forked from lijiext/lammps
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HTML
587 lines
34 KiB
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<title>pair_modify command — LAMMPS documentation</title>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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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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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_coeff.html">angle_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_style.html">angle_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atom_modify.html">atom_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="atom_style.html">atom_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="balance.html">balance command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_coeff.html">bond_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_style.html">bond_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_write.html">bond_write command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="clear.html">clear command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="comm_modify.html">comm_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="comm_style.html">comm_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute.html">compute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compute_modify.html">compute_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="create_atoms.html">create_atoms command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-h5md-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">h5md</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-movie-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">movie</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-molfile-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">molfile</span></code> command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_custom_vtk.html">dump custom/vtk command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_image.html">dump image command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_modify.html">dump_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dump_molfile.html">dump molfile command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="echo.html">echo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix.html">fix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="fix_modify.html">fix_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group.html">group command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="group2ndx.html">group2ndx command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="improper_coeff.html">improper_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="improper_style.html">improper_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kspace_modify.html">kspace_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="kspace_style.html">kspace_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="label.html">label command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="mass.html">mass command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_modify.html">min_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="min_style.html">min_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="minimize.html">minimize command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="molecule.html">molecule command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neb.html">neb command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neigh_modify.html">neigh_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="neighbor.html">neighbor command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="next.html">next command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="package.html">package command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pair_coeff.html">pair_coeff command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">pair_modify command</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
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<li class="toctree-l2"><a class="reference internal" href="shell.html">shell command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="special_bonds.html">special_bonds command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="suffix.html">suffix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo.html">thermo command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo_modify.html">thermo_modify command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="thermo_style.html">thermo_style command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timer.html">timer command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="timestep.html">timestep command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="uncompute.html">uncompute command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="undump.html">undump command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="unfix.html">unfix command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="velocity.html">velocity command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_coeff.html">write_coeff command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="write_data.html">write_data command</a></li>
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<li>pair_modify command</li>
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<div class="section" id="pair-modify-command">
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<span id="index-0"></span><h1>pair_modify command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<pre class="literal-block">
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pair_modify keyword values ...
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</pre>
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<ul>
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<li><p class="first">one or more keyword/value pairs may be listed</p>
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</li>
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<li><p class="first">keyword = <em>pair</em> or <em>shift</em> or <em>mix</em> or <em>table</em> or <em>table/disp</em> or <em>tabinner</em> or <em>tabinner/disp</em> or <em>tail</em> or <em>compute</em></p>
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<pre class="literal-block">
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<em>pair</em> values = sub-style N <em>special</em> which wt1 wt2 wt3
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sub-style = sub-style of <a class="reference internal" href="pair_hybrid.html"><span class="doc">pair hybrid</span></a>
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N = which instance of sub-style (only if sub-style is used multiple times)
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<em>special</em> which wt1 wt2 wt3 = override <em>special_bonds</em> settings (optional)
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which = <em>lj/coul</em> or <em>lj</em> or <em>coul</em>
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w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
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<em>mix</em> value = <em>geometric</em> or <em>arithmetic</em> or <em>sixthpower</em>
|
|
<em>shift</em> value = <em>yes</em> or <em>no</em>
|
|
<em>table</em> value = N
|
|
2^N = # of values in table
|
|
<em>table/disp</em> value = N
|
|
2^N = # of values in table
|
|
<em>tabinner</em> value = cutoff
|
|
cutoff = inner cutoff at which to begin table (distance units)
|
|
<em>tabinner/disp</em> value = cutoff
|
|
cutoff = inner cutoff at which to begin table (distance units)
|
|
<em>tail</em> value = <em>yes</em> or <em>no</em>
|
|
<em>compute</em> value = <em>yes</em> or <em>no</em>
|
|
</pre>
|
|
</li>
|
|
</ul>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<pre class="literal-block">
|
|
pair_modify shift yes mix geometric
|
|
pair_modify tail yes
|
|
pair_modify table 12
|
|
pair_modify pair lj/cut compute no
|
|
pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0
|
|
</pre>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Modify the parameters of the currently defined pair style. Not all
|
|
parameters are relevant to all pair styles.</p>
|
|
<p>If used, the <em>pair</em> keyword must appear first in the list of keywords.
|
|
It can only be used with the <a class="reference internal" href="pair_hybrid.html"><span class="doc">hybrid and hybrid/overlay</span></a> pair styles. It means that all the
|
|
following parameters will only be modified for the specified
|
|
sub-style. If the sub-style is defined multiple times, then an
|
|
additional numeric argument <em>N</em> must also be specified, which is a
|
|
number from 1 to M where M is the number of times the sub-style was
|
|
listed in the <a class="reference internal" href="pair_hybrid.html"><span class="doc">pair_style hybrid</span></a> command. The extra
|
|
number indicates which instance of the sub-style the remaining
|
|
keywords will be applied to. Note that if the <em>pair</em> keyword is not
|
|
used, and the pair style is <em>hybrid</em> or <em>hybrid/overlay</em>, then all the
|
|
specified keywords will be applied to all sub-styles.</p>
|
|
<p>The <em>special</em> keyword can only be used in conjunction with the <em>pair</em>
|
|
keyword and must directly follow it. It allows to override the
|
|
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> settings for the specified sub-style.
|
|
More details are given below.</p>
|
|
<p>The <em>mix</em> keyword affects pair coefficients for interactions between
|
|
atoms of type I and J, when I != J and the coefficients are not
|
|
explicitly set in the input script. Note that coefficients for I = J
|
|
must be set explicitly, either in the input script via the
|
|
“pair_coeff” command or in the “Pair Coeffs” section of the <a class="reference internal" href="read_data.html"><span class="doc">data file</span></a>. For some pair styles it is not necessary to
|
|
specify coefficients when I != J, since a “mixing” rule will create
|
|
them from the I,I and J,J settings. The pair_modify <em>mix</em> value
|
|
determines what formulas are used to compute the mixed coefficients.
|
|
In each case, the cutoff distance is mixed the same way as sigma.</p>
|
|
<p>Note that not all pair styles support mixing. Also, some mix options
|
|
are not available for certain pair styles. See the doc page for
|
|
individual pair styles for those restrictions. Note also that the
|
|
<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command also can be to directly set
|
|
coefficients for a specific I != J pairing, in which case no mixing is
|
|
performed.</p>
|
|
<p>mix <em>geometric</em></p>
|
|
<pre class="literal-block">
|
|
epsilon_ij = sqrt(epsilon_i * epsilon_j)
|
|
sigma_ij = sqrt(sigma_i * sigma_j)
|
|
</pre>
|
|
<p>mix <em>arithmetic</em></p>
|
|
<pre class="literal-block">
|
|
epsilon_ij = sqrt(epsilon_i * epsilon_j)
|
|
sigma_ij = (sigma_i + sigma_j) / 2
|
|
</pre>
|
|
<p>mix <em>sixthpower</em></p>
|
|
<pre class="literal-block">
|
|
epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
|
|
(sigma_i^6 + sigma_j^6)
|
|
sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
|
|
</pre>
|
|
<p>The <em>shift</em> keyword determines whether a Lennard-Jones potential is
|
|
shifted at its cutoff to 0.0. If so, this adds an energy term to each
|
|
pairwise interaction which will be included in the thermodynamic
|
|
output, but does not affect pair forces or atom trajectories. See the
|
|
doc page for individual pair styles to see which ones support this
|
|
option.</p>
|
|
<p>The <em>table</em> and <em>table/disp</em> keywords apply to pair styles with a
|
|
long-range Coulombic term or long-range dispersion term respectively;
|
|
see the doc page for individual styles to see which potentials support
|
|
these options. If N is non-zero, a table of length 2^N is
|
|
pre-computed for forces and energies, which can shrink their
|
|
computational cost by up to a factor of 2. The table is indexed via a
|
|
bit-mapping technique <a class="reference internal" href="pair_table_rx.html#wolff"><span class="std std-ref">(Wolff)</span></a> and a linear interpolation is
|
|
performed between adjacent table values. In our experiments with
|
|
different table styles (lookup, linear, spline), this method typically
|
|
gave the best performance in terms of speed and accuracy.</p>
|
|
<p>The choice of table length is a tradeoff in accuracy versus speed. A
|
|
larger N yields more accurate force computations, but requires more
|
|
memory which can slow down the computation due to cache misses. A
|
|
reasonable value of N is between 8 and 16. The default value of 12
|
|
(table of length 4096) gives approximately the same accuracy as the
|
|
no-table (N = 0) option. For N = 0, forces and energies are computed
|
|
directly, using a polynomial fit for the needed erfc() function
|
|
evaluation, which is what earlier versions of LAMMPS did. Values
|
|
greater than 16 typically slow down the simulation and will not
|
|
improve accuracy; values from 1 to 8 give unreliable results.</p>
|
|
<p>The <em>tabinner</em> and <em>tabinner/disp</em> keywords set an inner cutoff above
|
|
which the pairwise computation is done by table lookup (if tables are
|
|
invoked), for the corresponding Coulombic and dispersion tables
|
|
discussed with the <em>table</em> and <em>table/disp</em> keywords. The smaller the
|
|
cutoff is set, the less accurate the table becomes (for a given number
|
|
of table values), which can require use of larger tables. The default
|
|
cutoff value is sqrt(2.0) distance units which means nearly all
|
|
pairwise interactions are computed via table lookup for simulations
|
|
with “real” units, but some close pairs may be computed directly
|
|
(non-table) for simulations with “lj” units.</p>
|
|
<p>When the <em>tail</em> keyword is set to <em>yes</em>, certain pair styles will add
|
|
a long-range VanderWaals tail “correction” to the energy and pressure.
|
|
These corrections are bookkeeping terms which do not affect dynamics,
|
|
unless a constant-pressure simulation is being performed. See the doc
|
|
page for individual styles to see which support this option. These
|
|
corrections are included in the calculation and printing of
|
|
thermodynamic quantities (see the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a>
|
|
command). Their effect will also be included in constant NPT or NPH
|
|
simulations where the pressure influences the simulation box
|
|
dimensions (e.g. the <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a> and <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>
|
|
commands). The formulas used for the long-range corrections come from
|
|
equation 5 of <a class="reference internal" href="#sun"><span class="std std-ref">(Sun)</span></a>.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">The tail correction terms are computed at the beginning of each
|
|
run, using the current atom counts of each atom type. If atoms are
|
|
deleted (or lost) or created during a simulation, e.g. via the <a class="reference internal" href="fix_gcmc.html"><span class="doc">fix gcmc</span></a> command, the correction factors are not
|
|
re-computed. If you expect the counts to change dramatically, you can
|
|
break a run into a series of shorter runs so that the correction
|
|
factors are re-computed more frequently.</p>
|
|
</div>
|
|
<p>Several additional assumptions are inherent in using tail corrections,
|
|
including the following:</p>
|
|
<ul>
|
|
<li><p class="first">The simulated system is a 3d bulk homogeneous liquid. This option
|
|
should not be used for systems that are non-liquid, 2d, have a slab
|
|
geometry (only 2d periodic), or inhomogeneous.</p>
|
|
</li>
|
|
<li><p class="first">G(r), the radial distribution function (rdf), is unity beyond the
|
|
cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an
|
|
LJ fluid), and it is probably a good idea to verify this assumption by
|
|
checking the rdf. The rdf is not exactly unity beyond the cutoff for
|
|
each pair of interaction types, so the tail correction is necessarily
|
|
an approximation.</p>
|
|
<p>The tail corrections are computed at the beginning of each simulation
|
|
run. If the number of atoms changes during the run, e.g. due to atoms
|
|
leaving the simulation domain, or use of the <a class="reference internal" href="fix_gcmc.html"><span class="doc">fix gcmc</span></a>
|
|
command, then the corrections are not updates to relect the changed
|
|
atom count. If this is a large effect in your simulation, you should
|
|
break the long run into several short runs, so that the correction
|
|
factors are re-computed multiple times.</p>
|
|
</li>
|
|
<li><p class="first">Thermophysical properties obtained from calculations with this option
|
|
enabled will not be thermodynamically consistent with the truncated
|
|
force-field that was used. In other words, atoms do not feel any LJ
|
|
pair interactions beyond the cutoff, but the energy and pressure
|
|
reported by the simulation include an estimated contribution from
|
|
those interactions.</p>
|
|
</li>
|
|
</ul>
|
|
<p>The <em>compute</em> keyword allows pairwise computations to be turned off,
|
|
even though a <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> is defined. This is not
|
|
useful for running a real simulation, but can be useful for debugging
|
|
purposes or for performing a <a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a> simulation, when you
|
|
only wish to compute partial forces that do not include the pairwise
|
|
contribution.</p>
|
|
<p>Two examples are as follows. First, this option allows you to perform
|
|
a simulation with <a class="reference internal" href="pair_hybrid.html"><span class="doc">pair_style hybrid</span></a> with only a
|
|
subset of the hybrid sub-styles enabled. Second, this option allows
|
|
you to perform a simulation with only long-range interactions but no
|
|
short-range pairwise interactions. Doing this by simply not defining
|
|
a pair style will not work, because the
|
|
<a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> command requires a Kspace-compatible
|
|
pair style be defined.</p>
|
|
<hr class="docutils" />
|
|
<p>The <em>special</em> keyword allows to override the 1-2, 1-3, and 1-4
|
|
exclusion settings for individual sub-styles of a
|
|
<a class="reference internal" href="pair_hybrid.html"><span class="doc">hybrid pair style</span></a>. It requires 4 arguments similar
|
|
to the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command, <em>which</em> and
|
|
wt1,wt2,wt3. The <em>which</em> argument can be <em>lj</em> to change the
|
|
Lennard-Jones settings, <em>coul</em> to change the Coulombic settings,
|
|
or <em>lj/coul</em> to change both to the same set of 3 values. The wt1,wt2,wt3
|
|
values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
|
|
1-3, and 1-4 bond topology neighbors, respectively. The <em>special</em>
|
|
keyword can only be used in conjunction with the <em>pair</em> keyword
|
|
and has to directly follow it.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">The global settings specified by the
|
|
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command affect the construction of
|
|
neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
|
|
exclude those pairs from the neighbor list entirely. Weights of 1.0
|
|
store the neighbor with no weighting applied. Thus only global values
|
|
different from exactly 0.0 or 1.0 can be overridden and an error is
|
|
generated if the requested setting is not compatible with the global
|
|
setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is
|
|
usually a sufficient workaround in this case without causing a
|
|
significant error.</p>
|
|
</div>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<blockquote>
|
|
<div>none</div></blockquote>
|
|
<p>You cannot use <em>shift</em> yes with <em>tail</em> yes, since those are
|
|
conflicting options. You cannot use <em>tail</em> yes with 2d simulations.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</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="thermo_style.html"><span class="doc">thermo_style</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The option defaults are mix = geometric, shift = no, table = 12,
|
|
tabinner = sqrt(2.0), tail = no, and compute = yes.</p>
|
|
<p>Note that some pair styles perform mixing, but only a certain style of
|
|
mixing. See the doc pages for individual pair styles for details.</p>
|
|
<hr class="docutils" />
|
|
<p id="wolff"><strong>(Wolff)</strong> Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).</p>
|
|
<p id="sun"><strong>(Sun)</strong> Sun, J Phys Chem B, 102, 7338-7364 (1998).</p>
|
|
</div>
|
|
</div>
|
|
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<a href="pair_style.html" class="btn btn-neutral float-right" title="pair_style command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
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<a href="pair_coeff.html" class="btn btn-neutral" title="pair_coeff command" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
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