forked from lijiext/lammps
134 lines
5.4 KiB
HTML
134 lines
5.4 KiB
HTML
<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>bond_style table command
|
|
</H3>
|
|
<P><B>Syntax:</B>
|
|
</P>
|
|
<PRE>bond_style table style N
|
|
</PRE>
|
|
<UL><LI>style = <I>linear</I> or <I>spline</I> = method of interpolation
|
|
<LI>N = use N values in table
|
|
</UL>
|
|
<P><B>Examples:</B>
|
|
</P>
|
|
<PRE>bond_style table linear 1000
|
|
bond_coeff 1 file.table ENTRY1
|
|
</PRE>
|
|
<P><B>Description:</B>
|
|
</P>
|
|
<P>Style <I>table</I> creates interpolation tables of length <I>N</I> from bond
|
|
potential and force values listed in a file(s) as a function of bond
|
|
length. The files are read by the <A HREF = "bond_coeff.html">bond_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 2 styles: <I>linear</I> or <I>spline</I>.
|
|
</P>
|
|
<P>For the <I>linear</I> style, the bond length is used to find 2 surrounding
|
|
table values from which an energy or force is computed by linear
|
|
interpolation.
|
|
</P>
|
|
<P>For the <I>spline</I> style, a cubic spline coefficients are computed and
|
|
stored at each of the <I>N</I> values in the table. The bond length is
|
|
used to find the appropriate set of coefficients which are used to
|
|
evaluate a cubic polynomial which computes the energy or force.
|
|
</P>
|
|
<P>The following coefficients must be defined for each bond type via the
|
|
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above.
|
|
</P>
|
|
<UL><LI>filename
|
|
<LI>keyword
|
|
</UL>
|
|
<P>The filename specifies a file containing tabulated energy and force
|
|
values. The keyword specifies a section of the file. The format of
|
|
this file is described below.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>The format of a tabulated file is as follows (without the
|
|
parenthesized comments):
|
|
</P>
|
|
<PRE># Bond potential for harmonic (one or more comment or blank lines)
|
|
</PRE>
|
|
<PRE>HAM (keyword is the first text on line)
|
|
N 101 FP 0 0 EQ 0.5 (N, FP, EQ parameters)
|
|
(blank line)
|
|
1 0.00 338.0000 1352.0000 (index, bond-length, energy, force)
|
|
2 0.01 324.6152 1324.9600
|
|
...
|
|
101 1.00 338.0000 -1352.0000
|
|
</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
|
|
<A HREF = "bond_coeff.html">bond_coeff</A> 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>
|
|
<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 = "bond_style.html">bond_style table</A> command. Let
|
|
Ntable = <I>N</I> in the bond_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 bond lengths. 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
|
|
should set Ntable = Nfile.
|
|
</P>
|
|
<P>The "FP" parameter is optional. If used, it is followed by two values
|
|
fplo and fphi, which are the derivatives of the force at the innermost
|
|
and outermost bond lengths. These values are needed by the spline
|
|
construction routines. If not specified by the "FP" parameter, they
|
|
are estimated (less accurately) by the first two and last two force
|
|
values in the table.
|
|
</P>
|
|
<P>The "EQ" parameter is also optional. If used, it is followed by a the
|
|
equilibrium bond length, which is used, for example, by the <A HREF = "fix_shake.html">fix
|
|
shake</A> command. If not used, the equilibrium bond
|
|
length is set to 0.0.
|
|
</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
|
|
the bond length r (in distance units), the 3rd value is the energy (in
|
|
energy units), and the 4th is the force (in force units). The bond
|
|
lengths must range from a LO value to a HI value, and increase from
|
|
one line to the next. If the actual bond length is ever smaller than
|
|
the LO value or larger than the HI value, then the bond energy and
|
|
force is evaluated as if the bond were the LO or HI length.
|
|
</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>
|
|
<P><B>Restrictions:</B>
|
|
</P>
|
|
<P>This bond style can only be used if LAMMPS was built with the
|
|
MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
|
|
LAMMPS</A> section for more info on packages.
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
|
|
</P>
|
|
<P><B>Default:</B> none
|
|
</P>
|
|
</HTML>
|