forked from lijiext/lammps
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176 lines
7.2 KiB
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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>mix</I> value = <I>geometric</I> or <I>arithmetic</I> or <I>sixthpower</I>
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<I>shift</I> value = <I>yes</I> or <I>no</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>mix</I> keyword affects pair coefficients for interactions between
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atoms of type I and J, when I != J and the coefficients are not
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explicity set in the input script. Note that coefficients for I = J
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must be set explicitly, either in the input script via the
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"pair_coeff" command or in the "Pair Coeffs" section of the <A HREF = "read_data.html">data
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file</A>. For some pair styles is is not necessary to
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specify coefficients when I != J, since a "mixing" rule will create
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them from the I,I and J,J settings. The pair_modify <I>mix</I> value
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determines what formulas are used to compute the mixed coefficients.
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In each case, the cutoff distance is mixed the same way as sigma.
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</P>
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<P>Note that not all pair styles support mixing. Also, some mix options
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are not available for certain pair styles. See the doc page for
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individual pair styles for those restrictions. Note also that the
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<A HREF = "pair_coeff.html">pair_coeff</A> command also can be to directly set
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coefficients for a specific I != J pairing, in which case no mixing is
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performed.
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</P>
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<P>mix <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>mix <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>mix <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>The <I>shift</I> keyword determines whether a 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 included in the thermodynamic
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output, but does not affect pair forces or atom trajectories. See the
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doc page for individual pair styles to see which ones support this
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option.
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</P>
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<P>The <I>table</I> keyword applies to pair styles with a long-range Coulombic
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term; see the doc page for individual styles to see which potentials
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support this option. If N is non-zero, a table of length 2^N is
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pre-computed for forces and energies, which can shrink their
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computational cost by up to a factor of 2. The table is indexed via a
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bit-mapping technique <A HREF = "#Wolff">(Wolff)</A> and a linear interpolation is
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performed between adjacent table values. In our experiments with
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different table styles (lookup, linear, spline), this method typically
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gave the best performance in terms of speed and 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>, certain pair styles will add
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a long-range VanderWaals tail "correction" to the energy and pressure.
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See the doc page for individual styles to see which support this
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option. These corrections are included in the calculation and
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printing of thermodynamic quantities (see the
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<A HREF = "thermo_style.html">thermo_style</A> command). Their effect will also be
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included in constant NPT or NPH simulations where the pressure
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influences the simulation box dimensions (e.g. the <A HREF = "fix_npt.html">fix
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npt</A> and <A HREF = "fix_nph.html">fix nph</A> commands). The formulas
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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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<P>You cannot use <I>shift</I> yes with <I>tail</I> yes, since those are
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conflicting options. 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 mix = geometric, shift = no, table = 12,
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tabinner = sqrt(2.0), tail = no.
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</P>
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<P>Note that some pair styles perform mixing, but only a certain style of
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mixing. See the doc pages for individual pair styles for details.
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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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