2006-09-22 00:22:34 +08:00
|
|
|
<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>
|
|
|
|
|
</CENTER>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<H3>pair_modify command
|
|
|
|
|
</H3>
|
|
|
|
|
<P><B>Syntax:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>pair_modify keyword value ...
|
|
|
|
|
</PRE>
|
|
|
|
|
<UL><LI>one or more keyword/value pairs may be listed
|
|
|
|
|
|
|
|
|
|
<LI>keyword = <I>shift</I> or <I>mix</I> or <I>table</I> or <I>tabinner</I> or <I>tail</I>
|
|
|
|
|
|
2007-06-25 22:36:36 +08:00
|
|
|
<PRE> <I>mix</I> value = <I>geometric</I> or <I>arithmetic</I> or <I>sixthpower</I>
|
|
|
|
|
<I>shift</I> value = <I>yes</I> or <I>no</I>
|
2006-09-22 00:22:34 +08:00
|
|
|
<I>table</I> value = N
|
|
|
|
|
2^N = # of values in table
|
|
|
|
|
<I>tabinner</I> value = cutoff
|
|
|
|
|
cutoff = inner cutoff at which to begin table (distance units)
|
|
|
|
|
<I>tail</I> value = <I>yes</I> or <I>no</I>
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>pair_modify shift yes mix geometric
|
|
|
|
|
pair_modify tail yes
|
|
|
|
|
pair_modify table 12
|
|
|
|
|
</PRE>
|
|
|
|
|
<P><B>Description:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>Modify the parameters of the currently defined pair style. Not all
|
|
|
|
|
parameters are relevant to all pair styles.
|
|
|
|
|
</P>
|
2007-06-25 22:36:36 +08:00
|
|
|
<P>The <I>mix</I> keyword affects pair coefficients for interactions between
|
|
|
|
|
atoms of type I and J, when I != J and the coefficients are not
|
2008-03-01 09:13:20 +08:00
|
|
|
explicitly set in the input script. Note that coefficients for I = J
|
2007-06-25 22:36:36 +08:00
|
|
|
must be set explicitly, either in the input script via the
|
|
|
|
|
"pair_coeff" command or in the "Pair Coeffs" section of the <A HREF = "read_data.html">data
|
2010-04-15 23:06:47 +08:00
|
|
|
file</A>. For some pair styles it is not necessary to
|
2007-06-25 22:36:36 +08:00
|
|
|
specify coefficients when I != J, since a "mixing" rule will create
|
|
|
|
|
them from the I,I and J,J settings. The pair_modify <I>mix</I> 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 HREF = "pair_coeff.html">pair_coeff</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 <I>geometric</I>
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<PRE>epsilon_ij = sqrt(epsilon_i * epsilon_j)
|
|
|
|
|
sigma_ij = sqrt(sigma_i * sigma_j)
|
|
|
|
|
</PRE>
|
2007-06-25 22:36:36 +08:00
|
|
|
<P>mix <I>arithmetic</I>
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<PRE>epsilon_ij = sqrt(epsilon_i * epsilon_j)
|
|
|
|
|
sigma_ij = (sigma_i + sigma_j) / 2
|
|
|
|
|
</PRE>
|
2007-06-25 22:36:36 +08:00
|
|
|
<P>mix <I>sixthpower</I>
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<PRE>epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
|
|
|
|
|
(sigma_i^6 + sigma_j^6)
|
2007-04-20 07:25:27 +08:00
|
|
|
sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
|
2006-09-22 00:22:34 +08:00
|
|
|
</PRE>
|
2007-06-25 22:36:36 +08:00
|
|
|
<P>The <I>shift</I> 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>
|
2006-09-22 00:22:34 +08:00
|
|
|
<P>The <I>table</I> keyword applies to pair styles with a long-range Coulombic
|
2007-06-25 22:36:36 +08:00
|
|
|
term; see the doc page for individual styles to see which potentials
|
|
|
|
|
support this option. 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 HREF = "#Wolff">(Wolff)</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.
|
2006-09-22 00:22:34 +08:00
|
|
|
</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 <I>tabinner</I> keyword sets an inner cutoff above which the pairwise
|
|
|
|
|
computation is done by table lookup (if tables are invoked). The
|
|
|
|
|
smaller this value 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>
|
2007-06-25 22:36:36 +08:00
|
|
|
<P>When the <I>tail</I> keyword is set to <I>yes</I>, certain pair styles will add
|
|
|
|
|
a long-range VanderWaals tail "correction" to the energy and pressure.
|
|
|
|
|
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 HREF = "thermo_style.html">thermo_style</A> command). Their effect will also be
|
|
|
|
|
included in constant NPT or NPH simulations where the pressure
|
2010-04-03 00:51:06 +08:00
|
|
|
influences the simulation box dimensions (e.g. the <A HREF = "fix_nh.html">fix
|
|
|
|
|
npt</A> and <A HREF = "fix_nh.html">fix nph</A> commands). The formulas
|
2007-06-25 22:36:36 +08:00
|
|
|
used for the long-range corrections come from equation 5 of
|
2006-09-22 00:22:34 +08:00
|
|
|
<A HREF = "#Sun">(Sun)</A>.
|
|
|
|
|
</P>
|
|
|
|
|
<P>Several assumptions are inherent in using tail corrections, including
|
|
|
|
|
the following:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>The simulated system is a 3d bulk homogeneous liquid. This option
|
|
|
|
|
should not be used for systems that are non-liquid, 2d, have a slab
|
|
|
|
|
geometry (only 2d periodic), or inhomogeneous.
|
|
|
|
|
|
|
|
|
|
<LI>G(r), the radial distribution function (rdf), is unity beyond the
|
|
|
|
|
cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an
|
|
|
|
|
LJ fluid), and it is probably a good idea to verify this assumption by
|
|
|
|
|
checking the rdf. The rdf is not exactly unity beyond the cutoff for
|
|
|
|
|
each pair of interaction types, so the tail correction is necessarily
|
|
|
|
|
an approximation.
|
|
|
|
|
|
|
|
|
|
<LI>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.
|
|
|
|
|
</UL>
|
|
|
|
|
<P><B>Restrictions:</B> none
|
|
|
|
|
</P>
|
|
|
|
|
<P>You cannot use <I>shift</I> yes with <I>tail</I> yes, since those are
|
2007-06-25 22:36:36 +08:00
|
|
|
conflicting options. You cannot use <I>tail</I> yes with 2d simulations.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_coeff.html">pair_coeff</A>,
|
|
|
|
|
<A HREF = "thermo_style.html">thermo_style</A>
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B>
|
|
|
|
|
</P>
|
2007-06-25 22:36:36 +08:00
|
|
|
<P>The option defaults are mix = geometric, shift = no, table = 12,
|
|
|
|
|
tabinner = sqrt(2.0), tail = no.
|
|
|
|
|
</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.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<A NAME = "Wolff"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Wolff)</B> Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).
|
|
|
|
|
</P>
|
|
|
|
|
<A NAME = "Sun"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Sun)</B> Sun, J Phys Chem B, 102, 7338-7364 (1998).
|
|
|
|
|
</P>
|
|
|
|
|
</HTML>
|
