diff --git a/doc/html/compute_dpd.html b/doc/html/compute_dpd.html
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<div class="section" id="compute-dpd-command">
<span id="index-0"></span><h1>compute dpd command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">dpd</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
<li>dpd = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">dpd</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Define a computation that accumulates the total internal conductive
energy (U_cond), the total internal mechanical energy (U_mech), the
total internal energy (U) and the <em>harmonic</em> average of the internal
temperature (dpdTheta) for the entire system of particles. See the
<a class="reference internal" href="compute_dpd_atom.html"><span class="doc">compute dpd/atom</span></a> command if you want
per-particle internal energies and internal temperatures.</p>
<p>The system internal properties are computed according to the following
relations:</p>
<img alt="_images/compute_dpd.jpg" class="align-center" src="_images/compute_dpd.jpg" />
<p>where N is the number of particles in the system</p>
<hr class="docutils" />
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector of length 5 (U_cond, U_mech,
U, dpdTheta, N_particles), which can be accessed by indices 1-5. See
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS
output options.</p>
-<p>The vector values will be in energy and temperature <span class="xref doc">units</span>.</p>
+<p>The vector values will be in energy and temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>The compute <em>dpd</em> is only available if LAMMPS is built with the
USER-DPD package and requires the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a>.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="compute_dpd_atom.html"><span class="doc">compute dpd/atom</span></a>,
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="larentzos"><strong>(Larentzos)</strong> J.P. Larentzos, J.K. Brennan, J.D. Moore, and
W.D. Mattson, “LAMMPS Implementation of Constant Energy Dissipative
Particle Dynamics (DPD-E)”, ARL-TR-6863, U.S. Army Research
Laboratory, Aberdeen Proving Ground, MD (2014).</p>
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<div class="section" id="compute-gyration-command">
<span id="index-0"></span><h1>compute gyration command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">gyration</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
<li>gyration = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="n">molecule</span> <span class="n">gyration</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Define a computation that calculates the radius of gyration Rg of the
group of atoms, including all effects due to atoms passing thru
periodic boundaries.</p>
<p>Rg is a measure of the size of the group of atoms, and is computed as
the square root of the Rg^2 value in this formula</p>
<img alt="_images/compute_gyration.jpg" class="align-center" src="_images/compute_gyration.jpg" />
<p>where M is the total mass of the group, Rcm is the center-of-mass
position of the group, and the sum is over all atoms in the group.</p>
<p>A Rg^2 tensor, stored as a 6-element vector, is also calculated by
this compute. The formula for the components of the tensor is the
same as the above formula, except that (Ri - Rcm)^2 is replaced by
(Rix - Rcmx) * (Riy - Rcmy) for the xy component, etc. The 6
components of the vector are ordered xx, yy, zz, xy, xz, yz. Note
that unlike the scalar Rg, each of the 6 values of the tensor is
effectively a “squared” value, since the cross-terms may be negative
and taking a sqrt() would be invalid.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The coordinates of an atom contribute to Rg in “unwrapped” form,
by using the image flags associated with each atom. See the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command for a discussion of “unwrapped” coordinates.
See the Atoms section of the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command for a
discussion of image flags and how they are set for each atom. You can
reset the image flags (e.g. to 0) before invoking this compute by
using the <a class="reference internal" href="set.html"><span class="doc">set image</span></a> command.</p>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (Rg) and a global vector of
length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These
values can be used by any command that uses a global scalar value or
vector values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
<p>The scalar and vector values calculated by this compute are
“intensive”. The scalar and vector values will be in distance and
-distance^2 <span class="xref doc">units</span> respectively.</p>
+distance^2 <a class="reference internal" href="units.html"><span class="doc">units</span></a> respectively.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="compute_gyration_chunk.html"><span class="doc">compute gyration/chunk</span></a></p>
<p><strong>Default:</strong> none</p>
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<div class="section" id="compute-gyration-chunk-command">
<span id="index-0"></span><h1>compute gyration/chunk command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">gyration</span><span class="o">/</span><span class="n">chunk</span> <span class="n">chunkID</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
<li>gyration/chunk = style name of this compute command</li>
<li>chunkID = ID of <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>tensor</em></li>
</ul>
<pre class="literal-block">
<em>tensor</em> value = none
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="n">molecule</span> <span class="n">gyration</span><span class="o">/</span><span class="n">chunk</span> <span class="n">molchunk</span>
<span class="n">compute</span> <span class="mi">2</span> <span class="n">molecule</span> <span class="n">gyration</span><span class="o">/</span><span class="n">chunk</span> <span class="n">molchunk</span> <span class="n">tensor</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Define a computation that calculates the radius of gyration Rg for
multiple chunks of atoms.</p>
<p>In LAMMPS, chunks are collections of atoms defined by a <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> doc page and “<a class="reference internal" href="Section_howto.html#howto-23"><span class="std std-ref">Section_howto 23</span></a> for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.</p>
<p>This compute calculates the radius of gyration Rg for each chunk,
which includes all effects due to atoms passing thru periodic
boundaries.</p>
<p>Rg is a measure of the size of a chunk, and is computed by this
formula</p>
<img alt="_images/compute_gyration.jpg" class="align-center" src="_images/compute_gyration.jpg" />
<p>where M is the total mass of the chunk, Rcm is the center-of-mass
position of the chunk, and the sum is over all atoms in the
chunk.</p>
<p>Note that only atoms in the specified group contribute to the
calculation. The <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command
defines its own group; atoms will have a chunk ID = 0 if they are not
in that group, signifying they are not assigned to a chunk, and will
thus also not contribute to this calculation. You can specify the
“all” group for this command if you simply want to include atoms with
non-zero chunk IDs.</p>
<p>If the <em>tensor</em> keyword is specified, then the scalar Rg value is not
calculated, but an Rg tensor is instead calculated for each chunk.
The formula for the components of the tensor is the same as the above
formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy -
Rcmy) for the xy component, etc. The 6 components of the tensor are
ordered xx, yy, zz, xy, xz, yz.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The coordinates of an atom contribute to Rg in “unwrapped” form,
by using the image flags associated with each atom. See the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command for a discussion of “unwrapped” coordinates.
See the Atoms section of the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command for a
discussion of image flags and how they are set for each atom. You can
reset the image flags (e.g. to 0) before invoking this compute by
using the <a class="reference internal" href="set.html"><span class="doc">set image</span></a> command.</p>
</div>
<p>The simplest way to output the results of the compute gyration/chunk
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
command, for example:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">gyration</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
</pre></div>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector if the <em>tensor</em> keyword is not
specified and a global array if it is. The length of the vector or
number of rows in the array = the number of chunks <em>Nchunk</em> as
calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command. If the <em>tensor</em> keyword
is specified, the global array has 6 columns. The vector or array can
be accessed by any command that uses global values from a compute as
input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview
of LAMMPS output options.</p>
<p>All the vector or array values calculated by this compute are
“intensive”. The vector or array values will be in distance
-<span class="xref doc">units</span>, since they are the square root of values
+<a class="reference internal" href="units.html"><span class="doc">units</span></a>, since they are the square root of values
represented by the formula above.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
<p><strong>Related commands:</strong> none</p>
<p><a class="reference internal" href="compute_gyration.html"><span class="doc">compute gyration</span></a></p>
<p><strong>Default:</strong> none</p>
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diff --git a/doc/html/compute_heat_flux.html b/doc/html/compute_heat_flux.html
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<div class="section" id="compute-heat-flux-command">
<span id="index-0"></span><h1>compute heat/flux command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">heat</span><span class="o">/</span><span class="n">flux</span> <span class="n">ke</span><span class="o">-</span><span class="n">ID</span> <span class="n">pe</span><span class="o">-</span><span class="n">ID</span> <span class="n">stress</span><span class="o">-</span><span class="n">ID</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
<li>heat/flux = style name of this compute command</li>
<li>ke-ID = ID of a compute that calculates per-atom kinetic energy</li>
<li>pe-ID = ID of a compute that calculates per-atom potential energy</li>
<li>stress-ID = ID of a compute that calculates per-atom stress</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myFlux</span> <span class="nb">all</span> <span class="n">heat</span><span class="o">/</span><span class="n">flux</span> <span class="n">myKE</span> <span class="n">myPE</span> <span class="n">myStress</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Define a computation that calculates the heat flux vector based on
contributions from atoms in the specified group. This can be used by
itself to measure the heat flux into or out of a reservoir of atoms,
or to calculate a thermal conductivity using the Green-Kubo formalism.</p>
<p>See the <a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">fix thermal/conductivity</span></a>
command for details on how to compute thermal conductivity in an
alternate way, via the Muller-Plathe method. See the <a class="reference internal" href="fix_heat.html"><span class="doc">fix heat</span></a> command for a way to control the heat added or
subtracted to a group of atoms.</p>
<p>The compute takes three arguments which are IDs of other
<a class="reference internal" href="compute.html"><span class="doc">computes</span></a>. One calculates per-atom kinetic energy
(<em>ke-ID</em>), one calculates per-atom potential energy (<em>pe-ID)</em>, and the
third calcualtes per-atom stress (<em>stress-ID</em>). These should be
defined for the same group used by compute heat/flux, though LAMMPS
does not check for this.</p>
<p>The Green-Kubo formulas relate the ensemble average of the
auto-correlation of the heat flux J to the thermal conductivity kappa:</p>
<img alt="_images/heat_flux_J.jpg" class="align-center" src="_images/heat_flux_J.jpg" />
<img alt="_images/heat_flux_k.jpg" class="align-center" src="_images/heat_flux_k.jpg" />
<p>Ei in the first term of the equation for J is the per-atom energy
(potential and kinetic). This is calculated by the computes <em>ke-ID</em>
and <em>pe-ID</em>. Si in the second term of the equation for J is the
per-atom stress tensor calculated by the compute <em>stress-ID</em>. The
tensor multiplies Vi as a 3x3 matrix-vector multiply to yield a
vector. Note that as discussed below, the 1/V scaling factor in the
equation for J is NOT included in the calculation performed by this
compute; you need to add it for a volume appropriate to the atoms
included in the calculation.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The <a class="reference internal" href="compute_pe_atom.html"><span class="doc">compute pe/atom</span></a> and <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a> commands have options for which
terms to include in their calculation (pair, bond, etc). The heat
flux calculation will thus include exactly the same terms. Normally
you should use <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom virial</span></a>
so as not to include a kinetic energy term in the heat flux.</p>
</div>
<p>This compute calculates 6 quantities and stores them in a 6-component
vector. The first 3 components are the x, y, z components of the full
heat flux vector, i.e. (Jx, Jy, Jz). The next 3 components are the x,
y, z components of just the convective portion of the flux, i.e. the
first term in the equation for J above.</p>
<hr class="docutils" />
<p>The heat flux can be output every so many timesteps (e.g. via the
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command). Then as a
post-processing operation, an autocorrelation can be performed, its
integral estimated, and the Green-Kubo formula above evaluated.</p>
<p>The <a class="reference internal" href="fix_ave_correlate.html"><span class="doc">fix ave/correlate</span></a> command can calclate
the autocorrelation. The trap() function in the
<a class="reference internal" href="variable.html"><span class="doc">variable</span></a> command can calculate the integral.</p>
<p>An example LAMMPS input script for solid Ar is appended below. The
result should be: average conductivity ~0.29 in W/mK.</p>
<hr class="docutils" />
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector of length 6 (total heat flux
vector, followed by convective heat flux vector), which can be
accessed by indices 1-6. These values can be used by any command that
uses global vector values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The vector values calculated by this compute are “extensive”, meaning
they scale with the number of atoms in the simulation. They can be
divided by the appropriate volume to get a flux, which would then be
an “intensive” value, meaning independent of the number of atoms in
the simulation. Note that if the compute is “all”, then the
appropriate volume to divide by is the simulation box volume.
However, if a sub-group is used, it should be the volume containing
those atoms.</p>
-<p>The vector values will be in energy*velocity <span class="xref doc">units</span>. Once
+<p>The vector values will be in energy*velocity <a class="reference internal" href="units.html"><span class="doc">units</span></a>. Once
divided by a volume the units will be that of flux, namely
-energy/area/time <span class="xref doc">units</span></p>
+energy/area/time <a class="reference internal" href="units.html"><span class="doc">units</span></a></p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">fix thermal/conductivity</span></a>,
<a class="reference internal" href="fix_ave_correlate.html"><span class="doc">fix ave/correlate</span></a>,
<a class="reference internal" href="variable.html"><span class="doc">variable</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Sample LAMMPS input script for thermal conductivity of solid Ar</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span>units real
variable T equal 70
variable V equal vol
variable dt equal 4.0
variable p equal 200 # correlation length
variable s equal 10 # sample interval
variable d equal $p*$s # dump interval
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># convert from LAMMPS real units to SI</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span>variable kB equal 1.3806504e-23 # [J/K] Boltzmann
variable kCal2J equal 4186.0/6.02214e23
variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15
variable convert equal ${kCal2J}*${kCal2J}/${fs2s}/${A2m}
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># setup problem</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span>dimension 3
boundary p p p
lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region box block 0 4 0 4 0 4
create_box 1 box
create_atoms 1 box
mass 1 39.948
pair_style lj/cut 13.0
pair_coeff * * 0.2381 3.405
timestep ${dt}
thermo $d
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># equilibration and thermalization</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span>velocity all create $T 102486 mom yes rot yes dist gaussian
fix NVT all nvt temp $T $T 10 drag 0.2
run 8000
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># thermal conductivity calculation, switch to NVE if desired</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1">#unfix NVT</span>
<span class="c1">#fix NVE all nve</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span>reset_timestep 0
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom NULL virial
compute flux all heat/flux myKE myPE myStress
variable Jx equal c_flux[1]/vol
variable Jy equal c_flux[2]/vol
variable Jz equal c_flux[3]/vol
fix JJ all ave/correlate $s $p $d &
c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.dat ave running
variable scale equal ${convert}/${kB}/$T/$T/$V*$s*${dt}
variable k11 equal trap(f_JJ[3])*${scale}
variable k22 equal trap(f_JJ[4])*${scale}
variable k33 equal trap(f_JJ[5])*${scale}
thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
run 100000
variable k equal (v_k11+v_k22+v_k33)/3.0
variable ndens equal count(all)/vol
print "average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3"
</pre></div>
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index 056dd5907..a185b2a47 100644
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<div class="section" id="compute-msd-nongauss-command">
<span id="index-0"></span><h1>compute msd/nongauss command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">msd</span><span class="o">/</span><span class="n">nongauss</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
<li>msd/nongauss = style name of this compute command</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>com</em></li>
</ul>
<pre class="literal-block">
<em>com</em> value = <em>yes</em> or <em>no</em>
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">msd</span><span class="o">/</span><span class="n">nongauss</span>
<span class="n">compute</span> <span class="mi">1</span> <span class="n">upper</span> <span class="n">msd</span><span class="o">/</span><span class="n">nongauss</span> <span class="n">com</span> <span class="n">yes</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Define a computation that calculates the mean-squared displacement
(MSD) and non-Gaussian parameter (NGP) of the group of atoms,
including all effects due to atoms passing thru periodic boundaries.</p>
<p>A vector of three quantites is calculated by this compute. The first
element of the vector is the total squared dx,dy,dz displacements
drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the
fourth power of these displacements drfourth = (dx*dx + dy*dy +
dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the
group. The 3rd component is the nonGaussian diffusion paramter NGP =
3*drfourth/(5*drsquared*drsquared), i.e.</p>
<img alt="_images/compute_msd_nongauss.jpg" class="align-center" src="_images/compute_msd_nongauss.jpg" />
<p>The NGP is a commonly used quantity in studies of dynamical
heterogeneity. Its minimum theoretical value (-0.4) occurs when all
atoms have the same displacement magnitude. NGP=0 for Brownian
diffusion, while NGP > 0 when some mobile atoms move faster than
others.</p>
<p>If the <em>com</em> option is set to <em>yes</em> then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calcluated.</p>
<p>See the <a class="reference internal" href="compute_msd.html"><span class="doc">compute msd</span></a> doc page for further important
NOTEs, which also apply to this compute.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector of length 3, which can be
accessed by indices 1-3 by any command that uses global vector values
from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The vector values are “intensive”. The first vector value will be in
-distance^2 <span class="xref doc">units</span>, the second is in distance^4 units, and
+distance^2 <a class="reference internal" href="units.html"><span class="doc">units</span></a>, the second is in distance^4 units, and
the 3rd is dimensionless.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This compute is 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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="compute_msd.html"><span class="doc">compute msd</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>The option default is com = no.</p>
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<div class="section" id="compute-pressure-command">
<span id="index-0"></span><h1>compute pressure command</h1>
</div>
<div class="section" id="compute-pressure-cuda-command">
<h1>compute pressure/cuda command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">pressure</span> <span class="n">temp</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
<li>pressure = style name of this compute command</li>
<li>temp-ID = ID of compute that calculates temperature, can be NULL if not needed</li>
<li>zero or more keywords may be appended</li>
<li>keyword = <em>ke</em> or <em>pair</em> or <em>bond</em> or <em>angle</em> or <em>dihedral</em> or <em>improper</em> or <em>kspace</em> or <em>fix</em> or <em>virial</em></li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">thermo_temp</span>
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">NULL</span> <span class="n">pair</span> <span class="n">bond</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Define a computation that calculates the pressure of the entire system
of atoms. The specified group must be “all”. See the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a> command if you want per-atom
pressure (stress). These per-atom values could be summed for a group
of atoms via the <a class="reference internal" href="compute_reduce.html"><span class="doc">compute reduce</span></a> command.</p>
<p>The pressure is computed by the formula</p>
<img alt="_images/pressure.jpg" class="align-center" src="_images/pressure.jpg" />
<p>where N is the number of atoms in the system (see discussion of DOF
below), Kb is the Boltzmann constant, T is the temperature, d is the
dimensionality of the system (2 or 3 for 2d/3d), V is the system
volume (or area in 2d), and the second term is the virial, computed
within LAMMPS for all pairwise as well as 2-body, 3-body, and 4-body,
and long-range interactions. <a class="reference internal" href="fix.html"><span class="doc">Fixes</span></a> that impose constraints
(e.g. the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> command) also contribute to the
virial term.</p>
<p>A symmetric pressure tensor, stored as a 6-element vector, is also
calculated by this compute. The 6 components of the vector are
ordered xx, yy, zz, xy, xz, yz. The equation for the I,J components
(where I and J = x,y,z) is similar to the above formula, except that
the first term uses components of the kinetic energy tensor and the
second term uses components of the virial tensor:</p>
<img alt="_images/pressure_tensor.jpg" class="align-center" src="_images/pressure_tensor.jpg" />
<p>If no extra keywords are listed, the entire equations above are
calculated. This includes a kinetic energy (temperature) term and the
virial as the sum of pair, bond, angle, dihedral, improper, kspace
(long-range), and fix contributions to the force on each atom. If any
extra keywords are listed, then only those components are summed to
compute temperature or ke and/or the virial. The <em>virial</em> keyword
means include all terms except the kinetic energy <em>ke</em>.</p>
<p>Details of how LAMMPS computes the virial efficiently for the entire
system, including the effects of periodic boundary conditions is
discussed in <a class="reference internal" href="compute_stress_atom.html#thompson"><span class="std std-ref">(Thompson)</span></a>.</p>
<p>The temperature and kinetic energy tensor is not calculated by this
compute, but rather by the temperature compute specified with the
command. If the kinetic energy is not included in the pressure, than
the temperature compute is not used and can be specified as NULL.
Normally the temperature compute used by compute pressure should
calculate the temperature of all atoms for consistency with the virial
term, but any compute style that calculates temperature can be used,
e.g. one that excludes frozen atoms or other degrees of freedom.</p>
<p>Note that if desired the specified temperature compute can be one that
subtracts off a bias to calculate a temperature using only the thermal
velocity of the atoms, e.g. by subtracting a background streaming
velocity. See the doc pages for individual <a class="reference internal" href="compute.html"><span class="doc">compute commands</span></a> to determine which ones include a bias.</p>
<p>Also note that the N in the first formula above is really
degrees-of-freedom divided by d = dimensionality, where the DOF value
is calcluated by the temperature compute. See the various <a class="reference internal" href="compute.html"><span class="doc">compute temperature</span></a> styles for details.</p>
<p>A compute of this style with the ID of “thermo_press” is created when
LAMMPS starts up, as if this command were in the input script:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">thermo_temp</span>
</pre></div>
</div>
<p>where “thermo_temp” is the ID of a similarly defined compute of style
“temp”. See the “thermo_style” command for more details.</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"><span class="doc">Section_accelerate</span></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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<hr class="docutils" />
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (the pressure) and a global
vector of length 6 (pressure tensor), which can be accessed by indices
1-6. These values can be used by any command that uses global scalar
or vector values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The scalar and vector values calculated by this compute are
“intensive”. The scalar and vector values will be in pressure
-<span class="xref doc">units</span>.</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a>, <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>,
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a>,</p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="thompson"><strong>(Thompson)</strong> Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).</p>
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<div class="section" id="compute-stress-atom-command">
<span id="index-0"></span><h1>compute stress/atom command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">temp</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
<li>stress/atom = style name of this compute command</li>
<li>temp-ID = ID of compute that calculates temperature, can be NULL if not needed</li>
<li>zero or more keywords may be appended</li>
<li>keyword = <em>ke</em> or <em>pair</em> or <em>bond</em> or <em>angle</em> or <em>dihedral</em> or <em>improper</em> or <em>kspace</em> or <em>fix</em> or <em>virial</em></li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="n">mobile</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
<span class="n">compute</span> <span class="mi">1</span> <span class="n">mobile</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">myRamp</span>
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span> <span class="n">pair</span> <span class="n">bond</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Define a computation that computes the symmetric per-atom stress
tensor for each atom in a group. The tensor for each atom has 6
components and is stored as a 6-element vector in the following order:
xx, yy, zz, xy, xz, yz. See the <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> command if you want the stress tensor
(pressure) of the entire system.</p>
<p>The stress tensor for atom <em>I</em> is given by the following formula,
where <em>a</em> and <em>b</em> take on values x,y,z to generate the 6 components of
the symmetric tensor:</p>
<img alt="_images/stress_tensor.jpg" class="align-center" src="_images/stress_tensor.jpg" />
<p>The first term is a kinetic energy contribution for atom <em>I</em>. See
details below on how the specified <em>temp-ID</em> can affect the velocities
used in this calculation. The second term is a pairwise energy
contribution where <em>n</em> loops over the <em>Np</em> neighbors of atom <em>I</em>, <em>r1</em>
and <em>r2</em> are the positions of the 2 atoms in the pairwise interaction,
and <em>F1</em> and <em>F2</em> are the forces on the 2 atoms resulting from the
pairwise interaction. The third term is a bond contribution of
similar form for the <em>Nb</em> bonds which atom <em>I</em> is part of. There are
similar terms for the <em>Na</em> angle, <em>Nd</em> dihedral, and <em>Ni</em> improper
interactions atom <em>I</em> is part of. There is also a term for the KSpace
contribution from long-range Coulombic interactions, if defined.
Finally, there is a term for the <em>Nf</em> <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a> that apply
internal constraint forces to atom <em>I</em>. Currently, only the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> and <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> commands
contribute to this term.</p>
<p>As the coefficients in the formula imply, a virial contribution
produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
atoms in a Tersoff 3-body interaction) is assigned in equal portions
to each atom in the set. E.g. 1/4 of the dihedral virial to each of
the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied
to atoms in a a water molecule via the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a>
command.</p>
<p>If no extra keywords are listed, all of the terms in this formula are
included in the per-atom stress tensor. If any extra keywords are
listed, only those terms are summed to compute the tensor. The
<em>virial</em> keyword means include all terms except the kinetic energy
<em>ke</em>.</p>
<p>Note that the stress for each atom is due to its interaction with all
other atoms in the simulation, not just with other atoms in the group.</p>
<p>Details of how LAMMPS computes the virial for individual atoms for
either pairwise or manybody potentials, and including the effects of
periodic boundary conditions is discussed in <a class="reference internal" href="#thompson"><span class="std std-ref">(Thompson)</span></a>.
The basic idea for manybody potentials is to treat each component of
the force computation between a small cluster of atoms in the same
manner as in the formula above for bond, angle, dihedral, etc
interactions. Namely the quantity R dot F is summed over the atoms in
the interaction, with the R vectors unwrapped by periodic boundaries
so that the cluster of atoms is close together. The total
contribution for the cluster interaction is divided evenly among those
atoms.</p>
<p>The <a class="reference internal" href="dihedral_charmm.html"><span class="doc">dihedral_style charmm</span></a> style calculates
pairwise interactions between 1-4 atoms. The virial contribution of
these terms is included in the pair virial, not the dihedral virial.</p>
<p>The KSpace contribution is calculated using the method in
<a class="reference internal" href="#heyes"><span class="std std-ref">(Heyes)</span></a> for the Ewald method and by the methodology described
in <a class="reference internal" href="pair_srp.html#sirk"><span class="std std-ref">(Sirk)</span></a> for PPPM. The choice of KSpace solver is specified
by the <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style pppm</span></a> command. Note that for
PPPM, the calcluation requires 6 extra FFTs each timestep that
per-atom stress is calculated. Thus it can significantly increase the
cost of the PPPM calculation if it is needed on a large fraction of
the simulation timesteps.</p>
<p>The <em>temp-ID</em> argument can be used to affect the per-atom velocities
used in the kinetic energy contribution to the total stress. If the
kinetic energy is not included in the stress, than the temperature
compute is not used and can be specified as NULL. If the kinetic
energy is included and you wish to use atom velocities as-is, then
<em>temp-ID</em> can also be specified as NULL. If desired, the specified
temperature compute can be one that subtracts off a bias to leave each
atom with only a thermal velocity to use in the formula above, e.g. by
subtracting a background streaming velocity. See the doc pages for
individual <a class="reference internal" href="compute.html"><span class="doc">compute commands</span></a> to determine which ones
include a bias.</p>
<hr class="docutils" />
<p>Note that as defined in the formula, per-atom stress is the negative
of the per-atom pressure tensor. It is also really a stress*volume
formulation, meaning the computed quantity is in units of
pressure*volume. It would need to be divided by a per-atom volume to
have units of stress (pressure), but an individual atom’s volume is
not well defined or easy to compute in a deformed solid or a liquid.
See the <a class="reference internal" href="compute_voronoi_atom.html"><span class="doc">compute voronoi/atom</span></a> command for
one possible way to estimate a per-atom volume.</p>
<p>Thus, if the diagonal components of the per-atom stress tensor are
summed for all atoms in the system and the sum is divided by dV, where
d = dimension and V is the volume of the system, the result should be
-P, where P is the total pressure of the system.</p>
<p>These lines in an input script for a 3d system should yield that
result. I.e. the last 2 columns of thermo output will be the same:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">peratom</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
<span class="n">compute</span> <span class="n">p</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_peratom</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_peratom</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_peratom</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
<span class="n">variable</span> <span class="n">press</span> <span class="n">equal</span> <span class="o">-</span><span class="p">(</span><span class="n">c_p</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">c_p</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">+</span><span class="n">c_p</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span><span class="o">/</span><span class="p">(</span><span class="mi">3</span><span class="o">*</span><span class="n">vol</span><span class="p">)</span>
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">press</span> <span class="n">v_press</span>
</pre></div>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom array with 6 columns, which can be
accessed by indices 1-6 by any command that uses per-atom values from
a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
<p>The per-atom array values will be in pressure*volume
-<span class="xref doc">units</span> as discussed above.</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> as discussed above.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="compute_pe.html"><span class="doc">compute pe</span></a>, <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="heyes"><strong>(Heyes)</strong> Heyes, Phys Rev B 49, 755 (1994),</p>
<p id="sirk"><strong>(Sirk)</strong> Sirk, Moore, Brown, J Chem Phys, 138, 064505 (2013).</p>
<p id="thompson"><strong>(Thompson)</strong> Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).</p>
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<div class="section" id="create-atoms-command">
<span id="index-0"></span><h1>create_atoms command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">create_atoms</span> <span class="nb">type</span> <span class="n">style</span> <span class="n">args</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)</li>
<li>style = <em>box</em> or <em>region</em> or <em>single</em> or <em>random</em></li>
</ul>
<pre class="literal-block">
<em>box</em> args = none
<em>region</em> args = region-ID
region-ID = particles will only be created if contained in the region
<em>single</em> args = x y z
x,y,z = coordinates of a single particle (distance units)
<em>random</em> args = N seed region-ID
N = number of particles to create
seed = random # seed (positive integer)
region-ID = create atoms within this region, use NULL for entire simulation box
</pre>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>mol</em> or <em>basis</em> or <em>remap</em> or <em>var</em> or <em>set</em> or <em>units</em></li>
</ul>
<pre class="literal-block">
<em>mol</em> value = template-ID seed
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command
seed = random # seed (positive integer)
<em>basis</em> values = M itype
M = which basis atom
itype = atom type (1-N) to assign to this basis atom
<em>remap</em> value = <em>yes</em> or <em>no</em>
<em>var</em> value = name = variable name to evaluate for test of atom creation
<em>set</em> values = dim name
dim = <em>x</em> or <em>y</em> or <em>z</em>
name = name of variable to set with x, y, or z atom position
<em>rotate</em> values = Rx Ry Rz theta
Rx,Ry,Rz = rotation vector for single molecule
theta = rotation angle for single molecule (degrees)
<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
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">box</span>
<span class="n">create_atoms</span> <span class="mi">3</span> <span class="n">region</span> <span class="n">regsphere</span> <span class="n">basis</span> <span class="mi">2</span> <span class="mi">3</span>
<span class="n">create_atoms</span> <span class="mi">3</span> <span class="n">single</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">5</span>
<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">box</span> <span class="n">var</span> <span class="n">v</span> <span class="nb">set</span> <span class="n">x</span> <span class="n">xpos</span> <span class="nb">set</span> <span class="n">y</span> <span class="n">ypos</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>This command creates atoms (or molecules) on a lattice, or a single
atom (or molecule), or a random collection of atoms (or molecules), as
an alternative to reading in their coordinates explicitly via a
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
command. A simulation box must already exist, which is typically
created via the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command. Before using
this command, a lattice must also be defined using the
<a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command, unless you specify the <em>single</em> style
with units = box or the <em>random</em> style. For the remainder of this doc
page, a created atom or molecule is referred to as a “particle”.</p>
<p>If created particles are individual atoms, they are assigned the
specified atom <em>type</em>, though this can be altered via the <em>basis</em>
keyword as discussed below. If molecules are being created, the type
of each atom in the created molecule is specified in the file read by
the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command, and those values are added to
the specified atom <em>type</em>. E.g. if <em>type</em> = 2, and the file specifies
atom types 1,2,3, then each created molecule will have atom types
3,4,5.</p>
<p>For the <em>box</em> style, the create_atoms command fills the entire
simulation box with particles on the lattice. If your simulation box
is periodic, you should insure its size is a multiple of the lattice
spacings, to avoid unwanted atom overlaps at the box boundaries. If
your box is periodic and a multiple of the lattice spacing in a
particular dimension, LAMMPS is careful to put exactly one particle at
the boundary (on either side of the box), not zero or two.</p>
<p>For the <em>region</em> style, a geometric volume is filled with particles on
the lattice. This volume what is inside the simulation box and is
also consistent with the region volume. See the <a class="reference internal" href="region.html"><span class="doc">region</span></a>
command for details. Note that a region can be specified so that its
“volume” is either inside or outside a geometric boundary. Also note
that if your region is the same size as a periodic simulation box (in
some dimension), LAMMPS does not implement the same logic described
above as for the <em>box</em> style, to insure exactly one particle at
periodic boundaries. if this is what you desire, you should either
use the <em>box</em> style, or tweak the region size to get precisely the
particles you want.</p>
<p>For the <em>single</em> style, a single particle is added to the system at
the specified coordinates. This can be useful for debugging purposes
or to create a tiny system with a handful of particles at specified
positions.</p>
<p>For the <em>random</em> style, N particles are added to the system at
randomly generated coordinates, which can be useful for generating an
amorphous system. The particles are created one by one using the
speficied random number <em>seed</em>, resulting in the same set of particles
coordinates, independent of how many processors are being used in the
simulation. If the <em>region-ID</em> argument is specified as NULL, then
the created particles will be anywhere in the simulation box. If a
<em>region-ID</em> is specified, a geometric volume is filled which is both
inside the simulation box and is also consistent with the region
volume. See the <a class="reference internal" href="region.html"><span class="doc">region</span></a> command for details. Note that
a region can be specified so that its “volume” is either inside or
outside a geometric boundary.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Particles generated by the <em>random</em> style will typically be
highly overlapped which will cause many interatomic potentials to
compute large energies and forces. Thus you should either perform an
<a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a> or run dynamics with <a class="reference internal" href="fix_nve_limit.html"><span class="doc">fix nve/limit</span></a> to equilibrate such a system, before
running normal dynamics.</p>
</div>
<p>Note that this command adds particles to those that already exist.
This means it can be used to add particles to a system previously read
in from a data or restart file. Or the create_atoms command can be
used multiple times, to add multiple sets of particles to the
simulation. For example, grain boundaries can be created, by
interleaving create_atoms with <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> commands
specifying different orientations. By using the create_atoms command
in conjunction with the <a class="reference internal" href="delete_atoms.html"><span class="doc">delete_atoms</span></a> command,
reasonably complex geometries can be created, or a protein can be
solvated with a surrounding box of water molecules.</p>
<p>In all these cases, care should be taken to insure that new atoms do
not overlap existing atoms inappropriately, especially if molecules
are being added. The <a class="reference internal" href="delete_atoms.html"><span class="doc">delete_atoms</span></a> command can be
used to remove overlapping atoms or molecules.</p>
<hr class="docutils" />
<p>Individual atoms are inserted by this command, unless the <em>mol</em>
keyword is used. It specifies a <em>template-ID</em> previously defined
using the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command, which reads a file that
defines the molecule. The coordinates, atom types, charges, etc, as
well as any bond/angle/etc and special neighbor information for the
molecule can be specified in the molecule file. See the
<a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command for details. The only settings
required to be in this file are the coordinates and types of atoms in
the molecule.</p>
<p>Using a lattice to add molecules, e.g. via the <em>box</em> or <em>region</em> or
<em>single</em> styles, is exactly the same as adding atoms on lattice
points, except that entire molecules are added at each point, i.e. on
the point defined by each basis atom in the unit cell as it tiles the
simulation box or region. This is done by placing the geometric
center of the molecule at the lattice point, and giving the molecule a
random orientation about the point. The random <em>seed</em> specified with
the <em>mol</em> keyword is used for this operation, and the random numbers
generated by each processor are different. This means the coordinates
of individual atoms (in the molecules) will be different when running
on different numbers of processors, unlike when atoms are being
created in parallel.</p>
<p>Also note that because of the random rotations, it may be important to
use a lattice with a large enough spacing that adjacent molecules will
not overlap, regardless of their relative orientations.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command is used to create
the simulation box, followed by the create_atoms command with its
<em>mol</em> option for adding molecules, then you typically need to use the
optional keywords allowed by the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command
for extra bonds (angles,etc) or extra special neighbors. This is
because by default, the <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command sets up a
non-molecular system which doesn’t allow molecules to be added.</p>
</div>
<hr class="docutils" />
<p>This is the meaning of the other allowed keywords.</p>
<p>The <em>basis</em> keyword is only used when atoms (not molecules) are being
created. It specifies an atom type that will be assigned to specific
basis atoms as they are created. See the <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a>
command for specifics on how basis atoms are defined for the unit cell
of the lattice. By default, all created atoms are assigned the
argument <em>type</em> as their atom type.</p>
<p>The <em>remap</em> keyword only applies to the <em>single</em> style. If it is set
to <em>yes</em>, then if the specified position is outside the simulation
box, it will mapped back into the box, assuming the relevant
dimensions are periodic. If it is set to <em>no</em>, no remapping is done
and no particle is created if its position is outside the box.</p>
<p>The <em>var</em> and <em>set</em> keywords can be used together to provide a
criterion for accepting or rejecting the addition of an individual
atom, based on its coordinates. The <em>name</em> specified for the <em>var</em>
keyword is the name of an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> which
should evaluate to a zero or non-zero value based on one or two or
three variables which will store the x, y, or z coordinates of an atom
(one variable per coordinate). If used, these other variables must be
<a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a> defined in the input script, but
their formula can by anything. The <em>set</em> keyword is used to identify
the names of these other variables, one variable for the x-coordinate
of a created atom, one for y, and one for z.</p>
<p>When an atom is created, its x, y, or z coordinates override the
formula for any <em>set</em> variable that is defined. The <em>var</em> variable is
then evaluated. If the returned value is 0.0, the atom is not
created. If it is non-zero, the atom is created. After all atoms are
created, the formulas defined for all of the <em>set</em> variables are
restored to their original strings.</p>
<p>As an example, these commands can be used in a 2d simulation, to
create a sinusoidal surface. Note that the surface is “rough” due to
individual lattice points being “above” or “below” the mathematical
expression for the sinusoidal curve. If a finer lattice were used,
the sinusoid would appear to be “smoother”. Also note the use of the
“xlat” and “ylat” <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> keywords which
converts lattice spacings to distance. Click on the image for a
larger version.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>variable x equal 100
variable y equal 25
lattice hex 0.8442
region box block 0 $x 0 $y -0.5 0.5
create_box 1 box
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">xx</span> <span class="n">equal</span> <span class="mf">0.0</span>
<span class="n">variable</span> <span class="n">yy</span> <span class="n">equal</span> <span class="mf">0.0</span>
<span class="n">variable</span> <span class="n">v</span> <span class="n">equal</span> <span class="s2">"(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"</span>
<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">box</span> <span class="n">var</span> <span class="n">v</span> <span class="nb">set</span> <span class="n">x</span> <span class="n">xx</span> <span class="nb">set</span> <span class="n">y</span> <span class="n">yy</span>
</pre></div>
</div>
<a class=""
data-lightbox="group-default"
href="_images/sinusoid.jpg"
title=""
data-title=""
><img src="_images/sinusoid.jpg"
class="align-center"
width="25%"
height="auto"
alt=""/>
</a><p>The <em>rotate</em> keyword can be used with the <em>single</em> style, when adding
a single molecule to specify the orientation at which the molecule is
inserted. The axis of rotation is determined by the rotation vector
(Rx,Ry,Rz) that goes through the insertion point. The specified
<em>theta</em> determines the angle of rotation around that axis. Note that
the direction of rotation for the atoms around the rotation axis is
consistent with the right-hand rule: if your right-hand’s thumb points
along <em>R</em>, then your fingers wrap around the axis in the direction of
rotation.</p>
<p>The <em>units</em> keyword determines the meaning of the distance units used
to specify the coordinates of the one particle created by the <em>single</em>
style. A <em>box</em> value selects standard distance units as defined by
-the <span class="xref doc">units</span> command, e.g. Angstroms for units = real or
+the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command, e.g. Angstroms for units = real or
metal. A <em>lattice</em> value means the distance units are in lattice
spacings.</p>
<hr class="docutils" />
<p>Atom IDs are assigned to created atoms in the following way. The
collection of created atoms are assigned consecutive IDs that start
immediately following the largest atom ID existing before the
create_atoms command was invoked. When a simulation is performed on
different numbers of processors, there is no guarantee a particular
created atom will be assigned the same ID. If molecules are being
created, molecule IDs are assigned to created molecules in a similar
fashion.</p>
<p>Aside from their ID, atom type, and xyz position, other properties of
created atoms are set to default values, depending on which quantities
are defined by the chosen <a class="reference internal" href="atom_style.html"><span class="doc">atom style</span></a>. See the <a class="reference internal" href="atom_style.html"><span class="doc">atom style</span></a> command for more details. See the
<a class="reference internal" href="set.html"><span class="doc">set</span></a> and <a class="reference internal" href="velocity.html"><span class="doc">velocity</span></a> commands for info on how
to change these values.</p>
<ul class="simple">
<li>charge = 0.0</li>
<li>dipole moment magnitude = 0.0</li>
<li>diameter = 1.0</li>
<li>shape = 0.0 0.0 0.0</li>
<li>density = 1.0</li>
<li>volume = 1.0</li>
<li>velocity = 0.0 0.0 0.0</li>
<li>angular velocity = 0.0 0.0 0.0</li>
<li>angular momentum = 0.0 0.0 0.0</li>
<li>quaternion = (1,0,0,0)</li>
<li>bonds, angles, dihedrals, impropers = none</li>
</ul>
<p>If molecules are being created, these defaults can be overridden by
values specified in the file read by the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a>
command. E.g. the file typically defines bonds (angles,etc) between
atoms in the molecule, and can optionally define charges on each atom.</p>
<p>Note that the <em>sphere</em> atom style sets the default particle diameter
to 1.0 as well as the density. This means the mass for the particle
is not 1.0, but is PI/6 * diameter^3 = 0.5236.</p>
<p>Note that the <em>ellipsoid</em> atom style sets the default particle shape
to (0.0 0.0 0.0) and the density to 1.0 which means it is a point
particle, not an ellipsoid, and has a mass of 1.0.</p>
<p>Note that the <em>peri</em> style sets the default volume and density to 1.0
and thus also set the mass for the particle to 1.0.</p>
<p>The <a class="reference internal" href="set.html"><span class="doc">set</span></a> command can be used to override many of these
default settings.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>An <a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a> must be previously defined to use this
command.</p>
<p>A rotation vector specified for a single molecule must be in
the z-direction for a 2d model.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a>, <a class="reference internal" href="region.html"><span class="doc">region</span></a>, <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a>,
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>The default for the <em>basis</em> keyword is that all created atoms are
assigned the argument <em>type</em> as their atom type (when single atoms are
being created). The other defaults are <em>remap</em> = no, <em>rotate</em> =
random, and <em>units</em> = lattice.</p>
</div>
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<div class="section" id="dump-image-command">
<span id="index-0"></span><h1>dump image command</h1>
</div>
<div class="section" id="dump-movie-command">
<h1>dump movie command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style</span> <span class="n">N</span> <span class="n">file</span> <span class="n">color</span> <span class="n">diameter</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID = user-assigned name for the dump</li>
<li>group-ID = ID of the group of atoms to be imaged</li>
<li>style = <em>image</em> or <em>movie</em> = style of dump command (other styles <em>atom</em> or <em>cfg</em> or <em>dcd</em> or <em>xtc</em> or <em>xyz</em> or <em>local</em> or <em>custom</em> are discussed on the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> doc page)</li>
<li>N = dump every this many timesteps</li>
<li>file = name of file to write image to</li>
<li>color = atom attribute that determines color of each atom</li>
<li>diameter = atom attribute that determines size of each atom</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>atom</em> or <em>adiam</em> or <em>bond</em> or <em>line</em> or <em>tri</em> or <em>body</em> or <em>size</em> or <em>view</em> or <em>center</em> or <em>up</em> or <em>zoom</em> or <em>persp</em> or <em>box</em> or <em>axes</em> or <em>subbox</em> or <em>shiny</em> or <em>ssao</em></li>
</ul>
<pre class="literal-block">
<em>atom</em> = yes/no = do or do not draw atoms
<em>adiam</em> size = numeric value for atom diameter (distance units)
<em>bond</em> values = color width = color and width of bonds
color = <em>atom</em> or <em>type</em> or <em>none</em>
width = number or <em>atom</em> or <em>type</em> or <em>none</em>
number = numeric value for bond width (distance units)
<em>line</em> = color width
color = <em>type</em>
width = numeric value for line width (distance units)
<em>tri</em> = color tflag width
color = <em>type</em>
tflag = 1 for just triangle, 2 for just tri edges, 3 for both
width = numeric value for tringle edge width (distance units)
<em>body</em> = color bflag1 bflag2
color = <em>type</em>
bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
<em>size</em> values = width height = size of images
width = width of image in # of pixels
height = height of image in # of pixels
<em>view</em> values = theta phi = view of simulation box
theta = view angle from +z axis (degrees)
phi = azimuthal view angle (degrees)
theta or phi can be a variable (see below)
<em>center</em> values = flag Cx Cy Cz = center point of image
flag = "s" for static, "d" for dynamic
Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
Cx,Cy,Cz can be variables (see below)
<em>up</em> values = Ux Uy Uz = direction that is "up" in image
Ux,Uy,Uz = components of up vector
Ux,Uy,Uz can be variables (see below)
<em>zoom</em> value = zfactor = size that simulation box appears in image
zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
zfactor can be a variable (see below)
<em>persp</em> value = pfactor = amount of "perspective" in image
pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
pfactor can be a variable (see below)
<em>box</em> values = yes/no diam = draw outline of simulation box
yes/no = do or do not draw simulation box lines
diam = diameter of box lines as fraction of shortest box length
<em>axes</em> values = yes/no length diam = draw xyz axes
yes/no = do or do not draw xyz axes lines next to simulation box
length = length of axes lines as fraction of respective box lengths
diam = diameter of axes lines as fraction of shortest box length
<em>subbox</em> values = yes/no diam = draw outline of processor sub-domains
yes/no = do or do not draw sub-domain lines
diam = diameter of sub-domain lines as fraction of shortest box length
<em>shiny</em> value = sfactor = shinyness of spheres and cylinders
sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
<em>ssao</em> value = yes/no seed dfactor = SSAO depth shading
yes/no = turn depth shading on/off
seed = random # seed (positive integer)
dfactor = strength of shading from 0.0 to 1.0
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">d0</span> <span class="nb">all</span> <span class="n">image</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.*.</span><span class="n">jpg</span> <span class="nb">type</span> <span class="nb">type</span>
<span class="n">dump</span> <span class="n">d1</span> <span class="n">mobile</span> <span class="n">image</span> <span class="mi">500</span> <span class="n">snap</span><span class="o">.*.</span><span class="n">png</span> <span class="n">element</span> <span class="n">element</span> <span class="n">ssao</span> <span class="n">yes</span> <span class="mi">4539</span> <span class="mf">0.6</span>
<span class="n">dump</span> <span class="n">d2</span> <span class="nb">all</span> <span class="n">image</span> <span class="mi">200</span> <span class="n">img</span><span class="o">-*.</span><span class="n">ppm</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">zoom</span> <span class="mf">2.5</span> <span class="n">adiam</span> <span class="mf">1.5</span> <span class="n">size</span> <span class="mi">1280</span> <span class="mi">720</span>
<span class="n">dump</span> <span class="n">m0</span> <span class="nb">all</span> <span class="n">movie</span> <span class="mi">1000</span> <span class="n">movie</span><span class="o">.</span><span class="n">mpg</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">size</span> <span class="mi">640</span> <span class="mi">480</span>
<span class="n">dump</span> <span class="n">m1</span> <span class="nb">all</span> <span class="n">movie</span> <span class="mi">1000</span> <span class="n">movie</span><span class="o">.</span><span class="n">avi</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">size</span> <span class="mi">640</span> <span class="mi">480</span>
<span class="n">dump</span> <span class="n">m2</span> <span class="nb">all</span> <span class="n">movie</span> <span class="mi">100</span> <span class="n">movie</span><span class="o">.</span><span class="n">m4v</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">zoom</span> <span class="mf">1.8</span> <span class="n">adiam</span> <span class="n">v_value</span> <span class="n">size</span> <span class="mi">1280</span> <span class="mi">720</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Dump a high-quality rendered image of the atom configuration every N
timesteps and save the images either as a sequence of JPEG or PNG or
PPM files, or as a single movie file. The options for this command as
well as the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command control what is
included in the image or movie and how it appears. A series of such
images can easily be manually converted into an animated movie of your
simulation or the process can be automated without writing the
intermediate files using the dump movie style; see further details
below. Other dump styles store snapshots of numerical data asociated
with atoms in various formats, as discussed on the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a>
doc page.</p>
<p>Note that a set of images or a movie can be made after a simulation
has been run, using the <a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a> command to read snapshots
from an existing dump file, and using these dump commands in the rerun
script to generate the images/movie.</p>
<p>Here are two sample images, rendered as 1024x1024 JPEG files. Click
to see the full-size images:</p>
<DIV ALIGN=center><a class=""
data-lightbox="group-default"
href="_images/dump1.jpg"
title=""
data-title=""
><img src="_images/dump1.jpg"
class=""
width="25%"
height="auto"
alt=""/>
</a><a class=""
data-lightbox="group-default"
href="_images/dump2.jpg"
title=""
data-title=""
><img src="_images/dump2.jpg"
class=""
width="25%"
height="auto"
alt=""/>
</a></DIV><p>Only atoms in the specified group are rendered in the image. The
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify region and thresh</span></a> commands can also
alter what atoms are included in the image.
The filename suffix determines whether a JPEG, PNG, or PPM file is
created with the <em>image</em> dump style. If the suffix is ”.jpg” or
”.jpeg”, then a JPEG format file is created, if the suffix is ”.png”,
then a PNG format is created, else a PPM (aka NETPBM) format file is
created. The JPEG and PNG files are binary; PPM has a text mode
header followed by binary data. JPEG images have lossy compression;
PNG has lossless compression; and PPM files are uncompressed but can
be compressed with gzip, if LAMMPS has been compiled with
-DLAMMPS_GZIP and a ”.gz” suffix is used.</p>
<p>Similarly, the format of the resulting movie is chosen with the
<em>movie</em> dump style. This is handled by the underlying FFmpeg converter
and thus details have to be looked up in the FFmpeg documentation.
Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif
Additional settings of the movie compression like bitrate and
framerate can be set using the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command.</p>
<p>To write out JPEG and PNG format files, you must build LAMMPS with
support for the corresponding JPEG or PNG library. To convert images
into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG
flag. See <a class="reference internal" href="Section_start.html#start-2-4"><span class="std std-ref">this section</span></a> of the manual
for instructions on how to do this.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Because periodic boundary conditions are enforced only on
timesteps when neighbor lists are rebuilt, the coordinates of an atom
in the image may be slightly outside the simulation box.</p>
</div>
<hr class="docutils" />
<p>Dumps are performed on timesteps that are a multiple of N (including
timestep 0) and on the last timestep of a minimization if the
minimization converges. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of N. This behavior can be
changed via the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify first</span></a> command, which
can be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by
using the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify every</span></a> command.</p>
<p>Dump <em>image</em> filenames must contain a wildcard character “*”, so that
one image file per snapshot is written. The “*” character is replaced
with the timestep value. For example, tmp.dump.*.jpg becomes
tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note
that the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify pad</span></a> command can be used to
insure all timestep numbers are the same length (e.g. 00010), which
can make it easier to convert a series of images into a movie in the
correct ordering.</p>
<p>Dump <em>movie</em> filenames on the other hand, must not have any wildcard
character since only one file combining all images into a single
movie will be written by the movie encoder.</p>
<hr class="docutils" />
<p>The <em>color</em> and <em>diameter</em> settings determine the color and size of
atoms rendered in the image. They can be any atom attribute defined
for the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command, including <em>type</em> and
<em>element</em>. This includes per-atom quantities calculated by a
<a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix.html"><span class="doc">fix</span></a>, or <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>,
which are prefixed by “<a href="#id9"><span class="problematic" id="id10">c_</span></a>”, “<a href="#id11"><span class="problematic" id="id12">f_</span></a>”, or “<a href="#id13"><span class="problematic" id="id14">v_</span></a>” respectively. Note that the
<em>diameter</em> setting can be overridden with a numeric value applied to
all atoms by the optional <em>adiam</em> keyword.</p>
<p>If <em>type</em> is specified for the <em>color</em> setting, then the color of each
atom is determined by its atom type. By default the mapping of types
to colors is as follows:</p>
<ul class="simple">
<li>type 1 = red</li>
<li>type 2 = green</li>
<li>type 3 = blue</li>
<li>type 4 = yellow</li>
<li>type 5 = aqua</li>
<li>type 6 = cyan</li>
</ul>
<p>and repeats itself for types > 6. This mapping can be changed by the
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify acolor</span></a> command.</p>
<p>If <em>type</em> is specified for the <em>diameter</em> setting then the diameter of
each atom is determined by its atom type. By default all types have
diameter 1.0. This mapping can be changed by the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify adiam</span></a> command.</p>
<p>If <em>element</em> is specified for the <em>color</em> and/or <em>diameter</em> setting,
then the color and/or diameter of each atom is determined by which
element it is, which in turn is specified by the element-to-type
mapping specified by the “dump_modify element” command. By default
every atom type is C (carbon). Every element has a color and diameter
associated with it, which is the same as the colors and sizes used by
the <a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualization package.</p>
<p>If other atom attributes are used for the <em>color</em> or <em>diameter</em>
settings, they are interpreted in the following way.</p>
<p>If “vx”, for example, is used as the <em>color</em> setting, then the color
of the atom will depend on the x-component of its velocity. The
association of a per-atom value with a specific color is determined by
a “color map”, which can be specified via the
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command. The basic idea is that the
atom-attribute will be within a range of values, and every value
within the range is mapped to a specific color. Depending on how the
color map is defined, that mapping can take place via interpolation so
that a value of -3.2 is halfway between “red” and “blue”, or
discretely so that the value of -3.2 is “orange”.</p>
<p>If “vx”, for example, is used as the <em>diameter</em> setting, then the atom
will be rendered using the x-component of its velocity as the
diameter. If the per-atom value <= 0.0, them the atom will not be
drawn. Note that finite-size spherical particles, as defined by
<a class="reference internal" href="atom_style.html"><span class="doc">atom_style sphere</span></a> define a per-particle radius or
diameter, which can be used as the <em>diameter</em> setting.</p>
<hr class="docutils" />
<p>The various kewords listed above control how the image is rendered.
As listed below, all of the keywords have defaults, most of which you
will likely not need to change. The <a class="reference internal" href="dump_modify.html"><span class="doc">dump modify</span></a>
also has options specific to the dump image style, particularly for
assigning colors to atoms, bonds, and other image features.</p>
<hr class="docutils" />
<p>The <em>atom</em> keyword allow you to turn off the drawing of all atoms, if
the specified value is <em>no</em>. Note that this will not turn off the
drawing of particles that are represented as lines, triangles, or
bodies, as discussed below. These particles can be drawn separately
if the <em>line</em>, <em>tri</em>, or <em>body</em> keywords are used.</p>
<p>The <em>adiam</em> keyword allows you to override the <em>diameter</em> setting to
set a single numeric <em>size</em>. All atoms will be drawn with that
-diameter, e.g. 1.5, which is in whatever distance <span class="xref doc">units</span>
+diameter, e.g. 1.5, which is in whatever distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>
the input script defines, e.g. Angstroms.</p>
<p>The <em>bond</em> keyword allows to you to alter how bonds are drawn. A bond
is only drawn if both atoms in the bond are being drawn due to being
in the specified group and due to other selection criteria
(e.g. region, threshhold settings of the
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command). By default, bonds are drawn
if they are defined in the input data file as read by the
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command. Using <em>none</em> for both the bond
<em>color</em> and <em>width</em> value will turn off the drawing of all bonds.</p>
<p>If <em>atom</em> is specified for the bond <em>color</em> value, then each bond is
drawn in 2 halves, with the color of each half being the color of the
atom at that end of the bond.</p>
<p>If <em>type</em> is specified for the <em>color</em> value, then the color of each
bond is determined by its bond type. By default the mapping of bond
types to colors is as follows:</p>
<ul class="simple">
<li>type 1 = red</li>
<li>type 2 = green</li>
<li>type 3 = blue</li>
<li>type 4 = yellow</li>
<li>type 5 = aqua</li>
<li>type 6 = cyan</li>
</ul>
<p>and repeats itself for bond types > 6. This mapping can be changed by
the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify bcolor</span></a> command.</p>
<p>The bond <em>width</em> value can be a numeric value or <em>atom</em> or <em>type</em> (or
<em>none</em> as indicated above).</p>
<p>If a numeric value is specified, then all bonds will be drawn as
cylinders with that diameter, e.g. 1.0, which is in whatever distance
-<span class="xref doc">units</span> the input script defines, e.g. Angstroms.</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> the input script defines, e.g. Angstroms.</p>
<p>If <em>atom</em> is specified for the <em>width</em> value, then each bond
will be drawn with a width corresponding to the minimum diameter
of the 2 atoms in the bond.</p>
<p>If <em>type</em> is specified for the <em>width</em> value then the diameter of each
bond is determined by its bond type. By default all types have
diameter 0.5. This mapping can be changed by the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify bdiam</span></a> command.</p>
<p>The <em>line</em> keyword can be used when <a class="reference internal" href="atom_style.html"><span class="doc">atom_style line</span></a>
is used to define particles as line segments, and will draw them as
lines. If this keyword is not used, such particles will be drawn as
spheres, the same as if they were regular atoms. The only setting
currently allowed for the <em>color</em> value is <em>type</em>, which will color
the lines according to the atom type of the particle. By default the
mapping of types to colors is as follows:</p>
<ul class="simple">
<li>type 1 = red</li>
<li>type 2 = green</li>
<li>type 3 = blue</li>
<li>type 4 = yellow</li>
<li>type 5 = aqua</li>
<li>type 6 = cyan</li>
</ul>
<p>and repeats itself for types > 6. There is not yet an option to
change this via the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command.</p>
<p>The line <em>width</em> can only be a numeric value, which specifies that all
lines will be drawn as cylinders with that diameter, e.g. 1.0, which
-is in whatever distance <span class="xref doc">units</span> the input script defines,
+is in whatever distance <a class="reference internal" href="units.html"><span class="doc">units</span></a> the input script defines,
e.g. Angstroms.</p>
<p>The <em>tri</em> keyword can be used when <a class="reference internal" href="atom_style.html"><span class="doc">atom_style tri</span></a> is
used to define particles as triangles, and will draw them as triangles
or edges (3 lines) or both, depending on the setting for <em>tflag</em>. If
edges are drawn, the <em>width</em> setting determines the diameters of the
line segments. If this keyword is not used, triangle particles will
be drawn as spheres, the same as if they were regular atoms. The only
setting currently allowed for the <em>color</em> value is <em>type</em>, which will
color the triangles according to the atom type of the particle. By
default the mapping of types to colors is as follows:</p>
<ul class="simple">
<li>type 1 = red</li>
<li>type 2 = green</li>
<li>type 3 = blue</li>
<li>type 4 = yellow</li>
<li>type 5 = aqua</li>
<li>type 6 = cyan</li>
</ul>
<p>and repeats itself for types > 6. There is not yet an option to
change this via the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command.</p>
<p>The <em>body</em> keyword can be used when <a class="reference internal" href="atom_style.html"><span class="doc">atom_style body</span></a>
is used to define body particles with internal state
(e.g. sub-particles), and will drawn them in a manner specific to the
body style. If this keyword is not used, such particles will be drawn
as spheres, the same as if they were regular atoms.</p>
<p>The <a class="reference internal" href="body.html"><span class="doc">body</span></a> doc page descibes the body styles LAMMPS
currently supports, and provides more details as to the kind of body
particles they represent and how they are drawn by this dump image
command. For all the body styles, individual atoms can be either a
body particle or a usual point (non-body) particle. Non-body
particles will be drawn the same way they would be as a regular atom.
The <em>bflag1</em> and <em>bflag2</em> settings are numerical values which are
passed to the body style to affect how the drawing of a body particle
is done. See the <a class="reference internal" href="body.html"><span class="doc">body</span></a> doc page for a description of what
these parameters mean for each body style.</p>
<hr class="docutils" />
<p>The <em>size</em> keyword sets the width and height of the created images,
i.e. the number of pixels in each direction.</p>
<hr class="docutils" />
<p>The <em>view</em>, <em>center</em>, <em>up</em>, <em>zoom</em>, and <em>persp</em> values determine how
3d simulation space is mapped to the 2d plane of the image. Basically
they control how the simulation box appears in the image.</p>
<p>All of the <em>view</em>, <em>center</em>, <em>up</em>, <em>zoom</em>, and <em>persp</em> values can be
specified as numeric quantities, whose meaning is explained below.
Any of them can also be specified as an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a>, by using v_name as the value, where “name” is
the variable name. In this case the variable will be evaluated on the
timestep each image is created to create a new value. If the
equal-style variable is time-dependent, this is a means of changing
the way the simulation box appears from image to image, effectively
doing a pan or fly-by view of your simulation.</p>
<p>The <em>view</em> keyword determines the viewpoint from which the simulation
box is viewed, looking towards the <em>center</em> point. The <em>theta</em> value
is the vertical angle from the +z axis, and must be an angle from 0 to
180 degrees. The <em>phi</em> value is an azimuthal angle around the z axis
and can be positive or negative. A value of 0.0 is a view along the
+x axis, towards the <em>center</em> point. If <em>theta</em> or <em>phi</em> are
specified via variables, then the variable values should be in
degrees.</p>
<p>The <em>center</em> keyword determines the point in simulation space that
will be at the center of the image. <em>Cx</em>, <em>Cy</em>, and <em>Cz</em> are
speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is
the center of the simulation box. These values do not have to be
between 0.0 and 1.0, if you want the simulation box to be offset from
the center of the image. Note, however, that if you choose strange
values for <em>Cx</em>, <em>Cy</em>, or <em>Cz</em> you may get a blank image. Internally,
<em>Cx</em>, <em>Cy</em>, and <em>Cz</em> are converted into a point in simulation space.
If <em>flag</em> is set to “s” for static, then this conversion is done once,
at the time the dump command is issued. If <em>flag</em> is set to “d” for
dynamic then the conversion is performed every time a new image is
created. If the box size or shape is changing, this will adjust the
center point in simulation space.</p>
<p>The <em>up</em> keyword determines what direction in simulation space will be
“up” in the image. Internally it is stored as a vector that is in the
plane perpendicular to the view vector implied by the <em>theta</em> and
<em>pni</em> values, and which is also in the plane defined by the view
vector and user-specified up vector. Thus this internal vector is
computed from the user-specified <em>up</em> vector as</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">up_internal</span> <span class="o">=</span> <span class="n">view</span> <span class="n">cross</span> <span class="p">(</span><span class="n">up</span> <span class="n">cross</span> <span class="n">view</span><span class="p">)</span>
</pre></div>
</div>
<p>This means the only restriction on the specified <em>up</em> vector is that
it cannot be parallel to the <em>view</em> vector, implied by the <em>theta</em> and
<em>phi</em> values.</p>
<p>The <em>zoom</em> keyword scales the size of the simulation box as it appears
in the image. The default <em>zfactor</em> value of 1 should display an
image mostly filled by the atoms in the simulation box. A <em>zfactor</em> >
1 will make the simulation box larger; a <em>zfactor</em> < 1 will make it
smaller. <em>Zfactor</em> must be a value > 0.0.</p>
<p>The <em>persp</em> keyword determines how much depth perspective is present
in the image. Depth perspective makes lines that are parallel in
simulation space appear non-parallel in the image. A <em>pfactor</em> value
of 0.0 means that parallel lines will meet at infininty (1.0/pfactor),
which is an orthographic rendering with no persepctive. A <em>pfactor</em>
value between 0.0 and 1.0 will introduce more perspective. A <em>pfactor</em>
value > 1 will create a highly skewed image with a large amount of
perspective.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The <em>persp</em> keyword is not yet supported as an option.</p>
</div>
<hr class="docutils" />
<p>The <em>box</em> keyword determines if and how the simulation box boundaries
are rendered as thin cylinders in the image. If <em>no</em> is set, then the
box boundaries are not drawn and the <em>diam</em> setting is ignored. If
<em>yes</em> is set, the 12 edges of the box are drawn, with a diameter that
is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for
2d). The color of the box boundaries can be set with the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify boxcolor</span></a> command.</p>
<p>The <em>axes</em> keyword determines if and how the coordinate axes are
rendered as thin cylinders in the image. If <em>no</em> is set, then the
axes are not drawn and the <em>length</em> and <em>diam</em> settings are ignored.
If <em>yes</em> is set, 3 thin cylinders are drawn to represent the x,y,z
axes in colors red,green,blue. The origin of these cylinders will be
offset from the lower left corner of the box by 10%. The <em>length</em>
setting determines how long the cylinders will be as a fraction of the
respective box lengths. The <em>diam</em> setting determines their thickness
as a fraction of the shortest box length in x,y,z (for 3d) or x,y (for
2d).</p>
<p>The <em>subbox</em> keyword determines if and how processor sub-domain
boundaries are rendered as thin cylinders in the image. If <em>no</em> is
set (default), then the sub-domain boundaries are not drawn and the
<em>diam</em> setting is ignored. If <em>yes</em> is set, the 12 edges of each
processor sub-domain are drawn, with a diameter that is a fraction of
the shortest box length in x,y,z (for 3d) or x,y (for 2d). The color
of the sub-domain boundaries can be set with the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify boxcolor</span></a> command.</p>
<hr class="docutils" />
<p>The <em>shiny</em> keyword determines how shiny the objects rendered in the
image will appear. The <em>sfactor</em> value must be a value 0.0 <=
<em>sfactor</em> <= 1.0, where <em>sfactor</em> = 1 is a highly reflective surface
and <em>sfactor</em> = 0 is a rough non-shiny surface.</p>
<p>The <em>ssao</em> keyword turns on/off a screen space ambient occlusion
(SSAO) model for depth shading. If <em>yes</em> is set, then atoms further
away from the viewer are darkened via a randomized process, which is
perceived as depth. The calculation of this effect can increase the
cost of computing the image by roughly 2x. The strength of the effect
can be scaled by the <em>dfactor</em> parameter. If <em>no</em> is set, no depth
shading is performed.</p>
<hr class="docutils" />
<p>A series of JPEG, PNG, or PPM images can be converted into a movie
file and then played as a movie using commonly available tools. Using
dump style <em>movie</em> automates this step and avoids the intermediate
step of writing (many) image snapshot file. But LAMMPS has to be
compiled with -DLAMMPS_FFMPEG and an FFmpeg executable have to be
installed.</p>
<p>To manually convert JPEG, PNG or PPM files into an animated GIF or
MPEG or other movie file you can use:</p>
<ul class="simple">
<li><ol class="first loweralpha">
<li>Use the ImageMagick convert program.</li>
</ol>
</li>
</ul>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">convert</span> <span class="o">*.</span><span class="n">jpg</span> <span class="n">foo</span><span class="o">.</span><span class="n">gif</span>
<span class="o">%</span> <span class="n">convert</span> <span class="o">-</span><span class="n">loop</span> <span class="mi">1</span> <span class="o">*.</span><span class="n">ppm</span> <span class="n">foo</span><span class="o">.</span><span class="n">mpg</span>
</pre></div>
</div>
<p>Animated GIF files from ImageMagick are unoptimized. You can use a
program like gifsicle to optimize and massively shrink them.
MPEG files created by ImageMagick are in MPEG-1 format with rather
inefficient compression and low quality.</p>
<ul class="simple">
<li><ol class="first loweralpha" start="2">
<li>Use QuickTime.</li>
</ol>
</li>
</ul>
<p>Select “Open Image Sequence” under the File menu Load the images into
QuickTime to animate them Select “Export” under the File menu Save the
movie as a QuickTime movie (<a href="#id7"><span class="problematic" id="id8">*</span></a>.mov) or in another format. QuickTime
can generate very high quality and efficiently compressed movie
files. Some of the supported formats require to buy a license and some
are not readable on all platforms until specific runtime libraries are
installed.</p>
<ul class="simple">
<li><ol class="first loweralpha" start="3">
<li>Use FFmpeg</li>
</ol>
</li>
</ul>
<p>FFmpeg is a command line tool that is available on many platforms and
allows extremely flexible encoding and decoding of movies.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cat</span> <span class="n">snap</span><span class="o">.*.</span><span class="n">jpg</span> <span class="o">|</span> <span class="n">ffmpeg</span> <span class="o">-</span><span class="n">y</span> <span class="o">-</span><span class="n">f</span> <span class="n">image2pipe</span> <span class="o">-</span><span class="n">c</span><span class="p">:</span><span class="n">v</span> <span class="n">mjpeg</span> <span class="o">-</span><span class="n">i</span> <span class="o">-</span> <span class="o">-</span><span class="n">b</span><span class="p">:</span><span class="n">v</span> <span class="mi">2000</span><span class="n">k</span> <span class="n">movie</span><span class="o">.</span><span class="n">m4v</span>
<span class="n">cat</span> <span class="n">snap</span><span class="o">.*.</span><span class="n">ppm</span> <span class="o">|</span> <span class="n">ffmpeg</span> <span class="o">-</span><span class="n">y</span> <span class="o">-</span><span class="n">f</span> <span class="n">image2pipe</span> <span class="o">-</span><span class="n">c</span><span class="p">:</span><span class="n">v</span> <span class="n">ppm</span> <span class="o">-</span><span class="n">i</span> <span class="o">-</span> <span class="o">-</span><span class="n">b</span><span class="p">:</span><span class="n">v</span> <span class="mi">2400</span><span class="n">k</span> <span class="n">movie</span><span class="o">.</span><span class="n">avi</span>
</pre></div>
</div>
<p>Frontends for FFmpeg exist for multiple platforms. For more
information see the <a class="reference external" href="http://www.ffmpeg.org/">FFmpeg homepage</a></p>
<hr class="docutils" />
<p>Play the movie:</p>
<ul class="simple">
<li><ol class="first loweralpha">
<li>Use your browser to view an animated GIF movie.</li>
</ol>
</li>
</ul>
<p>Select “Open File” under the File menu
Load the animated GIF file</p>
<ul class="simple">
<li>b) Use the freely available mplayer or ffplay tool to view a
movie. Both are available for multiple OSes and support a large
variety of file formats and decoders.</li>
</ul>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">mplayer</span> <span class="n">foo</span><span class="o">.</span><span class="n">mpg</span>
<span class="o">%</span> <span class="n">ffplay</span> <span class="n">bar</span><span class="o">.</span><span class="n">avi</span>
</pre></div>
</div>
<ul class="simple">
<li>c) Use the <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a>
<a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza/doc/animate.html">animate tool</a>,
which works directly on a series of image files.</li>
</ul>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">a</span> <span class="o">=</span> <span class="n">animate</span><span class="p">(</span><span class="s2">"foo*.jpg"</span><span class="p">)</span>
</pre></div>
</div>
<ul class="simple">
<li>d) QuickTime and other Windows- or MacOS-based media players can
obviously play movie files directly. Similarly for corresponding tools
bundled with Linux desktop environments. However, due to licensing
issues with some file formats, the formats may require installing
additional libraries, purchasing a license, or may not be
supported.</li>
</ul>
<hr class="docutils" />
<p>See <a class="reference internal" href="Section_modify.html"><span class="doc">Section_modify</span></a> of the manual for information
on how to add new compute and fix styles to LAMMPS to calculate
per-atom quantities which could then be output into dump files.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>To write JPEG images, you must use the -DLAMMPS_JPEG switch when
building LAMMPS and link with a JPEG library. To write PNG images, you
must use the -DLAMMPS_PNG switch when building LAMMPS and link with a
PNG library.</p>
<p>To write <em>movie</em> dumps, you must use the -DLAMMPS_FFMPEG switch when
building LAMMPS and have the FFmpeg executable available on the
machine where LAMMPS is being run. Typically it’s name is lowercase,
i.e. ffmpeg.</p>
<p>See the <a class="reference internal" href="Section_start.html#start-2-4"><span class="std std-ref">Making LAMMPS</span></a> section of the
documentation for details on how to compile with optional switches.</p>
<p>Note that since FFmpeg is run as an external program via a pipe,
LAMMPS has limited control over its execution and no knowledge about
errors and warnings printed by it. Those warnings and error messages
will be printed to the screen only. Due to the way image data is
communicated to FFmpeg, it will often print the message</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pipe</span><span class="p">::</span> <span class="n">Input</span><span class="o">/</span><span class="n">output</span> <span class="n">error</span>
</pre></div>
</div>
<p>which can be safely ignored. Other warnings
and errors have to be addressed according to the FFmpeg documentation.
One known issue is that certain movie file formats (e.g. MPEG level 1
and 2 format streams) have video bandwith limits that can be crossed
when rendering too large of image sizes. Typical warnings look like
this:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="p">[</span><span class="n">mpeg</span> <span class="o">@</span> <span class="mh">0x98b5e0</span><span class="p">]</span> <span class="n">packet</span> <span class="n">too</span> <span class="n">large</span><span class="p">,</span> <span class="n">ignoring</span> <span class="n">buffer</span> <span class="n">limits</span> <span class="n">to</span> <span class="n">mux</span> <span class="n">it</span>
<span class="p">[</span><span class="n">mpeg</span> <span class="o">@</span> <span class="mh">0x98b5e0</span><span class="p">]</span> <span class="n">buffer</span> <span class="n">underflow</span> <span class="n">st</span><span class="o">=</span><span class="mi">0</span> <span class="n">bufi</span><span class="o">=</span><span class="mi">281407</span> <span class="n">size</span><span class="o">=</span><span class="mi">285018</span>
<span class="p">[</span><span class="n">mpeg</span> <span class="o">@</span> <span class="mh">0x98b5e0</span><span class="p">]</span> <span class="n">buffer</span> <span class="n">underflow</span> <span class="n">st</span><span class="o">=</span><span class="mi">0</span> <span class="n">bufi</span><span class="o">=</span><span class="mi">283448</span> <span class="n">size</span><span class="o">=</span><span class="mi">285018</span>
</pre></div>
</div>
<p>In this case it is recommended to either reduce the size of the image
or encode in a different format that is also supported by your copy of
FFmpeg, and which does not have this limitation (e.g. .avi, .mkv,
mp4).</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="dump.html"><span class="doc">dump</span></a>, <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a>, <a class="reference internal" href="undump.html"><span class="doc">undump</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>The defaults for the keywords are as follows:</p>
<ul class="simple">
<li>adiam = not specified (use diameter setting)</li>
<li>atom = yes</li>
<li>bond = none none (if no bonds in system)</li>
<li>bond = atom 0.5 (if bonds in system)</li>
<li>size = 512 512</li>
<li>view = 60 30 (for 3d)</li>
<li>view = 0 0 (for 2d)</li>
<li>center = s 0.5 0.5 0.5</li>
<li>up = 0 0 1 (for 3d)</li>
<li>up = 0 1 0 (for 2d)</li>
<li>zoom = 1.0</li>
<li>persp = 0.0</li>
<li>box = yes 0.02</li>
<li>axes = no 0.0 0.0</li>
<li>subbox no 0.0</li>
<li>shiny = 1.0</li>
<li>ssao = no</li>
</ul>
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<div class="section" id="fix-nvt-command">
<span id="index-0"></span><h1>fix nvt command</h1>
</div>
<div class="section" id="fix-nvt-cuda-command">
<h1>fix nvt/cuda command</h1>
</div>
<div class="section" id="fix-nvt-intel-command">
<h1>fix nvt/intel command</h1>
</div>
<div class="section" id="fix-nvt-kk-command">
<h1>fix nvt/kk command</h1>
</div>
<div class="section" id="fix-nvt-omp-command">
<h1>fix nvt/omp command</h1>
</div>
<div class="section" id="fix-npt-command">
<h1>fix npt command</h1>
</div>
<div class="section" id="fix-npt-cuda-command">
<h1>fix npt/cuda command</h1>
</div>
<div class="section" id="fix-npt-intel-command">
<h1>fix npt/intel command</h1>
</div>
<div class="section" id="fix-npt-kk-command">
<h1>fix npt/kk command</h1>
</div>
<div class="section" id="fix-npt-omp-command">
<h1>fix npt/omp command</h1>
</div>
<div class="section" id="fix-nph-command">
<h1>fix nph command</h1>
</div>
<div class="section" id="fix-nph-kk-command">
<h1>fix nph/kk command</h1>
</div>
<div class="section" id="fix-nph-omp-command">
<h1>fix nph/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style_name</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>style_name = <em>nvt</em> or <em>npt</em> or <em>nph</em></li>
<li>one or more keyword/value pairs may be appended</li>
</ul>
<pre class="literal-block">
keyword = <em>temp</em> or <em>iso</em> or <em>aniso</em> or <em>tri</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>yz</em> or <em>xz</em> or <em>couple</em> or <em>tchain</em> or <em>pchain</em> or <em>mtk</em> or <em>tloop</em> or <em>ploop</em> or <em>nreset</em> or <em>drag</em> or <em>dilate</em> or <em>scalexy</em> or <em>scaleyz</em> or <em>scalexz</em> or <em>flip</em> or <em>fixedpoint</em> or <em>update</em>
<em>temp</em> values = Tstart Tstop Tdamp
Tstart,Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units)
<em>iso</em> or <em>aniso</em> or <em>tri</em> values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
<em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>yz</em> or <em>xz</em> values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = stress damping parameter (time units)
<em>couple</em> = <em>none</em> or <em>xyz</em> or <em>xy</em> or <em>yz</em> or <em>xz</em>
<em>tchain</em> value = N
N = length of thermostat chain (1 = single thermostat)
<em>pchain</em> values = N
N length of thermostat chain on barostat (0 = no thermostat)
<em>mtk</em> value = <em>yes</em> or <em>no</em> = add in MTK adjustment term or not
<em>tloop</em> value = M
M = number of sub-cycles to perform on thermostat
<em>ploop</em> value = M
M = number of sub-cycles to perform on barostat thermostat
<em>nreset</em> value = reset reference cell every this many timesteps
<em>drag</em> value = Df
Df = drag factor added to barostat/thermostat (0.0 = no drag)
<em>dilate</em> value = dilate-group-ID
dilate-group-ID = only dilate atoms in this group due to barostat volume changes
<em>scalexy</em> value = <em>yes</em> or <em>no</em> = scale xy with ly
<em>scaleyz</em> value = <em>yes</em> or <em>no</em> = scale yz with lz
<em>scalexz</em> value = <em>yes</em> or <em>no</em> = scale xz with lz
<em>flip</em> value = <em>yes</em> or <em>no</em> = allow or disallow box flips when it becomes highly skewed
<em>fixedpoint</em> values = x y z
x,y,z = perform barostat dilation/contraction around this point (distance units)
<em>update</em> value = <em>dipole</em> update dipole orientation (only for sphere variants)
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">100.0</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="n">water</span> <span class="n">npt</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">100.0</span> <span class="n">iso</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">1000.0</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="n">jello</span> <span class="n">npt</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">100.0</span> <span class="n">tri</span> <span class="mf">5.0</span> <span class="mf">5.0</span> <span class="mf">1000.0</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="n">ice</span> <span class="n">nph</span> <span class="n">x</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.5</span> <span class="n">y</span> <span class="mf">2.0</span> <span class="mf">2.0</span> <span class="mf">0.5</span> <span class="n">z</span> <span class="mf">3.0</span> <span class="mf">3.0</span> <span class="mf">0.5</span> <span class="n">yz</span> <span class="mf">0.1</span> <span class="mf">0.1</span> <span class="mf">0.5</span> <span class="n">xz</span> <span class="mf">0.2</span> <span class="mf">0.2</span> <span class="mf">0.5</span> <span class="n">xy</span> <span class="mf">0.3</span> <span class="mf">0.3</span> <span class="mf">0.5</span> <span class="n">nreset</span> <span class="mi">1000</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>These commands perform time integration on Nose-Hoover style
non-Hamiltonian equations of motion which are designed to generate
positions and velocities sampled from the canonical (nvt),
isothermal-isobaric (npt), and isenthalpic (nph) ensembles. This
updates the position and velocity for atoms in the group each
timestep.</p>
<p>The thermostatting and barostatting is achieved by adding some dynamic
variables which are coupled to the particle velocities
(thermostatting) and simulation domain dimensions (barostatting). In
addition to basic thermostatting and barostatting, these fixes can
also create a chain of thermostats coupled to the particle thermostat,
and another chain of thermostats coupled to the barostat
variables. The barostat can be coupled to the overall box volume, or
to individual dimensions, including the <em>xy</em>, <em>xz</em> and <em>yz</em> tilt
dimensions. The external pressure of the barostat can be specified as
either a scalar pressure (isobaric ensemble) or as components of a
symmetric stress tensor (constant stress ensemble). When used
correctly, the time-averaged temperature and stress tensor of the
particles will match the target values specified by Tstart/Tstop and
Pstart/Pstop.</p>
<p>The equations of motion used are those of Shinoda et al in
<a class="reference internal" href="pair_sdk.html#shinoda"><span class="std std-ref">(Shinoda)</span></a>, which combine the hydrostatic equations of
-Martyna, Tobias and Klein in <a class="reference internal" href="fix_rigid.html#martyna"><span class="std std-ref">(Martyna)</span></a> with the strain
+Martyna, Tobias and Klein in <a class="reference internal" href="#martyna"><span class="std std-ref">(Martyna)</span></a> with the strain
energy proposed by Parrinello and Rahman in
-<a class="reference internal" href="fix_nh_eff.html#parrinello"><span class="std std-ref">(Parrinello)</span></a>. The time integration schemes closely
+<a class="reference internal" href="#parrinello"><span class="std std-ref">(Parrinello)</span></a>. The time integration schemes closely
follow the time-reversible measure-preserving Verlet and rRESPA
-integrators derived by Tuckerman et al in <a class="reference internal" href="run_style.html#tuckerman"><span class="std std-ref">(Tuckerman)</span></a>.</p>
+integrators derived by Tuckerman et al in <a class="reference internal" href="fix_pimd.html#tuckerman"><span class="std std-ref">(Tuckerman)</span></a>.</p>
<hr class="docutils" />
<p>The thermostat parameters for fix styles <em>nvt</em> and <em>npt</em> is specified
using the <em>temp</em> keyword. Other thermostat-related keywords are
<em>tchain</em>, <em>tloop</em> and <em>drag</em>, which are discussed below.</p>
<p>The thermostat is applied to only the translational degrees of freedom
for the particles. The translational degrees of freedom can also have
a bias velocity removed before thermostatting takes place; see the
description below. The desired temperature at each timestep is a
ramped value during the run from <em>Tstart</em> to <em>Tstop</em>. The <em>Tdamp</em>
parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, a value of 10.0 means to relax
the temperature in a timespan of (roughly) 10 time units (e.g. tau or
-fmsec or psec - see the <span class="xref doc">units</span> command). The atoms in the
+fmsec or psec - see the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command). The atoms in the
fix group are the only ones whose velocities and positions are updated
by the velocity/position update portion of the integration.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">A Nose-Hoover thermostat will not work well for arbitrary values
of <em>Tdamp</em>. If <em>Tdamp</em> is too small, the temperature can fluctuate
wildly; if it is too large, the temperature will take a very long time
to equilibrate. A good choice for many models is a <em>Tdamp</em> of around
100 timesteps. Note that this is NOT the same as 100 time units for
-most <span class="xref doc">units</span> settings.</p>
+most <a class="reference internal" href="units.html"><span class="doc">units</span></a> settings.</p>
</div>
<hr class="docutils" />
<p>The barostat parameters for fix styles <em>npt</em> and <em>nph</em> is specified
using one or more of the <em>iso</em>, <em>aniso</em>, <em>tri</em>, <em>x</em>, <em>y</em>, <em>z</em>, <em>xy</em>,
<em>xz</em>, <em>yz</em>, and <em>couple</em> keywords. These keywords give you the
ability to specify all 6 components of an external stress tensor, and
to couple various of these components together so that the dimensions
they represent are varied together during a constant-pressure
simulation.</p>
<p>Other barostat-related keywords are <em>pchain</em>, <em>mtk</em>, <em>ploop</em>,
<em>nreset</em>, <em>drag</em>, and <em>dilate</em>, which are discussed below.</p>
<p>Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
Triclinic (non-orthogonal) simulation boxes have 6 adjustable
dimensions (x,y,z,xy,xz,yz). The <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a>, <a class="reference internal" href="read_data.html"><span class="doc">read data</span></a>, and <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> commands
specify whether the simulation box is orthogonal or non-orthogonal
(triclinic) and explain the meaning of the xy,xz,yz tilt factors.</p>
<p>The target pressures for each of the 6 components of the stress tensor
can be specified independently via the <em>x</em>, <em>y</em>, <em>z</em>, <em>xy</em>, <em>xz</em>, <em>yz</em>
keywords, which correspond to the 6 simulation box dimensions. For
each component, the external pressure or tensor component at each
timestep is a ramped value during the run from <em>Pstart</em> to <em>Pstop</em>.
If a target pressure is specified for a component, then the
corresponding box dimension will change during a simulation. For
example, if the <em>y</em> keyword is used, the y-box length will change. If
the <em>xy</em> keyword is used, the xy tilt factor will change. A box
dimension will not change if that component is not specified, although
you have the option to change that dimension via the <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> command.</p>
<p>Note that in order to use the <em>xy</em>, <em>xz</em>, or <em>yz</em> keywords, the
simulation box must be triclinic, even if its initial tilt factors are
0.0.</p>
<p>For all barostat keywords, the <em>Pdamp</em> parameter operates like the
<em>Tdamp</em> parameter, determining the time scale on which pressure is
relaxed. For example, a value of 10.0 means to relax the pressure in
a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
-the <span class="xref doc">units</span> command).</p>
+the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command).</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">A Nose-Hoover barostat will not work well for arbitrary values
of <em>Pdamp</em>. If <em>Pdamp</em> is too small, the pressure and volume can
fluctuate wildly; if it is too large, the pressure will take a very
long time to equilibrate. A good choice for many models is a <em>Pdamp</em>
of around 1000 timesteps. However, note that <em>Pdamp</em> is specified in
time units, and that timesteps are NOT the same as time units for most
-<span class="xref doc">units</span> settings.</p>
+<a class="reference internal" href="units.html"><span class="doc">units</span></a> settings.</p>
</div>
<p>Regardless of what atoms are in the fix group (the only atoms which
are time integrated), a global pressure or stress tensor is computed
for all atoms. Similarly, when the size of the simulation box is
changed, all atoms are re-scaled to new positions, unless the keyword
<em>dilate</em> is specified with a <em>dilate-group-ID</em> for a group that
represents a subset of the atoms. This can be useful, for example, to
leave the coordinates of atoms in a solid substrate unchanged and
controlling the pressure of a surrounding fluid. This option should
be used with care, since it can be unphysical to dilate some atoms and
not others, because it can introduce large, instantaneous
displacements between a pair of atoms (one dilated, one not) that are
far from the dilation origin. Also note that for atoms not in the fix
group, a separate time integration fix like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or
<a class="reference internal" href="#"><span class="doc">fix nvt</span></a> can be used on them, independent of whether they
are dilated or not.</p>
<hr class="docutils" />
<p>The <em>couple</em> keyword allows two or three of the diagonal components of
the pressure tensor to be “coupled” together. The value specified
with the keyword determines which are coupled. For example, <em>xz</em>
means the <em>Pxx</em> and <em>Pzz</em> components of the stress tensor are coupled.
<em>Xyz</em> means all 3 diagonal components are coupled. Coupling means two
things: the instantaneous stress will be computed as an average of the
corresponding diagonal components, and the coupled box dimensions will
be changed together in lockstep, meaning coupled dimensions will be
dilated or contracted by the same percentage every timestep. The
<em>Pstart</em>, <em>Pstop</em>, <em>Pdamp</em> parameters for any coupled dimensions must
be identical. <em>Couple xyz</em> can be used for a 2d simulation; the <em>z</em>
dimension is simply ignored.</p>
<hr class="docutils" />
<p>The <em>iso</em>, <em>aniso</em>, and <em>tri</em> keywords are simply shortcuts that are
equivalent to specifying several other keywords together.</p>
<p>The keyword <em>iso</em> means couple all 3 diagonal components together when
pressure is computed (hydrostatic pressure), and dilate/contract the
dimensions together. Using “iso Pstart Pstop Pdamp” is the same as
specifying these 4 keywords:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
<span class="n">y</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
<span class="n">z</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
<span class="n">couple</span> <span class="n">xyz</span>
</pre></div>
</div>
<p>The keyword <em>aniso</em> means <em>x</em>, <em>y</em>, and <em>z</em> dimensions are controlled
independently using the <em>Pxx</em>, <em>Pyy</em>, and <em>Pzz</em> components of the
stress tensor as the driving forces, and the specified scalar external
pressure. Using “aniso Pstart Pstop Pdamp” is the same as specifying
these 4 keywords:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
<span class="n">y</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
<span class="n">z</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
<span class="n">couple</span> <span class="n">none</span>
</pre></div>
</div>
<p>The keyword <em>tri</em> means <em>x</em>, <em>y</em>, <em>z</em>, <em>xy</em>, <em>xz</em>, and <em>yz</em> dimensions
are controlled independently using their individual stress components
as the driving forces, and the specified scalar pressure as the
external normal stress. Using “tri Pstart Pstop Pdamp” is the same as
specifying these 7 keywords:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
<span class="n">y</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
<span class="n">z</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
<span class="n">xy</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="n">Pdamp</span>
<span class="n">yz</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="n">Pdamp</span>
<span class="n">xz</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="n">Pdamp</span>
<span class="n">couple</span> <span class="n">none</span>
</pre></div>
</div>
<hr class="docutils" />
<p>In some cases (e.g. for solids) the pressure (volume) and/or
temperature of the system can oscillate undesirably when a Nose/Hoover
barostat and thermostat is applied. The optional <em>drag</em> keyword will
damp these oscillations, although it alters the Nose/Hoover equations.
A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged.
A non-zero value adds a drag term; the larger the value specified, the
greater the damping effect. Performing a short run and monitoring the
pressure and temperature is the best way to determine if the drag term
is working. Typically a value between 0.2 to 2.0 is sufficient to
damp oscillations after a few periods. Note that use of the drag
keyword will interfere with energy conservation and will also change
the distribution of positions and velocities so that they do not
correspond to the nominal NVT, NPT, or NPH ensembles.</p>
<p>An alternative way to control initial oscillations is to use chain
thermostats. The keyword <em>tchain</em> determines the number of thermostats
in the particle thermostat. A value of 1 corresponds to the original
Nose-Hoover thermostat. The keyword <em>pchain</em> specifies the number of
thermostats in the chain thermostatting the barostat degrees of
freedom. A value of 0 corresponds to no thermostatting of the
barostat variables.</p>
<p>The <em>mtk</em> keyword controls whether or not the correction terms due to
Martyna, Tuckerman, and Klein are included in the equations of motion
-<a class="reference internal" href="fix_rigid.html#martyna"><span class="std std-ref">(Martyna)</span></a>. Specifying <em>no</em> reproduces the original
+<a class="reference internal" href="#martyna"><span class="std std-ref">(Martyna)</span></a>. Specifying <em>no</em> reproduces the original
Hoover barostat, whose volume probability distribution function
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence
using <em>yes</em> is more correct, but in many cases the difference is
negligible.</p>
<p>The keyword <em>tloop</em> can be used to improve the accuracy of integration
scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into <em>tloop</em> substeps, each of
length <em>dt</em>/<em>tloop</em>. This corresponds to using a first-order
-Suzuki-Yoshida scheme <a class="reference internal" href="run_style.html#tuckerman"><span class="std std-ref">(Tuckerman)</span></a>. The keyword <em>ploop</em>
+Suzuki-Yoshida scheme <a class="reference internal" href="fix_pimd.html#tuckerman"><span class="std std-ref">(Tuckerman)</span></a>. The keyword <em>ploop</em>
does the same thing for the barostat thermostat.</p>
<p>The keyword <em>nreset</em> controls how often the reference dimensions used
to define the strain energy are reset. If this keyword is not used,
or is given a value of zero, then the reference dimensions are set to
those of the initial simulation domain and are never changed. If the
simulation domain changes significantly during the simulation, then
the final average pressure tensor will differ significantly from the
specified values of the external stress tensor. A value of <em>nstep</em>
means that every <em>nstep</em> timesteps, the reference dimensions are set
to those of the current simulation domain.</p>
<p>The <em>scaleyz</em>, <em>scalexz</em>, and <em>scalexy</em> keywords control whether or
not the corresponding tilt factors are scaled with the associated box
dimensions when barostatting triclinic periodic cells. The default
values <em>yes</em> will turn on scaling, which corresponds to adjusting the
linear dimensions of the cell while preserving its shape. Choosing
<em>no</em> ensures that the tilt factors are not scaled with the box
dimensions. See below for restrictions and default values in different
situations. In older versions of LAMMPS, scaling of tilt factors was
not performed. The old behavior can be recovered by setting all three
scale keywords to <em>no</em>.</p>
<p>The <em>flip</em> keyword allows the tilt factors for a triclinic box to
exceed half the distance of the parallel box length, as discussed
below. If the <em>flip</em> value is set to <em>yes</em>, the bound is enforced by
flipping the box when it is exceeded. If the <em>flip</em> value is set to
<em>no</em>, the tilt will continue to change without flipping. Note that if
applied stress induces large deformations (e.g. in a liquid), this
means the box shape can tilt dramatically and LAMMPS will run less
efficiently, due to the large volume of communication needed to
acquire ghost atoms around a processor’s irregular-shaped sub-domain.
For extreme values of tilt, LAMMPS may also lose atoms and generate an
error.</p>
<p>The <em>fixedpoint</em> keyword specifies the fixed point for barostat volume
changes. By default, it is the center of the box. Whatever point is
chosen will not move during the simulation. For example, if the lower
periodic boundaries pass through (0,0,0), and this point is provided
to <em>fixedpoint</em>, then the lower periodic boundaries will remain at
(0,0,0), while the upper periodic boundaries will move twice as
far. In all cases, the particle trajectories are unaffected by the
chosen value, except for a time-dependent constant translation of
positions.</p>
<p>If the <em>update</em> keyword is used with the <em>dipole</em> value, then the
orientation of the dipole moment of each particle is also updated
during the time integration. This option should be used for models
where a dipole moment is assigned to finite-size particles,
e.g. spheroids via use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style hybrid sphere dipole</span></a> command.</p>
<hr class="docutils" />
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Using a barostat coupled to tilt dimensions <em>xy</em>, <em>xz</em>, <em>yz</em> can
sometimes result in arbitrarily large values of the tilt dimensions,
i.e. a dramatically deformed simulation box. LAMMPS allows the tilt
factors to grow a small amount beyond the normal limit of half the box
length (0.6 times the box length), and then performs a box “flip” to
an equivalent periodic cell. See the discussion of the <em>flip</em> keyword
above, to allow this bound to be exceeded, if desired.</p>
</div>
<p>The flip operation is described in more detail in the doc page for
<a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a>. Both the barostat dynamics and the atom
trajectories are unaffected by this operation. However, if a tilt
factor is incremented by a large amount (1.5 times the box length) on
a single timestep, LAMMPS can not accomodate this event and will
terminate the simulation with an error. This error typically indicates
that there is something badly wrong with how the simulation was
constructed, such as specifying values of <em>Pstart</em> that are too far
from the current stress value, or specifying a timestep that is too
large. Triclinic barostatting should be used with care. This also is
true for other barostat styles, although they tend to be more
forgiving of insults. In particular, it is important to recognize that
equilibrium liquids can not support a shear stress and that
equilibrium solids can not support shear stresses that exceed the
yield stress.</p>
<p>One exception to this rule is if the 1st dimension in the tilt factor
(x for xy) is non-periodic. In that case, the limits on the tilt
factor are not enforced, since flipping the box in that dimension does
not change the atom positions due to non-periodicity. In this mode,
if you tilt the system to extreme angles, the simulation will simply
become inefficient due to the highly skewed simulation box.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Unlike the <a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">fix temp/berendsen</span></a> command
which performs thermostatting but NO time integration, these fixes
perform thermostatting/barostatting AND time integration. Thus you
should not use any other time integration fix, such as <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> on atoms to which this fix is applied. Likewise,
fix nvt and fix npt should not normally be used on atoms that also
have their temperature controlled by another fix - e.g. by <a class="reference internal" href="#"><span class="doc">fix langevin</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>
commands.</p>
</div>
<p>See <a class="reference internal" href="Section_howto.html#howto-16"><span class="std std-ref">this howto section</span></a> of the manual for
a discussion of different ways to compute temperature and perform
thermostatting and barostatting.</p>
<hr class="docutils" />
<p>These fixes compute a temperature and pressure each timestep. To do
this, the fix creates its own computes of style “temp” and “pressure”,
as if one of these two sets of commands had been issued:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span>
<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span>
<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
</pre></div>
</div>
<p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
+ underscore + “press”. For fix nvt, the group for the new computes
is the same as the fix group. For fix nph and fix npt, the group for
the new computes is “all” since pressure is computed for the entire
system.</p>
<p>Note that these are NOT the computes used by thermodynamic output (see
the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command) with ID = <em>thermo_temp</em>
and <em>thermo_press</em>. This means you can change the attributes of this
fix’s temperature or pressure via the
<a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a> command or print this temperature
or pressure during thermodynamic output via the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command using the appropriate compute-ID.
It also means that changing attributes of <em>thermo_temp</em> or
<em>thermo_press</em> will have no effect on this fix.</p>
<p>Like other fixes that perform thermostatting, fix nvt and fix npt can
be used with <a class="reference internal" href="compute.html"><span class="doc">compute commands</span></a> that calculate a
temperature after removing a “bias” from the atom velocities.
E.g. removing the center-of-mass velocity from a group of atoms or
only calculating temperature on the x-component of velocity or only
calculating temperature for atoms in a geometric region. This is not
done by default, but only if the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> command
is used to assign a temperature compute to this fix that includes such
a bias term. See the doc pages for individual <a class="reference internal" href="compute.html"><span class="doc">compute commands</span></a> to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.</p>
<hr class="docutils" />
<p>These fixes can be used with either the <em>verlet</em> or <em>respa</em>
<a class="reference internal" href="run_style.html"><span class="doc">integrators</span></a>. When using one of the barostat fixes
with <em>respa</em>, LAMMPS uses an integrator constructed
according to the following factorization of the Liouville propagator
(for two rRESPA levels):</p>
<img alt="_images/fix_nh1.jpg" class="align-center" src="_images/fix_nh1.jpg" />
<p>This factorization differs somewhat from that of Tuckerman et al, in
that the barostat is only updated at the outermost rRESPA level,
whereas Tuckerman’s factorization requires splitting the pressure into
pieces corresponding to the forces computed at each rRESPA level. In
theory, the latter method will exhibit better numerical stability. In
practice, because Pdamp is normally chosen to be a large multiple of
the outermost rRESPA timestep, the barostat dynamics are not the
limiting factor for numerical stability. Both factorizations are
time-reversible and can be shown to preserve the phase space measure
of the underlying non-Hamiltonian equations of motion.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This implementation has been shown to conserve linear momentum
up to machine precision under NVT dynamics. Under NPT dynamics,
for a system with zero initial total linear momentum, the total
momentum fluctuates close to zero. It may occasionally undergo brief
excursions to non-negligible values, before returning close to zero.
Over long simulations, this has the effect of causing the center-of-mass
to undergo a slow random walk. This can be mitigated by resetting
the momentum at infrequent intervals using the
<a class="reference internal" href="fix_momentum.html"><span class="doc">fix momentum</span></a> command.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This implementation has been shown to conserve linear momentum
up to machine precision under NVT dynamics. Under NPT dynamics,
for a system with zero initial total linear momentum, the total
momentum fluctuates close to zero. It may occasionally undergo brief
excursions to non-negligible values, before returning close to zero.
Over long simulations, this has the effect of causing the center-of-mass
to undergo a slow random walk. This can be mitigated by resetting
the momentum at infrequent intervals using the
<a class="reference internal" href="fix_momentum.html"><span class="doc">fix momentum</span></a> command.</p>
</div>
<hr class="docutils" />
<p>The fix npt and fix nph commands can be used with rigid bodies or
mixtures of rigid bodies and non-rigid particles (e.g. solvent). But
there are also <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/npt</span></a> and <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/nph</span></a> commands, which are typically a more natural
choice. See the doc page for those commands for more discussion of
the various ways to do this.</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"><span class="doc">Section_accelerate</span></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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>These fixes writes the state of all the thermostat and barostat
variables to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> and <em>press</em> options are
supported by these fixes. You can use them to assign a
<a class="reference internal" href="compute.html"><span class="doc">compute</span></a> you have defined to this fix which will be used
in its thermostatting or barostatting procedure, as described above.
If you do this, note that the kinetic energy derived from the compute
temperature should be consistent with the virial term computed using
all atoms for the pressure. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If both the <em>temp</em> and <em>press</em> keywords are used in a single
thermo_modify command (or in two separate commands), then the order in
which the keywords are specified is important. Note that a <a class="reference internal" href="compute_pressure.html"><span class="doc">pressure compute</span></a> defines its own temperature compute as
an argument when it is specified. The <em>temp</em> keyword will override
this (for the pressure compute being used by fix npt), but only if the
<em>temp</em> keyword comes after the <em>press</em> keyword. If the <em>temp</em> keyword
comes before the <em>press</em> keyword, then the new pressure compute
specified by the <em>press</em> keyword will be unaffected by the <em>temp</em>
setting.</p>
</div>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by these
fixes to add the energy change induced by Nose/Hoover thermostatting
and barostatting to the system’s potential energy as part of
<a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
<p>These fixes compute a global scalar and a global vector of quantities,
which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The scalar value calculated by
these fixes is “extensive”; the vector values are “intensive”.</p>
<p>The scalar is the cumulative energy change due to the fix.</p>
<p>The vector stores internal Nose/Hoover thermostat and barostat
variables. The number and meaning of the vector values depends on
which fix is used and the settings for keywords <em>tchain</em> and <em>pchain</em>,
which specify the number of Nose/Hoover chains for the thermostat and
barostat. If no thermostatting is done, then <em>tchain</em> is 0. If no
barostatting is done, then <em>pchain</em> is 0. In the following list,
“ndof” is 0, 1, 3, or 6, and is the number of degrees of freedom in
the barostat. Its value is 0 if no barostat is used, else its value
is 6 if any off-diagonal stress tensor component is barostatted, else
its value is 1 if <em>couple xyz</em> is used or <em>couple xy</em> for a 2d
simulation, otherwise its value is 3.</p>
<p>The order of values in the global vector and their meaning is as
follows. The notation means there are tchain values for eta, followed
by tchain for eta_dot, followed by ndof for omega, etc:</p>
<ul class="simple">
<li>eta[tchain] = particle thermostat displacements (unitless)</li>
<li>eta_dot[tchain] = particle thermostat velocities (1/time units)</li>
<li>omega[ndof] = barostat displacements (unitless)</li>
<li>omega_dot[ndof] = barostat velocities (1/time units)</li>
<li>etap[pchain] = barostat thermostat displacements (unitless)</li>
<li>etap_dot[pchain] = barostat thermostat velocities (1/time units)</li>
<li>PE_eta[tchain] = potential energy of each particle thermostat displacement (energy units)</li>
<li>KE_eta_dot[tchain] = kinetic energy of each particle thermostat velocity (energy units)</li>
<li>PE_omega[ndof] = potential energy of each barostat displacement (energy units)</li>
<li>KE_omega_dot[ndof] = kinetic energy of each barostat velocity (energy units)</li>
<li>PE_etap[pchain] = potential energy of each barostat thermostat displacement (energy units)</li>
<li>KE_etap_dot[pchain] = kinetic energy of each barostat thermostat velocity (energy units)</li>
<li>PE_strain[1] = scalar strain energy (energy units)</li>
</ul>
<p>These fixes can ramp their external temperature and pressure over
multiple runs, using the <em>start</em> and <em>stop</em> keywords of the
<a class="reference internal" href="run.html"><span class="doc">run</span></a> command. See the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command for details of
how to do this.</p>
<p>These fixes are not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p><em>X</em>, <em>y</em>, <em>z</em> cannot be barostatted if the associated dimension is not
periodic. <em>Xy</em>, <em>xz</em>, and <em>yz</em> can only be barostatted if the
simulation domain is triclinic and the 2nd dimension in the keyword
(<em>y</em> dimension in <em>xy</em>) is periodic. <em>Z</em>, <em>xz</em>, and <em>yz</em>, cannot be
barostatted for 2D simulations. The <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a>,
<a class="reference internal" href="read_data.html"><span class="doc">read data</span></a>, and <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
commands specify whether the simulation box is orthogonal or
non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz
tilt factors.</p>
<p>For the <em>temp</em> keyword, the final Tstop cannot be 0.0 since it would
make the external T = 0.0 at some timestep during the simulation which
is not allowed in the Nose/Hoover formulation.</p>
<p>The <em>scaleyz yes</em> and <em>scalexz yes</em> keyword/value pairs can not be used
for 2D simulations. <em>scaleyz yes</em>, <em>scalexz yes</em>, and <em>scalexy yes</em> options
can only be used if the 2nd dimension in the keyword is periodic,
and if the tilt factor is not coupled to the barostat via keywords
<em>tri</em>, <em>yz</em>, <em>xz</em>, and <em>xy</em>.</p>
<p>These fixes can be used with dynamic groups as defined by the
<a class="reference internal" href="group.html"><span class="doc">group</span></a> command. Likewise they can be used with groups to
which atoms are added or deleted over time, e.g. a deposition
simulation. However, the conservation properties of the thermostat
and barostat are defined for systems with a static set of atoms. You
may observe odd behavior if the atoms in a group vary dramatically
over time or the atom count becomes very small.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a>,
<a class="reference internal" href="run_style.html"><span class="doc">run_style</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
not coupled to barostat, otherwise no.</p>
<hr class="docutils" />
<p id="martyna"><strong>(Martyna)</strong> Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).</p>
<p id="parrinello"><strong>(Parrinello)</strong> Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).</p>
<p id="tuckerman"><strong>(Tuckerman)</strong> Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
Martyna, J Phys A: Math Gen, 39, 5629 (2006).</p>
<p id="shinoda"><strong>(Shinoda)</strong> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).</p>
</div>
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<div class="section" id="fix-wall-lj93-command">
<span id="index-0"></span><h1>fix wall/lj93 command</h1>
</div>
<div class="section" id="fix-wall-lj126-command">
<h1>fix wall/lj126 command</h1>
</div>
<div class="section" id="fix-wall-lj1043-command">
<h1>fix wall/lj1043 command</h1>
</div>
<div class="section" id="fix-wall-colloid-command">
<h1>fix wall/colloid command</h1>
</div>
<div class="section" id="fix-wall-harmonic-command">
<h1>fix wall/harmonic command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style</span> <span class="n">face</span> <span class="n">args</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>style = <em>wall/lj93</em> or <em>wall/lj126</em> or <em>wall/lj1043</em> or <em>wall/colloid</em> or <em>wall/harmonic</em></li>
<li>one or more face/arg pairs may be appended</li>
<li>face = <em>xlo</em> or <em>xhi</em> or <em>ylo</em> or <em>yhi</em> or <em>zlo</em> or <em>zhi</em></li>
</ul>
<pre class="literal-block">
args = coord epsilon sigma cutoff
coord = position of wall = EDGE or constant or variable
EDGE = current lo or hi edge of simulation box
constant = number like 0.0 or -30.0 (distance units)
variable = <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> like v_x or v_wiggle
epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
epsilon can be a variable (see below)
sigma = size factor for wall-particle interaction (distance units)
sigma can be a variable (see below)
cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
</pre>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>units</em> or <em>fld</em></li>
</ul>
<pre class="literal-block">
<em>units</em> value = <em>lattice</em> or <em>box</em>
<em>lattice</em> = the wall position is defined in lattice units
<em>box</em> = the wall position is defined in simulation box units
<em>fld</em> value = <em>yes</em> or <em>no</em>
<em>yes</em> = invoke the wall constraint to be compatible with implicit FLD
<em>no</em> = invoke the wall constraint in the normal way
<em>pbc</em> value = <em>yes</em> or <em>no</em>
<em>yes</em> = allow periodic boundary in a wall dimension
<em>no</em> = require non-perioidic boundaries in any wall dimension
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">wallhi</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">lj93</span> <span class="n">xlo</span> <span class="o">-</span><span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="n">units</span> <span class="n">box</span>
<span class="n">fix</span> <span class="n">wallhi</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">lj93</span> <span class="n">xhi</span> <span class="n">EDGE</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
<span class="n">fix</span> <span class="n">wallhi</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">lj126</span> <span class="n">v_wiggle</span> <span class="mf">23.2</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
<span class="n">fix</span> <span class="n">zwalls</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">colloid</span> <span class="n">zlo</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.858</span> <span class="n">zhi</span> <span class="mf">40.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.858</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Bound the simulation domain on one or more of its faces with a flat
wall that interacts with the atoms in the group by generating a force
on the atom in a direction perpendicular to the wall. The energy of
wall-particle interactions depends on the style.</p>
<p>For style <em>wall/lj93</em>, the energy E is given by the 9/3 potential:</p>
<img alt="_images/fix_wall_lj93.jpg" class="align-center" src="_images/fix_wall_lj93.jpg" />
<p>For style <em>wall/lj126</em>, the energy E is given by the 12/6 potential:</p>
<img alt="_images/pair_lj.jpg" class="align-center" src="_images/pair_lj.jpg" />
<p>For style <em>wall/lj1043</em>, the energy E is given by the 10/4/3 potential:</p>
<img alt="_images/fix_wall_lj1043.jpg" class="align-center" src="_images/fix_wall_lj1043.jpg" />
<p>For style <em>wall/colloid</em>, the energy E is given by an integrated form
of the <a class="reference internal" href="pair_colloid.html"><span class="doc">pair_style colloid</span></a> potential:</p>
<img alt="_images/fix_wall_colloid.jpg" class="align-center" src="_images/fix_wall_colloid.jpg" />
<p>For style <em>wall/harmonic</em>, the energy E is given by a harmonic spring
potential:</p>
<img alt="_images/fix_wall_harmonic.jpg" class="align-center" src="_images/fix_wall_harmonic.jpg" />
<p>In all cases, <em>r</em> is the distance from the particle to the wall at
position <em>coord</em>, and Rc is the <em>cutoff</em> distance at which the
particle and wall no longer interact. The energy of the wall
potential is shifted so that the wall-particle interaction energy is
0.0 at the cutoff distance.</p>
<p>Up to 6 walls or faces can be specified in a single command: <em>xlo</em>,
<em>xhi</em>, <em>ylo</em>, <em>yhi</em>, <em>zlo</em>, <em>zhi</em>. A <em>lo</em> face interacts with
particles near the lower side of the simulation box in that dimension.
A <em>hi</em> face interacts with particles near the upper side of the
simulation box in that dimension.</p>
<p>The position of each wall can be specified in one of 3 ways: as the
EDGE of the simulation box, as a constant value, or as a variable. If
EDGE is used, then the corresponding boundary of the current
simulation box is used. If a numeric constant is specified then the
wall is placed at that position in the appropriate dimension (x, y, or
z). In both the EDGE and constant cases, the wall will never move.
If the wall position is a variable, it should be specified as v_name,
where name is an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> name. In this
case the variable is evaluated each timestep and the result becomes
the current position of the reflecting wall. Equal-style variables
can specify formulas with various mathematical functions, and include
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command keywords for the simulation
box parameters and timestep and elapsed time. Thus it is easy to
specify a time-dependent wall position. See examples below.</p>
<p>For the <em>wall/lj93</em> and <em>wall/lj126</em> and <em>wall/lj1043</em> styles,
<em>epsilon</em> and <em>sigma</em> are the usual Lennard-Jones parameters, which
determine the strength and size of the particle as it interacts with
the wall. Epsilon has energy units. Note that this <em>epsilon</em> and
<em>sigma</em> may be different than any <em>epsilon</em> or <em>sigma</em> values defined
for a pair style that computes particle-particle interactions.</p>
<p>The <em>wall/lj93</em> interaction is derived by integrating over a 3d
half-lattice of Lennard-Jones 12/6 particles. The <em>wall/lj126</em>
interaction is effectively a harder, more repulsive wall interaction.
The <em>wall/lj1043</em> interaction is yet a different form of wall
interaction, described in Magda et al in <a class="reference internal" href="#magda"><span class="std std-ref">(Magda)</span></a>.</p>
<p>For the <em>wall/colloid</em> style, <em>R</em> is the radius of the colloid
particle, <em>D</em> is the distance from the surface of the colloid particle
to the wall (r-R), and <em>sigma</em> is the size of a constituent LJ
particle inside the colloid particle and wall. Note that the cutoff
distance Rc in this case is the distance from the colloid particle
center to the wall. The prefactor <em>epsilon</em> can be thought of as an
effective Hamaker constant with energy units for the strength of the
colloid-wall interaction. More specifically, the <em>epsilon</em> pre-factor
= 4 * pi^2 * rho_wall * rho_colloid * epsilon * sigma^6, where epsilon
and sigma are the LJ parameters for the constituent LJ
particles. Rho_wall and rho_colloid are the number density of the
constituent particles, in the wall and colloid respectively, in units
of 1/volume.</p>
<p>The <em>wall/colloid</em> interaction is derived by integrating over
constituent LJ particles of size <em>sigma</em> within the colloid particle
and a 3d half-lattice of Lennard-Jones 12/6 particles of size <em>sigma</em>
in the wall. As mentioned in the preceeding paragraph, the density of
particles in the wall and colloid can be different, as specified by
the <em>epsilon</em> pre-factor.</p>
<p>For the <em>wall/harmonic</em> style, <em>epsilon</em> is effectively the spring
constant K, and has units (energy/distance^2). The input parameter
<em>sigma</em> is ignored. The minimum energy position of the harmonic
spring is at the <em>cutoff</em>. This is a repulsive-only spring since the
interaction is truncated at the <em>cutoff</em></p>
<p>For any wall, the <em>epsilon</em> and/or <em>sigma</em> parameter can be specified
as an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a>, in which case it should be
specified as v_name, where name is the variable name. As with a
variable wall position, the variable is evaluated each timestep and
the result becomes the current epsilon or sigma of the wall.
Equal-style variables can specify formulas with various mathematical
functions, and include <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent wall interaction.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">For all of the styles, you must insure that r is always > 0 for
all particles in the group, or LAMMPS will generate an error. This
means you cannot start your simulation with particles at the wall
position <em>coord</em> (r = 0) or with particles on the wrong side of the
wall (r < 0). For the <em>wall/lj93</em> and <em>wall/lj126</em> styles, the energy
of the wall/particle interaction (and hence the force on the particle)
blows up as r -> 0. The <em>wall/colloid</em> style is even more
restrictive, since the energy blows up as D = r-R -> 0. This means
the finite-size particles of radius R must be a distance larger than R
from the wall position <em>coord</em>. The <em>harmonic</em> style is a softer
potential and does not blow up as r -> 0, but you must use a large
enough <em>epsilon</em> that particles always reamin on the correct side of
the wall (r > 0).</p>
</div>
<p>The <em>units</em> keyword determines the meaning of the distance units used
to define a wall position, but only when a numeric constant or
variable is used. It is not relevant when EDGE is used to specify a
face position. In the variable case, the variable is assumed to
produce a value compatible with the <em>units</em> setting you specify.</p>
<p>A <em>box</em> value selects standard distance units as defined by the
-<span class="xref doc">units</span> command, e.g. Angstroms for units = real or metal.
+<a class="reference internal" href="units.html"><span class="doc">units</span></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"><span class="doc">lattice</span></a> command must have been previously used to
define the lattice spacings.</p>
<p>The <em>fld</em> keyword can be used with a <em>yes</em> setting to invoke the wall
constraint before pairwise interactions are computed. This allows an
implicit FLD model using <a class="reference internal" href="pair_lubricateU.html"><span class="doc">pair_style lubricateU</span></a>
to include the wall force in its calculations. If the setting is
<em>no</em>, wall forces are imposed after pairwise interactions, in the
usual manner.</p>
<p>The <em>pbc</em> keyword can be used with a <em>yes</em> setting to allow walls to
be specified in a periodic dimension. See the
<a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command for options on simulation box
boundaries. The default for <em>pbc</em> is <em>no</em>, which means the system
must be non-periodic when using a wall. But you may wish to use a
periodic box. E.g. to allow some particles to interact with the wall
via the fix group-ID, and others to pass through it and wrap around a
periodic box. In this case you should insure that the wall if
sufficiently far enough away from the box boundary. If you do not,
then particles may interact with both the wall and with periodic
images on the other side of the box, which is probably not what you
want.</p>
<hr class="docutils" />
<p>Here are examples of variable definitions that move the wall position
in a time-dependent fashion using equal-style
<a class="reference internal" href="variable.html"><span class="doc">variables</span></a>. The wall interaction parameters (epsilon,
sigma) could be varied with additional variable definitions.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">ramp</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span> <span class="n">xlo</span> <span class="n">v_ramp</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">linear</span> <span class="n">equal</span> <span class="n">vdisplace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">20</span><span class="p">)</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span> <span class="n">xlo</span> <span class="n">v_linear</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">wiggle</span> <span class="n">equal</span> <span class="n">swiggle</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">5.0</span><span class="p">,</span><span class="mf">3.0</span><span class="p">)</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span> <span class="n">xlo</span> <span class="n">v_wiggle</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">wiggle</span> <span class="n">equal</span> <span class="n">cwiggle</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">5.0</span><span class="p">,</span><span class="mf">3.0</span><span class="p">)</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span> <span class="n">xlo</span> <span class="n">v_wiggle</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
</pre></div>
</div>
<p>The ramp(lo,hi) function adjusts the wall position linearly from lo to
hi over the course of a run. The vdisplace(c0,velocity) function does
something similar using the equation position = c0 + velocity*delta,
where delta is the elapsed time.</p>
<p>The swiggle(c0,A,period) function causes the wall position to
oscillate sinusoidally according to this equation, where omega = 2 PI
/ period:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">position</span> <span class="o">=</span> <span class="n">c0</span> <span class="o">+</span> <span class="n">A</span> <span class="n">sin</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">)</span>
</pre></div>
</div>
<p>The cwiggle(c0,A,period) function causes the wall position to
oscillate sinusoidally according to this equation, which will have an
initial wall velocity of 0.0, and thus may impose a gentler
perturbation on the particles:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">position</span> <span class="o">=</span> <span class="n">c0</span> <span class="o">+</span> <span class="n">A</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">cos</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">))</span>
</pre></div>
</div>
</div>
<hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the energy of interaction between atoms and each wall to
the system’s potential energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
<p>This fix computes a global scalar energy and a global vector of
forces, which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. Note that the scalar energy is
the sum of interactions with all defined walls. If you want the
energy on a per-wall basis, you need to use multiple fix wall
commands. The length of the vector is equal to the number of walls
defined by the fix. Each vector value is the normal force on a
specific wall. Note that an outward force on a wall will be a
negative value for <em>lo</em> walls and a positive value for <em>hi</em> walls.
The scalar and vector values calculated by this fix are “extensive”.</p>
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.</p>
<p>The forces due to this fix are imposed during an energy minimization,
invoked by the <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> command.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you want the atom/wall interaction energy to be included in
the total potential energy of the system (the quantity being
minimized), you MUST enable the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em>
option for this fix.</p>
</div>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_wall_reflect.html"><span class="doc">fix wall/reflect</span></a>,
<a class="reference internal" href="fix_wall_gran.html"><span class="doc">fix wall/gran</span></a>,
<a class="reference internal" href="fix_wall_region.html"><span class="doc">fix wall/region</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>The option defaults units = lattice, fld = no, and pbc = no.</p>
<hr class="docutils" />
<p id="magda"><strong>(Magda)</strong> Magda, Tirrell, Davis, J Chem Phys, 83, 1888-1901 (1985);
erratum in JCP 84, 2901 (1986).</p>
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<a href="#A"><strong>A</strong></a>
| <a href="#B"><strong>B</strong></a>
| <a href="#C"><strong>C</strong></a>
| <a href="#D"><strong>D</strong></a>
| <a href="#E"><strong>E</strong></a>
| <a href="#F"><strong>F</strong></a>
| <a href="#G"><strong>G</strong></a>
| <a href="#I"><strong>I</strong></a>
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| <a href="#M"><strong>M</strong></a>
| <a href="#N"><strong>N</strong></a>
| <a href="#P"><strong>P</strong></a>
| <a href="#Q"><strong>Q</strong></a>
| <a href="#R"><strong>R</strong></a>
| <a href="#S"><strong>S</strong></a>
| <a href="#T"><strong>T</strong></a>
| <a href="#U"><strong>U</strong></a>
| <a href="#V"><strong>V</strong></a>
| <a href="#W"><strong>W</strong></a>
</div>
<h2 id="A">A</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="angle_coeff.html#index-0">angle_coeff</a>
</dt>
<dt><a href="angle_style.html#index-0">angle_style</a>
</dt>
<dt><a href="angle_charmm.html#index-0">angle_style charmm</a>
</dt>
<dt><a href="angle_class2.html#index-0">angle_style class2</a>
</dt>
<dt><a href="angle_cosine.html#index-0">angle_style cosine</a>
</dt>
<dt><a href="angle_cosine_delta.html#index-0">angle_style cosine/delta</a>
</dt>
<dt><a href="angle_cosine_periodic.html#index-0">angle_style cosine/periodic</a>
</dt>
<dt><a href="angle_cosine_shift.html#index-0">angle_style cosine/shift</a>
</dt>
<dt><a href="angle_cosine_shift_exp.html#index-0">angle_style cosine/shift/exp</a>
</dt>
<dt><a href="angle_cosine_squared.html#index-0">angle_style cosine/squared</a>
</dt>
<dt><a href="angle_dipole.html#index-0">angle_style dipole</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="angle_fourier.html#index-0">angle_style fourier</a>
</dt>
<dt><a href="angle_fourier_simple.html#index-0">angle_style fourier/simple</a>
</dt>
<dt><a href="angle_harmonic.html#index-0">angle_style harmonic</a>
</dt>
<dt><a href="angle_hybrid.html#index-0">angle_style hybrid</a>
</dt>
<dt><a href="angle_none.html#index-0">angle_style none</a>
</dt>
<dt><a href="angle_quartic.html#index-0">angle_style quartic</a>
</dt>
<dt><a href="angle_sdk.html#index-0">angle_style sdk</a>
</dt>
<dt><a href="angle_table.html#index-0">angle_style table</a>
</dt>
<dt><a href="angle_zero.html#index-0">angle_style zero</a>
</dt>
<dt><a href="atom_modify.html#index-0">atom_modify</a>
</dt>
<dt><a href="atom_style.html#index-0">atom_style</a>
</dt>
</dl></td>
</tr></table>
<h2 id="B">B</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="balance.html#index-0">balance</a>
</dt>
<dt><a href="bond_coeff.html#index-0">bond_coeff</a>
</dt>
<dt><a href="bond_style.html#index-0">bond_style</a>
</dt>
<dt><a href="bond_class2.html#index-0">bond_style class2</a>
</dt>
<dt><a href="bond_fene.html#index-0">bond_style fene</a>
</dt>
<dt><a href="bond_fene_expand.html#index-0">bond_style fene/expand</a>
</dt>
<dt><a href="bond_harmonic.html#index-0">bond_style harmonic</a>
</dt>
<dt><a href="bond_harmonic_shift.html#index-0">bond_style harmonic/shift</a>
</dt>
<dt><a href="bond_harmonic_shift_cut.html#index-0">bond_style harmonic/shift/cut</a>
</dt>
<dt><a href="bond_hybrid.html#index-0">bond_style hybrid</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="bond_morse.html#index-0">bond_style morse</a>
</dt>
<dt><a href="bond_none.html#index-0">bond_style none</a>
</dt>
<dt><a href="bond_nonlinear.html#index-0">bond_style nonlinear</a>
</dt>
<dt><a href="bond_quartic.html#index-0">bond_style quartic</a>
</dt>
<dt><a href="bond_table.html#index-0">bond_style table</a>
</dt>
<dt><a href="bond_zero.html#index-0">bond_style zero</a>
</dt>
<dt><a href="bond_write.html#index-0">bond_write</a>
</dt>
<dt><a href="boundary.html#index-0">boundary</a>
</dt>
<dt><a href="box.html#index-0">box</a>
</dt>
</dl></td>
</tr></table>
<h2 id="C">C</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="change_box.html#index-0">change_box</a>
</dt>
<dt><a href="clear.html#index-0">clear</a>
</dt>
<dt><a href="comm_modify.html#index-0">comm_modify</a>
</dt>
<dt><a href="comm_style.html#index-0">comm_style</a>
</dt>
<dt><a href="compute.html#index-0">compute</a>
</dt>
<dt><a href="compute_ackland_atom.html#index-0">compute ackland/atom</a>
</dt>
<dt><a href="compute_angle.html#index-0">compute angle</a>
</dt>
<dt><a href="compute_angle_local.html#index-0">compute angle/local</a>
</dt>
<dt><a href="compute_angmom_chunk.html#index-0">compute angmom/chunk</a>
</dt>
<dt><a href="compute_basal_atom.html#index-0">compute basal/atom</a>
</dt>
<dt><a href="compute_body_local.html#index-0">compute body/local</a>
</dt>
<dt><a href="compute_bond.html#index-0">compute bond</a>
</dt>
<dt><a href="compute_bond_local.html#index-0">compute bond/local</a>
</dt>
<dt><a href="compute_centro_atom.html#index-0">compute centro/atom</a>
</dt>
<dt><a href="compute_chunk_atom.html#index-0">compute chunk/atom</a>
</dt>
<dt><a href="compute_cluster_atom.html#index-0">compute cluster/atom</a>
</dt>
<dt><a href="compute_cna_atom.html#index-0">compute cna/atom</a>
</dt>
<dt><a href="compute_com.html#index-0">compute com</a>
</dt>
<dt><a href="compute_com_chunk.html#index-0">compute com/chunk</a>
</dt>
<dt><a href="compute_contact_atom.html#index-0">compute contact/atom</a>
</dt>
<dt><a href="compute_coord_atom.html#index-0">compute coord/atom</a>
</dt>
<dt><a href="compute_damage_atom.html#index-0">compute damage/atom</a>
</dt>
<dt><a href="compute_dihedral.html#index-0">compute dihedral</a>
</dt>
<dt><a href="compute_dihedral_local.html#index-0">compute dihedral/local</a>
</dt>
<dt><a href="compute_dilatation_atom.html#index-0">compute dilatation/atom</a>
</dt>
<dt><a href="compute_dipole_chunk.html#index-0">compute dipole/chunk</a>
</dt>
<dt><a href="compute_displace_atom.html#index-0">compute displace/atom</a>
</dt>
<dt><a href="compute_dpd.html#index-0">compute dpd</a>
</dt>
<dt><a href="compute_dpd_atom.html#index-0">compute dpd/atom</a>
</dt>
<dt><a href="compute_erotate_asphere.html#index-0">compute erotate/asphere</a>
</dt>
<dt><a href="compute_erotate_rigid.html#index-0">compute erotate/rigid</a>
</dt>
<dt><a href="compute_erotate_sphere.html#index-0">compute erotate/sphere</a>
</dt>
<dt><a href="compute_erotate_sphere_atom.html#index-0">compute erotate/sphere/atom</a>
</dt>
<dt><a href="compute_event_displace.html#index-0">compute event/displace</a>
</dt>
<dt><a href="compute_fep.html#index-0">compute fep</a>
</dt>
<dt><a href="compute_tally.html#index-0">compute force/tally</a>
</dt>
<dt><a href="compute_group_group.html#index-0">compute group/group</a>
</dt>
<dt><a href="compute_gyration.html#index-0">compute gyration</a>
</dt>
<dt><a href="compute_gyration_chunk.html#index-0">compute gyration/chunk</a>
</dt>
<dt><a href="compute_heat_flux.html#index-0">compute heat/flux</a>
</dt>
<dt><a href="compute_hexorder_atom.html#index-0">compute hexorder/atom</a>
</dt>
<dt><a href="compute_improper.html#index-0">compute improper</a>
</dt>
<dt><a href="compute_improper_local.html#index-0">compute improper/local</a>
</dt>
<dt><a href="compute_inertia_chunk.html#index-0">compute inertia/chunk</a>
</dt>
<dt><a href="compute_ke.html#index-0">compute ke</a>
</dt>
<dt><a href="compute_ke_atom.html#index-0">compute ke/atom</a>
</dt>
<dt><a href="compute_ke_atom_eff.html#index-0">compute ke/atom/eff</a>
</dt>
<dt><a href="compute_ke_eff.html#index-0">compute ke/eff</a>
</dt>
<dt><a href="compute_ke_rigid.html#index-0">compute ke/rigid</a>
</dt>
<dt><a href="compute_meso_e_atom.html#index-0">compute meso/e/atom</a>
</dt>
<dt><a href="compute_meso_rho_atom.html#index-0">compute meso/rho/atom</a>
</dt>
<dt><a href="compute_meso_t_atom.html#index-0">compute meso/t/atom</a>
</dt>
<dt><a href="compute_msd.html#index-0">compute msd</a>
</dt>
<dt><a href="compute_msd_chunk.html#index-0">compute msd/chunk</a>
</dt>
<dt><a href="compute_msd_nongauss.html#index-0">compute msd/nongauss</a>
</dt>
<dt><a href="compute_omega_chunk.html#index-0">compute omega/chunk</a>
</dt>
<dt><a href="compute_orientorder_atom.html#index-0">compute orientorder/atom</a>
</dt>
<dt><a href="compute_pair.html#index-0">compute pair</a>
</dt>
<dt><a href="compute_pair_local.html#index-0">compute pair/local</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="compute_pe.html#index-0">compute pe</a>
</dt>
<dt><a href="compute_pe_atom.html#index-0">compute pe/atom</a>
</dt>
<dt><a href="compute_plasticity_atom.html#index-0">compute plasticity/atom</a>
</dt>
<dt><a href="compute_pressure.html#index-0">compute pressure</a>
</dt>
<dt><a href="compute_property_atom.html#index-0">compute property/atom</a>
</dt>
<dt><a href="compute_property_chunk.html#index-0">compute property/chunk</a>
</dt>
<dt><a href="compute_property_local.html#index-0">compute property/local</a>
</dt>
<dt><a href="compute_rdf.html#index-0">compute rdf</a>
</dt>
<dt><a href="compute_reduce.html#index-0">compute reduce</a>
</dt>
<dt><a href="compute_saed.html#index-0">compute saed</a>
</dt>
<dt><a href="compute_slice.html#index-0">compute slice</a>
</dt>
<dt><a href="compute_smd_contact_radius.html#index-0">compute smd/contact/radius</a>
</dt>
<dt><a href="compute_smd_damage.html#index-0">compute smd/damage</a>
</dt>
<dt><a href="compute_smd_hourglass_error.html#index-0">compute smd/hourglass/error</a>
</dt>
<dt><a href="compute_smd_internal_energy.html#index-0">compute smd/internal/energy</a>
</dt>
<dt><a href="compute_smd_plastic_strain.html#index-0">compute smd/plastic/strain</a>
</dt>
<dt><a href="compute_smd_plastic_strain_rate.html#index-0">compute smd/plastic/strain/rate</a>
</dt>
<dt><a href="compute_smd_rho.html#index-0">compute smd/rho</a>
</dt>
<dt><a href="compute_smd_tlsph_defgrad.html#index-0">compute smd/tlsph/defgrad</a>
</dt>
<dt><a href="compute_smd_tlsph_dt.html#index-0">compute smd/tlsph/dt</a>
</dt>
<dt><a href="compute_smd_tlsph_num_neighs.html#index-0">compute smd/tlsph/num/neighs</a>
</dt>
<dt><a href="compute_smd_tlsph_shape.html#index-0">compute smd/tlsph/shape</a>
</dt>
<dt><a href="compute_smd_tlsph_strain.html#index-0">compute smd/tlsph/strain</a>
</dt>
<dt><a href="compute_smd_tlsph_strain_rate.html#index-0">compute smd/tlsph/strain/rate</a>
</dt>
<dt><a href="compute_smd_tlsph_stress.html#index-0">compute smd/tlsph/stress</a>
</dt>
<dt><a href="compute_smd_ulsph_num_neighs.html#index-0">compute smd/ulsph/num/neighs</a>
</dt>
<dt><a href="compute_smd_ulsph_strain.html#index-0">compute smd/ulsph/strain</a>
</dt>
<dt><a href="compute_smd_ulsph_strain_rate.html#index-0">compute smd/ulsph/strain/rate</a>
</dt>
<dt><a href="compute_smd_ulsph_stress.html#index-0">compute smd/ulsph/stress</a>
</dt>
<dt><a href="compute_smd_vol.html#index-0">compute smd/vol</a>
</dt>
<dt><a href="compute_sna_atom.html#index-0">compute sna/atom</a>
</dt>
<dt><a href="compute_stress_atom.html#index-0">compute stress/atom</a>
</dt>
<dt><a href="compute_temp.html#index-0">compute temp</a>
</dt>
<dt><a href="compute_temp_asphere.html#index-0">compute temp/asphere</a>
</dt>
<dt><a href="compute_temp_body.html#index-0">compute temp/body</a>
</dt>
<dt><a href="compute_temp_chunk.html#index-0">compute temp/chunk</a>
</dt>
<dt><a href="compute_temp_com.html#index-0">compute temp/com</a>
</dt>
<dt><a href="compute_temp_cs.html#index-0">compute temp/cs</a>
</dt>
<dt><a href="compute_temp_deform.html#index-0">compute temp/deform</a>
</dt>
<dt><a href="compute_temp_deform_eff.html#index-0">compute temp/deform/eff</a>
</dt>
<dt><a href="compute_temp_drude.html#index-0">compute temp/drude</a>
</dt>
<dt><a href="compute_temp_eff.html#index-0">compute temp/eff</a>
</dt>
<dt><a href="compute_temp_partial.html#index-0">compute temp/partial</a>
</dt>
<dt><a href="compute_temp_profile.html#index-0">compute temp/profile</a>
</dt>
<dt><a href="compute_temp_ramp.html#index-0">compute temp/ramp</a>
</dt>
<dt><a href="compute_temp_region.html#index-0">compute temp/region</a>
</dt>
<dt><a href="compute_temp_region_eff.html#index-0">compute temp/region/eff</a>
</dt>
<dt><a href="compute_temp_rotate.html#index-0">compute temp/rotate</a>
</dt>
<dt><a href="compute_temp_sphere.html#index-0">compute temp/sphere</a>
</dt>
<dt><a href="compute_ti.html#index-0">compute ti</a>
</dt>
<dt><a href="compute_torque_chunk.html#index-0">compute torque/chunk</a>
</dt>
<dt><a href="compute_vacf.html#index-0">compute vacf</a>
</dt>
<dt><a href="compute_vcm_chunk.html#index-0">compute vcm/chunk</a>
</dt>
<dt><a href="compute_voronoi_atom.html#index-0">compute voronoi/atom</a>
</dt>
<dt><a href="compute_xrd.html#index-0">compute xrd</a>
</dt>
<dt><a href="compute_modify.html#index-0">compute_modify</a>
</dt>
<dt><a href="create_atoms.html#index-0">create_atoms</a>
</dt>
<dt><a href="create_bonds.html#index-0">create_bonds</a>
</dt>
<dt><a href="create_box.html#index-0">create_box</a>
</dt>
</dl></td>
</tr></table>
<h2 id="D">D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="delete_atoms.html#index-0">delete_atoms</a>
</dt>
<dt><a href="delete_bonds.html#index-0">delete_bonds</a>
</dt>
<dt><a href="dielectric.html#index-0">dielectric</a>
</dt>
<dt><a href="dihedral_coeff.html#index-0">dihedral_coeff</a>
</dt>
<dt><a href="dihedral_style.html#index-0">dihedral_style</a>
</dt>
<dt><a href="dihedral_charmm.html#index-0">dihedral_style charmm</a>
</dt>
<dt><a href="dihedral_class2.html#index-0">dihedral_style class2</a>
</dt>
<dt><a href="dihedral_cosine_shift_exp.html#index-0">dihedral_style cosine/shift/exp</a>
</dt>
<dt><a href="dihedral_fourier.html#index-0">dihedral_style fourier</a>
</dt>
<dt><a href="dihedral_harmonic.html#index-0">dihedral_style harmonic</a>
</dt>
<dt><a href="dihedral_helix.html#index-0">dihedral_style helix</a>
</dt>
<dt><a href="dihedral_hybrid.html#index-0">dihedral_style hybrid</a>
</dt>
<dt><a href="dihedral_multi_harmonic.html#index-0">dihedral_style multi/harmonic</a>
</dt>
<dt><a href="dihedral_nharmonic.html#index-0">dihedral_style nharmonic</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="dihedral_none.html#index-0">dihedral_style none</a>
</dt>
<dt><a href="dihedral_opls.html#index-0">dihedral_style opls</a>
</dt>
<dt><a href="dihedral_quadratic.html#index-0">dihedral_style quadratic</a>
</dt>
<dt><a href="dihedral_table.html#index-0">dihedral_style table</a>
</dt>
<dt><a href="dihedral_zero.html#index-0">dihedral_style zero</a>
</dt>
<dt><a href="dimension.html#index-0">dimension</a>
</dt>
<dt><a href="displace_atoms.html#index-0">displace_atoms</a>
</dt>
<dt><a href="dump.html#index-0">dump</a>
</dt>
<dt><a href="dump_custom_vtk.html#index-0">dump custom/vtk</a>
</dt>
<dt><a href="dump_h5md.html#index-0">dump h5md</a>
</dt>
<dt><a href="dump_image.html#index-0">dump image</a>
</dt>
<dt><a href="dump_molfile.html#index-0">dump molfile</a>
</dt>
<dt><a href="dump_modify.html#index-0">dump_modify</a>
</dt>
</dl></td>
</tr></table>
<h2 id="E">E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="echo.html#index-0">echo</a>
</dt>
</dl></td>
</tr></table>
<h2 id="F">F</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="fix.html#index-0">fix</a>
</dt>
<dt><a href="fix_adapt.html#index-0">fix adapt</a>
</dt>
<dt><a href="fix_adapt_fep.html#index-0">fix adapt/fep</a>
</dt>
<dt><a href="fix_addforce.html#index-0">fix addforce</a>
</dt>
<dt><a href="fix_addtorque.html#index-0">fix addtorque</a>
</dt>
<dt><a href="fix_append_atoms.html#index-0">fix append/atoms</a>
</dt>
<dt><a href="fix_atc.html#index-0">fix atc</a>
</dt>
<dt><a href="fix_atom_swap.html#index-0">fix atom/swap</a>
</dt>
<dt><a href="fix_ave_atom.html#index-0">fix ave/atom</a>
</dt>
<dt><a href="fix_ave_chunk.html#index-0">fix ave/chunk</a>
</dt>
<dt><a href="fix_ave_correlate.html#index-0">fix ave/correlate</a>
</dt>
<dt><a href="fix_ave_correlate_long.html#index-0">fix ave/correlate/long</a>
</dt>
<dt><a href="fix_ave_histo.html#index-0">fix ave/histo</a>
</dt>
<dt><a href="fix_ave_spatial.html#index-0">fix ave/spatial</a>
</dt>
<dt><a href="fix_ave_spatial_sphere.html#index-0">fix ave/spatial/sphere</a>
</dt>
<dt><a href="fix_ave_time.html#index-0">fix ave/time</a>
</dt>
<dt><a href="fix_aveforce.html#index-0">fix aveforce</a>
</dt>
<dt><a href="fix_balance.html#index-0">fix balance</a>
</dt>
<dt><a href="fix_bond_break.html#index-0">fix bond/break</a>
</dt>
<dt><a href="fix_bond_create.html#index-0">fix bond/create</a>
</dt>
<dt><a href="fix_bond_swap.html#index-0">fix bond/swap</a>
</dt>
<dt><a href="fix_box_relax.html#index-0">fix box/relax</a>
</dt>
<dt><a href="fix_colvars.html#index-0">fix colvars</a>
</dt>
<dt><a href="fix_deform.html#index-0">fix deform</a>
</dt>
<dt><a href="fix_deposit.html#index-0">fix deposit</a>
</dt>
<dt><a href="fix_drag.html#index-0">fix drag</a>
</dt>
<dt><a href="fix_drude.html#index-0">fix drude</a>
</dt>
<dt><a href="fix_drude_transform.html#index-0">fix drude/transform/direct</a>
</dt>
<dt><a href="fix_dt_reset.html#index-0">fix dt/reset</a>
</dt>
<dt><a href="fix_efield.html#index-0">fix efield</a>
</dt>
<dt><a href="fix_enforce2d.html#index-0">fix enforce2d</a>
</dt>
<dt><a href="fix_eos_cv.html#index-0">fix eos/cv</a>
</dt>
<dt><a href="fix_eos_table.html#index-0">fix eos/table</a>
</dt>
<dt><a href="fix_evaporate.html#index-0">fix evaporate</a>
</dt>
<dt><a href="fix_external.html#index-0">fix external</a>
</dt>
<dt><a href="fix_freeze.html#index-0">fix freeze</a>
</dt>
<dt><a href="fix_gcmc.html#index-0">fix gcmc</a>
</dt>
<dt><a href="fix_gld.html#index-0">fix gld</a>
</dt>
<dt><a href="fix_gle.html#index-0">fix gle</a>
</dt>
<dt><a href="fix_gravity.html#index-0">fix gravity</a>
</dt>
<dt><a href="fix_heat.html#index-0">fix heat</a>
</dt>
<dt><a href="fix_imd.html#index-0">fix imd</a>
</dt>
<dt><a href="fix_indent.html#index-0">fix indent</a>
</dt>
<dt><a href="fix_ipi.html#index-0">fix ipi</a>
</dt>
<dt><a href="fix_langevin.html#index-0">fix langevin</a>
</dt>
<dt><a href="fix_langevin_drude.html#index-0">fix langevin/drude</a>
</dt>
<dt><a href="fix_langevin_eff.html#index-0">fix langevin/eff</a>
</dt>
<dt><a href="fix_lb_fluid.html#index-0">fix lb/fluid</a>
</dt>
<dt><a href="fix_lb_momentum.html#index-0">fix lb/momentum</a>
</dt>
<dt><a href="fix_lb_pc.html#index-0">fix lb/pc</a>
</dt>
<dt><a href="fix_lb_rigid_pc_sphere.html#index-0">fix lb/rigid/pc/sphere</a>
</dt>
<dt><a href="fix_lb_viscous.html#index-0">fix lb/viscous</a>
</dt>
<dt><a href="fix_lineforce.html#index-0">fix lineforce</a>
</dt>
<dt><a href="fix_meso.html#index-0">fix meso</a>
</dt>
<dt><a href="fix_meso_stationary.html#index-0">fix meso/stationary</a>
</dt>
<dt><a href="fix_momentum.html#index-0">fix momentum</a>
</dt>
<dt><a href="fix_move.html#index-0">fix move</a>
</dt>
<dt><a href="fix_msst.html#index-0">fix msst</a>
</dt>
<dt><a href="fix_neb.html#index-0">fix neb</a>
</dt>
<dt><a href="fix_nph_asphere.html#index-0">fix nph/asphere</a>
</dt>
<dt><a href="fix_nph_body.html#index-0">fix nph/body</a>
</dt>
<dt><a href="fix_nph_sphere.html#index-0">fix nph/sphere</a>
</dt>
<dt><a href="fix_nphug.html#index-0">fix nphug</a>
</dt>
<dt><a href="fix_npt_asphere.html#index-0">fix npt/asphere</a>
</dt>
<dt><a href="fix_npt_body.html#index-0">fix npt/body</a>
</dt>
<dt><a href="fix_npt_sphere.html#index-0">fix npt/sphere</a>
</dt>
<dt><a href="fix_nve.html#index-0">fix nve</a>
</dt>
<dt><a href="fix_nve_asphere.html#index-0">fix nve/asphere</a>
</dt>
<dt><a href="fix_nve_asphere_noforce.html#index-0">fix nve/asphere/noforce</a>
</dt>
<dt><a href="fix_nve_body.html#index-0">fix nve/body</a>
</dt>
<dt><a href="fix_nve_eff.html#index-0">fix nve/eff</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="fix_nve_limit.html#index-0">fix nve/limit</a>
</dt>
<dt><a href="fix_nve_line.html#index-0">fix nve/line</a>
</dt>
<dt><a href="fix_nve_noforce.html#index-0">fix nve/noforce</a>
</dt>
<dt><a href="fix_nve_sphere.html#index-0">fix nve/sphere</a>
</dt>
<dt><a href="fix_nve_tri.html#index-0">fix nve/tri</a>
</dt>
<dt><a href="fix_nh.html#index-0">fix nvt</a>
</dt>
<dt><a href="fix_nvt_asphere.html#index-0">fix nvt/asphere</a>
</dt>
<dt><a href="fix_nvt_body.html#index-0">fix nvt/body</a>
</dt>
<dt><a href="fix_nh_eff.html#index-0">fix nvt/eff</a>
</dt>
<dt><a href="fix_nvt_sllod.html#index-0">fix nvt/sllod</a>
</dt>
<dt><a href="fix_nvt_sllod_eff.html#index-0">fix nvt/sllod/eff</a>
</dt>
<dt><a href="fix_nvt_sphere.html#index-0">fix nvt/sphere</a>
</dt>
<dt><a href="fix_oneway.html#index-0">fix oneway</a>
</dt>
<dt><a href="fix_orient_fcc.html#index-0">fix orient/fcc</a>
</dt>
<dt><a href="fix_phonon.html#index-0">fix phonon</a>
</dt>
<dt><a href="fix_pimd.html#index-0">fix pimd</a>
</dt>
<dt><a href="fix_planeforce.html#index-0">fix planeforce</a>
</dt>
<dt><a href="fix_pour.html#index-0">fix pour</a>
</dt>
<dt><a href="fix_press_berendsen.html#index-0">fix press/berendsen</a>
</dt>
<dt><a href="fix_print.html#index-0">fix print</a>
</dt>
<dt><a href="fix_property_atom.html#index-0">fix property/atom</a>
</dt>
<dt><a href="fix_qbmsst.html#index-0">fix qbmsst</a>
</dt>
<dt><a href="fix_qeq_comb.html#index-0">fix qeq/comb</a>
</dt>
<dt><a href="fix_qeq.html#index-0">fix qeq/point</a>
</dt>
<dt><a href="fix_qeq_reax.html#index-0">fix qeq/reax</a>
</dt>
<dt><a href="fix_qmmm.html#index-0">fix qmmm</a>
</dt>
<dt><a href="fix_qtb.html#index-0">fix qtb</a>
</dt>
<dt><a href="fix_reax_bonds.html#index-0">fix reax/bonds</a>
</dt>
<dt><a href="fix_reaxc_species.html#index-0">fix reax/c/species</a>
</dt>
<dt><a href="fix_recenter.html#index-0">fix recenter</a>
</dt>
<dt><a href="fix_restrain.html#index-0">fix restrain</a>
</dt>
<dt><a href="fix_rigid.html#index-0">fix rigid</a>
</dt>
<dt><a href="fix_saed_vtk.html#index-0">fix saed/vtk</a>
</dt>
<dt><a href="fix_setforce.html#index-0">fix setforce</a>
</dt>
<dt><a href="fix_shake.html#index-0">fix shake</a>
</dt>
<dt><a href="fix_shardlow.html#index-0">fix shardlow</a>
</dt>
<dt><a href="fix_smd.html#index-0">fix smd</a>
</dt>
<dt><a href="fix_smd_adjust_dt.html#index-0">fix smd/adjust_dt</a>
</dt>
<dt><a href="fix_smd_integrate_tlsph.html#index-0">fix smd/integrate_tlsph</a>
</dt>
<dt><a href="fix_smd_integrate_ulsph.html#index-0">fix smd/integrate_ulsph</a>
</dt>
<dt><a href="fix_smd_move_triangulated_surface.html#index-0">fix smd/move_tri_surf</a>
</dt>
<dt><a href="fix_smd_setvel.html#index-0">fix smd/setvel</a>
</dt>
<dt><a href="fix_smd_wall_surface.html#index-0">fix smd/wall_surface</a>
</dt>
<dt><a href="fix_spring.html#index-0">fix spring</a>
</dt>
<dt><a href="fix_spring_rg.html#index-0">fix spring/rg</a>
</dt>
<dt><a href="fix_spring_self.html#index-0">fix spring/self</a>
</dt>
<dt><a href="fix_srd.html#index-0">fix srd</a>
</dt>
<dt><a href="fix_store_force.html#index-0">fix store/force</a>
</dt>
<dt><a href="fix_store_state.html#index-0">fix store/state</a>
</dt>
<dt><a href="fix_temp_berendsen.html#index-0">fix temp/berendsen</a>
</dt>
<dt><a href="fix_temp_csvr.html#index-0">fix temp/csvr</a>
</dt>
<dt><a href="fix_temp_rescale.html#index-0">fix temp/rescale</a>
</dt>
<dt><a href="fix_temp_rescale_eff.html#index-0">fix temp/rescale/eff</a>
</dt>
<dt><a href="fix_tfmc.html#index-0">fix tfmc</a>
</dt>
<dt><a href="fix_thermal_conductivity.html#index-0">fix thermal/conductivity</a>
</dt>
<dt><a href="fix_ti_rs.html#index-0">fix ti/rs</a>
</dt>
<dt><a href="fix_ti_spring.html#index-0">fix ti/spring</a>
</dt>
<dt><a href="fix_tmd.html#index-0">fix tmd</a>
</dt>
<dt><a href="fix_ttm.html#index-0">fix ttm</a>
</dt>
<dt><a href="fix_tune_kspace.html#index-0">fix tune/kspace</a>
</dt>
<dt><a href="fix_vector.html#index-0">fix vector</a>
</dt>
<dt><a href="fix_viscosity.html#index-0">fix viscosity</a>
</dt>
<dt><a href="fix_viscous.html#index-0">fix viscous</a>
</dt>
<dt><a href="fix_wall_gran.html#index-0">fix wall/gran</a>
</dt>
<dt><a href="fix_wall.html#index-0">fix wall/lj93</a>
</dt>
<dt><a href="fix_wall_piston.html#index-0">fix wall/piston</a>
</dt>
<dt><a href="fix_wall_reflect.html#index-0">fix wall/reflect</a>
</dt>
<dt><a href="fix_wall_region.html#index-0">fix wall/region</a>
</dt>
<dt><a href="fix_wall_srd.html#index-0">fix wall/srd</a>
</dt>
<dt><a href="fix_modify.html#index-0">fix_modify</a>
</dt>
</dl></td>
</tr></table>
<h2 id="G">G</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="group.html#index-0">group</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="group2ndx.html#index-0">group2ndx</a>
</dt>
</dl></td>
</tr></table>
<h2 id="I">I</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="if.html#index-0">if</a>
</dt>
<dt><a href="improper_coeff.html#index-0">improper_coeff</a>
</dt>
<dt><a href="improper_style.html#index-0">improper_style</a>
</dt>
<dt><a href="improper_class2.html#index-0">improper_style class2</a>
</dt>
<dt><a href="improper_cossq.html#index-0">improper_style cossq</a>
</dt>
<dt><a href="improper_cvff.html#index-0">improper_style cvff</a>
</dt>
<dt><a href="improper_distance.html#index-0">improper_style distance</a>
</dt>
<dt><a href="improper_fourier.html#index-0">improper_style fourier</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="improper_harmonic.html#index-0">improper_style harmonic</a>
</dt>
<dt><a href="improper_hybrid.html#index-0">improper_style hybrid</a>
</dt>
<dt><a href="improper_none.html#index-0">improper_style none</a>
</dt>
<dt><a href="improper_ring.html#index-0">improper_style ring</a>
</dt>
<dt><a href="improper_umbrella.html#index-0">improper_style umbrella</a>
</dt>
<dt><a href="improper_zero.html#index-0">improper_style zero</a>
</dt>
<dt><a href="include.html#index-0">include</a>
</dt>
<dt><a href="info.html#index-0">info</a>
</dt>
</dl></td>
</tr></table>
<h2 id="J">J</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="jump.html#index-0">jump</a>
</dt>
</dl></td>
</tr></table>
<h2 id="K">K</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="kspace_modify.html#index-0">kspace_modify</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="kspace_style.html#index-0">kspace_style</a>
</dt>
</dl></td>
</tr></table>
<h2 id="L">L</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="label.html#index-0">label</a>
</dt>
<dt><a href="lattice.html#index-0">lattice</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="log.html#index-0">log</a>
</dt>
</dl></td>
</tr></table>
<h2 id="M">M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="mass.html#index-0">mass</a>
</dt>
<dt><a href="min_modify.html#index-0">min_modify</a>
</dt>
<dt><a href="min_style.html#index-0">min_style</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="minimize.html#index-0">minimize</a>
</dt>
<dt><a href="molecule.html#index-0">molecule</a>
</dt>
</dl></td>
</tr></table>
<h2 id="N">N</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="neb.html#index-0">neb</a>
</dt>
<dt><a href="neigh_modify.html#index-0">neigh_modify</a>
</dt>
<dt><a href="neighbor.html#index-0">neighbor</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="newton.html#index-0">newton</a>
</dt>
<dt><a href="next.html#index-0">next</a>
</dt>
</dl></td>
</tr></table>
<h2 id="P">P</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="package.html#index-0">package</a>
</dt>
<dt><a href="pair_coeff.html#index-0">pair_coeff</a>
</dt>
<dt><a href="pair_modify.html#index-0">pair_modify</a>
</dt>
<dt><a href="pair_style.html#index-0">pair_style</a>
</dt>
<dt><a href="pair_adp.html#index-0">pair_style adp</a>
</dt>
<dt><a href="pair_airebo.html#index-0">pair_style airebo</a>
</dt>
<dt><a href="pair_awpmd.html#index-0">pair_style awpmd/cut</a>
</dt>
<dt><a href="pair_beck.html#index-0">pair_style beck</a>
</dt>
<dt><a href="pair_body.html#index-0">pair_style body</a>
</dt>
<dt><a href="pair_bop.html#index-0">pair_style bop</a>
</dt>
<dt><a href="pair_born.html#index-0">pair_style born</a>
</dt>
<dt><a href="pair_cs.html#index-0">pair_style born/coul/long/cs</a>
</dt>
<dt><a href="pair_brownian.html#index-0">pair_style brownian</a>
</dt>
<dt><a href="pair_buck.html#index-0">pair_style buck</a>
</dt>
<dt><a href="pair_buck_long.html#index-0">pair_style buck/long/coul/long</a>
</dt>
<dt><a href="pair_colloid.html#index-0">pair_style colloid</a>
</dt>
<dt><a href="pair_comb.html#index-0">pair_style comb</a>
</dt>
<dt><a href="pair_coul.html#index-0">pair_style coul/cut</a>
</dt>
<dt><a href="pair_coul_diel.html#index-0">pair_style coul/diel</a>
</dt>
<dt><a href="pair_dpd.html#index-0">pair_style dpd</a>
</dt>
<dt><a href="pair_dpd_conservative.html#index-0">pair_style dpd/conservative</a>
</dt>
<dt><a href="pair_dpd_fdt.html#index-0">pair_style dpd/fdt</a>
</dt>
<dt><a href="pair_dsmc.html#index-0">pair_style dsmc</a>
</dt>
<dt><a href="pair_eam.html#index-0">pair_style eam</a>
</dt>
<dt><a href="pair_edip.html#index-0">pair_style edip</a>
</dt>
<dt><a href="pair_eff.html#index-0">pair_style eff/cut</a>
</dt>
<dt><a href="pair_eim.html#index-0">pair_style eim</a>
</dt>
<dt><a href="pair_gauss.html#index-0">pair_style gauss</a>
</dt>
<dt><a href="pair_gayberne.html#index-0">pair_style gayberne</a>
</dt>
<dt><a href="pair_gran.html#index-0">pair_style gran/hooke</a>
</dt>
<dt><a href="pair_hbond_dreiding.html#index-0">pair_style hbond/dreiding/lj</a>
</dt>
<dt><a href="pair_hybrid.html#index-0">pair_style hybrid</a>
</dt>
<dt><a href="pair_kim.html#index-0">pair_style kim</a>
</dt>
<dt><a href="pair_lcbop.html#index-0">pair_style lcbop</a>
</dt>
<dt><a href="pair_line_lj.html#index-0">pair_style line/lj</a>
</dt>
<dt><a href="pair_list.html#index-0">pair_style list</a>
</dt>
<dt><a href="pair_charmm.html#index-0">pair_style lj/charmm/coul/charmm</a>
</dt>
<dt><a href="pair_class2.html#index-0">pair_style lj/class2</a>
</dt>
<dt><a href="pair_lj_cubic.html#index-0">pair_style lj/cubic</a>
</dt>
<dt><a href="pair_lj.html#index-0">pair_style lj/cut</a>
</dt>
<dt><a href="pair_dipole.html#index-0">pair_style lj/cut/dipole/cut</a>
</dt>
<dt><a href="pair_lj_soft.html#index-0">pair_style lj/cut/soft</a>
</dt>
<dt><a href="pair_lj_expand.html#index-0">pair_style lj/expand</a>
</dt>
<dt><a href="pair_gromacs.html#index-0">pair_style lj/gromacs</a>
</dt>
<dt><a href="pair_lj_long.html#index-0">pair_style lj/long/coul/long</a>
</dt>
<dt><a href="pair_mdf.html#index-0">pair_style lj/mdf</a>
</dt>
<dt><a href="pair_sdk.html#index-0">pair_style lj/sdk</a>
</dt>
<dt><a href="pair_lj_sf.html#index-0">pair_style lj/sf</a>
</dt>
<dt><a href="pair_lj_smooth.html#index-0">pair_style lj/smooth</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="pair_lj_smooth_linear.html#index-0">pair_style lj/smooth/linear</a>
</dt>
<dt><a href="pair_lj96.html#index-0">pair_style lj96/cut</a>
</dt>
<dt><a href="pair_lubricate.html#index-0">pair_style lubricate</a>
</dt>
<dt><a href="pair_lubricateU.html#index-0">pair_style lubricateU</a>
</dt>
<dt><a href="pair_meam.html#index-0">pair_style meam</a>
</dt>
<dt><a href="pair_mgpt.html#index-0">pair_style mgpt</a>
</dt>
<dt><a href="pair_mie.html#index-0">pair_style mie/cut</a>
</dt>
<dt><a href="pair_morse.html#index-0">pair_style morse</a>
</dt>
<dt><a href="pair_nb3b_harmonic.html#index-0">pair_style nb3b/harmonic</a>
</dt>
<dt><a href="pair_nm.html#index-0">pair_style nm/cut</a>
</dt>
<dt><a href="pair_none.html#index-0">pair_style none</a>
</dt>
<dt><a href="pair_peri.html#index-0">pair_style peri/pmb</a>
</dt>
<dt><a href="pair_polymorphic.html#index-0">pair_style polymorphic</a>
</dt>
<dt><a href="pair_quip.html#index-0">pair_style quip</a>
</dt>
<dt><a href="pair_reax.html#index-0">pair_style reax</a>
</dt>
<dt><a href="pair_reax_c.html#index-0">pair_style reax/c</a>
</dt>
<dt><a href="pair_resquared.html#index-0">pair_style resquared</a>
</dt>
<dt><a href="pair_smd_hertz.html#index-0">pair_style smd/hertz</a>
</dt>
<dt><a href="pair_smd_tlsph.html#index-0">pair_style smd/tlsph</a>
</dt>
<dt><a href="pair_smd_triangulated_surface.html#index-0">pair_style smd/tri_surface</a>
</dt>
<dt><a href="pair_smd_ulsph.html#index-0">pair_style smd/ulsph</a>
</dt>
<dt><a href="pair_smtbq.html#index-0">pair_style smtbq</a>
</dt>
<dt><a href="pair_snap.html#index-0">pair_style snap</a>
</dt>
<dt><a href="pair_soft.html#index-0">pair_style soft</a>
</dt>
<dt><a href="pair_sph_heatconduction.html#index-0">pair_style sph/heatconduction</a>
</dt>
<dt><a href="pair_sph_idealgas.html#index-0">pair_style sph/idealgas</a>
</dt>
<dt><a href="pair_sph_lj.html#index-0">pair_style sph/lj</a>
</dt>
<dt><a href="pair_sph_rhosum.html#index-0">pair_style sph/rhosum</a>
</dt>
<dt><a href="pair_sph_taitwater.html#index-0">pair_style sph/taitwater</a>
</dt>
<dt><a href="pair_sph_taitwater_morris.html#index-0">pair_style sph/taitwater/morris</a>
</dt>
<dt><a href="pair_srp.html#index-0">pair_style srp</a>
</dt>
<dt><a href="pair_sw.html#index-0">pair_style sw</a>
</dt>
<dt><a href="pair_table.html#index-0">pair_style table</a>
</dt>
<dt><a href="pair_tersoff.html#index-0">pair_style tersoff</a>
</dt>
<dt><a href="pair_tersoff_mod.html#index-0">pair_style tersoff/mod</a>
</dt>
<dt><a href="pair_tersoff_zbl.html#index-0">pair_style tersoff/zbl</a>
</dt>
<dt><a href="pair_thole.html#index-0">pair_style thole</a>
</dt>
<dt><a href="pair_tri_lj.html#index-0">pair_style tri/lj</a>
</dt>
<dt><a href="pair_vashishta.html#index-0">pair_style vashishta</a>
</dt>
<dt><a href="pair_yukawa.html#index-0">pair_style yukawa</a>
</dt>
<dt><a href="pair_yukawa_colloid.html#index-0">pair_style yukawa/colloid</a>
</dt>
<dt><a href="pair_zbl.html#index-0">pair_style zbl</a>
</dt>
<dt><a href="pair_zero.html#index-0">pair_style zero</a>
</dt>
<dt><a href="pair_write.html#index-0">pair_write</a>
</dt>
<dt><a href="partition.html#index-0">partition</a>
</dt>
<dt><a href="prd.html#index-0">prd</a>
</dt>
<dt><a href="print.html#index-0">print</a>
</dt>
<dt><a href="processors.html#index-0">processors</a>
</dt>
<dt><a href="python.html#index-0">python</a>
</dt>
</dl></td>
</tr></table>
<h2 id="Q">Q</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="quit.html#index-0">quit</a>
</dt>
</dl></td>
</tr></table>
<h2 id="R">R</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="read_data.html#index-0">read_data</a>
</dt>
<dt><a href="read_dump.html#index-0">read_dump</a>
</dt>
<dt><a href="read_restart.html#index-0">read_restart</a>
</dt>
<dt><a href="region.html#index-0">region</a>
</dt>
<dt><a href="replicate.html#index-0">replicate</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="rerun.html#index-0">rerun</a>
</dt>
<dt><a href="reset_timestep.html#index-0">reset_timestep</a>
</dt>
<dt><a href="restart.html#index-0">restart</a>
</dt>
<dt><a href="run.html#index-0">run</a>
</dt>
<dt><a href="run_style.html#index-0">run_style</a>
</dt>
</dl></td>
</tr></table>
<h2 id="S">S</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="set.html#index-0">set</a>
</dt>
<dt><a href="shell.html#index-0">shell</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="special_bonds.html#index-0">special_bonds</a>
</dt>
<dt><a href="suffix.html#index-0">suffix</a>
</dt>
</dl></td>
</tr></table>
<h2 id="T">T</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="tad.html#index-0">tad</a>
</dt>
<dt><a href="temper.html#index-0">temper</a>
</dt>
<dt><a href="thermo.html#index-0">thermo</a>
</dt>
<dt><a href="thermo_modify.html#index-0">thermo_modify</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="thermo_style.html#index-0">thermo_style</a>
</dt>
<dt><a href="timer.html#index-0">timer</a>
</dt>
<dt><a href="timestep.html#index-0">timestep</a>
</dt>
</dl></td>
</tr></table>
<h2 id="U">U</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="uncompute.html#index-0">uncompute</a>
</dt>
<dt><a href="undump.html#index-0">undump</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="unfix.html#index-0">unfix</a>
</dt>
+
+ <dt><a href="units.html#index-0">units</a>
+ </dt>
+
</dl></td>
</tr></table>
<h2 id="V">V</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="variable.html#index-0">variable</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="velocity.html#index-0">velocity</a>
</dt>
</dl></td>
</tr></table>
<h2 id="W">W</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="write_coeff.html#index-0">write_coeff</a>
</dt>
<dt><a href="write_data.html#index-0">write_data</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="write_dump.html#index-0">write_dump</a>
</dt>
<dt><a href="write_restart.html#index-0">write_restart</a>
</dt>
</dl></td>
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<div class="section" id="pair-style-airebo-command">
<span id="index-0"></span><h1>pair_style airebo command</h1>
</div>
<div class="section" id="pair-style-airebo-omp-command">
<h1>pair_style airebo/omp command</h1>
</div>
<div class="section" id="pair-style-airebo-morse-command">
<h1>pair_style airebo/morse command</h1>
</div>
<div class="section" id="pair-style-airebo-morse-omp-command">
<h1>pair_style airebo/morse/omp command</h1>
</div>
<div class="section" id="pair-style-rebo-command">
<h1>pair_style rebo command</h1>
</div>
<div class="section" id="pair-style-rebo-omp-command">
<h1>pair_style rebo/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">cutoff</span> <span class="n">LJ_flag</span> <span class="n">TORSION_flag</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>airebo</em> or <em>airebo/morse</em> or <em>rebo</em></li>
<li>cutoff = LJ or Morse cutoff (sigma scale factor) (AIREBO and AIREBO-M only)</li>
<li>LJ_flag = 0/1 to turn off/on the LJ or Morse term (AIREBO and AIREBO-M only, optional)</li>
<li>TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO and AIREBO-M only, optional)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">airebo</span> <span class="mf">3.0</span>
<span class="n">pair_style</span> <span class="n">airebo</span> <span class="mf">2.5</span> <span class="mi">1</span> <span class="mi">0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">CH</span><span class="o">.</span><span class="n">airebo</span> <span class="n">H</span> <span class="n">C</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">airebo</span><span class="o">/</span><span class="n">morse</span> <span class="mf">3.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">CH</span><span class="o">.</span><span class="n">airebo</span><span class="o">-</span><span class="n">m</span> <span class="n">H</span> <span class="n">C</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">rebo</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">CH</span><span class="o">.</span><span class="n">airebo</span> <span class="n">H</span> <span class="n">C</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>The <em>airebo</em> pair style computes the Adaptive Intermolecular Reactive
Empirical Bond Order (AIREBO) Potential of <a class="reference internal" href="#stuart"><span class="std std-ref">(Stuart)</span></a> for a
system of carbon and/or hydrogen atoms. Note that this is the initial
formulation of AIREBO from 2000, not the later formulation.</p>
<p>The <em>airebo/morse</em> pair style computes the AIREBO-M potential, which
is equivalent to AIREBO, but replaces the LJ term with a Morse potential.
The Morse potentials are parameterized by high-quality quantum chemistry
(MP2) calculations and do not diverge as quickly as particle density
increases. This allows AIREBO-M to retain accuracy to much higher pressures
than AIREBO (up to 40 GPa for Polyethylene). Details for this potential
and its parameterization are given in <a class="reference internal" href="#oconnor"><span class="std std-ref">(O’Conner)</span></a>.</p>
<p>The <em>rebo</em> pair style computes the Reactive Empirical Bond Order (REBO)
Potential of <a class="reference internal" href="#brenner"><span class="std std-ref">(Brenner)</span></a>. Note that this is the so-called
2nd generation REBO from 2002, not the original REBO from 1990.
As discussed below, 2nd generation REBO is closely related to the
intial AIREBO; it is just a subset of the potential energy terms.</p>
<p>The AIREBO potential consists of three terms:</p>
<img alt="_images/pair_airebo.jpg" class="align-center" src="_images/pair_airebo.jpg" />
<p>By default, all three terms are included. For the <em>airebo</em> style, if
the two optional flag arguments to the pair_style command are
included, the LJ and torsional terms can be turned off. Note that
both or neither of the flags must be included. If both of the LJ an
torsional terms are turned off, it becomes the 2nd-generation REBO
potential, with a small caveat on the spline fitting procedure
mentioned below. This can be specified directly as pair_style <em>rebo</em>
with no additional arguments.</p>
<p>The detailed formulas for this potential are given in
<a class="reference internal" href="#stuart"><span class="std std-ref">(Stuart)</span></a>; here we provide only a brief description.</p>
<p>The E_REBO term has the same functional form as the hydrocarbon REBO
potential developed in <a class="reference internal" href="#brenner"><span class="std std-ref">(Brenner)</span></a>. The coefficients for
E_REBO in AIREBO are essentially the same as Brenner’s potential, but
a few fitted spline values are slightly different. For most cases the
E_REBO term in AIREBO will produce the same energies, forces and
statistical averages as the original REBO potential from which it was
derived. The E_REBO term in the AIREBO potential gives the model its
reactive capabilities and only describes short-ranged C-C, C-H and H-H
interactions (r < 2 Angstroms). These interactions have strong
coordination-dependence through a bond order parameter, which adjusts
the attraction between the I,J atoms based on the position of other
nearby atoms and thus has 3- and 4-body dependence.</p>
<p>The E_LJ term adds longer-ranged interactions (2 < r < cutoff) using a
form similar to the standard <a class="reference internal" href="pair_lj.html"><span class="doc">Lennard Jones potential</span></a>.
The E_LJ term in AIREBO contains a series of switching functions so
that the short-ranged LJ repulsion (1/r^12) does not interfere with
the energetics captured by the E_REBO term. The extent of the E_LJ
interactions is determined by the <em>cutoff</em> argument to the pair_style
command which is a scale factor. For each type pair (C-C, C-H, H-H)
the cutoff is obtained by multiplying the scale factor by the sigma
value defined in the potential file for that type pair. In the
standard AIREBO potential, sigma_CC = 3.4 Angstroms, so with a scale
factor of 3.0 (the argument in pair_style), the resulting E_LJ cutoff
would be 10.2 Angstroms.</p>
<p>The E_TORSION term is an explicit 4-body potential that describes
various dihedral angle preferences in hydrocarbon configurations.</p>
<hr class="docutils" />
<p>Only a single pair_coeff command is used with the <em>airebo</em>, <em>airebo</em>
or <em>rebo</em> style which specifies an AIREBO or AIREBO-M potential file
with parameters for C and H. Note that the <em>rebo</em> style in LAMMPS
uses the same AIREBO-formatted potential file. 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 AIREBO elements to atom types</li>
</ul>
<p>See the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></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, and the 4th to be H, you would use the following
pair_coeff command:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">CH</span><span class="o">.</span><span class="n">airebo</span> <span class="n">C</span> <span class="n">C</span> <span class="n">C</span> <span class="n">H</span>
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three C arguments map LAMMPS atom types 1,2,3 to the C
element in the AIREBO file. The final H argument maps LAMMPS atom
type 4 to the H 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>airebo</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 AIREBO potentials are listed in
the CH.airebo file to agree with the original <a class="reference internal" href="#stuart"><span class="std std-ref">(Stuart)</span></a>
paper. Thus the parameters are specific to this potential and the way
it was fit, so modifying the file should be done cautiously.</p>
<p>Similarly the parameters/coefficients for the AIREBO-M potentials are
listed in the CH.airebo-m file to agree with the <a class="reference internal" href="#oconnor"><span class="std std-ref">(O’Connor)</span></a>
paper. Thus the parameters are specific to this potential and the way
it was fit, so modifying the file should be done cautiously. The
AIREBO-M Morse potentials were parameterized using a cutoff of
3.0 (sigma). Modifying this cutoff may impact simulation accuracy.</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"><span class="doc">Section_accelerate</span></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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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 the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a>
mix, shift, table, and tail options.</p>
<p>These pair styles do not write their information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, 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>These pair styles can only be used via the <em>pair</em> keyword of the
<a class="reference internal" href="run_style.html"><span class="doc">run_style respa</span></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</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 class="std std-ref">Making LAMMPS</span></a> section
for more info.</p>
<p>These pair potentials require the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be
“on” for pair interactions.</p>
<p>The CH.airebo and CH.airebo-m potential files provided with LAMMPS
-(see the potentials directory) are parameterized for metal <span class="xref doc">units</span>.
+(see the potentials directory) are parameterized for metal <a class="reference internal" href="units.html"><span class="doc">units</span></a>.
You can use the AIREBO, AIREBO-M or REBO potential with any LAMMPS units,
but you would need to create your own AIREBO or AIREBO-M potential file
with coefficients listed in the appropriate units, if your simulation
doesn’t use “metal” units.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="stuart"><strong>(Stuart)</strong> Stuart, Tutein, Harrison, J Chem Phys, 112, 6472-6486
(2000).</p>
<p id="brenner"><strong>(Brenner)</strong> Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J
Physics: Condensed Matter, 14, 783-802 (2002).</p>
<p id="oconnor"><strong>(O’Connor)</strong> O’Connor et al., J. Chem. Phys. 142, 024903 (2015).</p>
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<div class="section" id="pair-style-bop-command">
<span id="index-0"></span><h1>pair_style bop command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">bop</span> <span class="n">keyword</span> <span class="o">...</span>
</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-default"><div class="highlight"><pre><span></span><span class="n">save</span> <span class="o">=</span> <span class="n">pre</span><span class="o">-</span><span class="n">compute</span> <span class="ow">and</span> <span class="n">save</span> <span class="n">some</span> <span class="n">values</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">bop</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">CdTe_bop</span> <span class="n">Cd</span> <span class="n">Te</span>
<span class="n">pair_style</span> <span class="n">bop</span> <span class="n">save</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">CdTe</span><span class="o">.</span><span class="n">bop</span><span class="o">.</span><span class="n">table</span> <span class="n">Cd</span> <span class="n">Te</span> <span class="n">Te</span>
<span class="n">comm_modify</span> <span class="n">cutoff</span> <span class="mf">14.70</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</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 class="std std-ref">Murdick</span></a>, <a class="reference internal" href="#ward"><span class="std std-ref">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 class="std std-ref">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’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"><span class="doc">mass</span></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"><span class="doc">mass</span></a> command after using the
<span class="xref doc">pair_coeff</span> 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-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">CdTe</span> <span class="n">Cd</span> <span class="n">Cd</span> <span class="n">Cd</span> <span class="n">Te</span>
</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 ”.bop” 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 class="std std-ref">Ward</span></a>) and Zhou (<a class="reference internal" href="pair_polymorphic.html#zhou"><span class="std std-ref">Zhou</span></a>). Each header line containing a
”:” 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 class="std std-ref">Ward</span></a>). This format also
assumes the angular functions have the formulation of (<a class="reference internal" href="#ward"><span class="std std-ref">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->N, j=i->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->N, j=0->N, k=j->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 class="std std-ref">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->N, j=i->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 class="std std-ref">Ward</span></a>). This format also
assumes the angular functions have the formulation of (<a class="reference internal" href="pair_polymorphic.html#zhou"><span class="std std-ref">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->N, j=i->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->N, j=0->N, k=j->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 class="std std-ref">Ward</span></a>). This format also
assumes the angular functions have the formulation of (<a class="reference internal" href="pair_polymorphic.html#zhou"><span class="std std-ref">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->N, j=i->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->N, j=0->N, k=j->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"><span class="doc">pair_modify</span></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"><span class="doc">binary restart files</span></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"><span class="doc">run_style respa</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more
info.</p>
<p>These pair potentials require the <a class="reference internal" href="newton.html"><span class="doc">newtion</span></a> setting to be
“on” for pair interactions.</p>
<p>The CdTe.bop and GaAs.bop potential files provided with LAMMPS (see the
-potentials directory) are parameterized for metal <span class="xref doc">units</span>.
+potentials directory) are parameterized for metal <a class="reference internal" href="units.html"><span class="doc">units</span></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 “metal” units.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</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>
</div>
</div>
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<div class="section" id="pair-style-comb-command">
<span id="index-0"></span><h1>pair_style comb command</h1>
</div>
<div class="section" id="pair-style-comb-omp-command">
<h1>pair_style comb/omp command</h1>
</div>
<div class="section" id="pair-style-comb3-command">
<h1>pair_style comb3 command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">comb</span>
<span class="n">pair_style</span> <span class="n">comb3</span> <span class="n">keyword</span>
</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</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">comb</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">comb</span> <span class="n">Si</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">comb</span> <span class="n">Hf</span> <span class="n">Si</span> <span class="n">O</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">comb3</span> <span class="n">polar_off</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">comb3</span> <span class="n">O</span> <span class="n">Cu</span> <span class="n">N</span> <span class="n">C</span> <span class="n">O</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</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 class="std std-ref">(COMB)</span></a> and <a class="reference internal" href="#comb3"><span class="std std-ref">(COMB3)</span></a>. Briefly, the total energy
<em>E<sub>T</sub></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<sub>i</sub><sup>self</sup></em> is the self-energy of atom <em>i</em>
(including atomic ionization energies and electron affinities),
<em>E<sub>ij</sub><sup>short</sup></em> is the bond-order potential between
atoms <em>i</em> and <em>j</em>,
<em>E<sub>ij</sub><sup>Coul</sup></em> is the Coulomb interactions,
<em>E<sup>polar</sup></em> is the polarization term for organic systems
(style <em>comb3</em> only),
<em>E<sup>vdW</sup></em> is the van der Waals energy (style <em>comb3</em> only),
<em>E<sup>barr</sup></em> is a charge barrier function, and
<em>E<sup>corr</sup></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 class="std std-ref">Rick</span></a> for
further details. This is implemented by the <a class="reference internal" href="fix_qeq_comb.html"><span class="doc">fix qeq/comb</span></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"><span class="doc">fix qeq/comb</span></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<sub>2</sub>/
HfO<sub>2</sub> 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-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">comb</span> <span class="n">Si</span> <span class="n">Hf</span> <span class="n">O</span> <span class="n">Si</span>
</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<sub>2</sub>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"><span class="doc">pair_coeff</span></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"><span class="doc">Section_accelerate</span></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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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"><span class="doc">pair_modify</span></a>
shift, table, and tail options.</p>
<p>These pair styles do not write its information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></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"><span class="doc">fix qeq/comb</span></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"><span class="doc">run_style respa</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>These pair styles requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be “on”
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
-<span class="xref doc">units</span>. You can use the COMB potential with any LAMMPS
+<a class="reference internal" href="units.html"><span class="doc">units</span></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’t use “metal” units.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a>, <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a>,
<a class="reference internal" href="fix_qeq_comb.html"><span class="doc">fix qeq/comb</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="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. & 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>
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diff --git a/doc/html/pair_dipole.html b/doc/html/pair_dipole.html
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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</h1>
</div>
<div class="section" id="pair-style-lj-cut-dipole-cut-gpu-command">
<h1>pair_style lj/cut/dipole/cut/gpu command</h1>
</div>
<div class="section" id="pair-style-lj-cut-dipole-cut-omp-command">
<h1>pair_style lj/cut/dipole/cut/omp command</h1>
</div>
<div class="section" id="pair-style-lj-sf-dipole-sf-command">
<h1>pair_style lj/sf/dipole/sf command</h1>
</div>
<div class="section" id="pair-style-lj-sf-dipole-sf-gpu-command">
<h1>pair_style lj/sf/dipole/sf/gpu command</h1>
</div>
<div class="section" id="pair-style-lj-sf-dipole-sf-omp-command">
<h1>pair_style lj/sf/dipole/sf/omp command</h1>
</div>
<div class="section" id="pair-style-lj-cut-dipole-long-command">
<h1>pair_style lj/cut/dipole/long command</h1>
</div>
<div class="section" id="pair-style-lj-long-dipole-long-command">
<h1>pair_style lj/long/dipole/long command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">cut</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">sf</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">sf</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">long</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">long</span> <span class="n">flag_lj</span> <span class="n">flag_coul</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</span>
</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</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mf">4.0</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">sf</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">sf</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mf">4.0</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mf">4.0</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">long</span> <span class="n">long</span> <span class="n">long</span> <span class="mf">3.5</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mf">4.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</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 class="std std-ref">(Allen)</span></a> and in <a class="reference internal" href="#toukmaji"><span class="std std-ref">(Toukmaji)</span></a>.</p>
<p>Style <em>lj/sf/dipole/sf</em> computes “shifted-force” 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 class="std std-ref">(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 class="std std-ref">(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 class="std std-ref">(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 class="std std-ref">(Allen)</span></a>. The formulas for the corresponding forces and
torques have been obtained by applying the ‘chain rule’ as in appendix
C.3 of <a class="reference internal" href="pair_gayberne.html#allen"><span class="std std-ref">(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 class="std std-ref">(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"><span class="doc">kspace_style</span></a> must be defined to
use this pair style. Currently, only <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style ewald/disp</span></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 class="std std-ref">(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"><span class="doc">kspace_style ewald_disp</span></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"><span class="doc">pair_style lj/cut</span></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"><span class="doc">kspace_style</span></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"><span class="doc">fix nve/sphere update dipole</span></a> command to rotate the
dipole moments. The <em>omega</em> option on the <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> command can be used to thermostat the
rotational motion. The <a class="reference internal" href="compute_temp_sphere.html"><span class="doc">compute temp/sphere</span></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"><span class="doc">atom_style dipole</span></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
<span class="xref doc">dipole</span> command or in the “Dipoles” section of the data
file read in by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command. Their initial
orientation can be defined by the <a class="reference internal" href="set.html"><span class="doc">set dipole</span></a> command or in
the “Atoms” 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"><span class="doc">pair_coeff</span></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"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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"><span class="doc">Section_accelerate</span></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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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 “pair_modify” 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 “pair_modify” command for details.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></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"><span class="doc">pair_modify</span></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"><span class="doc">pair_modify</span></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"><span class="doc">binary restart files</span></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"><span class="doc">run_style respa</span></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</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 class="std std-ref">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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
-<p>Using dipole pair styles with <em>electron</em> <span class="xref doc">units</span> is not
+<p>Using dipole pair styles with <em>electron</em> <a class="reference internal" href="units.html"><span class="doc">units</span></a> is not
currently supported.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="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-eam-command">
<span id="index-0"></span><h1>pair_style eam command</h1>
</div>
<div class="section" id="pair-style-eam-cuda-command">
<h1>pair_style eam/cuda command</h1>
</div>
<div class="section" id="pair-style-eam-gpu-command">
<h1>pair_style eam/gpu command</h1>
</div>
<div class="section" id="pair-style-eam-kk-command">
<h1>pair_style eam/kk command</h1>
</div>
<div class="section" id="pair-style-eam-omp-command">
<h1>pair_style eam/omp command</h1>
</div>
<div class="section" id="pair-style-eam-opt-command">
<h1>pair_style eam/opt command</h1>
</div>
<div class="section" id="pair-style-eam-alloy-command">
<h1>pair_style eam/alloy command</h1>
</div>
<div class="section" id="pair-style-eam-alloy-cuda-command">
<h1>pair_style eam/alloy/cuda command</h1>
</div>
<div class="section" id="pair-style-eam-alloy-gpu-command">
<h1>pair_style eam/alloy/gpu command</h1>
</div>
<div class="section" id="pair-style-eam-alloy-kk-command">
<h1>pair_style eam/alloy/kk command</h1>
</div>
<div class="section" id="pair-style-eam-alloy-omp-command">
<h1>pair_style eam/alloy/omp command</h1>
</div>
<div class="section" id="pair-style-eam-alloy-opt-command">
<h1>pair_style eam/alloy/opt command</h1>
</div>
<div class="section" id="pair-style-eam-cd-command">
<h1>pair_style eam/cd command</h1>
</div>
<div class="section" id="pair-style-eam-cd-omp-command">
<h1>pair_style eam/cd/omp command</h1>
</div>
<div class="section" id="pair-style-eam-fs-command">
<h1>pair_style eam/fs command</h1>
</div>
<div class="section" id="pair-style-eam-fs-cuda-command">
<h1>pair_style eam/fs/cuda command</h1>
</div>
<div class="section" id="pair-style-eam-fs-gpu-command">
<h1>pair_style eam/fs/gpu command</h1>
</div>
<div class="section" id="pair-style-eam-fs-kk-command">
<h1>pair_style eam/fs/kk command</h1>
</div>
<div class="section" id="pair-style-eam-fs-omp-command">
<h1>pair_style eam/fs/omp command</h1>
</div>
<div class="section" id="pair-style-eam-fs-opt-command">
<h1>pair_style eam/fs/opt command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span>
</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</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eam</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">cuu3</span>
<span class="n">pair_coeff</span> <span class="mi">1</span><span class="o">*</span><span class="mi">3</span> <span class="mi">1</span><span class="o">*</span><span class="mi">3</span> <span class="n">niu3</span><span class="o">.</span><span class="n">eam</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eam</span><span class="o">/</span><span class="n">alloy</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">NiAlH_jea</span><span class="o">.</span><span class="n">eam</span><span class="o">.</span><span class="n">alloy</span> <span class="n">Ni</span> <span class="n">Al</span> <span class="n">Ni</span> <span class="n">Ni</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eam</span><span class="o">/</span><span class="n">cd</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">FeCr</span><span class="o">.</span><span class="n">cdeam</span> <span class="n">Fe</span> <span class="n">Cr</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eam</span><span class="o">/</span><span class="n">fs</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">NiAlH_jea</span><span class="o">.</span><span class="n">eam</span><span class="o">.</span><span class="n">fs</span> <span class="n">Ni</span> <span class="n">Al</span> <span class="n">Ni</span> <span class="n">Ni</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</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 class="std std-ref">(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"><span class="doc">pair_coeff</span></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
“potentials” directory of the LAMMPS distribution. All of these files
-are parameterized in terms of LAMMPS <span class="xref doc">metal units</span>.</p>
+are parameterized in terms of LAMMPS <a class="reference internal" href="units.html"><span class="doc">metal units</span></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"><span class="doc">mass</span></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-default"><div class="highlight"><pre><span></span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">www</span><span class="o">.</span><span class="n">ctcms</span><span class="o">.</span><span class="n">nist</span><span class="o">.</span><span class="n">gov</span><span class="o">/</span><span class="n">potentials</span>
<span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">cst</span><span class="o">-</span><span class="n">www</span><span class="o">.</span><span class="n">nrl</span><span class="o">.</span><span class="n">navy</span><span class="o">.</span><span class="n">mil</span><span class="o">/</span><span class="n">ccm6</span><span class="o">/</span><span class="n">ap</span>
<span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">enpub</span><span class="o">.</span><span class="n">fulton</span><span class="o">.</span><span class="n">asu</span><span class="o">.</span><span class="n">edu</span><span class="o">/</span><span class="n">cms</span><span class="o">/</span><span class="n">potentials</span><span class="o">/</span><span class="n">main</span><span class="o">/</span><span class="n">main</span><span class="o">.</span><span class="n">htm</span>
</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 “D” values in it for exponents.
C only recognizes “e” or “E” 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-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span><span class="mi">2</span> <span class="mi">1</span><span class="o">*</span><span class="mi">2</span> <span class="n">cuu3</span><span class="o">.</span><span class="n">eam</span>
</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"><span class="doc">pair_coeff</span></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 ”.eam” 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 <span class="xref doc">units</span>, e.g. mass number or grams/mole for metal
+in mass <a class="reference internal" href="units.html"><span class="doc">units</span></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’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 “atomic charge” 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-default"><div class="highlight"><pre><span></span><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"><span class="doc">pair_coeff</span></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 “D”
values in it for exponents. C only recognizes “e” or “E” 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"><span class="doc">pair_coeff</span></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-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">NiAlH_jea</span><span class="o">.</span><span class="n">eam</span><span class="o">.</span><span class="n">alloy</span> <span class="n">Ni</span> <span class="n">Ni</span> <span class="n">Ni</span> <span class="n">Al</span>
</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 ”.eam.alloy” 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 <span class="xref doc">units</span>,
+<p>As with the <em>funcfl</em> files, only the mass (in mass <a class="reference internal" href="units.html"><span class="doc">units</span></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 >= 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 class="std std-ref">(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 ”.cdeam” 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 class="std std-ref">(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"><span class="doc">pair_coeff</span></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 class="std std-ref">(Ackland1)</span></a>. An example of such a potential is the same
author’s Fe-P FS potential <a class="reference internal" href="#ackland2"><span class="std std-ref">(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-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">NiAlH_jea</span><span class="o">.</span><span class="n">eam</span><span class="o">.</span><span class="n">fs</span> <span class="n">Ni</span> <span class="n">Ni</span> <span class="n">Ni</span> <span class="n">Al</span>
</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"><span class="doc">pair_coeff</span></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 ”.eam.fs” 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 >= 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"><span class="doc">Section_accelerate</span></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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accerlate</span></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"><span class="doc">pair_modify</span></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"><span class="doc">binary restart files</span></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"><span class="doc">run_style respa</span></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</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 class="std std-ref">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 class="std std-ref">Making LAMMPS</span></a>
section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></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 & 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</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">edip</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">edip</span><span class="o">/</span><span class="n">omp</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<p>pair_style edip
pair_coeff * * Si.edip Si</p>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>The <em>edip</em> style computes a 3-body <a class="reference internal" href="#edip"><span class="std std-ref">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"><span class="doc">Stillinger-Weber</span></a> or
<a class="reference internal" href="pair_tersoff.html"><span class="doc">Tersoff</span></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 < 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"><span class="doc">pair_coeff</span></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 ”.edip” 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"><span class="doc">Section_accelerate</span></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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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"><span class="doc">pair_modify</span></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></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"><span class="doc">run_style respa</span></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</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 class="std std-ref">Making LAMMPS</span></a>
section for more info on packages.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be “on”
for pair interactions.</p>
<p>The EDIP potential files provided with LAMMPS (see the potentials directory)
-are parameterized for metal <span class="xref doc">units</span>.
+are parameterized for metal <a class="reference internal" href="units.html"><span class="doc">units</span></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’t use “metal” units.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="edip"><strong>(EDIP)</strong> J. F. Justo et al., Phys. Rev. B 58, 2539 (1998).</p>
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<div class="section" id="pair-style-eff-cut-command">
<span id="index-0"></span><h1>pair_style eff/cut command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eff</span><span class="o">/</span><span class="n">cut</span> <span class="n">cutoff</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
</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</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eff</span><span class="o">/</span><span class="n">cut</span> <span class="mf">39.7</span>
<span class="n">pair_style</span> <span class="n">eff</span><span class="o">/</span><span class="n">cut</span> <span class="mf">40.0</span> <span class="n">limit</span><span class="o">/</span><span class="n">eradius</span>
<span class="n">pair_style</span> <span class="n">eff</span><span class="o">/</span><span class="n">cut</span> <span class="mf">40.0</span> <span class="n">limit</span><span class="o">/</span><span class="n">eradius</span> <span class="n">pressure</span><span class="o">/</span><span class="n">evirials</span>
<span class="n">pair_style</span> <span class="n">eff</span><span class="o">/</span><span class="n">cut</span> <span class="mf">40.0</span> <span class="n">ecp</span> <span class="mi">1</span> <span class="n">Si</span> <span class="mi">3</span> <span class="n">C</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mf">20.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="n">s</span> <span class="mf">0.320852</span> <span class="mf">2.283269</span> <span class="mf">0.814857</span>
<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="n">p</span> <span class="mf">22.721015</span> <span class="mf">0.728733</span> <span class="mf">1.103199</span> <span class="mf">17.695345</span> <span class="mf">6.693621</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</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 class="std std-ref">(Jaramillo-Botero)</span></a>. The eFF for Z<6
was first introduced by <a class="reference internal" href="#su"><span class="std std-ref">(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’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 class="std std-ref">(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 <span class="xref doc">electron_units</span>). The
+according to the units chosen (see <a class="reference internal" href="units.html"><span class="doc">electron_units</span></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"><span class="doc">kspace_style</span></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"><span class="doc">atom_style electron</span></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"><span class="doc">pair_coeff</span></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"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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"><span class="doc">pair_coeff</span></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 > 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 “ecp” 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 “s” ECP form requires 3 parameters and the “p” 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 ‘rigid’ 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 “all electron”
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<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 “pair_modify” command for details.</p>
<p>The <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></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"><span class="doc">pair_modify</span></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"><span class="doc">pair_modify</span></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"><span class="doc">binary restart files</span></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"><span class="doc">run_style respa</span></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</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 class="std std-ref">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"><span class="doc">atom_style</span></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"><span class="doc">comm_modify vel yes</span></a> command so that velocites are stored by ghost
atoms.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</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>
</div>
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<div class="section" id="pair-style-eim-command">
<span id="index-0"></span><h1>pair_style eim command</h1>
</div>
<div class="section" id="pair-style-eim-omp-command">
<h1>pair_style eim/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>eim</em></li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eim</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Na</span> <span class="n">Cl</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">eim</span> <span class="n">Na</span> <span class="n">Cl</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Na</span> <span class="n">Cl</span> <span class="n">ffield</span><span class="o">.</span><span class="n">eim</span> <span class="n">Na</span> <span class="n">Na</span> <span class="n">Na</span> <span class="n">Cl</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Na</span> <span class="n">Cl</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">eim</span> <span class="n">Cl</span> <span class="n">NULL</span> <span class="n">Na</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</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 class="std std-ref">(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"><span class="doc">atom_style</span></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"><span class="doc">pair_coeff</span></a> command. This is an
ASCII text file in a format described below. The “ffield.eim” file
included in the “potentials” 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 <span class="xref doc">metal units</span>.</p>
+file is parameterized in terms of LAMMPS <a class="reference internal" href="units.html"><span class="doc">metal units</span></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"><span class="doc">mass</span></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"><span class="doc">pair_coeff</span></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-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Na</span> <span class="n">Cl</span> <span class="n">ffield</span><span class="o">.</span><span class="n">eim</span> <span class="n">Na</span> <span class="n">Na</span> <span class="n">Na</span> <span class="n">Cl</span>
</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 “global:” 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 “element:” 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 “pair:” 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"><span class="doc">Section_accelerate</span></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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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</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</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="zhou"><strong>(Zhou)</strong> Zhou, submitted for publication (2010). Please contact
Xiaowang Zhou (Sandia) for details via email at xzhou at sandia.gov.</p>
</div>
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<div class="section" id="pair-style-meam-command">
<span id="index-0"></span><h1>pair_style meam command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">meam</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">meam</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">library</span><span class="o">.</span><span class="n">meam</span> <span class="n">Si</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">si</span><span class="o">.</span><span class="n">meam</span> <span class="n">Si</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">library</span><span class="o">.</span><span class="n">meam</span> <span class="n">Ni</span> <span class="n">Al</span> <span class="n">NULL</span> <span class="n">Ni</span> <span class="n">Al</span> <span class="n">Ni</span> <span class="n">Ni</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</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 class="std std-ref">(Baskes)</span></a>. Conceptually, it is an extension to the original
<a class="reference internal" href="pair_eam.html"><span class="doc">EAM potentials</span></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 class="std std-ref">(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"><span class="doc">pair_coeff</span></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 “potentials” directory of the LAMMPS
distribution with a ”.meam” suffix. All of these are parameterized in
-terms of LAMMPS <span class="xref doc">metal units</span>.</p>
+terms of LAMMPS <a class="reference internal" href="units.html"><span class="doc">metal units</span></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"><span class="doc">pair_coeff</span></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-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">library</span><span class="o">.</span><span class="n">meam</span> <span class="n">Si</span> <span class="n">C</span> <span class="n">sic</span><span class="o">.</span><span class="n">meam</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">C</span>
</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 “meamf” 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 “elt” and “lat” 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 “elt” 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 “elt” 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 = "A" parameter for MEAM (see e.g. <a class="reference internal" href="#baskes"><span class="std std-ref">(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 class="std std-ref">(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 class="std std-ref">(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-default"><div class="highlight"><pre><span></span> <span class="mi">0</span> <span class="o">=></span> <span class="n">G</span> <span class="o">=</span> <span class="n">sqrt</span><span class="p">(</span><span class="mi">1</span><span class="o">+</span><span class="n">Gamma</span><span class="p">)</span>
<span class="mi">1</span> <span class="o">=></span> <span class="n">G</span> <span class="o">=</span> <span class="n">exp</span><span class="p">(</span><span class="n">Gamma</span><span class="o">/</span><span class="mi">2</span><span class="p">)</span>
<span class="mi">2</span> <span class="o">=></span> <span class="ow">not</span> <span class="n">implemented</span>
<span class="mi">3</span> <span class="o">=></span> <span class="n">G</span> <span class="o">=</span> <span class="mi">2</span><span class="o">/</span><span class="p">(</span><span class="mi">1</span><span class="o">+</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="n">Gamma</span><span class="p">))</span>
<span class="mi">4</span> <span class="o">=></span> <span class="n">G</span> <span class="o">=</span> <span class="n">sqrt</span><span class="p">(</span><span class="mi">1</span><span class="o">+</span><span class="n">Gamma</span><span class="p">)</span>
<span class="o">-</span><span class="mi">5</span> <span class="o">=></span> <span class="n">G</span> <span class="o">=</span> <span class="o">+-</span><span class="n">sqrt</span><span class="p">(</span><span class="nb">abs</span><span class="p">(</span><span class="mi">1</span><span class="o">+</span><span class="n">Gamma</span><span class="p">))</span>
</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 ”.meam” 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-default"><div class="highlight"><pre><span></span><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<=J); default = 2.8
Cmin(I,J,K) = Cmin screening parameter when I-J pair is screened
by K (I<=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 class="std std-ref">(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 class="std std-ref">(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-default"><div class="highlight"><pre><span></span><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 class="std std-ref">(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-default"><div class="highlight"><pre><span></span><span class="n">astar</span> <span class="o">=</span> <span class="n">alpha</span> <span class="o">*</span> <span class="p">(</span><span class="n">r</span><span class="o">/</span><span class="n">re</span> <span class="o">-</span> <span class="mf">1.</span><span class="n">d0</span><span class="p">)</span>
<span class="k">if</span> <span class="n">erose_form</span> <span class="o">=</span> <span class="mi">0</span><span class="p">:</span> <span class="n">erose</span> <span class="o">=</span> <span class="o">-</span><span class="n">Ec</span><span class="o">*</span><span class="p">(</span><span class="mi">1</span><span class="o">+</span><span class="n">astar</span><span class="o">+</span><span class="n">a3</span><span class="o">*</span><span class="p">(</span><span class="n">astar</span><span class="o">**</span><span class="mi">3</span><span class="p">)</span><span class="o">/</span><span class="p">(</span><span class="n">r</span><span class="o">/</span><span class="n">re</span><span class="p">))</span><span class="o">*</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="n">astar</span><span class="p">)</span>
<span class="k">if</span> <span class="n">erose_form</span> <span class="o">=</span> <span class="mi">1</span><span class="p">:</span> <span class="n">erose</span> <span class="o">=</span> <span class="o">-</span><span class="n">Ec</span><span class="o">*</span><span class="p">(</span><span class="mi">1</span><span class="o">+</span><span class="n">astar</span><span class="o">+</span><span class="p">(</span><span class="o">-</span><span class="n">attrac</span><span class="o">+</span><span class="n">repuls</span><span class="o">/</span><span class="n">r</span><span class="p">)</span><span class="o">*</span><span class="p">(</span><span class="n">astar</span><span class="o">**</span><span class="mi">3</span><span class="p">))</span><span class="o">*</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="n">astar</span><span class="p">)</span>
<span class="k">if</span> <span class="n">erose_form</span> <span class="o">=</span> <span class="mi">2</span><span class="p">:</span> <span class="n">erose</span> <span class="o">=</span> <span class="o">-</span><span class="n">Ec</span><span class="o">*</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span><span class="n">astar</span> <span class="o">+</span> <span class="n">a3</span><span class="o">*</span><span class="p">(</span><span class="n">astar</span><span class="o">**</span><span class="mi">3</span><span class="p">))</span><span class="o">*</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="n">astar</span><span class="p">)</span>
<span class="n">a3</span> <span class="o">=</span> <span class="n">repuls</span><span class="p">,</span> <span class="n">astar</span> <span class="o"><</span> <span class="mi">0</span>
<span class="n">a3</span> <span class="o">=</span> <span class="n">attrac</span><span class="p">,</span> <span class="n">astar</span> <span class="o">>=</span> <span class="mi">0</span>
</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 class="std std-ref">(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"><span class="doc">pair_modify</span></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></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"><span class="doc">run_style respa</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a>, <a class="reference internal" href="pair_eam.html"><span class="doc">pair_style eam</span></a>,
<a class="reference internal" href="pair_meam_spline.html"><span class="doc">pair_style meam/spline</span></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, “Stopping and Ranges
of Ions in Matter”, Vol 1, 1985, Pergamon Press.</p>
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diff --git a/doc/html/pair_meam_spline.html b/doc/html/pair_meam_spline.html
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--- a/doc/html/pair_meam_spline.html
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@@ -1,309 +1,309 @@
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<div class="section" id="pair-style-meam-spline">
<h1>pair_style meam/spline</h1>
</div>
<div class="section" id="pair-style-meam-spline-omp">
<h1>pair_style meam/spline/omp</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">meam</span><span class="o">/</span><span class="n">spline</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">meam</span><span class="o">/</span><span class="n">spline</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ti</span><span class="o">.</span><span class="n">meam</span><span class="o">.</span><span class="n">spline</span> <span class="n">Ti</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ti</span><span class="o">.</span><span class="n">meam</span><span class="o">.</span><span class="n">spline</span> <span class="n">Ti</span> <span class="n">Ti</span> <span class="n">Ti</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</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 class="std std-ref">(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"><span class="doc">pair_coeff</span></a> command. Parameter files for different
elements are included in the “potentials” directory of the LAMMPS
distribution and have a ”.meam.spline” file suffix. All of these
-files are parameterized in terms of LAMMPS <span class="xref doc">metal units</span>.</p>
+files are parameterized in terms of LAMMPS <a class="reference internal" href="units.html"><span class="doc">metal units</span></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"><span class="doc">mass</span></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"><span class="doc">pair_coeff</span></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-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ti</span><span class="o">.</span><span class="n">meam</span><span class="o">.</span><span class="n">spline</span> <span class="n">Ti</span> <span class="n">Ti</span> <span class="n">Ti</span>
</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"><span class="doc">Section_accelerate</span></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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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"><span class="doc">pair_modify</span></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"><span class="doc">binary restart files</span></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"><span class="doc">run_style respa</span></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</h2>
<p>This pair style requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be “on”
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 class="std std-ref">Making LAMMPS</span></a> section
for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a>, <a class="reference internal" href="pair_meam.html"><span class="doc">pair_style meam</span></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</h1>
</div>
<div class="section" id="pair-style-meam-sw-spline-omp">
<h1>pair_style meam/sw/spline/omp</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">meam</span><span class="o">/</span><span class="n">sw</span><span class="o">/</span><span class="n">spline</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">meam</span><span class="o">/</span><span class="n">sw</span><span class="o">/</span><span class="n">spline</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ti</span><span class="o">.</span><span class="n">meam</span><span class="o">.</span><span class="n">sw</span><span class="o">.</span><span class="n">spline</span> <span class="n">Ti</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ti</span><span class="o">.</span><span class="n">meam</span><span class="o">.</span><span class="n">sw</span><span class="o">.</span><span class="n">spline</span> <span class="n">Ti</span> <span class="n">Ti</span> <span class="n">Ti</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</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 class="std std-ref">(Lenosky)</span></a> with an additional Stillinger-Weber (SW) term
<a class="reference internal" href="pair_sw.html#stillinger"><span class="std std-ref">(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 class="std std-ref">(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"><span class="doc">pair_coeff</span></a> command. Parameter files for different
elements are included in the “potentials” directory of the LAMMPS
distribution and have a ”.meam.sw.spline” file suffix. All of these
-files are parameterized in terms of LAMMPS <span class="xref doc">metal units</span>.</p>
+files are parameterized in terms of LAMMPS <a class="reference internal" href="units.html"><span class="doc">metal units</span></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"><span class="doc">mass</span></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"><span class="doc">pair_coeff</span></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"><span class="doc">pair_modify</span></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"><span class="doc">binary restart files</span></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"><span class="doc">run_style respa</span></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</h2>
<p>This pair style requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be “on”
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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a>, <a class="reference internal" href="pair_meam.html"><span class="doc">pair_style meam</span></a>,
<a class="reference internal" href="pair_meam_spline.html"><span class="doc">pair_style meam/spline</span></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</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">mgpt</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">mgpt</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ta6</span><span class="o">.</span><span class="mi">8</span><span class="n">x</span><span class="o">.</span><span class="n">mgpt</span><span class="o">.</span><span class="n">parmin</span> <span class="n">Ta6</span><span class="o">.</span><span class="mi">8</span><span class="n">x</span><span class="o">.</span><span class="n">mgpt</span><span class="o">.</span><span class="n">potin</span> <span class="n">Omega</span>
<span class="n">cp</span> <span class="o">~/</span><span class="n">lammps</span><span class="o">/</span><span class="n">potentials</span><span class="o">/</span><span class="n">Ta6</span><span class="o">.</span><span class="mi">8</span><span class="n">x</span><span class="o">.</span><span class="n">mgpt</span><span class="o">.</span><span class="n">parmin</span> <span class="n">parmin</span>
<span class="n">cp</span> <span class="o">~/</span><span class="n">lammps</span><span class="o">/</span><span class="n">potentials</span><span class="o">/</span><span class="n">Ta6</span><span class="o">.</span><span class="mi">8</span><span class="n">x</span><span class="o">.</span><span class="n">mgpt</span><span class="o">.</span><span class="n">potin</span> <span class="n">potin</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">parmin</span> <span class="n">potin</span> <span class="n">Omega</span> <span class="n">volpress</span> <span class="n">yes</span> <span class="n">nbody</span> <span class="mi">1234</span> <span class="n">precision</span> <span class="n">double</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">parmin</span> <span class="n">potin</span> <span class="n">Omega</span> <span class="n">volpress</span> <span class="n">yes</span> <span class="n">nbody</span> <span class="mi">12</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Within DFT quantum mechanics, generalized pseudopotential theory (GPT)
(<a class="reference internal" href="#moriarty1"><span class="std std-ref">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 class="std std-ref">Moriarty2</span></a>,
<a class="reference internal" href="#moriarty3"><span class="std std-ref">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 class="std std-ref">Moriarty2</span></a>) and matrix
(<a class="reference internal" href="#moriarty3"><span class="std std-ref">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 class="std std-ref">Glosli</span></a>, <a class="reference internal" href="#moriarty3"><span class="std std-ref">Moriarty3</span></a>) and by Oppelstrup
(<a class="reference internal" href="#oppelstrup"><span class="std std-ref">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"><span class="doc">pair_coeff</span></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"><span class="doc">pair_coeff</span></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., “make bgq”) should enable the optimized algebra
routines. For x-86 machines, the here provided Makefile.mpi_fastmgpt
(build with “make mpi_fastmgpt”) 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"><span class="doc">pair_coeff</span></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 “README” 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 “-O3 -msse3 -funroll-loops” 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"><span class="doc">pair_modify</span></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"><span class="doc">binary restart files</span></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"><span class="doc">run_style respa</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>The MGPT potentials require the <a class="reference internal" href="newton.html"><span class="doc">newtion</span></a> setting to be
“on” for pair style interactions.</p>
<p>The stored parmin and potin potential files provided with LAMMPS in
the “potentials” 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 <span class="xref doc">units</span>.</p>
+compatible with LAMMPS electron <a class="reference internal" href="units.html"><span class="doc">units</span></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 “potentials” 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</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>The options defaults for the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></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>
</div>
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<div class="section" id="pair-style-polymorphic-command">
<span id="index-0"></span><h1>pair_style polymorphic command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">polymorphic</span>
</pre></div>
</div>
<p>style = <em>polymorphic</em></p>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">polymorphic</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">TlBr_msw</span><span class="o">.</span><span class="n">polymorphic</span> <span class="n">Tl</span> <span class="n">Br</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">AlCu_eam</span><span class="o">.</span><span class="n">polymorphic</span> <span class="n">Al</span> <span class="n">Cu</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">GaN_tersoff</span><span class="o">.</span><span class="n">polymorphic</span> <span class="n">Ga</span> <span class="n">N</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">GaN_sw</span><span class="o">.</span><span class="n">polymorphic</span> <span class="n">GaN</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>The <em>polymorphic</em> pair style computes a 3-body free-form potential
(<a class="reference internal" href="#zhou"><span class="std std-ref">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’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 class="std std-ref">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 class="std std-ref">Tersoff</span></a> or <a class="reference internal" href="pair_tersoff_zbl.html#albe"><span class="std std-ref">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 class="std std-ref">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 class="std std-ref">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
“poly” 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-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC_tersoff</span><span class="o">.</span><span class="n">polymorphic</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">C</span>
</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 ”.poly” suffix. At the beginning of the files, an unlimited
number of lines starting with ‘#’ are used to describe the potential
and are ignored by LAMMPS. The next line lists two numbers:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">ntypes</span> <span class="n">eta</span>
</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-default"><div class="highlight"><pre><span></span><span class="n">atomic_number</span> <span class="n">atomic</span><span class="o">-</span><span class="n">mass</span> <span class="n">element</span> <span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="n">atomic_number</span> <span class="n">atomic</span><span class="o">-</span><span class="n">mass</span> <span class="n">element</span> <span class="p">(</span><span class="mi">2</span><span class="p">)</span>
<span class="o">...</span>
<span class="n">atomic_number</span> <span class="n">atomic</span><span class="o">-</span><span class="n">mass</span> <span class="n">element</span> <span class="p">(</span><span class="n">ntypes</span><span class="p">)</span>
</pre></div>
</div>
<p>The next ntypes*(ntypes+1)/2 lines contain two numbers:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cut</span> <span class="n">xi</span> <span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="n">cut</span> <span class="n">xi</span> <span class="p">(</span><span class="mi">2</span><span class="p">)</span>
<span class="o">...</span>
<span class="n">cut</span> <span class="n">xi</span> <span class="p">(</span><span class="n">ntypes</span><span class="o">*</span><span class="p">(</span><span class="n">ntypes</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span><span class="o">/</span><span class="mi">2</span><span class="p">)</span>
</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 <= r <= cut for the U(r), V(r), W(r)
functions, -cutmax <= delta_r <= cutmax for the P(delta_r) functions,
-1 <= costheta <= 1 for the G(costheta) functions, and 0 <= X <= 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"><span class="doc">pair_modify</span></a>
shift, table, and tail options.</p>
<p>This pair style does not write their information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>This pair potential requires the <a class="reference internal" href="newton.html"><span class="doc">newtion</span></a> setting to be
“on” for pair interactions.</p>
<p>The potential files provided with LAMMPS (see the potentials
-directory) are parameterized for metal <span class="xref doc">units</span>. You can use
+directory) are parameterized for metal <a class="reference internal" href="units.html"><span class="doc">units</span></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</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></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>
</div>
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diff --git a/doc/html/pair_sw.html b/doc/html/pair_sw.html
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<div class="section" id="pair-style-sw-command">
<span id="index-0"></span><h1>pair_style sw command</h1>
</div>
<div class="section" id="pair-style-sw-cuda-command">
<h1>pair_style sw/cuda command</h1>
</div>
<div class="section" id="pair-style-sw-gpu-command">
<h1>pair_style sw/gpu command</h1>
</div>
<div class="section" id="pair-style-sw-intel-command">
<h1>pair_style sw/intel command</h1>
</div>
<div class="section" id="pair-style-sw-kk-command">
<h1>pair_style sw/kk command</h1>
</div>
<div class="section" id="pair-style-sw-omp-command">
<h1>pair_style sw/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">sw</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">sw</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">si</span><span class="o">.</span><span class="n">sw</span> <span class="n">Si</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">GaN</span><span class="o">.</span><span class="n">sw</span> <span class="n">Ga</span> <span class="n">N</span> <span class="n">Ga</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>The <em>sw</em> style computes a 3-body <a class="reference internal" href="#stillinger"><span class="std std-ref">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"><span class="doc">pair_coeff</span></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-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">sw</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">C</span>
</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 ”.sw” 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"><span class="doc">Section_accelerate</span></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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></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"><span class="doc">Section_accelerate</span></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"><span class="doc">pair_modify</span></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></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"><span class="doc">run_style respa</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be “on”
for pair interactions.</p>
<p>The Stillinger-Weber potential files provided with LAMMPS (see the
-potentials directory) are parameterized for metal <span class="xref doc">units</span>.
+potentials directory) are parameterized for metal <a class="reference internal" href="units.html"><span class="doc">units</span></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’t use “metal” units.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="stillinger"><strong>(Stillinger)</strong> Stillinger and Weber, Phys Rev B, 31, 5262 (1985).</p>
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<div class="section" id="pair-style-tersoff-command">
<span id="index-0"></span><h1>pair_style tersoff command</h1>
</div>
<div class="section" id="pair-style-tersoff-table-command">
<h1>pair_style tersoff/table command</h1>
</div>
<div class="section" id="pair-style-tersoff-cuda">
<h1>pair_style tersoff/cuda</h1>
</div>
<div class="section" id="pair-style-tersoff-gpu">
<h1>pair_style tersoff/gpu</h1>
</div>
<div class="section" id="pair-style-tersoff-intel">
<h1>pair_style tersoff/intel</h1>
</div>
<div class="section" id="pair-style-tersoff-kk">
<h1>pair_style tersoff/kk</h1>
</div>
<div class="section" id="pair-style-tersoff-omp">
<h1>pair_style tersoff/omp</h1>
</div>
<div class="section" id="pair-style-tersoff-table-omp-command">
<h1>pair_style tersoff/table/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span>
</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</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tersoff</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Si</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">Si</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">Si</span> <span class="n">C</span> <span class="n">Si</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tersoff</span><span class="o">/</span><span class="n">table</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiCGe</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">Si</span><span class="p">(</span><span class="n">D</span><span class="p">)</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</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 class="std std-ref">(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"><span class="doc">pair_coeff</span></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-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">C</span>
</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 ”.tersoff” 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 < -1 or > 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 class="std std-ref">(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 class="std std-ref">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 class="std std-ref">(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’+S’)/2 and D=(S’-R’)/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’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"><span class="doc">Section_accelerate</span></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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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"><span class="doc">pair_modify</span></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></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"><span class="doc">run_style respa</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be “on”
for pair interactions.</p>
<p>The Tersoff potential files provided with LAMMPS (see the potentials
-directory) are parameterized for metal <span class="xref doc">units</span>. You can
+directory) are parameterized for metal <a class="reference internal" href="units.html"><span class="doc">units</span></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’t use “metal” units.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="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</h1>
</div>
<div class="section" id="pair-style-tersoff-mod-gpu-command">
<h1>pair_style tersoff/mod/gpu command</h1>
</div>
<div class="section" id="pair-style-tersoff-mod-kk-command">
<h1>pair_style tersoff/mod/kk command</h1>
</div>
<div class="section" id="pair-style-tersoff-mod-omp-command">
<h1>pair_style tersoff/mod/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tersoff</span><span class="o">/</span><span class="n">mod</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tersoff</span><span class="o">/</span><span class="n">mod</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Si</span><span class="o">.</span><span class="n">tersoff</span><span class="o">.</span><span class="n">mod</span> <span class="n">Si</span> <span class="n">Si</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>The <em>tersoff/mod</em> style computes a bond-order type interatomic
potential <a class="reference internal" href="#kumagai"><span class="std std-ref">(Kumagai)</span></a> based on a 3-body Tersoff potential
<a class="reference internal" href="pair_tersoff_zbl.html#tersoff-1"><span class="std std-ref">(Tersoff_1)</span></a>, <a class="reference internal" href="pair_tersoff_zbl.html#tersoff-2"><span class="std std-ref">(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 class="std std-ref">(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 class="std std-ref">(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-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Si</span><span class="o">.</span><span class="n">tersoff_mod</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span>
</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 ”.tersoff.mod” 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"><span class="doc">Section_accelerate</span></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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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"><span class="doc">pair_modify</span></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></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"><span class="doc">run_style respa</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be “on”
for pair interactions.</p>
<p>The Tersoff/MOD potential files provided with LAMMPS (see the potentials
-directory) are parameterized for metal <span class="xref doc">units</span>. You can
+directory) are parameterized for metal <a class="reference internal" href="units.html"><span class="doc">units</span></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’t use “metal” units.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="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</h1>
</div>
<div class="section" id="pair-style-tersoff-zbl-gpu-command">
<h1>pair_style tersoff/zbl/gpu command</h1>
</div>
<div class="section" id="pair-style-tersoff-zbl-kk-command">
<h1>pair_style tersoff/zbl/kk command</h1>
</div>
<div class="section" id="pair-style-tersoff-zbl-omp-command">
<h1>pair_style tersoff/zbl/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tersoff</span><span class="o">/</span><span class="n">zbl</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tersoff</span><span class="o">/</span><span class="n">zbl</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">tersoff</span><span class="o">.</span><span class="n">zbl</span> <span class="n">Si</span> <span class="n">C</span> <span class="n">Si</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>The <em>tersoff/zbl</em> style computes a 3-body Tersoff potential
<a class="reference internal" href="#tersoff-1"><span class="std std-ref">(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 class="std std-ref">(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 “sharp”
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"><span class="doc">pair_coeff</span></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-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">C</span>
</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 ”.tersoff.zbl” 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 < -1 or > 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 class="std std-ref">(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 class="std std-ref">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 class="std std-ref">(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’+S’)/2 and D=(S’-R’)/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’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"><span class="doc">Section_accelerate</span></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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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"><span class="doc">pair_modify</span></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></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"><span class="doc">run_style respa</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be “on”
for pair interactions.</p>
<p>The Tersoff/ZBL potential files provided with LAMMPS (see the
-potentials directory) are parameterized for metal <span class="xref doc">units</span>.
+potentials directory) are parameterized for metal <a class="reference internal" href="units.html"><span class="doc">units</span></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’t use “metal”
units.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="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, ‘Stopping and Ranges
of Ions in Matter’ 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>
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diff --git a/doc/html/pair_vashishta.html b/doc/html/pair_vashishta.html
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<div class="section" id="pair-style-vashishta-command">
<span id="index-0"></span><h1>pair_style vashishta command</h1>
</div>
<div class="section" id="pair-style-vashishta-omp-command">
<h1>pair_style vashishta/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">vashishta</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">vashishta</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">vashishta</span> <span class="n">Si</span> <span class="n">C</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</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 class="std std-ref">Vashishta1990</span></a>,
SiC <a class="reference internal" href="#vashishta2007"><span class="std std-ref">Vashishta2007</span></a>,
and InP <a class="reference internal" href="#branicio2009"><span class="std std-ref">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 class="std std-ref">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"><span class="doc">pair_coeff</span></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-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">vashishta</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">C</span>
</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 ”.vashishta” 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"><span class="doc">Section_accelerate</span></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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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"><span class="doc">pair_modify</span></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></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"><span class="doc">run_style respa</span></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</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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be “on”
for pair interactions.</p>
<p>The Vashishta potential files provided with LAMMPS (see the
-potentials directory) are parameterized for metal <span class="xref doc">units</span>.
+potentials directory) are parameterized for metal <a class="reference internal" href="units.html"><span class="doc">units</span></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’t use “metal” units.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="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>
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<div class="section" id="pair-style-zbl-command">
<span id="index-0"></span><h1>pair_style zbl command</h1>
</div>
<div class="section" id="pair-style-zbl-gpu-command">
<h1>pair_style zbl/gpu command</h1>
</div>
<div class="section" id="pair-style-zbl-omp-command">
<h1>pair_style zbl/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">zbl</span> <span class="n">inner</span> <span class="n">outer</span>
</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</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">zbl</span> <span class="mf">3.0</span> <span class="mf">4.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">73.0</span> <span class="mf">73.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">14.0</span> <span class="mf">14.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</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 class="std std-ref">(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"><span class="doc">pair_style lj/gromacs</span></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"><span class="doc">pair_coeff</span></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"><span class="doc">hybrid/overlay</span></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 <span class="xref doc">units</span> setting. The values of Z should
+specified LAMMPS <a class="reference internal" href="units.html"><span class="doc">units</span></a> setting. The values of Z should
always be given as multiples of a proton’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"><span class="doc">Section_accelerate</span></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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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"><span class="doc">hybrid/overlay</span></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"><span class="doc">pair_modify</span></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"><span class="doc">pair_modify</span></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"><span class="doc">pair_modify</span></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"><span class="doc">pair_modify</span></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"><span class="doc">binary restart files</span></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"><span class="doc">run_style respa</span></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</h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="ziegler"><strong>(Ziegler)</strong> J.F. Ziegler, J. P. Biersack and U. Littmark, “The
Stopping and Range of Ions in Matter,” Volume 1, Pergamon, 1985.</p>
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