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_style table command
|
|
|
|
|
</H3>
|
2012-01-26 00:00:02 +08:00
|
|
|
<H3>pair_style table/gpu command
|
|
|
|
|
</H3>
|
2011-10-07 01:32:51 +08:00
|
|
|
<H3>pair_style table/omp command
|
|
|
|
|
</H3>
|
2006-09-22 00:22:34 +08:00
|
|
|
<P><B>Syntax:</B>
|
|
|
|
|
</P>
|
2013-04-24 06:19:03 +08:00
|
|
|
<PRE>pair_style table style N keyword ...
|
2006-09-22 00:22:34 +08:00
|
|
|
</PRE>
|
|
|
|
|
<UL><LI>style = <I>lookup</I> or <I>linear</I> or <I>spline</I> or <I>bitmap</I> = method of interpolation
|
|
|
|
|
<LI>N = use N values in <I>lookup</I>, <I>linear</I>, <I>spline</I> tables
|
2013-04-24 06:19:03 +08:00
|
|
|
<LI>N = use 2^N values in <I>bitmap</I> tables
|
|
|
|
|
<LI>zero or more keywords may be appended
|
|
|
|
|
<LI>keyword = <I>ewald</I> or <I>pppm</I> or <I>msm</I> or <I>dispersion</I> or <I>tip4p</I>
|
2006-09-22 00:22:34 +08:00
|
|
|
</UL>
|
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>pair_style table linear 1000
|
2013-04-24 06:19:03 +08:00
|
|
|
pair_style table linear 1000 pppm
|
2006-09-22 00:22:34 +08:00
|
|
|
pair_style table bitmap 12
|
|
|
|
|
pair_coeff * 3 morse.table ENTRY1
|
|
|
|
|
pair_coeff * 3 morse.table ENTRY1 7.0
|
|
|
|
|
</PRE>
|
|
|
|
|
<P><B>Description:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>Style <I>table</I> creates interpolation tables of length <I>N</I> from pair
|
|
|
|
|
potential and force values listed in a file(s) as a function of
|
|
|
|
|
distance. The files are read by the <A HREF = "pair_coeff.html">pair_coeff</A>
|
|
|
|
|
command.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The interpolation tables are created by fitting cubic splines to the
|
|
|
|
|
file values and interpolating energy and force values at each of <I>N</I>
|
|
|
|
|
distances. During a simulation, these tables are used to interpolate
|
|
|
|
|
energy and force values as needed. The interpolation is done in one
|
|
|
|
|
of 4 styles: <I>lookup</I>, <I>linear</I>, <I>spline</I>, or <I>bitmap</I>.
|
|
|
|
|
</P>
|
|
|
|
|
<P>For the <I>lookup</I> style, the distance between 2 atoms is used to find
|
|
|
|
|
the nearest table entry, which is the energy or force.
|
|
|
|
|
</P>
|
2009-08-11 04:13:44 +08:00
|
|
|
<P>For the <I>linear</I> style, the pair distance is used to find 2
|
|
|
|
|
surrounding table values from which an energy or force is computed by
|
|
|
|
|
linear interpolation.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P>For the <I>spline</I> style, a cubic spline coefficients are computed and
|
2009-08-11 04:13:44 +08:00
|
|
|
stored at each of the <I>N</I> values in the table. The pair distance is
|
|
|
|
|
used to find the appropriate set of coefficients which are used to
|
|
|
|
|
evaluate a cubic polynomial which computes the energy or force.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P>For the <I>bitmap</I> style, the N means to create interpolation tables
|
2009-08-11 04:13:44 +08:00
|
|
|
that are 2^N in length. <The pair distance is used to index into the
|
2006-09-22 00:22:34 +08:00
|
|
|
table via a fast bit-mapping technique <A HREF = "#Wolff">(Wolff)</A> and a linear
|
|
|
|
|
interpolation is performed between adjacent table values.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The following coefficients must be defined for each pair of atoms
|
|
|
|
|
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
|
2009-08-11 04:13:44 +08:00
|
|
|
above.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<UL><LI>filename
|
|
|
|
|
<LI>keyword
|
|
|
|
|
<LI>cutoff (distance units)
|
|
|
|
|
</UL>
|
|
|
|
|
<P>The filename specifies a file containing tabulated energy and force
|
|
|
|
|
values. The keyword specifies a section of the file. The cutoff is
|
|
|
|
|
an optional coefficient. If not specified, the outer cutoff in the
|
|
|
|
|
table itself (see below) will be used to build an interpolation table
|
2008-03-01 09:13:20 +08:00
|
|
|
that extend to the largest tabulated distance. If specified, only
|
2006-09-22 00:22:34 +08:00
|
|
|
file values up to the cutoff are used to create the interpolation
|
2008-04-03 07:05:25 +08:00
|
|
|
table. The format of this file is described below.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2013-04-24 06:19:03 +08:00
|
|
|
<P>If your tabulated potential(s) are designed to be used as the
|
|
|
|
|
short-range part of one of the long-range solvers specified by the
|
|
|
|
|
<A HREF = "kspace_style.html">kspace_style</A> command, then you must use one or
|
|
|
|
|
more of the optional keywords listed above for the pair_style command.
|
|
|
|
|
These are <I>ewald</I> or <I>pppm</I> or <I>msm</I> or <I>dispersion</I> or <I>tip4p</I>. This
|
|
|
|
|
is so LAMMPS can insure the short-range potential and long-range
|
|
|
|
|
solver are compatible with each other, as it does for other
|
|
|
|
|
short-range pair styles, such as <A HREF = "pair_lj.html">pair_style
|
|
|
|
|
lj/cut/coul/long</A>. Note that it is up to you to insure
|
|
|
|
|
the tabulated values for each pair of atom types has the correct
|
|
|
|
|
functional form to be compatible with the matching long-range solver.
|
|
|
|
|
</P>
|
2008-04-03 07:05:25 +08:00
|
|
|
<HR>
|
|
|
|
|
|
2008-04-03 07:07:12 +08:00
|
|
|
<P>Here are some guidelines for using the pair_style table command to
|
|
|
|
|
best effect:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>Vary the number of table points; you may need to use more than you think
|
2008-04-03 07:05:25 +08:00
|
|
|
to get good resolution.
|
|
|
|
|
|
|
|
|
|
<LI>Always use the <A HREF = "pair_write.html">pair_write</A> command to produce a plot
|
|
|
|
|
of what the final interpolated potential looks like. This can show up
|
2008-04-03 07:07:12 +08:00
|
|
|
interpolation "features" you may not like.
|
2008-04-03 07:05:25 +08:00
|
|
|
|
|
|
|
|
<LI>Start with the linear style; it's the style least likely to have problems.
|
|
|
|
|
|
2009-08-11 04:13:44 +08:00
|
|
|
<LI>Use <I>N</I> in the pair_style command equal to the "N" in the tabulation
|
2010-04-15 05:45:05 +08:00
|
|
|
file, and use the "RSQ" or "BITMAP" parameter, so additional interpolation
|
|
|
|
|
is not needed. See discussion below.
|
2009-08-11 04:13:44 +08:00
|
|
|
|
2012-04-11 01:11:48 +08:00
|
|
|
<LI>Make sure that your tabulated forces and tabulated energies are consistent
|
|
|
|
|
(dE/dr = -F) along the entire range of r values.
|
|
|
|
|
|
2008-04-03 07:05:25 +08:00
|
|
|
<LI>Use as large an inner cutoff as possible. This avoids fitting splines
|
|
|
|
|
to very steep parts of the potential.
|
2008-04-03 07:07:12 +08:00
|
|
|
</UL>
|
2008-04-03 07:05:25 +08:00
|
|
|
<HR>
|
|
|
|
|
|
2006-09-22 00:22:34 +08:00
|
|
|
<P>The format of a tabulated file is as follows (without the
|
|
|
|
|
parenthesized comments):
|
|
|
|
|
</P>
|
|
|
|
|
<PRE># Morse potential for Fe (one or more comment or blank lines)
|
|
|
|
|
</PRE>
|
|
|
|
|
<PRE>MORSE_FE (keyword is first text on line)
|
|
|
|
|
N 500 R 1.0 10.0 (N, R, RSQ, BITMAP, FPRIME parameters)
|
|
|
|
|
(blank)
|
|
|
|
|
1 1.0 25.5 102.34 (index, r, energy, force)
|
|
|
|
|
2 1.02 23.4 98.5
|
|
|
|
|
...
|
|
|
|
|
500 10.0 0.001 0.003
|
|
|
|
|
</PRE>
|
|
|
|
|
<P>A section begins with a non-blank line whose 1st character is not a
|
|
|
|
|
"#"; blank lines or lines starting with "#" can be used as comments
|
|
|
|
|
between sections. The first line begins with a keyword which
|
|
|
|
|
identifies the section. The line can contain additional text, but the
|
|
|
|
|
initial text must match the argument specified in the pair_coeff
|
|
|
|
|
command. The next line lists (in any order) one or more parameters
|
|
|
|
|
for the table. Each parameter is a keyword followed by one or more
|
|
|
|
|
numeric values.
|
|
|
|
|
</P>
|
2009-08-11 04:13:44 +08:00
|
|
|
<P>The parameter "N" is required and its value is the number of table
|
|
|
|
|
entries that follow. Note that this may be different than the <I>N</I>
|
|
|
|
|
specified in the <A HREF = "pair_style.html">pair_style table</A> command. Let
|
|
|
|
|
Ntable = <I>N</I> in the pair_style command, and Nfile = "N" in the
|
|
|
|
|
tabulated file. What LAMMPS does is a preliminary interpolation by
|
|
|
|
|
creating splines using the Nfile tabulated values as nodal points. It
|
|
|
|
|
uses these to interpolate as needed to generate energy and force
|
|
|
|
|
values at Ntable different points. The resulting tables of length
|
|
|
|
|
Ntable are then used as described above, when computing energy and
|
|
|
|
|
force for individual pair distances. This means that if you want the
|
|
|
|
|
interpolation tables of length Ntable to match exactly what is in the
|
|
|
|
|
tabulated file (with effectively no preliminary interpolation), you
|
2010-04-15 05:45:05 +08:00
|
|
|
should set Ntable = Nfile, and use the "RSQ" or "BITMAP" parameter.
|
2012-04-11 01:11:48 +08:00
|
|
|
The internal table abscissa is RSQ (separation distance squared).
|
2009-08-11 04:13:44 +08:00
|
|
|
</P>
|
|
|
|
|
<P>All other parameters are optional. If "R" or "RSQ" or "BITMAP" does
|
|
|
|
|
not appear, then the distances in each line of the table are used
|
|
|
|
|
as-is to perform spline interpolation. In this case, the table values
|
|
|
|
|
can be spaced in <I>r</I> uniformly or however you wish to position table
|
|
|
|
|
values in regions of large gradients.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P>If used, the parameters "R" or "RSQ" are followed by 2 values <I>rlo</I>
|
|
|
|
|
and <I>rhi</I>. If specified, the distance associated with each energy and
|
|
|
|
|
force value is computed from these 2 values (at high accuracy), rather
|
|
|
|
|
than using the (low-accuracy) value listed in each line of the table.
|
2012-04-11 01:11:48 +08:00
|
|
|
The distance values in the table file are ignored in this case.
|
2006-09-22 00:22:34 +08:00
|
|
|
For "R", distances uniformly spaced between <I>rlo</I> and <I>rhi</I> are
|
|
|
|
|
computed; for "RSQ", squared distances uniformly spaced between
|
|
|
|
|
<I>rlo*rlo</I> and <I>rhi*rhi</I> are computed.
|
|
|
|
|
</P>
|
|
|
|
|
<P>If used, the parameter "BITMAP" is also followed by 2 values <I>rlo</I> and
|
|
|
|
|
<I>rhi</I>. These values, along with the "N" value determine the ordering
|
|
|
|
|
of the N lines that follow and what distance is associated with each.
|
|
|
|
|
This ordering is complex, so it is not documented here, since this
|
|
|
|
|
file is typically produced by the <A HREF = "pair_write.html">pair_write</A> command
|
|
|
|
|
with its <I>bitmap</I> option. When the table is in BITMAP format, the "N"
|
|
|
|
|
parameter in the file must be equal to 2^M where M is the value
|
|
|
|
|
specified in the pair_style command. Also, a cutoff parameter cannot
|
|
|
|
|
be used as an optional 3rd argument in the pair_coeff command; the
|
|
|
|
|
entire table extent as specified in the file must be used.
|
|
|
|
|
</P>
|
|
|
|
|
<P>If used, the parameter "FPRIME" is followed by 2 values <I>fplo</I> and
|
|
|
|
|
<I>fphi</I> which are the derivative of the force at the innermost and
|
|
|
|
|
outermost distances listed in the table. These values are needed by
|
|
|
|
|
the spline construction routines. If not specified by the "FPRIME"
|
|
|
|
|
parameter, they are estimated (less accurately) by the first 2 and
|
|
|
|
|
last 2 force values in the table. This parameter is not used by
|
|
|
|
|
BITMAP tables.
|
|
|
|
|
</P>
|
|
|
|
|
<P>Following a blank line, the next N lines list the tabulated values.
|
|
|
|
|
On each line, the 1st value is the index from 1 to N, the 2nd value is
|
|
|
|
|
r (in distance units), the 3rd value is the energy (in energy units),
|
|
|
|
|
and the 4th is the force (in force units). The r values must increase
|
|
|
|
|
from one line to the next (unless the BITMAP parameter is specified).
|
|
|
|
|
</P>
|
|
|
|
|
<P>Note that one file can contain many sections, each with a tabulated
|
|
|
|
|
potential. LAMMPS reads the file section by section until it finds
|
|
|
|
|
one that matches the specified keyword.
|
|
|
|
|
</P>
|
2007-06-26 08:03:39 +08:00
|
|
|
<HR>
|
|
|
|
|
|
2011-12-14 04:35:35 +08:00
|
|
|
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally
|
|
|
|
|
the same as the corresponding style without the suffix. They have
|
|
|
|
|
been optimized to run faster, depending on your available hardware, as
|
|
|
|
|
discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A> of the
|
|
|
|
|
manual. The accelerated styles take the same arguments and should
|
|
|
|
|
produce the same results, except for round-off and precision issues.
|
2011-10-07 01:32:51 +08:00
|
|
|
</P>
|
|
|
|
|
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
|
|
|
|
|
packages, respectively. They are only enabled if LAMMPS was built with
|
|
|
|
|
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
|
|
|
|
|
section for more info.
|
|
|
|
|
</P>
|
|
|
|
|
<P>You can specify the accelerated styles explicitly in your input script
|
2012-01-28 07:39:14 +08:00
|
|
|
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
|
2011-10-07 01:32:51 +08:00
|
|
|
switch</A> when you invoke LAMMPS, or you can
|
|
|
|
|
use the <A HREF = "suffix.html">suffix</A> command in your input script.
|
|
|
|
|
</P>
|
2011-12-14 04:35:35 +08:00
|
|
|
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
|
|
|
|
|
more instructions on how to use the accelerated styles effectively.
|
2011-10-07 01:32:51 +08:00
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2008-01-22 02:12:34 +08:00
|
|
|
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
2007-06-26 08:03:39 +08:00
|
|
|
</P>
|
|
|
|
|
<P>This pair style does not support mixing. Thus, coefficients for all
|
|
|
|
|
I,J pairs must be specified explicitly.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The <A HREF = "pair_modify.html">pair_modify</A> shift, table, and tail options are
|
|
|
|
|
not relevant for this pair style.
|
2006-09-28 03:12:31 +08:00
|
|
|
</P>
|
2007-06-26 08:03:39 +08:00
|
|
|
<P>This pair style writes the settings for the "pair_style table" command
|
|
|
|
|
to <A HREF = "restart.html">binary restart files</A>, so a pair_style command does
|
|
|
|
|
not need to specified in an input script that reads a restart file.
|
|
|
|
|
However, the coefficient information is not stored in the restart
|
|
|
|
|
file, since it is tabulated in the potential files. Thus, pair_coeff
|
|
|
|
|
commands do need to be specified in the restart input script.
|
|
|
|
|
</P>
|
2007-10-04 08:21:14 +08:00
|
|
|
<P>This pair style can only be used via the <I>pair</I> keyword of the
|
|
|
|
|
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
|
2007-10-12 07:09:49 +08:00
|
|
|
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
|
2007-10-04 08:21:14 +08:00
|
|
|
</P>
|
2007-06-26 08:03:39 +08:00
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><B>Restrictions:</B> none
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "pair_coeff.html">pair_coeff</A>
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B> none
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<A NAME = "Wolff"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Wolff)</B> Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).
|
|
|
|
|
</P>
|
|
|
|
|
</HTML>
|
