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doc/accelerate_kokkos.html
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@ -196,7 +196,7 @@ following kinds of hardware:</p>
<li>GPU: on the GPUs of a node with additional OpenMP threading on the CPUs</li>
</ul>
<p>Kokkos support within LAMMPS must be built with a C++11 compatible
compiler. For example, gcc 4.7.2 or later.</p>
compiler. If using gcc, version 4.8.1 or later is required.</p>
<p>Note that Intel Xeon Phi coprocessors are supported in &#8220;native&#8221; mode,
not &#8220;offload&#8221; mode like the USER-INTEL package supports.</p>
<p>Only NVIDIA GPUs are currently supported.</p>

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<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<H3>compute temp/region command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID temp/region region-ID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>temp/region = style name of this compute command
<LI>region-ID = ID of region to use for choosing atoms
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute mine flow temp/region boundary
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
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<div class="section" id="compute-temp-region-command">
<span id="index-0"></span><h1>compute temp/region command<a class="headerlink" href="#compute-temp-region-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID temp/region region-ID
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>temp/region = style name of this compute command</li>
<li>region-ID = ID of region to use for choosing atoms</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute mine flow temp/region boundary
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that calculates the temperature of a group of
atoms in a geometric region. This can be useful for thermostatting
one portion of the simulation box. E.g. a McDLT simulation where one
side is cooled, and the other side is heated. A compute of this style
can be used by any command that computes a temperature,
e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, etc.
</P>
<P>Note that a <I>region</I>-style temperature can be used to thermostat with
<A HREF = "fix_temp_rescale.html">fix temp/rescale</A> or <A HREF = "fix_langevin.html">fix
langevin</A>, but should probably not be used with
Nose/Hoover style fixes (<A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_nh.html">fix
npt</A>, or <A HREF = "fix_nh.html">fix nph</A>), if the
degrees-of-freedom included in the computed T varies with time.
</P>
<P>The temperature is calculated by the formula KE = dim/2 N k T, where
e.g. <a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a>, <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a>, etc.</p>
<p>Note that a <em>region</em>-style temperature can be used to thermostat with
<a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a> or <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a>, but should probably not be used with
Nose/Hoover style fixes (<a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a>, or <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a>), if the
degrees-of-freedom included in the computed T varies with time.</p>
<p>The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in both the group and region, k = Boltzmann constant, and T =
temperature.
</P>
<P>A kinetic energy tensor, stored as a 6-element vector, is also
temperature.</p>
<p>A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that v^2 is replaced by vx*vy for the xy
component, etc. The 6 components of the vector are ordered xx, yy,
zz, xy, xz, yz.
</P>
<P>The number of atoms contributing to the temperature is calculated each
zz, xy, xz, yz.</p>
<p>The number of atoms contributing to the temperature is calculated each
time the temperature is evaluated since it is assumed atoms can
enter/leave the region. Thus there is no need to use the <I>dynamic</I>
option of the <A HREF = "compute_modify.html">compute_modify</A> command for this
compute style.
</P>
<P>The removal of atoms outside the region by this fix is essentially
computing the temperature after a "bias" has been removed, which in
enter/leave the region. Thus there is no need to use the <em>dynamic</em>
option of the <a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command for this
compute style.</p>
<p>The removal of atoms outside the region by this fix is essentially
computing the temperature after a &#8220;bias&#8221; has been removed, which in
this case is the velocity of any atoms outside the region. If this
compute is used with a fix command that performs thermostatting then
this bias will be subtracted from each atom, thermostatting of the
remaining thermal velocity will be performed, and the bias will be
added back in. Thermostatting fixes that work in this way include
<A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
langevin</A>. This means that when this compute
<a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a>, <a class="reference internal" href="fix_temp_berendsen.html"><em>fix temp/berendsen</em></a>, and <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a>. This means that when this compute
is used to calculate the temperature for any of the thermostatting
fixes via the <A HREF = "fix_modify.html">fix modify temp</A> command, the thermostat
will operate only on atoms that are currently in the geometric
region.
</P>
<P>Unlike other compute styles that calculate temperature, this compute
fixes via the <a class="reference internal" href="fix_modify.html"><em>fix modify temp</em></a> command, the thermostat
will operate only on atoms that are currently in the geometric
region.</p>
<p>Unlike other compute styles that calculate temperature, this compute
does not subtract out degrees-of-freedom due to fixes that constrain
motion, such as <A HREF = "fix_shake.html">fix shake</A> and <A HREF = "fix_rigid.html">fix
rigid</A>. This is because those degrees of freedom
motion, such as <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> and <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a>. This is because those degrees of freedom
(e.g. a constrained bond) could apply to sets of atoms that straddle
the region boundary, and hence the concept is somewhat ill-defined.
If needed the number of subtracted degrees-of-freedom can be set
explicitly using the <I>extra</I> option of the
<A HREF = "compute_modify.html">compute_modify</A> command.
</P>
<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
explicitly using the <em>extra</em> option of the
<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command.</p>
<p>See <a class="reference internal" href="Section_howto.html#howto-16"><span>this howto section</span></a> of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the temperature) and a global
thermostatting.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE 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 HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
</P>
<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_pressure.html">compute
pressure</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
vector values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The scalar value calculated by this compute is &#8220;intensive&#8221;. The
vector values are &#8220;extensive&#8221;.</p>
<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><em>units</em></a>. The
vector values will be in energy <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_temp.html"><em>compute temp</em></a>, <a class="reference internal" href="compute_pressure.html"><em>compute pressure</em></a></p>
<p><strong>Default:</strong> none</p>
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<H3>fix atom/swap command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID atom/swap N X seed T keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>atom/swap = style name of this fix command
<LI>N = invoke this fix every N steps
<LI>X = number of swaps to attempt every N steps
<LI>seed = random # seed (positive integer)
<LI>T = scaling temperature of the MC swaps (temperature units)
<LI>one or more keyword/value pairs may be appended to args
<LI>keyword = <I>types</I> or <I>mu</I> or <I>ke</I> or <I>semi-grand</I> or <I>region</I>
<PRE> <I>types</I> values = two or more atom types
<I>mu</I> values = chemical potential of swap types (energy units)
<I>ke</I> value = <I>no</I> or <I>yes</I>
<I>no</I> = no conservation of kinetic energy after atom swaps
<I>yes</I> = kinetic energy is conserved after atom swaps
<I>semi-grand</I> value = <I>no</I> or <I>yes</I>
<I>no</I> = particle type counts and fractions conserved
<I>yes</I> = semi-grand canonical ensemble, particle fractions not conserved
<I>region</I> value = region-ID
region-ID = ID of region to use as an exchange/move volume
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 4.3 -5.0
</PRE>
<P><B>Description:</B>
</P>
<P>This fix performs Monte Carlo swaps of atoms of one given atom type
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<div class="section" id="fix-atom-swap-command">
<span id="index-0"></span><h1>fix atom/swap command<a class="headerlink" href="#fix-atom-swap-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID atom/swap N X seed T keyword values ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
<li>atom/swap = style name of this fix command</li>
<li>N = invoke this fix every N steps</li>
<li>X = number of swaps to attempt every N steps</li>
<li>seed = random # seed (positive integer)</li>
<li>T = scaling temperature of the MC swaps (temperature units)</li>
<li>one or more keyword/value pairs may be appended to args</li>
<li>keyword = <em>types</em> or <em>mu</em> or <em>ke</em> or <em>semi-grand</em> or <em>region</em></li>
</ul>
<pre class="literal-block">
<em>types</em> values = two or more atom types
<em>mu</em> values = chemical potential of swap types (energy units)
<em>ke</em> value = <em>no</em> or <em>yes</em>
<em>no</em> = no conservation of kinetic energy after atom swaps
<em>yes</em> = kinetic energy is conserved after atom swaps
<em>semi-grand</em> value = <em>no</em> or <em>yes</em>
<em>no</em> = particle type counts and fractions conserved
<em>yes</em> = semi-grand canonical ensemble, particle fractions not conserved
<em>region</em> value = region-ID
region-ID = ID of region to use as an exchange/move volume
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 4.3 -5.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>This fix performs Monte Carlo swaps of atoms of one given atom type
with atoms of the other given atom types. The specified T is used in
the Metropolis criterion dictating swap probabilities.
</P>
<P>Perform X swaps of atoms of one type with atoms of another type
the Metropolis criterion dictating swap probabilities.</p>
<p>Perform X swaps of atoms of one type with atoms of another type
according to a Monte Carlo probability. Swap candidates must be in the
fix group, must be in the region (if specified), and must be of one of
the listed types. Swaps are attempted between candidates that are
chosen randomly with equal probability among the candidate
atoms. Swaps are not attempted between atoms of the same type since
nothing would happen.
</P>
<P>All atoms in the simulation domain can be moved using regular time
integration displacements, e.g. via <A HREF = "fix_nvt.html">fix_nvt</A>, resulting
nothing would happen.</p>
<p>All atoms in the simulation domain can be moved using regular time
integration displacements, e.g. via <code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>, resulting
in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
be needed when running such a hybrid simulation, especially if the
swapped atoms are not well equilibrated.
</P>
<P>The <I>types</I> keyword is required. At least two atom types must be
specified.
</P>
<P>The <I>ke</I> keyword can be set to <I>no</I> to turn off kinetic energy
conservation for swaps. The default is <I>yes</I>, which means that swapped
swapped atoms are not well equilibrated.</p>
<p>The <em>types</em> keyword is required. At least two atom types must be
specified.</p>
<p>The <em>ke</em> keyword can be set to <em>no</em> to turn off kinetic energy
conservation for swaps. The default is <em>yes</em>, which means that swapped
atoms have their velocities scaled by the ratio of the masses of the
swapped atom types. This ensures that the kinetic energy of each atom
is the same after the swap as it was before the swap, even though the
atom masses have changed.
</P>
<P>The <I>semi-grand</I> keyword can be set to <I>yes</I> to switch to the
semi-grand canonical ensemble as discussed in <A HREF = "#Sadigh">(Sadigh)</A>. This
atom masses have changed.</p>
<p>The <em>semi-grand</em> keyword can be set to <em>yes</em> to switch to the
semi-grand canonical ensemble as discussed in <a class="reference internal" href="#sadigh"><span>(Sadigh)</span></a>. This
means that the total number of each particle type does not need to be
conserved. The default is <I>no</I>, which means that the only kind of swap
conserved. The default is <em>no</em>, which means that the only kind of swap
allowed exchanges an atom of one type with an atom of a different
given type. In other words, the relative mole fractions of the swapped
atoms remains constant. Whereas in the semi-grand canonical ensemble,
the composition of the system can change. Note that when using
<I>semi-grand</I>, atoms in the fix group whose type is not listed
in the <I>types</I> keyword are ineligible for attempted
conversion. An attempt is made to switch
the selected atom (if eligible) to one of the other listed types
with equal probability. Acceptance of each attempt depends upon the Metropolis criterion.
</P>
<P>The <I>mu</I> keyword allows users to specify chemical
potentials. This is required and allowed only when using <I>semi-grand</I>.
All chemical potentials are absolute, so there is one for
each swap type listed following the <I>types</I> keyword.
In semi-grand canonical ensemble simulations the chemical composition
<em>semi-grand</em>, atoms in the fix group whose type is not listed
in the <em>types</em> keyword are ineligible for attempted
conversion. An attempt is made to switch
the selected atom (if eligible) to one of the other listed types
with equal probability. Acceptance of each attempt depends upon the Metropolis criterion.</p>
<p>The <em>mu</em> keyword allows users to specify chemical
potentials. This is required and allowed only when using <em>semi-grand</em>.
All chemical potentials are absolute, so there is one for
each swap type listed following the <em>types</em> keyword.
In semi-grand canonical ensemble simulations the chemical composition
of the system is controlled by the difference in these values. So
shifting all values by a constant amount will have no effect
on the simulation.
</P>
<P>This command may optionally use the <I>region</I> keyword to define swap
on the simulation.</p>
<p>This command may optionally use the <em>region</em> keyword to define swap
volume. The specified region must have been previously defined with a
<A HREF = "region.html">region</A> command. It must be defined with side = <I>in</I>.
<a class="reference internal" href="region.html"><em>region</em></a> command. It must be defined with side = <em>in</em>.
Swap attempts occur only between atoms that are both within the
specified region. Swaps are not otherwise attempted.
</P>
<P>You should ensure you do not swap atoms belonging to a molecule, or
specified region. Swaps are not otherwise attempted.</p>
<p>You should ensure you do not swap atoms belonging to a molecule, or
LAMMPS will soon generate an error when it tries to find those atoms.
LAMMPS will warn you if any of the atoms eligible for swapping have a
non-zero molecule ID, but does not check for this at the time of
swapping.
</P>
<P>If not using <I>semi-grand</I> this fix checks to ensure all atoms of the
given types have the same atomic charge. LAMMPS doesn't enforce this
in general, but it is needed for this fix to simplify the
swapping procedure. Successful swaps will swap the atom type and charge
of the swapped atoms. Conversely, when using <I>semi-grand</I>, it is assumed that all the atom
swapping.</p>
<p>If not using <em>semi-grand</em> this fix checks to ensure all atoms of the
given types have the same atomic charge. LAMMPS doesn&#8217;t enforce this
in general, but it is needed for this fix to simplify the
swapping procedure. Successful swaps will swap the atom type and charge
of the swapped atoms. Conversely, when using <em>semi-grand</em>, it is assumed that all the atom
types involved in switches have the same charge. Otherwise, charge
would not be conserved. As a consequence, no checks on atomic charges are
performed, and successful switches update the atom type but not the
atom charge. While it is possible to use <I>semi-grand</I> with groups of
atom charge. While it is possible to use <em>semi-grand</em> with groups of
atoms that have different charges, these charges will not be changed when the
atom types change.
</P>
<P>Since this fix computes total potential energies before and after
atom types change.</p>
<p>Since this fix computes total potential energies before and after
proposed swaps, so even complicated potential energy calculations are
OK, including the following:
</P>
<UL><LI> long-range electrostatics (kspace)
<LI> many body pair styles
<LI> hybrid pair styles
<LI> eam pair styles
<LI> triclinic systems
<LI> need to include potential energy contributions from other fixes
</UL>
<P>Some fixes have an associated potential energy. Examples of such fixes
include: <A HREF = "fix_efield.html">efield</A>, <A HREF = "fix_gravity.html">gravity</A>,
<A HREF = "fix_addforce.html">addforce</A>, <A HREF = "fix_langevin.html">langevin</A>,
<A HREF = "fix_restrain.html">restrain</A>, <A HREF = "fix_temp_berendsen.html">temp/berendsen</A>,
<A HREF = "fix_temp_rescale.html">temp/rescale</A>, and <A HREF = "fix_wall.html">wall fixes</A>.
For that energy to be included in the total potential energy of the
OK, including the following:</p>
<ul class="simple">
<li>long-range electrostatics (kspace)</li>
<li>many body pair styles</li>
<li>hybrid pair styles</li>
<li>eam pair styles</li>
<li>triclinic systems</li>
<li>need to include potential energy contributions from other fixes</li>
</ul>
<p>Some fixes have an associated potential energy. Examples of such fixes
include: <a class="reference internal" href="fix_efield.html"><em>efield</em></a>, <a class="reference internal" href="fix_gravity.html"><em>gravity</em></a>,
<a class="reference internal" href="fix_addforce.html"><em>addforce</em></a>, <a class="reference internal" href="fix_langevin.html"><em>langevin</em></a>,
<a class="reference internal" href="fix_restrain.html"><em>restrain</em></a>, <a class="reference internal" href="fix_temp_berendsen.html"><em>temp/berendsen</em></a>,
<a class="reference internal" href="fix_temp_rescale.html"><em>temp/rescale</em></a>, and <a class="reference internal" href="fix_wall.html"><em>wall fixes</em></a>.
For that energy to be included in the total potential energy of the
system (the quantity used when performing GCMC moves),
you MUST enable the <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for
that fix. The doc pages for individual <A HREF = "fix.html">fix</A> commands
specify if this should be done.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the fix to <A HREF = "restart.html">binary restart
files</A>. This includes information about the random
you MUST enable the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> option for
that fix. The doc pages for individual <a class="reference internal" href="fix.html"><em>fix</em></a> commands
specify if this should be done.</p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline"></a></h2>
<p>This fix writes the state of the fix to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. This includes information about the random
number generator seed, the next timestep for MC exchanges, etc. See
the <A HREF = "read_restart.html">read_restart</A> command for info on how to
the <a class="reference internal" href="read_restart.html"><em>read_restart</em></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>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
fix.
</P>
<P>This fix computes a global vector of length 2, which can be accessed
by various <A HREF = "Section_howto.html#howto_15">output commands</A>. The vector
values are the following global cumulative quantities:
</P>
<UL><LI>1 = swap attempts
<LI>2 = swap successes
</UL>
<P>The vector values calculated by this fix are "extensive".
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nvt.html">fix_nvt</A>, <A HREF = "neighbor.html">neighbor</A>,
<A HREF = "fix_deposit.html">fix_deposit</A>, <A HREF = "fix_evaporate.html">fix_evaporate</A>,
<A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "fix_gcmc.html">fix_gcmc</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are ke = yes, semi-grand = no, mu = 0.0 for
all atom types.
</P>
<HR>
the operation of the fix continues in an uninterrupted fashion.</p>
<p>None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options are relevant to this
fix.</p>
<p>This fix computes a global vector of length 2, which can be accessed
by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The vector
values are the following global cumulative quantities:</p>
<ul class="simple">
<li>1 = swap attempts</li>
<li>2 = swap successes</li>
</ul>
<p>The vector values calculated by this fix are &#8220;extensive&#8221;.</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"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>, <a class="reference internal" href="neighbor.html"><em>neighbor</em></a>,
<a class="reference internal" href="fix_deposit.html"><em>fix_deposit</em></a>, <a class="reference internal" href="fix_evaporate.html"><em>fix_evaporate</em></a>,
<a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a>, <a class="reference internal" href="fix_gcmc.html"><em>fix_gcmc</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option defaults are ke = yes, semi-grand = no, mu = 0.0 for
all atom types.</p>
<hr class="docutils" />
<p id="sadigh"><strong>(Sadigh)</strong> B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and
L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012).</p>
</div>
</div>
<A NAME = "Sadigh"></A>
<P><B>(Sadigh)</B> B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and
L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012).
</P>
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<H3>pair_style zbl command
</H3>
<H3>pair_style zbl/gpu command
</H3>
<H3>pair_style zbl/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style zbl inner outer
</PRE>
<UL><LI>inner = distance where switching function begins
<LI>outer = global cutoff for ZBL interaction
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style zbl 3.0 4.0
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<div class="section" id="pair-style-zbl-command">
<span id="index-0"></span><h1>pair_style zbl command<a class="headerlink" href="#pair-style-zbl-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-zbl-gpu-command">
<h1>pair_style zbl/gpu command<a class="headerlink" href="#pair-style-zbl-gpu-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-zbl-omp-command">
<h1>pair_style zbl/omp command<a class="headerlink" href="#pair-style-zbl-omp-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style zbl inner outer
</pre></div>
</div>
<ul class="simple">
<li>inner = distance where switching function begins</li>
<li>outer = global cutoff for ZBL interaction</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style zbl 3.0 4.0
pair_coeff * * 73.0 73.0
pair_coeff 1 1 14.0 14.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>zbl</I> computes the Ziegler-Biersack-Littmark (ZBL) screened nuclear
pair_coeff 1 1 14.0 14.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>zbl</em> computes the Ziegler-Biersack-Littmark (ZBL) screened nuclear
repulsion for describing high-energy collisions between atoms.
<A HREF = "#Ziegler">(Ziegler)</A>. It includes an additional switching function
that ramps the energy, force, and curvature smoothly to zero
<a class="reference internal" href="#ziegler"><span>(Ziegler)</span></a>. It includes an additional switching function
that ramps the energy, force, and curvature smoothly to zero
between an inner and outer cutoff. The potential
energy due to a pair of atoms at a distance r_ij is given by:
</P>
<CENTER><IMG SRC = "Eqs/pair_zbl.jpg">
</CENTER>
<P>where e is the electron charge, epsilon_0 is the electrical
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 HREF = "pair_gromacs.html">pair_style lj/gromacs</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 HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above,
or in the LAMMPS data file.
</P>
<UL><LI>Z_i (atomic number for first atom type, e.g. 13.0 for aluminum)
</UL>
<UL><LI>Z_j (ditto for second atom type)
</UL>
<P>The values of Z_i and Z_j are normally equal to the atomic
<a class="reference internal" href="pair_gromacs.html"><em>pair_style lj/gromacs</em></a>. Here, the inner and outer
cutoff are the same for all pairs of atom types.</p>
<p>The following coefficients must be defined for each pair of atom types
via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above,
or in the LAMMPS data file.</p>
<ul class="simple">
<li>Z_i (atomic number for first atom type, e.g. 13.0 for aluminum)</li>
<li>Z_j (ditto for second atom type)</li>
</ul>
<p>The values of Z_i and Z_j are normally equal to the atomic
numbers of the two atom types. Thus, the user may optionally
specify only the coefficients for each I==I pair, and rely
on the obvious mixing rule for cross interactions (see below).
Note that when I==I it is required that Z_i == Z_j. When used
with <A HREF = "pair_hybrid.html">hybrid/overlay</A> and pairs are assigned
with <a class="reference internal" href="pair_hybrid.html"><em>hybrid/overlay</em></a> and pairs are assigned
to more than one sub-style, the mixing rule is not used and
each pair of types interacting with the ZBL sub-style must
be included in a pair_coeff command.
</P>
<P>IMPORTANT NOTE: The numerical values of the exponential decay
be included in a pair_coeff command.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The numerical values of the exponential decay
constants in the screening function depend on the unit of distance. In
the above equation they are given for units of angstroms. LAMMPS will
automatically convert these values to the distance unit of the
specified LAMMPS <A HREF = "units.html">units</A> setting. The values of Z should
always be given as multiples of a proton's charge, e.g. 29.0 for
copper.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
specified LAMMPS <a class="reference internal" href="units.html"><em>units</em></a> setting. The values of Z should
always be given as multiples of a proton&#8217;s charge, e.g. 29.0 for
copper.</p>
</div>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
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 HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the Z_i and Z_j coefficients
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, the Z_i and Z_j coefficients
can be mixed by taking Z_i and Z_j from the values specified for
I == I and J == J cases. When used
with <A HREF = "pair_hybrid.html">hybrid/overlay</A> and pairs are assigned
with <a class="reference internal" href="pair_hybrid.html"><em>hybrid/overlay</em></a> and pairs are assigned
to more than one sub-style, the mixing rule is not used and
each pair of types interacting with the ZBL sub-style
each pair of types interacting with the ZBL sub-style
must be included in a pair_coeff command.
The <A HREF = "pair_modify.html">pair_modify</A> mix option has no effect on
the mixing behavior
</P>
<P>The ZBL pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> mix option has no effect on
the mixing behavior</p>
<p>The ZBL pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option, since the ZBL interaction is already smoothed to 0.0 at
the cutoff.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant for
this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
the cutoff.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant for
this pair style.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
tail option for adding long-range tail corrections to energy and
pressure, since there are no corrections for a potential that goes to
0.0 at the cutoff.
</P>
<P>This pair style does not write information to <A HREF = "restart.html">binary restart
files</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 <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
0.0 at the cutoff.</p>
<p>This pair style does not write information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands must be
specified in an input script that reads a restart file.</p>
<p>This pair style can only be used via the <em>pair</em> keyword of the
<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="ziegler"><strong>(Ziegler)</strong> J.F. Ziegler, J. P. Biersack and U. Littmark, &#8220;The
Stopping and Range of Ions in Matter,&#8221; Volume 1, Pergamon, 1985.</p>
</div>
</div>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Ziegler"></A>
</div>
</div>
<footer>
<P><B>(Ziegler)</B> 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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