forked from lijiext/lammps
154 lines
6.1 KiB
Plaintext
154 lines
6.1 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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bond_style table command :h3
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bond_style table/omp command :h3
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[Syntax:]
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bond_style table style N :pre
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style = {linear} or {spline} = method of interpolation
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N = use N values in table :ul
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[Examples:]
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bond_style table linear 1000
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bond_coeff 1 file.table ENTRY1 :pre
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[Description:]
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Style {table} creates interpolation tables of length {N} 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 "bond_coeff"_bond_coeff.html
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command.
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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 {N}
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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: {linear} or {spline}.
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For the {linear} 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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For the {spline} style, a cubic spline coefficients are computed and
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stored at each of the {N} 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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The following coefficients must be defined for each bond type via the
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"bond_coeff"_bond_coeff.html command as in the example above.
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filename
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keyword :ul
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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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:line
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The format of a tabulated file is as follows (without the
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parenthesized comments):
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# Bond potential for harmonic (one or more comment or blank lines) :pre
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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 :pre
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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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"bond_coeff"_bond_coeff.html 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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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 {N}
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specified in the "bond_style table"_bond_style.html command. Let
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Ntable = {N} 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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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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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 "fix
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shake"_fix_shake.html command. If not used, the equilibrium bond
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length is set to 0.0.
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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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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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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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:line
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Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally
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the same as the corresponding style without the suffix. They have
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been optimized to run faster, depending on your available hardware, as
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discussed in "Section_accelerate"_Section_accelerate.html of the
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manual. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision issues.
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These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
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packages, respectively. They are only enabled if LAMMPS was built with
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those packages. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the "-suffix command-line
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switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
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use the "suffix"_suffix.html command in your input script.
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See "Section_accelerate"_Section_accelerate.html of the manual for
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more instructions on how to use the accelerated styles effectively.
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:line
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[Restrictions:]
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This bond style can only be used if LAMMPS was built with the
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MOLECULAR package (which it is by default). See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info on packages.
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[Related commands:]
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"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
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[Default:] none
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