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<title>pair_style snap command — LAMMPS 15 May 2015 version documentation</title>
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<div class="section" id="pair-style-snap-command">
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<span id="index-0"></span><h1>pair_style snap command<a class="headerlink" href="#pair-style-snap-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>pair_style snap
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</pre></div>
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</div>
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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>pair_style snap
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pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P
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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>snap</em> computes interactions
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using the spectral neighbor analysis potential (SNAP)
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<a class="reference internal" href="#thompson2014"><span>(Thompson)</span></a>. Like the GAP framework of Bartok et al.
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<a class="reference internal" href="#bartok2010"><span>(Bartok2010)</span></a>, <a class="reference internal" href="#bartok2013"><span>(Bartok2013)</span></a>
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it uses bispectrum components
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to characterize the local neighborhood of each atom
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in a very general way. The mathematical definition of the
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bispectrum calculation used by SNAP is identical
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to that used of <a class="reference internal" href="compute_sna_atom.html"><em>compute sna/atom</em></a>.
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In SNAP, the total energy is decomposed into a sum over
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atom energies. The energy of atom <em>i</em> is
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expressed as a weighted sum over bispectrum components.</p>
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<img alt="_images/pair_snap.jpg" class="align-center" src="_images/pair_snap.jpg" />
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<p>where <em>B_k^i</em> is the <em>k</em>-th bispectrum component of atom <em>i</em>,
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and <em>beta_k^alpha_i</em> is the corresponding linear coefficient
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that depends on <em>alpha_i</em>, the SNAP element of atom <em>i</em>. The
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number of bispectrum components used and their definitions
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depend on the values of <em>twojmax</em> and <em>diagonalstyle</em>
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defined in the SNAP parameter file described below.
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The bispectrum calculation is described in more detail
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in <a class="reference internal" href="compute_sna_atom.html"><em>compute sna/atom</em></a>.</p>
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<p>Note that unlike for other potentials, cutoffs for SNAP potentials are
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not set in the pair_style or pair_coeff command; they are specified in
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the SNAP potential files themselves.</p>
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<p>Only a single pair_coeff command is used with the <em>snap</em> style which
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specifies two SNAP files and the list SNAP element(s) to be
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extracted.
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The SNAP elements are mapped to LAMMPS atom types by specifying
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N additional arguments after the 2nd filename in the pair_coeff
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command, where N is the number of LAMMPS atom types:</p>
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<ul class="simple">
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<li>SNAP element file</li>
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<li>Elem1, Elem2, ...</li>
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<li>SNAP parameter file</li>
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<li>N element names = mapping of SNAP elements to atom types</li>
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</ul>
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<p>As an example, if a LAMMPS indium phosphide simulation has 4 atoms
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types, with the first two being indium and the 3rd and 4th being
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phophorous, the pair_coeff command would look like this:</p>
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<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P
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</pre></div>
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</div>
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<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
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The two filenames are for the element and parameter files, respectively.
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The ‘In’ and ‘P’ arguments (between the file names) are the two elements
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which will be extracted from the element file. The
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two trailing ‘In’ arguments map LAMMPS atom types 1 and 2 to the
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SNAP ‘In’ element. The two trailing ‘P’ arguments map LAMMPS atom types
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3 and 4 to the SNAP ‘P’ element.</p>
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<p>If a SNAP mapping value is
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specified as NULL, the mapping is not performed.
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This can be used when a <em>snap</em> potential is used as part of the
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<em>hybrid</em> pair style. The NULL values are placeholders for atom types
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that will be used with other potentials.</p>
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<p>The name of the SNAP element file usually ends in the
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”.snapcoeff” extension. It may contain coefficients
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for many SNAP elements.
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Only those elements listed in the pair_coeff command are extracted.
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The name of the SNAP parameter file usually ends in the ”.snapparam”
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extension. It contains a small number
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of parameters that define the overall form of the SNAP potential.
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See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc page for alternate ways
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to specify the path for these files.</p>
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<p>Quite commonly,
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SNAP potentials are combined with one or more other LAMMPS pair styles
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using the <em>hybrid/overlay</em> pair style. As an example, the SNAP
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tantalum potential provided in the LAMMPS potentials directory
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combines the <em>snap</em> and <em>zbl</em> pair styles. It is invoked
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by the following commands:</p>
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<div class="highlight-python"><div class="highlight"><pre>variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 73
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pair_style hybrid/overlay &
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zbl ${zblcutinner} ${zblcutouter} snap
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pair_coeff * * zbl 0.0
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pair_coeff 1 1 zbl ${zblz}
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pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
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../potentials/Ta06A.snapparam Ta
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</pre></div>
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</div>
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<p>It is convenient to keep these commands in a separate file that can
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be inserted in any LAMMPS input script using the <a class="reference internal" href="include.html"><em>include</em></a>
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command.</p>
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<p>The top of the SNAP element file can contain any number of blank and comment
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lines (start with #), but follows a strict
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format after that. The first non-blank non-comment
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line must contain two integers:</p>
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<ul class="simple">
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<li>nelem = Number of elements</li>
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<li>ncoeff = Number of coefficients</li>
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</ul>
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<p>This is followed by one block for each of the <em>nelem</em> elements.
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The first line of each block contains three entries:</p>
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<ul class="simple">
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<li>Element symbol (text string)</li>
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<li>R = Element radius (distance units)</li>
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<li>w = Element weight (dimensionless)</li>
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</ul>
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<p>This line is followed by <em>ncoeff</em> coefficients, one per line.</p>
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<p>The SNAP parameter file can contain blank and comment lines (start
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with #) anywhere. Each non-blank non-comment line must contain one
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keyword/value pair. The required keywords are <em>rcutfac</em> and
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<em>twojmax</em>. Optional keywords are <em>rfac0</em>, <em>rmin0</em>, <em>diagonalstyle</em>,
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and <em>switchflag</em>.</p>
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<p>The default values for these keywords are</p>
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<ul class="simple">
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<li><em>rfac0</em> = 0.99363</li>
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<li><em>rmin0</em> = 0.0</li>
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<li><em>diagonalstyle</em> = 3</li>
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<li><em>switchflag</em> = 0</li>
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</ul>
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<p>Detailed definitions of these keywords are given on the <a class="reference internal" href="compute_sna_atom.html"><em>compute sna/atom</em></a> doc page.</p>
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<hr class="docutils" />
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<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
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<p>For atom type pairs I,J and I != J, where types I and J correspond to
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two different element types, mixing is performed by LAMMPS with
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user-specifiable parameters as described above. You never need to
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specify a pair_coeff command with I != J arguments for this style.</p>
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<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
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shift, table, and tail options.</p>
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<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
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need to re-specify the pair_style and pair_coeff commands in an input
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script that reads a restart file.</p>
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<p>This pair style can only be used via the <em>pair</em> keyword of the
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<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command. It does not support the
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<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</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 style is part of the SNAP package. It is only enabled if
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LAMMPS was built with that package. 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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</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="compute_sna_atom.html"><em>compute sna/atom</em></a>,
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<a class="reference internal" href="compute_sna_atom.html"><em>compute snad/atom</em></a>,
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<a class="reference internal" href="compute_sna_atom.html"><em>compute snav/atom</em></a></p>
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<p><strong>Default:</strong> none</p>
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<hr class="docutils" />
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<p id="thompson2014"><strong>(Thompson)</strong> Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
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available at <a class="reference external" href="http://arxiv.org/abs/1409.3880">arXiv:1409.3880</a></p>
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<p id="bartok2010"><strong>(Bartok2010)</strong> Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).</p>
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<p id="bartok2013"><strong>(Bartok2013)</strong> Bartok, Gillan, Manby, Csanyi, Phys Rev B 87, 184115 (2013).</p>
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