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doc/Manual.html
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@ -238,23 +238,24 @@ it gives quick access to documentation for all LAMMPS commands.</p>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.17. USER-COLVARS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.18. USER-CUDA package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.19. USER-DIFFRACTION package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.20. USER-DRUDE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.21. USER-EFF package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.22. USER-FEP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-h5md-package">4.23. USER-H5MD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.24. USER-INTEL package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.25. USER-LB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-mgpt-package">4.26. USER-MGPT package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.27. USER-MISC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.28. USER-MOLFILE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.29. USER-OMP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.30. USER-PHONON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.31. USER-QMMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.32. USER-QTB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.33. USER-REAXC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smd-package">4.34. USER-SMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smtbq-package">4.35. USER-SMTBQ package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.36. USER-SPH package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-dpd-package">4.20. USER-DPD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.21. USER-DRUDE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.22. USER-EFF package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.23. USER-FEP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-h5md-package">4.24. USER-H5MD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.25. USER-INTEL package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.26. USER-LB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-mgpt-package">4.27. USER-MGPT package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.28. USER-MISC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.29. USER-MOLFILE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.30. USER-OMP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.31. USER-PHONON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.32. USER-QMMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.33. USER-QTB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.34. USER-REAXC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smd-package">4.35. USER-SMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smtbq-package">4.36. USER-SMTBQ package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.37. USER-SPH package</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>

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@ -97,23 +97,24 @@
<li class="toctree-l2"><a class="reference internal" href="#user-colvars-package">4.17. USER-COLVARS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-cuda-package">4.18. USER-CUDA package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-diffraction-package">4.19. USER-DIFFRACTION package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-drude-package">4.20. USER-DRUDE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-eff-package">4.21. USER-EFF package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-fep-package">4.22. USER-FEP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-h5md-package">4.23. USER-H5MD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-intel-package">4.24. USER-INTEL package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-lb-package">4.25. USER-LB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-mgpt-package">4.26. USER-MGPT package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-misc-package">4.27. USER-MISC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-molfile-package">4.28. USER-MOLFILE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-omp-package">4.29. USER-OMP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-phonon-package">4.30. USER-PHONON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-qmmm-package">4.31. USER-QMMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-qtb-package">4.32. USER-QTB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-reaxc-package">4.33. USER-REAXC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-smd-package">4.34. USER-SMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-smtbq-package">4.35. USER-SMTBQ package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-sph-package">4.36. USER-SPH package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-dpd-package">4.20. USER-DPD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-drude-package">4.21. USER-DRUDE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-eff-package">4.22. USER-EFF package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-fep-package">4.23. USER-FEP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-h5md-package">4.24. USER-H5MD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-intel-package">4.25. USER-INTEL package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-lb-package">4.26. USER-LB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-mgpt-package">4.27. USER-MGPT package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-misc-package">4.28. USER-MISC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-molfile-package">4.29. USER-MOLFILE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-omp-package">4.30. USER-OMP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-phonon-package">4.31. USER-PHONON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-qmmm-package">4.32. USER-QMMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-qtb-package">4.33. USER-QTB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-reaxc-package">4.34. USER-REAXC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-smd-package">4.35. USER-SMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-smtbq-package">4.36. USER-SMTBQ package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-sph-package">4.37. USER-SPH package</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
@ -741,7 +742,21 @@ serial.</p>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-DRUDE</td>
<tr class="row-even"><td>USER-DPD</td>
<td>dissipative particle dynamics (DPD)</td>
<td>Larentzos &amp; Mattox &amp; Brennan (5)</td>
<td>src/USER-DPD/README</td>
<td>USER/dpd</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-DRUDE</td>
<td>Drude oscillators</td>
<td>Dequidt &amp; Devemy &amp; Padua (3)</td>
<td><a class="reference internal" href="tutorial_drude.html"><em>tutorial</em></a></td>
@ -755,7 +770,7 @@ serial.</p>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-EFF</td>
<tr class="row-even"><td>USER-EFF</td>
<td>electron force field</td>
<td>Andres Jaramillo-Botero (Caltech)</td>
<td><a class="reference internal" href="pair_eff.html"><em>pair_style eff/cut</em></a></td>
@ -766,7 +781,7 @@ serial.</p>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-FEP</td>
<tr class="row-odd"><td>USER-FEP</td>
<td>free energy perturbation</td>
<td>Agilio Padua (U Blaise Pascal Clermont-Ferrand)</td>
<td><a class="reference internal" href="compute_fep.html"><em>compute fep</em></a></td>
@ -780,7 +795,7 @@ serial.</p>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-H5MD</td>
<tr class="row-even"><td>USER-H5MD</td>
<td>dump output via HDF5</td>
<td>Pierre de Buyl (KU Leuven)</td>
<td><a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a></td>
@ -794,7 +809,7 @@ serial.</p>
</td>
<td>lib/h5md</td>
</tr>
<tr class="row-even"><td>USER-INTEL</td>
<tr class="row-odd"><td>USER-INTEL</td>
<td>Vectorized CPU and Intel(R) coprocessor styles</td>
<td><ol class="first last upperalpha simple" start="23">
<li>Michael Brown (Intel)</li>
@ -811,7 +826,7 @@ serial.</p>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-LB</td>
<tr class="row-even"><td>USER-LB</td>
<td>Lattice Boltzmann fluid</td>
<td>Colin Denniston (U Western Ontario)</td>
<td><a class="reference internal" href="fix_lb_fluid.html"><em>fix lb/fluid</em></a></td>
@ -825,7 +840,7 @@ serial.</p>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-MGPT</td>
<tr class="row-odd"><td>USER-MGPT</td>
<td>fast MGPT multi-ion potentials</td>
<td>Tomas Oppelstrup &amp; John Moriarty (LLNL)</td>
<td><a class="reference internal" href="pair_mgpt.html"><em>pair_style mgpt</em></a></td>
@ -839,7 +854,7 @@ serial.</p>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-MISC</td>
<tr class="row-even"><td>USER-MISC</td>
<td>single-file contributions</td>
<td>USER-MISC/README</td>
<td>USER-MISC/README</td>
@ -856,7 +871,7 @@ serial.</p>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-MOLFILE</td>
<tr class="row-odd"><td>USER-MOLFILE</td>
<td><a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a> molfile plug-ins</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="dump_molfile.html"><em>dump molfile</em></a></td>
@ -870,7 +885,7 @@ serial.</p>
</td>
<td>VMD-MOLFILE</td>
</tr>
<tr class="row-odd"><td>USER-OMP</td>
<tr class="row-even"><td>USER-OMP</td>
<td>OpenMP threaded styles</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="accelerate_omp.html"><em>Section accelerate</em></a></td>
@ -887,7 +902,7 @@ serial.</p>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-PHONON</td>
<tr class="row-odd"><td>USER-PHONON</td>
<td>phonon dynamical matrix</td>
<td>Ling-Ti Kong (Shanghai Jiao Tong U)</td>
<td><a class="reference internal" href="fix_phonon.html"><em>fix phonon</em></a></td>
@ -901,7 +916,7 @@ serial.</p>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-QMMM</td>
<tr class="row-even"><td>USER-QMMM</td>
<td>QM/MM coupling</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="fix_qmmm.html"><em>fix qmmm</em></a></td>
@ -912,7 +927,7 @@ serial.</p>
</td>
<td>lib/qmmm</td>
</tr>
<tr class="row-even"><td>USER-QTB</td>
<tr class="row-odd"><td>USER-QTB</td>
<td>quantum nuclear effects</td>
<td>Yuan Shen (Stanford)</td>
<td><a class="reference internal" href="fix_qtb.html"><em>fix qtb</em></a> <a class="reference internal" href="fix_qbmsst.html"><em>fix_qbmsst</em></a></td>
@ -926,7 +941,7 @@ serial.</p>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-QUIP</td>
<tr class="row-even"><td>USER-QUIP</td>
<td>QUIP/libatoms interface</td>
<td>Albert Bartok-Partay (U Cambridge)</td>
<td><a class="reference internal" href="pair_quip.html"><em>pair_style quip</em></a></td>
@ -937,7 +952,7 @@ serial.</p>
</td>
<td>lib/quip</td>
</tr>
<tr class="row-even"><td>USER-REAXC</td>
<tr class="row-odd"><td>USER-REAXC</td>
<td>C version of ReaxFF</td>
<td>Metin Aktulga (LBNL)</td>
<td><a class="reference internal" href="pair_reax_c.html"><em>pair_style reaxc</em></a></td>
@ -951,7 +966,7 @@ serial.</p>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-SMD</td>
<tr class="row-even"><td>USER-SMD</td>
<td>smoothed Mach dynamics</td>
<td>Georg Ganzenmuller (EMI)</td>
<td><a class="reference external" href="PDF/SMD_LAMMPS_userguide.pdf">userguide.pdf</a></td>
@ -965,7 +980,7 @@ serial.</p>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-SMTBQ</td>
<tr class="row-odd"><td>USER-SMTBQ</td>
<td>Second Moment Tight Binding - QEq potential</td>
<td>Salles &amp; Maras &amp; Politano &amp; Tetot (4)</td>
<td><a class="reference internal" href="pair_smtbq.html"><em>pair_style smtbq</em></a></td>
@ -979,7 +994,7 @@ serial.</p>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-SPH</td>
<tr class="row-even"><td>USER-SPH</td>
<td>smoothed particle hydrodynamics</td>
<td>Georg Ganzenmuller (EMI)</td>
<td><a class="reference external" href="PDF/SPH_LAMMPS_userguide.pdf">userguide.pdf</a></td>
@ -990,7 +1005,7 @@ serial.</p>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-TALLY</td>
<tr class="row-odd"><td>USER-TALLY</td>
<td>Pairwise tallied computes</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><code class="xref doc docutils literal"><span class="pre">compute</span></code></td>
@ -1004,7 +1019,7 @@ serial.</p>
</ul>
</td>
</tr>
<tr class="row-odd"><td>&nbsp;</td>
<tr class="row-even"><td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
@ -1026,6 +1041,8 @@ Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
(U Blaise Pascal).</p>
<p>(4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
Olivier Politano, and Robert Tetot (LAAS-CNRS, France).</p>
<p>(4) The USER-DPD package was created by James Larentzos, Timothy
Mattox, and John Brennan (Army Research Lab (ARL) and Engility Corp).</p>
<p>If the Library is not listed as lib/package, then it is a third-party
library not included in the LAMMPS distribution. See the
src/package/Makefile.lammps file for info on where to download the
@ -1200,8 +1217,32 @@ theory.</p>
Arkansas. Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-dpd-package">
<h2>4.20. USER-DPD package<a class="headerlink" href="#user-dpd-package" title="Permalink to this headline"></a></h2>
<p>This package implements the dissipative particle dynamics (DPD) method
under isothermal, isoenergetic, isobaric and isenthalpic conditions.
The DPD equations of motion are integrated efficiently through the
Shardlow splitting algorithm.</p>
<p>See these doc pages and their related commands to get started:</p>
<ul class="simple">
<li><a class="reference internal" href="compute_dpd.html"><em>compute dpd</em></a></li>
<li><a class="reference internal" href="compute_dpd_atom.html"><em>compute dpd/atom</em></a></li>
<li><a class="reference internal" href="fix_eos_table.html"><em>fix_eos/cv</em></a></li>
<li><a class="reference internal" href="fix_eos_table.html"><em>fix_eos/table</em></a></li>
<li><a class="reference internal" href="fix_shardlow.html"><em>fix_shardlow</em></a></li>
<li><a class="reference internal" href="pair_dpd_conservative.html"><em>pair_dpd/conservative</em></a></li>
<li><a class="reference internal" href="pair_dpd_fdt.html"><em>pair_dpd/fdt</em></a></li>
<li><a class="reference internal" href="pair_dpd_fdt.html"><em>pair_dpd/fdt/energy</em></a></li>
</ul>
<p>There are example scripts for using this package in examples/USER/dpd.</p>
<p>The people who created this package are James Larentzos
(james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at
engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil).
Contact them directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-drude-package">
<h2>4.20. USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline"></a></h2>
<h2>4.21. USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline"></a></h2>
<p>This package implements methods for simulating polarizable systems
in LAMMPS using thermalized Drude oscillators.</p>
<p>See these doc pages and their related commands to get started:</p>
@ -1221,7 +1262,7 @@ Agilio Padua.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-eff-package">
<h2>4.21. USER-EFF package<a class="headerlink" href="#user-eff-package" title="Permalink to this headline"></a></h2>
<h2>4.22. USER-EFF package<a class="headerlink" href="#user-eff-package" title="Permalink to this headline"></a></h2>
<p>This package contains a LAMMPS implementation of the electron Force
Field (eFF) currently under development at Caltech, as described in
A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
@ -1255,7 +1296,7 @@ have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-fep-package">
<h2>4.22. USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline"></a></h2>
<h2>4.23. USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline"></a></h2>
<p>This package provides methods for performing free energy perturbation
simulations with soft-core pair potentials in LAMMPS.</p>
<p>See these doc pages and their related commands to get started:</p>
@ -1270,7 +1311,7 @@ Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-h5md-package">
<h2>4.23. USER-H5MD package<a class="headerlink" href="#user-h5md-package" title="Permalink to this headline"></a></h2>
<h2>4.24. USER-H5MD package<a class="headerlink" href="#user-h5md-package" title="Permalink to this headline"></a></h2>
<p>This package contains a <a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a> command for
performing a dump of atom properties in HDF5 format. <a class="reference external" href="http://www.hdfgroup.org/HDF5/">HDF5 files</a> are binary, portable and self-describing and can be
examined and used by a variety of auxiliary tools. The output HDF5
@ -1284,7 +1325,7 @@ directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-intel-package">
<h2>4.24. USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline"></a></h2>
<h2>4.25. USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline"></a></h2>
<p>This package provides options for performing neighbor list and
non-bonded force calculations in single, mixed, or double precision
and also a capability for accelerating calculations with an
@ -1296,7 +1337,7 @@ Intel(R) Xeon Phi(TM) coprocessor.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-lb-package">
<h2>4.25. USER-LB package<a class="headerlink" href="#user-lb-package" title="Permalink to this headline"></a></h2>
<h2>4.26. USER-LB package<a class="headerlink" href="#user-lb-package" title="Permalink to this headline"></a></h2>
<p>This package contains a LAMMPS implementation of a background
Lattice-Boltzmann fluid, which can be used to model MD particles
influenced by hydrodynamic forces.</p>
@ -1308,7 +1349,7 @@ Western Ontario. Contact them directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-mgpt-package">
<h2>4.26. USER-MGPT package<a class="headerlink" href="#user-mgpt-package" title="Permalink to this headline"></a></h2>
<h2>4.27. USER-MGPT package<a class="headerlink" href="#user-mgpt-package" title="Permalink to this headline"></a></h2>
<p>This package contains a fast implementation for LAMMPS of
quantum-based MGPT multi-ion potentials. The MGPT or model GPT method
derives from first-principles DFT-based generalized pseudopotential
@ -1331,7 +1372,7 @@ Contact them directly if you have any questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-misc-package">
<h2>4.27. USER-MISC package<a class="headerlink" href="#user-misc-package" title="Permalink to this headline"></a></h2>
<h2>4.28. USER-MISC package<a class="headerlink" href="#user-misc-package" title="Permalink to this headline"></a></h2>
<p>The files in this package are a potpourri of (mostly) unrelated
features contributed to LAMMPS by users. Each feature is a single
pair of files (<a href="#id2"><span class="problematic" id="id3">*</span></a>.cpp and <a href="#id4"><span class="problematic" id="id5">*</span></a>.h).</p>
@ -1348,7 +1389,7 @@ about the feature or its coding.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-molfile-package">
<h2>4.28. USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline"></a></h2>
<h2>4.29. USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline"></a></h2>
<p>This package contains a dump molfile command which uses molfile
plugins that are bundled with the
<a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a> molecular visualization and
@ -1367,7 +1408,7 @@ application itself.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-omp-package">
<h2>4.29. USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline"></a></h2>
<h2>4.30. USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline"></a></h2>
<p>This package provides OpenMP multi-threading support and
other optimizations of various LAMMPS pair styles, dihedral
styles, and fix styles.</p>
@ -1378,7 +1419,7 @@ styles, and fix styles.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-phonon-package">
<h2>4.30. USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline"></a></h2>
<h2>4.31. USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline"></a></h2>
<p>This package contains a fix phonon command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
relations, directly from molecular dynamics simulations.</p>
@ -1390,7 +1431,7 @@ if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-qmmm-package">
<h2>4.31. USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline"></a></h2>
<h2>4.32. USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline"></a></h2>
<p>This package provides a fix qmmm command which allows LAMMPS to be
used in a QM/MM simulation, currently only in combination with pw.x
code from the <a class="reference external" href="http://www.quantum-espresso.org">Quantum ESPRESSO</a> package.</p>
@ -1407,7 +1448,7 @@ without changes to LAMMPS itself.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-qtb-package">
<h2>4.32. USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline"></a></h2>
<h2>4.33. USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline"></a></h2>
<p>This package provides a self-consistent quantum treatment of the
vibrational modes in a classical molecular dynamics simulation. By
coupling the MD simulation to a colored thermostat, it introduces zero
@ -1429,7 +1470,7 @@ have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-reaxc-package">
<h2>4.33. USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline"></a></h2>
<h2>4.34. USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline"></a></h2>
<p>This package contains a implementation for LAMMPS of the ReaxFF force
field. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
@ -1457,7 +1498,7 @@ questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-smd-package">
<h2>4.34. USER-SMD package<a class="headerlink" href="#user-smd-package" title="Permalink to this headline"></a></h2>
<h2>4.35. USER-SMD package<a class="headerlink" href="#user-smd-package" title="Permalink to this headline"></a></h2>
<p>This package implements smoothed Mach dynamics (SMD) in
LAMMPS. Currently, the package has the following features:</p>
<ul class="simple">
@ -1481,7 +1522,7 @@ you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-smtbq-package">
<h2>4.35. USER-SMTBQ package<a class="headerlink" href="#user-smtbq-package" title="Permalink to this headline"></a></h2>
<h2>4.36. USER-SMTBQ package<a class="headerlink" href="#user-smtbq-package" title="Permalink to this headline"></a></h2>
<p>This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
potential for the description of ionocovalent bonds in oxides.</p>
<p>There are example scripts for using this package in
@ -1495,7 +1536,7 @@ them directly if you have any questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-sph-package">
<h2>4.36. USER-SPH package<a class="headerlink" href="#user-sph-package" title="Permalink to this headline"></a></h2>
<h2>4.37. USER-SPH package<a class="headerlink" href="#user-sph-package" title="Permalink to this headline"></a></h2>
<p>This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:</p>
<ul class="simple">

31
doc/Section_packages.txt
View File

@ -201,6 +201,7 @@ USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sd
USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda
USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
USER-DPD, dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
USER-DRUDE, Drude oscillators, Dequidt & Devemy & Padua (3), "tutorial"_tutorial_drude.html, USER/drude, -, -
USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
@ -245,6 +246,9 @@ Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
(4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
Olivier Politano, and Robert Tetot (LAAS-CNRS, France).
(4) The USER-DPD package was created by James Larentzos, Timothy
Mattox, and John Brennan (Army Research Lab (ARL) and Engility Corp).
If the Library is not listed as lib/package, then it is a third-party
library not included in the LAMMPS distribution. See the
src/package/Makefile.lammps file for info on where to download the
@ -455,6 +459,33 @@ Arkansas. Contact him directly if you have questions.
:line
USER-DPD package :h4
This package implements the dissipative particle dynamics (DPD) method
under isothermal, isoenergetic, isobaric and isenthalpic conditions.
The DPD equations of motion are integrated efficiently through the
Shardlow splitting algorithm.
See these doc pages and their related commands to get started:
"compute dpd"_compute_dpd.html
"compute dpd/atom"_compute_dpd_atom.html
"fix_eos/cv"_fix_eos_table.html
"fix_eos/table"_fix_eos_table.html
"fix_shardlow"_fix_shardlow.html
"pair_dpd/conservative"_pair_dpd_conservative.html
"pair_dpd/fdt"_pair_dpd_fdt.html
"pair_dpd/fdt/energy"_pair_dpd_fdt.html :ul
There are example scripts for using this package in examples/USER/dpd.
The people who created this package are James Larentzos
(james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at
engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil).
Contact them directly if you have questions.
:line
USER-DRUDE package :h4
This package implements methods for simulating polarizable systems

35
doc/_sources/Section_packages.txt
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@ -246,6 +246,8 @@ The current list of user-contributed packages is as follows:
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-DIFFRACTION | virutal x-ray and electron diffraction | Shawn Coleman (ARL) | :doc:`compute xrd <compute_xrd>` | USER/diffraction | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-DPD | dissipative particle dynamics (DPD) | Larentzos & Mattox & Brennan (5) | src/USER-DPD/README | USER/dpd | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-DRUDE | Drude oscillators | Dequidt & Devemy & Padua (3) | :doc:`tutorial <tutorial_drude>` | USER/drude | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-EFF | electron force field | Andres Jaramillo-Botero (Caltech) | :doc:`pair_style eff/cut <pair_eff>` | USER/eff | `eff <eff_>`_ | - |
@ -324,6 +326,9 @@ Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
(4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
Olivier Politano, and Robert Tetot (LAAS-CNRS, France).
(4) The USER-DPD package was created by James Larentzos, Timothy
Mattox, and John Brennan (Army Research Lab (ARL) and Engility Corp).
If the Library is not listed as lib/package, then it is a third-party
library not included in the LAMMPS distribution. See the
src/package/Makefile.lammps file for info on where to download the
@ -557,6 +562,36 @@ Arkansas. Contact him directly if you have questions.
----------
USER-DPD package
----------------
This package implements the dissipative particle dynamics (DPD) method
under isothermal, isoenergetic, isobaric and isenthalpic conditions.
The DPD equations of motion are integrated efficiently through the
Shardlow splitting algorithm.
See these doc pages and their related commands to get started:
* :doc:`compute dpd <compute_dpd>`
* :doc:`compute dpd/atom <compute_dpd_atom>`
* :doc:`fix_eos/cv <fix_eos_table>`
* :doc:`fix_eos/table <fix_eos_table>`
* :doc:`fix_shardlow <fix_shardlow>`
* :doc:`pair_dpd/conservative <pair_dpd_conservative>`
* :doc:`pair_dpd/fdt <pair_dpd_fdt>`
* :doc:`pair_dpd/fdt/energy <pair_dpd_fdt>`
There are example scripts for using this package in examples/USER/dpd.
The people who created this package are James Larentzos
(james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at
engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil).
Contact them directly if you have questions.
----------
USER-DRUDE package
------------------

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