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Merge remote branch 'lammps-ro/master' into lammps-icms

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Axel Kohlmeyer
2016-02-18 13:21:49 +01:00
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doc/Manual.html
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@ -235,66 +235,7 @@ it gives quick access to documentation for all LAMMPS commands.</p>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#standard-packages">4.1. Standard packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#asphere-package">4.2. ASPHERE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#body-package">4.3. BODY package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#class2-package">4.4. CLASS2 package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#colloid-package">4.5. COLLOID package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#compress-package">4.6. COMPRESS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#coreshell-package">4.7. CORESHELL package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#dipole-package">4.8. DIPOLE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#fld-package">4.9. FLD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#gpu-package">4.10. GPU package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#granular-package">4.11. GRANULAR package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#kim-package">4.12. KIM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#kokkos-package">4.13. KOKKOS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#kspace-package">4.14. KSPACE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#manybody-package">4.15. MANYBODY package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#mc-package">4.16. MC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#meam-package">4.17. MEAM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#misc-package">4.18. MISC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#molecule-package">4.19. MOLECULE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#mpiio-package">4.20. MPIIO package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#opt-package">4.21. OPT package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#peri-package">4.22. PERI package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#poems-package">4.23. POEMS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#python-package">4.24. PYTHON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#qeq-package">4.25. QEQ package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#reax-package">4.26. REAX package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#replica-package">4.27. REPLICA package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#rigid-package">4.28. RIGID package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#shock-package">4.29. SHOCK package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#snap-package">4.30. SNAP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#srd-package">4.31. SRD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#voronoi-package">4.32. VORONOI package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#xtc-package">4.33. XTC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.34. User packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-atc-package">4.35. USER-ATC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-awpmd-package">4.36. USER-AWPMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cg-cmm-package">4.37. USER-CG-CMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.38. USER-COLVARS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.39. USER-CUDA package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.40. USER-DIFFRACTION package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-dpd-package">4.41. USER-DPD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.42. USER-DRUDE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.43. USER-EFF package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.44. USER-FEP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-h5md-package">4.45. USER-H5MD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.46. USER-INTEL package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.47. USER-LB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-mgpt-package">4.48. USER-MGPT package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.49. USER-MISC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.50. USER-MOLFILE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.51. USER-OMP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.52. USER-PHONON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.53. USER-QMMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.54. USER-QTB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-quip-package">4.55. USER-QUIP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.56. USER-REAXC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smd-package">4.57. USER-SMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smtbq-package">4.58. USER-SMTBQ package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.59. USER-SPH package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-tally-package">4.60. USER-TALLY package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-vtk-package">4.61. USER-VTK package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.2. User packages</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>

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@ -6477,7 +6477,7 @@ of two and the number of grid points in one or more directions have been
adjusted to meet this requirement.</dd>
<dt><em>OMP_NUM_THREADS environment is not set.</em></dt>
<dd>This environment variable must be set appropriately to use the
USER-OMP pacakge.</dd>
USER-OMP package.</dd>
<dt><em>One or more atoms are time integrated more than once</em></dt>
<dd>This is probably an error since you typically do not want to
advance the positions or velocities of an atom more than once

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@ -263,7 +263,7 @@ section of the <a class="reference external" href="http://lammps.sandia.gov">LAM
<td>parallel replica dynamics of vacancy diffusion in bulk Si</td>
</tr>
<tr class="row-even"><td>qeq</td>
<td>use of the QEQ pacakge for charge equilibration</td>
<td>use of the QEQ package for charge equilibration</td>
</tr>
<tr class="row-odd"><td>reax</td>
<td>RDX and TATB models using the ReaxFF</td>

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@ -78,67 +78,71 @@
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">4. Packages</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#standard-packages">4.1. Standard packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="#asphere-package">4.2. ASPHERE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#body-package">4.3. BODY package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#class2-package">4.4. CLASS2 package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#colloid-package">4.5. COLLOID package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#compress-package">4.6. COMPRESS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#coreshell-package">4.7. CORESHELL package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#dipole-package">4.8. DIPOLE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#fld-package">4.9. FLD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#gpu-package">4.10. GPU package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#granular-package">4.11. GRANULAR package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#kim-package">4.12. KIM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#kokkos-package">4.13. KOKKOS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#kspace-package">4.14. KSPACE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#manybody-package">4.15. MANYBODY package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#mc-package">4.16. MC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#meam-package">4.17. MEAM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#misc-package">4.18. MISC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#molecule-package">4.19. MOLECULE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#mpiio-package">4.20. MPIIO package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#opt-package">4.21. OPT package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#peri-package">4.22. PERI package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#poems-package">4.23. POEMS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#python-package">4.24. PYTHON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#qeq-package">4.25. QEQ package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#reax-package">4.26. REAX package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#replica-package">4.27. REPLICA package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#rigid-package">4.28. RIGID package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#shock-package">4.29. SHOCK package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#snap-package">4.30. SNAP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#srd-package">4.31. SRD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#voronoi-package">4.32. VORONOI package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#xtc-package">4.33. XTC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-packages">4.34. User packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-atc-package">4.35. USER-ATC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-awpmd-package">4.36. USER-AWPMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-cg-cmm-package">4.37. USER-CG-CMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-colvars-package">4.38. USER-COLVARS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-cuda-package">4.39. USER-CUDA package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-diffraction-package">4.40. USER-DIFFRACTION package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-dpd-package">4.41. USER-DPD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-drude-package">4.42. USER-DRUDE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-eff-package">4.43. USER-EFF package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-fep-package">4.44. USER-FEP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-h5md-package">4.45. USER-H5MD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-intel-package">4.46. USER-INTEL package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-lb-package">4.47. USER-LB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-mgpt-package">4.48. USER-MGPT package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-misc-package">4.49. USER-MISC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-molfile-package">4.50. USER-MOLFILE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-omp-package">4.51. USER-OMP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-phonon-package">4.52. USER-PHONON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-qmmm-package">4.53. USER-QMMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-qtb-package">4.54. USER-QTB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-quip-package">4.55. USER-QUIP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-reaxc-package">4.56. USER-REAXC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-smd-package">4.57. USER-SMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-smtbq-package">4.58. USER-SMTBQ package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-sph-package">4.59. USER-SPH package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-tally-package">4.60. USER-TALLY package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-vtk-package">4.61. USER-VTK package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#standard-packages">4.1. Standard packages</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#asphere-package">4.1.1. ASPHERE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#body-package">4.1.2. BODY package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#class2-package">4.1.3. CLASS2 package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#colloid-package">4.1.4. COLLOID package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#compress-package">4.1.5. COMPRESS package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#coreshell-package">4.1.6. CORESHELL package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#dipole-package">4.1.7. DIPOLE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#fld-package">4.1.8. FLD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#gpu-package">4.1.9. GPU package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#granular-package">4.1.10. GRANULAR package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#kim-package">4.1.11. KIM package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#kokkos-package">4.1.12. KOKKOS package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#kspace-package">4.1.13. KSPACE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#manybody-package">4.1.14. MANYBODY package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#mc-package">4.1.15. MC package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#meam-package">4.1.16. MEAM package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#misc-package">4.1.17. MISC package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#molecule-package">4.1.18. MOLECULE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#mpiio-package">4.1.19. MPIIO package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#opt-package">4.1.20. OPT package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#peri-package">4.1.21. PERI package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#poems-package">4.1.22. POEMS package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#python-package">4.1.23. PYTHON package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#qeq-package">4.1.24. QEQ package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#reax-package">4.1.25. REAX package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#replica-package">4.1.26. REPLICA package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#rigid-package">4.1.27. RIGID package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#shock-package">4.1.28. SHOCK package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#snap-package">4.1.29. SNAP package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#srd-package">4.1.30. SRD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#voronoi-package">4.1.31. VORONOI package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#xtc-package">4.1.32. XTC package</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#user-packages">4.2. User packages</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#user-atc-package">4.2.1. USER-ATC package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-awpmd-package">4.2.2. USER-AWPMD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-cg-cmm-package">4.2.3. USER-CG-CMM package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-colvars-package">4.2.4. USER-COLVARS package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-cuda-package">4.2.5. USER-CUDA package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-diffraction-package">4.2.6. USER-DIFFRACTION package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-dpd-package">4.2.7. USER-DPD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-drude-package">4.2.8. USER-DRUDE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-eff-package">4.2.9. USER-EFF package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-fep-package">4.2.10. USER-FEP package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-h5md-package">4.2.11. USER-H5MD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-intel-package">4.2.12. USER-INTEL package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-lb-package">4.2.13. USER-LB package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-mgpt-package">4.2.14. USER-MGPT package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-misc-package">4.2.15. USER-MISC package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-molfile-package">4.2.16. USER-MOLFILE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-omp-package">4.2.17. USER-OMP package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-phonon-package">4.2.18. USER-PHONON package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-qmmm-package">4.2.19. USER-QMMM package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-qtb-package">4.2.20. USER-QTB package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-quip-package">4.2.21. USER-QUIP package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-reaxc-package">4.2.22. USER-REAXC package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-smd-package">4.2.23. USER-SMD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-smtbq-package">4.2.24. USER-SMTBQ package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-sph-package">4.2.25. USER-SPH package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-tally-package">4.2.26. USER-TALLY package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-vtk-package">4.2.27. USER-VTK package</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
@ -200,26 +204,35 @@
<div class="section" id="packages">
<h1>4. Packages<a class="headerlink" href="#packages" title="Permalink to this headline"></a></h1>
<p>This section gives an overview of the add-on packages that extend
LAMMPS functionality. Two tables, for standard and user packages, are
below. A brief sub-section for each package follows, with a summary
of what the package contains, how to install it, and pointers to
examples of its use or documentation provided in the LAMMPS
distribution.</p>
<p>This section gives an overview of the add-on optional packages that
extend LAMMPS functionality. Packages are groups of files that enable
a specific set of features. For example, force fields for molecular
systems or granular systems are in packages. You can see the list of
all packages by typing &#8220;make package&#8221; from within the src directory of
the LAMMPS distribution.</p>
<p>Here are links for two tables below, which list standard and user
packages.</p>
<div class="line-block">
<div class="line">4.1 <a class="reference internal" href="#pkg-1"><span>Standard packages</span></a></div>
<div class="line">4.2 <a class="reference internal" href="#pkg-2"><span>User packages</span></a></div>
<div class="line"><br /></div>
</div>
<p>LAMMPS includes many optional packages, which are groups of files that
enable a specific set of features. For example, force fields for
molecular systems or granular systems are in packages. You can see
the list of all packages by typing &#8220;make package&#8221; from within the src
directory of the LAMMPS distribution.</p>
<p>See <a class="reference internal" href="Section_start.html#start-3"><span>Section_start 3</span></a> of the manual for
details on how to include/exclude specific packages as part of the
LAMMPS build process, and for more details about the differences
between standard packages and user packages.</p>
<p><a class="reference internal" href="Section_start.html#start-3"><span>Section_start 3</span></a> of the manual describes
the difference between standard packages and user packages. It also
has general details on how to include/exclude specific packages as
part of the LAMMPS build process, and on how to build auxiliary
libraries or modify a machine Makefile if a package requires it.</p>
<p>Following the two tables below, is a sub-section for each package. It
has a summary of what the package contains. It has specific
instructions on how to install it, build or obtain any auxiliary
library it requires, and any Makefile.machine changes it requires. It
also lists pointers to examples of its use or documentation provided
in the LAMMPS distribution.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The sub-sections below are still being filled in, as of Feb
2016.</p>
</div>
<p>Unless otherwise noted below, every package is independent of all the
others. I.e. any package can be included or excluded in a LAMMPS
build, independent of all other packages. However, note that some
@ -229,18 +242,14 @@ package will also not be installed when you include the new one.
E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package
will not be installed as part of the USER-OMP package if the KSPACE
package is not also installed, since it contains the pair
lj/cut/coul/long command. If you later install the KSPACE pacakge and
lj/cut/coul/long command. If you later install the KSPACE package and
the USER-OMP package is already installed, both the pair
lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.</p>
<p>The two tables below list currently available packages in LAMMPS, with
a one-line descriptions of each. The sub-sections below give more
details.</p>
<hr class="docutils" />
<div class="section" id="standard-packages">
<span id="pkg-1"></span><h2>4.1. Standard packages<a class="headerlink" href="#standard-packages" title="Permalink to this headline"></a></h2>
<p>The current list of standard packages is as follows. Each package
name links to a sub-section below with more details on how to build
with the package and pointers to additional info.</p>
name links to a sub-section below with more details.</p>
<table border="1" class="docutils">
<colgroup>
<col width="16%" />
@ -630,11 +639,11 @@ 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>
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>
<div class="section" id="asphere-package">
<span id="asphere"></span><h2>4.2. ASPHERE package<a class="headerlink" href="#asphere-package" title="Permalink to this headline"></a></h2>
<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>
@ -658,7 +667,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="body-package">
<span id="body"></span><h2>4.3. BODY package<a class="headerlink" href="#body-package" title="Permalink to this headline"></a></h2>
<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
@ -680,7 +689,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="class2-package">
<span id="class2"></span><h2>4.4. CLASS2 package<a class="headerlink" href="#class2-package" title="Permalink to this headline"></a></h2>
<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
@ -702,7 +711,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="colloid-package">
<span id="colloid"></span><h2>4.5. COLLOID package<a class="headerlink" href="#colloid-package" title="Permalink to this headline"></a></h2>
<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
@ -724,7 +733,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="compress-package">
<span id="compress"></span><h2>4.6. COMPRESS package<a class="headerlink" href="#compress-package" title="Permalink to this headline"></a></h2>
<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
@ -746,7 +755,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="coreshell-package">
<span id="coreshell"></span><h2>4.7. CORESHELL package<a class="headerlink" href="#coreshell-package" title="Permalink to this headline"></a></h2>
<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
@ -768,7 +777,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="dipole-package">
<span id="dipole"></span><h2>4.8. DIPOLE package<a class="headerlink" href="#dipole-package" title="Permalink to this headline"></a></h2>
<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
@ -790,7 +799,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="fld-package">
<span id="fld"></span><h2>4.9. FLD package<a class="headerlink" href="#fld-package" title="Permalink to this headline"></a></h2>
<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
@ -812,7 +821,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="gpu-package">
<span id="gpu"></span><h2>4.10. GPU package<a class="headerlink" href="#gpu-package" title="Permalink to this headline"></a></h2>
<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
@ -834,7 +843,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="granular-package">
<span id="granular"></span><h2>4.11. GRANULAR package<a class="headerlink" href="#granular-package" title="Permalink to this headline"></a></h2>
<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
@ -856,7 +865,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="kim-package">
<span id="kim"></span><h2>4.12. KIM package<a class="headerlink" href="#kim-package" title="Permalink to this headline"></a></h2>
<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
@ -878,7 +887,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="kokkos-package">
<span id="kokkos"></span><h2>4.13. KOKKOS package<a class="headerlink" href="#kokkos-package" title="Permalink to this headline"></a></h2>
<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
@ -920,7 +929,7 @@ Makefile.</p>
<hr class="docutils" />
</div>
<div class="section" id="kspace-package">
<span id="kspace"></span><h2>4.14. KSPACE package<a class="headerlink" href="#kspace-package" title="Permalink to this headline"></a></h2>
<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
@ -944,7 +953,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="manybody-package">
<span id="manybody"></span><h2>4.15. MANYBODY package<a class="headerlink" href="#manybody-package" title="Permalink to this headline"></a></h2>
<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
@ -967,7 +976,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="mc-package">
<span id="mc"></span><h2>4.16. MC package<a class="headerlink" href="#mc-package" title="Permalink to this headline"></a></h2>
<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
@ -989,7 +998,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="meam-package">
<span id="meam"></span><h2>4.17. MEAM package<a class="headerlink" href="#meam-package" title="Permalink to this headline"></a></h2>
<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
@ -1011,7 +1020,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="misc-package">
<span id="misc"></span><h2>4.18. MISC package<a class="headerlink" href="#misc-package" title="Permalink to this headline"></a></h2>
<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
@ -1033,7 +1042,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="molecule-package">
<span id="molecule"></span><h2>4.19. MOLECULE package<a class="headerlink" href="#molecule-package" title="Permalink to this headline"></a></h2>
<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
@ -1055,7 +1064,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="mpiio-package">
<span id="mpiio"></span><h2>4.20. MPIIO package<a class="headerlink" href="#mpiio-package" title="Permalink to this headline"></a></h2>
<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
@ -1077,7 +1086,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="opt-package">
<span id="opt"></span><h2>4.21. OPT package<a class="headerlink" href="#opt-package" title="Permalink to this headline"></a></h2>
<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
@ -1104,7 +1113,7 @@ settings for CCFLAGS.</p>
<hr class="docutils" />
</div>
<div class="section" id="peri-package">
<span id="peri"></span><h2>4.22. PERI package<a class="headerlink" href="#peri-package" title="Permalink to this headline"></a></h2>
<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
@ -1126,7 +1135,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="poems-package">
<span id="poems"></span><h2>4.23. POEMS package<a class="headerlink" href="#poems-package" title="Permalink to this headline"></a></h2>
<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
@ -1148,7 +1157,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="python-package">
<span id="python"></span><h2>4.24. PYTHON package<a class="headerlink" href="#python-package" title="Permalink to this headline"></a></h2>
<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
@ -1170,7 +1179,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="qeq-package">
<span id="qeq"></span><h2>4.25. QEQ package<a class="headerlink" href="#qeq-package" title="Permalink to this headline"></a></h2>
<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
@ -1192,7 +1201,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="reax-package">
<span id="reax"></span><h2>4.26. REAX package<a class="headerlink" href="#reax-package" title="Permalink to this headline"></a></h2>
<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
@ -1214,7 +1223,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="replica-package">
<span id="replica"></span><h2>4.27. REPLICA package<a class="headerlink" href="#replica-package" title="Permalink to this headline"></a></h2>
<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
@ -1236,7 +1245,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="rigid-package">
<span id="rigid"></span><h2>4.28. RIGID package<a class="headerlink" href="#rigid-package" title="Permalink to this headline"></a></h2>
<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
@ -1258,7 +1267,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="shock-package">
<span id="shock"></span><h2>4.29. SHOCK package<a class="headerlink" href="#shock-package" title="Permalink to this headline"></a></h2>
<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
@ -1280,7 +1289,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="snap-package">
<span id="snap"></span><h2>4.30. SNAP package<a class="headerlink" href="#snap-package" title="Permalink to this headline"></a></h2>
<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
@ -1302,7 +1311,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="srd-package">
<span id="srd"></span><h2>4.31. SRD package<a class="headerlink" href="#srd-package" title="Permalink to this headline"></a></h2>
<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
@ -1324,7 +1333,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="voronoi-package">
<span id="voronoi"></span><h2>4.32. VORONOI package<a class="headerlink" href="#voronoi-package" title="Permalink to this headline"></a></h2>
<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
@ -1346,7 +1355,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="xtc-package">
<span id="xtc"></span><h2>4.33. XTC package<a class="headerlink" href="#xtc-package" title="Permalink to this headline"></a></h2>
<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
@ -1367,8 +1376,9 @@ make machine
<p>Supporting info:</p>
<hr class="docutils" />
</div>
</div>
<div class="section" id="user-packages">
<span id="pkg-2"></span><h2>4.34. User packages<a class="headerlink" href="#user-packages" title="Permalink to this headline"></a></h2>
<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>
@ -1785,9 +1795,8 @@ 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>
<div class="section" id="user-atc-package">
<span id="user-atc"></span><h2>4.35. USER-ATC package<a class="headerlink" href="#user-atc-package" title="Permalink to this headline"></a></h2>
<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>
@ -1812,7 +1821,7 @@ you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-awpmd-package">
<span id="user-awpmd"></span><h2>4.36. USER-AWPMD package<a class="headerlink" href="#user-awpmd-package" title="Permalink to this headline"></a></h2>
<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>
@ -1832,7 +1841,7 @@ have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-cg-cmm-package">
<span id="user-cg-cmm"></span><h2>4.37. USER-CG-CMM package<a class="headerlink" href="#user-cg-cmm-package" title="Permalink to this headline"></a></h2>
<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
@ -1886,7 +1895,7 @@ simulation systems.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-colvars-package">
<span id="user-colvars"></span><h2>4.38. USER-COLVARS package<a class="headerlink" href="#user-colvars-package" title="Permalink to this headline"></a></h2>
<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>
@ -1924,7 +1933,7 @@ beta quality.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-cuda-package">
<span id="user-cuda"></span><h2>4.39. USER-CUDA package<a class="headerlink" href="#user-cuda-package" title="Permalink to this headline"></a></h2>
<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>
@ -1947,7 +1956,7 @@ tu-ilmenau.de). Contact him directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-diffraction-package">
<span id="user-diffraction"></span><h2>4.40. USER-DIFFRACTION package<a class="headerlink" href="#user-diffraction-package" title="Permalink to this headline"></a></h2>
<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>
@ -1982,7 +1991,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="user-dpd-package">
<span id="user-dpd"></span><h2>4.41. USER-DPD package<a class="headerlink" href="#user-dpd-package" title="Permalink to this headline"></a></h2>
<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
@ -2023,7 +2032,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="user-drude-package">
<span id="user-drude"></span><h2>4.42. USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline"></a></h2>
<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>
@ -2065,7 +2074,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="user-eff-package">
<span id="user-eff"></span><h2>4.43. USER-EFF package<a class="headerlink" href="#user-eff-package" title="Permalink to this headline"></a></h2>
<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>
@ -2120,7 +2129,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="user-fep-package">
<span id="user-fep"></span><h2>4.44. USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline"></a></h2>
<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>
@ -2156,7 +2165,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="user-h5md-package">
<span id="user-h5md"></span><h2>4.45. USER-H5MD package<a class="headerlink" href="#user-h5md-package" title="Permalink to this headline"></a></h2>
<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>
@ -2174,7 +2183,7 @@ directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-intel-package">
<span id="user-intel"></span><h2>4.46. USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline"></a></h2>
<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>
@ -2209,7 +2218,7 @@ your Makefile.machine for CCFLAGS and LINKFLAGS.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-lb-package">
<span id="user-lb"></span><h2>4.47. USER-LB package<a class="headerlink" href="#user-lb-package" title="Permalink to this headline"></a></h2>
<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>
@ -2242,7 +2251,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="user-mgpt-package">
<span id="user-mgpt"></span><h2>4.48. USER-MGPT package<a class="headerlink" href="#user-mgpt-package" title="Permalink to this headline"></a></h2>
<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>
@ -2286,7 +2295,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="user-misc-package">
<span id="user-misc"></span><h2>4.49. USER-MISC package<a class="headerlink" href="#user-misc-package" title="Permalink to this headline"></a></h2>
<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>
@ -2324,7 +2333,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="user-molfile-package">
<span id="user-molfile"></span><h2>4.50. USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline"></a></h2>
<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>
@ -2347,7 +2356,7 @@ application itself.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-omp-package">
<span id="user-omp"></span><h2>4.51. USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline"></a></h2>
<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>
@ -2369,7 +2378,7 @@ settings for CCFLAGS and LINKFLAGS.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-phonon-package">
<span id="user-phonon"></span><h2>4.52. USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline"></a></h2>
<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>
@ -2398,7 +2407,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="user-qmmm-package">
<span id="user-qmmm"></span><h2>4.53. USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline"></a></h2>
<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>
@ -2419,7 +2428,7 @@ without changes to LAMMPS itself.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-qtb-package">
<span id="user-qtb"></span><h2>4.54. USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline"></a></h2>
<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>
@ -2462,7 +2471,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="user-quip-package">
<span id="user-quip"></span><h2>4.55. USER-QUIP package<a class="headerlink" href="#user-quip-package" title="Permalink to this headline"></a></h2>
<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>
@ -2471,7 +2480,7 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="user-reaxc-package">
<span id="user-reaxc"></span><h2>4.56. USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline"></a></h2>
<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
@ -2518,7 +2527,7 @@ questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-smd-package">
<span id="user-smd"></span><h2>4.57. USER-SMD package<a class="headerlink" href="#user-smd-package" title="Permalink to this headline"></a></h2>
<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>
@ -2547,7 +2556,7 @@ you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-smtbq-package">
<span id="user-smtbq"></span><h2>4.58. USER-SMTBQ package<a class="headerlink" href="#user-smtbq-package" title="Permalink to this headline"></a></h2>
<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
@ -2580,7 +2589,7 @@ them directly if you have any questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-sph-package">
<span id="user-sph"></span><h2>4.59. USER-SPH package<a class="headerlink" href="#user-sph-package" title="Permalink to this headline"></a></h2>
<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
@ -2621,7 +2630,7 @@ you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-tally-package">
<span id="user-tally"></span><h2>4.60. USER-TALLY package<a class="headerlink" href="#user-tally-package" title="Permalink to this headline"></a></h2>
<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
@ -2644,13 +2653,14 @@ make machine
<hr class="docutils" />
</div>
<div class="section" id="user-vtk-package">
<span id="user-vtk"></span><h2>4.61. USER-VTK package<a class="headerlink" href="#user-vtk-package" title="Permalink to this headline"></a></h2>
<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>

164
doc/Section_packages.txt
View File

@ -10,26 +10,34 @@ Section"_Section_accelerate.html :c
4. Packages :h3
This section gives an overview of the add-on packages that extend
LAMMPS functionality. Two tables, for standard and user packages, are
below. A brief sub-section for each package follows, with a summary
of what the package contains, how to install it, and pointers to
examples of its use or documentation provided in the LAMMPS
distribution.
This section gives an overview of the add-on optional packages that
extend LAMMPS functionality. Packages are groups of files that enable
a specific set of features. For example, force fields for molecular
systems or granular systems are in packages. You can see the list of
all packages by typing "make package" from within the src directory of
the LAMMPS distribution.
Here are links for two tables below, which list standard and user
packages.
4.1 "Standard packages"_#pkg_1
4.2 "User packages"_#pkg_2 :all(b)
LAMMPS includes many optional packages, which are groups of files that
enable a specific set of features. For example, force fields for
molecular systems or granular systems are in packages. You can see
the list of all packages by typing "make package" from within the src
directory of the LAMMPS distribution.
"Section_start 3"_Section_start.html#start_3 of the manual describes
the difference between standard packages and user packages. It also
has general details on how to include/exclude specific packages as
part of the LAMMPS build process, and on how to build auxiliary
libraries or modify a machine Makefile if a package requires it.
See "Section_start 3"_Section_start.html#start_3 of the manual for
details on how to include/exclude specific packages as part of the
LAMMPS build process, and for more details about the differences
between standard packages and user packages.
Following the two tables below, is a sub-section for each package. It
has a summary of what the package contains. It has specific
instructions on how to install it, build or obtain any auxiliary
library it requires, and any Makefile.machine changes it requires. It
also lists pointers to examples of its use or documentation provided
in the LAMMPS distribution.
NOTE: The sub-sections below are still being filled in, as of Feb
2016.
Unless otherwise noted below, every package is independent of all the
others. I.e. any package can be included or excluded in a LAMMPS
@ -44,17 +52,12 @@ lj/cut/coul/long command. If you later install the KSPACE package and
the USER-OMP package is already installed, both the pair
lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.
The two tables below list currently available packages in LAMMPS, with
a one-line descriptions of each. The sub-sections below give more
details.
:line
4.1 Standard packages :h4,link(pkg_1)
The current list of standard packages is as follows. Each package
name links to a sub-section below with more details on how to build
with the package and pointers to additional info.
name links to a sub-section below with more details.
Package, Description, Author(s), Doc page, Example, Library
"ASPHERE"_#ASPHERE, aspherical particles, -, "Section_howto 6.14"_Section_howto.html#howto_14, ellipse, -
@ -120,10 +123,11 @@ 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? ;-)
:line
ASPHERE package :link(ASPHERE),h4
ASPHERE package :link(ASPHERE),h5
Contents: Aspherical particle models for ellipsoids, 2d lines, 3d
triangles.
@ -147,7 +151,7 @@ Supporting info: examples/ASPHERE, examples/ellipse, Section howto
:line
BODY package :link(BODY),h4
BODY package :link(BODY),h5
Contents:
@ -169,7 +173,7 @@ Supporting info: examples/body
:line
CLASS2 package :link(CLASS2),h4
CLASS2 package :link(CLASS2),h5
Contents:
@ -191,7 +195,7 @@ Supporting info:
:line
COLLOID package :link(COLLOID),h4
COLLOID package :link(COLLOID),h5
Contents:
@ -213,7 +217,7 @@ Supporting info: examples/colloid, examples/srd
:line
COMPRESS package :link(COMPRESS),h4
COMPRESS package :link(COMPRESS),h5
Contents:
@ -235,7 +239,7 @@ Supporting info:
:line
CORESHELL package :link(CORESHELL),h4
CORESHELL package :link(CORESHELL),h5
Contents:
@ -257,7 +261,7 @@ Supporting info: examples/coreshell, Section howto 6.26
:line
DIPOLE package :link(DIPOLE),h4
DIPOLE package :link(DIPOLE),h5
Contents:
@ -279,7 +283,7 @@ Supporting info: examples/dipole
:line
FLD package :link(FLD),h4
FLD package :link(FLD),h5
Contents:
@ -301,7 +305,7 @@ Supporting info:
:line
GPU package :link(GPU),h4
GPU package :link(GPU),h5
Contents:
@ -323,7 +327,7 @@ Supporting info: examples/accelerate, bench/FERMI, bench/KEPLER
:line
GRANULAR package :link(GRANULAR),h4
GRANULAR package :link(GRANULAR),h5
Contents:
@ -345,7 +349,7 @@ Supporting info: examples/pour, bench/in.chute, Section howto 6.6
:line
KIM package :link(KIM),h4
KIM package :link(KIM),h5
Contents:
@ -367,7 +371,7 @@ Supporting info: examples/kim
:line
KOKKOS package :link(KOKKOS),h4
KOKKOS package :link(KOKKOS),h5
Contents:
@ -411,7 +415,7 @@ Examples: examples/accelerate, bench/FERMI, bench/KEPLER
:line
KSPACE package :link(KSPACE),h4
KSPACE package :link(KSPACE),h5
Contents:
@ -437,7 +441,7 @@ Doc: Section howto 6.7, Section howto 6.8, Section howto 6.9
:line
MANYBODY package :link(MANYBODY),h4
MANYBODY package :link(MANYBODY),h5
Contents:
@ -461,7 +465,7 @@ Examples: examples/comb, examples/eim, examples/nb3d, examples/vashishta
:line
MC package :link(MC),h4
MC package :link(MC),h5
Contents:
@ -483,7 +487,7 @@ Supporting info:
:line
MEAM package :link(MEAM),h4
MEAM package :link(MEAM),h5
Contents:
@ -505,7 +509,7 @@ Supporting info: examples/meam
:line
MISC package :link(MISC),h4
MISC package :link(MISC),h5
Contents:
@ -527,7 +531,7 @@ Supporting info: examples/misc
:line
MOLECULE package :link(MOLECULE),h4
MOLECULE package :link(MOLECULE),h5
Contents:
@ -549,7 +553,7 @@ Supporting info: examples/micelle, examples/peptide, bench/in.chain, bench/in.rh
:line
MPIIO package :link(MPIIO),h4
MPIIO package :link(MPIIO),h5
Contents:
@ -571,7 +575,7 @@ Supporting info:
:line
OPT package :link(OPT),h4
OPT package :link(OPT),h5
Contents:
@ -598,7 +602,7 @@ CCFLAGS: add -restrict :ul
:line
PERI package :link(PERI),h4
PERI package :link(PERI),h5
Contents:
@ -620,7 +624,7 @@ Supporting info: examples/peri
:line
POEMS package :link(POEMS),h4
POEMS package :link(POEMS),h5
Contents:
@ -642,7 +646,7 @@ Supporting info: examples/rigid
:line
PYTHON package :link(PYTHON),h4
PYTHON package :link(PYTHON),h5
Contents:
@ -664,7 +668,7 @@ Supporting info: examples/python
:line
QEQ package :link(QEQ),h4
QEQ package :link(QEQ),h5
Contents:
@ -686,7 +690,7 @@ Supporting info: examples/qeq
:line
REAX package :link(REAX),h4
REAX package :link(REAX),h5
Contents:
@ -708,7 +712,7 @@ Supporting info: examples/reax
:line
REPLICA package :link(REPLICA),h4
REPLICA package :link(REPLICA),h5
Contents:
@ -730,7 +734,7 @@ Supporting info: examples/neb, examples/prd, examples/tad, Section howto 6.5
:line
RIGID package :link(RIGID),h4
RIGID package :link(RIGID),h5
Contents:
@ -752,7 +756,7 @@ Supporting info: examples/ASPHERE, examples/rigid
:line
SHOCK package :link(SHOCK),h4
SHOCK package :link(SHOCK),h5
Contents:
@ -774,7 +778,7 @@ Supporting info: examples/hugoniostat, examples/msst
:line
SNAP package :link(SNAP),h4
SNAP package :link(SNAP),h5
Contents:
@ -796,7 +800,7 @@ Supporting info: examples/snap
:line
SRD package :link(SRD),h4
SRD package :link(SRD),h5
Contents:
@ -818,7 +822,7 @@ Supporting info:
:line
VORONOI package :link(VORONOI),h4
VORONOI package :link(VORONOI),h5
Contents:
@ -840,7 +844,7 @@ Supporting info: examples/voronoi
:line
XTC package :link(XTC),h4
XTC package :link(XTC),h5
Contents:
@ -945,7 +949,7 @@ See details on all of this below for individual packages.
:line
USER-ATC package :link(USER-ATC),h4
USER-ATC package :link(USER-ATC),h5
Contents:
@ -980,7 +984,7 @@ Examples: examples/USER/atc
:line
USER-AWPMD package :link(USER-AWPMD),h4
USER-AWPMD package :link(USER-AWPMD),h5
Contents:
@ -1010,7 +1014,7 @@ Examples: examples/USER/awpmd
:line
USER-CG-CMM package :link(USER-CG-CMM),h4
USER-CG-CMM package :link(USER-CG-CMM),h5
Contents:
@ -1071,7 +1075,7 @@ Examples: examples/USER/cg-cmm
:line
USER-COLVARS package :link(USER-COLVARS),h4
USER-COLVARS package :link(USER-COLVARS),h5
Contents:
@ -1123,7 +1127,7 @@ Supporting info:
:line
USER-CUDA package :link(USER-CUDA),h4
USER-CUDA package :link(USER-CUDA),h5
This package provides acceleration of various LAMMPS pair styles, fix
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
@ -1157,7 +1161,7 @@ Supporting info:
:line
USER-DIFFRACTION package :link(USER-DIFFRACTION),h4
USER-DIFFRACTION package :link(USER-DIFFRACTION),h5
This package contains the commands neeed to calculate x-ray and
electron diffraction intensities based on kinematic diffraction
@ -1195,7 +1199,7 @@ Supporting info:
:line
USER-DPD package :link(USER-DPD),h4
USER-DPD package :link(USER-DPD),h5
This package implements the dissipative particle dynamics (DPD) method
under isothermal, isoenergetic, isobaric and isenthalpic conditions.
@ -1238,7 +1242,7 @@ Examples: examples/USER/dpd
:line
USER-DRUDE package :link(USER-DRUDE),h4
USER-DRUDE package :link(USER-DRUDE),h5
Contents:
@ -1287,7 +1291,7 @@ Doc: Section howto 6.27
:line
USER-EFF package :link(USER-EFF),h4
USER-EFF package :link(USER-EFF),h5
Contents:
@ -1352,7 +1356,7 @@ Examples: examples/USER/eff
:line
USER-FEP package :link(USER-FEP),h4
USER-FEP package :link(USER-FEP),h5
Contents:
@ -1393,7 +1397,7 @@ Examples: examples/USER/fep
:line
USER-H5MD package :link(USER-H5MD),h4
USER-H5MD package :link(USER-H5MD),h5
Contents:
@ -1420,7 +1424,7 @@ directly if you have questions.
:line
USER-INTEL package :link(USER-INTEL),h4
USER-INTEL package :link(USER-INTEL),h5
Contents:
@ -1465,7 +1469,7 @@ Examples: examples/accelerate, bench/KEPLER
:line
USER-LB package :link(USER-LB),h4
USER-LB package :link(USER-LB),h5
Contents:
@ -1505,7 +1509,7 @@ Examples: examples/USER/lb
:line
USER-MGPT package :link(USER-MGPT),h4
USER-MGPT package :link(USER-MGPT),h5
Contents:
@ -1557,7 +1561,7 @@ Examples: examples/USER/mgpt
:line
USER-MISC package :link(USER-MISC),h4
USER-MISC package :link(USER-MISC),h5
Contents:
@ -1604,7 +1608,7 @@ Examples: examples/USER/misc
:line
USER-MOLFILE package :link(USER-MOLFILE),h4
USER-MOLFILE package :link(USER-MOLFILE),h5
Contents:
@ -1636,7 +1640,7 @@ The person who created this package is Axel Kohlmeyer at Temple U
:line
USER-OMP package :link(USER-OMP),h4
USER-OMP package :link(USER-OMP),h5
Contents:
@ -1667,7 +1671,7 @@ Examples: examples/accelerate, bench/KEPLER
:line
USER-PHONON package :link(USER-PHONON),h4
USER-PHONON package :link(USER-PHONON),h5
This package contains a fix phonon command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
@ -1699,7 +1703,7 @@ Examples: examples/USER/phonon
:line
USER-QMMM package :link(USER-QMMM),h4
USER-QMMM package :link(USER-QMMM),h5
Contents:
@ -1732,7 +1736,7 @@ The person who created this package is Axel Kohlmeyer at Temple U
:line
USER-QTB package :link(USER-QTB),h4
USER-QTB package :link(USER-QTB),h5
Contents:
@ -1783,7 +1787,7 @@ Examples: examples/USER/qtb
:line
USER-QUIP package :link(USER-QUIP),h4
USER-QUIP package :link(USER-QUIP),h5
Contents:
@ -1797,7 +1801,7 @@ Examples: examples/USER/quip
:line
USER-REAXC package :link(USER-REAXC),h4
USER-REAXC package :link(USER-REAXC),h5
Contents:
@ -1852,7 +1856,7 @@ Examples: examples/reax
:line
USER-SMD package :link(USER-SMD),h4
USER-SMD package :link(USER-SMD),h5
Contents:
@ -1893,7 +1897,7 @@ Examples: examples/USER/smd
:line
USER-SMTBQ package :link(USER-SMTBQ),h4
USER-SMTBQ package :link(USER-SMTBQ),h5
Contents:
@ -1932,7 +1936,7 @@ Examples: examples/USER/smtbq
:line
USER-SPH package :link(USER-SPH),h4
USER-SPH package :link(USER-SPH),h5
Contents:
@ -1981,7 +1985,7 @@ Examples: examples/USER/sph
:line
USER-TALLY package :link(USER-TALLY),h4
USER-TALLY package :link(USER-TALLY),h5
Contents:
@ -2005,7 +2009,7 @@ Examples: examples/USER/tally
:line
USER-VTK package :link(USER-VTK),h4
USER-VTK package :link(USER-VTK),h5
Contents:

2
doc/Section_python.html
View File

@ -273,7 +273,7 @@ previous section 11.1. This means it can issue LAMMPS input script
commands or query and set internal LAMMPS state. As an example, this
can be useful in an input script to create a more complex loop with
branching logic, than can be created using the simple looping and
brancing logic enabled by the <a class="reference internal" href="next.html"><em>next</em></a> and <a class="reference internal" href="if.html"><em>if</em></a>
branching logic enabled by the <a class="reference internal" href="next.html"><em>next</em></a> and <a class="reference internal" href="if.html"><em>if</em></a>
commands.</p>
<p>See the <a class="reference internal" href="python.html"><em>python</em></a> doc page and the <a class="reference internal" href="variable.html"><em>variable</em></a>
doc page for its python-style variables for more info, including

3
doc/Section_start.html
View File

@ -211,7 +211,8 @@ sub-directories:</p>
</tr>
</tbody>
</table>
<p>Note that the <a class="reference external" href="http://lammps.sandia.gov/download.html">download page</a> also has links to download
<p>Note that the <a class="reference external" href="http://lammps.sandia.gov/download.html">download page</a>
also has links to download
Windows exectubles and installers, as well as pre-built executables
for a few specific Linux distributions. It also has instructions for
how to download/install LAMMPS for Macs (via Homebrew), and to

2
doc/_sources/Section_errors.txt
View File

@ -8972,7 +8972,7 @@ Warnings:
*OMP_NUM_THREADS environment is not set.*
This environment variable must be set appropriately to use the
USER-OMP pacakge.
USER-OMP package.
*One or more atoms are time integrated more than once*
This is probably an error since you typically do not want to

2
doc/_sources/Section_example.txt
View File

@ -96,7 +96,7 @@ These are the sample problems in the examples sub-directories:
+-------------+----------------------------------------------------------------------------+
| prd | parallel replica dynamics of vacancy diffusion in bulk Si |
+-------------+----------------------------------------------------------------------------+
| qeq | use of the QEQ pacakge for charge equilibration |
| qeq | use of the QEQ package for charge equilibration |
+-------------+----------------------------------------------------------------------------+
| reax | RDX and TATB models using the ReaxFF |
+-------------+----------------------------------------------------------------------------+

168
doc/_sources/Section_packages.txt
View File

@ -1,27 +1,37 @@
Packages
========
This section gives an overview of the add-on packages that extend
LAMMPS functionality. Two tables, for standard and user packages, are
below. A brief sub-section for each package follows, with a summary
of what the package contains, how to install it, and pointers to
examples of its use or documentation provided in the LAMMPS
distribution.
This section gives an overview of the add-on optional packages that
extend LAMMPS functionality. Packages are groups of files that enable
a specific set of features. For example, force fields for molecular
systems or granular systems are in packages. You can see the list of
all packages by typing "make package" from within the src directory of
the LAMMPS distribution.
Here are links for two tables below, which list standard and user
packages.
| 4.1 :ref:`Standard packages <pkg_1>`
| 4.2 :ref:`User packages <pkg_2>`
|
LAMMPS includes many optional packages, which are groups of files that
enable a specific set of features. For example, force fields for
molecular systems or granular systems are in packages. You can see
the list of all packages by typing "make package" from within the src
directory of the LAMMPS distribution.
:ref:`Section_start 3 <start_3>` of the manual describes
the difference between standard packages and user packages. It also
has general details on how to include/exclude specific packages as
part of the LAMMPS build process, and on how to build auxiliary
libraries or modify a machine Makefile if a package requires it.
See :ref:`Section_start 3 <start_3>` of the manual for
details on how to include/exclude specific packages as part of the
LAMMPS build process, and for more details about the differences
between standard packages and user packages.
Following the two tables below, is a sub-section for each package. It
has a summary of what the package contains. It has specific
instructions on how to install it, build or obtain any auxiliary
library it requires, and any Makefile.machine changes it requires. It
also lists pointers to examples of its use or documentation provided
in the LAMMPS distribution.
.. note::
The sub-sections below are still being filled in, as of Feb
2016.
Unless otherwise noted below, every package is independent of all the
others. I.e. any package can be included or excluded in a LAMMPS
@ -32,14 +42,10 @@ package will also not be installed when you include the new one.
E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package
will not be installed as part of the USER-OMP package if the KSPACE
package is not also installed, since it contains the pair
lj/cut/coul/long command. If you later install the KSPACE pacakge and
lj/cut/coul/long command. If you later install the KSPACE package and
the USER-OMP package is already installed, both the pair
lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.
The two tables below list currently available packages in LAMMPS, with
a one-line descriptions of each. The sub-sections below give more
details.
----------
@ -50,8 +56,7 @@ Standard packages
-----------------------------
The current list of standard packages is as follows. Each package
name links to a sub-section below with more details on how to build
with the package and pointers to additional info.
name links to a sub-section below with more details.
+------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| Package | Description | Author(s) | Doc page | Example | Library |
@ -150,6 +155,7 @@ 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? ;-)
----------
@ -158,7 +164,7 @@ See details on all of this below for individual packages.
.. _ASPHERE:
ASPHERE package
---------------
^^^^^^^^^^^^^^^
Contents: Aspherical particle models for ellipsoids, 2d lines, 3d
triangles.
@ -195,7 +201,7 @@ Supporting info: examples/ASPHERE, examples/ellipse, Section howto
.. _BODY:
BODY package
------------
^^^^^^^^^^^^
Contents:
@ -230,7 +236,7 @@ Supporting info: examples/body
.. _CLASS2:
CLASS2 package
--------------
^^^^^^^^^^^^^^
Contents:
@ -265,7 +271,7 @@ Supporting info:
.. _COLLOID:
COLLOID package
---------------
^^^^^^^^^^^^^^^
Contents:
@ -300,7 +306,7 @@ Supporting info: examples/colloid, examples/srd
.. _COMPRESS:
COMPRESS package
----------------
^^^^^^^^^^^^^^^^
Contents:
@ -335,7 +341,7 @@ Supporting info:
.. _CORESHELL:
CORESHELL package
-----------------
^^^^^^^^^^^^^^^^^
Contents:
@ -370,7 +376,7 @@ Supporting info: examples/coreshell, Section howto 6.26
.. _DIPOLE:
DIPOLE package
--------------
^^^^^^^^^^^^^^
Contents:
@ -405,7 +411,7 @@ Supporting info: examples/dipole
.. _FLD:
FLD package
-----------
^^^^^^^^^^^
Contents:
@ -440,7 +446,7 @@ Supporting info:
.. _GPU:
GPU package
-----------
^^^^^^^^^^^
Contents:
@ -475,7 +481,7 @@ Supporting info: examples/accelerate, bench/FERMI, bench/KEPLER
.. _GRANULAR:
GRANULAR package
----------------
^^^^^^^^^^^^^^^^
Contents:
@ -510,7 +516,7 @@ Supporting info: examples/pour, bench/in.chute, Section howto 6.6
.. _KIM:
KIM package
-----------
^^^^^^^^^^^
Contents:
@ -545,7 +551,7 @@ Supporting info: examples/kim
.. _KOKKOS:
KOKKOS package
--------------
^^^^^^^^^^^^^^
Contents:
@ -604,7 +610,7 @@ Examples: examples/accelerate, bench/FERMI, bench/KEPLER
.. _KSPACE:
KSPACE package
--------------
^^^^^^^^^^^^^^
Contents:
@ -643,7 +649,7 @@ Doc: Section howto 6.7, Section howto 6.8, Section howto 6.9
.. _MANYBODY:
MANYBODY package
----------------
^^^^^^^^^^^^^^^^
Contents:
@ -680,7 +686,7 @@ Examples: examples/comb, examples/eim, examples/nb3d, examples/vashishta
.. _MC:
MC package
----------
^^^^^^^^^^
Contents:
@ -715,7 +721,7 @@ Supporting info:
.. _MEAM:
MEAM package
------------
^^^^^^^^^^^^
Contents:
@ -750,7 +756,7 @@ Supporting info: examples/meam
.. _MISC:
MISC package
------------
^^^^^^^^^^^^
Contents:
@ -785,7 +791,7 @@ Supporting info: examples/misc
.. _MOLECULE:
MOLECULE package
----------------
^^^^^^^^^^^^^^^^
Contents:
@ -820,7 +826,7 @@ Supporting info: examples/micelle, examples/peptide, bench/in.chain, bench/in.rh
.. _MPIIO:
MPIIO package
-------------
^^^^^^^^^^^^^
Contents:
@ -855,7 +861,7 @@ Supporting info:
.. _OPT:
OPT package
-----------
^^^^^^^^^^^
Contents:
@ -895,7 +901,7 @@ settings for CCFLAGS.
.. _PERI:
PERI package
------------
^^^^^^^^^^^^
Contents:
@ -930,7 +936,7 @@ Supporting info: examples/peri
.. _POEMS:
POEMS package
-------------
^^^^^^^^^^^^^
Contents:
@ -965,7 +971,7 @@ Supporting info: examples/rigid
.. _PYTHON:
PYTHON package
--------------
^^^^^^^^^^^^^^
Contents:
@ -1000,7 +1006,7 @@ Supporting info: examples/python
.. _QEQ:
QEQ package
-----------
^^^^^^^^^^^
Contents:
@ -1035,7 +1041,7 @@ Supporting info: examples/qeq
.. _REAX:
REAX package
------------
^^^^^^^^^^^^
Contents:
@ -1070,7 +1076,7 @@ Supporting info: examples/reax
.. _REPLICA:
REPLICA package
---------------
^^^^^^^^^^^^^^^
Contents:
@ -1105,7 +1111,7 @@ Supporting info: examples/neb, examples/prd, examples/tad, Section howto 6.5
.. _RIGID:
RIGID package
-------------
^^^^^^^^^^^^^
Contents:
@ -1140,7 +1146,7 @@ Supporting info: examples/ASPHERE, examples/rigid
.. _SHOCK:
SHOCK package
-------------
^^^^^^^^^^^^^
Contents:
@ -1175,7 +1181,7 @@ Supporting info: examples/hugoniostat, examples/msst
.. _SNAP:
SNAP package
------------
^^^^^^^^^^^^
Contents:
@ -1210,7 +1216,7 @@ Supporting info: examples/snap
.. _SRD:
SRD package
-----------
^^^^^^^^^^^
Contents:
@ -1245,7 +1251,7 @@ Supporting info:
.. _VORONOI:
VORONOI package
---------------
^^^^^^^^^^^^^^^
Contents:
@ -1280,7 +1286,7 @@ Supporting info: examples/voronoi
.. _XTC:
XTC package
-----------
^^^^^^^^^^^
Contents:
@ -1447,7 +1453,7 @@ See details on all of this below for individual packages.
.. _USER-ATC:
USER-ATC package
----------------
^^^^^^^^^^^^^^^^
Contents:
@ -1487,7 +1493,7 @@ Examples: examples/USER/atc
.. _USER-AWPMD:
USER-AWPMD package
------------------
^^^^^^^^^^^^^^^^^^
Contents:
@ -1522,7 +1528,7 @@ Examples: examples/USER/awpmd
.. _USER-CG-CMM:
USER-CG-CMM package
-------------------
^^^^^^^^^^^^^^^^^^^
Contents:
@ -1596,7 +1602,7 @@ Examples: examples/USER/cg-cmm
.. _USER-COLVARS:
USER-COLVARS package
--------------------
^^^^^^^^^^^^^^^^^^^^
Contents:
@ -1653,7 +1659,7 @@ Supporting info:
.. _USER-CUDA:
USER-CUDA package
-----------------
^^^^^^^^^^^^^^^^^
This package provides acceleration of various LAMMPS pair styles, fix
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
@ -1692,7 +1698,7 @@ Supporting info:
.. _USER-DIFFRACTION:
USER-DIFFRACTION package
------------------------
^^^^^^^^^^^^^^^^^^^^^^^^
This package contains the commands neeed to calculate x-ray and
electron diffraction intensities based on kinematic diffraction
@ -1743,7 +1749,7 @@ Supporting info:
.. _USER-DPD:
USER-DPD package
----------------
^^^^^^^^^^^^^^^^
This package implements the dissipative particle dynamics (DPD) method
under isothermal, isoenergetic, isobaric and isenthalpic conditions.
@ -1799,7 +1805,7 @@ Examples: examples/USER/dpd
.. _USER-DRUDE:
USER-DRUDE package
------------------
^^^^^^^^^^^^^^^^^^
Contents:
@ -1861,7 +1867,7 @@ Doc: Section howto 6.27
.. _USER-EFF:
USER-EFF package
----------------
^^^^^^^^^^^^^^^^
Contents:
@ -1939,7 +1945,7 @@ Examples: examples/USER/eff
.. _USER-FEP:
USER-FEP package
----------------
^^^^^^^^^^^^^^^^
Contents:
@ -1993,7 +1999,7 @@ Examples: examples/USER/fep
.. _USER-H5MD:
USER-H5MD package
-----------------
^^^^^^^^^^^^^^^^^
Contents:
@ -2026,7 +2032,7 @@ directly if you have questions.
.. _USER-INTEL:
USER-INTEL package
------------------
^^^^^^^^^^^^^^^^^^
Contents:
@ -2078,7 +2084,7 @@ Examples: examples/accelerate, bench/KEPLER
.. _USER-LB:
USER-LB package
---------------
^^^^^^^^^^^^^^^
Contents:
@ -2131,7 +2137,7 @@ Examples: examples/USER/lb
.. _USER-MGPT:
USER-MGPT package
-----------------
^^^^^^^^^^^^^^^^^
Contents:
@ -2196,7 +2202,7 @@ Examples: examples/USER/mgpt
.. _USER-MISC:
USER-MISC package
-----------------
^^^^^^^^^^^^^^^^^
Contents:
@ -2256,7 +2262,7 @@ Examples: examples/USER/misc
.. _USER-MOLFILE:
USER-MOLFILE package
--------------------
^^^^^^^^^^^^^^^^^^^^
Contents:
@ -2293,7 +2299,7 @@ The person who created this package is Axel Kohlmeyer at Temple U
.. _USER-OMP:
USER-OMP package
----------------
^^^^^^^^^^^^^^^^
Contents:
@ -2329,7 +2335,7 @@ Examples: examples/accelerate, bench/KEPLER
.. _USER-PHONON:
USER-PHONON package
-------------------
^^^^^^^^^^^^^^^^^^^
This package contains a fix phonon command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
@ -2374,7 +2380,7 @@ Examples: examples/USER/phonon
.. _USER-QMMM:
USER-QMMM package
-----------------
^^^^^^^^^^^^^^^^^
Contents:
@ -2414,7 +2420,7 @@ The person who created this package is Axel Kohlmeyer at Temple U
.. _USER-QTB:
USER-QTB package
----------------
^^^^^^^^^^^^^^^^
Contents:
@ -2478,7 +2484,7 @@ Examples: examples/USER/qtb
.. _USER-QUIP:
USER-QUIP package
-----------------
^^^^^^^^^^^^^^^^^
Contents:
@ -2497,7 +2503,7 @@ Examples: examples/USER/quip
.. _USER-REAXC:
USER-REAXC package
------------------
^^^^^^^^^^^^^^^^^^
Contents:
@ -2565,7 +2571,7 @@ Examples: examples/reax
.. _USER-SMD:
USER-SMD package
----------------
^^^^^^^^^^^^^^^^
Contents:
@ -2611,7 +2617,7 @@ Examples: examples/USER/smd
.. _USER-SMTBQ:
USER-SMTBQ package
------------------
^^^^^^^^^^^^^^^^^^
Contents:
@ -2663,7 +2669,7 @@ Examples: examples/USER/smtbq
.. _USER-SPH:
USER-SPH package
----------------
^^^^^^^^^^^^^^^^
Contents:
@ -2725,7 +2731,7 @@ Examples: examples/USER/sph
.. _USER-TALLY:
USER-TALLY package
------------------
^^^^^^^^^^^^^^^^^^
Contents:
@ -2762,7 +2768,7 @@ Examples: examples/USER/tally
.. _USER-VTK:
USER-VTK package
----------------
^^^^^^^^^^^^^^^^
Contents:

2
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@ -147,7 +147,7 @@ previous section 11.1. This means it can issue LAMMPS input script
commands or query and set internal LAMMPS state. As an example, this
can be useful in an input script to create a more complex loop with
branching logic, than can be created using the simple looping and
brancing logic enabled by the :doc:`next <next>` and :doc:`if <if>`
branching logic enabled by the :doc:`next <next>` and :doc:`if <if>`
commands.
See the :doc:`python <python>` doc page and the :doc:`variable <variable>`

3
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View File

@ -54,7 +54,8 @@ sub-directories:
| tools | pre- and post-processing tools |
+------------+--------------------------------------------+
Note that the `download page <download_>`_ also has links to download
Note that the `download page <http://lammps.sandia.gov/download.html>`_
also has links to download
Windows exectubles and installers, as well as pre-built executables
for a few specific Linux distributions. It also has instructions for
how to download/install LAMMPS for Macs (via Homebrew), and to

2
doc/_sources/accelerate_opt.txt
View File

@ -15,7 +15,7 @@ follow.
.. parsed-literal::
make yes-opt
make mpi # build with the OPT pacakge
make mpi # build with the OPT package
Make.py -v -p opt -o mpi -a file mpi # or one-line build via Make.py
.. parsed-literal::

2
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View File

@ -290,7 +290,7 @@ with a specific package, as listed below. See the :ref:`Making LAMMPS <start_3>
The *angle*, *bond*, *full*, *molecular*, and *template* styles are
part of the MOLECULE package.
The *line* and *tri* styles are part of the ASPHERE pacakge.
The *line* and *tri* styles are part of the ASPHERE package.
The *body* style is part of the BODY package.

4
doc/_sources/fix_langevin.txt
View File

@ -23,9 +23,9 @@ Syntax
* keyword = *angmom* or *omega* or *scale* or *tally* or *zero*
.. parsed-literal::
*angmom* value = *no* or scale
*angmom* value = *no* or factor
*no* = do not thermostat rotational degrees of freedom via the angular momentum
factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric factor as discussed below
factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below
*gjf* value = *no* or *yes*
*no* = use standard formulation
*yes* = use Gronbech-Jensen/Farago formulation

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@ -34,7 +34,7 @@ Syntax
*slab* value = volfactor or *nozforce*
volfactor = ratio of the total extended volume used in the
2d approximation compared with the volume of the simulation domain
*nozforce* turns off kspace forces in the z direction
*nozforce* turns off kspace forces in the z direction
*compute* value = *yes* or *no*
*cutoff/adjust* value = *yes* or *no*
*pressure/scalar* value = *yes* or *no*

12
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@ -38,11 +38,13 @@ Syntax
Examples
""""""""
pair_modify shift yes mix geometric
pair_modify tail yes
pair_modify table 12
pair_modify pair lj/cut compute no
pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0:pre
.. parsed-literal::
pair_modify shift yes mix geometric
pair_modify tail yes
pair_modify table 12
pair_modify pair lj/cut compute no
pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0
Description
"""""""""""

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@ -135,7 +135,7 @@ due to if tests and other conditional code.</p>
<p>Here is a quick overview of how to use the OPT package. More details
follow.</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-opt
make mpi # build with the OPT pacakge
make mpi # build with the OPT package
Make.py -v -p opt -o mpi -a file mpi # or one-line build via Make.py
</pre></div>
</div>

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@ -416,7 +416,7 @@ more instructions on how to use the accelerated styles effectively.</p>
with a specific package, as listed below. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>The <em>angle</em>, <em>bond</em>, <em>full</em>, <em>molecular</em>, and <em>template</em> styles are
part of the MOLECULE package.</p>
<p>The <em>line</em> and <em>tri</em> styles are part of the ASPHERE pacakge.</p>
<p>The <em>line</em> and <em>tri</em> styles are part of the ASPHERE package.</p>
<p>The <em>body</em> style is part of the BODY package.</p>
<p>The <em>dipole</em> style is part of the DIPOLE package.</p>
<p>The <em>peri</em> style is part of the PERI package for Peridynamics.</p>

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@ -145,9 +145,9 @@
<li>keyword = <em>angmom</em> or <em>omega</em> or <em>scale</em> or <em>tally</em> or <em>zero</em></li>
</ul>
<pre class="literal-block">
<em>angmom</em> value = <em>no</em> or scale
<em>angmom</em> value = <em>no</em> or factor
<em>no</em> = do not thermostat rotational degrees of freedom via the angular momentum
factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric factor as discussed below
factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below
<em>gjf</em> value = <em>no</em> or <em>yes</em>
<em>no</em> = use standard formulation
<em>yes</em> = use Gronbech-Jensen/Farago formulation
@ -175,7 +175,7 @@ fix 1 all langevin 1.0 1.1 100.0 48279 angmom 3.333
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Apply a Langevin thermostat as described in <a class="reference internal" href="fix_langevin_eff.html#schneider"><span>(Schneider)</span></a>
<p>Apply a Langevin thermostat as described in <a class="reference internal" href="#schneider"><span>(Schneider)</span></a>
to a group of atoms which models an interaction with a background
implicit solvent. Used with <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a>, this command
performs Brownian dynamics (BD), since the total force on each atom
@ -203,7 +203,7 @@ dt damp), where Kb is the Boltzmann constant, T is the desired
temperature, m is the mass of the particle, dt is the timestep size,
and damp is the damping factor. Random numbers are used to randomize
the direction and magnitude of this force as described in
<a class="reference internal" href="fix_langevin_eff.html#dunweg"><span>(Dunweg)</span></a>, where a uniform random number is used (instead of
<a class="reference internal" href="#dunweg"><span>(Dunweg)</span></a>, where a uniform random number is used (instead of
a Gaussian random number) for speed.</p>
<p>Note that unless you use the <em>omega</em> or <em>angmom</em> keywords, the
thermostat effect of this fix is applied to only the translational

4
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@ -21,9 +21,9 @@ damp = damping parameter (time units) :l
seed = random number seed to use for white noise (positive integer) :l
zero or more keyword/value pairs may be appended :l
keyword = {angmom} or {omega} or {scale} or {tally} or {zero} :l
{angmom} value = {no} or scale
{angmom} value = {no} or factor
{no} = do not thermostat rotational degrees of freedom via the angular momentum
factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric factor as discussed below
factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below
{gjf} value = {no} or {yes}
{no} = use standard formulation
{yes} = use Gronbech-Jensen/Farago formulation

10
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@ -156,7 +156,7 @@ keyword = <em>mesh</em> or <em>order</em> or <em>order/disp</em> or <em>mix/disp
<em>slab</em> value = volfactor or <em>nozforce</em>
volfactor = ratio of the total extended volume used in the
2d approximation compared with the volume of the simulation domain
<em>nozforce</em> turns off kspace forces in the z direction
<em>nozforce</em> turns off kspace forces in the z direction
<em>compute</em> value = <em>yes</em> or <em>no</em>
<em>cutoff/adjust</em> value = <em>yes</em> or <em>no</em>
<em>pressure/scalar</em> value = <em>yes</em> or <em>no</em>
@ -310,7 +310,7 @@ beginning of the run to give the desired estimated error. Other
cutoffs such as LJ will not be affected. If the grid is not set using
the <em>mesh</em> command, this command will also attempt to use the optimal
grid that minimizes cost using an estimate given by
<a class="reference internal" href="kspace_style.html#hardy"><span>(Hardy)</span></a>. Note that this cost estimate is not exact, somewhat
<a class="reference internal" href="#hardy"><span>(Hardy)</span></a>. Note that this cost estimate is not exact, somewhat
experimental, and still may not yield the optimal parameters.</p>
<p>The <em>pressure/scalar</em> keyword applies only to MSM. If this option is
turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will
@ -335,7 +335,7 @@ collective operations and adequate hardware.</p>
<p>The <em>diff</em> keyword specifies the differentiation scheme used by the
PPPM method to compute forces on particles given electrostatic
potentials on the PPPM mesh. The <em>ik</em> approach is the default for
PPPM and is the original formulation used in <a class="reference internal" href="kspace_style.html#hockney"><span>(Hockney)</span></a>. It
PPPM and is the original formulation used in <a class="reference internal" href="#hockney"><span>(Hockney)</span></a>. It
performs differentiation in Kspace, and uses 3 FFTs to transfer each
component of the computed fields back to real space for total of 4
FFTs per timestep.</p>
@ -370,7 +370,7 @@ speed-up the simulations but introduces some error in the force
computations, as shown in <a class="reference internal" href="#wennberg"><span>(Wennberg)</span></a>. With <em>none</em>, it is
assumed that no mixing rule is applicable. Splitting of the dispersion
coefficients will be performed as described in
<a class="reference internal" href="kspace_style.html#isele-holder"><span>(Isele-Holder)</span></a>. This splitting can be influenced with
<a class="reference internal" href="#isele-holder"><span>(Isele-Holder)</span></a>. This splitting can be influenced with
the <em>splittol</em> keywords. Only the eigenvalues that are larger than tol
compared to the largest eigenvalues are included. Using this keywords
the original matrix of dispersion coefficients is approximated. This
@ -378,7 +378,7 @@ leads to faster computations, but the accuracy in the reciprocal space
computations of the dispersion part is decreased.</p>
<p>The <em>force/disp/real</em> and <em>force/disp/kspace</em> keywords set the force
accuracy for the real and space computations for the dispersion part
of pppm/disp. As shown in <a class="reference internal" href="kspace_style.html#isele-holder"><span>(Isele-Holder)</span></a>, optimal
of pppm/disp. As shown in <a class="reference internal" href="#isele-holder"><span>(Isele-Holder)</span></a>, optimal
performance and accuracy in the results is obtained when these values
are different.</p>
<p>The <em>disp/auto</em> option controlls whether the pppm/disp is allowed to

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@ -158,11 +158,13 @@
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<p>pair_modify shift yes mix geometric
<div class="highlight-python"><div class="highlight"><pre>pair_modify shift yes mix geometric
pair_modify tail yes
pair_modify table 12
pair_modify pair lj/cut compute no
pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0:pre</p>
pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
@ -226,7 +228,7 @@ see the doc page for individual styles to see which potentials support
these options. If N is non-zero, a table of length 2^N is
pre-computed for forces and energies, which can shrink their
computational cost by up to a factor of 2. The table is indexed via a
bit-mapping technique <a class="reference internal" href="pair_table.html#wolff"><span>(Wolff)</span></a> and a linear interpolation is
bit-mapping technique <a class="reference internal" href="#wolff"><span>(Wolff)</span></a> and a linear interpolation is
performed between adjacent table values. In our experiments with
different table styles (lookup, linear, spline), this method typically
gave the best performance in terms of speed and accuracy.</p>

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