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<li class="toctree-l2"><a class="reference internal" href="bond_bpm_rotational.html">bond_style bpm/rotational command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_bpm_spring.html">bond_style bpm/spring command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_class2.html">bond_style class2 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_fene.html">bond_style fene command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_fene.html#bond-style-fene-nm-command">bond_style fene/nm command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_fene_expand.html">bond_style fene/expand command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_gaussian.html">bond_style gaussian command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_gromos.html">bond_style gromos command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_harmonic.html">bond_style harmonic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_harmonic_restrain.html">bond_style harmonic/restrain command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_harmonic_shift.html">bond_style harmonic/shift command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_harmonic_shift_cut.html">bond_style harmonic/shift/cut command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_hybrid.html">bond_style hybrid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_lepton.html">bond_style lepton command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_mesocnt.html">bond_style mesocnt command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_mm3.html">bond_style mm3 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_morse.html">bond_style morse command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_none.html">bond_style none command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_nonlinear.html">bond_style nonlinear command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_oxdna.html">bond_style oxdna/fene command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_oxdna.html#bond-style-oxdna2-fene-command">bond_style oxdna2/fene command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_oxdna.html#bond-style-oxrna2-fene-command">bond_style oxrna2/fene command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_quartic.html">bond_style quartic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_rheo_shell.html">bond_style rheo/shell command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_special.html">bond_style special command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">bond_style table command</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
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<li class="toctree-l2"><a class="reference internal" href="bond_zero.html">bond_style zero command</a></li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="bond-style-table-command">
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<span id="index-1"></span><span id="index-0"></span><h1>bond_style table command<a class="headerlink" href="#bond-style-table-command" title="Link to this heading"></a></h1>
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<p>Accelerator Variants: <em>table/omp</em></p>
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<section id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Link to this heading"></a></h2>
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">bond_style</span><span class="w"> </span><span class="n">table</span><span class="w"> </span><span class="n">style</span><span class="w"> </span><span class="n">N</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li><p>style = <em>linear</em> or <em>spline</em> = method of interpolation</p></li>
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<li><p>N = use N values in table</p></li>
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</ul>
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</section>
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<section id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">bond_style</span><span class="w"> </span><span class="n">table</span><span class="w"> </span><span class="n">linear</span><span class="w"> </span><span class="m">1000</span>
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<span class="k">bond_coeff</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">file.table</span><span class="w"> </span><span class="n">ENTRY1</span>
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</pre></div>
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</div>
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</section>
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<section id="description">
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<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
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<p>Style <em>table</em> creates interpolation tables of length <em>N</em> 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 class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>
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command.</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 <em>N</em>
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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: <em>linear</em> or <em>spline</em>.</p>
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<p>For the <em>linear</em> 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.</p>
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<p>For the <em>spline</em> style, a cubic spline coefficients are computed and
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stored at each of the <em>N</em> 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.</p>
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<p>The following coefficients must be defined for each bond type via the
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<a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a> command as in the example above.</p>
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<ul class="simple">
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<li><p>filename</p></li>
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<li><p>keyword</p></li>
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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.</p>
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<hr class="docutils" />
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<p>Suitable tables for use with this bond style can be created by LAMMPS
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itself from existing bond styles using the <a class="reference internal" href="bond_write.html"><span class="doc">bond_write</span></a> command. This can be useful to have a template file for
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testing the bond style settings and to build a compatible custom file.
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Another option to generate tables is the Python code in the
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<code class="docutils literal notranslate"><span class="pre">tools/tabulate</span></code> folder of the LAMMPS source code distribution.</p>
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<p>The format of a tabulated file is as follows (without the
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parenthesized comments):</p>
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<div class="highlight-none notranslate"><div class="highlight"><pre><span></span># Bond potential for harmonic (one or more comment or blank lines)
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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
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</pre></div>
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</div>
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<p>A section begins with a non-blank line whose first 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 class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></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.</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 <em>N</em>
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specified in the <a class="reference internal" href="bond_style.html"><span class="doc">bond_style table</span></a> command. Let
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Ntable = <em>N</em> 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.</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.</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 class="reference internal" href="fix_shake.html"><span class="doc">fix
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shake</span></a> command. If not used, the equilibrium bond length is
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to the distance in the table with the lowest potential energy.</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 first value is the index from 1 to N, the second value is
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the bond length r (in distance units), the third value is the energy (in
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energy units), and the fourth 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 calculation is
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aborted with an error, so it is advisable to cover the whole range
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of possible bond lengths.</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.</p>
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<hr class="docutils" />
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<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> 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 on the <a class="reference internal" href="Speed_packages.html"><span class="doc">Accelerator packages</span></a>
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page. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision issues.</p>
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<p>These accelerated styles are part of the GPU, INTEL, KOKKOS,
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OPENMP, and OPT packages, respectively. They are only enabled if
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LAMMPS was built with those packages. See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> page for more info.</p>
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<p>You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the <a class="reference internal" href="Run_options.html"><span class="doc">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can use the
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<a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
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<p>See the <a class="reference internal" href="Speed_packages.html"><span class="doc">Accelerator packages</span></a> page for more
|
|
instructions on how to use the accelerated styles effectively.</p>
|
|
</section>
|
|
<hr class="docutils" />
|
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<section id="restart-info">
|
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<h2>Restart info<a class="headerlink" href="#restart-info" title="Link to this heading"></a></h2>
|
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<p>This bond style writes the settings for the “bond_style table” command
|
|
to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so a bond_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, bond_coeff commands
|
|
do need to be specified in the restart input script.</p>
|
|
</section>
|
|
<section id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
|
<p>This bond style can only be used if LAMMPS was built with the MOLECULE
|
|
package. See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> page for more
|
|
info.</p>
|
|
</section>
|
|
<section id="related-commands">
|
|
<h2>Related commands<a class="headerlink" href="#related-commands" title="Link to this heading"></a></h2>
|
|
<p><a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a>,
|
|
<a class="reference internal" href="bond_write.html"><span class="doc">bond_write</span></a></p>
|
|
</section>
|
|
<section id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
|
<p>none</p>
|
|
</section>
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