2006-09-22 00:22:34 +08:00
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<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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<HR>
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<H3>pair_modify command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_modify keyword value ...
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</PRE>
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<UL><LI>one or more keyword/value pairs may be listed
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<LI>keyword = <I>shift</I> or <I>mix</I> or <I>table</I> or <I>tabinner</I> or <I>tail</I>
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<PRE> <I>shift</I> value = <I>yes</I> or <I>no</I>
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<I>mix</I> value = <I>geometric</I> or <I>arithmetic</I> or <I>sixthpower</I>
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<I>table</I> value = N
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2^N = # of values in table
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<I>tabinner</I> value = cutoff
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cutoff = inner cutoff at which to begin table (distance units)
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<I>tail</I> value = <I>yes</I> or <I>no</I>
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_modify shift yes mix geometric
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pair_modify tail yes
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pair_modify table 12
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Modify the parameters of the currently defined pair style. Not all
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parameters are relevant to all pair styles.
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</P>
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<P>The <I>shift</I> keyword determines whether the Lennard-Jones potential is
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shifted at its cutoff to 0.0. If so, this adds an energy term to each
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pairwise interaction which will be printed in the thermodynamic
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output, but does not affect atom dynamics (forces). Pair styles that
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are already 0.0 at their cutoff such as <I>lj/charmm/coul/charmm</I> are
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not affected by this setting.
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</P>
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<P>The <I>mix</I> keyword affects how Lennard-Jones coefficients for epsilon
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and sigma are generated for interactions between atoms of type I and
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J, when I != J. (I = J coefficients are set explicitly in the data
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file or input script.) The <A HREF = "pair_coeff.html">pair_coeff</A> command can
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be used in the input script to specify epilon/sigma for a specific I,J
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pairing, which overrides the setting of the <I>mix</I> keyword. In each
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case, the LJ cutoff is mixed the same way as sigma.
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</P>
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<P>These are the formulas used by the 3 <I>mix</I> options:
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</P>
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<P><I>geometric</I>
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</P>
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<PRE>epsilon_ij = sqrt(epsilon_i * epsilon_j)
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sigma_ij = sqrt(sigma_i * sigma_j)
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</PRE>
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<P><I>arithmetic</I>
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</P>
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<PRE>epsilon_ij = sqrt(epsilon_i * epsilon_j)
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sigma_ij = (sigma_i + sigma_j) / 2
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</PRE>
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<P><I>sixthpower</I>
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</P>
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<PRE>epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
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(sigma_i^6 + sigma_j^6)
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sigma_ij= ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
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</PRE>
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<P>Style <I>soft</I> only uses a pre-factor coefficient, which is always mixed
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geometrically, regardless of the <I>mix</I> setting. The <I>charmm</I> styles
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are always mixed arithmetically, regardless of the <I>mix</I> setting. The
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<I>class2</I> styles are always mixed as a sixthpower, regardless of the
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<I>mix</I> setting, except that the cutoff is mixed according to the mix
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setting. Style <I>lj/expand</I> always mixes its delta coefficient using
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the rule
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</P>
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<PRE>delta_ij = (delta_i + delta_j) / 2
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</PRE>
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<P>The <I>table</I> keyword applies to pair styles with a long-range Coulombic
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term (lj/cut/coul/long and lj/charmm/coul/long). If N is non-zero, a
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table of length 2^N is pre-computed for forces and energies, which can
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shrink their computational cost by up to a factor of 2. The table is
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indexed via a bit-mapping technique <A HREF = "#Wolff">(Wolff)</A> and a linear
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interpolation is performed between adjacent table values. In our
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experiments with different table styles (lookup, linear, spline), this
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method typically gave the best performance in terms of speed and
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accuracy.
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</P>
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<P>The choice of table length is a tradeoff in accuracy versus speed. A
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larger N yields more accurate force computations, but requires more
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memory which can slow down the computation due to cache misses. A
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reasonable value of N is between 8 and 16. The default value of 12
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(table of length 4096) gives approximately the same accuracy as the
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no-table (N = 0) option. For N = 0, forces and energies are computed
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directly, using a polynomial fit for the needed erfc() function
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evaluation, which is what earlier versions of LAMMPS did. Values
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greater than 16 typically slow down the simulation and will not
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improve accuracy; values from 1 to 8 give unreliable results.
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</P>
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<P>The <I>tabinner</I> keyword sets an inner cutoff above which the pairwise
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computation is done by table lookup (if tables are invoked). The
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smaller this value is set, the less accurate the table becomes (for a
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given number of table values), which can require use of larger tables.
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The default cutoff value is sqrt(2.0) distance units which means
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nearly all pairwise interactions are computed via table lookup for
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simulations with "real" units, but some close pairs may be computed
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directly (non-table) for simulations with "lj" units.
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</P>
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<P>When the <I>tail</I> keyword is set to <I>yes</I>, long-range VanderWaals tail
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"corrections" are added to the energy and pressure. These are
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included in the calculation and printing of thermodynamic quantities
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(see the <A HREF = "thermo_style.html">thermo_style</A> command). Their effect will
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also be included in constant NPT or NPH simulations where the pressure
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influences the simulation box dimensions (see the <A HREF = "fix_npt.html">fix
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npt</A> and <A HREF = "fix_nph.html">fix nph</A> commands).
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</P>
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<P>The <I>tail</I> keyword is only supported by <A HREF = "pair_style.html">pair_style</A>
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pairwise potentials which include Lennard-Jones interactions which are
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cutoff at a non-zero energy. This does not include the LJ CHARMM
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potentials or <I>lj/smooth</I> since they go to zero at the cutoff. The
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formulas used for the long-range corrections come from equation 5 of
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<A HREF = "#Sun">(Sun)</A>.
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</P>
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<P>Several assumptions are inherent in using tail corrections, including
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the following:
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</P>
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<UL><LI>The simulated system is a 3d bulk homogeneous liquid. This option
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should not be used for systems that are non-liquid, 2d, have a slab
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geometry (only 2d periodic), or inhomogeneous.
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<LI>G(r), the radial distribution function (rdf), is unity beyond the
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cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an
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LJ fluid), and it is probably a good idea to verify this assumption by
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checking the rdf. The rdf is not exactly unity beyond the cutoff for
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each pair of interaction types, so the tail correction is necessarily
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an approximation.
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<LI>Thermophysical properties obtained from calculations with this option
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enabled will not be thermodynamically consistent with the truncated
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force-field that was used. In other words, atoms do not feel any LJ
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pair interactions beyond the cutoff, but the energy and pressure
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reported by the simulation include an estimated contribution from
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those interactions.
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</UL>
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<P><B>Restrictions:</B> none
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</P>
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2006-09-28 03:12:31 +08:00
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<P>Not all pair styles support mixing. See the doc page for individual
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pair styles for details.
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</P>
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2006-09-22 00:22:34 +08:00
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<P>You cannot use <I>shift</I> yes with <I>tail</I> yes, since those are
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conflicting options.
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</P>
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<P>You cannot use <I>tail</I> yes with 2d simulations.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_coeff.html">pair_coeff</A>,
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<A HREF = "thermo_style.html">thermo_style</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are shift = no, mix = arithmetic (for lj/charmm
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pair styles), mix = geometric (for other pair styles), table = 12,
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and tabinner = sqrt(2.0), tail = no.
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</P>
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<HR>
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<A NAME = "Wolff"></A>
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<P><B>(Wolff)</B> Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).
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</P>
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<A NAME = "Sun"></A>
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<P><B>(Sun)</B> Sun, J Phys Chem B, 102, 7338-7364 (1998).
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</P>
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</HTML>
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