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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<div class="section" id="dihedral-style-table-command">
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<span id="index-0"></span><h1>dihedral_style table command<a class="headerlink" href="#dihedral-style-table-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="dihedral-style-table-omp-command">
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<h1>dihedral_style table/omp command<a class="headerlink" href="#dihedral-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>dihedral_style table style Ntable
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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>Ntable = size of the internal lookup 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>dihedral_style table spline 400
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dihedral_style table linear 1000
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dihedral_coeff 1 file.table DIH_TABLE1
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dihedral_coeff 2 file.table DIH_TABLE2
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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>The <em>table</em> dihedral style creates interpolation tables of length
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<em>Ntable</em> from dihedral potential and derivative values listed in a
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file(s) as a function of the dihedral angle “phi”. The files are read
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by the <a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a> 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 derivative values at each of
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<em>Ntable</em> dihedral angles. During a simulation, these tables are used
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to interpolate energy and force values on individual atoms as
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needed. The interpolation is done in one of 2 styles: <em>linear</em> or
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<em>spline</em>.</p>
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<p>For the <em>linear</em> style, the dihedral angle (phi) is used to find 2
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surrounding table values from which an energy or its derivative is
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computed by linear interpolation.</p>
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<p>For the <em>spline</em> style, cubic spline coefficients are computed and
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stored at each of the <em>Ntable</em> evenly-spaced values in the
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interpolated table. For a given dihedral angle (phi), the appropriate
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coefficients are chosen from this list, and a cubic polynomial is used
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to compute the energy and the derivative at this angle.</p>
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<p>The following coefficients must be defined for each dihedral type via
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the <a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a> command as in the example
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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
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derivative values. The keyword specifies a section of the file. The
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format of 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). It can begin with one or more comment
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or blank lines.</p>
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<div class="highlight-python"><div class="highlight"><pre><span class="c"># Table of the potential and its negative derivative</span>
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>DIH_TABLE1 (keyword is the first text on line)
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N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F)
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(blank line)
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1 -168.0 -1.40351172223 -0.0423346818422
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2 -156.0 -1.70447981034 -0.00811786522531
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3 -144.0 -1.62956100432 0.0184129719987
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...
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30 180.0 -0.707106781187 -0.0719306095245
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre><span class="c"># Example 2: table of the potential. Forces omitted</span>
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>DIH_TABLE2
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N 30 NOF CHECKU testU.dat CHECKF testF.dat
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>1 -168.0 -1.40351172223
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2 -156.0 -1.70447981034
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3 -144.0 -1.62956100432
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...
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30 180.0 -0.707106781187
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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="dihedral_coeff.html"><em>dihedral_coeff</em></a> command. The next line lists (in
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any 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>Following a blank line, the next N lines list the tabulated values. On
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each line, the 1st value is the index from 1 to N, the 2nd value is
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the angle value, the 3rd value is the energy (in energy units), and
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the 4th is -dE/d(phi) also in energy units). The 3rd term is the
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energy of the 4-atom configuration for the specified angle. The 4th
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term (when present) is the negative derivative of the energy with
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respect to the angle (in degrees, or radians depending on whether the
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user selected DEGREES or RADIANS). Thus the units of the last term
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are still energy, not force. The dihedral angle values must increase
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from one line to the next.</p>
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<p>Dihedral table splines are cyclic. There is no discontinuity at 180
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degrees (or at any other angle). Although in the examples above, the
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angles range from -180 to 180 degrees, in general, the first angle in
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the list can have any value (positive, zero, or negative). However
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the <em>range</em> of angles represented in the table must be <em>strictly</em> less
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than 360 degrees (2pi radians) to avoid angle overlap. (You may not
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supply entries in the table for both 180 and -180, for example.) If
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the user’s table covers only a narrow range of dihedral angles,
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strange numerical behavior can occur in the large remaining gap.</p>
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<p><strong>Parameters:</strong></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 N
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specified in the <a class="reference internal" href="dihedral_style.html"><em>dihedral_style table</em></a> command.
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Let <em>Ntable</em> is the number of table entries requested dihedral_style
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command, and let <em>Nfile</em> be the parameter following “N” in the
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tabulated file (“30” in the sparse example above). What LAMMPS does
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is a preliminary interpolation by creating splines using the <em>Nfile</em>
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tabulated values as nodal points. It uses these to interpolate as
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needed to generate energy and derivative values at <em>Ntable</em> different
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points (which are evenly spaced over a 360 degree range, even if the
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angles in the file are not). The resulting tables of length <em>Ntable</em>
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are then used as described above, when computing energy and force for
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individual dihedral angles and their atoms. This means that if you
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want the interpolation tables of length <em>Ntable</em> to match exactly what
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is in the tabulated file (with effectively nopreliminary
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interpolation), you should set <em>Ntable</em> = <em>Nfile</em>. To insure the
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nodal points in the user’s file are aligned with the interpolated
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table entries, the angles in the table should be integer multiples of
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360/<em>Ntable</em> degrees, or 2*PI/<em>Ntable</em> radians (depending on your
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choice of angle units).</p>
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<p>The optional “NOF” keyword allows the user to omit the forces
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(negative energy derivatives) from the table file (normally located in
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the 4th column). In their place, forces will be calculated
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automatically by differentiating the potential energy function
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indicated by the 3rd column of the table (using either linear or
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spline interpolation).</p>
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<p>The optional “DEGREES” keyword allows the user to specify angles in
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degrees instead of radians (default).</p>
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<p>The optional “RADIANS” keyword allows the user to specify angles in
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radians instead of degrees. (Note: This changes the way the forces
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are scaled in the 4th column of the data file.)</p>
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<p>The optional “CHECKU” keyword is followed by a filename. This allows
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the user to save all of the the <em>Ntable</em> different entries in the
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interpolated energy table to a file to make sure that the interpolated
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function agrees with the user’s expectations. (Note: You can
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temporarily increase the <em>Ntable</em> parameter to a high value for this
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purpose. “<em>Ntable</em>” is explained above.)</p>
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<p>The optional “CHECKF” keyword is analogous to the “CHECKU” keyword.
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It is followed by a filename, and it allows the user to check the
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interpolated force table. This option is available even if the user
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selected the “NOF” option.</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 one
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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-6"><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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<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 dihedral style can only be used if LAMMPS was built with the
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USER-MISC package. See the <span class="xref std std-ref">Making LAMMPS</span>
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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="dihedral_coeff.html"><em>dihedral_coeff</em></a></p>
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<p><strong>Default:</strong> none</p>
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