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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_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="">4. Packages</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#standard-packages">4.1. Standard packages</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#asphere-package">4.1.1. ASPHERE package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#body-package">4.1.2. BODY package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#class2-package">4.1.3. CLASS2 package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#colloid-package">4.1.4. COLLOID package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#compress-package">4.1.5. COMPRESS package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#coreshell-package">4.1.6. CORESHELL package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#dipole-package">4.1.7. DIPOLE package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#fld-package">4.1.8. FLD package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#gpu-package">4.1.9. GPU package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#granular-package">4.1.10. GRANULAR package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#kim-package">4.1.11. KIM package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#kokkos-package">4.1.12. KOKKOS package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#kspace-package">4.1.13. KSPACE package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#manybody-package">4.1.14. MANYBODY package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#mc-package">4.1.15. MC package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#meam-package">4.1.16. MEAM package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#misc-package">4.1.17. MISC package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#molecule-package">4.1.18. MOLECULE package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#mpiio-package">4.1.19. MPIIO package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#opt-package">4.1.20. OPT package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#peri-package">4.1.21. PERI package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#poems-package">4.1.22. POEMS package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#python-package">4.1.23. PYTHON package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#qeq-package">4.1.24. QEQ package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#reax-package">4.1.25. REAX package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#replica-package">4.1.26. REPLICA package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#rigid-package">4.1.27. RIGID package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#shock-package">4.1.28. SHOCK package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#snap-package">4.1.29. SNAP package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#srd-package">4.1.30. SRD package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#voronoi-package">4.1.31. VORONOI package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#xtc-package">4.1.32. XTC package</a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="#user-packages">4.2. User packages</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#user-atc-package">4.2.1. USER-ATC package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-awpmd-package">4.2.2. USER-AWPMD package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-cg-cmm-package">4.2.3. USER-CG-CMM package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-colvars-package">4.2.4. USER-COLVARS package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-cuda-package">4.2.5. USER-CUDA package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-diffraction-package">4.2.6. USER-DIFFRACTION package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-dpd-package">4.2.7. USER-DPD package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-drude-package">4.2.8. USER-DRUDE package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-eff-package">4.2.9. USER-EFF package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-fep-package">4.2.10. USER-FEP package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-h5md-package">4.2.11. USER-H5MD package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-intel-package">4.2.12. USER-INTEL package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-lb-package">4.2.13. USER-LB package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-mgpt-package">4.2.14. USER-MGPT package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-misc-package">4.2.15. USER-MISC package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-molfile-package">4.2.16. USER-MOLFILE package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-omp-package">4.2.17. USER-OMP package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-phonon-package">4.2.18. USER-PHONON package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-qmmm-package">4.2.19. USER-QMMM package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-qtb-package">4.2.20. USER-QTB package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-quip-package">4.2.21. USER-QUIP package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-reaxc-package">4.2.22. USER-REAXC package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-smd-package">4.2.23. USER-SMD package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-smtbq-package">4.2.24. USER-SMTBQ package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-sph-package">4.2.25. USER-SPH package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-tally-package">4.2.26. USER-TALLY package</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#user-vtk-package">4.2.27. USER-VTK package</a></li>
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</ul>
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</li>
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</ul>
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</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_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</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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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<div class="section" id="packages">
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<h1>4. Packages<a class="headerlink" href="#packages" title="Permalink to this headline">¶</a></h1>
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<p>This section gives an overview of the add-on optional packages that
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extend LAMMPS functionality. Packages are groups of files that enable
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a specific set of features. For example, force fields for molecular
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systems or granular systems are in packages. You can see the list of
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all packages by typing “make package” from within the src directory of
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the LAMMPS distribution.</p>
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<p>Here are links for two tables below, which list standard and user
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packages.</p>
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<div class="line-block">
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<div class="line">4.1 <a class="reference internal" href="#pkg-1"><span>Standard packages</span></a></div>
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<div class="line">4.2 <a class="reference internal" href="#pkg-2"><span>User packages</span></a></div>
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<div class="line"><br /></div>
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</div>
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<p><a class="reference internal" href="Section_start.html#start-3"><span>Section_start 3</span></a> of the manual describes
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the difference between standard packages and user packages. It also
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has general details on how to include/exclude specific packages as
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part of the LAMMPS build process, and on how to build auxiliary
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libraries or modify a machine Makefile if a package requires it.</p>
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<p>Following the two tables below, is a sub-section for each package. It
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has a summary of what the package contains. It has specific
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instructions on how to install it, build or obtain any auxiliary
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library it requires, and any Makefile.machine changes it requires. It
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also lists pointers to examples of its use or documentation provided
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in the LAMMPS distribution.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">The sub-sections below are still being filled in, as of Feb
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2016.</p>
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</div>
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<p>Unless otherwise noted below, every package is independent of all the
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others. I.e. any package can be included or excluded in a LAMMPS
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build, independent of all other packages. However, note that some
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packages include commands derived from commands in other packages. If
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the other package is not installed, the derived command from the new
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package will also not be installed when you include the new one.
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E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package
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will not be installed as part of the USER-OMP package if the KSPACE
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package is not also installed, since it contains the pair
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lj/cut/coul/long command. If you later install the KSPACE pacakge and
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the USER-OMP package is already installed, both the pair
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lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.</p>
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<hr class="docutils" />
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<div class="section" id="standard-packages">
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<span id="pkg-1"></span><h2>4.1. Standard packages<a class="headerlink" href="#standard-packages" title="Permalink to this headline">¶</a></h2>
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<p>The current list of standard packages is as follows. Each package
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name links to a sub-section below with more details.</p>
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<table border="1" class="docutils">
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<colgroup>
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<col width="16%" />
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<col width="21%" />
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<col width="22%" />
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<col width="28%" />
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<col width="6%" />
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<col width="7%" />
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td>Package</td>
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<td>Description</td>
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<td>Author(s)</td>
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<td>Doc page</td>
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<td>Example</td>
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<td>Library</td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="#asphere"><span>ASPHERE</span></a></td>
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<td>aspherical particles</td>
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<td><ul class="first last simple">
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<li></li>
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</ul>
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</td>
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<td><a class="reference internal" href="Section_howto.html#howto-14"><span>Section_howto 6.14</span></a></td>
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<td>ellipse</td>
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<td><ul class="first last simple">
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<li></li>
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</ul>
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</td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="#body"><span>BODY</span></a></td>
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<td>body-style particles</td>
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<td><ul class="first last simple">
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<li></li>
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</ul>
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</td>
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<td><a class="reference internal" href="body.html"><em>body</em></a></td>
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<td>body</td>
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<td><ul class="first last simple">
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<li></li>
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</ul>
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</td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="#class2"><span>CLASS2</span></a></td>
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<td>class 2 force fields</td>
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<td><ul class="first last simple">
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<li></li>
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</ul>
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</td>
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<td><a class="reference internal" href="pair_class2.html"><em>pair_style lj/class2</em></a></td>
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<td><ul class="first last simple">
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<li></li>
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</ul>
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</td>
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<td><ul class="first last simple">
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<li></li>
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</ul>
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</td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="#colloid"><span>COLLOID</span></a></td>
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<td>colloidal particles</td>
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<td><ul class="first last simple">
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<li></li>
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</ul>
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</td>
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<td><a class="reference internal" href="atom_style.html"><em>atom_style colloid</em></a></td>
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<td>colloid</td>
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<td><ul class="first last simple">
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<li></li>
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</ul>
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</td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="#compress"><span>COMPRESS</span></a></td>
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<td>I/O compression</td>
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<td>Axel Kohlmeyer (Temple U)</td>
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<td><a class="reference internal" href="dump.html"><em>dump */gz</em></a></td>
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<td><ul class="first last simple">
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<li></li>
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</ul>
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</td>
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<td><ul class="first last simple">
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<li></li>
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</ul>
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</td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="#coreshell"><span>CORESHELL</span></a></td>
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<td>adiabatic core/shell model</td>
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<td>Hendrik Heenen (Technical U of Munich)</td>
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<td><a class="reference internal" href="Section_howto.html#howto-25"><span>Section_howto 6.25</span></a></td>
|
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<td>coreshell</td>
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<td><ul class="first last simple">
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<li></li>
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</ul>
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</td>
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</tr>
|
|
<tr class="row-even"><td><a class="reference internal" href="#dipole"><span>DIPOLE</span></a></td>
|
|
<td>point dipole particles</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td><a class="reference internal" href="pair_dipole.html"><em>pair_style dipole/cut</em></a></td>
|
|
<td>dipole</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#fld"><span>FLD</span></a></td>
|
|
<td>Fast Lubrication Dynamics</td>
|
|
<td>Kumar & Bybee & Higdon (1)</td>
|
|
<td><a class="reference internal" href="pair_lubricateU.html"><em>pair_style lubricateU</em></a></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-even"><td><a class="reference internal" href="#gpu"><span>GPU</span></a></td>
|
|
<td>GPU-enabled styles</td>
|
|
<td>Mike Brown (ORNL)</td>
|
|
<td><a class="reference internal" href="accelerate_gpu.html"><em>Section accelerate</em></a></td>
|
|
<td>gpu</td>
|
|
<td>lib/gpu</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#granular"><span>GRANULAR</span></a></td>
|
|
<td>granular systems</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td><a class="reference internal" href="Section_howto.html#howto-6"><span>Section_howto 6.6</span></a></td>
|
|
<td>pour</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
</tr>
|
|
<tr class="row-even"><td><a class="reference internal" href="#kim"><span>KIM</span></a></td>
|
|
<td>openKIM potentials</td>
|
|
<td>Smirichinski & Elliot & Tadmor (3)</td>
|
|
<td><a class="reference internal" href="pair_kim.html"><em>pair_style kim</em></a></td>
|
|
<td>kim</td>
|
|
<td>KIM</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#kokkos"><span>KOKKOS</span></a></td>
|
|
<td>Kokkos-enabled styles</td>
|
|
<td>Trott & Edwards (4)</td>
|
|
<td><a class="reference internal" href="accelerate_kokkos.html"><em>Section_accelerate</em></a></td>
|
|
<td>kokkos</td>
|
|
<td>lib/kokkos</td>
|
|
</tr>
|
|
<tr class="row-even"><td><a class="reference internal" href="#kspace"><span>KSPACE</span></a></td>
|
|
<td>long-range Coulombic solvers</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td><a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a></td>
|
|
<td>peptide</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#manybody"><span>MANYBODY</span></a></td>
|
|
<td>many-body potentials</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td><a class="reference internal" href="pair_tersoff.html"><em>pair_style tersoff</em></a></td>
|
|
<td>shear</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
</tr>
|
|
<tr class="row-even"><td><a class="reference internal" href="#meam"><span>MEAM</span></a></td>
|
|
<td>modified EAM potential</td>
|
|
<td>Greg Wagner (Sandia)</td>
|
|
<td><a class="reference internal" href="pair_meam.html"><em>pair_style meam</em></a></td>
|
|
<td>meam</td>
|
|
<td>lib/meam</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#mc"><span>MC</span></a></td>
|
|
<td>Monte Carlo options</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td><a class="reference internal" href="fix_gcmc.html"><em>fix gcmc</em></a></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-even"><td><a class="reference internal" href="#molecule"><span>MOLECULE</span></a></td>
|
|
<td>molecular system force fields</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td><a class="reference internal" href="Section_howto.html#howto-3"><span>Section_howto 6.3</span></a></td>
|
|
<td>peptide</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#opt"><span>OPT</span></a></td>
|
|
<td>optimized pair styles</td>
|
|
<td>Fischer & Richie & Natoli (2)</td>
|
|
<td><a class="reference internal" href="accelerate_opt.html"><em>Section accelerate</em></a></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-even"><td><a class="reference internal" href="#peri"><span>PERI</span></a></td>
|
|
<td>Peridynamics models</td>
|
|
<td>Mike Parks (Sandia)</td>
|
|
<td><a class="reference internal" href="pair_peri.html"><em>pair_style peri</em></a></td>
|
|
<td>peri</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#poems"><span>POEMS</span></a></td>
|
|
<td>coupled rigid body motion</td>
|
|
<td>Rudra Mukherjee (JPL)</td>
|
|
<td><a class="reference internal" href="fix_poems.html"><em>fix poems</em></a></td>
|
|
<td>rigid</td>
|
|
<td>lib/poems</td>
|
|
</tr>
|
|
<tr class="row-even"><td><a class="reference internal" href="#python"><span>PYTHON</span></a></td>
|
|
<td>embed Python code in an input script</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td><a class="reference internal" href="python.html"><em>python</em></a></td>
|
|
<td>python</td>
|
|
<td>lib/python</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#reax"><span>REAX</span></a></td>
|
|
<td>ReaxFF potential</td>
|
|
<td>Aidan Thompson (Sandia)</td>
|
|
<td><a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a></td>
|
|
<td>reax</td>
|
|
<td>lib/reax</td>
|
|
</tr>
|
|
<tr class="row-even"><td><a class="reference internal" href="#replica"><span>REPLICA</span></a></td>
|
|
<td>multi-replica methods</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td><a class="reference internal" href="Section_howto.html#howto-5"><span>Section_howto 6.5</span></a></td>
|
|
<td>tad</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#rigid"><span>RIGID</span></a></td>
|
|
<td>rigid bodies</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td><a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a></td>
|
|
<td>rigid</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
</tr>
|
|
<tr class="row-even"><td><a class="reference internal" href="#shock"><span>SHOCK</span></a></td>
|
|
<td>shock loading methods</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td><a class="reference internal" href="fix_msst.html"><em>fix msst</em></a></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><a class="reference internal" href="#snap"><span>SNAP</span></a></td>
|
|
<td>quantum-fit potential</td>
|
|
<td>Aidan Thompson (Sandia)</td>
|
|
<td><a class="reference internal" href="pair_snap.html"><em>pair snap</em></a></td>
|
|
<td>snap</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
</tr>
|
|
<tr class="row-even"><td><a class="reference internal" href="#srd"><span>SRD</span></a></td>
|
|
<td>stochastic rotation dynamics</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td><a class="reference internal" href="fix_srd.html"><em>fix srd</em></a></td>
|
|
<td>srd</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#voronoi"><span>VORONOI</span></a></td>
|
|
<td>Voronoi tesselations</td>
|
|
<td>Daniel Schwen (LANL)</td>
|
|
<td><a class="reference internal" href="compute_voronoi_atom.html"><em>compute voronoi/atom</em></a></td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td>Voro++</td>
|
|
</tr>
|
|
<tr class="row-even"><td><a class="reference internal" href="#xtc"><span>XTC</span></a></td>
|
|
<td>dumps in XTC format</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td><a class="reference internal" href="dump.html"><em>dump</em></a></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> </td>
|
|
<td> </td>
|
|
<td> </td>
|
|
<td> </td>
|
|
<td> </td>
|
|
<td> </td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<p>The “Authors” column lists a name(s) if a specific person is
|
|
responible for creating and maintaining the package.</p>
|
|
<p>(1) The FLD package was created by Amit Kumar and Michael Bybee from
|
|
Jonathan Higdon’s group at UIUC.</p>
|
|
<p>(2) The OPT package was created by James Fischer (High Performance
|
|
Technologies), David Richie, and Vincent Natoli (Stone Ridge
|
|
Technolgy).</p>
|
|
<p>(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
|
|
and Ellad Tadmor (U Minn).</p>
|
|
<p>(4) The KOKKOS package was created primarily by Christian Trott
|
|
(Sandia). It uses the Kokkos library which was developed by Carter
|
|
Edwards, Christian, and collaborators at Sandia.</p>
|
|
<p>The “Doc page” column links to either a sub-section of the
|
|
<a class="reference internal" href="Section_howto.html"><em>Section_howto</em></a> of the manual, or an input script
|
|
command implemented as part of the package, or to additional
|
|
documentation provided within the package.</p>
|
|
<p>The “Example” column is a sub-directory in the examples directory of
|
|
the distribution which has an input script that uses the package.
|
|
E.g. “peptide” refers to the examples/peptide directory.</p>
|
|
<p>The “Library” column lists an external library which must be built
|
|
first and which LAMMPS links to when it is built. If it is listed as
|
|
lib/package, then the code for the library is under the lib directory
|
|
of the LAMMPS distribution. See the lib/package/README file for info
|
|
on how to build the library. If it is not listed as lib/package, then
|
|
it is a third-party library not included in the LAMMPS distribution.
|
|
See details on all of this below for individual packages.
|
|
p.s.: are we ever going to get commit messages from you? ;-)</p>
|
|
<hr class="docutils" />
|
|
<div class="section" id="asphere-package">
|
|
<span id="asphere"></span><h3>4.1.1. ASPHERE package<a class="headerlink" href="#asphere-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents: Aspherical particle models for ellipsoids, 2d lines, 3d
|
|
triangles.</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-asphere
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p asphere -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-asphere
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^asphere -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/ASPHERE, examples/ellipse, Section howto
|
|
6.14, pair gayberne</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="body-package">
|
|
<span id="body"></span><h3>4.1.2. BODY package<a class="headerlink" href="#body-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/body</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="class2-package">
|
|
<span id="class2"></span><h3>4.1.3. CLASS2 package<a class="headerlink" href="#class2-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-class2
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p class2 -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-class2
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^class2 -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info:</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="colloid-package">
|
|
<span id="colloid"></span><h3>4.1.4. COLLOID package<a class="headerlink" href="#colloid-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-colloid
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p colloid -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-colloid
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^colloid -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/colloid, examples/srd</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="compress-package">
|
|
<span id="compress"></span><h3>4.1.5. COMPRESS package<a class="headerlink" href="#compress-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-compress
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p compress -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-compress
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^compress -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info:</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="coreshell-package">
|
|
<span id="coreshell"></span><h3>4.1.6. CORESHELL package<a class="headerlink" href="#coreshell-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-coreshell
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p coreshell -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-coreshell
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^coreshell -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/coreshell, Section howto 6.26</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="dipole-package">
|
|
<span id="dipole"></span><h3>4.1.7. DIPOLE package<a class="headerlink" href="#dipole-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-dipole
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p dipole -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-dipole
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^dipole -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/dipole</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="fld-package">
|
|
<span id="fld"></span><h3>4.1.8. FLD package<a class="headerlink" href="#fld-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-fld
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p fld -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-fld
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^fld -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info:</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="gpu-package">
|
|
<span id="gpu"></span><h3>4.1.9. GPU package<a class="headerlink" href="#gpu-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-gpu
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p gpu -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-gpu
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^gpu -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/accelerate, bench/FERMI, bench/KEPLER</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="granular-package">
|
|
<span id="granular"></span><h3>4.1.10. GRANULAR package<a class="headerlink" href="#granular-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-granular
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p granular -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-granular
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^granular -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/pour, bench/in.chute, Section howto 6.6</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="kim-package">
|
|
<span id="kim"></span><h3>4.1.11. KIM package<a class="headerlink" href="#kim-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-kim
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p kim -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-kim
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^kim -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/kim</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="kokkos-package">
|
|
<span id="kokkos"></span><h3>4.1.12. KOKKOS package<a class="headerlink" href="#kokkos-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-kokkow
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p kokkow -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-kokkow
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^kokkow -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info:</p>
|
|
<p>For the KOKKOS package, you have 3 choices when building. You can
|
|
build with OMP or Cuda or Phi support. Phi support uses Xeon Phi
|
|
chips in “native” mode. This can be done by setting the following
|
|
variables in your Makefile.machine:</p>
|
|
<ul class="simple">
|
|
<li>for OMP support, set OMP = yes</li>
|
|
<li>for Cuda support, set OMP = yes and CUDA = yes</li>
|
|
<li>for Phi support, set OMP = yes and MIC = yes</li>
|
|
</ul>
|
|
<p>These can also be set as additional arguments to the make command, e.g.</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make g++ OMP=yes MIC=yes
|
|
</pre></div>
|
|
</div>
|
|
<p>Building the KOKKOS package with CUDA support requires a Makefile
|
|
machine that uses the NVIDIA “nvcc” compiler, as well as an
|
|
appropriate “arch” setting appropriate to the GPU hardware and NVIDIA
|
|
software you have on your machine. See
|
|
src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine
|
|
Makefile.</p>
|
|
<p>Examples: examples/accelerate, bench/FERMI, bench/KEPLER</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="kspace-package">
|
|
<span id="kspace"></span><h3>4.1.13. KSPACE package<a class="headerlink" href="#kspace-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-kspace
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p kspace -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-kspace
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^kspace -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info:</p>
|
|
<p>Examples: examples/peptide, bench/in.rhodo</p>
|
|
<p>Doc: Section howto 6.7, Section howto 6.8, Section howto 6.9</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="manybody-package">
|
|
<span id="manybody"></span><h3>4.1.14. MANYBODY package<a class="headerlink" href="#manybody-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-manybody
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p manybody -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-manybody
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^manybody -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info:</p>
|
|
<p>Examples: examples/comb, examples/eim, examples/nb3d, examples/vashishta</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="mc-package">
|
|
<span id="mc"></span><h3>4.1.15. MC package<a class="headerlink" href="#mc-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-mc
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p mc -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-mc
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^mc -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info:</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="meam-package">
|
|
<span id="meam"></span><h3>4.1.16. MEAM package<a class="headerlink" href="#meam-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-meam
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p meam -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-meam
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^meam -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/meam</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="misc-package">
|
|
<span id="misc"></span><h3>4.1.17. MISC package<a class="headerlink" href="#misc-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-misc
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p misc -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-misc
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^misc -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/misc</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="molecule-package">
|
|
<span id="molecule"></span><h3>4.1.18. MOLECULE package<a class="headerlink" href="#molecule-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-molecule
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p molecule -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-molecule
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^molecule -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo, Section howto 6.3</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="mpiio-package">
|
|
<span id="mpiio"></span><h3>4.1.19. MPIIO package<a class="headerlink" href="#mpiio-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-mpiio
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p mpiio -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-mpiio
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^mpiio -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info:</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="opt-package">
|
|
<span id="opt"></span><h3>4.1.20. OPT package<a class="headerlink" href="#opt-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-opt
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p opt -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-opt
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^opt -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/accelerate, bench/KEPLER</p>
|
|
<p>For the OPT package, your Makefile.machine needs an additional
|
|
settings for CCFLAGS.</p>
|
|
<ul class="simple">
|
|
<li>CCFLAGS: add -restrict</li>
|
|
</ul>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="peri-package">
|
|
<span id="peri"></span><h3>4.1.21. PERI package<a class="headerlink" href="#peri-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-peri
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p peri -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-peri
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^peri -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/peri</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="poems-package">
|
|
<span id="poems"></span><h3>4.1.22. POEMS package<a class="headerlink" href="#poems-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-poems
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p poems -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-poems
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^poems -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/rigid</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="python-package">
|
|
<span id="python"></span><h3>4.1.23. PYTHON package<a class="headerlink" href="#python-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-python
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p python -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-python
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^python -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/python</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="qeq-package">
|
|
<span id="qeq"></span><h3>4.1.24. QEQ package<a class="headerlink" href="#qeq-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-qeq
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p qeq -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-qeq
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^qeq -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/qeq</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="reax-package">
|
|
<span id="reax"></span><h3>4.1.25. REAX package<a class="headerlink" href="#reax-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-reax
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p reax -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-reax
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^reax -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/reax</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="replica-package">
|
|
<span id="replica"></span><h3>4.1.26. REPLICA package<a class="headerlink" href="#replica-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-replica
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p replica -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-replica
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^replica -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/neb, examples/prd, examples/tad, Section howto 6.5</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="rigid-package">
|
|
<span id="rigid"></span><h3>4.1.27. RIGID package<a class="headerlink" href="#rigid-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-rigid
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p rigid -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-rigid
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^rigid -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/ASPHERE, examples/rigid</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="shock-package">
|
|
<span id="shock"></span><h3>4.1.28. SHOCK package<a class="headerlink" href="#shock-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-shock
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p shock -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-shock
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^shock -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/hugoniostat, examples/msst</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="snap-package">
|
|
<span id="snap"></span><h3>4.1.29. SNAP package<a class="headerlink" href="#snap-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-snap
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p snap -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-snap
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^snap -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/snap</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="srd-package">
|
|
<span id="srd"></span><h3>4.1.30. SRD package<a class="headerlink" href="#srd-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-srd
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p srd -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-srd
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^srd -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info:</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="voronoi-package">
|
|
<span id="voronoi"></span><h3>4.1.31. VORONOI package<a class="headerlink" href="#voronoi-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-voronoi
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p voronoi -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-voronoi
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^voronoi -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info: examples/voronoi</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="xtc-package">
|
|
<span id="xtc"></span><h3>4.1.32. XTC package<a class="headerlink" href="#xtc-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-xtc
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p xtc -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-xtc
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^xtc -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info:</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
</div>
|
|
<div class="section" id="user-packages">
|
|
<span id="pkg-2"></span><h2>4.2. User packages<a class="headerlink" href="#user-packages" title="Permalink to this headline">¶</a></h2>
|
|
<p>The current list of user-contributed packages is as follows:</p>
|
|
<table border="1" class="docutils">
|
|
<colgroup>
|
|
<col width="18%" />
|
|
<col width="19%" />
|
|
<col width="20%" />
|
|
<col width="23%" />
|
|
<col width="7%" />
|
|
<col width="9%" />
|
|
<col width="5%" />
|
|
</colgroup>
|
|
<tbody valign="top">
|
|
<tr class="row-odd"><td>Package</td>
|
|
<td>Description</td>
|
|
<td>Author(s)</td>
|
|
<td>Doc page</td>
|
|
<td>Example</td>
|
|
<td>Pic/movie</td>
|
|
<td>Library</td>
|
|
</tr>
|
|
<tr class="row-even"><td><a class="reference internal" href="#user-atc"><span>USER-ATC</span></a></td>
|
|
<td>atom-to-continuum coupling</td>
|
|
<td>Jones & Templeton & Zimmerman (1)</td>
|
|
<td><a class="reference internal" href="fix_atc.html"><em>fix atc</em></a></td>
|
|
<td>USER/atc</td>
|
|
<td><a class="reference external" href="http://lammps.sandia.gov/pictures.html#atc">atc</a></td>
|
|
<td>lib/atc</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#user-awpmd"><span>USER-AWPMD</span></a></td>
|
|
<td>wave-packet MD</td>
|
|
<td>Ilya Valuev (JIHT)</td>
|
|
<td><a class="reference internal" href="pair_awpmd.html"><em>pair_style awpmd/cut</em></a></td>
|
|
<td>USER/awpmd</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td>lib/awpmd</td>
|
|
</tr>
|
|
<tr class="row-even"><td><a class="reference internal" href="#user-cg-cmm"><span>USER-CG-CMM</span></a></td>
|
|
<td>coarse-graining model</td>
|
|
<td>Axel Kohlmeyer (Temple U)</td>
|
|
<td><a class="reference internal" href="pair_sdk.html"><em>pair_style lj/sdk</em></a></td>
|
|
<td>USER/cg-cmm</td>
|
|
<td><a class="reference external" href="http://lammps.sandia.gov/pictures.html#cg">cg</a></td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#user-colvars"><span>USER-COLVARS</span></a></td>
|
|
<td>collective variables</td>
|
|
<td>Fiorin & Henin & Kohlmeyer (2)</td>
|
|
<td><a class="reference internal" href="fix_colvars.html"><em>fix colvars</em></a></td>
|
|
<td>USER/colvars</td>
|
|
<td><a class="reference external" href="colvars">colvars</a></td>
|
|
<td>lib/colvars</td>
|
|
</tr>
|
|
<tr class="row-even"><td><a class="reference internal" href="#user-cuda"><span>USER-CUDA</span></a></td>
|
|
<td>NVIDIA GPU styles</td>
|
|
<td>Christian Trott (U Tech Ilmenau)</td>
|
|
<td><a class="reference internal" href="accelerate_cuda.html"><em>Section accelerate</em></a></td>
|
|
<td>USER/cuda</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td>lib/cuda</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#user-diffraction"><span>USER-DIFFRACTION</span></a></td>
|
|
<td>virutal x-ray and electron diffraction</td>
|
|
<td>Shawn Coleman (ARL)</td>
|
|
<td><a class="reference internal" href="compute_xrd.html"><em>compute xrd</em></a></td>
|
|
<td>USER/diffraction</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-even"><td><a class="reference internal" href="#user-dpd"><span>USER-DPD</span></a></td>
|
|
<td>dissipative particle dynamics (DPD)</td>
|
|
<td>Larentzos & Mattox & 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><a class="reference internal" href="#user-drude"><span>USER-DRUDE</span></a></td>
|
|
<td>Drude oscillators</td>
|
|
<td>Dequidt & Devemy & Padua (3)</td>
|
|
<td><a class="reference internal" href="tutorial_drude.html"><em>tutorial</em></a></td>
|
|
<td>USER/drude</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-even"><td><a class="reference internal" href="#user-eff"><span>USER-EFF</span></a></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>
|
|
<td>USER/eff</td>
|
|
<td><a class="reference external" href="http://lammps.sandia.gov/movies.html#eff">eff</a></td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#user-fep"><span>USER-FEP</span></a></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>
|
|
<td>USER/fep</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-even"><td><a class="reference internal" href="#user-h5md"><span>USER-H5MD</span></a></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>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td>lib/h5md</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#user-intel"><span>USER-INTEL</span></a></td>
|
|
<td>Vectorized CPU and Intel(R) coprocessor styles</td>
|
|
<td><ol class="first last upperalpha simple" start="23">
|
|
<li>Michael Brown (Intel)</li>
|
|
</ol>
|
|
</td>
|
|
<td><a class="reference internal" href="accelerate_intel.html"><em>Section accelerate</em></a></td>
|
|
<td>examples/intel</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-even"><td><a class="reference internal" href="#user-lb"><span>USER-LB</span></a></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>
|
|
<td>USER/lb</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><a class="reference internal" href="#user-mgpt"><span>USER-MGPT</span></a></td>
|
|
<td>fast MGPT multi-ion potentials</td>
|
|
<td>Tomas Oppelstrup & John Moriarty (LLNL)</td>
|
|
<td><a class="reference internal" href="pair_mgpt.html"><em>pair_style mgpt</em></a></td>
|
|
<td>USER/mgpt</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-even"><td><a class="reference internal" href="#user-misc"><span>USER-MISC</span></a></td>
|
|
<td>single-file contributions</td>
|
|
<td>USER-MISC/README</td>
|
|
<td>USER-MISC/README</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</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><a class="reference internal" href="#user-molfile"><span>USER-MOLFILE</span></a></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>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td>VMD-MOLFILE</td>
|
|
</tr>
|
|
<tr class="row-even"><td><a class="reference internal" href="#user-omp"><span>USER-OMP</span></a></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>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</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><a class="reference internal" href="#user-phonon"><span>USER-PHONON</span></a></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>
|
|
<td>USER/phonon</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-even"><td><a class="reference internal" href="#user-qmmm"><span>USER-QMMM</span></a></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>
|
|
<td>USER/qmmm</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td>lib/qmmm</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#user-qtb"><span>USER-QTB</span></a></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>
|
|
<td>qtb</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-even"><td><a class="reference internal" href="#user-quip"><span>USER-QUIP</span></a></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>
|
|
<td>USER/quip</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td>lib/quip</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#user-reaxc"><span>USER-REAXC</span></a></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>
|
|
<td>reax</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-even"><td><a class="reference internal" href="#user-smd"><span>USER-SMD</span></a></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>
|
|
<td>USER/smd</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><a class="reference internal" href="#user-smtbq"><span>USER-SMTBQ</span></a></td>
|
|
<td>Second Moment Tight Binding - QEq potential</td>
|
|
<td>Salles & Maras & Politano & Tetot (4)</td>
|
|
<td><a class="reference internal" href="pair_smtbq.html"><em>pair_style smtbq</em></a></td>
|
|
<td>USER/smtbq</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-even"><td><a class="reference internal" href="#user-sph"><span>USER-SPH</span></a></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>
|
|
<td>USER/sph</td>
|
|
<td><a class="reference external" href="http://lammps.sandia.gov/movies.html#sph">sph</a></td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
</tr>
|
|
<tr class="row-odd"><td><a class="reference internal" href="#user-tally"><span>USER-TALLY</span></a></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>
|
|
<td>USER/tally</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-even"><td><a class="reference internal" href="#user-vtk"><span>USER-VTK</span></a></td>
|
|
<td>VTK-style dumps</td>
|
|
<td>Berger and Queteschiner (6)</td>
|
|
<td><code class="xref doc docutils literal"><span class="pre">compute</span> <span class="pre">custom/vtk</span></code></td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td><ul class="first last simple">
|
|
<li></li>
|
|
</ul>
|
|
</td>
|
|
<td>lib/vtk</td>
|
|
</tr>
|
|
<tr class="row-odd"><td> </td>
|
|
<td> </td>
|
|
<td> </td>
|
|
<td> </td>
|
|
<td> </td>
|
|
<td> </td>
|
|
<td> </td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<p>The “Authors” column lists a name(s) if a specific person is
|
|
responible for creating and maintaining the package.</p>
|
|
<p>(1) The ATC package was created by Reese Jones, Jeremy Templeton, and
|
|
Jon Zimmerman (Sandia).</p>
|
|
<p>(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
|
|
the colvars module library written by Giacomo Fiorin (Temple U) and
|
|
Jerome Henin (LISM, Marseille, France).</p>
|
|
<p>(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal
|
|
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>(5) The USER-DPD package was created by James Larentzos (ARL), Timothy
|
|
Mattox (Engility), and John Brennan (ARL).</p>
|
|
<p>(6) The USER-VTK package was created by Richard Berger (JKU) and
|
|
Daniel Queteschiner (DCS Computing).</p>
|
|
<p>The “Doc page” column links to either a sub-section of the
|
|
<a class="reference internal" href="Section_howto.html"><em>Section_howto</em></a> of the manual, or an input script
|
|
command implemented as part of the package, or to additional
|
|
documentation provided within the package.</p>
|
|
<p>The “Example” column is a sub-directory in the examples directory of
|
|
the distribution which has an input script that uses the package.
|
|
E.g. “peptide” refers to the examples/peptide directory. USER/cuda
|
|
refers to the examples/USER/cuda directory.</p>
|
|
<p>The “Library” column lists an external library which must be built
|
|
first and which LAMMPS links to when it is built. If it is listed as
|
|
lib/package, then the code for the library is under the lib directory
|
|
of the LAMMPS distribution. See the lib/package/README file for info
|
|
on how to build the library. If it is not listed as lib/package, then
|
|
it is a third-party library not included in the LAMMPS distribution.
|
|
See details on all of this below for individual packages.</p>
|
|
<hr class="docutils" />
|
|
<div class="section" id="user-atc-package">
|
|
<span id="user-atc"></span><h3>4.2.1. USER-ATC package<a class="headerlink" href="#user-atc-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<p>This package implements a “fix atc” command which can be used in a
|
|
LAMMPS input script. This fix can be employed to either do concurrent
|
|
coupling of MD with FE-based physics surrogates or on-the-fly
|
|
post-processing of atomic information to continuum fields.</p>
|
|
<p>See the doc page for the fix atc command to get started. At the
|
|
bottom of the doc page are many links to additional documentation
|
|
contained in the doc/USER/atc directory.</p>
|
|
<p>There are example scripts for using this package in examples/USER/atc.</p>
|
|
<p>This package uses an external library in lib/atc which must be
|
|
compiled before making LAMMPS. See the lib/atc/README file and the
|
|
LAMMPS manual for information on building LAMMPS with external
|
|
libraries.</p>
|
|
<p>The primary people who created this package are Reese Jones (rjones at
|
|
sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
|
|
Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
|
|
you have questions.</p>
|
|
<p>Examples: examples/USER/atc</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-awpmd-package">
|
|
<span id="user-awpmd"></span><h3>4.2.2. USER-AWPMD package<a class="headerlink" href="#user-awpmd-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<p>This package contains a LAMMPS implementation of the Antisymmetrized
|
|
Wave Packet Molecular Dynamics (AWPMD) method.</p>
|
|
<p>See the doc page for the pair_style awpmd/cut command to get started.</p>
|
|
<p>There are example scripts for using this package in examples/USER/awpmd.</p>
|
|
<p>This package uses an external library in lib/awpmd which must be
|
|
compiled before making LAMMPS. See the lib/awpmd/README file and the
|
|
LAMMPS manual for information on building LAMMPS with external
|
|
libraries.</p>
|
|
<p>The person who created this package is Ilya Valuev at the JIHT in
|
|
Russia (valuev at physik.hu-berlin.de). Contact him directly if you
|
|
have questions.</p>
|
|
<p>Examples: examples/USER/awpmd</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-cg-cmm-package">
|
|
<span id="user-cg-cmm"></span><h3>4.2.3. USER-CG-CMM package<a class="headerlink" href="#user-cg-cmm-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info:</p>
|
|
<p>This package implements 3 commands which can be used in a LAMMPS input
|
|
script:</p>
|
|
<ul class="simple">
|
|
<li>pair_style lj/sdk</li>
|
|
<li>pair_style lj/sdk/coul/long</li>
|
|
<li>angle_style sdk</li>
|
|
</ul>
|
|
<p>These styles allow coarse grained MD simulations with the
|
|
parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
|
|
(SDK), with extensions to simulate ionic liquids, electrolytes, lipids
|
|
and charged amino acids.</p>
|
|
<p>See the doc pages for these commands for details.</p>
|
|
<p>There are example scripts for using this package in
|
|
examples/USER/cg-cmm.</p>
|
|
<p>This is the second generation implementation reducing the the clutter
|
|
of the previous version. For many systems with electrostatics, it will
|
|
be faster to use pair_style hybrid/overlay with lj/sdk and coul/long
|
|
instead of the combined lj/sdk/coul/long style. since the number of
|
|
charged atom types is usually small. For any other coulomb
|
|
interactions this is now required. To exploit this property, the use
|
|
of the kspace_style pppm/cg is recommended over regular pppm. For all
|
|
new styles, input file backward compatibility is provided. The old
|
|
implementation is still available through appending the /old
|
|
suffix. These will be discontinued and removed after the new
|
|
implementation has been fully validated.</p>
|
|
<p>The current version of this package should be considered beta
|
|
quality. The CG potentials work correctly for “normal” situations, but
|
|
have not been testing with all kinds of potential parameters and
|
|
simulation systems.</p>
|
|
<p>The person who created this package is Axel Kohlmeyer at Temple U
|
|
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
|
|
<p>Examples: examples/USER/cg-cmm</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-colvars-package">
|
|
<span id="user-colvars"></span><h3>4.2.4. USER-COLVARS package<a class="headerlink" href="#user-colvars-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<p>This package implements the “fix colvars” command which can be
|
|
used in a LAMMPS input script.</p>
|
|
<p>This fix allows to use “collective variables” to implement
|
|
Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
|
|
Sampling and Restraints. This code consists of two parts:</p>
|
|
<ul class="simple">
|
|
<li>A portable collective variable module library written and maintained</li>
|
|
<li>by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and</li>
|
|
<li>Jerome Henin (LISM, CNRS, Marseille, France). This code is located in</li>
|
|
<li>the directory lib/colvars and needs to be compiled first. The colvars</li>
|
|
<li>fix and an interface layer, exchanges information between LAMMPS and</li>
|
|
<li>the collective variable module.</li>
|
|
</ul>
|
|
<p>See the doc page of <a class="reference internal" href="fix_colvars.html"><em>fix colvars</em></a> for more details.</p>
|
|
<p>There are example scripts for using this package in
|
|
examples/USER/colvars</p>
|
|
<p>This is a very new interface that does not yet support all
|
|
features in the module and will see future optimizations
|
|
and improvements. The colvars module library is also available
|
|
in NAMD has been thoroughly used and tested there. Bugs and
|
|
problems are likely due to the interface layers code.
|
|
Thus the current version of this package should be considered
|
|
beta quality.</p>
|
|
<p>The person who created this package is Axel Kohlmeyer at Temple U
|
|
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
|
|
<p>Examples: examples/USER/colvars</p>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-cuda-package">
|
|
<span id="user-cuda"></span><h3>4.2.5. USER-CUDA package<a class="headerlink" href="#user-cuda-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>This package provides acceleration of various LAMMPS pair styles, fix
|
|
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
|
|
GPUs.</p>
|
|
<p>See this section of the manual to get started:</p>
|
|
<p><span class="xref std std-ref">Section_accelerate</span></p>
|
|
<p>There are example scripts for using this package in
|
|
examples/USER/cuda.</p>
|
|
<p>This package uses an external library in lib/cuda which must be
|
|
compiled before making LAMMPS. See the lib/cuda/README file and the
|
|
LAMMPS manual for information on building LAMMPS with external
|
|
libraries.</p>
|
|
<p>The person who created this package is Christian Trott at the
|
|
University of Technology Ilmenau, Germany (christian.trott at
|
|
tu-ilmenau.de). Contact him directly if you have questions.</p>
|
|
<p>Examples: examples/accelerate, bench/FERMI, bench/KEPLER</p>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-diffraction-package">
|
|
<span id="user-diffraction"></span><h3>4.2.6. USER-DIFFRACTION package<a class="headerlink" href="#user-diffraction-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>This package contains the commands neeed to calculate x-ray and
|
|
electron diffraction intensities based on kinematic diffraction
|
|
theory.</p>
|
|
<p>See these doc pages and their related commands to get started:</p>
|
|
<ul class="simple">
|
|
<li><a class="reference internal" href="compute_xrd.html"><em>compute xrd</em></a></li>
|
|
<li><a class="reference internal" href="compute_saed.html"><em>compute saed</em></a></li>
|
|
<li><a class="reference internal" href="fix_saed_vtk.html"><em>fix saed/vtk</em></a></li>
|
|
</ul>
|
|
<p>The person who created this package is Shawn P. Coleman
|
|
(shawn.p.coleman8.ctr at mail.mil) while at the University of
|
|
Arkansas. Contact him directly if you have questions.</p>
|
|
<p>Examples: examples/USER/diffraction</p>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info:</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-dpd-package">
|
|
<span id="user-dpd"></span><h3>4.2.7. USER-DPD package<a class="headerlink" href="#user-dpd-package" title="Permalink to this headline">¶</a></h3>
|
|
<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>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Examples: examples/USER/dpd</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-drude-package">
|
|
<span id="user-drude"></span><h3>4.2.8. USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<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>
|
|
<ul class="simple">
|
|
<li><a class="reference internal" href="tutorial_drude.html"><em>Drude tutorial</em></a></li>
|
|
<li><a class="reference internal" href="fix_drude.html"><em>fix drude</em></a></li>
|
|
<li><a class="reference internal" href="compute_temp_drude.html"><em>compute temp/drude</em></a></li>
|
|
<li><a class="reference internal" href="fix_langevin_drude.html"><em>fix langevin/drude</em></a></li>
|
|
<li><a class="reference internal" href="fix_drude_transform.html"><em>fix drude/transform/...</em></a></li>
|
|
<li><a class="reference internal" href="pair_thole.html"><em>pair thole</em></a></li>
|
|
</ul>
|
|
<p>There are auxiliary tools for using this package in tools/drude.</p>
|
|
<p>The person who created this package is Alain Dequidt at Universite
|
|
Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
|
|
Contact him directly if you have questions. Co-authors: Julien Devemy,
|
|
Agilio Padua.</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Examples: examples/USER/drude</p>
|
|
<p>Doc: Section howto 6.27</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-eff-package">
|
|
<span id="user-eff"></span><h3>4.2.9. USER-EFF package<a class="headerlink" href="#user-eff-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<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,
|
|
2010. The eFF potential was first introduced by Su and Goddard, in
|
|
2007.</p>
|
|
<p>eFF can be viewed as an approximation to QM wave packet dynamics and
|
|
Fermionic molecular dynamics, combining the ability of electronic
|
|
structure methods to describe atomic structure, bonding, and chemistry
|
|
in materials, and of plasma methods to describe nonequilibrium
|
|
dynamics of large systems with a large number of highly excited
|
|
electrons. We classify it as a mixed QM-classical approach rather than
|
|
a conventional force field method, which introduces QM-based terms (a
|
|
spin-dependent repulsion term to account for the Pauli exclusion
|
|
principle and the electron wavefunction kinetic energy associated with
|
|
the Heisenberg principle) that reduce, along with classical
|
|
electrostatic terms between nuclei and electrons, to the sum of a set
|
|
of effective pairwise potentials. This makes eFF uniquely suited to
|
|
simulate materials over a wide range of temperatures and pressures
|
|
where electronically excited and ionized states of matter can occur
|
|
and coexist.</p>
|
|
<p>The necessary customizations to the LAMMPS core are in place to
|
|
enable the correct handling of explicit electron properties during
|
|
minimization and dynamics.</p>
|
|
<p>See the doc page for the pair_style eff/cut command to get started.</p>
|
|
<p>There are example scripts for using this package in
|
|
examples/USER/eff.</p>
|
|
<p>There are auxiliary tools for using this package in tools/eff.</p>
|
|
<p>The person who created this package is Andres Jaramillo-Botero at
|
|
CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
|
|
have questions.</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Examples: examples/USER/eff</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-fep-package">
|
|
<span id="user-fep"></span><h3>4.2.10. USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<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>
|
|
<ul class="simple">
|
|
<li><a class="reference internal" href="fix_adapt_fep.html"><em>fix adapt/fep</em></a></li>
|
|
<li><a class="reference internal" href="compute_fep.html"><em>compute fep</em></a></li>
|
|
<li><a class="reference internal" href="pair_lj_soft.html"><em>soft pair styles</em></a></li>
|
|
</ul>
|
|
<p>The person who created this package is Agilio Padua at Universite
|
|
Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
|
|
Contact him directly if you have questions.</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Examples: examples/USER/fep</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-h5md-package">
|
|
<span id="user-h5md"></span><h3>4.2.11. USER-H5MD package<a class="headerlink" href="#user-h5md-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<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
|
|
files are structured in a format called H5MD, which was designed to
|
|
store molecular data, and can be used and produced by various MD and
|
|
MD-related codes. The <code class="xref doc docutils literal"><span class="pre">dump</span> <span class="pre">h5md</span></code> command gives a
|
|
citation to a paper describing the format.</p>
|
|
<p>The person who created this package and the underlying H5MD format is
|
|
Pierre de Buyl at KU Leuven (see <a class="reference external" href="http://pdebuyl.be">http://pdebuyl.be</a>). Contact him
|
|
directly if you have questions.</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-intel-package">
|
|
<span id="user-intel"></span><h3>4.2.12. USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<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
|
|
Intel(R) Xeon Phi(TM) coprocessor.</p>
|
|
<p>See this section of the manual to get started:</p>
|
|
<p><span class="xref std std-ref">Section_accelerate</span></p>
|
|
<p>The person who created this package is W. Michael Brown at Intel
|
|
(michael.w.brown at intel.com). Contact him directly if you have questions.</p>
|
|
<p>For the USER-INTEL package, you have 2 choices when building. You can
|
|
build with CPU or Phi support. The latter uses Xeon Phi chips in
|
|
“offload” mode. Each of these modes requires additional settings in
|
|
your Makefile.machine for CCFLAGS and LINKFLAGS.</p>
|
|
<p>For CPU mode (if using an Intel compiler):</p>
|
|
<ul class="simple">
|
|
<li>CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits</li>
|
|
<li>LINKFLAGS: add -fopenmp</li>
|
|
</ul>
|
|
<p>For Phi mode add the following in addition to the CPU mode flags:</p>
|
|
<ul class="simple">
|
|
<li>CCFLAGS: add -DLMP_INTEL_OFFLOAD and</li>
|
|
<li>LINKFLAGS: add -offload</li>
|
|
</ul>
|
|
<p>And also add this to CCFLAGS:</p>
|
|
<pre class="literal-block">
|
|
-offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs="gather_scatter_loop_unroll=4""
|
|
</pre>
|
|
<p>Examples: examples/accelerate, bench/KEPLER</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-lb-package">
|
|
<span id="user-lb"></span><h3>4.2.13. USER-LB package<a class="headerlink" href="#user-lb-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<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>
|
|
<p>See this doc page and its related commands to get started:</p>
|
|
<p><a class="reference internal" href="fix_lb_fluid.html"><em>fix lb/fluid</em></a></p>
|
|
<p>The people who created this package are Frances Mackay (fmackay at
|
|
uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
|
|
Western Ontario. Contact them directly if you have questions.</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Examples: examples/USER/lb</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-mgpt-package">
|
|
<span id="user-mgpt"></span><h3>4.2.14. USER-MGPT package<a class="headerlink" href="#user-mgpt-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<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
|
|
theory (GPT) through a series of systematic approximations valid for
|
|
mid-period transition metals with nearly half-filled d bands. The
|
|
MGPT method was originally developed by John Moriarty at Lawrence
|
|
Livermore National Lab (LLNL).</p>
|
|
<p>In the general matrix representation of MGPT, which can also be
|
|
applied to f-band actinide metals, the multi-ion potentials are
|
|
evaluated on the fly during a simulation through d- or f-state matrix
|
|
multiplication, and the forces that move the ions are determined
|
|
analytically. The <em>mgpt</em> pair style in this package calculates forces
|
|
and energies using an optimized matrix-MGPT algorithm due to Tomas
|
|
Oppelstrup at LLNL.</p>
|
|
<p>See this doc page to get started:</p>
|
|
<p><a class="reference internal" href="pair_mgpt.html"><em>pair_style mgpt</em></a></p>
|
|
<p>The persons who created the USER-MGPT package are Tomas Oppelstrup
|
|
(<a class="reference external" href="mailto:oppelstrup2%40llnl.gov">oppelstrup2<span>@</span>llnl<span>.</span>gov</a>) and John Moriarty (<a class="reference external" href="mailto:moriarty2%40llnl.gov">moriarty2<span>@</span>llnl<span>.</span>gov</a>)
|
|
Contact them directly if you have any questions.</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Examples: examples/USER/mgpt</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-misc-package">
|
|
<span id="user-misc"></span><h3>4.2.15. USER-MISC package<a class="headerlink" href="#user-misc-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<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>
|
|
<p>More information about each feature can be found by reading its doc
|
|
page in the LAMMPS doc directory. The doc page which lists all LAMMPS
|
|
input script commands is as follows:</p>
|
|
<p><a class="reference internal" href="Section_commands.html#cmd-5"><span>Section_commands</span></a></p>
|
|
<p>User-contributed features are listed at the bottom of the fix,
|
|
compute, pair, etc sections.</p>
|
|
<p>The list of features and author of each is given in the
|
|
src/USER-MISC/README file.</p>
|
|
<p>You should contact the author directly if you have specific questions
|
|
about the feature or its coding.</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Examples: examples/USER/misc</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-molfile-package">
|
|
<span id="user-molfile"></span><h3>4.2.16. USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<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
|
|
analysis program, to enable LAMMPS to dump its information in formats
|
|
compatible with various molecular simulation tools.</p>
|
|
<p>The package only provides the interface code, not the plugins. These
|
|
can be obtained from a VMD installation which has to match the
|
|
platform that you are using to compile LAMMPS for. By adding plugins
|
|
to VMD, support for new file formats can be added to LAMMPS (or VMD or
|
|
other programs that use them) without having to recompile the
|
|
application itself.</p>
|
|
<p>See this doc page to get started:</p>
|
|
<p><span class="xref std std-ref">dump molfile</span></p>
|
|
<p>The person who created this package is Axel Kohlmeyer at Temple U
|
|
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-omp-package">
|
|
<span id="user-omp"></span><h3>4.2.17. USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<p>This package provides OpenMP multi-threading support and
|
|
other optimizations of various LAMMPS pair styles, dihedral
|
|
styles, and fix styles.</p>
|
|
<p>See this section of the manual to get started:</p>
|
|
<p><span class="xref std std-ref">Section_accelerate</span></p>
|
|
<p>The person who created this package is Axel Kohlmeyer at Temple U
|
|
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
|
|
<p>For the USER-OMP package, your Makefile.machine needs additional
|
|
settings for CCFLAGS and LINKFLAGS.</p>
|
|
<ul class="simple">
|
|
<li>CCFLAGS: add -fopenmp and -restrict</li>
|
|
<li>LINKFLAGS: add -fopenmp</li>
|
|
</ul>
|
|
<p>Examples: examples/accelerate, bench/KEPLER</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-phonon-package">
|
|
<span id="user-phonon"></span><h3>4.2.18. USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline">¶</a></h3>
|
|
<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>
|
|
<p>See this doc page to get started:</p>
|
|
<p><a class="reference internal" href="fix_phonon.html"><em>fix phonon</em></a></p>
|
|
<p>The person who created this package is Ling-Ti Kong (konglt at
|
|
sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly
|
|
if you have questions.</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Examples: examples/USER/phonon</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-qmmm-package">
|
|
<span id="user-qmmm"></span><h3>4.2.19. USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<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>
|
|
<p>The current implementation only supports an ONIOM style mechanical
|
|
coupling to the Quantum ESPRESSO plane wave DFT package.
|
|
Electrostatic coupling is in preparation and the interface has been
|
|
written in a manner that coupling to other QM codes should be possible
|
|
without changes to LAMMPS itself.</p>
|
|
<p>See this doc page to get started:</p>
|
|
<p><a class="reference internal" href="fix_qmmm.html"><em>fix qmmm</em></a></p>
|
|
<p>as well as the lib/qmmm/README file.</p>
|
|
<p>The person who created this package is Axel Kohlmeyer at Temple U
|
|
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-qtb-package">
|
|
<span id="user-qtb"></span><h3>4.2.20. USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<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
|
|
point energy into the system, alter the energy power spectrum and the
|
|
heat capacity towards their quantum nature. This package could be of
|
|
interest if one wants to model systems at temperatures lower than
|
|
their classical limits or when temperatures ramp up across the
|
|
classical limits in the simulation.</p>
|
|
<p>See these two doc pages to get started:</p>
|
|
<p><a class="reference internal" href="fix_qtb.html"><em>fix qtb</em></a> provides quantum nulcear correction through a
|
|
colored thermostat and can be used with other time integration schemes
|
|
like <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> or <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a>.</p>
|
|
<p><a class="reference internal" href="fix_qbmsst.html"><em>fix qbmsst</em></a> enables quantum nuclear correction of a
|
|
multi-scale shock technique simulation by coupling the quantum thermal
|
|
bath with the shocked system.</p>
|
|
<p>The person who created this package is Yuan Shen (sy0302 at
|
|
stanford.edu) at Stanford University. Contact him directly if you
|
|
have questions.</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Examples: examples/USER/qtb</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-quip-package">
|
|
<span id="user-quip"></span><h3>4.2.21. USER-QUIP package<a class="headerlink" href="#user-quip-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<p>Examples: examples/USER/quip</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-reaxc-package">
|
|
<span id="user-reaxc"></span><h3>4.2.22. USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info:</p>
|
|
<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
|
|
energy. It was originally developed by Adri van Duin and the Goddard
|
|
group at CalTech.</p>
|
|
<p>The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
|
|
C, should give identical or very similar results to pair_style reax,
|
|
which is a ReaxFF implementation on top of a Fortran library, a
|
|
version of which library was originally authored by Adri van Duin.</p>
|
|
<p>The reax/c version should be somewhat faster and more scalable,
|
|
particularly with respect to the charge equilibration calculation. It
|
|
should also be easier to build and use since there are no complicating
|
|
issues with Fortran memory allocation or linking to a Fortran library.</p>
|
|
<p>For technical details about this implemention of ReaxFF, see
|
|
this paper:</p>
|
|
<p>Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
|
|
and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
|
|
S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011).</p>
|
|
<p>See the doc page for the pair_style reax/c command for details
|
|
of how to use it in LAMMPS.</p>
|
|
<p>The person who created this package is Hasan Metin Aktulga (hmaktulga
|
|
at lbl.gov), while at Purdue University. Contact him directly, or
|
|
Aidan Thompson at Sandia (athomps at sandia.gov), if you have
|
|
questions.</p>
|
|
<p>Examples: examples/reax</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-smd-package">
|
|
<span id="user-smd"></span><h3>4.2.23. USER-SMD package<a class="headerlink" href="#user-smd-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<p>This package implements smoothed Mach dynamics (SMD) in
|
|
LAMMPS. Currently, the package has the following features:</p>
|
|
<ul class="simple">
|
|
<li>Does liquids via traditional Smooth Particle Hydrodynamics (SPH)</li>
|
|
<li>Also solves solids mechanics problems via a state of the art
|
|
stabilized meshless method with hourglass control.</li>
|
|
<li>Can specify hydrostatic interactions independently from material
|
|
strength models, i.e. pressure and deviatoric stresses are separated.</li>
|
|
<li>Many material models available (Johnson-Cook, plasticity with
|
|
hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
|
|
material models.</li>
|
|
<li>Rigid boundary conditions (walls) can be loaded as surface geometries
|
|
from <a href="#id7"><span class="problematic" id="id8">*</span></a>.STL files.</li>
|
|
</ul>
|
|
<p>See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.</p>
|
|
<p>There are example scripts for using this package in examples/USER/smd.</p>
|
|
<p>The person who created this package is Georg Ganzenmuller at the
|
|
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
|
|
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
|
|
you have questions.</p>
|
|
<p>Examples: examples/USER/smd</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-smtbq-package">
|
|
<span id="user-smtbq"></span><h3>4.2.24. USER-SMTBQ package<a class="headerlink" href="#user-smtbq-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info:</p>
|
|
<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
|
|
examples/USER/smtbq.</p>
|
|
<p>See this doc page to get started:</p>
|
|
<p><a class="reference internal" href="pair_smtbq.html"><em>pair_style smtbq</em></a></p>
|
|
<p>The persons who created the USER-SMTBQ package are Nicolas Salles,
|
|
Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at
|
|
these email addreses: <a class="reference external" href="mailto:lammps%40u-bourgogne.fr">lammps<span>@</span>u-bourgogne<span>.</span>fr</a>, <a class="reference external" href="mailto:nsalles%40laas.fr">nsalles<span>@</span>laas<span>.</span>fr</a>. Contact
|
|
them directly if you have any questions.</p>
|
|
<p>Examples: examples/USER/smtbq</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-sph-package">
|
|
<span id="user-sph"></span><h3>4.2.25. USER-SPH package<a class="headerlink" href="#user-sph-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info:</p>
|
|
<p>This package implements smoothed particle hydrodynamics (SPH) in
|
|
LAMMPS. Currently, the package has the following features:</p>
|
|
<ul class="simple">
|
|
<li>Tait, ideal gas, Lennard-Jones equation of states, full support for
|
|
complete (i.e. internal-energy dependent) equations of state</li>
|
|
<li>Plain or Monaghans XSPH integration of the equations of motion</li>
|
|
<li>Density continuity or density summation to propagate the density field</li>
|
|
<li>Commands to set internal energy and density of particles from the
|
|
input script</li>
|
|
<li>Output commands to access internal energy and density for dumping and
|
|
thermo output</li>
|
|
</ul>
|
|
<p>See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.</p>
|
|
<p>There are example scripts for using this package in examples/USER/sph.</p>
|
|
<p>The person who created this package is Georg Ganzenmuller at the
|
|
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
|
|
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
|
|
you have questions.</p>
|
|
<p>Examples: examples/USER/sph</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-tally-package">
|
|
<span id="user-tally"></span><h3>4.2.26. USER-TALLY package<a class="headerlink" href="#user-tally-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make yes-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>make no-body
|
|
make machine
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
|
|
</pre></div>
|
|
</div>
|
|
<p>Supporting info:</p>
|
|
<p>Examples: examples/USER/tally</p>
|
|
<hr class="docutils" />
|
|
</div>
|
|
<div class="section" id="user-vtk-package">
|
|
<span id="user-vtk"></span><h3>4.2.27. USER-VTK package<a class="headerlink" href="#user-vtk-package" title="Permalink to this headline">¶</a></h3>
|
|
<p>Contents:</p>
|
|
<p>To install via make or Make.py:</p>
|
|
<p>To un-install via make or Make.py:</p>
|
|
<p>Supporting info:</p>
|
|
<p>Examples: examples/USER/tally</p>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
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|
|
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