<p>where <spanclass="math">\(w_i\)</span> are weights of a numerical quadrature. The <aclass="reference internal"href="fix_adapt.html"><spanclass="doc">fix adapt</span></a> command can be used to define the stages of
<spanclass="math">\(\lambda\)</span> at which the derivative is calculated and averaged.</p>
<p>The value of the free energy difference is determined by numerical
root finding to establish the equality.</p>
<p>Concerning the choice of how the atomic parameters are perturbed in
order to setup an alchemical transformation route, several strategies
are available, such as single-topology or double-topology strategies
<aclass="reference internal"href="#pearlman"><spanclass="std std-ref">(Pearlman)</span></a>. The latter does not require modification of
bond lengths, angles or other internal coordinates.</p>
<p>NOTES: This compute command does not take kinetic energy into account,
therefore the masses of the particles should not be modified between
the reference and perturbed states, or along the alchemical
transformation route. This compute command does not change bond
lengths or other internal coordinates <aclass="reference internal"href="#boreschkarplus"><spanclass="std std-ref">(Boresch, Karplus)</span></a>.</p>
<hrclass="docutils"/>
<p>The <em>pair</em> attribute enables various parameters of potentials defined
by the <aclass="reference internal"href="pair_style.html"><spanclass="doc">pair_style</span></a> and <aclass="reference internal"href="pair_coeff.html"><spanclass="doc">pair_coeff</span></a>
commands to be changed, if the pair style supports it.</p>
<p>The <em>pstyle</em> argument is the name of the pair style. For example,
<em>pstyle</em> could be specified as “lj/cut”. The <em>pparam</em> argument is the
name of the parameter to change. This is a (non-exclusive) list of
pair styles and parameters that can be used with this compute. See
the doc pages for individual pair styles and their energy formulas for
the number of atom types, then an asterisk with no numeric values
means all types from 1 to N. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive). Note that only type pairs with I <= J are considered; if
asterisks imply type pairs where J < I, they are ignored.</p>
<p>If <aclass="reference internal"href="pair_hybrid.html"><spanclass="doc">pair_style hybrid or hybrid/overlay</span></a> is being
used, then the <em>pstyle</em> will be a sub-style name. You must specify
I,J arguments that correspond to type pair values defined (via the
<aclass="reference internal"href="pair_coeff.html"><spanclass="doc">pair_coeff</span></a> command) for that sub-style.</p>
<p>The <em>v_name</em> argument for keyword <em>pair</em> is the name of an
<aclass="reference internal"href="variable.html"><spanclass="doc">equal-style variable</span></a> which will be evaluated each time
this compute is invoked. It should be specified as v_name, where name
is the variable name.</p>
<hrclass="docutils"/>
<p>The <em>atom</em> attribute enables atom properties to be changed. The
<em>aparam</em> argument is the name of the parameter to change. This is the
current list of atom parameters that can be used with this compute:</p>
<ulclass="simple">
<li>charge = charge on particle</li>
</ul>
<p>The <em>v_name</em> argument for keyword <em>pair</em> is the name of an
<aclass="reference internal"href="variable.html"><spanclass="doc">equal-style variable</span></a> which will be evaluated each time
this compute is invoked. It should be specified as v_name, where name
is the variable name.</p>
<hrclass="docutils"/>
<p>The <em>tail</em> keyword controls the calculation of the tail correction to
“van der Waals” pair energies beyond the cutoff, if this has been
activated via the <aclass="reference internal"href="pair_modify.html"><spanclass="doc">pair_modify</span></a> command. If the
perturbation is small, the tail contribution to the energy difference
between the reference and perturbed systems should be negligible.</p>
<p>If the keyword <em>volume</em> = <em>yes</em>, then the Boltzmann term is multiplied
by the volume so that correct ensemble averaging can be performed over
trajectories during which the volume fluctuates or changes <aclass="reference internal"href="#allentildesley"><spanclass="std std-ref">(Allen and Tildesley)</span></a>:</p>
unperturbed parameters. The energies include kspace terms if these
are used in the simulation.</p>
<p>These output results can be used by any command that uses a global
scalar or vector from a compute as input. See <aclass="reference internal"href="Section_howto.html#howto-15"><spanclass="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
options. For example, the computed values can be averaged using <aclass="reference internal"href="fix_ave_time.html"><spanclass="doc">fix ave/time</span></a>.</p>
<p>The values calculated by this compute are “extensive”.</p>
</div>
<divclass="section"id="restrictions">
<h2>Restrictions</h2>
<p>This compute is distributed as the USER-FEP package. It is only
enabled if LAMMPS was built with that package. See the <aclass="reference internal"href="Section_start.html#start-3"><spanclass="std std-ref">Making LAMMPS</span></a> section for more info.</p>
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