</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 sph/taitwater/morris style computes pressure forces between SPH
particles according to Tait&#8217;s equation of state:</p>
<img alt="_images/pair_sph_tait.jpg" class="align-center" src="_images/pair_sph_tait.jpg" />
<p>where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the
reference density and c_0 the reference speed of sound.</p>
<p>This pair style also computes laminar viscosity <a class="reference internal" href="#morris"><span>(Morris)</span></a>.</p>
<p>See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to using SPH in
LAMMPS.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above.</p>
<ul class="simple">
<li>rho0 reference density (mass/volume units)</li>
<li>c0 reference soundspeed (distance/time units)</li>
<li>nu dynamic viscosity (mass*distance/time units)</li>
<li>h kernel function cutoff (distance units)</li>
</ul>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>This style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This style does not write information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. Thus, you need to re-specify the pair_style and
pair_coeff commands in an input script that reads a restart file.</p>
<p>This style 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. It does not support the <em>inner</em>,
<em>middle</em>, <em>outer</em> keywords.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style is part of the USER-SPH package. It is only enabled
if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</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>, pair_sph/rhosum</p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="morris"><strong>(Morris)</strong> Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997).</p>
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<div class="section" id="pair-style-srp-command">
<span id="index-0"></span><h1>pair_style srp command<a class="headerlink" href="#pair-style-srp-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>
<p>pair_style srp cutoff btype dist keyword value ...</p>
<ul class="simple">
<li>cutoff = global cutoff for SRP interactions (distance units)</li>
<li>btype = bond type to apply SRP interactions to (can be wildcard, see below)</li>
<li>distance = <em>min</em> or <em>mid</em></li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>exclude</em></li>
</ul>
<pre class="literal-block">
<em>bptype</em> value = atom type for bond particles
<em>exclude</em> value = <em>yes</em> or <em>no</em>
</pre>
</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 dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
pair_coeff 1 1 dpd 60.0 4.5 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0 0.8
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
pair_coeff 1 1 dpd 60.0 50 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp 40.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid srp 0.8 2 mid
pair_coeff 1 1 none
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0 0.8
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>srp</em> computes a soft segmental repulsive potential (SRP) that
acts between pairs of bonds. This potential is useful for preventing
bonds from passing through one another when a soft non-bonded
potential acts between beads in, for example, DPD polymer chains. An
example input script that uses this command is provided in
examples/USER/srp.</p>
<p>Bonds of specified type <em>btype</em> interact with one another through a
bond-pairwise potential, such that the force on bond <em>i</em> due to bond
<em>j</em> is as follows</p>
<img alt="_images/pair_srp1.jpg" class="align-center" src="_images/pair_srp1.jpg" />
<p>where <em>r</em> and <em>rij</em> are the distance and unit vector between the two
bonds. Note that <em>btype</em> can be specified as an asterisk &#8220;*&#8221;, which
case the interaction is applied to all bond types. The <em>mid</em> option
computes <em>r</em> and <em>rij</em> from the midpoint distance between bonds. The
<em>min</em> option computes <em>r</em> and <em>rij</em> from the minimum distance between
bonds. The force acting on a bond is mapped onto the two bond atoms
according to the lever rule,</p>
<img alt="_images/pair_srp2.jpg" class="align-center" src="_images/pair_srp2.jpg" />
<p>where <em>L</em> is the normalized distance from the atom to the point of
closest approach of bond <em>i</em> and <em>j</em>. The <em>mid</em> option takes <em>L</em> as
0.5 for each interaction as described in <a class="reference internal" href="#sirk"><span>(Sirk)</span></a>.</p>
<p>The following coefficients must be defined via the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above, or in
the data file or restart file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li><em>C</em> (force units)</li>
<li><em>rc</em> (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global cutoff
is used.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Pair style srp considers each bond of type <em>btype</em> to be a
fictitious &#8220;particle&#8221; of type <em>bptype</em>, where <em>bptype</em> is either the
largest atom type in the system, or the type set by the <em>bptype</em> flag.
Any actual existing particles with this atom type will be deleted at
the beginning of a run. This means you must specify the number of
types in your system accordingly; usually to be one larger than what
would normally be the case, e.g. via the <a class="reference internal" href="create_box.html"><em>create_box</em></a>
or by changing the header in your <a class="reference internal" href="read_data.html"><em>data file</em></a>. The
ficitious &#8220;bond particles&#8221; are inserted at the beginning of the run,
and serve as placeholders that define the position of the bonds. This
allows neighbor lists to be constructed and pairwise interactions to
be computed in almost the same way as is done for actual particles.
Because bonds interact only with other bonds, <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> should be used to turn off interactions
between atom type <em>bptype</em> and all other types of atoms. An error
will be flagged if <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> is not used.</p>
</div>
<p>The optional <em>exclude</em> keyword determines if forces are computed
between first neighbor (directly connected) bonds. For a setting of
<em>no</em>, first neighbor forces are computed; for <em>yes</em> they are not
computed. A setting of <em>no</em> cannot be used with the <em>min</em> option for
distance calculation because the the minimum distance between directly
connected bonds is zero.</p>
<p>Pair style <em>srp</em> turns off normalization of thermodynamic properties
by particle number, as if the command <a class="reference internal" href="thermo_modify.html"><em>thermo_modify norm no</em></a> had been issued.</p>
<p>The pairwise energy associated with style <em>srp</em> is shifted to be zero
at the cutoff distance <em>rc</em>.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair styles does not support mixing.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option for the energy of the pair interaction. Note that as
discussed above, the energy term is already shifted to be 0.0 at the
cutoff distance <em>rc</em>.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant for
this pair style.</p>
<p>This pair style does 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>This pair style writes global and per-atom information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. Pair srp should be used with <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a>, thus the pair_coeff commands need to be
specified in the input script when reading a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style is part of the USER-MISC package. It is only enabled
if LAMMPS was built with that package. See the Making LAMMPS section
for more info.</p>
<p>This pair style must be used with <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a>.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><em>newton</em></a> command to be <em>on</em>
for non-bonded interactions.</p>
</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_hybrid.html"><em>pair_style hybrid</em></a>, <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>,
<a class="reference internal" href="pair_dpd.html"><em>pair dpd</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The default keyword value is exclude = yes.</p>
<hr class="docutils" />
<p id="sirk"><strong>(Sirk)</strong> Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J
Chem Phys, 136 (13) 134903, 2012.</p>
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<div class="section" id="pair-style-command">
<span id="index-0"></span><h1>pair_style command<a class="headerlink" href="#pair-style-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 args
</pre></div>
</div>
<ul class="simple">
<li>style = one of the styles from the list below</li>
<li>args = arguments used by a particular style</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 lj/cut 2.5
pair_style eam/alloy
pair_style hybrid lj/charmm/coul/long 10.0 eam
pair_style table linear 1000
pair_style none
</pre></div>
</div>
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<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Set the formula(s) LAMMPS uses to compute pairwise interactions. In
LAMMPS, pair potentials are defined between pairs of atoms that are
within a cutoff distance and the set of active interactions typically
changes over time. See the <a class="reference internal" href="bond_style.html"><em>bond_style</em></a> command to
define potentials between pairs of bonded atoms, which typically
remain in place for the duration of a simulation.</p>
<p>In LAMMPS, pairwise force fields encompass a variety of interactions,
some of which include many-body effects, e.g. EAM, Stillinger-Weber,
Tersoff, REBO potentials. They are still classified as &#8220;pairwise&#8221;
potentials because the set of interacting atoms changes with time
(unlike molecular bonds) and thus a neighbor list is used to find
nearby interacting atoms.</p>
<p>Hybrid models where specified pairs of atom types interact via
different pair potentials can be setup using the <em>hybrid</em> pair style.</p>
<p>The coefficients associated with a pair style are typically set for
each pair of atom types, and are specified by the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command or read from a file by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> command sets options for mixing of
type I-J interaction coefficients and adding energy offsets or tail
corrections to Lennard-Jones potentials. Details on these options as
they pertain to individual potentials are described on the doc page
for the potential. Likewise, info on whether the potential
information is stored in a <a class="reference internal" href="write_restart.html"><em>restart file</em></a> is listed
on the potential doc page.</p>
<p>In the formulas listed for each pair style, <em>E</em> is the energy of a
pairwise interaction between two atoms separated by a distance <em>r</em>.
The force between the atoms is the negative derivative of this
expression.</p>
<p>If the pair_style command has a cutoff argument, it sets global
cutoffs for all pairs of atom types. The distance(s) can be smaller
or larger than the dimensions of the simulation box.</p>
<p>Typically, the global cutoff value can be overridden for a specific
pair of atom types by the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command. The
pair style settings (including global cutoffs) can be changed by a
subsequent pair_style command using the same style. This will reset
the cutoffs for all atom type pairs, including those previously set
explicitly by a <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command. The exceptions
to this are that pair_style <em>table</em> and <em>hybrid</em> settings cannot be
reset. A new pair_style command for these styles will wipe out all
previously specified pair_coeff values.</p>
<hr class="docutils" />
<p>Here is an alphabetic list of pair styles defined in LAMMPS. They are
also given in more compact form in the pair section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<p>Click on the style to display the formula it computes, arguments
specified in the pair_style command, and coefficients specified by the
associated <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command.</p>
<p>There are also additional pair styles (not listed here) submitted by
users which are included in the LAMMPS distribution. The list of
these with links to the individual styles are given in the pair
section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<p>There are also additional accelerated pair styles (not listed here)
included in the LAMMPS distribution for faster performance on CPUs and
GPUs. The list of these with links to the individual styles are given
in the pair section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<ul class="simple">
<li><a class="reference internal" href="pair_none.html"><em>pair_style none</em></a> - turn off pairwise interactions</li>
<li><a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> - multiple styles of pairwise interactions</li>
<li><a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a> - multiple styles of superposed pairwise interactions</li>
<li><a class="reference internal" href="pair_zero.html"><em>pair_style zero</em></a> - neighbor list but no interactions</li>
<li><a class="reference internal" href="pair_adp.html"><em>pair_style adp</em></a> - angular dependent potential (ADP) of Mishin</li>
<li><a class="reference internal" href="pair_airebo.html"><em>pair_style airebo</em></a> - AIREBO potential of Stuart</li>
<li><a class="reference internal" href="pair_airebo.html"><em>pair_style airebo/morse</em></a> - AIREBO with Morse instead of LJ</li>
<li><a class="reference internal" href="pair_beck.html"><em>pair_style beck</em></a> - Beck potential</li>
<li><a class="reference internal" href="pair_body.html"><em>pair_style body</em></a> - interactions between body particles</li>
<li><a class="reference internal" href="pair_bop.html"><em>pair_style bop</em></a> - BOP potential of Pettifor</li>
<li><a class="reference internal" href="pair_born.html"><em>pair_style born</em></a> - Born-Mayer-Huggins potential</li>
<li><a class="reference internal" href="pair_born.html"><em>pair_style born/coul/long</em></a> - Born-Mayer-Huggins with long-range Coulombics</li>
<li><a class="reference internal" href="pair_born.html"><em>pair_style born/coul/long/cs</em></a> - Born-Mayer-Huggins with long-range Coulombics and core/shell</li>
<li><a class="reference internal" href="pair_born.html"><em>pair_style born/coul/msm</em></a> - Born-Mayer-Huggins with long-range MSM Coulombics</li>
<li><a class="reference internal" href="pair_born.html"><em>pair_style born/coul/wolf</em></a> - Born-Mayer-Huggins with Coulombics via Wolf potential</li>
<li><a class="reference internal" href="pair_brownian.html"><em>pair_style brownian</em></a> - Brownian potential for Fast Lubrication Dynamics</li>
<li><a class="reference internal" href="pair_brownian.html"><em>pair_style brownian/poly</em></a> - Brownian potential for Fast Lubrication Dynamics with polydispersity</li>
<li><a class="reference internal" href="pair_buck.html"><em>pair_style buck</em></a> - Buckingham potential</li>
<li><a class="reference internal" href="pair_buck.html"><em>pair_style buck/coul/cut</em></a> - Buckingham with cutoff Coulomb</li>
<li><a class="reference internal" href="pair_buck.html"><em>pair_style buck/coul/long</em></a> - Buckingham with long-range Coulombics</li>
<li><a class="reference internal" href="pair_buck.html"><em>pair_style buck/coul/long/cs</em></a> - Buckingham with long-range Coulombics and core/shell</li>
<li><a class="reference internal" href="pair_buck.html"><em>pair_style buck/coul/msm</em></a> - Buckingham long-range MSM Coulombics</li>
<li><a class="reference internal" href="pair_buck_long.html"><em>pair_style buck/long/coul/long</em></a> - long-range Buckingham with long-range Coulombics</li>
<li><a class="reference internal" href="pair_colloid.html"><em>pair_style colloid</em></a> - integrated colloidal potential</li>
<li><a class="reference internal" href="pair_comb.html"><em>pair_style comb</em></a> - charge-optimized many-body (COMB) potential</li>
<li><a class="reference internal" href="pair_comb.html"><em>pair_style comb3</em></a> - charge-optimized many-body (COMB3) potential</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style coul/cut</em></a> - cutoff Coulombic potential</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style coul/debye</em></a> - cutoff Coulombic potential with Debye screening</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style coul/dsf</em></a> - Coulombics via damped shifted forces</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style coul/long</em></a> - long-range Coulombic potential</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style coul/long/cs</em></a> - long-range Coulombic potential and core/shell</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style coul/msm</em></a> - long-range MSM Coulombics</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style coul/streitz</em></a> - Coulombics via Streitz/Mintmire Slater orbitals</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style coul/wolf</em></a> - Coulombics via Wolf potential</li>
<li><a class="reference internal" href="pair_dpd.html"><em>pair_style dpd</em></a> - dissipative particle dynamics (DPD)</li>
<li><a class="reference internal" href="pair_dpd.html"><em>pair_style dpd/tstat</em></a> - DPD thermostatting</li>
<li><a class="reference internal" href="pair_dsmc.html"><em>pair_style dsmc</em></a> - Direct Simulation Monte Carlo (DSMC)</li>
<li><a class="reference internal" href="pair_eam.html"><em>pair_style eam</em></a> - embedded atom method (EAM)</li>
<li><a class="reference internal" href="pair_eam.html"><em>pair_style eam/alloy</em></a> - alloy EAM</li>
<li><a class="reference internal" href="pair_eam.html"><em>pair_style eam/fs</em></a> - Finnis-Sinclair EAM</li>
<li><a class="reference internal" href="pair_eim.html"><em>pair_style eim</em></a> - embedded ion method (EIM)</li>
<li><a class="reference internal" href="pair_gauss.html"><em>pair_style gauss</em></a> - Gaussian potential</li>
<li><a class="reference internal" href="pair_gayberne.html"><em>pair_style gayberne</em></a> - Gay-Berne ellipsoidal potential</li>
<li><a class="reference internal" href="pair_gran.html"><em>pair_style gran/hertz/history</em></a> - granular potential with Hertzian interactions</li>
<li><a class="reference internal" href="pair_gran.html"><em>pair_style gran/hooke</em></a> - granular potential with history effects</li>
<li><a class="reference internal" href="pair_gran.html"><em>pair_style gran/hooke/history</em></a> - granular potential without history effects</li>
<li><a class="reference internal" href="pair_hbond_dreiding.html"><em>pair_style hbond/dreiding/lj</em></a> - DREIDING hydrogen bonding LJ potential</li>
<li><a class="reference internal" href="pair_hbond_dreiding.html"><em>pair_style hbond/dreiding/morse</em></a> - DREIDING hydrogen bonding Morse potential</li>
<li><a class="reference internal" href="pair_kim.html"><em>pair_style kim</em></a> - interface to potentials provided by KIM project</li>
<li><a class="reference internal" href="pair_lcbop.html"><em>pair_style lcbop</em></a> - long-range bond-order potential (LCBOP)</li>
<li><a class="reference internal" href="pair_line_lj.html"><em>pair_style line/lj</em></a> - LJ potential between line segments</li>
<li><a class="reference internal" href="pair_charmm.html"><em>pair_style lj/charmm/coul/charmm</em></a> - CHARMM potential with cutoff Coulomb</li>
<li><a class="reference internal" href="pair_charmm.html"><em>pair_style lj/charmm/coul/charmm/implicit</em></a> - CHARMM for implicit solvent</li>
<li><a class="reference internal" href="pair_charmm.html"><em>pair_style lj/charmm/coul/long</em></a> - CHARMM with long-range Coulomb</li>
<li><a class="reference internal" href="pair_charmm.html"><em>pair_style lj/charmm/coul/msm</em></a> - CHARMM with long-range MSM Coulombics</li>
<li><a class="reference internal" href="pair_class2.html"><em>pair_style lj/class2</em></a> - COMPASS (class 2) force field with no Coulomb</li>
<li><a class="reference internal" href="pair_class2.html"><em>pair_style lj/class2/coul/cut</em></a> - COMPASS with cutoff Coulomb</li>
<li><a class="reference internal" href="pair_class2.html"><em>pair_style lj/class2/coul/long</em></a> - COMPASS with long-range Coulomb</li>
<li><a class="reference internal" href="pair_lj_cubic.html"><em>pair_style lj/cubic</em></a> - LJ with cubic after inflection point</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut</em></a> - cutoff Lennard-Jones potential with no Coulomb</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/cut</em></a> - LJ with cutoff Coulomb</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/debye</em></a> - LJ with Debye screening added to Coulomb</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/dsf</em></a> - LJ with Coulombics via damped shifted forces</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/long</em></a> - LJ with long-range Coulombics</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/long/cs</em></a> - LJ with long-range Coulombics and core/shell</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/msm</em></a> - LJ with long-range MSM Coulombics</li>
<li><a class="reference internal" href="pair_dipole.html"><em>pair_style lj/cut/dipole/cut</em></a> - point dipoles with cutoff</li>
<li><a class="reference internal" href="pair_dipole.html"><em>pair_style lj/cut/dipole/long</em></a> - point dipoles with long-range Ewald</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/tip4p/cut</em></a> - LJ with cutoff Coulomb for TIP4P water</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/tip4p/long</em></a> - LJ with long-range Coulomb for TIP4P water</li>
<li><a class="reference internal" href="pair_lj_expand.html"><em>pair_style lj/expand</em></a> - Lennard-Jones for variable size particles</li>
<li><a class="reference internal" href="pair_gromacs.html"><em>pair_style lj/gromacs</em></a> - GROMACS-style Lennard-Jones potential</li>
<li><a class="reference internal" href="pair_gromacs.html"><em>pair_style lj/gromacs/coul/gromacs</em></a> - GROMACS-style LJ and Coulombic potential</li>
<li><a class="reference internal" href="pair_lj_long.html"><em>pair_style lj/long/coul/long</em></a> - long-range LJ and long-range Coulombics</li>
<li><a class="reference internal" href="pair_dipole.html"><em>pair_style lj/long/dipole/long</em></a> - long-range LJ and long-range point dipoles</li>
<li><a class="reference internal" href="pair_lj_long.html"><em>pair_style lj/long/tip4p/long</em></a> - long-range LJ and long-range Coulomb for TIP4P water</li>
<li><a class="reference internal" href="pair_lj_smooth.html"><em>pair_style lj/smooth</em></a> - smoothed Lennard-Jones potential</li>
<li><a class="reference internal" href="pair_lj_smooth_linear.html"><em>pair_style lj/smooth/linear</em></a> - linear smoothed Lennard-Jones potential</li>
<li><a class="reference internal" href="pair_lj96.html"><em>pair_style lj96/cut</em></a> - Lennard-Jones 9/6 potential</li>
<li><a class="reference internal" href="pair_lubricate.html"><em>pair_style lubricate</em></a> - hydrodynamic lubrication forces</li>
<li><a class="reference internal" href="pair_lubricate.html"><em>pair_style lubricate/poly</em></a> - hydrodynamic lubrication forces with polydispersity</li>
<li><a class="reference internal" href="pair_lubricateU.html"><em>pair_style lubricateU</em></a> - hydrodynamic lubrication forces for Fast Lubrication Dynamics</li>
<li><a class="reference internal" href="pair_lubricateU.html"><em>pair_style lubricateU/poly</em></a> - hydrodynamic lubrication forces for Fast Lubrication with polydispersity</li>
<li><a class="reference internal" href="pair_meam.html"><em>pair_style meam</em></a> - modified embedded atom method (MEAM)</li>
<li><a class="reference internal" href="pair_mie.html"><em>pair_style mie/cut</em></a> - Mie potential</li>
<li><a class="reference internal" href="pair_morse.html"><em>pair_style morse</em></a> - Morse potential</li>
<li><a class="reference internal" href="pair_nb3b_harmonic.html"><em>pair_style nb3b/harmonic</em></a> - nonbonded 3-body harmonic potential</li>
<li><a class="reference internal" href="pair_nm.html"><em>pair_style nm/cut</em></a> - N-M potential</li>
<li><a class="reference internal" href="pair_nm.html"><em>pair_style nm/cut/coul/cut</em></a> - N-M potential with cutoff Coulomb</li>
<li><a class="reference internal" href="pair_nm.html"><em>pair_style nm/cut/coul/long</em></a> - N-M potential with long-range Coulombics</li>
<li><a class="reference internal" href="pair_peri.html"><em>pair_style peri/eps</em></a> - peridynamic EPS potential</li>
<li><a class="reference internal" href="pair_peri.html"><em>pair_style peri/lps</em></a> - peridynamic LPS potential</li>
<li><a class="reference internal" href="pair_peri.html"><em>pair_style peri/pmb</em></a> - peridynamic PMB potential</li>
<li><a class="reference internal" href="pair_peri.html"><em>pair_style peri/ves</em></a> - peridynamic VES potential</li>
<li><a class="reference internal" href="pair_polymorphic.html"><em>pair_style polymorphic</em></a> - polymorphic 3-body potential</li>
<li><a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a> - ReaxFF potential</li>
<li><a class="reference internal" href="pair_airebo.html"><em>pair_style rebo</em></a> - 2nd generation REBO potential of Brenner</li>
<li><a class="reference internal" href="pair_resquared.html"><em>pair_style resquared</em></a> - Everaers RE-Squared ellipsoidal potential</li>
<li><a class="reference internal" href="pair_snap.html"><em>pair_style snap</em></a> - SNAP quantum-accurate potential</li>
<li><a class="reference internal" href="pair_soft.html"><em>pair_style soft</em></a> - Soft (cosine) potential</li>
<li><a class="reference internal" href="pair_sw.html"><em>pair_style sw</em></a> - Stillinger-Weber 3-body potential</li>
<li><a class="reference internal" href="pair_table.html"><em>pair_style table</em></a> - tabulated pair potential</li>
<li><a class="reference internal" href="pair_tersoff.html"><em>pair_style tersoff</em></a> - Tersoff 3-body potential</li>
<li><a class="reference internal" href="pair_tersoff_mod.html"><em>pair_style tersoff/mod</em></a> - modified Tersoff 3-body potential</li>
<li><a class="reference internal" href="pair_tersoff_zbl.html"><em>pair_style tersoff/zbl</em></a> - Tersoff/ZBL 3-body potential</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style tip4p/cut</em></a> - Coulomb for TIP4P water w/out LJ</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style tip4p/long</em></a> - long-range Coulombics for TIP4P water w/out LJ</li>
<li><a class="reference internal" href="pair_tri_lj.html"><em>pair_style tri/lj</em></a> - LJ potential between triangles</li>
<li><a class="reference internal" href="pair_vashishta.html"><em>pair_style vashishta</em></a> - Vashishta 2-body and 3-body potential</li>
<li><a class="reference internal" href="pair_yukawa.html"><em>pair_style yukawa</em></a> - Yukawa potential</li>
<li><a class="reference internal" href="pair_yukawa_colloid.html"><em>pair_style yukawa/colloid</em></a> - screened Yukawa potential for finite-size particles</li>
<li><a class="reference internal" href="pair_zbl.html"><em>pair_style zbl</em></a> - Ziegler-Biersack-Littmark potential</li>
</ul>
</div>
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<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This command must be used before any coefficients are set by the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="read_data.html"><em>read_data</em></a>, or
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands.</p>
<p>Some pair styles are part of specific packages. They are only enabled
if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.
The doc pages for individual pair potentials tell if it is part of a
package.</p>
</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>, <a class="reference internal" href="read_data.html"><em>read_data</em></a>,
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>, <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a>,
<a class="reference internal" href="dielectric.html"><em>dielectric</em></a>, <a class="reference internal" href="pair_write.html"><em>pair_write</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style none
</pre></div>
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<div class="section" id="pair-style-sw-command">
<span id="index-0"></span><h1>pair_style sw command<a class="headerlink" href="#pair-style-sw-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-sw-cuda-command">
<h1>pair_style sw/cuda command<a class="headerlink" href="#pair-style-sw-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-sw-gpu-command">
<h1>pair_style sw/gpu command<a class="headerlink" href="#pair-style-sw-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-sw-intel-command">
<h1>pair_style sw/intel command<a class="headerlink" href="#pair-style-sw-intel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-sw-kk-command">
<h1>pair_style sw/kk command<a class="headerlink" href="#pair-style-sw-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-sw-omp-command">
<h1>pair_style sw/omp command<a class="headerlink" href="#pair-style-sw-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 sw
</pre></div>
</div>
</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 sw
pair_coeff * * si.sw Si
pair_coeff * * GaN.sw Ga N Ga
</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>sw</em> style computes a 3-body <a class="reference internal" href="#stillinger"><span>Stillinger-Weber</span></a>
potential for the energy E of a system of atoms as</p>
<img alt="_images/pair_sw.jpg" class="align-center" src="_images/pair_sw.jpg" />
<p>where phi2 is a two-body term and phi3 is a three-body term. The
summations in the formula are over all neighbors J and K of atom I
within a cutoff distance = a*sigma.</p>
<p>Only a single pair_coeff command is used with the <em>sw</em> style which
specifies a Stillinger-Weber potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N element names = mapping of SW elements to atom types</li>
</ul>
<p>See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc page for alternate ways
to specify the path for the potential file.</p>
<p>As an example, imagine a file SiC.sw has Stillinger-Weber values for
Si and C. If your LAMMPS simulation has 4 atoms types and you want
the 1st 3 to be Si, and the 4th to be C, you would use the following
pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * SiC.sw Si Si Si C
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
element in the SW file. The final C argument maps LAMMPS atom type 4
to the C element in the SW file. If a mapping value is specified as
NULL, the mapping is not performed. This can be used when a <em>sw</em>
potential is used as part of the <em>hybrid</em> pair style. The NULL values
are placeholders for atom types that will be used with other
potentials.</p>
<p>Stillinger-Weber files in the <em>potentials</em> directory of the LAMMPS
distribution have a &#8221;.sw&#8221; suffix. Lines that are not blank or
comments (starting with #) define parameters for a triplet of
elements. The parameters in a single entry correspond to the two-body
and three-body coefficients in the formula above:</p>
<ul class="simple">
<li>element 1 (the center atom in a 3-body interaction)</li>
<li>element 2</li>
<li>element 3</li>
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>a</li>
<li>lambda</li>
<li>gamma</li>
<li>costheta0</li>
<li>A</li>
<li>B</li>
<li>p</li>
<li>q</li>
<li>tol</li>
</ul>
<p>The A, B, p, and q parameters are used only for two-body
interactions. The lambda and costheta0 parameters are used only for
three-body interactions. The epsilon, sigma and a parameters are used
for both two-body and three-body interactions. gamma is used only in the
three-body interactions, but is defined for pairs of atoms.
The non-annotated parameters are unitless.</p>
<p>LAMMPS introduces an additional performance-optimization parameter tol
that is used for both two-body and three-body interactions. In the
Stillinger-Weber potential, the interaction energies become negligibly
small at atomic separations substantially less than the theoretical
cutoff distances. LAMMPS therefore defines a virtual cutoff distance
based on a user defined tolerance tol. The use of the virtual cutoff
distance in constructing atom neighbor lists can significantly reduce
the neighbor list sizes and therefore the computational cost. LAMMPS
provides a <em>tol</em> value for each of the three-body entries so that they
can be separately controlled. If tol = 0.0, then the standard
Stillinger-Weber cutoff is used.</p>
<p>The Stillinger-Weber potential file must contain entries for all the
elements listed in the pair_coeff command. It can also contain
entries for additional elements not being used in a particular
simulation; LAMMPS ignores those entries.</p>
<p>For a single-element simulation, only a single entry is required
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
specify SW parameters for all permutations of the two elements
interacting in three-body configurations. Thus for 3 elements, 27
entries would be required, etc.</p>
<p>As annotated above, the first element in the entry is the center atom
in a three-body interaction. Thus an entry for SiCC means a Si atom
with 2 C atoms as neighbors. The parameter values used for the
two-body interaction come from the entry where the 2nd and 3rd
elements are the same. Thus the two-body parameters for Si
interacting with C, comes from the SiCC entry. The three-body
parameters can in principle be specific to the three elements of the
configuration. In the literature, however, the three-body parameters
are usually defined by simple formulas involving two sets of pair-wise
parameters, corresponding to the ij and ik pairs, where i is the
center atom. The user must ensure that the correct combining rule is
used to calculate the values of the threebody parameters for
alloys. Note also that the function phi3 contains two exponential
screening factors with parameter values from the ij pair and ik
pairs. So phi3 for a C atom bonded to a Si atom and a second C atom
will depend on the three-body parameters for the CSiC entry, and also
on the two-body parameters for the CCC and CSiSi entries. Since the
order of the two neighbors is arbitrary, the threebody parameters for
entries CSiC and CCSi should be the same. Similarly, the two-body
parameters for entries SiCC and CSiSi should also be the same. The
parameters used only for two-body interactions (A, B, p, and q) in
entries whose 2nd and 3rd element are different (e.g. SiCSi) are not
used for anything and can be set to 0.0 if desired.
This is also true for the parameters in phi3 that are
taken from the ij and ik pairs (sigma, a, gamma)</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>When using the USER-INTEL package with this style, there is an
additional 5 to 10 percent performance improvement when the
Stillinger-Weber parameters p and q are set to 4 and 0 respectively.
These parameters are common for modeling silicon and water.</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>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><em>newton</em></a> setting to be &#8220;on&#8221;
for pair interactions.</p>
<p>The Stillinger-Weber potential files provided with LAMMPS (see the
potentials directory) are parameterized for metal <a class="reference internal" href="units.html"><em>units</em></a>.
You can use the SW potential with any LAMMPS units, but you would need
to create your own SW potential file with coefficients listed in the
appropriate units if your simulation doesn&#8217;t use &#8220;metal&#8221; units.</p>
</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="stillinger"><strong>(Stillinger)</strong> Stillinger and Weber, Phys Rev B, 31, 5262 (1985).</p>
</div>
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<div class="section" id="pair-style-table-command">
<span id="index-0"></span><h1>pair_style table command<a class="headerlink" href="#pair-style-table-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-table-gpu-command">
<h1>pair_style table/gpu command<a class="headerlink" href="#pair-style-table-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-table-kk-command">
<h1>pair_style table/kk command<a class="headerlink" href="#pair-style-table-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-table-omp-command">
<h1>pair_style table/omp command<a class="headerlink" href="#pair-style-table-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 table style N keyword ...
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lookup</em> or <em>linear</em> or <em>spline</em> or <em>bitmap</em> = method of interpolation</li>
<li>N = use N values in <em>lookup</em>, <em>linear</em>, <em>spline</em> tables</li>
<li>N = use 2^N values in <em>bitmap</em> tables</li>
<li>zero or more keywords may be appended</li>
<li>keyword = <em>ewald</em> or <em>pppm</em> or <em>msm</em> or <em>dispersion</em> or <em>tip4p</em></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 table linear 1000
pair_style table linear 1000 pppm
pair_style table bitmap 12
pair_coeff * 3 morse.table ENTRY1
pair_coeff * 3 morse.table ENTRY1 7.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>table</em> creates interpolation tables from potential energy and
force values listed in a file(s) as a function of distance. When
performing dynamics or minimation, the interpolation tables are used
to evaluate energy and forces for pairwise interactions between
particles, similar to how analytic formulas are used for other pair
styles.</p>
<p>The interpolation tables are created as a pre-computation by fitting
cubic splines to the file values and interpolating energy and force
values at each of <em>N</em> distances. During a simulation, the tables are
used to interpolate energy and force values as needed for each pair of
particles separated by a distance <em>R</em>. The interpolation is done in
one of 4 styles: <em>lookup</em>, <em>linear</em>, <em>spline</em>, or <em>bitmap</em>.</p>
<p>For the <em>lookup</em> style, the distance <em>R</em> is used to find the nearest
table entry, which is the energy or force.</p>
<p>For the <em>linear</em> style, the distance <em>R</em> is used to find the 2
surrounding table values from which an energy or force is computed by
linear interpolation.</p>
<p>For the <em>spline</em> style, a cubic spline coefficients are computed and
stored for each of the <em>N</em> values in the table, one set of splines for
energy, another for force. Note that these splines are different than
the ones used to pre-compute the <em>N</em> values. Those splines were fit
to the <em>Nfile</em> values in the tabulated file, where often <em>Nfile</em> &lt;
<em>N</em>. The distance <em>R</em> is used to find the appropriate set of spline
coefficients which are used to evaluate a cubic polynomial which
computes the energy or force.</p>
<p>For the <em>bitmap</em> style, the specified <em>N</em> is used to create
interpolation tables that are 2^N in length. The distance <em>R</em> is used
to index into the table via a fast bit-mapping technique due to
<a class="reference internal" href="#wolff"><span>(Wolff)</span></a>, and a linear interpolation is performed between
adjacent table values.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above.</p>
<ul class="simple">
<li>filename</li>
<li>keyword</li>
<li>cutoff (distance units)</li>
</ul>
<p>The filename specifies a file containing tabulated energy and force
values. The keyword specifies a section of the file. The cutoff is
an optional coefficient. If not specified, the outer cutoff in the
table itself (see below) will be used to build an interpolation table
that extend to the largest tabulated distance. If specified, only
file values up to the cutoff are used to create the interpolation
table. The format of this file is described below.</p>
<p>If your tabulated potential(s) are designed to be used as the
short-range part of one of the long-range solvers specified by the
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command, then you must use one or
more of the optional keywords listed above for the pair_style command.
These are <em>ewald</em> or <em>pppm</em> or <em>msm</em> or <em>dispersion</em> or <em>tip4p</em>. This
is so LAMMPS can insure the short-range potential and long-range
solver are compatible with each other, as it does for other
short-range pair styles, such as <a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/long</em></a>. Note that it is up to you to insure
the tabulated values for each pair of atom types has the correct
functional form to be compatible with the matching long-range solver.</p>
<hr class="docutils" />
<p>Here are some guidelines for using the pair_style table command to
best effect:</p>
<ul class="simple">
<li>Vary the number of table points; you may need to use more than you think
to get good resolution.</li>
<li>Always use the <a class="reference internal" href="pair_write.html"><em>pair_write</em></a> command to produce a plot
of what the final interpolated potential looks like. This can show up
interpolation &#8220;features&#8221; you may not like.</li>
<li>Start with the linear style; it&#8217;s the style least likely to have problems.</li>
<li>Use <em>N</em> in the pair_style command equal to the &#8220;N&#8221; in the tabulation
file, and use the &#8220;RSQ&#8221; or &#8220;BITMAP&#8221; parameter, so additional interpolation
is not needed. See discussion below.</li>
<li>Make sure that your tabulated forces and tabulated energies are
consistent (dE/dr = -F) over the entire range of r values. LAMMPS
will warn if this is not the case.</li>
<li>Use as large an inner cutoff as possible. This avoids fitting splines
to very steep parts of the potential.</li>
</ul>
<hr class="docutils" />
<p>The format of a tabulated file is a series of one or more sections,
defined as follows (without the parenthesized comments):</p>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># Morse potential for Fe (one or more comment or blank lines)</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>MORSE_FE (keyword is first text on line)
N 500 R 1.0 10.0 (N, R, RSQ, BITMAP, FPRIME parameters)
(blank)
1 1.0 25.5 102.34 (index, r, energy, force)
2 1.02 23.4 98.5
...
500 10.0 0.001 0.003
</pre></div>
</div>
<p>A section begins with a non-blank line whose 1st character is not a
&#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the pair_coeff
command. The next line lists (in any order) one or more parameters
for the table. Each parameter is a keyword followed by one or more
numeric values.</p>
<p>The parameter &#8220;N&#8221; is required and its value is the number of table
entries that follow. Note that this may be different than the <em>N</em>
specified in the <a class="reference internal" href="pair_style.html"><em>pair_style table</em></a> command. Let
Ntable = <em>N</em> in the pair_style command, and Nfile = &#8220;N&#8221; in the
tabulated file. What LAMMPS does is a preliminary interpolation by
creating splines using the Nfile tabulated values as nodal points. It
uses these to interpolate energy and force values at Ntable different
points. The resulting tables of length Ntable are then used as
described above, when computing energy and force for individual pair
distances. This means that if you want the interpolation tables of
length Ntable to match exactly what is in the tabulated file (with
effectively no preliminary interpolation), you should set Ntable =
Nfile, and use the &#8220;RSQ&#8221; or &#8220;BITMAP&#8221; parameter. This is because the
internal table abscissa is always RSQ (separation distance squared),
for efficient lookup.</p>
<p>All other parameters are optional. If &#8220;R&#8221; or &#8220;RSQ&#8221; or &#8220;BITMAP&#8221; does
not appear, then the distances in each line of the table are used
as-is to perform spline interpolation. In this case, the table values
can be spaced in <em>r</em> uniformly or however you wish to position table
values in regions of large gradients.</p>
<p>If used, the parameters &#8220;R&#8221; or &#8220;RSQ&#8221; are followed by 2 values <em>rlo</em>
and <em>rhi</em>. If specified, the distance associated with each energy and
force value is computed from these 2 values (at high accuracy), rather
than using the (low-accuracy) value listed in each line of the table.
The distance values in the table file are ignored in this case.
For &#8220;R&#8221;, distances uniformly spaced between <em>rlo</em> and <em>rhi</em> are
computed; for &#8220;RSQ&#8221;, squared distances uniformly spaced between
<em>rlo*rlo</em> and <em>rhi*rhi</em> are computed.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you use &#8220;R&#8221; or &#8220;RSQ&#8221;, the tabulated distance values in the
file are effectively ignored, and replaced by new values as described
in the previous paragraph. If the distance value in the table is not
very close to the new value (i.e. round-off difference), then you will
be assingning energy/force values to a different distance, which is
probably not what you want. LAMMPS will warn if this is occurring.</p>
</div>
<p>If used, the parameter &#8220;BITMAP&#8221; is also followed by 2 values <em>rlo</em> and
<em>rhi</em>. These values, along with the &#8220;N&#8221; value determine the ordering
of the N lines that follow and what distance is associated with each.
This ordering is complex, so it is not documented here, since this
file is typically produced by the <a class="reference internal" href="pair_write.html"><em>pair_write</em></a> command
with its <em>bitmap</em> option. When the table is in BITMAP format, the &#8220;N&#8221;
parameter in the file must be equal to 2^M where M is the value
specified in the pair_style command. Also, a cutoff parameter cannot
be used as an optional 3rd argument in the pair_coeff command; the
entire table extent as specified in the file must be used.</p>
<p>If used, the parameter &#8220;FPRIME&#8221; is followed by 2 values <em>fplo</em> and
<em>fphi</em> which are the derivative of the force at the innermost and
outermost distances listed in the table. These values are needed by
the spline construction routines. If not specified by the &#8220;FPRIME&#8221;
parameter, they are estimated (less accurately) by the first 2 and
last 2 force values in the table. This parameter is not used by
BITMAP tables.</p>
<p>Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
r (in distance units), the 3rd value is the energy (in energy units),
and the 4th is the force (in force units). The r values must increase
from one line to the next (unless the BITMAP parameter is specified).</p>
<p>Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds
one that matches the specified keyword.</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>This pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift, table, and tail options are
not relevant for this pair style.</p>
<p>This pair style writes the settings for the &#8220;pair_style table&#8221; command
to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so a pair_style command does
not need to specified in an input script that reads a restart file.
However, the coefficient information is not stored in the restart
file, since it is tabulated in the potential files. Thus, pair_coeff
commands do need to be specified in the restart input script.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</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>, <a class="reference internal" href="pair_write.html"><em>pair_write</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="wolff"><strong>(Wolff)</strong> Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).</p>
</div>
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<div class="section" id="pair-style-tersoff-command">
<span id="index-0"></span><h1>pair_style tersoff command<a class="headerlink" href="#pair-style-tersoff-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tersoff-table-command">
<h1>pair_style tersoff/table command<a class="headerlink" href="#pair-style-tersoff-table-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tersoff-cuda">
<h1>pair_style tersoff/cuda<a class="headerlink" href="#pair-style-tersoff-cuda" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tersoff-gpu">
<h1>pair_style tersoff/gpu<a class="headerlink" href="#pair-style-tersoff-gpu" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tersoff-intel">
<h1>pair_style tersoff/intel<a class="headerlink" href="#pair-style-tersoff-intel" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tersoff-kk">
<h1>pair_style tersoff/kk<a class="headerlink" href="#pair-style-tersoff-kk" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tersoff-omp">
<h1>pair_style tersoff/omp<a class="headerlink" href="#pair-style-tersoff-omp" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tersoff-table-omp-command">
<h1>pair_style tersoff/table/omp command<a class="headerlink" href="#pair-style-tersoff-table-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
</pre></div>
</div>
<p>style = <em>tersoff</em> or <em>tersoff/table</em> or <em>tersoff/cuda</em> or <em>tersoff/gpu</em> or <em>tersoff/omp</em> or <em>tersoff/table/omp</em></p>
</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 tersoff
pair_coeff * * Si.tersoff Si
pair_coeff * * SiC.tersoff Si C Si
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style tersoff/table
pair_coeff * * SiCGe.tersoff Si(D)
</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>tersoff</em> style computes a 3-body Tersoff potential
<a class="reference internal" href="pair_tersoff_zbl.html#tersoff-1"><span>(Tersoff_1)</span></a> for the energy E of a system of atoms as</p>
<img alt="_images/pair_tersoff_1.jpg" class="align-center" src="_images/pair_tersoff_1.jpg" />
<p>where f_R is a two-body term and f_A includes three-body interactions.
The summations in the formula are over all neighbors J and K of atom I
within a cutoff distance = R + D.</p>
<p>The <em>tersoff/table</em> style uses tabulated forms for the two-body,
environment and angular functions. Linear interpolation is performed
between adjacent table entries. The table length is chosen to be
accurate within 10^-6 with respect to the <em>tersoff</em> style energy.
The <em>tersoff/table</em> should give better performance in terms of speed.</p>
<p>Only a single pair_coeff command is used with the <em>tersoff</em> style
which specifies a Tersoff potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N element names = mapping of Tersoff elements to atom types</li>
</ul>
<p>See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc page for alternate ways
to specify the path for the potential file.</p>
<p>As an example, imagine the SiC.tersoff file has Tersoff values for Si
and C. If your LAMMPS simulation has 4 atoms types and you want the
1st 3 to be Si, and the 4th to be C, you would use the following
pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * SiC.tersoff Si Si Si C
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
element in the Tersoff file. The final C argument maps LAMMPS atom
type 4 to the C element in the Tersoff file. If a mapping value is
specified as NULL, the mapping is not performed. This can be used
when a <em>tersoff</em> potential is used as part of the <em>hybrid</em> pair style.
The NULL values are placeholders for atom types that will be used with
other potentials.</p>
<p>Tersoff files in the <em>potentials</em> directory of the LAMMPS distribution
have a &#8221;.tersoff&#8221; suffix. Lines that are not blank or comments
(starting with #) define parameters for a triplet of elements. The
parameters in a single entry correspond to coefficients in the formula
above:</p>
<ul class="simple">
<li>element 1 (the center atom in a 3-body interaction)</li>
<li>element 2 (the atom bonded to the center atom)</li>
<li>element 3 (the atom influencing the 1-2 bond in a bond-order sense)</li>
<li>m</li>
<li>gamma</li>
<li>lambda3 (1/distance units)</li>
<li>c</li>
<li>d</li>
<li>costheta0 (can be a value &lt; -1 or &gt; 1)</li>
<li>n</li>
<li>beta</li>
<li>lambda2 (1/distance units)</li>
<li>B (energy units)</li>
<li>R (distance units)</li>
<li>D (distance units)</li>
<li>lambda1 (1/distance units)</li>
<li>A (energy units)</li>
</ul>
<p>The n, beta, lambda2, B, lambda1, and A parameters are only used for
two-body interactions. The m, gamma, lambda3, c, d, and costheta0
parameters are only used for three-body interactions. The R and D
parameters are used for both two-body and three-body interactions. The
non-annotated parameters are unitless. The value of m must be 3 or 1.</p>
<p>The Tersoff potential file must contain entries for all the elements
listed in the pair_coeff command. It can also contain entries for
additional elements not being used in a particular simulation; LAMMPS
ignores those entries.</p>
<p>For a single-element simulation, only a single entry is required
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
specify Tersoff parameters for all permutations of the two elements
interacting in three-body configurations. Thus for 3 elements, 27
entries would be required, etc.</p>
<p>As annotated above, the first element in the entry is the center atom
in a three-body interaction and it is bonded to the 2nd atom and the
bond is influenced by the 3rd atom. Thus an entry for SiCC means Si
bonded to a C with another C atom influencing the bond. Thus
three-body parameters for SiCSi and SiSiC entries will not, in
general, be the same. The parameters used for the two-body
interaction come from the entry where the 2nd element is repeated.
Thus the two-body parameters for Si interacting with C, comes from the
SiCC entry.</p>
<p>The parameters used for a particular
three-body interaction come from the entry with the corresponding
three elements. The parameters used only for two-body interactions
(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd
element are different (e.g. SiCSi) are not used for anything and can
be set to 0.0 if desired.</p>
<p>Note that the twobody parameters in entries such as SiCC and CSiSi
are often the same, due to the common use of symmetric mixing rules,
but this is not always the case. For example, the beta and n parameters in
Tersoff_2 <a class="reference internal" href="pair_tersoff_zbl.html#tersoff-2"><span>(Tersoff_2)</span></a> are not symmetric.</p>
<p>We chose the above form so as to enable users to define all commonly
used variants of the Tersoff potential. In particular, our form
reduces to the original Tersoff form when m = 3 and gamma = 1, while
it reduces to the form of <a class="reference internal" href="pair_tersoff_zbl.html#albe"><span>Albe et al.</span></a> when beta = 1 and m = 1.
Note that in the current Tersoff implementation in LAMMPS, m must be
specified as either 3 or 1. Tersoff used a slightly different but
equivalent form for alloys, which we will refer to as Tersoff_2
potential <a class="reference internal" href="pair_tersoff_zbl.html#tersoff-2"><span>(Tersoff_2)</span></a>. The <em>tersoff/table</em> style implements
Tersoff_2 parameterization only.</p>
<p>LAMMPS parameter values for Tersoff_2 can be obtained as follows:
gamma_ijk = omega_ik, lambda3 = 0 and the value of
m has no effect. The parameters for species i and j can be calculated
using the Tersoff_2 mixing rules:</p>
<img alt="_images/pair_tersoff_2.jpg" class="align-center" src="_images/pair_tersoff_2.jpg" />
<p>Tersoff_2 parameters R and S must be converted to the LAMMPS
parameters R and D (R is different in both forms), using the following
relations: R=(R&#8217;+S&#8217;)/2 and D=(S&#8217;-R&#8217;)/2, where the primes indicate the
Tersoff_2 parameters.</p>
<p>In the potentials directory, the file SiCGe.tersoff provides the
LAMMPS parameters for Tersoff&#8217;s various versions of Si, as well as his
alloy parameters for Si, C, and Ge. This file can be used for pure Si,
(three different versions), pure C, pure Ge, binary SiC, and binary
SiGe. LAMMPS will generate an error if this file is used with any
combination involving C and Ge, since there are no entries for the GeC
interactions (Tersoff did not publish parameters for this
cross-interaction.) Tersoff files are also provided for the SiC alloy
(SiC.tersoff) and the GaN (GaN.tersoff) alloys.</p>
<p>Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou
for helping clarify how Tersoff parameters for alloys have been
defined in various papers.</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>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><em>newton</em></a> setting to be &#8220;on&#8221;
for pair interactions.</p>
<p>The Tersoff potential files provided with LAMMPS (see the potentials
directory) are parameterized for metal <a class="reference internal" href="units.html"><em>units</em></a>. You can
use the Tersoff potential with any LAMMPS units, but you would need to
create your own Tersoff potential file with coefficients listed in the
appropriate units if your simulation doesn&#8217;t use &#8220;metal&#8221; units.</p>
</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="tersoff-1"><strong>(Tersoff_1)</strong> J. Tersoff, Phys Rev B, 37, 6991 (1988).</p>
<p id="albe"><strong>(Albe)</strong> J. Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.:
Condens. Matter, 15, 5649(2003).</p>
<p id="tersoff-2"><strong>(Tersoff_2)</strong> J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)</p>
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<div class="section" id="pair-style-tersoff-mod-command">
<span id="index-0"></span><h1>pair_style tersoff/mod command<a class="headerlink" href="#pair-style-tersoff-mod-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tersoff-mod-gpu-command">
<h1>pair_style tersoff/mod/gpu command<a class="headerlink" href="#pair-style-tersoff-mod-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tersoff-mod-kk-command">
<h1>pair_style tersoff/mod/kk command<a class="headerlink" href="#pair-style-tersoff-mod-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tersoff-mod-omp-command">
<h1>pair_style tersoff/mod/omp command<a class="headerlink" href="#pair-style-tersoff-mod-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 tersoff/mod
</pre></div>
</div>
</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 tersoff/mod
pair_coeff * * Si.tersoff.mod Si Si
</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>tersoff/mod</em> style computes a bond-order type interatomic
potential <a class="reference internal" href="#kumagai"><span>(Kumagai)</span></a> based on a 3-body Tersoff potential
<a class="reference internal" href="pair_tersoff_zbl.html#tersoff-1"><span>(Tersoff_1)</span></a>, <a class="reference internal" href="pair_tersoff_zbl.html#tersoff-2"><span>(Tersoff_2)</span></a> with modified
cutoff function and angular-dependent term, giving the energy E of a
system of atoms as</p>
<img alt="_images/pair_tersoff_mod.jpg" class="align-center" src="_images/pair_tersoff_mod.jpg" />
<p>where f_R is a two-body term and f_A includes three-body interactions.
The summations in the formula are over all neighbors J and K of atom I
within a cutoff distance = R + D.</p>
<p>The modified cutoff function f_C proposed by <a class="reference internal" href="#murty"><span>(Murty)</span></a> and
having a continuous second-order differential is employed. The
angular-dependent term g(theta) was modified to increase the
flexibility of the potential.</p>
<p>The <em>tersoff/mod</em> potential is fitted to both the elastic constants
and melting point by employing the modified Tersoff potential function
form in which the angular-dependent term is improved. The model
performs extremely well in describing the crystalline, liquid, and
amorphous phases <a class="reference internal" href="#schelling"><span>(Schelling)</span></a>.</p>
<p>Only a single pair_coeff command is used with the <em>tersoff/mod</em> style
which specifies a Tersoff/MOD potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N element names = mapping of Tersoff/MOD elements to atom types</li>
</ul>
<p>As an example, imagine the Si.tersoff_mod file has Tersoff values for Si.
If your LAMMPS simulation has 3 Si atoms types, you would use the following
pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * Si.tersoff_mod Si Si Si
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The three Si arguments map LAMMPS atom types 1,2,3 to the Si element
in the Tersoff/MOD file. If a mapping value is specified as NULL, the
mapping is not performed. This can be used when a <em>tersoff/mod</em>
potential is used as part of the <em>hybrid</em> pair style. The NULL values
are placeholders for atom types that will be used with other
potentials.</p>
<p>Tersoff/MOD file in the <em>potentials</em> directory of the LAMMPS
distribution have a &#8221;.tersoff.mod&#8221; suffix. Lines that are not blank
or comments (starting with #) define parameters for a triplet of
elements. The parameters in a single entry correspond to coefficients
in the formula above:</p>
<ul class="simple">
<li>element 1 (the center atom in a 3-body interaction)</li>
<li>element 2 (the atom bonded to the center atom)</li>
<li>element 3 (the atom influencing the 1-2 bond in a bond-order sense)</li>
<li>beta</li>
<li>alpha</li>
<li>h</li>
<li>eta</li>
<li>beta_ters = 1 (dummy parameter)</li>
<li>lambda2 (1/distance units)</li>
<li>B (energy units)</li>
<li>R (distance units)</li>
<li>D (distance units)</li>
<li>lambda1 (1/distance units)</li>
<li>A (energy units)</li>
<li>n</li>
<li>c1</li>
<li>c2</li>
<li>c3</li>
<li>c4</li>
<li>c5</li>
</ul>
<p>The n, eta, lambda2, B, lambda1, and A parameters are only used for
two-body interactions. The beta, alpha, c1, c2, c3, c4, c5, h
parameters are only used for three-body interactions. The R and D
parameters are used for both two-body and three-body interactions. The
non-annotated parameters are unitless.</p>
<p>The Tersoff/MOD potential file must contain entries for all the elements
listed in the pair_coeff command. It can also contain entries for
additional elements not being used in a particular simulation; LAMMPS
ignores those entries.</p>
<p>For a single-element simulation, only a single entry is required
(e.g. SiSiSi). As annotated above, the first element in the entry is
the center atom in a three-body interaction and it is bonded to the
2nd atom and the bond is influenced by the 3rd atom. Thus an entry
for SiSiSi means Si bonded to a Si with another Si atom influencing the bond.</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>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><em>newton</em></a> setting to be &#8220;on&#8221;
for pair interactions.</p>
<p>The Tersoff/MOD potential files provided with LAMMPS (see the potentials
directory) are parameterized for metal <a class="reference internal" href="units.html"><em>units</em></a>. You can
use the Tersoff/MOD potential with any LAMMPS units, but you would need to
create your own Tersoff/MOD potential file with coefficients listed in the
appropriate units if your simulation doesn&#8217;t use &#8220;metal&#8221; units.</p>
</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="kumagai"><strong>(Kumagai)</strong> T. Kumagai, S. Izumi, S. Hara, S. Sakai,
Comp. Mat. Science, 39, 457 (2007).</p>
<p id="tersoff-1"><strong>(Tersoff_1)</strong> J. Tersoff, Phys Rev B, 37, 6991 (1988).</p>
<p id="tersoff-2"><strong>(Tersoff_2)</strong> J. Tersoff, Phys Rev B, 38, 9902 (1988).</p>
<p id="murty"><strong>(Murty)</strong> M.V.R. Murty, H.A. Atwater, Phys Rev B, 51, 4889 (1995).</p>
<p id="schelling"><strong>(Schelling)</strong> Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008).</p>
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<div class="section" id="pair-style-tersoff-zbl-command">
<span id="index-0"></span><h1>pair_style tersoff/zbl command<a class="headerlink" href="#pair-style-tersoff-zbl-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tersoff-zbl-gpu-command">
<h1>pair_style tersoff/zbl/gpu command<a class="headerlink" href="#pair-style-tersoff-zbl-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tersoff-zbl-kk-command">
<h1>pair_style tersoff/zbl/kk command<a class="headerlink" href="#pair-style-tersoff-zbl-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tersoff-zbl-omp-command">
<h1>pair_style tersoff/zbl/omp command<a class="headerlink" href="#pair-style-tersoff-zbl-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 tersoff/zbl
</pre></div>
</div>
</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 tersoff/zbl
pair_coeff * * SiC.tersoff.zbl Si C Si
</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>tersoff/zbl</em> style computes a 3-body Tersoff potential
<a class="reference internal" href="#tersoff-1"><span>(Tersoff_1)</span></a> with a close-separation pairwise modification
based on a Coulomb potential and the Ziegler-Biersack-Littmark
universal screening function <a class="reference internal" href="#zbl"><span>(ZBL)</span></a>, giving the energy E of a
system of atoms as</p>
<img alt="_images/pair_tersoff_zbl.jpg" class="align-center" src="_images/pair_tersoff_zbl.jpg" />
<p>The f_F term is a fermi-like function used to smoothly connect the ZBL
repulsive potential with the Tersoff potential. There are 2
parameters used to adjust it: A_F and r_C. A_F controls how &#8220;sharp&#8221;
the transition is between the two, and r_C is essentially the cutoff
for the ZBL potential.</p>
<p>For the ZBL portion, there are two terms. The first is the Coulomb
repulsive term, with Z1, Z2 as the number of protons in each nucleus,
e as the electron charge (1 for metal and real units) and epsilon0 as
the permittivity of vacuum. The second part is the ZBL universal
screening function, with a0 being the Bohr radius (typically 0.529
Angstroms), and the remainder of the coefficients provided by the
original paper. This screening function should be applicable to most
systems. However, it is only accurate for small separations
(i.e. less than 1 Angstrom).</p>
<p>For the Tersoff portion, f_R is a two-body term and f_A includes
three-body interactions. The summations in the formula are over all
neighbors J and K of atom I within a cutoff distance = R + D.</p>
<p>Only a single pair_coeff command is used with the <em>tersoff/zbl</em> style
which specifies a Tersoff/ZBL potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N element names = mapping of Tersoff/ZBL elements to atom types</li>
</ul>
<p>See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc page for alternate ways
to specify the path for the potential file.</p>
<p>As an example, imagine the SiC.tersoff.zbl file has Tersoff/ZBL values
for Si and C. If your LAMMPS simulation has 4 atoms types and you
want the 1st 3 to be Si, and the 4th to be C, you would use the
following pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * SiC.tersoff Si Si Si C
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
element in the Tersoff/ZBL file. The final C argument maps LAMMPS
atom type 4 to the C element in the Tersoff/ZBL file. If a mapping
value is specified as NULL, the mapping is not performed. This can be
used when a <em>tersoff/zbl</em> potential is used as part of the <em>hybrid</em>
pair style. The NULL values are placeholders for atom types that will
be used with other potentials.</p>
<p>Tersoff/ZBL files in the <em>potentials</em> directory of the LAMMPS
distribution have a &#8221;.tersoff.zbl&#8221; suffix. Lines that are not blank
or comments (starting with #) define parameters for a triplet of
elements. The parameters in a single entry correspond to coefficients
in the formula above:</p>
<ul class="simple">
<li>element 1 (the center atom in a 3-body interaction)</li>
<li>element 2 (the atom bonded to the center atom)</li>
<li>element 3 (the atom influencing the 1-2 bond in a bond-order sense)</li>
<li>m</li>
<li>gamma</li>
<li>lambda3 (1/distance units)</li>
<li>c</li>
<li>d</li>
<li>costheta0 (can be a value &lt; -1 or &gt; 1)</li>
<li>n</li>
<li>beta</li>
<li>lambda2 (1/distance units)</li>
<li>B (energy units)</li>
<li>R (distance units)</li>
<li>D (distance units)</li>
<li>lambda1 (1/distance units)</li>
<li>A (energy units)</li>
<li>Z_i</li>
<li>Z_j</li>
<li>ZBLcut (distance units)</li>
<li>ZBLexpscale (1/distance units)</li>
</ul>
<p>The n, beta, lambda2, B, lambda1, and A parameters are only used for
two-body interactions. The m, gamma, lambda3, c, d, and costheta0
parameters are only used for three-body interactions. The R and D
parameters are used for both two-body and three-body interactions. The
Z_i,Z_j, ZBLcut, ZBLexpscale parameters are used in the ZBL repulsive
portion of the potential and in the Fermi-like function. The
non-annotated parameters are unitless. The value of m must be 3 or 1.</p>
<p>The Tersoff/ZBL potential file must contain entries for all the
elements listed in the pair_coeff command. It can also contain
entries for additional elements not being used in a particular
simulation; LAMMPS ignores those entries.</p>
<p>For a single-element simulation, only a single entry is required
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
specify Tersoff parameters for all permutations of the two elements
interacting in three-body configurations. Thus for 3 elements, 27
entries would be required, etc.</p>
<p>As annotated above, the first element in the entry is the center atom
in a three-body interaction and it is bonded to the 2nd atom and the
bond is influenced by the 3rd atom. Thus an entry for SiCC means Si
bonded to a C with another C atom influencing the bond. Thus
three-body parameters for SiCSi and SiSiC entries will not, in
general, be the same. The parameters used for the two-body
interaction come from the entry where the 2nd element is repeated.
Thus the two-body parameters for Si interacting with C, comes from the
SiCC entry.</p>
<p>The parameters used for a particular
three-body interaction come from the entry with the corresponding
three elements. The parameters used only for two-body interactions
(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd
element are different (e.g. SiCSi) are not used for anything and can
be set to 0.0 if desired.</p>
<p>Note that the twobody parameters in entries such as SiCC and CSiSi
are often the same, due to the common use of symmetric mixing rules,
but this is not always the case. For example, the beta and n parameters in
Tersoff_2 <a class="reference internal" href="#tersoff-2"><span>(Tersoff_2)</span></a> are not symmetric.</p>
<p>We chose the above form so as to enable users to define all commonly
used variants of the Tersoff portion of the potential. In particular,
our form reduces to the original Tersoff form when m = 3 and gamma =
1, while it reduces to the form of <a class="reference internal" href="#albe"><span>Albe et al.</span></a> when beta = 1
and m = 1. Note that in the current Tersoff implementation in LAMMPS,
m must be specified as either 3 or 1. Tersoff used a slightly
different but equivalent form for alloys, which we will refer to as
Tersoff_2 potential <a class="reference internal" href="#tersoff-2"><span>(Tersoff_2)</span></a>.</p>
<p>LAMMPS parameter values for Tersoff_2 can be obtained as follows:
gamma = omega_ijk, lambda3 = 0 and the value of
m has no effect. The parameters for species i and j can be calculated
using the Tersoff_2 mixing rules:</p>
<img alt="_images/pair_tersoff_2.jpg" class="align-center" src="_images/pair_tersoff_2.jpg" />
<p>Tersoff_2 parameters R and S must be converted to the LAMMPS
parameters R and D (R is different in both forms), using the following
relations: R=(R&#8217;+S&#8217;)/2 and D=(S&#8217;-R&#8217;)/2, where the primes indicate the
Tersoff_2 parameters.</p>
<p>In the potentials directory, the file SiCGe.tersoff provides the
LAMMPS parameters for Tersoff&#8217;s various versions of Si, as well as his
alloy parameters for Si, C, and Ge. This file can be used for pure Si,
(three different versions), pure C, pure Ge, binary SiC, and binary
SiGe. LAMMPS will generate an error if this file is used with any
combination involving C and Ge, since there are no entries for the GeC
interactions (Tersoff did not publish parameters for this
cross-interaction.) Tersoff files are also provided for the SiC alloy
(SiC.tersoff) and the GaN (GaN.tersoff) alloys.</p>
<p>Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou
for helping clarify how Tersoff parameters for alloys have been
defined in various papers. Also thanks to Ram Devanathan for
providing the base ZBL implementation.</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>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><em>newton</em></a> setting to be &#8220;on&#8221;
for pair interactions.</p>
<p>The Tersoff/ZBL potential files provided with LAMMPS (see the
potentials directory) are parameterized for metal <a class="reference internal" href="units.html"><em>units</em></a>.
You can use the Tersoff potential with any LAMMPS units, but you would
need to create your own Tersoff potential file with coefficients
listed in the appropriate units if your simulation doesn&#8217;t use &#8220;metal&#8221;
units.</p>
</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="tersoff-1"><strong>(Tersoff_1)</strong> J. Tersoff, Phys Rev B, 37, 6991 (1988).</p>
<p id="zbl"><strong>(ZBL)</strong> J.F. Ziegler, J.P. Biersack, U. Littmark, &#8216;Stopping and Ranges
of Ions in Matter&#8217; Vol 1, 1985, Pergamon Press.</p>
<p id="albe"><strong>(Albe)</strong> J. Nord, K. Albe, P. Erhart and K. Nordlund, J. Phys.:
Condens. Matter, 15, 5649(2003).</p>
<p id="tersoff-2"><strong>(Tersoff_2)</strong> J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)</p>
</div>
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<div class="section" id="pair-style-thole-command">
<span id="index-0"></span><h1>pair_style thole command<a class="headerlink" href="#pair-style-thole-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-thole-long-command">
<h1>pair_style lj/cut/thole/long command<a class="headerlink" href="#pair-style-lj-cut-thole-long-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lj-cut-thole-long-omp-command">
<h1>pair_style lj/cut/thole/long/omp command<a class="headerlink" href="#pair-style-lj-cut-thole-long-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 args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>thole</em> or <em>lj/cut/thole/long</em> or <em>lj/cut/thole/long/omp</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>thole</em> args = damp cutoff
damp = global damping parameter
cutoff = global cutoff (distance units)
<em>lj/cut/thole/long</em> or <em>lj/cut/thole/long/omp</em> args = damp cutoff (cutoff2)
damp = global damping parameter
cutoff = global cutoff for LJ (and Thole if only 1 arg) (distance units)
cutoff2 = global cutoff for Thole (optional) (distance units)
</pre>
</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 ... thole 2.6 12.0
pair_coeff 1 1 thole 1.0
pair_coeff 1 2 thole 1.0 2.6 10.0
pair_coeff * 2 thole 1.0 2.6
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/thole/long 2.6 12.0
</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>thole</em> pair styles are meant to be used with force fields that
include explicit polarization through Drude dipoles. This link
describes how to use the <a class="reference internal" href="tutorial_drude.html"><em>thermalized Drude oscillator model</em></a> in LAMMPS and polarizable models in LAMMPS
are discussed in <a class="reference internal" href="Section_howto.html#howto-25"><span>this Section</span></a>.</p>
<p>The <em>thole</em> pair style should be used as a sub-style within in the
<a class="reference internal" href="pair_hybrid.html"><em>pair_hybrid/overlay</em></a> command, in conjunction with a
main pair style including Coulomb interactions, i.e. any pair style
containing <em>coul/cut</em> or <em>coul/long</em> in its style name.</p>
<p>The <em>lj/cut/thole/long</em> pair style is equivalent to, but more convenient that
the frequent combination <em>hybrid/overlay lj/cut/coul/long cutoff thole damp
cutoff2</em>. It is not only a shorthand for this pair_style combination, but
it also allows for mixing pair coefficients instead of listing them all.
The <em>lj/cut/thole/long</em> pair style is also a bit faster because it avoids an
overlay and can benefit from OMP acceleration. Moreover, it uses a more
precise approximation of the direct Coulomb interaction at short range similar
to <code class="xref doc docutils literal"><span class="pre">coul/long/cs</span></code>, which stabilizes the temperature of
Drude particles.</p>
<p>The <em>thole</em> pair styles compute the Coulomb interaction damped at
short distances by a function</p>
<div class="math">
\[\begin{equation} T_{ij}(r_{ij}) = 1 - \left( 1 +
\frac{s_{ij} r_{ij} }{2} \right)
\exp \left( - s_{ij} r_{ij} \right) \end{equation}\]</div>
<p>This function results from an adaptation to point charges
<a class="reference internal" href="tutorial_drude.html#noskov"><span>(Noskov)</span></a> of the dipole screening scheme originally proposed
by <a class="reference internal" href="tutorial_drude.html#thole"><span>Thole</span></a>. The scaling coefficient <span class="math">\(s_{ij}\)</span> is determined
by the polarizability of the atoms, <span class="math">\(\alpha_i\)</span>, and by a Thole
damping parameter <span class="math">\(a\)</span>. This Thole damping parameter usually takes
a value of 2.6, but in certain force fields the value can depend upon
the atom types. The mixing rule for Thole damping parameters is the
arithmetic average, and for polarizabilities the geometric average
between the atom-specific values.</p>
<div class="math">
\[\begin{equation} s_{ij} = \frac{ a_{ij} }{
(\alpha_{ij})^{1/3} } = \frac{ (a_i + a_j)/2 }{
[(\alpha_i\alpha_j)^{1/2}]^{1/3} } \end{equation}\]</div>
<p>The damping function is only applied to the interactions between the
point charges representing the induced dipoles on polarizable sites,
that is, charges on Drude particles, <span class="math">\(q_{D,i}\)</span>, and opposite
charges, <span class="math">\(-q_{D,i}\)</span>, located on the respective core particles
(to which each Drude particle is bonded). Therefore, Thole screening
is not applied to the full charge of the core particle <span class="math">\(q_i\)</span>, but
only to the <span class="math">\(-q_{D,i}\)</span> part of it.</p>
<p>The interactions between core charges are subject to the weighting
factors set by the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command. The
interactions between Drude particles and core charges or
non-polarizable atoms are also subject to these weighting factors. The
Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from
their respective cores.</p>
<p>For pair_style <em>thole</em>, the following coefficients must be defined for
each pair of atoms types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command
as in the example above.</p>
<ul class="simple">
<li>alpha (distance units^3)</li>
<li>damp</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last two coefficients are optional. If not specified the global
Thole damping parameter or global cutoff specified in the pair_style
command are used. In order to specify a cutoff (third argument) a damp
parameter (second argument) must also be specified.</p>
<p>For pair style <em>lj/cut/thole/long</em>, the following coefficients must be
defined for each pair of atoms types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>
command.</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (length units)</li>
<li>alpha (distance units^3)</li>
<li>damps</li>
<li>LJ cutoff (distance units)</li>
</ul>
<p>The last two coefficients are optional and default to the global values from
the <em>pair_style</em> command line.</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>
<p><strong>Mixing</strong>:</p>
<p>The <em>thole</em> pair style does not support mixing. Thus, coefficients
for all I,J pairs must be specified explicitly.</p>
<p>The <em>lj/cut/thole/long</em> pair style does support mixing. Mixed coefficients
are defined using</p>
<div class="math">
\[\begin{equation} \alpha_{ij} = \sqrt{\alpha_i\alpha_j}\end{equation}\]</div>
<div class="math">
\[\begin{equation} a_{ij} = \frac 1 2 (a_i + a_j)\end{equation}\]</div>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>These pair styles are part of the USER-DRUDE 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>Making LAMMPS</span></a> section for more info.</p>
<p>This pair_style should currently not be used with the <a class="reference internal" href="dihedral_charmm.html"><em>charmm dihedral style</em></a> if the latter has non-zero 1-4 weighting
factors. This is because the <em>thole</em> pair style does not know which
pairs are 1-4 partners of which dihedrals.</p>
<p>The <em>lj/cut/thole/long</em> pair style should be used with a <a class="reference internal" href="kspace_style.html"><em>Kspace solver</em></a>
like PPPM or Ewald, which is only enabled if LAMMPS was built with the kspace
package.</p>
</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="fix_drude.html"><em>fix drude</em></a>, <a class="reference internal" href="fix_langevin_drude.html"><em>fix langevin/drude</em></a>, <a class="reference internal" href="fix_drude_transform.html"><em>fix drude/transform</em></a>, <a class="reference internal" href="compute_temp_drude.html"><em>compute temp/drude</em></a>
<a class="reference external" href="pair_lj_cut_coul_long">pair_style lj/cut/coul/long</a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="noskov"><strong>(Noskov)</strong> Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005).</p>
<p id="thole"><strong>(Thole)</strong> Chem Phys, 59, 341 (1981).</p>
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<div class="section" id="pair-style-tri-lj-command">
<span id="index-0"></span><h1>pair_style tri/lj command<a class="headerlink" href="#pair-style-tri-lj-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 tri/lj cutoff
</pre></div>
</div>
<p>cutoff = global cutoff for interactions (distance units)</p>
</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 tri/lj 3.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.5 2.5
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>tri/lj</em> treats particles which are triangles as a set of small
spherical particles that tile the triangle surface as explained below.
Interactions between two triangles, each with N1 and N2 spherical
particles, are calculated as the pairwise sum of N1*N2 Lennard-Jones
interactions. Interactions between a triangle with N spherical
particles and a point particle are treated as the pairwise sum of N
Lennard-Jones interactions. See the <a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut</em></a>
doc page for the definition of Lennard-Jones interactions.</p>
<p>The cutoff distance for an interaction between 2 triangles, or between
a triangle and a point particle, is calculated from the position of
the triangle (its centroid), not between pairs of individual spheres
comprising the triangle. Thus an interaction is either calculated in
its entirety or not at all.</p>
<p>The set of non-overlapping spherical particles that represent a
triangle, for purposes of this pair style, are generated in the
following manner. Assume the triangle is of type I, and sigma_II has
been specified. We want a set of spheres with centers in the plane of
the triangle, none of them larger in diameter than sigma_II, which
completely cover the triangle&#8217;s area, but with minimial overlap and a
minimal total number of spheres. This is done in a recursive manner.
Place a sphere at the centroid of the original triangle. Calculate
what diameter it must have to just cover all 3 corner points of the
triangle. If that diameter is equal to or smaller than sigma_II, then
include a sphere of the calculated diameter in the set of covering
spheres. It the diameter is larger than sigma_II, then split the
triangle into 2 triangles by bisecting its longest side. Repeat the
process on each sub-triangle, recursing as far as needed to generate a
set of covering spheres. When finished, the original criteria are
met, and the set of covering spheres shoule be near minimal in number
and overlap, at least for input triangles with a reasonable
aspect-ratio.</p>
<p>The LJ interaction between 2 spheres on different triangles of types
I,J is computed with an arithmetic mixing of the sigma values of the 2
spheres and using the specified epsilon value for I,J atom types.
Note that because the sigma values for triangles spheres is computed
using only sigma_II values, specific to the triangles&#8217;s type, this
means that any specified sigma_IJ values (for I != J) are effectively
ignored.</p>
<p>For style <em>tri/lj</em>, the following coefficients must be defined for
each pair of atoms types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command
as in the examples above, or in the data file or restart files read by
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global cutoff
is used.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of this pair style can be mixed. The
default mix value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command for
details.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This style is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
<p>Defining particles to be triangles so they participate in tri/tri or
tri/particle interactions requires the use the <a class="reference internal" href="atom_style.html"><em>atom_style tri</em></a> command.</p>
</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>, <a class="reference internal" href="pair_line_lj.html"><em>pair_style line/lj</em></a></p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="pair-style-vashishta-command">
<span id="index-0"></span><h1>pair_style vashishta command<a class="headerlink" href="#pair-style-vashishta-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-vashishta-omp-command">
<h1>pair_style vashishta/omp command<a class="headerlink" href="#pair-style-vashishta-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 vashishta
</pre></div>
</div>
</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 vashishta
pair_coeff * * SiC.vashishta Si C
</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>vashishta</em> style computes the combined 2-body and 3-body
family of potentials developed in the group of Vashishta and
co-workers. By combining repulsive, screened Coulombic,
screened charge-dipole, and dispersion interactions with a
bond-angle energy based on the Stillinger-Weber potential,
this potential has been used to describe a variety of inorganic
compounds, including SiO2 <a class="reference internal" href="#vashishta1990"><span>Vashishta1990</span></a>,
SiC <a class="reference internal" href="#vashishta2007"><span>Vashishta2007</span></a>,
and InP <a class="reference internal" href="#branicio2009"><span>Branicio2009</span></a>.</p>
<p>The potential for the energy U of a system of atoms is</p>
<img alt="_images/pair_vashishta.jpg" class="align-center" src="_images/pair_vashishta.jpg" />
<p>where we follow the notation used in <a class="reference internal" href="#branicio2009"><span>Branicio2009</span></a>.
U2 is a two-body term and U3 is a three-body term. The
summation over two-body terms is over all neighbors J within
a cutoff distance = <em>rc</em>. The twobody terms are shifted and
tilted by a linear function so that the energy and force are
both zero at <em>rc</em>. The summation over three-body terms
is over all neighbors J and K within a cut-off distance = <em>r0</em>,
where the exponential screening function becomes zero.</p>
<p>Only a single pair_coeff command is used with the <em>vashishta</em> style which
specifies a Vashishta potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N element names = mapping of Vashishta elements to atom types</li>
</ul>
<p>See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc page for alternate ways
to specify the path for the potential file.</p>
<p>As an example, imagine a file SiC.vashishta has parameters for
Si and C. If your LAMMPS simulation has 4 atoms types and you want
the 1st 3 to be Si, and the 4th to be C, you would use the following
pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * SiC.vashishta Si Si Si C
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
element in the file. The final C argument maps LAMMPS atom type 4
to the C element in the file. If a mapping value is specified as
NULL, the mapping is not performed. This can be used when a <em>vashishta</em>
potential is used as part of the <em>hybrid</em> pair style. The NULL values
are placeholders for atom types that will be used with other
potentials.</p>
<p>Vashishta files in the <em>potentials</em> directory of the LAMMPS
distribution have a &#8221;.vashishta&#8221; suffix. Lines that are not blank or
comments (starting with #) define parameters for a triplet of
elements. The parameters in a single entry correspond to the two-body
and three-body coefficients in the formulae above:</p>
<ul class="simple">
<li>element 1 (the center atom in a 3-body interaction)</li>
<li>element 2</li>
<li>element 3</li>
<li>H (energy units)</li>
<li>eta</li>
<li>Zi (electron charge units)</li>
<li>Zj (electron charge units)</li>
<li>lambda1 (distance units)</li>
<li>D (energy units)</li>
<li>lambda4 (distance units)</li>
<li>W (energy units)</li>
<li>rc (distance units)</li>
<li>B (energy units)</li>
<li>gamma</li>
<li>r0 (distance units)</li>
<li>C</li>
<li>costheta0</li>
</ul>
<p>The non-annotated parameters are unitless.
The Vashishta potential file must contain entries for all the
elements listed in the pair_coeff command. It can also contain
entries for additional elements not being used in a particular
simulation; LAMMPS ignores those entries.
For a single-element simulation, only a single entry is required
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
specify parameters for all permutations of the two elements
interacting in three-body configurations. Thus for 3 elements, 27
entries would be required, etc.</p>
<p>Depending on the particular version of the Vashishta potential,
the values of these parameters may be keyed to the identities of
zero, one, two, or three elements.
In order to make the input file format unambiguous, general,
and simple to code,
LAMMPS uses a slightly confusing method for specifying parameters.
All parameters are divided into two classes: two-body and three-body.
Two-body and three-body parameters are handled differently,
as described below.
The two-body parameters are H, eta, lambda1, D, lambda4, W, rc, gamma, and r0.
They appear in the above formulae with two subscripts.
The parameters Zi and Zj are also classified as two-body parameters,
even though they only have 1 subscript.
The three-body parameters are B, C, costheta0.
They appear in the above formulae with three subscripts.
Two-body and three-body parameters are handled differently,
as described below.</p>
<p>The first element in each entry is the center atom
in a three-body interaction, while the second and third elements
are two neighbor atoms. Three-body parameters for a central atom I
and two neighbors J and K are taken from the IJK entry.
Note that even though three-body parameters do not depend on the order of
J and K, LAMMPS stores three-body parameters for both IJK and IKJ.
The user must ensure that these values are equal.
Two-body parameters for an atom I interacting with atom J are taken from
the IJJ entry, where the 2nd and 3rd
elements are the same. Thus the two-body parameters
for Si interacting with C come from the SiCC entry. Note that even
though two-body parameters (except possibly gamma and r0 in U3)
do not depend on the order of the two elements,
LAMMPS will get the Si-C value from the SiCC entry
and the C-Si value from the CSiSi entry. The user must ensure
that these values are equal. Two-body parameters appearing
in entries where the 2nd and 3rd elements are different are
stored but never used. It is good practice to enter zero for
these values. Note that the three-body function U3 above
contains the two-body parameters gamma and r0. So U3 for a
central C atom bonded to an Si atom and a second C atom
will take three-body parameters from the CSiC entry, but
two-body parameters from the CCC and CSiSi entries.</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>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><em>newton</em></a> setting to be &#8220;on&#8221;
for pair interactions.</p>
<p>The Vashishta potential files provided with LAMMPS (see the
potentials directory) are parameterized for metal <a class="reference internal" href="units.html"><em>units</em></a>.
You can use the Vashishta potential with any LAMMPS units, but you would need
to create your own Vashishta potential file with coefficients listed in the
appropriate units if your simulation doesn&#8217;t use &#8220;metal&#8221; units.</p>
</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="vashishta1990"><strong>(Vashishta1990)</strong> P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B 41, 12197 (1990).</p>
<p id="vashishta2007"><strong>(Vashishta2007)</strong> P. Vashishta, R. K. Kalia, A. Nakano, J. P. Rino. J. Appl. Phys. 101, 103515 (2007).</p>
<p id="branicio2009"><strong>(Branicio2009)</strong> Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002</p>
</div>
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<div class="section" id="pair-write-command">
<span id="index-0"></span><h1>pair_write command<a class="headerlink" href="#pair-write-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_write itype jtype N style inner outer file keyword Qi Qj
</pre></div>
</div>
<ul class="simple">
<li>itype,jtype = 2 atom types</li>
<li>N = # of values</li>
<li>style = <em>r</em> or <em>rsq</em> or <em>bitmap</em></li>
<li>inner,outer = inner and outer cutoff (distance units)</li>
<li>file = name of file to write values to</li>
<li>keyword = section name in file for this set of tabulated values</li>
<li>Qi,Qj = 2 atom charges (charge units) (optional)</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_write 1 3 500 r 1.0 10.0 table.txt LJ
pair_write 1 1 1000 rsq 2.0 8.0 table.txt Yukawa_1_1 -0.5 0.5
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Write energy and force values to a file as a function of distance for
the currently defined pair potential. This is useful for plotting the
potential function or otherwise debugging its values. If the file
already exists, the table of values is appended to the end of the file
to allow multiple tables of energy and force to be included in one
file.</p>
<p>The energy and force values are computed at distances from inner to
outer for 2 interacting atoms of type itype and jtype, using the
appropriate <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> coefficients. If the style
is <em>r</em>, then N distances are used, evenly spaced in r; if the style is
<em>rsq</em>, N distances are used, evenly spaced in r^2.</p>
<p>For example, for N = 7, style = <em>r</em>, inner = 1.0, and outer = 4.0,
values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0.</p>
<p>If the style is <em>bitmap</em>, then 2^N values are written to the file in a
format and order consistent with how they are read in by the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command for pair style <em>table</em>. For
reasonable accuracy in a bitmapped table, choose N &gt;= 12, an <em>inner</em>
value that is smaller than the distance of closest approach of 2
atoms, and an <em>outer</em> value &lt;= cutoff of the potential.</p>
<p>If the pair potential is computed between charged atoms, the charges
of the pair of interacting atoms can optionally be specified. If not
specified, values of Qi = Qj = 1.0 are used.</p>
<p>The file is written in the format used as input for the
<a class="reference internal" href="pair_style.html"><em>pair_style</em></a> <em>table</em> option with <em>keyword</em> as the
section name. Each line written to the file lists an index number
(1-N), a distance (in distance units), an energy (in energy units),
and a force (in force units).</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>All force field coefficients for pair and other kinds of interactions
must be set before this command can be invoked.</p>
<p>Due to how the pairwise force is computed, an inner value &gt; 0.0 must
be specified even if the potential has a finite value at r = 0.0.</p>
<p>For EAM potentials, the pair_write command only tabulates the
pairwise portion of the potential, not the embedding portion.</p>
</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_table.html"><em>pair_style table</em></a>,
<a class="reference internal" href="pair_style.html"><em>pair_style</em></a>, <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="pair-style-yukawa-command">
<span id="index-0"></span><h1>pair_style yukawa command<a class="headerlink" href="#pair-style-yukawa-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-yukawa-gpu-command">
<h1>pair_style yukawa/gpu command<a class="headerlink" href="#pair-style-yukawa-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-yukawa-omp-command">
<h1>pair_style yukawa/omp command<a class="headerlink" href="#pair-style-yukawa-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 yukawa kappa cutoff
</pre></div>
</div>
<ul class="simple">
<li>kappa = screening length (inverse distance units)</li>
<li>cutoff = global cutoff for Yukawa interactions (distance units)</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 yukawa 2.0 2.5
pair_coeff 1 1 100.0 2.3
pair_coeff * * 100.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>yukawa</em> computes pairwise interactions with the formula</p>
<img alt="_images/pair_yukawa.jpg" class="align-center" src="_images/pair_yukawa.jpg" />
<p>Rc is the cutoff.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>A (energy*distance units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global yukawa
cutoff is used.</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>For atom type pairs I,J and I != J, the A coefficient and cutoff
distance for this pair style can be mixed. A is an energy value mixed
like a LJ epsilon. The default mix value is <em>geometric</em>. See the
&#8220;pair_modify&#8221; command for details.</p>
<p>This pair style supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the pair interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>This pair style does 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>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
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<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>
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<div class="section" id="pair-style-yukawa-colloid-command">
<span id="index-0"></span><h1>pair_style yukawa/colloid command<a class="headerlink" href="#pair-style-yukawa-colloid-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-yukawa-colloid-gpu-command">
<h1>pair_style yukawa/colloid/gpu command<a class="headerlink" href="#pair-style-yukawa-colloid-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-yukawa-colloid-omp-command">
<h1>pair_style yukawa/colloid/omp command<a class="headerlink" href="#pair-style-yukawa-colloid-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 yukawa/colloid kappa cutoff
</pre></div>
</div>
<ul class="simple">
<li>kappa = screening length (inverse distance units)</li>
<li>cutoff = global cutoff for colloidal Yukawa interactions (distance units)</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 yukawa/colloid 2.0 2.5
pair_coeff 1 1 100.0 2.3
pair_coeff * * 100.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>yukawa/colloid</em> computes pairwise interactions with the formula</p>
<img alt="_images/pair_yukawa_colloid.jpg" class="align-center" src="_images/pair_yukawa_colloid.jpg" />
<p>where Ri and Rj are the radii of the two particles and Rc is the
cutoff.</p>
<p>In contrast to <a class="reference internal" href="pair_yukawa.html"><em>pair_style yukawa</em></a>, this functional
form arises from the Coulombic interaction between two colloid
particles, screened due to the presence of an electrolyte, see the
book by <a class="reference internal" href="#safran"><span>Safran</span></a> for a derivation in the context of DVLO
theory. <a class="reference internal" href="pair_yukawa.html"><em>Pair_style yukawa</em></a> is a screened Coulombic
potential between two point-charges and uses no such approximation.</p>
<p>This potential applies to nearby particle pairs for which the Derjagin
approximation holds, meaning h &lt;&lt; Ri + Rj, where h is the
surface-to-surface separation of the two particles.</p>
<p>When used in combination with <a class="reference internal" href="pair_colloid.html"><em>pair_style colloid</em></a>,
the two terms become the so-called DLVO potential, which combines
electrostatic repulsion and van der Waals attraction.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>A (energy/distance units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The prefactor A is determined from the relationship between surface
charge and surface potential due to the presence of electrolyte. Note
that the A for this potential style has different units than the A
used in <a class="reference internal" href="pair_yukawa.html"><em>pair_style yukawa</em></a>. For low surface
potentials, i.e. less than about 25 mV, A can be written as:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">A</span> <span class="o">=</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">PI</span> <span class="o">*</span> <span class="n">R</span><span class="o">*</span><span class="n">eps</span><span class="o">*</span><span class="n">eps0</span> <span class="o">*</span> <span class="n">kappa</span> <span class="o">*</span> <span class="n">psi</span><span class="o">^</span><span class="mi">2</span>
</pre></div>
</div>
<p>where</p>
<ul class="simple">
<li>R = colloid radius (distance units)</li>
<li>eps0 = permittivity of free space (charge^2/energy/distance units)</li>
<li>eps = relative permittivity of fluid medium (dimensionless)</li>
<li>kappa = inverse screening length (1/distance units)</li>
<li>psi = surface potential (energy/charge units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global
yukawa/colloid cutoff is used.</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>For atom type pairs I,J and I != J, the A coefficient and cutoff
distance for this pair style can be mixed. A is an energy value mixed
like a LJ epsilon. The default mix value is <em>geometric</em>. See the
&#8220;pair_modify&#8221; command for details.</p>
<p>This pair style supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the pair interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>This pair style does 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>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This style is part of the COLLOID package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>This pair style requires that atoms be finite-size spheres with a
diameter, as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style sphere</em></a>
command.</p>
<p>Per-particle polydispersity is not yet supported by this pair style;
per-type polydispersity is allowed. This means all particles of the
same type must have the same diameter. Each type can have a different
diameter.</p>
</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="safran"><strong>(Safran)</strong> Safran, Statistical Thermodynamics of Surfaces, Interfaces,
And Membranes, Westview Press, ISBN: 978-0813340791 (2003).</p>
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<div class="section" id="pair-style-zbl-command">
<span id="index-0"></span><h1>pair_style zbl command<a class="headerlink" href="#pair-style-zbl-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-zbl-gpu-command">
<h1>pair_style zbl/gpu command<a class="headerlink" href="#pair-style-zbl-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-zbl-omp-command">
<h1>pair_style zbl/omp command<a class="headerlink" href="#pair-style-zbl-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 zbl inner outer
</pre></div>
</div>
<ul class="simple">
<li>inner = distance where switching function begins</li>
<li>outer = global cutoff for ZBL interaction</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 zbl 3.0 4.0
pair_coeff * * 73.0 73.0
pair_coeff 1 1 14.0 14.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>zbl</em> computes the Ziegler-Biersack-Littmark (ZBL) screened nuclear
repulsion for describing high-energy collisions between atoms.
<a class="reference internal" href="#ziegler"><span>(Ziegler)</span></a>. It includes an additional switching function
that ramps the energy, force, and curvature smoothly to zero
between an inner and outer cutoff. The potential
energy due to a pair of atoms at a distance r_ij is given by:</p>
<img alt="_images/pair_zbl.jpg" class="align-center" src="_images/pair_zbl.jpg" />
<p>where e is the electron charge, epsilon_0 is the electrical
permittivity of vacuum, and Z_i and Z_j are the nuclear charges of the
two atoms. The switching function S(r) is identical to that used by
<a class="reference internal" href="pair_gromacs.html"><em>pair_style lj/gromacs</em></a>. Here, the inner and outer
cutoff are the same for all pairs of atom types.</p>
<p>The following coefficients must be defined for each pair of atom types
via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above,
or in the LAMMPS data file.</p>
<ul class="simple">
<li>Z_i (atomic number for first atom type, e.g. 13.0 for aluminum)</li>
<li>Z_j (ditto for second atom type)</li>
</ul>
<p>The values of Z_i and Z_j are normally equal to the atomic
numbers of the two atom types. Thus, the user may optionally
specify only the coefficients for each I==I pair, and rely
on the obvious mixing rule for cross interactions (see below).
Note that when I==I it is required that Z_i == Z_j. When used
with <a class="reference internal" href="pair_hybrid.html"><em>hybrid/overlay</em></a> and pairs are assigned
to more than one sub-style, the mixing rule is not used and
each pair of types interacting with the ZBL sub-style must
be included in a pair_coeff command.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The numerical values of the exponential decay constants in the
screening function depend on the unit of distance. In the above
equation they are given for units of angstroms. LAMMPS will
automatically convert these values to the distance unit of the
specified LAMMPS <a class="reference internal" href="units.html"><em>units</em></a> setting. The values of Z should
always be given as multiples of a proton&#8217;s charge, e.g. 29.0 for
copper.</p>
</div>
<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>For atom type pairs I,J and I != J, the Z_i and Z_j coefficients
can be mixed by taking Z_i and Z_j from the values specified for
I == I and J == J cases. When used
with <a class="reference internal" href="pair_hybrid.html"><em>hybrid/overlay</em></a> and pairs are assigned
to more than one sub-style, the mixing rule is not used and
each pair of types interacting with the ZBL sub-style
must be included in a pair_coeff command.
The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> mix option has no effect on
the mixing behavior</p>
<p>The ZBL pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option, since the ZBL interaction is already smoothed to 0.0 at
the cutoff.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant for
this pair style.</p>
<p>This pair style does 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, since there are no corrections for a potential that goes to
0.0 at the cutoff.</p>
<p>This pair style does not write information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands must be
specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</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="ziegler"><strong>(Ziegler)</strong> J.F. Ziegler, J. P. Biersack and U. Littmark, &#8220;The
Stopping and Range of Ions in Matter,&#8221; Volume 1, Pergamon, 1985.</p>
</div>
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<div class="section" id="pair-style-zero-command">
<span id="index-0"></span><h1>pair_style zero command<a class="headerlink" href="#pair-style-zero-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>
<pre class="literal-block">
pair_style zero cutoff <em>nocoeff</em>
</pre>
<ul class="simple">
<li>zero = style name of this pair style
cutoff = global cutoff (distance units)
nocoeff = ignore all pair_coeff parameters (optional)</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 zero 10.0
pair_style zero 5.0 nocoeff
pair_coeff * *
pair_coeff 1 2*4 3.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a global or per-type cutoff length for the purpose of
building a neighbor list and acquiring ghost atoms, but do
not compute any pairwise forces or energies.</p>
<p>This can be useful for fixes or computes which require a neighbor list
to enumerate pairs of atoms within some cutoff distance, but when
pairwise forces are not otherwise needed. Examples are the <a class="reference internal" href="fix_bond_create.html"><em>fix bond/create</em></a>, <a class="reference internal" href="compute_rdf.html"><em>compute rdf</em></a>,
<a class="reference internal" href="compute_voronoi_atom.html"><em>compute voronoi/atom</em></a> commands.</p>
<p>Note that the <a class="reference internal" href="comm_modify.html"><em>comm_modify cutoff</em></a> command can be
used to insure communication of ghost atoms even when a pair style is
not defined, but it will not trigger neighbor list generation.</p>
<p>The optional <em>nocoeff</em> flag allows to read data files with a PairCoeff
section for any pair style. Similarly, any pair_coeff commands
will only be checked for the atom type numbers and the rest ignored.
In this case, only the global cutoff will be used.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>cutoff (distance units)</li>
</ul>
<p>This coefficient is optional. If not specified, the global cutoff
specified in the pair_style command is used. If the pair_style has
been specified with the optional <em>nocoeff</em> flag, then a cutoff
pair coefficient is ignored.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>The cutoff distance for this pair style can be mixed. The default mix
value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command for details.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style 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. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</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_none.html"><em>pair_style none</em></a></p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="partition-command">
<span id="index-0"></span><h1>partition command<a class="headerlink" href="#partition-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>partition style N command ...
</pre></div>
</div>
<ul class="simple">
<li>style = <em>yes</em> or <em>no</em></li>
<li>N = partition number (see asterisk form below)</li>
<li>command = any LAMMPS command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<pre class="literal-block">
partition yes 1 processors 4 10 6
partition no 5 print &quot;Active partition&quot;
partition yes <em>5 fix all nve
partition yes 6</em> fix all nvt temp 1.0 1.0 0.1
</pre>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>This command invokes the specified command on a subset of the
partitions of processors you have defined via the -partition
command-line switch. See <a class="reference internal" href="Section_start.html#start-7"><span>Section_start 6</span></a>
for an explanation of the switch.</p>
<p>Normally, every input script command in your script is invoked by
every partition. This behavior can be modified by defining world- or
universe-style <a class="reference internal" href="variable.html"><em>variables</em></a> that have different values
for each partition. This mechanism can be used to cause your script
to jump to different input script files on different partitions, if
such a variable is used in a <a class="reference internal" href="jump.html"><em>jump</em></a> command.</p>
<p>The &#8220;partition&#8221; command is another mechanism for having as input
script operate differently on different partitions. It is basically a
prefix on any LAMMPS command. The commmand will only be invoked on
the partition(s) specified by the <em>style</em> and <em>N</em> arguments.</p>
<p>If the <em>style</em> is <em>yes</em>, the command will be invoked on any partition
which matches the <em>N</em> argument. If the <em>style</em> is <em>no</em> the command
will be invoked on all the partitions which do not match the Np
argument.</p>
<p>Partitions are numbered from 1 to Np, where Np is the number of
partitions specified by the <a class="reference internal" href="Section_start.html#start-7"><span>-partition command-line switch</span></a>.</p>
<p><em>N</em> can be specified in one of two ways. An explicit numeric value
can be used, as in the 1st example above. Or a wild-card asterisk can
be used to span a range of partition numbers. This takes the form &#8220;*&#8221;
or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;. An asterisk with no numeric values means
all partitions from 1 to Np. A leading asterisk means all partitions
from 1 to n (inclusive). A trailing asterisk means all partitions
from n to Np (inclusive). A middle asterisk means all partitions from
m to n (inclusive).</p>
<p>This command can be useful for the &#8220;run_style verlet/split&#8221; command
which imposed requirements on how the <a class="reference internal" href="processors.html"><em>processors</em></a>
command lays out a 3d grid of processors in each of 2 partitions.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<blockquote>
<div>none</div></blockquote>
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<div class="section" id="prd-command">
<span id="index-0"></span><h1>prd command<a class="headerlink" href="#prd-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>prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ...
</pre></div>
</div>
<ul class="simple">
<li>N = # of timesteps to run (not including dephasing/quenching)</li>
<li>t_event = timestep interval between event checks</li>
<li>n_dephase = number of velocity randomizations to perform in each dephase run</li>
<li>t_dephase = number of timesteps to run dynamics after each velocity randomization during dephase</li>
<li>t_correlate = number of timesteps within which 2 consecutive events are considered to be correlated</li>
<li>compute-ID = ID of the compute used for event detection</li>
<li>random_seed = random # seed (positive integer)</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>min</em> or <em>temp</em> or <em>vel</em></li>
</ul>
<pre class="literal-block">
<em>min</em> values = etol ftol maxiter maxeval
etol = stopping tolerance for energy, used in quenching
ftol = stopping tolerance for force, used in quenching
maxiter = max iterations of minimize, used in quenching
maxeval = max number of force/energy evaluations, used in quenching
<em>temp</em> value = Tdephase
Tdephase = target temperature for velocity randomization, used in dephasing
<em>vel</em> values = loop dist
loop = <em>all</em> or <em>local</em> or <em>geom</em>, used in dephasing
dist = <em>uniform</em> or <em>gaussian</em>, used in dephasing
<em>time</em> value = <em>steps</em> or <em>clock</em>
<em>steps</em> = simulation runs for N timesteps on each replica (default)
<em>clock</em> = simulation runs for N timesteps across all replicas
</pre>
</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>prd 5000 100 10 10 100 1 54982
prd 5000 100 10 10 100 1 54982 min 0.1 0.1 100 200
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Run a parallel replica dynamics (PRD) simulation using multiple
replicas of a system. One or more replicas can be used. The total
number of steps <em>N</em> to run can be interpreted in one of two ways; see
discussion of the <em>time</em> keyword below.</p>
<p>PRD is described in <a class="reference internal" href="tad.html#voter"><span>this paper</span></a> by Art Voter. It is a method
for performing accelerated dynamics that is suitable for
infrequent-event systems that obey first-order kinetics. A good
overview of accelerated dynamics methods for such systems in given in
<a class="reference internal" href="tad.html#voter2"><span>this review paper</span></a> from the same group. To quote from the
paper: &#8220;The dynamical evolution is characterized by vibrational
excursions within a potential basin, punctuated by occasional
transitions between basins.&#8221; The transition probability is
characterized by p(t) = k*exp(-kt) where k is the rate constant.
Running multiple replicas gives an effective enhancement in the
timescale spanned by the multiple simulations, while waiting for an
event to occur.</p>
<p>Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see <a class="reference internal" href="Section_start.html#start-7"><span>Section_start 6</span></a> of the
manual. Note that if you have MPI installed, you can run a
multi-replica simulation with more replicas (partitions) than you have
physical processors, e.g you can run a 10-replica simulation on one or
two processors. For PRD, this makes little sense, since this offers
no effective parallel speed-up in searching for infrequent events. See
<a class="reference internal" href="Section_howto.html#howto-5"><span>Section_howto 5</span></a> of the manual for further
discussion.</p>
<p>When a PRD simulation is performed, it is assumed that each replica is
running the same model, though LAMMPS does not check for this.
I.e. the simulation domain, the number of atoms, the interaction
potentials, etc should be the same for every replica.</p>
<p>A PRD run has several stages, which are repeated each time an &#8220;event&#8221;
occurs in one of the replicas, as defined below. The logic for a PRD
run is as follows:</p>
<div class="highlight-python"><div class="highlight"><pre>while (time remains):
dephase for n_dephase*t_dephase steps
until (event occurs on some replica):
run dynamics for t_event steps
quench
check for uncorrelated event on any replica
until (no correlated event occurs):
run dynamics for t_correlate steps
quench
check for correlated event on this replica
event replica shares state with all replicas
</pre></div>
</div>
<p>Before this loop begins, the state of the system on replica 0 is
shared with all replicas, so that all replicas begin from the same
initial state. The first potential energy basin is identified by
quenching (an energy minimization, see below) the initial state and
storing the resulting coordinates for reference.</p>
<p>In the first stage, dephasing is performed by each replica
independently to eliminate correlations between replicas. This is
done by choosing a random set of velocities, based on the
<em>random_seed</em> that is specified, and running <em>t_dephase</em> timesteps of
dynamics. This is repeated <em>n_dephase</em> times. At each of the
<em>n_dephase</em> stages, if an event occurs during the <em>t_dephase</em> steps of
dynamics for a particular replica, the replica repeats the stage until
no event occurs.</p>
<p>If the <em>temp</em> keyword is not specified, the target temperature for
velocity randomization for each replica is the current temperature of
that replica. Otherwise, it is the specified <em>Tdephase</em> temperature.
The style of velocity randomization is controlled using the keyword
<em>vel</em> with arguments that have the same meaning as their counterparts
in the <a class="reference internal" href="velocity.html"><em>velocity</em></a> command.</p>
<p>In the second stage, each replica runs dynamics continuously, stopping
every <em>t_event</em> steps to check if a transition event has occurred.
This check is performed by quenching the system and comparing the
resulting atom coordinates to the coordinates from the previous basin.
The first time through the PRD loop, the &#8220;previous basin&#8221; is the set
of quenched coordinates from the initial state of the system.</p>
<p>A quench is an energy minimization and is performed by whichever
algorithm has been defined by the <a class="reference internal" href="min_style.html"><em>min_style</em></a> command.
Minimization parameters may be set via the
<a class="reference internal" href="min_modify.html"><em>min_modify</em></a> command and by the <em>min</em> keyword of the
PRD command. The latter are the settings that would be used with the
<a class="reference internal" href="minimize.html"><em>minimize</em></a> command. Note that typically, you do not
need to perform a highly-converged minimization to detect a transition
event.</p>
<p>The event check is performed by a compute with the specified
<em>compute-ID</em>. Currently there is only one compute that works with the
PRD commmand, which is the <a class="reference internal" href="compute_event_displace.html"><em>compute event/displace</em></a> command. Other
event-checking computes may be added. <a class="reference internal" href="compute_event_displace.html"><em>Compute event/displace</em></a> checks whether any atom in
the compute group has moved further than a specified threshold
distance. If so, an &#8220;event&#8221; has occurred.</p>
<p>In the third stage, the replica on which the event occurred (event
replica) continues to run dynamics to search for correlated events.
This is done by running dynamics for <em>t_correlate</em> steps, quenching
every <em>t_event</em> steps, and checking if another event has occurred.</p>
<p>The first time no correlated event occurs, the final state of the
event replica is shared with all replicas, the new basin reference
coordinates are updated with the quenched state, and the outer loop
begins again. While the replica event is searching for correlated
events, all the other replicas also run dynamics and event checking
with the same schedule, but the final states are always overwritten by
the state of the event replica.</p>
<p>The outer loop of the pseudo-code above continues until <em>N</em> steps of
dynamics have been performed. Note that <em>N</em> only includes the
dynamics of stages 2 and 3, not the steps taken during dephasing or
the minimization iterations of quenching. The specified <em>N</em> is
interpreted in one of two ways, depending on the <em>time</em> keyword. If
the <em>time</em> value is <em>steps</em>, which is the default, then each replica
runs for <em>N</em> timesteps. If the <em>time</em> value is <em>clock</em>, then the
simulation runs until <em>N</em> aggregate timesteps across all replicas have
elapsed. This aggregate time is the &#8220;clock&#8221; time defined below, which
typically advances nearly M times faster than the timestepping on a
single replica.</p>
<hr class="docutils" />
<p>Four kinds of output can be generated during a PRD run: event
statistics, thermodynamic output by each replica, dump files, and
restart files.</p>
<p>When running with multiple partitions (each of which is a replica in
this case), the print-out to the screen and master log.lammps file is
limited to event statistics. Note that if a PRD run is performed on
only a single replica then the event statistics will be intermixed
with the usual thermodynamic output discussed below.</p>
<p>The quantities printed each time an event occurs are the timestep, CPU
time, clock, event number, a correlation flag, the number of
coincident events, and the replica number of the chosen event.</p>
<p>The timestep is the usual LAMMPS timestep, except that time does not
advance during dephasing or quenches, but only during dynamics. Note
that are two kinds of dynamics in the PRD loop listed above. The
first is when all replicas are performing independent dynamics,
waiting for an event to occur. The second is when correlated events
are being searched for and only one replica is running dynamics.</p>
<p>The CPU time is the total processor time since the start of the PRD
run.</p>
<p>The clock is the same as the timestep except that it advances by M
steps every timestep during the first kind of dynamics when the M
replicas are running independently. The clock advances by only 1 step
per timestep during the second kind of dynamics, since only a single
replica is checking for a correlated event. Thus &#8220;clock&#8221; time
represents the aggregate time (in steps) that effectively elapses
during a PRD simulation on M replicas. If most of the PRD run is
spent in the second stage of the loop above, searching for infrequent
events, then the clock will advance nearly M times faster than it
would if a single replica was running. Note the clock time between
events will be drawn from p(t).</p>
<p>The event number is a counter that increments with each event, whether
it is uncorrelated or correlated.</p>
<p>The correlation flag will be 0 when an uncorrelated event occurs
during the second stage of the loop listed above, i.e. when all
replicas are running independently. The correlation flag will be 1
when a correlated event occurs during the third stage of the loop
listed above, i.e. when only one replica is running dynamics.</p>
<p>When more than one replica detects an event at the end of the second
stage, then one of them is chosen at random. The number of coincident
events is the number of replicas that detected an event. Normally, we
expect this value to be 1. If it is often greater than 1, then either
the number of replicas is too large, or <em>t_event</em> is too large.</p>
<p>The replica number is the ID of the replica (from 0 to M-1) that
found the event.</p>
<hr class="docutils" />
<p>When running on multiple partitions, LAMMPS produces additional log
files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For
the PRD command, these contain the thermodynamic output for each
replica. You will see short runs and minimizations corresponding to
the dynamics and quench operations of the loop listed above. The
timestep will be reset aprpopriately depending on whether the
operation advances time or not.</p>
<p>After the PRD command completes, timing statistics for the PRD run are
printed in each replica&#8217;s log file, giving a breakdown of how much CPU
time was spent in each stage (dephasing, dynamics, quenching, etc).</p>
<hr class="docutils" />
<p>Any <a class="reference internal" href="dump.html"><em>dump files</em></a> defined in the input script, will be
written to during a PRD run at timesteps corresponding to both
uncorrelated and correlated events. This means the the requested dump
frequency in the <a class="reference internal" href="dump.html"><em>dump</em></a> command is ignored. There will be
one dump file (per dump command) created for all partitions.</p>
<p>The atom coordinates of the dump snapshot are those of the minimum
energy configuration resulting from quenching following a transition
event. The timesteps written into the dump files correspond to the
timestep at which the event occurred and NOT the clock. A dump
snapshot corresponding to the initial minimum state used for event
detection is written to the dump file at the beginning of each PRD
run.</p>
<hr class="docutils" />
<p>If the <a class="reference internal" href="restart.html"><em>restart</em></a> command is used, a single restart file
for all the partitions is generated, which allows a PRD run to be
continued by a new input script in the usual manner.</p>
<p>The restart file is generated at the end of the loop listed above. If
no correlated events are found, this means it contains a snapshot of
the system at time T + <em>t_correlate</em>, where T is the time at which the
uncorrelated event occurred. If correlated events were found, then it
contains a snapshot of the system at time T + <em>t_correlate</em>, where T
is the time of the last correlated event.</p>
<p>The restart frequency specified in the <a class="reference internal" href="restart.html"><em>restart</em></a> command
is interpreted differently when performing a PRD run. It does not
mean the timestep interval between restart files. Instead it means an
event interval for uncorrelated events. Thus a frequency of 1 means
write a restart file every time an uncorrelated event occurs. A
frequency of 10 means write a restart file every 10th uncorrelated
event.</p>
<p>When an input script reads a restart file from a previous PRD run, the
new script can be run on a different number of replicas or processors.
However, it is assumed that <em>t_correlate</em> in the new PRD command is
the same as it was previously. If not, the calculation of the &#8220;clock&#8221;
value for the first event in the new run will be slightly off.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This command can only be used if LAMMPS was built with the REPLICA
package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
for more info on packages.</p>
<p><em>N</em> and <em>t_correlate</em> settings must be integer multiples of
<em>t_event</em>.</p>
<p>Runs restarted from restart file written during a PRD run will not
produce identical results due to changes in the random numbers used
for dephasing.</p>
<p>This command cannot be used when any fixes are defined that keep track
of elapsed time to perform time-dependent operations. Examples
include the &#8220;ave&#8221; fixes such as <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a>. Also <a class="reference internal" href="fix_dt_reset.html"><em>fix dt/reset</em></a> and <a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a>.</p>
</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="compute_event_displace.html"><em>compute event/displace</em></a>,
<a class="reference internal" href="min_modify.html"><em>min_modify</em></a>, <a class="reference internal" href="min_style.html"><em>min_style</em></a>,
<a class="reference internal" href="run_style.html"><em>run_style</em></a>, <a class="reference internal" href="minimize.html"><em>minimize</em></a>,
<a class="reference internal" href="velocity.html"><em>velocity</em></a>, <a class="reference internal" href="temper.html"><em>temper</em></a>, <a class="reference internal" href="neb.html"><em>neb</em></a>,
<a class="reference internal" href="tad.html"><em>tad</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option defaults are min = 0.1 0.1 40 50, no temp setting, vel =
geom gaussian, and time = steps.</p>
<hr class="docutils" />
<p id="voter"><strong>(Voter)</strong> Voter, Phys Rev B, 57, 13985 (1998).</p>
<p id="voter2"><strong>(Voter2)</strong> Voter, Montalenti, Germann, Annual Review of Materials
Research 32, 321 (2002).</p>
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<div class="section" id="print-command">
<span id="index-0"></span><h1>print command<a class="headerlink" href="#print-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>print string keyword value
</pre></div>
</div>
<ul class="simple">
<li>string = text string to print, which may contain variables</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>file</em> or <em>append</em> or <em>screen</em></li>
</ul>
<pre class="literal-block">
<em>file</em> value = filename
<em>append</em> value = filename
<em>screen</em> value = <em>yes</em> or <em>no</em>
</pre>
</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>print &quot;Done with equilibration&quot; file info.dat
print Vol=$v append info.dat screen no
print &quot;The system volume is now $v&quot;
print &#39;The system volume is now $v&#39;
print &quot;&quot;&quot;
System volume = $v
System temperature = $t
&quot;&quot;&quot;
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Print a text string to the screen and logfile. The text string must
be a single argument, so if it is one line but more than one word, it
should be enclosed in single or double quotes. To generate multiple
lines of output, the string can be enclosed in triple quotes, as in
the last example above. If the text string contains variables, they
will be evaluated and their current values printed.</p>
<p>If the <em>file</em> or <em>append</em> keyword is used, a filename is specified to
which the output will be written. If <em>file</em> is used, then the
filename is overwritten if it already exists. If <em>append</em> is used,
then the filename is appended to if it already exists, or created if
it does not exist.</p>
<p>If the <em>screen</em> keyword is used, output to the screen and logfile can
be turned on or off as desired.</p>
<p>If you want the print command to be executed multiple times (with
changing variable values), there are 3 options. First, consider using
the <a class="reference internal" href="fix_print.html"><em>fix print</em></a> command, which will print a string
periodically during a simulation. Second, the print command can be
used as an argument to the <em>every</em> option of the <a class="reference internal" href="run.html"><em>run</em></a>
command. Third, the print command could appear in a section of the
input script that is looped over (see the <a class="reference internal" href="jump.html"><em>jump</em></a> and
<a class="reference internal" href="next.html"><em>next</em></a> commands).</p>
<p>See the <a class="reference internal" href="variable.html"><em>variable</em></a> command for a description of <em>equal</em>
style variables which are typically the most useful ones to use with
the print command. Equal-style variables can calculate formulas
involving mathematical operations, atom properties, group properties,
thermodynamic properties, global values calculated by a
<a class="reference internal" href="compute.html"><em>compute</em></a> or <a class="reference internal" href="fix.html"><em>fix</em></a>, or references to other
<a class="reference internal" href="variable.html"><em>variables</em></a>.</p>
</div>
<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="fix_print.html"><em>fix print</em></a>, <a class="reference internal" href="variable.html"><em>variable</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option defaults are no file output and screen = yes.</p>
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<div class="section" id="processors-command">
<span id="index-0"></span><h1>processors command<a class="headerlink" href="#processors-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>processors Px Py Pz keyword args ...
</pre></div>
</div>
<ul class="simple">
<li>Px,Py,Pz = # of processors in each dimension of 3d grid overlaying the simulation domain</li>
<li>zero or more keyword/arg pairs may be appended</li>
<li>keyword = <em>grid</em> or <em>map</em> or <em>part</em> or <em>file</em></li>
</ul>
<pre class="literal-block">
<em>grid</em> arg = gstyle params ...
gstyle = <em>onelevel</em> or <em>twolevel</em> or <em>numa</em> or <em>custom</em>
onelevel params = none
twolevel params = Nc Cx Cy Cz
Nc = number of cores per node
Cx,Cy,Cz = # of cores in each dimension of 3d sub-grid assigned to each node
numa params = none
custom params = infile
infile = file containing grid layout
<em>map</em> arg = <em>cart</em> or <em>cart/reorder</em> or <em>xyz</em> or <em>xzy</em> or <em>yxz</em> or <em>yzx</em> or <em>zxy</em> or <em>zyx</em>
cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0
cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1
xyz,xzy,yxz,yzx,zxy,zyx = map procesors to 3d grid in IJK ordering
<em>numa</em> arg = none
<em>part</em> args = Psend Precv cstyle
Psend = partition # (1 to Np) which will send its processor layout
Precv = partition # (1 to Np) which will recv the processor layout
cstyle = <em>multiple</em>
<em>multiple</em> = Psend grid will be multiple of Precv grid in each dimension
<em>file</em> arg = outfile
outfile = name of file to write 3d grid of processors to
</pre>
</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>processors * * 5
processors 2 4 4
processors * * 8 map xyz
processors * * * grid numa
processors * * * grid twolevel 4 * * 1
processors 4 8 16 grid custom myfile
processors * * * part 1 2 multiple
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Specify how processors are mapped as a regular 3d grid to the global
simulation box. The mapping involves 2 steps. First if there are P
processors it means choosing a factorization P = Px by Py by Pz so
that there are Px processors in the x dimension, and similarly for the
y and z dimensions. Second, the P processors are mapped to the
regular 3d grid. The arguments to this command control each of these
2 steps.</p>
<p>The Px, Py, Pz parameters affect the factorization. Any of the 3
parameters can be specified with an asterisk &#8220;*&#8221;, which means LAMMPS
will choose the number of processors in that dimension of the grid.
It will do this based on the size and shape of the global simulation
box so as to minimize the surface-to-volume ratio of each processor&#8217;s
sub-domain.</p>
<p>Choosing explicit values for Px or Py or Pz can be used to override
the default manner in which LAMMPS will create the regular 3d grid of
processors, if it is known to be sub-optimal for a particular problem.
E.g. a problem where the extent of atoms will change dramatically in a
particular dimension over the course of the simulation.</p>
<p>The product of Px, Py, Pz must equal P, the total # of processors
LAMMPS is running on. For a <a class="reference internal" href="dimension.html"><em>2d simulation</em></a>, Pz must
equal 1.</p>
<p>Note that if you run on a prime number of processors P, then a grid
such as 1 x P x 1 will be required, which may incur extra
communication costs due to the high surface area of each processor&#8217;s
sub-domain.</p>
<p>Also note that if multiple partitions are being used then P is the
number of processors in this partition; see <a class="reference internal" href="Section_start.html#start-7"><span>this section</span></a> for an explanation of the
-partition command-line switch. Also note that you can prefix the
processors command with the <a class="reference internal" href="partition.html"><em>partition</em></a> command to
easily specify different Px,Py,Pz values for different partitions.</p>
<p>You can use the <a class="reference internal" href="partition.html"><em>partition</em></a> command to specify
different processor grids for different partitions, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>partition yes 1 processors 4 4 4
partition yes 2 processors 2 3 2
</pre></div>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This command only affects the initial regular 3d grid created
when the simulation box is first specified via a
<a class="reference internal" href="create_box.html"><em>create_box</em></a> or <a class="reference internal" href="read_data.html"><em>read_data</em></a> or
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command. Or if the simulation box is
re-created via the <a class="reference internal" href="replicate.html"><em>replicate</em></a> command. The same
regular grid is initially created, regardless of which
<a class="reference internal" href="comm_style.html"><em>comm_style</em></a> command is in effect.</p>
</div>
<p>If load-balancing is never invoked via the <a class="reference internal" href="balance.html"><em>balance</em></a> or
<a class="reference internal" href="fix_balance.html"><em>fix balance</em></a> commands, then the initial regular grid
will persist for all simulations. If balancing is performed, some of
the methods invoked by those commands retain the logical toplogy of
the initial 3d grid, and the mapping of processors to the grid
specified by the processors command. However the grid spacings in
different dimensions may change, so that processors own sub-domains of
different sizes. If the <a class="reference internal" href="comm_style.html"><em>comm_style tiled</em></a> command is
used, methods invoked by the balancing commands may discard the 3d
grid of processors and tile the simulation domain with sub-domains of
different sizes and shapes which no longer have a logical 3d
connectivity. If that occurs, all the information specified by the
processors command is ignored.</p>
<hr class="docutils" />
<p>The <em>grid</em> keyword affects the factorization of P into Px,Py,Pz and it
can also affect how the P processor IDs are mapped to the 3d grid of
processors.</p>
<p>The <em>onelevel</em> style creates a 3d grid that is compatible with the
Px,Py,Pz settings, and which minimizes the surface-to-volume ratio of
each processor&#8217;s sub-domain, as described above. The mapping of
processors to the grid is determined by the <em>map</em> keyword setting.</p>
<p>The <em>twolevel</em> style can be used on machines with multicore nodes to
minimize off-node communication. It insures that contiguous
sub-sections of the 3d grid are assigned to all the cores of a node.
For example if <em>Nc</em> is 4, then 2x2x1 or 2x1x2 or 1x2x2 sub-sections of
the 3d grid will correspond to the cores of each node. This affects
both the factorization and mapping steps.</p>
<p>The <em>Cx</em>, <em>Cy</em>, <em>Cz</em> settings are similar to the <em>Px</em>, <em>Py</em>, <em>Pz</em>
settings, only their product should equal <em>Nc</em>. Any of the 3
parameters can be specified with an asterisk &#8220;*&#8221;, which means LAMMPS
will choose the number of cores in that dimension of the node&#8217;s
sub-grid. As with Px,Py,Pz, it will do this based on the size and
shape of the global simulation box so as to minimize the
surface-to-volume ratio of each processor&#8217;s sub-domain.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">For the <em>twolevel</em> style to work correctly, it assumes the MPI
ranks of processors LAMMPS is running on are ordered by core and then
by node. E.g. if you are running on 2 quad-core nodes, for a total of
8 processors, then it assumes processors 0,1,2,3 are on node 1, and
processors 4,5,6,7 are on node 2. This is the default rank ordering
for most MPI implementations, but some MPIs provide options for this
ordering, e.g. via environment variable settings.</p>
</div>
<p>The <em>numa</em> style operates similar to the <em>twolevel</em> keyword except
that it auto-detects which cores are running on which nodes.
Currently, it does this in only 2 levels, but it may be extended in
the future to account for socket topology and other non-uniform memory
access (NUMA) costs. It also uses a different algorithm than the
<em>twolevel</em> keyword for doing the two-level factorization of the
simulation box into a 3d processor grid to minimize off-node
communication, and it does its own MPI-based mapping of nodes and
cores to the regular 3d grid. Thus it may produce a different layout
of the processors than the <em>twolevel</em> options.</p>
<p>The <em>numa</em> style will give an error if the number of MPI processes is
not divisible by the number of cores used per node, or any of the Px
or Py of Pz values is greater than 1.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Unlike the <em>twolevel</em> style, the <em>numa</em> style does not require
any particular ordering of MPI ranks i norder to work correctly. This
is because it auto-detects which processes are running on which nodes.</p>
</div>
<p>The <em>custom</em> style uses the file <em>infile</em> to define both the 3d
factorization and the mapping of processors to the grid.</p>
<p>The file should have the following format. Any number of initial
blank or comment lines (starting with a &#8220;#&#8221; character) can be present.
The first non-blank, non-comment line should have
3 values:</p>
<div class="highlight-python"><div class="highlight"><pre>Px Py Py
</pre></div>
</div>
<p>These must be compatible with the total number of processors
and the Px, Py, Pz settings of the processors commmand.</p>
<p>This line should be immediately followed by
P = Px*Py*Pz lines of the form:</p>
<div class="highlight-python"><div class="highlight"><pre>ID I J K
</pre></div>
</div>
<p>where ID is a processor ID (from 0 to P-1) and I,J,K are the
processors location in the 3d grid. I must be a number from 1 to Px
(inclusive) and similarly for J and K. The P lines can be listed in
any order, but no processor ID should appear more than once.</p>
<hr class="docutils" />
<p>The <em>map</em> keyword affects how the P processor IDs (from 0 to P-1) are
mapped to the 3d grid of processors. It is only used by the
<em>onelevel</em> and <em>twolevel</em> grid settings.</p>
<p>The <em>cart</em> style uses the family of MPI Cartesian functions to perform
the mapping, namely MPI_Cart_create(), MPI_Cart_get(),
MPI_Cart_shift(), and MPI_Cart_rank(). It invokes the
MPI_Cart_create() function with its reorder flag = 0, so that MPI is
not free to reorder the processors.</p>
<p>The <em>cart/reorder</em> style does the same thing as the <em>cart</em> style
except it sets the reorder flag to 1, so that MPI can reorder
processors if it desires.</p>
<p>The <em>xyz</em>, <em>xzy</em>, <em>yxz</em>, <em>yzx</em>, <em>zxy</em>, and <em>zyx</em> styles are all
similar. If the style is IJK, then it maps the P processors to the
grid so that the processor ID in the I direction varies fastest, the
processor ID in the J direction varies next fastest, and the processor
ID in the K direction varies slowest. For example, if you select
style <em>xyz</em> and you have a 2x2x2 grid of 8 processors, the assignments
of the 8 octants of the simulation domain will be:</p>
<div class="highlight-python"><div class="highlight"><pre>proc 0 = lo x, lo y, lo z octant
proc 1 = hi x, lo y, lo z octant
proc 2 = lo x, hi y, lo z octant
proc 3 = hi x, hi y, lo z octant
proc 4 = lo x, lo y, hi z octant
proc 5 = hi x, lo y, hi z octant
proc 6 = lo x, hi y, hi z octant
proc 7 = hi x, hi y, hi z octant
</pre></div>
</div>
<p>Note that, in principle, an MPI implementation on a particular machine
should be aware of both the machine&#8217;s network topology and the
specific subset of processors and nodes that were assigned to your
simulation. Thus its MPI_Cart calls can optimize the assignment of
MPI processes to the 3d grid to minimize communication costs. In
practice, however, few if any MPI implementations actually do this.
So it is likely that the <em>cart</em> and <em>cart/reorder</em> styles simply give
the same result as one of the IJK styles.</p>
<p>Also note, that for the <em>twolevel</em> grid style, the <em>map</em> setting is
used to first map the nodes to the 3d grid, then again to the cores
within each node. For the latter step, the <em>cart</em> and <em>cart/reorder</em>
styles are not supported, so an <em>xyz</em> style is used in their place.</p>
<hr class="docutils" />
<p>The <em>part</em> keyword affects the factorization of P into Px,Py,Pz.</p>
<p>It can be useful when running in multi-partition mode, e.g. with the
<a class="reference internal" href="run_style.html"><em>run_style verlet/split</em></a> command. It specifies a
dependency bewteen a sending partition <em>Psend</em> and a receiving
partition <em>Precv</em> which is enforced when each is setting up their own
mapping of their processors to the simulation box. Each of <em>Psend</em>
and <em>Precv</em> must be integers from 1 to Np, where Np is the number of
partitions you have defined via the <a class="reference internal" href="Section_start.html#start-7"><span>-partition command-line switch</span></a>.</p>
<p>A &#8220;dependency&#8221; means that the sending partition will create its
regular 3d grid as Px by Py by Pz and after it has done this, it will
send the Px,Py,Pz values to the receiving partition. The receiving
partition will wait to receive these values before creating its own
regular 3d grid and will use the sender&#8217;s Px,Py,Pz values as a
constraint. The nature of the constraint is determined by the
<em>cstyle</em> argument.</p>
<p>For a <em>cstyle</em> of <em>multiple</em>, each dimension of the sender&#8217;s processor
grid is required to be an integer multiple of the corresponding
dimension in the receiver&#8217;s processor grid. This is a requirement of
the <a class="reference internal" href="run_style.html"><em>run_style verlet/split</em></a> command.</p>
<p>For example, assume the sending partition creates a 4x6x10 grid = 240
processor grid. If the receiving partition is running on 80
processors, it could create a 4x2x10 grid, but it will not create a
2x4x10 grid, since in the y-dimension, 6 is not an integer multiple of
4.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you use the <a class="reference internal" href="partition.html"><em>partition</em></a> command to invoke
different &#8220;processsors&#8221; commands on different partitions, and you also
use the <em>part</em> keyword, then you must insure that both the sending and
receiving partitions invoke the &#8220;processors&#8221; command that connects the
2 partitions via the <em>part</em> keyword. LAMMPS cannot easily check for
this, but your simulation will likely hang in its setup phase if this
error has been made.</p>
</div>
<hr class="docutils" />
<p>The <em>file</em> keyword writes the mapping of the factorization of P
processors and their mapping to the 3d grid to the specified file
<em>outfile</em>. This is useful to check that you assigned physical
processors in the manner you desired, which can be tricky to figure
out, especially when running on multiple partitions or on, a multicore
machine or when the processor ranks were reordered by use of the
<a class="reference internal" href="Section_start.html#start-7"><span>-reorder command-line switch</span></a> or due to
use of MPI-specific launch options such as a config file.</p>
<p>If you have multiple partitions you should insure that each one writes
to a different file, e.g. using a <a class="reference internal" href="variable.html"><em>world-style variable</em></a>
for the filename. The file has a self-explanatory header, followed by
one-line per processor in this format:</p>
<p>world-ID universe-ID original-ID: I J K: name</p>
<p>The IDs are the processor&#8217;s rank in this simulation (the world), the
universe (of multiple simulations), and the original MPI communicator
used to instantiate LAMMPS, respectively. The world and universe IDs
will only be different if you are running on more than one partition;
see the <a class="reference internal" href="Section_start.html#start-7"><span>-partition command-line switch</span></a>.
The universe and original IDs will only be different if you used the
<a class="reference internal" href="Section_start.html#start-7"><span>-reorder command-line switch</span></a> to reorder
the processors differently than their rank in the original
communicator LAMMPS was instantiated with.</p>
<p>I,J,K are the indices of the processor in the regular 3d grid, each
from 1 to Nd, where Nd is the number of processors in that dimension
of the grid.</p>
<p>The <em>name</em> is what is returned by a call to MPI_Get_processor_name()
and should represent an identifier relevant to the physical processors
in your machine. Note that depending on the MPI implementation,
multiple cores can have the same <em>name</em>.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This command cannot be used after the simulation box is defined by a
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="create_box.html"><em>create_box</em></a> command.
It can be used before a restart file is read to change the 3d
processor grid from what is specified in the restart file.</p>
<p>The <em>grid numa</em> keyword only currently works with the <em>map cart</em>
option.</p>
<p>The <em>part</em> keyword (for the receiving partition) only works with the
<em>grid onelevel</em> or <em>grid twolevel</em> options.</p>
</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="partition.html"><em>partition</em></a>, <a class="reference internal" href="Section_start.html#start-7"><span>-reorder command-line switch</span></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option defaults are Px Py Pz = * * <a href="#id1"><span class="problematic" id="id2">*</span></a>, grid = onelevel, and map =
cart.</p>
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<div class="section" id="python-command">
<span id="index-0"></span><h1>python command<a class="headerlink" href="#python-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>python func keyword args ...
</pre></div>
</div>
<ul class="simple">
<li>func = name of Python function</li>
<li>one or more keyword/args pairs must be appended</li>
</ul>
<pre class="literal-block">
keyword = <em>invoke</em> or <em>input</em> or <em>return</em> or <em>format</em> or <em>file</em> or <em>here</em> or <em>exists</em>
<em>invoke</em> arg = none = invoke the previously defined Python function
<em>input</em> args = N i1 i2 ... iN
N = # of inputs to function
i1,...,iN = value, SELF, or LAMMPS variable name
value = integer number, floating point number, or string
SELF = reference to LAMMPS itself which can be accessed by Python function
variable = v_name, where name = name of LAMMPS variable, e.g. v_abc
<em>return</em> arg = varReturn
varReturn = v_name = LAMMPS variable name which return value of function will be assigned to
<em>format</em> arg = fstring with M characters
M = N if no return value, where N = # of inputs
M = N+1 if there is a return value
fstring = each character (i,f,s,p) corresponds in order to an input or return value
'i' = integer, 'f' = floating point, 's' = string, 'p' = SELF
<em>file</em> arg = filename
filename = file of Python code, which defines func
<em>here</em> arg = inline
inline = one or more lines of Python code which defines func
must be a single argument, typically enclosed between triple quotes
<em>exists</em> arg = none = Python code has been loaded by previous python command
</pre>
</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>python pForce input 2 v_x 20.0 return v_f format fff file force.py
python pForce invoke
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>python factorial input 1 myN return v_fac format ii here &quot;&quot;&quot;
def factorial(n):
if n == 1: return n
return n * factorial(n-1)
&quot;&quot;&quot;
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>python loop input 1 SELF return v_value format -f here &quot;&quot;&quot;
def loop(lmpptr,N,cut0):
from lammps import lammps
lmp = lammps(ptr=lmpptr)
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># loop N times, increasing cutoff each time</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre> for i in range(N):
cut = cut0 + i*0.1
lmp.set_variable(&quot;cut&quot;,cut) # set a variable in LAMMPS
lmp.command(&quot;pair_style lj/cut ${cut}&quot;) # LAMMPS commands
lmp.command(&quot;pair_coeff * * 1.0 1.0&quot;)
lmp.command(&quot;run 100&quot;)
&quot;&quot;&quot;
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">It is not currently possible to use the <a class="reference internal" href=""><em>python</em></a>
command described in this section with Python 3, only with Python 2.
The C API changed from Python 2 to 3 and the LAMMPS code is not
compatible with both.</p>
</div>
<p>Define a Python function or execute a previously defined function.
Arguments, including LAMMPS variables, can be passed to the function
from the LAMMPS input script and a value returned by the Python
function to a LAMMPS variable. The Python code for the function can
be included directly in the input script or in a separate Python file.
The function can be standard Python code or it can make &#8220;callbacks&#8221; to
LAMMPS through its library interface to query or set internal values
within LAMMPS. This is a powerful mechanism for performing complex
operations in a LAMMPS input script that are not possible with the
simple input script and variable syntax which LAMMPS defines. Thus
your input script can operate more like a true programming language.</p>
<p>Use of this command requires building LAMMPS with the PYTHON package
which links to the Python library so that the Python interpreter is
embedded in LAMMPS. More details about this process are given below.</p>
<p>There are two ways to invoke a Python function once it has been
defined. One is using the <em>invoke</em> keyword. The other is to assign
the function to a <a class="reference internal" href="variable.html"><em>python-style variable</em></a> defined in
your input script. Whenever the variable is evaluated, it will
execute the Python function to assign a value to the variable. Note
that variables can be evaluated in many different ways within LAMMPS.
They can be substituted for directly in an input script. Or they can
be passed to various commands as arguments, so that the variable is
evaluated during a simulation run.</p>
<p>A broader overview of how Python can be used with LAMMPS is
given in <a class="reference internal" href="Section_python.html"><em>Section python</em></a>. There is an
examples/python directory which illustrates use of the python
command.</p>
<hr class="docutils" />
<p>The <em>func</em> setting specifies the name of the Python function. The
code for the function is defined using the <em>file</em> or <em>here</em> keywords
as explained below.</p>
<p>If the <em>invoke</em> keyword is used, no other keywords can be used, and a
previous python command must have defined the Python function
referenced by this command. This invokes the Python function with the
previously defined arguments and return value processed as explained
below. You can invoke the function as many times as you wish in your
input script.</p>
<p>The <em>input</em> keyword defines how many arguments <em>N</em> the Python function
expects. If it takes no arguments, then the <em>input</em> keyword should
not be used. Each argument can be specified directly as a value,
e.g. 6 or 3.14159 or abc (a string of characters). The type of each
argument is specified by the <em>format</em> keyword as explained below, so
that Python will know how to interpret the value. If the word SELF is
used for an argument it has a special meaning. A pointer is passed to
the Python function which it converts into a reference to LAMMPS
itself. This enables the function to call back to LAMMPS through its
library interface as explained below. This allows the Python function
to query or set values internal to LAMMPS which can affect the
subsequent execution of the input script. A LAMMPS variable can also
be used as an argument, specified as v_name, where &#8220;name&#8221; is the name
of the variable. Any style of LAMMPS variable can be used, as defined
by the <a class="reference internal" href="variable.html"><em>variable</em></a> command. Each time the Python
function is invoked, the LAMMPS variable is evaluated and its value is
passed to the Python function.</p>
<p>The <em>return</em> keyword is only needed if the Python function returns a
value. The specified <em>varReturn</em> must be of the form v_name, where
&#8220;name&#8221; is the name of a python-style LAMMPS variable, defined by the
<a class="reference internal" href="variable.html"><em>variable</em></a> command. The Python function can return a
numeric or string value, as specified by the <em>format</em> keyword.</p>
<p>As explained on the <a class="reference internal" href="variable.html"><em>variable</em></a> doc page, the definition
of a python-style variable associates a Python function name with the
variable. This must match the <em>func</em> setting for this command. For
exampe these two commands would be self-consistent:</p>
<div class="highlight-python"><div class="highlight"><pre>variable foo python myMultiply
python myMultiply return v_foo format f file funcs.py
</pre></div>
</div>
<p>The two commands can appear in either order in the input script so
long as both are specified before the Python function is invoked for
the first time.</p>
<p>The <em>format</em> keyword must be used if the <em>input</em> or <em>return</em> keyword
is used. It defines an <em>fstring</em> with M characters, where M = sum of
number of inputs and outputs. The order of characters corresponds to
the N inputs, followed by the return value (if it exists). Each
character must be one of the following: &#8220;i&#8221; for integer, &#8220;f&#8221; for
floating point, &#8220;s&#8221; for string, or &#8220;p&#8221; for SELF. Each character
defines the type of the corresponding input or output value of the
Python function and affects the type conversion that is performed
internally as data is passed back and forth between LAMMPS and Python.
Note that it is permissible to use a <a class="reference internal" href="variable.html"><em>python-style variable</em></a> in a LAMMPS command that allows for an
equal-style variable as an argument, but only if the output of the
Python function is flagged as a numeric value (&#8220;i&#8221; or &#8220;f&#8221;) via the
<em>format</em> keyword.</p>
<p>Either the <em>file</em>, <em>here</em>, or <em>exists</em> keyword must be used, but only
one of them. These keywords specify what Python code to load into the
Python interpreter. The <em>file</em> keyword gives the name of a file,
which should end with a &#8221;.py&#8221; suffix, which contains Python code. The
code will be immediately loaded into and run in the &#8220;main&#8221; module of
the Python interpreter. Note that Python code which contains a
function definition does not &#8220;execute&#8221; the function when it is run; it
simply defines the function so that it can be invoked later.</p>
<p>The <em>here</em> keyword does the same thing, except that the Python code
follows as a single argument to the <em>here</em> keyword. This can be done
using triple quotes as delimiters, as in the examples above. This
allows Python code to be listed verbatim in your input script, with
proper indentation, blank lines, and comments, as desired. See
<a class="reference internal" href="Section_commands.html#cmd-2"><span>Section 3.2</span></a>, for an explanation of how
triple quotes can be used as part of input script syntax.</p>
<p>The <em>exists</em> keyword takes no argument. It means that Python code
containing the required Python function defined by the <em>func</em> setting,
is assumed to have been previously loaded by another python command.</p>
<p>Note that the Python code that is loaded and run must contain a
function with the specified <em>func</em> name. To operate properly when
later invoked, the the function code must match the <em>input</em> and
<em>return</em> and <em>format</em> keywords specified by the python command.
Otherwise Python will generate an error.</p>
<hr class="docutils" />
<p>This section describes how Python code can be written to work with
LAMMPS.</p>
<p>Whether you load Python code from a file or directly from your input
script, via the <em>file</em> and <em>here</em> keywords, the code can be identical.
It must be indented properly as Python requires. It can contain
comments or blank lines. If the code is in your input script, it
cannot however contain triple-quoted Python strings, since that will
conflict with the triple-quote parsing that the LAMMPS input script
performs.</p>
<p>All the Python code you specify via one or more python commands is
loaded into the Python &#8220;main&#8221; module, i.e. __main__. The code can
define global variables or statements that are outside of function
definitions. It can contain multiple functions, only one of which
matches the <em>func</em> setting in the python command. This means you can
use the <em>file</em> keyword once to load several functions, and the
<em>exists</em> keyword thereafter in subsequent python commands to access
the other functions previously loaded.</p>
<p>A Python function you define (or more generally, the code you load)
can import other Python modules or classes, it can make calls to other
system functions or functions you define, and it can access or modify
global variables (in the &#8220;main&#8221; module) which will persist between
successive function calls. The latter can be useful, for example, to
prevent a function from being invoke multiple times per timestep by
different commands in a LAMMPS input script that access the returned
python-style variable associated with the function. For example,
consider this function loaded with two global variables defined
outside the function:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">nsteplast</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">nvaluelast</span> <span class="o">=</span> <span class="mi">0</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="k">def</span> <span class="nf">expensive</span><span class="p">(</span><span class="n">nstep</span><span class="p">):</span>
<span class="k">global</span> <span class="n">nsteplast</span><span class="p">,</span><span class="n">nvaluelast</span>
<span class="k">if</span> <span class="n">nstep</span> <span class="o">==</span> <span class="n">nsteplast</span><span class="p">:</span> <span class="k">return</span> <span class="n">nvaluelast</span>
<span class="n">nsteplast</span> <span class="o">=</span> <span class="n">nstep</span>
<span class="c"># perform complicated calculation</span>
<span class="n">nvalue</span> <span class="o">=</span> <span class="o">...</span>
<span class="n">nvaluelast</span> <span class="o">=</span> <span class="n">nvalue</span>
<span class="k">return</span> <span class="n">nvalue</span>
</pre></div>
</div>
<p>Nsteplast stores the previous timestep the function was invoked
(passed as an argument to the function). Nvaluelast stores the return
value computed on the last function invocation. If the function is
invoked again on the same timestep, the previous value is simply
returned, without re-computing it. The &#8220;global&#8221; statement inside the
Python function allows it to overwrite the global variables.</p>
<p>Note that if you load Python code multiple times (via multiple python
commands), you can overwrite previously loaded variables and functions
if you are not careful. E.g. if the code above were loaded twice, the
global variables would be re-initialized, which might not be what you
want. Likewise, if a function with the same name exists in two chunks
of Python code you load, the function loaded second will override the
function loaded first.</p>
<p>It&#8217;s important to realize that if you are running LAMMPS in parallel,
each MPI task will load the Python interpreter and execute a local
copy of the Python function(s) you define. There is no connection
between the Python interpreters running on different processors.
This implies three important things.</p>
<p>First, if you put a print statement in your Python function, you will
see P copies of the output, when running on P processors. If the
prints occur at (nearly) the same time, the P copies of the output may
be mixed together. Welcome to the world of parallel programming and
debugging.</p>
<p>Second, if your Python code loads modules that are not pre-loaded by
the Python library, then it will load the module from disk. This may
be a bottleneck if 1000s of processors try to load a module at the
same time. On some large supercomputers, loading of modules from disk
by Python may be disabled. In this case you would need to pre-build a
Python library that has the required modules pre-loaded and link
LAMMPS with that library.</p>
<p>Third, if your Python code calls back to LAMMPS (discussed in the
next section) and causes LAMMPS to perform an MPI operation requires
global communication (e.g. via MPI_Allreduce), such as computing the
global temperature of the system, then you must insure all your Python
functions (running independently on different processors) call back to
LAMMPS. Otherwise the code may hang.</p>
<hr class="docutils" />
<p>Your Python function can &#8220;call back&#8221; to LAMMPS through its
library interface, if you use the SELF input to pass Python
a pointer to LAMMPS. The mechanism for doing this in your
Python function is as follows:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="k">def</span> <span class="nf">foo</span><span class="p">(</span><span class="n">lmpptr</span><span class="p">,</span><span class="o">...</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">lammps</span> <span class="kn">import</span> <span class="n">lammps</span>
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">ptr</span><span class="o">=</span><span class="n">lmpptr</span><span class="p">)</span>
<span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s">&#39;print &quot;Hello from inside Python&quot;&#39;</span><span class="p">)</span>
<span class="o">...</span>
</pre></div>
</div>
<p>The function definition must include a variable (lmpptr in this case)
which corresponds to SELF in the python command. The first line of
the function imports the Python module lammps.py in the python dir of
the distribution. The second line creates a Python object &#8220;lmp&#8221; which
wraps the instance of LAMMPS that called the function. The
&#8220;ptr=lmpptr&#8221; argument is what makes that happen. The thrid line
invokes the command() function in the LAMMPS library interface. It
takes a single string argument which is a LAMMPS input script command
for LAMMPS to execute, the same as if it appeared in your input
script. In this case, LAMMPS should output</p>
<div class="highlight-python"><div class="highlight"><pre>Hello from inside Python
</pre></div>
</div>
<p>to the screen and log file. Note that since the LAMMPS print command
itself takes a string in quotes as its argument, the Python string
must be delimited with a different style of quotes.</p>
<p><a class="reference internal" href="Section_python.html#py-7"><span>Section 11.7</span></a> describes the syntax for how
Python wraps the various functions included in the LAMMPS library
interface.</p>
<p>A more interesting example is in the examples/python/in.python script
which loads and runs the following function from examples/python/funcs.py:</p>
<div class="highlight-python"><div class="highlight"><pre>def loop(N,cut0,thresh,lmpptr):
print &quot;LOOP ARGS&quot;,N,cut0,thresh,lmpptr
from lammps import lammps
lmp = lammps(ptr=lmpptr)
natoms = lmp.get_natoms()
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">N</span><span class="p">):</span>
<span class="n">cut</span> <span class="o">=</span> <span class="n">cut0</span> <span class="o">+</span> <span class="n">i</span><span class="o">*</span><span class="mf">0.1</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="n">lmp</span><span class="o">.</span><span class="n">set_variable</span><span class="p">(</span><span class="s">&quot;cut&quot;</span><span class="p">,</span><span class="n">cut</span><span class="p">)</span> <span class="c"># set a variable in LAMMPS</span>
<span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s">&quot;pair_style lj/cut ${cut}&quot;</span><span class="p">)</span> <span class="c"># LAMMPS command</span>
<span class="c">#lmp.command(&quot;pair_style lj/cut %d&quot; % cut) # LAMMPS command option</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>lmp.command(&quot;pair_coeff * * 1.0 1.0&quot;) # ditto
lmp.command(&quot;run 10&quot;) # ditto
pe = lmp.extract_compute(&quot;thermo_pe&quot;,0,0) # extract total PE from LAMMPS
print &quot;PE&quot;,pe/natoms,thresh
if pe/natoms &lt; thresh: return
</pre></div>
</div>
<p>with these input script commands:</p>
<div class="highlight-python"><div class="highlight"><pre>python loop input 4 10 1.0 -4.0 SELF format iffp file funcs.py
python loop invoke
</pre></div>
</div>
<p>This has the effect of looping over a series of 10 short runs (10
timesteps each) where the pair style cutoff is increased from a value
of 1.0 in distance units, in increments of 0.1. The looping stops
when the per-atom potential energy falls below a threshhold of -4.0 in
energy units. More generally, Python can be used to implement a loop
with complex logic, much more so than can be created using the LAMMPS
<a class="reference internal" href="jump.html"><em>jump</em></a> and <a class="reference internal" href="if.html"><em>if</em></a> commands.</p>
<p>Several LAMMPS library functions are called from the loop function.
Get_natoms() returns the number of atoms in the simulation, so that it
can be used to normalize the potential energy that is returned by
extract_compute() for the &#8220;thermo_pe&#8221; compute that is defined by
default for LAMMPS thermodynamic output. Set_variable() sets the
value of a string variable defined in LAMMPS. This library function
is a useful way for a Python function to return multiple values to
LAMMPS, more than the single value that can be passed back via a
return statement. This cutoff value in the &#8220;cut&#8221; variable is then
substituted (by LAMMPS) in the pair_style command that is executed
next. Alternatively, the &#8220;LAMMPS command option&#8221; line could be used
in place of the 2 preceeding lines, to have Python insert the value
into the LAMMPS command string.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">When using the callback mechanism just described, recognize that
there are some operations you should not attempt because LAMMPS cannot
execute them correctly. If the Python function is invoked between
runs in the LAMMPS input script, then it should be OK to invoke any
LAMMPS input script command via the library interface command() or
file() functions, so long as the command would work if it were
executed in the LAMMPS input script directly at the same point.</p>
</div>
<p>However, a Python function can also be invoked during a run, whenever
an associated LAMMPS variable it is assigned to is evaluted. If the
variable is an input argument to another LAMMPS command (e.g. <a class="reference internal" href="fix_setforce.html"><em>fix setforce</em></a>), then the Python function will be invoked
inside the class for that command, in one of its methods that is
invoked in the middle of a timestep. You cannot execute arbitrary
input script commands from the Python function (again, via the
command() or file() functions) at that point in the run and expect it
to work. Other library functions such as those that invoke computes
or other variables may have hidden side effects as well. In these
cases, LAMMPS has no simple way to check that something illogical is
being attempted.</p>
<hr class="docutils" />
<p>If you run Python code directly on your workstation, either
interactively or by using Python to launch a Python script stored in a
file, and your code has an error, you will typically see informative
error messages. That is not the case when you run Python code from
LAMMPS using an embedded Python interpreter. The code will typically
fail silently. LAMMPS will catch some errors but cannot tell you
where in the Python code the problem occurred. For example, if the
Python code cannot be loaded and run because it has syntax or other
logic errors, you may get an error from Python pointing to the
offending line, or you may get one of these generic errors from
LAMMPS:</p>
<div class="highlight-python"><div class="highlight"><pre>Could not process Python file
Could not process Python string
</pre></div>
</div>
<p>When the Python function is invoked, if it does not return properly,
you will typically get this generic error from LAMMPS:</p>
<div class="highlight-python"><div class="highlight"><pre>Python function evaluation failed
</pre></div>
</div>
<p>Here are three suggestions for debugging your Python code while
running it under LAMMPS.</p>
<p>First, don&#8217;t run it under LAMMPS, at least to start with! Debug it
using plain Python. Load and invoke your function, pass it arguments,
check return values, etc.</p>
<p>Second, add Python print statements to the function to check how far
it gets and intermediate values it calculates. See the discussion
above about printing from Python when running in parallel.</p>
<p>Third, use Python exception handling. For example, say this statement
in your Python function is failing, because you have not initialized the
variable foo:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">foo</span> <span class="o">+=</span> <span class="mi">1</span>
</pre></div>
</div>
<p>If you put one (or more) statements inside a &#8220;try&#8221; statement,
like this:</p>
<div class="highlight-python"><div class="highlight"><pre>import exceptions
print &quot;Inside simple function&quot;
try:
foo += 1 # one or more statements here
except Exception, e:
print &quot;FOO error:&quot;,e
</pre></div>
</div>
<p>then you will get this message printed to the screen:</p>
<div class="highlight-python"><div class="highlight"><pre>FOO error: local variable &#39;foo&#39; referenced before assignment
</pre></div>
</div>
<p>If there is no error in the try statements, then nothing is printed.
Either way the function continues on (unless you put a return or
sys.exit() in the except clause).</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This command is part of the PYTHON package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>Building LAMMPS with the PYTHON package will link LAMMPS with the
Python library on your system. Settings to enable this are in the
lib/python/Makefile.lammps file. See the lib/python/README file for
information on those settings.</p>
<p>If you use Python code which calls back to LAMMPS, via the SELF input
argument explained above, there is an extra step required when
building LAMMPS. LAMMPS must also be built as a shared library and
your Python function must be able to to load the Python module in
python/lammps.py that wraps the LAMMPS library interface. These are
the same steps required to use Python by itself to wrap LAMMPS.
Details on these steps are explained in <code class="xref doc docutils literal"><span class="pre">Section</span> <span class="pre">python</span></code>. Note that it is important that the
stand-alone LAMMPS executable and the LAMMPS shared library be
consistent (built from the same source code files) in order for this
to work. If the two have been built at different times using
different source files, problems may occur.</p>
<p>As described above, you can use the python command to invoke a Python
function which calls back to LAMMPS through its Python-wrapped library
interface. However you cannot do the opposite. I.e. you cannot call
LAMMPS from Python and invoke the python command to &#8220;callback&#8221; to
Python and execute a Python function. LAMMPS will generate an error
if you try to do that. Note that we think there actually should be a
way to do that, but haven&#8217;t yet been able to figure out how to do it
successfully.</p>
</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="shell.html"><em>shell</em></a>, <a class="reference internal" href="variable.html"><em>variable</em></a></p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="quit-command">
<span id="index-0"></span><h1>quit command<a class="headerlink" href="#quit-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>quit status
</pre></div>
</div>
<p>status = numerical exit status (optional)</p>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<p>quit
if &#8220;$n &gt; 10000&#8221; then &#8220;quit 1&#8221;:pre</p>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>This command causes LAMMPS to exit, after shutting down all output
cleanly.</p>
<p>It can be used as a debug statement in an input script, to terminate
the script at some intermediate point.</p>
<p>It can also be used as an invoked command inside the &#8220;then&#8221; or &#8220;else&#8221;
portion of an <a class="reference internal" href="if.html"><em>if</em></a> command.</p>
<p>The optional status argument is an integer which signals the return
status to a program calling LAMMPS. A return status of 0 usually
indicates success. A status != 0 is failure, where the specified
value can be used to distinguish the kind of error, e.g. where in the
input script the quit was invoked. If not specified, a status of 0 is
returned.</p>
</div>
<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="if.html"><em>if</em></a></p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="read-dump-command">
<span id="index-0"></span><h1>read_dump command<a class="headerlink" href="#read-dump-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>read_dump file Nstep field1 field2 ... keyword values ...
</pre></div>
</div>
<ul class="simple">
<li>file = name of dump file to read</li>
<li>Nstep = snapshot timestep to read from file</li>
<li>one or more fields may be appended</li>
</ul>
<pre class="literal-block">
field = <em>x</em> or <em>y</em> or <em>z</em> or <em>vx</em> or <em>vy</em> or <em>vz</em> or <em>q</em> or <em>ix</em> or <em>iy</em> or <em>iz</em>
<em>x</em>,*y*,*z* = atom coordinates
<em>vx</em>,*vy*,*vz* = velocity components
<em>q</em> = charge
<em>ix</em>,*iy*,*iz* = image flags in each dimension
</pre>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>box</em> or <em>replace</em> or <em>purge</em> or <em>trim</em> or <em>add</em> or <em>label</em> or <em>scaled</em> or <em>wrapped</em> or <em>format</em></li>
</ul>
<pre class="literal-block">
<em>box</em> value = <em>yes</em> or <em>no</em> = replace simulation box with dump box
<em>replace</em> value = <em>yes</em> or <em>no</em> = overwrite atoms with dump atoms
<em>purge</em> value = <em>yes</em> or <em>no</em> = delete all atoms before adding dump atoms
<em>trim</em> value = <em>yes</em> or <em>no</em> = trim atoms not in dump snapshot
<em>add</em> value = <em>yes</em> or <em>no</em> = add new dump atoms to system
<em>label</em> value = field column
field = one of the listed fields or <em>id</em> or <em>type</em>
column = label on corresponding column in dump file
<em>scaled</em> value = <em>yes</em> or <em>no</em> = coords in dump file are scaled/unscaled
<em>wrapped</em> value = <em>yes</em> or <em>no</em> = coords in dump file are wrapped/unwrapped
<em>format</em> values = format of dump file, must be last keyword if used
<em>native</em> = native LAMMPS dump file
<em>xyz</em> = XYZ file
<em>molfile</em> style path = VMD molfile plugin interface
style = <em>dcd</em> or <em>xyz</em> or others supported by molfile plugins
path = optional path for location of molfile plugins
</pre>
</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>read_dump dump.file 5000 x y z
read_dump dump.xyz 5 x y z box no format xyz
read_dump dump.xyz 10 x y z box no format molfile xyz &quot;../plugins&quot;
read_dump dump.dcd 0 x y z box yes format molfile dcd
read_dump dump.file 1000 x y z vx vy vz box yes format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
read_dump dump.file 5000 x y vx vy trim yes
read_dump ../run7/dump.file.gz 10000 x y z box yes
read_dump dump.xyz 10 x y z box no format molfile xyz ../plugins
read_dump dump.dcd 0 x y z format molfile dcd
read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Read atom information from a dump file to overwrite the current atom
coordinates, and optionally the atom velocities and image flags and
the simluation box dimensions. This is useful for restarting a run
from a particular snapshot in a dump file. See the
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> and <a class="reference internal" href="read_data.html"><em>read_data</em></a>
commands for alternative methods to do this. Also see the
<a class="reference internal" href="rerun.html"><em>rerun</em></a> command for a means of reading multiple snapshots
from a dump file.</p>
<p>Note that a simulation box must already be defined before using the
read_dump command. This can be done by the
<a class="reference internal" href="create_box.html"><em>create_box</em></a>, <a class="reference internal" href="read_data.html"><em>read_data</em></a>, or
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands. The read_dump command can
reset the simulation box dimensions, as explained below.</p>
<p>Also note that reading per-atom information from a dump snapshot is
limited to the atom coordinates, velocities and image flags, as
explained below. Other atom properties, which may be necessary to run
a valid simulation, such as atom charge, or bond topology information
for a molecular system, are not read from (or even contained in) dump
files. Thus this auxiliary information should be defined in the usual
way, e.g. in a data file read in by a <a class="reference internal" href="read_data.html"><em>read_data</em></a>
command, before using the read_dump command, or by the <a class="reference internal" href="set.html"><em>set</em></a>
command, after the dump snapshot is read.</p>
<hr class="docutils" />
<p>If the dump filename specified as <em>file</em> ends with &#8221;.gz&#8221;, the dump
file is read in gzipped format. You cannot (yet) read a dump file
that was written in binary format with a &#8221;.bin&#8221; suffix, or to multiple
files via the &#8220;%&#8221; option in the dump file name. See the
<a class="reference internal" href="dump.html"><em>dump</em></a> command for details.</p>
<p>The format of the dump file is selected through the <em>format</em> keyword.
If specified, it must be the last keyword used, since all remaining
arguments are passed on to the dump reader. The <em>native</em> format is
for native LAMMPS dump files, written with a <a class="reference internal" href="dump.html"><em>dump atom</em></a> or
<a class="reference internal" href="dump.html"><em>dump custom</em></a> command. The <em>xyz</em> format is for generic XYZ
formatted dump files. These formats take no additional values.</p>
<p>The <em>molfile</em> format supports reading data through using the <a class="reference external" href="vmd">VMD</a>
molfile plugin interface. This dump reader format is only available,
if the USER-MOLFILE package has been installed when compiling
LAMMPS.</p>
<p>The <em>molfile</em> format takes one or two additional values. The <em>style</em>
value determines the file format to be used and can be any format that
the molfile plugins support, such as DCD or XYZ. Note that DCD dump
files can be written by LAMMPS via the <a class="reference internal" href="dump.html"><em>dump dcd</em></a> command.
The <em>path</em> value specifies a list of directories which LAMMPS will
search for the molfile plugins appropriate to the specified <em>style</em>.
The syntax of the <em>path</em> value is like other search paths: it can
contain multiple directories separated by a colon (or semi-colon on
windows). The <em>path</em> keyword is optional and defaults to &#8221;.&#8221;,
i.e. the current directory.</p>
<p>Support for other dump format readers may be added in the future.</p>
<hr class="docutils" />
<p>Global information is first read from the dump file, namely timestep
and box information.</p>
<p>The dump file is scanned for a snapshot with a time stamp that matches
the specified <em>Nstep</em>. This means the LAMMPS timestep the dump file
snapshot was written on for the <em>native</em> format. Note that the <em>xyz</em>
and <em>molfile</em> formats do not store the timestep. For these formats,
timesteps are numbered logically, in a sequential manner, starting
from 0. Thus to access the 10th snapshot in an <em>xyz</em> or <em>mofile</em>
formatted dump file, use <em>Nstep</em> = 9.</p>
<p>The dimensions of the simulation box for the selected snapshot are
also read; see the <em>box</em> keyword discussion below. For the <em>native</em>
format, an error is generated if the snapshot is for a triclinic box
and the current simulation box is orthogonal or vice versa. A warning
will be generated if the snapshot box boundary conditions (periodic,
shrink-wrapped, etc) do not match the current simulation boundary
conditions, but the boundary condition information in the snapshot is
otherwise ignored. See the &#8220;boundary&#8221; command for more details.</p>
<p>For the <em>xyz</em> format, no information about the box is available, so
you must set the <em>box</em> flag to <em>no</em>. See details below.</p>
<p>For the <em>molfile</em> format, reading simulation box information is
typically supported, but the location of the simulation box origin is
lost and no explicit information about periodicity or
orthogonal/triclinic box shape is available. The USER-MOLFILE package
makes a best effort to guess based on heuristics, but this may not
always work perfectly.</p>
<hr class="docutils" />
<p>Per-atom information from the dump file snapshot is then read from the
dump file snapshot. This corresponds to the specified <em>fields</em> listed
in the read_dump command. It is an error to specify a z-dimension
field, namely <em>z</em>, <em>vz</em>, or <em>iz</em>, for a 2d simulation.</p>
<p>For dump files in <em>native</em> format, each column of per-atom data has a
text label listed in the file. A matching label for each field must
appear, e.g. the label &#8220;vy&#8221; for the field <em>vy</em>. For the <em>x</em>, <em>y</em>, <em>z</em>
fields any of the following labels are considered a match:</p>
<pre class="literal-block">
x, xs, xu, xsu for field <em>x</em>
y, ys, yu, ysu for field <em>y</em>
z, zs, zu, zsu for field <em>z</em>
</pre>
<p>The meaning of xs (scaled), xu (unwrapped), and xsu (scaled and
unwrapped) is explained on the <a class="reference internal" href="dump.html"><em>dump</em></a> command doc page.
These labels are searched for in the list of column labels in the dump
file, in order, until a match is found.</p>
<p>The dump file must also contain atom IDs, with a column label of &#8220;id&#8221;.</p>
<p>If the <em>add</em> keyword is specified with a value of <em>yes</em>, as discussed
below, the dump file must contain atom types, with a column label of
&#8220;type&#8221;.</p>
<p>If a column label you want to read from the dump file is not a match
to a specified field, the <em>label</em> keyword can be used to specify the
specific column label from the dump file to associate with that field.
An example is if a time-averaged coordinate is written to the dump
file via the <a class="reference internal" href="fix_ave_atom.html"><em>fix ave/atom</em></a> command. The column
will then have a label corresponding to the fix-ID rather than &#8220;x&#8221; or
&#8220;xs&#8221;. The <em>label</em> keyword can also be used to specify new column
labels for fields <em>id</em> and <em>type</em>.</p>
<p>For dump files in <em>xyz</em> format, only the <em>x</em>, <em>y</em>, and <em>z</em> fields are
supported. The dump file does not store atom IDs, so these are
assigned consecutively to the atoms as they appear in the dump file,
starting from 1. Thus you should insure that order of atoms is
consistent from snapshot to snapshot in the the XYZ dump file. See
the <a class="reference internal" href="dump_modify.html"><em>dump_modify sort</em></a> command if the XYZ dump file
was written by LAMMPS.</p>
<p>For dump files in <em>molfile</em> format, the <em>x</em>, <em>y</em>, <em>z</em>, <em>vx</em>, <em>vy</em>, and
<em>vz</em> fields can be specified. However, not all molfile formats store
velocities, or their respective plugins may not support reading of
velocities. The molfile dump files do not store atom IDs, so these
are assigned consecutively to the atoms as they appear in the dump
file, starting from 1. Thus you should insure that order of atoms are
consistent from snapshot to snapshot in the the molfile dump file.
See the <a class="reference internal" href="dump_modify.html"><em>dump_modify sort</em></a> command if the dump file
was written by LAMMPS.</p>
<hr class="docutils" />
<p>Information from the dump file snapshot is used to overwrite or
replace properties of the current system. There are various options
for how this is done, determined by the specified fields and optional
keywords.</p>
<p>The timestep of the snapshot becomes the current timestep for the
simulation. See the <a class="reference internal" href="reset_timestep.html"><em>reset_timestep</em></a> command if
you wish to change this after the dump snapshot is read.</p>
<p>If the <em>box</em> keyword is specified with a <em>yes</em> value, then the current
simulation box dimensions are replaced by the dump snapshot box
dimensions. If the <em>box</em> keyword is specified with a <em>no</em> value, the
current simulatoin box is unchanged.</p>
<p>If the <em>purge</em> keyword is specified with a <em>yes</em> value, then all
current atoms in the system are deleted before any of the operations
invoked by the <em>replace</em>, <em>trim</em>, or <em>add</em> keywords take place.</p>
<p>If the <em>replace</em> keyword is specified with a <em>yes</em> value, then atoms
with IDs that are in both the current system and the dump snapshot
have their properties overwritten by field values. If the <em>replace</em>
keyword is specified with a <em>no</em> value, atoms with IDs that are in
both the current system and the dump snapshot are not modified.</p>
<p>If the <em>trim</em> keyword is specified with a <em>yes</em> value, then atoms with
IDs that are in the current system but not in the dump snapshot are
deleted. These atoms are unaffected if the <em>trim</em> keyword is
specified with a <em>no</em> value.</p>
<p>If the <em>add</em> keyword is specified with a <em>yes</em> value, then atoms with
IDs that are in the dump snapshot, but not in the current system are
added to the system. These dump atoms are ignored if the <em>add</em>
keyword is specified with a <em>no</em> value.</p>
<p>Note that atoms added via the <em>add</em> keyword will have only the
attributes read from the dump file due to the <em>field</em> arguments. If
<em>x</em> or <em>y</em> or <em>z</em> is not specified as a field, a value of 0.0 is used
for added atoms. Added atoms must have an atom type, so this value
must appear in the dump file.</p>
<p>Any other attributes (e.g. charge or particle diameter for spherical
particles) will be set to default values, the same as if the
<a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a> command were used.</p>
<p>Note that atom IDs are not preserved for new dump snapshot atoms added
via the <em>add</em> keyword. The procedure for assigning new atom IDS to
added atoms is the same as is described for the
<a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a> command.</p>
<hr class="docutils" />
<p>Atom coordinates read from the dump file are first converted into
unscaled coordinates, relative to the box dimensions of the snapshot.
These coordinates are then be assigned to an existing or new atom in
the current simulation. The coordinates will then be remapped to the
simulation box, whether it is the original box or the dump snapshot
box. If periodic boundary conditions apply, this means the atom will
be remapped back into the simulation box if necessary. If shrink-wrap
boundary conditions apply, the new coordinates may change the
simulation box dimensions. If fixed boundary conditions apply, the
atom will be lost if it is outside the simulation box.</p>
<p>For <em>native</em> format dump files, the 3 xyz image flags for an atom in
the dump file are set to the corresponding values appearing in the
dump file if the <em>ix</em>, <em>iy</em>, <em>iz</em> fields are specified. If not
specified, the image flags for replaced atoms are not changed and
image flags for new atoms are set to default values. If coordinates
read from the dump file are in unwrapped format (e.g. <em>xu</em>) then the
image flags for read-in atoms are also set to default values. The
remapping procedure described in the previous paragraph will then
change images flags for all atoms (old and new) if periodic boundary
conditions are applied to remap an atom back into the simulation box.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you get a warning about inconsistent image flags after
reading in a dump snapshot, it means one or more pairs of bonded atoms
now have inconsistent image flags. As discussed in <a class="reference internal" href="Section_errors.html"><em>Section errors</em></a> this may or may not cause problems for
subsequent simulations, One way this can happen is if you read image
flag fields from the dump file but do not also use the dump file box
parameters.</p>
</div>
<p>LAMMPS knows how to compute unscaled and remapped coordinates for the
snapshot column labels discussed above, e.g. <em>x</em>, <em>xs</em>, <em>xu</em>, <em>xsu</em>.
If another column label is assigned to the <em>x</em> or <em>y</em> or <em>z</em> field via
the <em>label</em> keyword, e.g. for coordinates output by the <a class="reference internal" href="fix_ave_atom.html"><em>fix ave/atom</em></a> command, then LAMMPS needs to know whether
the coordinate information in the dump file is scaled and/or wrapped.
This can be set via the <em>scaled</em> and <em>wrapped</em> keywords. Note that
the value of the <em>scaled</em> and <em>wrapped</em> keywords is ignored for fields
<em>x</em> or <em>y</em> or <em>z</em> if the <em>label</em> keyword is not used to assign a
column label to that field.</p>
<p>The scaled/unscaled and wrapped/unwrapped setting must be identical
for any of the <em>x</em>, <em>y</em>, <em>z</em> fields that are specified. Thus you
cannot read <em>xs</em> and <em>yu</em> from the dump file. Also, if the dump file
coordinates are scaled and the simulation box is triclinic, then all 3
of the <em>x</em>, <em>y</em>, <em>z</em> fields must be specified, since they are all
needed to generate absolute, unscaled coordinates.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>To read gzipped dump files, you must compile LAMMPS with the
-DLAMMPS_GZIP option - see the <a class="reference internal" href="Section_start.html#start-2"><span>Making LAMMPS</span></a> section of the documentation.</p>
<p>The <em>molfile</em> dump file formats are part of the USER-MOLFILE package.
They are only enabled if LAMMPS was built with that packages. See the
<a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</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="dump.html"><em>dump</em></a>, <a class="reference internal" href="dump_molfile.html"><em>dump molfile</em></a>,
<a class="reference internal" href="read_data.html"><em>read_data</em></a>, <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>,
<a class="reference internal" href="rerun.html"><em>rerun</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option defaults are box = yes, replace = yes, purge = no, trim =
no, add = no, scaled = no, wrapped = yes, and format = native.</p>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<div class="section" id="read-restart-command">
<span id="index-0"></span><h1>read_restart command<a class="headerlink" href="#read-restart-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>read_restart file flag
</pre></div>
</div>
<ul class="simple">
<li>file = name of binary restart file to read in</li>
<li>flag = remap (optional)</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>read_restart save.10000
read_restart save.10000 remap
read_restart restart.*
read_restart restart.*.mpiio
read_restart poly.*.% remap
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Read in a previously saved system configuration from a restart file.
This allows continuation of a previous run. Details about what
information is stored (and not stored) in a restart file is given
below. Basically this operation will re-create the simulation box
with all its atoms and their attributes as well as some related global
settings, at the point in time it was written to the restart file by a
previous simluation. The simulation box will be partitioned into a
regular 3d grid of rectangular bricks, one per processor, based on the
number of processors in the current simulation and the settings of the
<a class="reference internal" href="processors.html"><em>processors</em></a> command. The partitioning can later be
changed by the <a class="reference internal" href="balance.html"><em>balance</em></a> or <a class="reference internal" href="fix_balance.html"><em>fix balance</em></a> commands.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Normally, restart files are written by the
<a class="reference internal" href="restart.html"><em>restart</em></a> or <a class="reference internal" href="write_restart.html"><em>write_restart</em></a> commands
so that all atoms in the restart file are inside the simulation box.
If this is not the case, the read_restart command will print an error
that atoms were &#8220;lost&#8221; when the file is read. This error should be
reported to the LAMMPS developers so the invalid writing of the
restart file can be fixed. If you still wish to use the restart file,
the optional <em>remap</em> flag can be appended to the read_restart command.
This should avoid the error, by explicitly remapping each atom back
into the simulation box, updating image flags for the atom
appropriately.</p>
</div>
<p>Restart files are saved in binary format to enable exact restarts,
meaning that the trajectories of a restarted run will precisely match
those produced by the original run had it continued on.</p>
<p>Several things can prevent exact restarts due to round-off effects, in
which case the trajectories in the 2 runs will slowly diverge. These
include running on a different number of processors or changing
certain settings such as those set by the <a class="reference internal" href="newton.html"><em>newton</em></a> or
<a class="reference internal" href="processors.html"><em>processors</em></a> commands. LAMMPS will issue a warning in
these cases.</p>
<p>Certain fixes will not restart exactly, though they should provide
statistically similar results. These include <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> and <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a>.</p>
<p>Certain pair styles will not restart exactly, though they should
provide statistically similar results. This is because the forces
they compute depend on atom velocities, which are used at half-step
values every timestep when forces are computed. When a run restarts,
forces are initially evaluated with a full-step velocity, which is
different than if the run had continued. These pair styles include
<a class="reference internal" href="pair_gran.html"><em>granular pair styles</em></a>, <a class="reference internal" href="pair_dpd.html"><em>pair dpd</em></a>, and
<a class="reference internal" href="pair_lubricate.html"><em>pair lubricate</em></a>.</p>
<p>If a restarted run is immediately different than the run which
produced the restart file, it could be a LAMMPS bug, so consider
<a class="reference internal" href="Section_errors.html#err-2"><span>reporting it</span></a> if you think the behavior is
wrong.</p>
<p>Because restart files are binary, they may not be portable to other
machines. In this case, you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-restart command-line switch</span></a> to convert a restart file to a data
file.</p>
<p>Similar to how restart files are written (see the
<a class="reference internal" href="write_restart.html"><em>write_restart</em></a> and <a class="reference internal" href="restart.html"><em>restart</em></a>
commands), the restart filename can contain two wild-card characters.
If a &#8220;*&#8221; appears in the filename, the directory is searched for all
filenames that match the pattern where &#8220;*&#8221; is replaced with a timestep
value. The file with the largest timestep value is read in. Thus,
this effectively means, read the latest restart file. It&#8217;s useful if
you want your script to continue a run from where it left off. See
the <a class="reference internal" href="run.html"><em>run</em></a> command and its &#8220;upto&#8221; option for how to specify
the run command so it doesn&#8217;t need to be changed either.</p>
<p>If a &#8220;%&#8221; character appears in the restart filename, LAMMPS expects a
set of multiple files to exist. The <a class="reference internal" href="restart.html"><em>restart</em></a> and
<a class="reference internal" href="write_restart.html"><em>write_restart</em></a> commands explain how such sets are
created. Read_restart will first read a filename where &#8220;%&#8221; is
replaced by &#8220;base&#8221;. This file tells LAMMPS how many processors
created the set and how many files are in it. Read_restart then reads
the additional files. For example, if the restart file was specified
as save.% when it was written, then read_restart reads the files
save.base, save.0, save.1, ... save.P-1, where P is the number of
processors that created the restart file.</p>
<p>Note that P could be the total number of processors in the previous
simulation, or some subset of those processors, if the <em>fileper</em> or
<em>nfile</em> options were used when the restart file was written; see the
<a class="reference internal" href="restart.html"><em>restart</em></a> and <a class="reference internal" href="write_restart.html"><em>write_restart</em></a> commands
for details. The processors in the current LAMMPS simulation share
the work of reading these files; each reads a roughly equal subset of
the files. The number of processors which created the set can be
different the number of processors in the current LAMMPS simulation.
This can be a fast mode of input on parallel machines that support
parallel I/O.</p>
<p>A restart file can also be read in parallel as one large binary file
via the MPI-IO library, assuming it was also written with MPI-IO.
MPI-IO is part of the MPI standard for versions 2.0 and above. Using
MPI-IO requires two steps. First, build LAMMPS with its MPIIO package
installed, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-mpiio # installs the MPIIO package
make g++ # build LAMMPS for your platform
</pre></div>
</div>
<p>Second, use a restart filename which contains &#8221;.mpiio&#8221;. Note that it
does not have to end in &#8221;.mpiio&#8221;, just contain those characters.
Unlike MPI-IO dump files, a particular restart file must be both
written and read using MPI-IO.</p>
<hr class="docutils" />
<p>Here is the list of information included in a restart file, which
means these quantities do not need to be re-specified in the input
script that reads the restart file, though you can redefine many of
these settings after the restart file is read.</p>
<ul class="simple">
<li><a class="reference internal" href="units.html"><em>units</em></a></li>
<li><a class="reference internal" href="atom_style.html"><em>atom style</em></a> and <a class="reference internal" href="atom_modify.html"><em>atom_modify</em></a> settings id, map, sort</li>
<li><a class="reference internal" href="comm_style.html"><em>comm style</em></a> and <a class="reference external" href="comm_modify">comm_modify</a> settings mode, cutoff, vel</li>
<li><a class="reference internal" href="timestep.html"><em>timestep</em></a></li>
<li>simulation box size and shape and <a class="reference internal" href="boundary.html"><em>boundary</em></a> settings</li>
<li>atom <a class="reference internal" href="group.html"><em>group</em></a> definitions</li>
<li>per-type atom settings such as <a class="reference external" href="mass.thml">mass</a></li>
<li>per-atom attributes including their group assignments and molecular topology attributes (bonds, angles, etc)</li>
<li>force field styles (<a class="reference internal" href="pair_style.html"><em>pair</em></a>, <a class="reference internal" href="bond_style.html"><em>bond</em></a>, <a class="reference internal" href="angle_style.html"><em>angle</em></a>, etc)</li>
<li>force field coefficients (<a class="reference internal" href="pair_coeff.html"><em>pair</em></a>, <a class="reference internal" href="bond_coeff.html"><em>bond</em></a>, <a class="reference internal" href="angle_coeff.html"><em>angle</em></a>, etc) in some cases (see below)</li>
<li><a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> settings, except the compute option</li>
<li><a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> settings</li>
</ul>
<p>Here is a list of information not stored in a restart file, which
means you must re-issue these commands in your input script, after
reading the restart file.</p>
<ul class="simple">
<li><a class="reference internal" href="fix.html"><em>fix</em></a> commands (see below)</li>
<li><a class="reference internal" href="compute.html"><em>compute</em></a> commands (see below)</li>
<li><a class="reference internal" href="variable.html"><em>variable</em></a> commands</li>
<li><a class="reference internal" href="region.html"><em>region</em></a> commands</li>
<li><a class="reference internal" href="neighbor.html"><em>neighbor list</em></a> criteria including <a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a> settings</li>
<li><a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> and <a class="reference internal" href="kspace_modify.html"><em>kspace_modify</em></a> settings</li>
<li>info for <a class="reference internal" href="thermo_style.html"><em>thermodynamic</em></a>, <a class="reference internal" href="dump.html"><em>dump</em></a>, or <a class="reference internal" href="restart.html"><em>restart</em></a> output</li>
</ul>
<p>Note that some force field styles (pair, bond, angle, etc) do not
store their coefficient info in restart files. Typically these are
many-body or tabulated potentials which read their parameters from
separate files. In these cases you will need to re-specify the &#8220;pair
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, etc
commands in your restart input script. The doc pages for individual
force field styles mention if this is the case. This is also true of
<a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> (bond hybrid, angle hybrid, etc)
commands; they do not store coefficient info.</p>
<p>As indicated in the above list, the <a class="reference internal" href="fix.html"><em>fixes</em></a> used for a
simulation are not stored in the restart file. This means the new
input script should specify all fixes it will use. However, note that
some fixes store an internal &#8220;state&#8221; which is written to the restart
file. This allows the fix to continue on with its calculations in a
restarted simulation. To re-enable such a fix, the fix command in the
new input script must use the same fix-ID and group-ID as was used in
the input script that wrote the restart file. If a match is found,
LAMMPS prints a message indicating that the fix is being re-enabled.
If no match is found before the first run or minimization is performed
by the new script, the &#8220;state&#8221; information for the saved fix is
discarded. See the doc pages for individual fixes for info on which
ones can be restarted in this manner.</p>
<p>Likewise, the <a class="reference internal" href="fix.html"><em>computes</em></a> used for a simulation are not stored
in the restart file. This means the new input script should specify
all computes it will use. However, some computes create a fix
internally to store &#8220;state&#8221; information that persists from timestep to
timestep. An example is the <a class="reference internal" href="compute_msd.html"><em>compute msd</em></a> command
which uses a fix to store a reference coordinate for each atom, so
that a displacement can be calculated at any later time. If the
compute command in the new input script uses the same compute-ID and
group-ID as was used in the input script that wrote the restart file,
then it will create the same fix in the restarted run. This means the
re-created fix will be re-enabled with the stored state information as
described in the previous paragraph, so that the compute can continue
its calculations in a consistent manner.</p>
<p>Some pair styles, like the <a class="reference internal" href="pair_gran.html"><em>granular pair styles</em></a>, also
use a fix to store &#8220;state&#8221; information that persists from timestep to
timestep. In the case of granular potentials, it is contact
information between pairs of touching particles. This info will also
be re-enabled in the restart script, assuming you re-use the same
granular pair style.</p>
<p>LAMMPS allows bond interactions (angle, etc) to be turned off or
deleted in various ways, which can affect how their info is stored in
a restart file.</p>
<p>If bonds (angles, etc) have been turned off by the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> or <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a> command,
their info will be written to a restart file as if they are turned on.
This means they will need to be turned off again in a new run after
the restart file is read.</p>
<p>Bonds that are broken (e.g. by a bond-breaking potential) are written
to the restart file as broken bonds with a type of 0. Thus these
bonds will still be broken when the restart file is read.</p>
<p>Bonds that have been broken by the <a class="reference internal" href="fix_bond_break.html"><em>fix bond/break</em></a> command have disappeared from the
system. No information about these bonds is written to the restart
file.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>To write and read restart files in parallel with MPI-IO, the MPIIO
package must be installed.</p>
</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="read_data.html"><em>read_data</em></a>, <a class="reference internal" href="read_dump.html"><em>read_dump</em></a>,
<a class="reference internal" href="write_restart.html"><em>write_restart</em></a>, <a class="reference internal" href="restart.html"><em>restart</em></a></p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="region-command">
<span id="index-0"></span><h1>region command<a class="headerlink" href="#region-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>region ID style args keyword arg ...
</pre></div>
</div>
<ul class="simple">
<li>ID = user-assigned name for the region</li>
<li>style = <em>delete</em> or <em>block</em> or <em>cone</em> or <em>cylinder</em> or <em>plane</em> or <em>prism</em> or <em>sphere</em> or <em>union</em> or <em>intersect</em></li>
</ul>
<pre class="literal-block">
<em>delete</em> = no args
<em>block</em> args = xlo xhi ylo yhi zlo zhi
xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units)
<em>cone</em> args = dim c1 c2 radlo radhi lo hi
dim = <em>x</em> or <em>y</em> or <em>z</em> = axis of cone
c1,c2 = coords of cone axis in other 2 dimensions (distance units)
radlo,radhi = cone radii at lo and hi end (distance units)
lo,hi = bounds of cone in dim (distance units)
<em>cylinder</em> args = dim c1 c2 radius lo hi
dim = <em>x</em> or <em>y</em> or <em>z</em> = axis of cylinder
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
radius = cylinder radius (distance units)
radius can be a variable (see below)
lo,hi = bounds of cylinder in dim (distance units)
<em>plane</em> args = px py pz nx ny nz
px,py,pz = point on the plane (distance units)
nx,ny,nz = direction normal to plane (distance units)
<em>prism</em> args = xlo xhi ylo yhi zlo zhi xy xz yz
xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
xy = distance to tilt y in x direction (distance units)
xz = distance to tilt z in x direction (distance units)
yz = distance to tilt z in y direction (distance units)
<em>sphere</em> args = x y z radius
x,y,z = center of sphere (distance units)
radius = radius of sphere (distance units)
radius can be a variable (see below)
<em>union</em> args = N reg-ID1 reg-ID2 ...
N = # of regions to follow, must be 2 or greater
reg-ID1,reg-ID2, ... = IDs of regions to join together
<em>intersect</em> args = N reg-ID1 reg-ID2 ...
N = # of regions to follow, must be 2 or greater
reg-ID1,reg-ID2, ... = IDs of regions to intersect
</pre>
<ul class="simple">
<li>zero or more keyword/arg pairs may be appended</li>
<li>keyword = <em>side</em> or <em>units</em> or <em>move</em> or <em>rotate</em></li>
</ul>
<pre class="literal-block">
<em>side</em> value = <em>in</em> or <em>out</em>
<em>in</em> = the region is inside the specified geometry
<em>out</em> = the region is outside the specified geometry
<em>units</em> value = <em>lattice</em> or <em>box</em>
<em>lattice</em> = the geometry is defined in lattice units
<em>box</em> = the geometry is defined in simulation box units
<em>move</em> args = v_x v_y v_z
v_x,v_y,v_z = equal-style variables for x,y,z displacement of region over time
<em>rotate</em> args = v_theta Px Py Pz Rx Ry Rz
v_theta = equal-style variable for rotaton of region over time (in radians)
Px,Py,Pz = origin for axis of rotation (distance units)
Rx,Ry,Rz = axis of rotation vector
</pre>
<ul class="simple">
<li>accelerated styles (with same args) = <em>block/kk</em></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>region 1 block -3.0 5.0 INF 10.0 INF INF
region 2 sphere 0.0 0.0 0.0 5 side out
region void cylinder y 2 3 5 -5.0 EDGE units box
region 1 prism 0 10 0 10 0 10 2 0 0
region outside union 4 side1 side2 side3 side4
region 2 sphere 0.0 0.0 0.0 5 side out move v_left v_up NULL
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>This command defines a geometric region of space. Various other
commands use regions. For example, the region can be filled with
atoms via the <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a> command. Or a bounding
box around the region, can be used to define the simulation box via
the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command. Or the atoms in the region
can be identified as a group via the <a class="reference internal" href="group.html"><em>group</em></a> command, or
deleted via the <a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a> command. Or the
surface of the region can be used as a boundary wall via the <a class="reference internal" href="fix_wall_region.html"><em>fix wall/region</em></a> command.</p>
<p>Commands which use regions typically test whether an atom&#8217;s position
is contained in the region or not. For this purpose, coordinates
exactly on the region boundary are considered to be interior to the
region. This means, for example, for a spherical region, an atom on
the sphere surface would be part of the region if the sphere were
defined with the <em>side in</em> keyword, but would not be part of the
region if it were defined using the <em>side out</em> keyword. See more
details on the <em>side</em> keyword below.</p>
<p>Normally, regions in LAMMPS are &#8220;static&#8221;, meaning their geometric
extent does not change with time. If the <em>move</em> or <em>rotate</em> keyword
is used, as described below, the region becomes &#8220;dynamic&#8221;, meaning
it&#8217;s location or orientation changes with time. This may be useful,
for example, when thermostatting a region, via the compute temp/region
command, or when the fix wall/region command uses a region surface as
a bounding wall on particle motion, i.e. a rotating container.</p>
<p>The <em>delete</em> style removes the named region. Since there is little
overhead to defining extra regions, there is normally no need to do
this, unless you are defining and discarding large numbers of regions
in your input script.</p>
<p>The lo/hi values for <em>block</em> or <em>cone</em> or <em>cylinder</em> or <em>prism</em> styles
can be specified as EDGE or INF. EDGE means they extend all the way
to the global simulation box boundary. Note that this is the current
box boundary; if the box changes size during a simulation, the region
does not. INF means a large negative or positive number (1.0e20), so
it should encompass the simulation box even if it changes size. If a
region is defined before the simulation box has been created (via
<a class="reference internal" href="create_box.html"><em>create_box</em></a> or <a class="reference internal" href="read_data.html"><em>read_data</em></a> or
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands), then an EDGE or INF
parameter cannot be used. For a <em>prism</em> region, a non-zero tilt
factor in any pair of dimensions cannot be used if both the lo/hi
values in either of those dimensions are INF. E.g. if the xy tilt is
non-zero, then xlo and xhi cannot both be INF, nor can ylo and yhi.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Regions in LAMMPS do not get wrapped across periodic boundaries,
as specified by the <a class="reference internal" href="boundary.html"><em>boundary</em></a> command. For example, a
spherical region that is defined so that it overlaps a periodic
boundary is not treated as 2 half-spheres, one on either side of the
simulation box.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Regions in LAMMPS are always 3d geometric objects, regardless of
whether the <a class="reference internal" href="dimension.html"><em>dimension</em></a> of a simulation is 2d or 3d.
Thus when using regions in a 2d simulation, you should be careful to
define the region so that its intersection with the 2d x-y plane of
the simulation has the 2d geometric extent you want.</p>
</div>
<p>For style <em>cone</em>, an axis-aligned cone is defined which is like a
<em>cylinder</em> except that two different radii (one at each end) can be
defined. Either of the radii (but not both) can be 0.0.</p>
<p>For style <em>cone</em> and <em>cylinder</em>, the c1,c2 params are coordinates in
the 2 other dimensions besides the cylinder axis dimension. For dim =
x, c1/c2 = y/z; for dim = y, c1/c2 = x/z; for dim = z, c1/c2 = x/y.
Thus the third example above specifies a cylinder with its axis in the
y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and
extending in the y-direction from -5.0 to the upper box boundary.</p>
<p>For style <em>plane</em>, a plane is defined which contain the point
(px,py,pz) and has a normal vector (nx,ny,nz). The normal vector does
not have to be of unit length. The &#8220;inside&#8221; of the plane is the
half-space in the direction of the normal vector; see the discussion
of the <em>side</em> option below.</p>
<p>For style <em>prism</em>, a parallelepiped is defined (it&#8217;s too hard to spell
parallelepiped in an input script!). The parallelepiped has its
&#8220;origin&#8221; at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
(xz,yz,zhi-zlo). <em>Xy,xz,yz</em> can be 0.0 or positive or negative values
and are called &#8220;tilt factors&#8221; because they are the amount of
displacement applied to faces of an originally orthogonal box to
transform it into the parallelepiped.</p>
<p>A prism region that will be used with the <a class="reference internal" href="create_box.html"><em>create_box</em></a>
command to define a triclinic simulation box must have tilt factors
(xy,xz,yz) that do not skew the box more than half the distance of
corresponding the parallel box length. For example, if xlo = 2 and
xhi = 12, then the x box length is 10 and the xy tilt factor must be
between -5 and 5. Similarly, both xz and yz must be between
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
since if the maximum tilt factor is 5 (as in this example), then
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
geometrically equivalent.</p>
<p>The <em>radius</em> value for style <em>sphere</em> and <em>cylinder</em> can be specified
as an equal-style <a class="reference internal" href="variable.html"><em>variable</em></a>. If the value is a
variable, it should be specified as v_name, where name is the variable
name. In this case, the variable will be evaluated each timestep, and
its value used to determine the radius of the region.</p>
<p>Equal-style variables can specify formulas with various mathematical
functions, and include <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent radius.</p>
<p>See <a class="reference internal" href="Section_howto.html#howto-12"><span>Section_howto 12</span></a> of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
triclinic representations.</p>
<p>The <em>union</em> style creates a region consisting of the volume of all the
listed regions combined. The <em>intersect</em> style creates a region
consisting of the volume that is common to all the listed regions.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The <em>union</em> and <em>intersect</em> regions operate by invoking methods
from their list of sub-regions. Thus you cannot delete the
sub-regions after defining the <em>union</em> or <em>intersection</em> region.</p>
</div>
<hr class="docutils" />
<p>The <em>side</em> keyword determines whether the region is considered to be
inside or outside of the specified geometry. Using this keyword in
conjunction with <em>union</em> and <em>intersect</em> regions, complex geometries
can be built up. For example, if the interior of two spheres were
each defined as regions, and a <em>union</em> style with <em>side</em> = out was
constructed listing the region-IDs of the 2 spheres, the resulting
region would be all the volume in the simulation box that was outside
both of the spheres.</p>
<p>The <em>units</em> keyword determines the meaning of the distance units used
to define the region for any argument above listed as having distance
units. It also affects the scaling of the velocity vector specfied
with the <em>vel</em> keyword, the amplitude vector specified with the
<em>wiggle</em> keyword, and the rotation point specified with the <em>rotate</em>
keyword, since they each involve a distance metric.</p>
<p>A <em>box</em> value selects standard distance units as defined by the
<a class="reference internal" href="units.html"><em>units</em></a> command, e.g. Angstroms for units = real or metal.
A <em>lattice</em> value means the distance units are in lattice spacings.
The <a class="reference internal" href="lattice.html"><em>lattice</em></a> command must have been previously used to
define the lattice spacings which are used as follows:</p>
<ul class="simple">
<li>For style <em>block</em>, the lattice spacing in dimension x is applied to
xlo and xhi, similarly the spacings in dimensions y,z are applied to
ylo/yhi and zlo/zhi.</li>
<li>For style <em>cone</em>, the lattice spacing in argument <em>dim</em> is applied to
lo and hi. The spacings in the two radial dimensions are applied to
c1 and c2. The two cone radii are scaled by the lattice
spacing in the dimension corresponding to c1.</li>
<li>For style <em>cylinder</em>, the lattice spacing in argument <em>dim</em> is applied
to lo and hi. The spacings in the two radial dimensions are applied
to c1 and c2. The cylinder radius is scaled by the lattice
spacing in the dimension corresponding to c1.</li>
<li>For style <em>plane</em>, the lattice spacing in dimension x is applied to
px and nx, similarly the spacings in dimensions y,z are applied to
py/ny and pz/nz.</li>
<li>For style <em>prism</em>, the lattice spacing in dimension x is applied to
xlo and xhi, similarly for ylo/yhi and zlo/zhi. The lattice spacing
in dimension x is applied to xy and xz, and the spacing in dimension y
to yz.</li>
<li>For style <em>sphere</em>, the lattice spacing in dimensions x,y,z are
applied to the sphere center x,y,z. The spacing in dimension x is
applied to the sphere radius.</li>
</ul>
<hr class="docutils" />
<p>If the <em>move</em> or <em>rotate</em> keywords are used, the region is &#8220;dynamic&#8221;,
meaning its location or orientation changes with time. These keywords
cannot be used with a <em>union</em> or <em>intersect</em> style region. Instead,
the keywords should be used to make the individual sub-regions of the
<em>union</em> or <em>intersect</em> region dynamic. Normally, each sub-region
should be &#8220;dynamic&#8221; in the same manner (e.g. rotate around the same
point), though this is not a requirement.</p>
<p>The <em>move</em> keyword allows one or more <a class="reference internal" href="variable.html"><em>equal-style variables</em></a> to be used to specify the x,y,z displacement
of the region, typically as a function of time. A variable is
specified as v_name, where name is the variable name. Any of the
three variables can be specified as NULL, in which case no
displacement is calculated in that dimension.</p>
<p>Note that equal-style variables can specify formulas with various
mathematical functions, and include <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a>
command keywords for the simulation box parameters and timestep and
elapsed time. Thus it is easy to specify a region displacement that
change as a function of time or spans consecutive runs in a continuous
fashion. For the latter, see the <em>start</em> and <em>stop</em> keywords of the
<a class="reference internal" href="run.html"><em>run</em></a> command and the <em>elaplong</em> keyword of <a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> for details.</p>
<p>For example, these commands would displace a region from its initial
position, in the positive x direction, effectively at a constant
velocity:</p>
<div class="highlight-python"><div class="highlight"><pre>variable dx equal ramp(0,10)
region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL
</pre></div>
</div>
<p>Note that the initial displacemet is 0.0, though that is not required.</p>
<p>Either of these varaibles would &#8220;wiggle&#8221; the region back and forth in
the y direction:</p>
<div class="highlight-python"><div class="highlight"><pre>variable dy equal swiggle(0,5,100)
variable dysame equal 5*sin(2*PI*elaplong*dt/100)
region 2 sphere 10.0 10.0 0.0 5 move NULL v_dy NULL
</pre></div>
</div>
<p>The <em>rotate</em> keyword rotates the region around a rotation axis <em>R</em> =
(Rx,Ry,Rz) that goes thru a point <em>P</em> = (Px,Py,Pz). The rotation
angle is calculated, presumably as a function of time, by a variable
specified as v_theta, where theta is the variable name. The variable
should generate its result in radians. The direction of rotation for
the region around the rotation axis is consistent with the right-hand
rule: if your right-hand thumb points along <em>R</em>, then your fingers
wrap around the axis in the direction of rotation.</p>
<p>The <em>move</em> and <em>rotate</em> keywords can be used together. In this case,
the displacement specified by the <em>move</em> keyword is applied to the <em>P</em>
point of the <em>rotate</em> keyword.</p>
<hr class="docutils" />
<p>Styles with a <em>kk</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>The code using the region (such as a fix or compute) must also be supported
by Kokkos or no acceleration will occur. Currently, only <em>block</em> style
regions are supported by Kokkos.</p>
<p>These accelerated styles are part of the Kokkos 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>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>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>A prism cannot be of 0.0 thickness in any dimension; use a small z
thickness for 2d simulations. For 2d simulations, the xz and yz
parameters must be 0.0.</p>
</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="lattice.html"><em>lattice</em></a>, <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a>,
<a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a>, <a class="reference internal" href="group.html"><em>group</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option defaults are side = in, units = lattice, and no move or
rotation.</p>
</div>
</div>
</div>
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