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<title>bond_style table command — LAMMPS 15 May 2015 version documentation</title>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<div class="section" id="bond-style-table-command">
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<span id="index-0"></span><h1>bond_style table command<a class="headerlink" href="#bond-style-table-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="bond-style-table-omp-command">
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<h1>bond_style table/omp command<a class="headerlink" href="#bond-style-table-omp-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>bond_style table style N
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</pre></div>
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</div>
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<ul class="simple">
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<li>style = <em>linear</em> or <em>spline</em> = method of interpolation</li>
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<li>N = use N values in table</li>
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</ul>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>bond_style table linear 1000
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bond_coeff 1 file.table ENTRY1
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</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"><em>bond_coeff</em></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"><em>bond_coeff</em></a> command as in the example above.</p>
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<ul class="simple">
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<li>filename</li>
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<li>keyword</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>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-python"><div class="highlight"><pre><span class="c"># Bond potential for harmonic (one or more comment or blank lines)</span>
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><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></div>
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</div>
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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 class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></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"><em>bond_style table</em></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"><em>fix shake</em></a> command. If not used, the equilibrium bond
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length is set to 0.0.</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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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.</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>cuda</em>, <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 in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></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.</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 class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section 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="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
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use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
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<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
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more instructions on how to use the accelerated styles effectively.</p>
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</div>
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<hr class="docutils" />
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<p>This bond style can only be used if LAMMPS was built with the
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MOLECULE package (which it is by default). See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a></p>
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<p><strong>Default:</strong> none</p>
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