2009-08-11 04:13:44 +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>bond_style table command
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</H3>
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2011-12-01 23:35:32 +08:00
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<H3>bond_style table/omp command
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</H3>
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2009-08-11 04:13:44 +08:00
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<P><B>Syntax:</B>
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</P>
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<PRE>bond_style table style N
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</PRE>
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<UL><LI>style = <I>linear</I> or <I>spline</I> = method of interpolation
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<LI>N = use N values in table
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>bond_style table linear 1000
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bond_coeff 1 file.table ENTRY1
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Style <I>table</I> creates interpolation tables of length <I>N</I> from bond
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potential and force values listed in a file(s) as a function of bond
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length. The files are read by the <A HREF = "bond_coeff.html">bond_coeff</A>
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command.
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</P>
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<P>The interpolation tables are created by fitting cubic splines to the
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file values and interpolating energy and force values at each of <I>N</I>
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distances. During a simulation, these tables are used to interpolate
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energy and force values as needed. The interpolation is done in one
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of 2 styles: <I>linear</I> or <I>spline</I>.
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</P>
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<P>For the <I>linear</I> style, the bond length is used to find 2 surrounding
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table values from which an energy or force is computed by linear
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interpolation.
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</P>
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<P>For the <I>spline</I> style, a cubic spline coefficients are computed and
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stored at each of the <I>N</I> values in the table. The bond length is
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used to find the appropriate set of coefficients which are used to
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evaluate a cubic polynomial which computes the energy or force.
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</P>
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<P>The following coefficients must be defined for each bond type via the
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<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above.
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</P>
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<UL><LI>filename
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<LI>keyword
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</UL>
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<P>The filename specifies a file containing tabulated energy and force
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values. The keyword specifies a section of the file. The format of
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this file is described below.
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</P>
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<HR>
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<P>The format of a tabulated file is as follows (without the
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parenthesized comments):
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</P>
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<PRE># Bond potential for harmonic (one or more comment or blank lines)
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</PRE>
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<PRE>HAM (keyword is the first text on line)
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N 101 FP 0 0 EQ 0.5 (N, FP, EQ parameters)
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(blank line)
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1 0.00 338.0000 1352.0000 (index, bond-length, energy, force)
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2 0.01 324.6152 1324.9600
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...
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101 1.00 338.0000 -1352.0000
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</PRE>
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<P>A section begins with a non-blank line whose 1st character is not a
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"#"; blank lines or lines starting with "#" can be used as comments
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between sections. The first line begins with a keyword which
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identifies the section. The line can contain additional text, but the
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initial text must match the argument specified in the
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<A HREF = "bond_coeff.html">bond_coeff</A> command. The next line lists (in any
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order) one or more parameters for the table. Each parameter is a
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keyword followed by one or more numeric values.
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</P>
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<P>The parameter "N" is required and its value is the number of table
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entries that follow. Note that this may be different than the <I>N</I>
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specified in the <A HREF = "bond_style.html">bond_style table</A> command. Let
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Ntable = <I>N</I> in the bond_style command, and Nfile = "N" in the
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tabulated file. What LAMMPS does is a preliminary interpolation by
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creating splines using the Nfile tabulated values as nodal points. It
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uses these to interpolate as needed to generate energy and force
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values at Ntable different points. The resulting tables of length
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Ntable are then used as described above, when computing energy and
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force for individual bond lengths. This means that if you want the
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interpolation tables of length Ntable to match exactly what is in the
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tabulated file (with effectively no preliminary interpolation), you
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should set Ntable = Nfile.
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</P>
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<P>The "FP" parameter is optional. If used, it is followed by two values
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fplo and fphi, which are the derivatives of the force at the innermost
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and outermost bond lengths. These values are needed by the spline
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construction routines. If not specified by the "FP" parameter, they
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are estimated (less accurately) by the first two and last two force
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values in the table.
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</P>
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<P>The "EQ" parameter is also optional. If used, it is followed by a the
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equilibrium bond length, which is used, for example, by the <A HREF = "fix_shake.html">fix
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shake</A> command. If not used, the equilibrium bond
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length is set to 0.0.
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</P>
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<P>Following a blank line, the next N lines list the tabulated values.
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On each line, the 1st value is the index from 1 to N, the 2nd value is
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the bond length r (in distance units), the 3rd value is the energy (in
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energy units), and the 4th is the force (in force units). The bond
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2010-06-16 23:36:21 +08:00
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lengths must range from a LO value to a HI value, and increase from
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one line to the next. If the actual bond length is ever smaller than
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the LO value or larger than the HI value, then the bond energy and
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force is evaluated as if the bond were the LO or HI length.
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2009-08-11 04:13:44 +08:00
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</P>
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<P>Note that one file can contain many sections, each with a tabulated
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potential. LAMMPS reads the file section by section until it finds
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one that matches the specified keyword.
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</P>
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2011-12-01 23:35:32 +08:00
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<HR>
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2014-08-15 00:30:25 +08:00
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<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.
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</P>
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<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
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KOKKOS, USER-OMP and OPT packages, respectively. They are only
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enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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2011-12-01 23:35:32 +08:00
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</P>
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<P>You can specify the accelerated styles explicitly in your input script
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2012-01-28 07:39:14 +08:00
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by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
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2011-12-01 23:35:32 +08:00
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switch</A> when you invoke LAMMPS, or you can
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use the <A HREF = "suffix.html">suffix</A> command in your input script.
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</P>
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2011-12-14 04:35:35 +08:00
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<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
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more instructions on how to use the accelerated styles effectively.
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2011-12-01 23:35:32 +08:00
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</P>
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<HR>
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2009-08-11 04:13:44 +08:00
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<P><B>Restrictions:</B>
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</P>
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<P>This bond style can only be used if LAMMPS was built with the
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2011-08-27 02:53:00 +08:00
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MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
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2009-08-11 04:13:44 +08:00
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LAMMPS</A> section for more info on packages.
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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 = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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