Skip to content
Snippets Groups Projects
Commit d205583a authored by sjplimp's avatar sjplimp
Browse files

'' 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13775 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent dc536d88
No related branches found
No related tags found
No related merge requests found
Expand all Hide whitespace changes
Inline Side-by-side
Showing
with 542 additions and 1048 deletions
doc/Manual.html
+ 12
− 205
View file @ d205583a
......@@ -32,8 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="next" title="1. Introduction" href="Section_intro.html"/>
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
......@@ -72,22 +71,16 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<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"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">LAMMPS Documentation</a><ul>
<li><a class="reference internal" href="#jul-2015-version">27 Jul 2015 version</a></li>
<li><a class="reference internal" href="#version-info">Version info:</a></li>
</ul>
</li>
<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
</ul>
</div>
</div>
......@@ -172,192 +165,13 @@ we can improve the LAMMPS documentation.</p>
it gives quick access to documentation for all LAMMPS commands.</p>
<p><a class="reference external" href="Manual.pdf">PDF file</a> of the entire manual, generated by
<a class="reference external" href="http://freecode.com/projects/htmldoc">htmldoc</a></p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-features">1.2. LAMMPS features</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-non-features">1.3. LAMMPS non-features</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#open-source-distribution">1.4. Open source distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#what-s-in-the-lammps-distribution">2.1. What&#8217;s in the LAMMPS distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps">2.2. Making LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps-with-optional-packages">2.3. Making LAMMPS with optional packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-via-the-make-py-script">2.4. Building LAMMPS via the Make.py script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-as-a-library">2.5. Building LAMMPS as a library</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#running-lammps">2.6. Running LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#command-line-options">2.7. Command-line options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#lammps-screen-output">2.8. LAMMPS screen output</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#tips-for-users-of-previous-lammps-versions">2.9. Tips for users of previous LAMMPS versions</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#lammps-input-script">3.1. LAMMPS input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#parsing-rules">3.2. Parsing rules</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#input-script-structure">3.3. Input script structure</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#commands-listed-by-category">3.4. Commands listed by category</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#individual-commands">3.5. Individual commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#fix-styles">3.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#compute-styles">3.7. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#pair-style-potentials">3.8. Pair_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#bond-style-potentials">3.9. Bond_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#angle-style-potentials">3.10. Angle_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#improper-style-potentials">3.12. Improper_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#kspace-solvers">3.13. Kspace solvers</a></li>
</ul>
</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#user-packages">4.2. User packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-atc-package">4.3. USER-ATC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-awpmd-package">4.4. USER-AWPMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cg-cmm-package">4.5. USER-CG-CMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.6. USER-COLVARS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.7. USER-CUDA package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.8. USER-DIFFRACTION package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.9. USER-DRUDE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.10. USER-EFF package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.11. USER-FEP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.12. USER-INTEL package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.13. USER-LB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.14. USER-MISC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.15. USER-MOLFILE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.16. USER-OMP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.17. USER-PHONON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.18. USER-QMMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.19. USER-QTB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.20. USER-REAXC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.21. USER-SPH package</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#measuring-performance">5.1. Measuring performance</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#general-strategies">5.2. General strategies</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#restarting-a-simulation">6.1. Restarting a simulation</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#d-simulations">6.2. 2d simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#charmm-amber-and-dreiding-force-fields">6.3. CHARMM, AMBER, and DREIDING force fields</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#running-multiple-simulations-from-one-input-script">6.4. Running multiple simulations from one input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#granular-models">6.6. Granular models</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip3p-water-model">6.7. TIP3P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip4p-water-model">6.8. TIP4P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#spc-water-model">6.9. SPC water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#nemd-simulations">6.13. NEMD simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#finite-size-spherical-and-aspherical-particles">6.14. Finite-size spherical and aspherical particles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#output-from-lammps-thermo-dumps-computes-fixes-variables">6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#walls">6.17. Walls</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#elastic-constants">6.18. Elastic constants</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-viscosity">6.21. Calculating viscosity</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#using-chunks-to-calculate-system-properties">6.23. Using chunks to calculate system properties</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#setting-parameters-for-the-kspace-style-pppm-disp-command">6.24. Setting parameters for the <code class="docutils literal"><span class="pre">kspace_style</span> <span class="pre">pppm/disp</span></code> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#polarizable-models">6.25. Polarizable models</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#binary2txt-tool">9.2. binary2txt tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ch2lmp-tool">9.3. ch2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#chain-tool">9.4. chain tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#colvars-tools">9.5. colvars tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#createatoms-tool">9.6. createatoms tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#data2xmovie-tool">9.7. data2xmovie tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-database-tool">9.8. eam database tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-generate-tool">9.9. eam generate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eff-tool">9.10. eff tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#fep-tool">9.12. fep tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#i-pi-tool">9.13. i-pi tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ipp-tool">9.14. ipp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#kate-tool">9.15. kate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2arc-tool">9.16. lmp2arc tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#matlab-tool">9.19. matlab tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#micelle2d-tool">9.20. micelle2d tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#moltemplate-tool">9.21. moltemplate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#msi2lmp-tool">9.22. msi2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#phonon-tool">9.23. phonon tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#python-tool">9.26. python tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#reax-tool">9.27. reax tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#restart2data-tool">9.28. restart2data tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#vim-tool">9.29. vim tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmgrace-tool">9.30. xmgrace tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmovie-tool">9.31. xmovie tool</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#atom-styles">10.1. Atom styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#compute-styles">10.3. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-styles">10.4. Dump styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-custom-output-options">10.5. Dump custom output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#fix-styles">10.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#input-script-commands">10.7. Input script commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#kspace-computations">10.8. Kspace computations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#minimization-styles">10.9. Minimization styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#region-styles">10.11. Region styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#body-styles">10.12. Body styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#variable-options">10.14. Variable options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#extending-python-with-mpi-to-run-in-parallel">11.5. Extending Python with MPI to run in parallel</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#common-problems">12.1. Common problems</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#reporting-bugs">12.2. Reporting bugs</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error-warning-messages">12.3. Error &amp; warning messages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error">12.4. Errors:</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#warnings">12.5. Warnings:</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#coming-attractions">13.1. Coming attractions</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#past-versions">13.2. Past versions</a></li>
</ul>
</li>
</ul>
</div>
</div>
</div>
<div class="section" id="indices-and-tables">
<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline"></a></h1>
<ul class="simple">
<li><a class="reference internal" href="genindex.html"><span>Index</span></a></li>
<li><a class="reference internal" href="search.html"><span>Search Page</span></a></li>
<li><a class="reference internal" href="genindex.html"><span>Index</span></a> // comment</li>
<li><a class="reference internal" href="search.html"><span>Search Page</span></a> // comment</li>
</ul>
</BODY></div>
......@@ -366,13 +180,6 @@ it gives quick access to documentation for all LAMMPS commands.</p>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_intro.html" class="btn btn-neutral float-right" title="1. Introduction" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
</div>
<hr/>
......
doc/Section_accelerate.html
+ 18
− 40
View file @ d205583a
......@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>5. Accelerating LAMMPS performance &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>Accelerating LAMMPS performance &mdash; LAMMPS 15 May 2015 version documentation</title>
......@@ -32,9 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="next" title="6. How-to discussions" href="Section_howto.html"/>
<link rel="prev" title="4. Packages" href="Section_packages.html"/>
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
......@@ -73,31 +71,20 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<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"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">5. Accelerating LAMMPS performance</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#measuring-performance">5.1. Measuring performance</a></li>
<li class="toctree-l2"><a class="reference internal" href="#general-strategies">5.2. General strategies</a></li>
<li class="toctree-l2"><a class="reference internal" href="#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#examples">5.4.1. Examples</a></li>
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Accelerating LAMMPS performance</a><ul>
<li><a class="reference internal" href="#measuring-performance">Measuring performance</a></li>
<li><a class="reference internal" href="#general-strategies">General strategies</a></li>
<li><a class="reference internal" href="#packages-with-optimized-styles">Packages with optimized styles</a></li>
<li><a class="reference internal" href="#comparison-of-various-accelerator-packages">Comparison of various accelerator packages</a><ul>
<li><a class="reference internal" href="#examples">Examples</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
......@@ -120,7 +107,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>5. Accelerating LAMMPS performance</li>
<li>Accelerating LAMMPS performance</li>
<li class="wy-breadcrumbs-aside">
......@@ -135,7 +122,7 @@
<div itemprop="articleBody">
<div class="section" id="accelerating-lammps-performance">
<h1>5. Accelerating LAMMPS performance<a class="headerlink" href="#accelerating-lammps-performance" title="Permalink to this headline"></a></h1>
<h1>Accelerating LAMMPS performance<a class="headerlink" href="#accelerating-lammps-performance" title="Permalink to this headline"></a></h1>
<p>This section describes various methods for improving LAMMPS
performance for different classes of problems running on different
kinds of machines.</p>
......@@ -163,7 +150,7 @@ packages discussed in Section 5.2, for several of the standard LAMMPS
benchmark problems, as a function of problem size and number of
compute nodes, on different hardware platforms.</p>
<div class="section" id="measuring-performance">
<span id="acc-1"></span><h2>5.1. Measuring performance<a class="headerlink" href="#measuring-performance" title="Permalink to this headline"></a></h2>
<span id="acc-1"></span><h2>Measuring performance<a class="headerlink" href="#measuring-performance" title="Permalink to this headline"></a></h2>
<p>Before trying to make your simulation run faster, you should
understand how it currently performs and where the bottlenecks are.</p>
<p>The best way to do this is run the your system (actual number of
......@@ -204,7 +191,7 @@ LAMMPS, to obtain synchronized timings.</p>
<hr class="docutils" />
</div>
<div class="section" id="general-strategies">
<span id="acc-2"></span><h2>5.2. General strategies<a class="headerlink" href="#general-strategies" title="Permalink to this headline"></a></h2>
<span id="acc-2"></span><h2>General strategies<a class="headerlink" href="#general-strategies" title="Permalink to this headline"></a></h2>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">this section 5.2 is still a work in progress</p>
......@@ -257,7 +244,7 @@ such as when using a barostat.</p>
<hr class="docutils" />
</div>
<div class="section" id="packages-with-optimized-styles">
<span id="acc-3"></span><h2>5.3. Packages with optimized styles<a class="headerlink" href="#packages-with-optimized-styles" title="Permalink to this headline"></a></h2>
<span id="acc-3"></span><h2>Packages with optimized styles<a class="headerlink" href="#packages-with-optimized-styles" title="Permalink to this headline"></a></h2>
<p>Accelerated versions of various <a class="reference internal" href="pair_style.html"><em>pair_style</em></a>,
<a class="reference internal" href="fix.html"><em>fixes</em></a>, <a class="reference internal" href="compute.html"><em>computes</em></a>, and other commands have
been added to LAMMPS, which will typically run faster than the
......@@ -449,7 +436,7 @@ CPU.</li>
<hr class="docutils" />
</div>
<div class="section" id="comparison-of-various-accelerator-packages">
<span id="acc-4"></span><h2>5.4. Comparison of various accelerator packages<a class="headerlink" href="#comparison-of-various-accelerator-packages" title="Permalink to this headline"></a></h2>
<span id="acc-4"></span><h2>Comparison of various accelerator packages<a class="headerlink" href="#comparison-of-various-accelerator-packages" title="Permalink to this headline"></a></h2>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">this section still needs to be re-worked with additional KOKKOS
......@@ -520,7 +507,7 @@ is generally not a problem since typical runs are computation-limited
rather than memory-limited.</li>
</ul>
<div class="section" id="examples">
<h3>5.4.1. Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h3>
<h3>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h3>
<p>The LAMMPS distribution has two directories with sample input scripts
for the GPU and USER-CUDA packages.</p>
<ul class="simple">
......@@ -538,15 +525,6 @@ to benchmark the performance of both packages on your system.</p>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_howto.html" class="btn btn-neutral float-right" title="6. How-to discussions" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Section_packages.html" class="btn btn-neutral" title="4. Packages" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<hr/>
......
doc/Section_commands.html
+ 34
− 56
View file @ d205583a
......@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>3. Commands &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>Commands &mdash; LAMMPS 15 May 2015 version documentation</title>
......@@ -32,9 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="next" title="4. Packages" href="Section_packages.html"/>
<link rel="prev" title="2. Getting Started" href="Section_start.html"/>
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
......@@ -73,37 +71,26 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">3. Commands</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#lammps-input-script">3.1. LAMMPS input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="#parsing-rules">3.2. Parsing rules</a></li>
<li class="toctree-l2"><a class="reference internal" href="#input-script-structure">3.3. Input script structure</a></li>
<li class="toctree-l2"><a class="reference internal" href="#commands-listed-by-category">3.4. Commands listed by category</a></li>
<li class="toctree-l2"><a class="reference internal" href="#individual-commands">3.5. Individual commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="#fix-styles">3.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#compute-styles">3.7. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#pair-style-potentials">3.8. Pair_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#bond-style-potentials">3.9. Bond_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#angle-style-potentials">3.10. Angle_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#improper-style-potentials">3.12. Improper_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#kspace-solvers">3.13. Kspace solvers</a></li>
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Commands</a><ul>
<li><a class="reference internal" href="#lammps-input-script">LAMMPS input script</a></li>
<li><a class="reference internal" href="#parsing-rules">Parsing rules</a></li>
<li><a class="reference internal" href="#input-script-structure">Input script structure</a></li>
<li><a class="reference internal" href="#commands-listed-by-category">Commands listed by category</a></li>
<li><a class="reference internal" href="#individual-commands">Individual commands</a></li>
<li><a class="reference internal" href="#fix-styles">Fix styles</a></li>
<li><a class="reference internal" href="#compute-styles">Compute styles</a></li>
<li><a class="reference internal" href="#pair-style-potentials">Pair_style potentials</a></li>
<li><a class="reference internal" href="#bond-style-potentials">Bond_style potentials</a></li>
<li><a class="reference internal" href="#angle-style-potentials">Angle_style potentials</a></li>
<li><a class="reference internal" href="#dihedral-style-potentials">Dihedral_style potentials</a></li>
<li><a class="reference internal" href="#improper-style-potentials">Improper_style potentials</a></li>
<li><a class="reference internal" href="#kspace-solvers">Kspace solvers</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
......@@ -126,7 +113,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>3. Commands</li>
<li>Commands</li>
<li class="wy-breadcrumbs-aside">
......@@ -141,7 +128,7 @@
<div itemprop="articleBody">
<div class="section" id="commands">
<h1>3. Commands<a class="headerlink" href="#commands" title="Permalink to this headline"></a></h1>
<h1>Commands<a class="headerlink" href="#commands" title="Permalink to this headline"></a></h1>
<p>This section describes how a LAMMPS input script is formatted and the
input script commands used to define a LAMMPS simulation.</p>
<div class="line-block">
......@@ -153,7 +140,7 @@ input script commands used to define a LAMMPS simulation.</p>
<div class="line"><br /></div>
</div>
<div class="section" id="lammps-input-script">
<span id="cmd-1"></span><h2>3.1. LAMMPS input script<a class="headerlink" href="#lammps-input-script" title="Permalink to this headline"></a></h2>
<span id="cmd-1"></span><h2>LAMMPS input script<a class="headerlink" href="#lammps-input-script" title="Permalink to this headline"></a></h2>
<p>LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
command causes LAMMPS to take some action. It may set an internal
......@@ -200,7 +187,7 @@ command lists restrictions on how the command can be used.</p>
<hr class="docutils" />
</div>
<div class="section" id="parsing-rules">
<span id="cmd-2"></span><h2>3.2. Parsing rules<a class="headerlink" href="#parsing-rules" title="Permalink to this headline"></a></h2>
<span id="cmd-2"></span><h2>Parsing rules<a class="headerlink" href="#parsing-rules" title="Permalink to this headline"></a></h2>
<p>Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
are specified command arguments. Upper case letters may be used in
......@@ -304,7 +291,7 @@ allowed, but that should be sufficient for most use cases.</p>
<hr class="docutils" />
</div>
<div class="section" id="input-script-structure">
<span id="cmd-3"></span><h2>3.3. Input script structure<a class="headerlink" href="#input-script-structure" title="Permalink to this headline"></a></h2>
<span id="cmd-3"></span><h2>Input script structure<a class="headerlink" href="#input-script-structure" title="Permalink to this headline"></a></h2>
<p>This section describes the structure of a typical LAMMPS input script.
The &#8220;examples&#8221; directory in the LAMMPS distribution contains many
sample input scripts; the corresponding problems are discussed in
......@@ -383,7 +370,7 @@ the <a class="reference internal" href="minimize.html"><em>minimize</em></a> com
<hr class="docutils" />
</div>
<div class="section" id="commands-listed-by-category">
<span id="cmd-4"></span><h2>3.4. Commands listed by category<a class="headerlink" href="#commands-listed-by-category" title="Permalink to this headline"></a></h2>
<span id="cmd-4"></span><h2>Commands listed by category<a class="headerlink" href="#commands-listed-by-category" title="Permalink to this headline"></a></h2>
<p>This section lists all LAMMPS commands, grouped by category. The
<a class="reference internal" href="#cmd-5"><span>next section</span></a> lists the same commands alphabetically. Note
that some style options for some commands are part of specific LAMMPS
......@@ -442,7 +429,7 @@ in the command&#8217;s documentation.</p>
<hr class="docutils" />
</div>
<div class="section" id="individual-commands">
<span id="comm"></span><span id="cmd-5"></span><h2>3.5. Individual commands<a class="headerlink" href="#individual-commands" title="Permalink to this headline"></a></h2>
<span id="comm"></span><span id="cmd-5"></span><h2>Individual commands<a class="headerlink" href="#individual-commands" title="Permalink to this headline"></a></h2>
<p>This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The <a class="reference internal" href="#cmd-4"><span>previous section</span></a> lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
......@@ -588,7 +575,7 @@ in the command&#8217;s documentation.</p>
</div>
<hr class="docutils" />
<div class="section" id="fix-styles">
<h2>3.6. Fix styles<a class="headerlink" href="#fix-styles" title="Permalink to this headline"></a></h2>
<h2>Fix styles<a class="headerlink" href="#fix-styles" title="Permalink to this headline"></a></h2>
<p>See the <a class="reference internal" href="fix.html"><em>fix</em></a> command for one-line descriptions of each style
or click on the style itself for a full description. Some of the
styles have accelerated versions, which can be used if LAMMPS is built
......@@ -810,7 +797,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
</div>
<hr class="docutils" />
<div class="section" id="compute-styles">
<h2>3.7. Compute styles<a class="headerlink" href="#compute-styles" title="Permalink to this headline"></a></h2>
<h2>Compute styles<a class="headerlink" href="#compute-styles" title="Permalink to this headline"></a></h2>
<p>See the <a class="reference internal" href="compute.html"><em>compute</em></a> command for one-line descriptions of
each style or click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
......@@ -944,7 +931,7 @@ used if <a class="reference internal" href="Section_start.html#start-3"><span>LA
</div>
<hr class="docutils" />
<div class="section" id="pair-style-potentials">
<h2>3.8. Pair_style potentials<a class="headerlink" href="#pair-style-potentials" title="Permalink to this headline"></a></h2>
<h2>Pair_style potentials<a class="headerlink" href="#pair-style-potentials" title="Permalink to this headline"></a></h2>
<p>See the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command for an overview of pair
potentials. Click on the style itself for a full description. Many
of the styles have accelerated versions, which can be used if LAMMPS
......@@ -1156,7 +1143,7 @@ if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS
</div>
<hr class="docutils" />
<div class="section" id="bond-style-potentials">
<h2>3.9. Bond_style potentials<a class="headerlink" href="#bond-style-potentials" title="Permalink to this headline"></a></h2>
<h2>Bond_style potentials<a class="headerlink" href="#bond-style-potentials" title="Permalink to this headline"></a></h2>
<p>See the <a class="reference internal" href="bond_style.html"><em>bond_style</em></a> command for an overview of bond
potentials. Click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
......@@ -1204,7 +1191,7 @@ if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS
</div>
<hr class="docutils" />
<div class="section" id="angle-style-potentials">
<h2>3.10. Angle_style potentials<a class="headerlink" href="#angle-style-potentials" title="Permalink to this headline"></a></h2>
<h2>Angle_style potentials<a class="headerlink" href="#angle-style-potentials" title="Permalink to this headline"></a></h2>
<p>See the <a class="reference internal" href="angle_style.html"><em>angle_style</em></a> command for an overview of
angle potentials. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
......@@ -1261,7 +1248,7 @@ if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS
</div>
<hr class="docutils" />
<div class="section" id="dihedral-style-potentials">
<h2>3.11. Dihedral_style potentials<a class="headerlink" href="#dihedral-style-potentials" title="Permalink to this headline"></a></h2>
<h2>Dihedral_style potentials<a class="headerlink" href="#dihedral-style-potentials" title="Permalink to this headline"></a></h2>
<p>See the <a class="reference internal" href="dihedral_style.html"><em>dihedral_style</em></a> command for an overview
of dihedral potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
......@@ -1313,7 +1300,7 @@ used if <a class="reference internal" href="Section_start.html#start-3"><span>LA
</div>
<hr class="docutils" />
<div class="section" id="improper-style-potentials">
<h2>3.12. Improper_style potentials<a class="headerlink" href="#improper-style-potentials" title="Permalink to this headline"></a></h2>
<h2>Improper_style potentials<a class="headerlink" href="#improper-style-potentials" title="Permalink to this headline"></a></h2>
<p>See the <a class="reference internal" href="improper_style.html"><em>improper_style</em></a> command for an overview
of improper potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
......@@ -1358,7 +1345,7 @@ used if <a class="reference internal" href="Section_start.html#start-3"><span>LA
</div>
<hr class="docutils" />
<div class="section" id="kspace-solvers">
<h2>3.13. Kspace solvers<a class="headerlink" href="#kspace-solvers" title="Permalink to this headline"></a></h2>
<h2>Kspace solvers<a class="headerlink" href="#kspace-solvers" title="Permalink to this headline"></a></h2>
<p>See the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command for an overview of
Kspace solvers. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
......@@ -1398,15 +1385,6 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_packages.html" class="btn btn-neutral float-right" title="4. Packages" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Section_start.html" class="btn btn-neutral" title="2. Getting Started" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<hr/>
......
doc/Section_errors.html
+ 18
− 40
View file @ d205583a
......@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>12. Errors &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>Errors &mdash; LAMMPS 15 May 2015 version documentation</title>
......@@ -32,9 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="next" title="13. Future and history" href="Section_history.html"/>
<link rel="prev" title="11. Python interface to LAMMPS" href="Section_python.html"/>
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
......@@ -73,29 +71,18 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<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"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">12. Errors</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#common-problems">12.1. Common problems</a></li>
<li class="toctree-l2"><a class="reference internal" href="#reporting-bugs">12.2. Reporting bugs</a></li>
<li class="toctree-l2"><a class="reference internal" href="#error-warning-messages">12.3. Error &amp; warning messages</a></li>
<li class="toctree-l2"><a class="reference internal" href="#error">12.4. Errors:</a></li>
<li class="toctree-l2"><a class="reference internal" href="#warnings">12.5. Warnings:</a></li>
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Errors</a><ul>
<li><a class="reference internal" href="#common-problems">Common problems</a></li>
<li><a class="reference internal" href="#reporting-bugs">Reporting bugs</a></li>
<li><a class="reference internal" href="#error-warning-messages">Error &amp; warning messages</a></li>
<li><a class="reference internal" href="#error">Errors:</a></li>
<li><a class="reference internal" href="#warnings">Warnings:</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
......@@ -118,7 +105,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>12. Errors</li>
<li>Errors</li>
<li class="wy-breadcrumbs-aside">
......@@ -133,7 +120,7 @@
<div itemprop="articleBody">
<div class="section" id="errors">
<h1>12. Errors<a class="headerlink" href="#errors" title="Permalink to this headline"></a></h1>
<h1>Errors<a class="headerlink" href="#errors" title="Permalink to this headline"></a></h1>
<p>This section describes the errors you can encounter when using LAMMPS,
either conceptually, or as printed out by the program.</p>
<div class="line-block">
......@@ -143,7 +130,7 @@ either conceptually, or as printed out by the program.</p>
<div class="line"><br /></div>
</div>
<div class="section" id="common-problems">
<span id="err-1"></span><h2>12.1. Common problems<a class="headerlink" href="#common-problems" title="Permalink to this headline"></a></h2>
<span id="err-1"></span><h2>Common problems<a class="headerlink" href="#common-problems" title="Permalink to this headline"></a></h2>
<p>If two LAMMPS runs do not produce the same answer on different
machines or different numbers of processors, this is typically not a
bug. In theory you should get identical answers on any number of
......@@ -232,7 +219,7 @@ buffering or boost the sizes of messages that can be buffered.</p>
<hr class="docutils" />
</div>
<div class="section" id="reporting-bugs">
<span id="err-2"></span><h2>12.2. Reporting bugs<a class="headerlink" href="#reporting-bugs" title="Permalink to this headline"></a></h2>
<span id="err-2"></span><h2>Reporting bugs<a class="headerlink" href="#reporting-bugs" title="Permalink to this headline"></a></h2>
<p>If you are confident that you have found a bug in LAMMPS, follow these
steps.</p>
<p>Check the <a class="reference external" href="http://lammps.sandia.gov/bug.html">New features and bug fixes</a> section of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW site</a> to see if the bug has already been reported or fixed or the
......@@ -254,7 +241,7 @@ causing the problem.</p>
<hr class="docutils" />
</div>
<div class="section" id="error-warning-messages">
<span id="err-3"></span><h2>12.3. Error &amp; warning messages<a class="headerlink" href="#error-warning-messages" title="Permalink to this headline"></a></h2>
<span id="err-3"></span><h2>Error &amp; warning messages<a class="headerlink" href="#error-warning-messages" title="Permalink to this headline"></a></h2>
<p>These are two alphabetic lists of the <a class="reference internal" href="#error"><span>ERROR</span></a> and
<a class="reference internal" href="#warn"><span>WARNING</span></a> messages LAMMPS prints out and the reason why. If the
explanation here is not sufficient, the documentation for the
......@@ -269,7 +256,7 @@ error occurs and is not self-explanatory, you&#8217;ll need to look in the
source code or contact the author of the package.</p>
</div>
<div class="section" id="error">
<span id="id2"></span><h2>12.4. Errors:<a class="headerlink" href="#error" title="Permalink to this headline"></a></h2>
<span id="id2"></span><h2>Errors:<a class="headerlink" href="#error" title="Permalink to this headline"></a></h2>
<dl class="docutils">
<dt><em>1-3 bond count is inconsistent</em></dt>
<dd>An inconsistency was detected when computing the number of 1-3
......@@ -5788,7 +5775,7 @@ read_restart, or create_box command.</dd>
</dl>
</div>
<div class="section" id="warnings">
<span id="warn"></span><h2>12.5. Warnings:<a class="headerlink" href="#warnings" title="Permalink to this headline"></a></h2>
<span id="warn"></span><h2>Warnings:<a class="headerlink" href="#warnings" title="Permalink to this headline"></a></h2>
<dl class="docutils">
<dt><em>Adjusting Coulombic cutoff for MSM, new cutoff = %g</em></dt>
<dd>The adjust/cutoff command is turned on and the Coulombic cutoff has been
......@@ -6299,15 +6286,6 @@ infinity.</dd>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_history.html" class="btn btn-neutral float-right" title="13. Future and history" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Section_python.html" class="btn btn-neutral" title="11. Python interface to LAMMPS" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<hr/>
......
doc/Section_example.html
+ 8
− 30
View file @ d205583a
......@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>7. Example problems &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>Example problems &mdash; LAMMPS 15 May 2015 version documentation</title>
......@@ -32,9 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="next" title="8. Performance &amp; scalability" href="Section_perf.html"/>
<link rel="prev" title="6. How-to discussions" href="Section_howto.html"/>
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
......@@ -73,22 +71,11 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<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"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Example problems</a></li>
</ul>
</div>
</div>
......@@ -111,7 +98,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>7. Example problems</li>
<li>Example problems</li>
<li class="wy-breadcrumbs-aside">
......@@ -126,7 +113,7 @@
<div itemprop="articleBody">
<div class="section" id="example-problems">
<h1>7. Example problems<a class="headerlink" href="#example-problems" title="Permalink to this headline"></a></h1>
<h1>Example problems<a class="headerlink" href="#example-problems" title="Permalink to this headline"></a></h1>
<p>The LAMMPS distribution includes an examples sub-directory with
several sample problems. Each problem is in a sub-directory of its
own. Most are 2d models so that they run quickly, requiring at most a
......@@ -318,15 +305,6 @@ packages.</p>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_perf.html" class="btn btn-neutral float-right" title="8. Performance &amp; scalability" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Section_howto.html" class="btn btn-neutral" title="6. How-to discussions" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<hr/>
......
doc/Section_history.html
+ 12
− 31
View file @ d205583a
......@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>13. Future and history &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>Future and history &mdash; LAMMPS 15 May 2015 version documentation</title>
......@@ -32,8 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="prev" title="12. Errors" href="Section_errors.html"/>
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
......@@ -72,26 +71,15 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<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"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">13. Future and history</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#coming-attractions">13.1. Coming attractions</a></li>
<li class="toctree-l2"><a class="reference internal" href="#past-versions">13.2. Past versions</a></li>
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Future and history</a><ul>
<li><a class="reference internal" href="#coming-attractions">Coming attractions</a></li>
<li><a class="reference internal" href="#past-versions">Past versions</a></li>
</ul>
</li>
</ul>
</div>
</div>
......@@ -114,7 +102,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>13. Future and history</li>
<li>Future and history</li>
<li class="wy-breadcrumbs-aside">
......@@ -129,7 +117,7 @@
<div itemprop="articleBody">
<div class="section" id="future-and-history">
<h1>13. Future and history<a class="headerlink" href="#future-and-history" title="Permalink to this headline"></a></h1>
<h1>Future and history<a class="headerlink" href="#future-and-history" title="Permalink to this headline"></a></h1>
<p>This section lists features we plan to add to LAMMPS, features of
previous versions of LAMMPS, and features of other parallel molecular
dynamics codes our group has distributed.</p>
......@@ -139,7 +127,7 @@ dynamics codes our group has distributed.</p>
<div class="line"><br /></div>
</div>
<div class="section" id="coming-attractions">
<span id="hist-1"></span><h2>13.1. Coming attractions<a class="headerlink" href="#coming-attractions" title="Permalink to this headline"></a></h2>
<span id="hist-1"></span><h2>Coming attractions<a class="headerlink" href="#coming-attractions" title="Permalink to this headline"></a></h2>
<p>The <a class="reference external" href="http://lammps.sandia.gov/future.html">Wish list link</a> on the
LAMMPS WWW page gives a list of features we are hoping to add to
LAMMPS in the future, including contact names of individuals you can
......@@ -150,7 +138,7 @@ your wish to the list.</p>
<hr class="docutils" />
</div>
<div class="section" id="past-versions">
<span id="hist-2"></span><h2>13.2. Past versions<a class="headerlink" href="#past-versions" title="Permalink to this headline"></a></h2>
<span id="hist-2"></span><h2>Past versions<a class="headerlink" href="#past-versions" title="Permalink to this headline"></a></h2>
<p>LAMMPS development began in the mid 1990s under a cooperative research
&amp; development agreement (CRADA) between two DOE labs (Sandia and LLNL)
and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
......@@ -238,13 +226,6 @@ internally. A brief listing of their features is given here.</p>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_errors.html" class="btn btn-neutral" title="12. Errors" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<hr/>
......
doc/Section_howto.html
+ 102
− 124
View file @ d205583a
This diff is collapsed.
doc/Section_intro.html
+ 40
− 62
View file @ d205583a
......@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>1. Introduction &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>Introduction &mdash; LAMMPS 15 May 2015 version documentation</title>
......@@ -32,9 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="next" title="2. Getting Started" href="Section_start.html"/>
<link rel="prev" title="LAMMPS Documentation" href="Manual.html"/>
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
......@@ -73,42 +71,31 @@
<ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="">1. Introduction</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#what-is-lammps">1.1. What is LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="#lammps-features">1.2. LAMMPS features</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#general-features">1.2.1. General features</a></li>
<li class="toctree-l3"><a class="reference internal" href="#particle-and-model-types">1.2.2. Particle and model types</a></li>
<li class="toctree-l3"><a class="reference internal" href="#force-fields">1.2.3. Force fields</a></li>
<li class="toctree-l3"><a class="reference internal" href="#atom-creation">1.2.4. Atom creation</a></li>
<li class="toctree-l3"><a class="reference internal" href="#ensembles-constraints-and-boundary-conditions">1.2.5. Ensembles, constraints, and boundary conditions</a></li>
<li class="toctree-l3"><a class="reference internal" href="#integrators">1.2.6. Integrators</a></li>
<li class="toctree-l3"><a class="reference internal" href="#diagnostics">1.2.7. Diagnostics</a></li>
<li class="toctree-l3"><a class="reference internal" href="#output">1.2.8. Output</a></li>
<li class="toctree-l3"><a class="reference internal" href="#multi-replica-models">1.2.9. Multi-replica models</a></li>
<li class="toctree-l3"><a class="reference internal" href="#pre-and-post-processing">1.2.10. Pre- and post-processing</a></li>
<li class="toctree-l3"><a class="reference internal" href="#specialized-features">1.2.11. Specialized features</a></li>
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Introduction</a><ul>
<li><a class="reference internal" href="#what-is-lammps">What is LAMMPS</a></li>
<li><a class="reference internal" href="#lammps-features">LAMMPS features</a><ul>
<li><a class="reference internal" href="#general-features">General features</a></li>
<li><a class="reference internal" href="#particle-and-model-types">Particle and model types</a></li>
<li><a class="reference internal" href="#force-fields">Force fields</a></li>
<li><a class="reference internal" href="#atom-creation">Atom creation</a></li>
<li><a class="reference internal" href="#ensembles-constraints-and-boundary-conditions">Ensembles, constraints, and boundary conditions</a></li>
<li><a class="reference internal" href="#integrators">Integrators</a></li>
<li><a class="reference internal" href="#diagnostics">Diagnostics</a></li>
<li><a class="reference internal" href="#output">Output</a></li>
<li><a class="reference internal" href="#multi-replica-models">Multi-replica models</a></li>
<li><a class="reference internal" href="#pre-and-post-processing">Pre- and post-processing</a></li>
<li><a class="reference internal" href="#specialized-features">Specialized features</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#lammps-non-features">1.3. LAMMPS non-features</a></li>
<li class="toctree-l2"><a class="reference internal" href="#open-source-distribution">1.4. Open source distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
<li><a class="reference internal" href="#lammps-non-features">LAMMPS non-features</a></li>
<li><a class="reference internal" href="#open-source-distribution">Open source distribution</a></li>
<li><a class="reference internal" href="#acknowledgments-and-citations">Acknowledgments and citations</a></li>
</ul>
</li>
<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"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
......@@ -131,7 +118,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>1. Introduction</li>
<li>Introduction</li>
<li class="wy-breadcrumbs-aside">
......@@ -146,7 +133,7 @@
<div itemprop="articleBody">
<div class="section" id="introduction">
<h1>1. Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline"></a></h1>
<h1>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline"></a></h1>
<p>This section provides an overview of what LAMMPS can and can&#8217;t do,
describes what it means for LAMMPS to be an open-source code, and
acknowledges the funding and people who have contributed to LAMMPS
......@@ -160,7 +147,7 @@ over the years.</p>
<div class="line"><br /></div>
</div>
<div class="section" id="what-is-lammps">
<span id="intro-1"></span><h2>1.1. What is LAMMPS<a class="headerlink" href="#what-is-lammps" title="Permalink to this headline"></a></h2>
<span id="intro-1"></span><h2>What is LAMMPS<a class="headerlink" href="#what-is-lammps" title="Permalink to this headline"></a></h2>
<p>LAMMPS is a classical molecular dynamics code that models an ensemble
of particles in a liquid, solid, or gaseous state. It can model
atomic, polymeric, biological, metallic, granular, and coarse-grained
......@@ -211,14 +198,14 @@ LAMMPS are listed in <a class="reference internal" href="#intro-5"><span>this se
<hr class="docutils" />
</div>
<div class="section" id="lammps-features">
<span id="intro-2"></span><h2>1.2. LAMMPS features<a class="headerlink" href="#lammps-features" title="Permalink to this headline"></a></h2>
<span id="intro-2"></span><h2>LAMMPS features<a class="headerlink" href="#lammps-features" title="Permalink to this headline"></a></h2>
<p>This section highlights LAMMPS features, with pointers to specific
commands which give more details. If LAMMPS doesn&#8217;t have your
favorite interatomic potential, boundary condition, or atom type, see
<a class="reference internal" href="Section_modify.html"><em>Section_modify</em></a>, which describes how you can add
it to LAMMPS.</p>
<div class="section" id="general-features">
<h3>1.2.1. General features<a class="headerlink" href="#general-features" title="Permalink to this headline"></a></h3>
<h3>General features<a class="headerlink" href="#general-features" title="Permalink to this headline"></a></h3>
<ul class="simple">
<li>runs on a single processor or in parallel</li>
<li>distributed-memory message-passing parallelism (MPI)</li>
......@@ -237,7 +224,7 @@ it to LAMMPS.</p>
</ul>
</div>
<div class="section" id="particle-and-model-types">
<h3>1.2.2. Particle and model types<a class="headerlink" href="#particle-and-model-types" title="Permalink to this headline"></a></h3>
<h3>Particle and model types<a class="headerlink" href="#particle-and-model-types" title="Permalink to this headline"></a></h3>
<p>(<a class="reference internal" href="atom_style.html"><em>atom style</em></a> command)</p>
<ul class="simple">
<li>atoms</li>
......@@ -255,7 +242,7 @@ it to LAMMPS.</p>
</ul>
</div>
<div class="section" id="force-fields">
<h3>1.2.3. Force fields<a class="headerlink" href="#force-fields" title="Permalink to this headline"></a></h3>
<h3>Force fields<a class="headerlink" href="#force-fields" title="Permalink to this headline"></a></h3>
<p>(<a class="reference internal" href="pair_style.html"><em>pair style</em></a>, <a class="reference internal" href="bond_style.html"><em>bond style</em></a>,
<a class="reference internal" href="angle_style.html"><em>angle style</em></a>, <a class="reference internal" href="dihedral_style.html"><em>dihedral style</em></a>,
<a class="reference internal" href="improper_style.html"><em>improper style</em></a>, <a class="reference internal" href="kspace_style.html"><em>kspace style</em></a>
......@@ -284,7 +271,7 @@ commands)</p>
</ul>
</div>
<div class="section" id="atom-creation">
<h3>1.2.4. Atom creation<a class="headerlink" href="#atom-creation" title="Permalink to this headline"></a></h3>
<h3>Atom creation<a class="headerlink" href="#atom-creation" title="Permalink to this headline"></a></h3>
<p>(<a class="reference internal" href="read_data.html"><em>read_data</em></a>, <a class="reference internal" href="lattice.html"><em>lattice</em></a>,
<a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a>, <a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a>,
<a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a>, <a class="reference internal" href="replicate.html"><em>replicate</em></a> commands)</p>
......@@ -297,7 +284,7 @@ commands)</p>
</ul>
</div>
<div class="section" id="ensembles-constraints-and-boundary-conditions">
<h3>1.2.5. Ensembles, constraints, and boundary conditions<a class="headerlink" href="#ensembles-constraints-and-boundary-conditions" title="Permalink to this headline"></a></h3>
<h3>Ensembles, constraints, and boundary conditions<a class="headerlink" href="#ensembles-constraints-and-boundary-conditions" title="Permalink to this headline"></a></h3>
<p>(<a class="reference internal" href="fix.html"><em>fix</em></a> command)</p>
<ul class="simple">
<li>2d or 3d systems</li>
......@@ -317,7 +304,7 @@ commands)</p>
</ul>
</div>
<div class="section" id="integrators">
<h3>1.2.6. Integrators<a class="headerlink" href="#integrators" title="Permalink to this headline"></a></h3>
<h3>Integrators<a class="headerlink" href="#integrators" title="Permalink to this headline"></a></h3>
<p>(<a class="reference internal" href="run.html"><em>run</em></a>, <a class="reference internal" href="run_style.html"><em>run_style</em></a>, <a class="reference internal" href="minimize.html"><em>minimize</em></a> commands)</p>
<ul class="simple">
<li>velocity-Verlet integrator</li>
......@@ -329,13 +316,13 @@ commands)</p>
</ul>
</div>
<div class="section" id="diagnostics">
<h3>1.2.7. Diagnostics<a class="headerlink" href="#diagnostics" title="Permalink to this headline"></a></h3>
<h3>Diagnostics<a class="headerlink" href="#diagnostics" title="Permalink to this headline"></a></h3>
<ul class="simple">
<li>see the various flavors of the <a class="reference internal" href="fix.html"><em>fix</em></a> and <a class="reference internal" href="compute.html"><em>compute</em></a> commands</li>
</ul>
</div>
<div class="section" id="output">
<h3>1.2.8. Output<a class="headerlink" href="#output" title="Permalink to this headline"></a></h3>
<h3>Output<a class="headerlink" href="#output" title="Permalink to this headline"></a></h3>
<p>(<a class="reference internal" href="dump.html"><em>dump</em></a>, <a class="reference internal" href="restart.html"><em>restart</em></a> commands)</p>
<ul class="simple">
<li>log file of thermodynamic info</li>
......@@ -350,14 +337,14 @@ commands)</p>
</ul>
</div>
<div class="section" id="multi-replica-models">
<h3>1.2.9. Multi-replica models<a class="headerlink" href="#multi-replica-models" title="Permalink to this headline"></a></h3>
<h3>Multi-replica models<a class="headerlink" href="#multi-replica-models" title="Permalink to this headline"></a></h3>
<p><a class="reference internal" href="neb.html"><em>nudged elastic band</em></a>
<a class="reference internal" href="prd.html"><em>parallel replica dynamics</em></a>
<a class="reference internal" href="tad.html"><em>temperature accelerated dynamics</em></a>
<a class="reference internal" href="temper.html"><em>parallel tempering</em></a></p>
</div>
<div class="section" id="pre-and-post-processing">
<h3>1.2.10. Pre- and post-processing<a class="headerlink" href="#pre-and-post-processing" title="Permalink to this headline"></a></h3>
<h3>Pre- and post-processing<a class="headerlink" href="#pre-and-post-processing" title="Permalink to this headline"></a></h3>
<ul class="simple">
<li>Various pre- and post-processing serial tools are packaged
with LAMMPS; see these <a class="reference internal" href="Section_tools.html"><em>doc pages</em></a>.</li>
......@@ -368,7 +355,7 @@ written in <a class="reference external" href="http://www.python.org">Python</a>
</ul>
</div>
<div class="section" id="specialized-features">
<h3>1.2.11. Specialized features<a class="headerlink" href="#specialized-features" title="Permalink to this headline"></a></h3>
<h3>Specialized features<a class="headerlink" href="#specialized-features" title="Permalink to this headline"></a></h3>
<p>These are LAMMPS capabilities which you may not think of as typical
molecular dynamics options:</p>
<ul class="simple">
......@@ -392,7 +379,7 @@ molecular dynamics options:</p>
</div>
</div>
<div class="section" id="lammps-non-features">
<span id="intro-3"></span><h2>1.3. LAMMPS non-features<a class="headerlink" href="#lammps-non-features" title="Permalink to this headline"></a></h2>
<span id="intro-3"></span><h2>LAMMPS non-features<a class="headerlink" href="#lammps-non-features" title="Permalink to this headline"></a></h2>
<p>LAMMPS is designed to efficiently compute Newton&#8217;s equations of motion
for a system of interacting particles. Many of the tools needed to
pre- and post-process the data for such simulations are not included
......@@ -485,7 +472,7 @@ spatial-decomposition version exist.</p>
<hr class="docutils" />
</div>
<div class="section" id="open-source-distribution">
<span id="intro-4"></span><h2>1.4. Open source distribution<a class="headerlink" href="#open-source-distribution" title="Permalink to this headline"></a></h2>
<span id="intro-4"></span><h2>Open source distribution<a class="headerlink" href="#open-source-distribution" title="Permalink to this headline"></a></h2>
<p>LAMMPS comes with no warranty of any kind. As each source file states
in its header, it is a copyrighted code that is distributed free-of-
charge, under the terms of the <a class="reference external" href="http://www.gnu.org/copyleft/gpl.html">GNU Public License</a> (GPL). This
......@@ -547,7 +534,7 @@ encouraged.</li>
<hr class="docutils" />
</div>
<div class="section" id="acknowledgments-and-citations">
<span id="intro-5"></span><h2>1.5. Acknowledgments and citations<a class="headerlink" href="#acknowledgments-and-citations" title="Permalink to this headline"></a></h2>
<span id="intro-5"></span><h2>Acknowledgments and citations<a class="headerlink" href="#acknowledgments-and-citations" title="Permalink to this headline"></a></h2>
<p>LAMMPS development has been funded by the <a class="reference external" href="http://www.doe.gov">US Department of Energy</a> (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
programs and its <a class="reference external" href="http://www.sc.doe.gov/ascr/home.html">OASCR</a> and <a class="reference external" href="http://www.er.doe.gov/production/ober/ober_top.html">OBER</a> offices.</p>
<p>Specifically, work on the latest version was funded in part by the US
......@@ -616,15 +603,6 @@ version of LAMMPS were the following:</p>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_start.html" class="btn btn-neutral float-right" title="2. Getting Started" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Manual.html" class="btn btn-neutral" title="LAMMPS Documentation" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<hr/>
......
doc/Section_modify.html
+ 38
− 60
View file @ d205583a
......@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>10. Modifying &amp; extending LAMMPS &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>Modifying &amp; extending LAMMPS &mdash; LAMMPS 15 May 2015 version documentation</title>
......@@ -32,9 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="next" title="11. Python interface to LAMMPS" href="Section_python.html"/>
<link rel="prev" title="9. Additional tools" href="Section_tools.html"/>
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
......@@ -73,39 +71,28 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<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"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">10. Modifying &amp; extending LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#atom-styles">10.1. Atom styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#compute-styles">10.3. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#dump-styles">10.4. Dump styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#dump-custom-output-options">10.5. Dump custom output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="#fix-styles">10.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#input-script-commands">10.7. Input script commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="#kspace-computations">10.8. Kspace computations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#minimization-styles">10.9. Minimization styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#pairwise-potentials">10.10. Pairwise potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#region-styles">10.11. Region styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#body-styles">10.12. Body styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="#variable-options">10.14. Variable options</a></li>
<li class="toctree-l2"><a class="reference internal" href="#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li>
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Modifying &amp; extending LAMMPS</a><ul>
<li><a class="reference internal" href="#atom-styles">Atom styles</a></li>
<li><a class="reference internal" href="#bond-angle-dihedral-improper-potentials">Bond, angle, dihedral, improper potentials</a></li>
<li><a class="reference internal" href="#compute-styles">Compute styles</a></li>
<li><a class="reference internal" href="#dump-styles">Dump styles</a></li>
<li><a class="reference internal" href="#dump-custom-output-options">Dump custom output options</a></li>
<li><a class="reference internal" href="#fix-styles">Fix styles</a></li>
<li><a class="reference internal" href="#input-script-commands">Input script commands</a></li>
<li><a class="reference internal" href="#kspace-computations">Kspace computations</a></li>
<li><a class="reference internal" href="#minimization-styles">Minimization styles</a></li>
<li><a class="reference internal" href="#pairwise-potentials">Pairwise potentials</a></li>
<li><a class="reference internal" href="#region-styles">Region styles</a></li>
<li><a class="reference internal" href="#body-styles">Body styles</a></li>
<li><a class="reference internal" href="#thermodynamic-output-options">Thermodynamic output options</a></li>
<li><a class="reference internal" href="#variable-options">Variable options</a></li>
<li><a class="reference internal" href="#submitting-new-features-for-inclusion-in-lammps">Submitting new features for inclusion in LAMMPS</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
......@@ -128,7 +115,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>10. Modifying &amp; extending LAMMPS</li>
<li>Modifying &amp; extending LAMMPS</li>
<li class="wy-breadcrumbs-aside">
......@@ -143,7 +130,7 @@
<div itemprop="articleBody">
<div class="section" id="modifying-extending-lammps">
<h1>10. Modifying &amp; extending LAMMPS<a class="headerlink" href="#modifying-extending-lammps" title="Permalink to this headline"></a></h1>
<h1>Modifying &amp; extending LAMMPS<a class="headerlink" href="#modifying-extending-lammps" title="Permalink to this headline"></a></h1>
<p>This section describes how to customize LAMMPS by modifying
and extending its source code.</p>
<div class="line-block">
......@@ -253,7 +240,7 @@ interested in adding it to the LAMMPS distribution. See further
details on this at the bottom of this page.</li>
</ul>
<div class="section" id="atom-styles">
<span id="mod-1"></span><h2>10.1. Atom styles<a class="headerlink" href="#atom-styles" title="Permalink to this headline"></a></h2>
<span id="mod-1"></span><h2>Atom styles<a class="headerlink" href="#atom-styles" title="Permalink to this headline"></a></h2>
<p>Classes that define an <a class="reference internal" href="atom_style.html"><em>atom style</em></a> are derived from
the AtomVec class and managed by the Atom class. The atom style
determines what attributes are associated with an atom. A new atom
......@@ -400,7 +387,7 @@ which store the attributes of individual atoms.</p>
<hr class="docutils" />
</div>
<div class="section" id="bond-angle-dihedral-improper-potentials">
<span id="mod-2"></span><h2>10.2. Bond, angle, dihedral, improper potentials<a class="headerlink" href="#bond-angle-dihedral-improper-potentials" title="Permalink to this headline"></a></h2>
<span id="mod-2"></span><h2>Bond, angle, dihedral, improper potentials<a class="headerlink" href="#bond-angle-dihedral-improper-potentials" title="Permalink to this headline"></a></h2>
<p>Classes that compute molecular interactions are derived from the Bond,
Angle, Dihedral, and Improper classes. New styles can be created to
add new potentials to LAMMPS.</p>
......@@ -451,7 +438,7 @@ for details and specific additional methods.</p>
<hr class="docutils" />
</div>
<div class="section" id="compute-styles">
<span id="mod-3"></span><h2>10.3. Compute styles<a class="headerlink" href="#compute-styles" title="Permalink to this headline"></a></h2>
<span id="mod-3"></span><h2>Compute styles<a class="headerlink" href="#compute-styles" title="Permalink to this headline"></a></h2>
<p>Classes that compute scalar and vector quantities like temperature
and the pressure tensor, as well as classes that compute per-atom
quantities like kinetic energy and the centro-symmetry parameter
......@@ -518,10 +505,10 @@ class. See compute.h for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="dump-styles">
<span id="mod-4"></span><h2>10.4. Dump styles<a class="headerlink" href="#dump-styles" title="Permalink to this headline"></a></h2>
<span id="mod-4"></span><h2>Dump styles<a class="headerlink" href="#dump-styles" title="Permalink to this headline"></a></h2>
</div>
<div class="section" id="dump-custom-output-options">
<span id="mod-5"></span><h2>10.5. Dump custom output options<a class="headerlink" href="#dump-custom-output-options" title="Permalink to this headline"></a></h2>
<span id="mod-5"></span><h2>Dump custom output options<a class="headerlink" href="#dump-custom-output-options" title="Permalink to this headline"></a></h2>
<p>Classes that dump per-atom info to files are derived from the Dump
class. To dump new quantities or in a new format, a new derived dump
class can be added, but it is typically simpler to modify the
......@@ -560,7 +547,7 @@ half-dozen or so locations where code will need to be added.</p>
<hr class="docutils" />
</div>
<div class="section" id="fix-styles">
<span id="mod-6"></span><h2>10.6. Fix styles<a class="headerlink" href="#fix-styles" title="Permalink to this headline"></a></h2>
<span id="mod-6"></span><h2>Fix styles<a class="headerlink" href="#fix-styles" title="Permalink to this headline"></a></h2>
<p>In LAMMPS, a &#8220;fix&#8221; is any operation that is computed during
timestepping that alters some property of the system. Essentially
everything that happens during a simulation besides force computation,
......@@ -768,7 +755,7 @@ quantities and/or to be summed to the potential energy of the system.</p>
<hr class="docutils" />
</div>
<div class="section" id="input-script-commands">
<span id="mod-7"></span><h2>10.7. Input script commands<a class="headerlink" href="#input-script-commands" title="Permalink to this headline"></a></h2>
<span id="mod-7"></span><h2>Input script commands<a class="headerlink" href="#input-script-commands" title="Permalink to this headline"></a></h2>
<p>New commands can be added to LAMMPS input scripts by adding new
classes that have a &#8220;command&#8221; method. For example, the create_atoms,
read_data, velocity, and run commands are all implemented in this
......@@ -794,7 +781,7 @@ needed.</p>
<hr class="docutils" />
</div>
<div class="section" id="kspace-computations">
<span id="mod-8"></span><h2>10.8. Kspace computations<a class="headerlink" href="#kspace-computations" title="Permalink to this headline"></a></h2>
<span id="mod-8"></span><h2>Kspace computations<a class="headerlink" href="#kspace-computations" title="Permalink to this headline"></a></h2>
<p>Classes that compute long-range Coulombic interactions via K-space
representations (Ewald, PPPM) are derived from the KSpace class. New
styles can be created to add new K-space options to LAMMPS.</p>
......@@ -824,7 +811,7 @@ class. See kspace.h for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="minimization-styles">
<span id="mod-9"></span><h2>10.9. Minimization styles<a class="headerlink" href="#minimization-styles" title="Permalink to this headline"></a></h2>
<span id="mod-9"></span><h2>Minimization styles<a class="headerlink" href="#minimization-styles" title="Permalink to this headline"></a></h2>
<p>Classes that perform energy minimization derived from the Min class.
New styles can be created to add new minimization algorithms to
LAMMPS.</p>
......@@ -851,7 +838,7 @@ class. See min.h for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="pairwise-potentials">
<span id="mod-10"></span><h2>10.10. Pairwise potentials<a class="headerlink" href="#pairwise-potentials" title="Permalink to this headline"></a></h2>
<span id="mod-10"></span><h2>Pairwise potentials<a class="headerlink" href="#pairwise-potentials" title="Permalink to this headline"></a></h2>
<p>Classes that compute pairwise interactions are derived from the Pair
class. In LAMMPS, pairwise calculation include manybody potentials
such as EAM or Tersoff where particles interact without a static bond
......@@ -899,7 +886,7 @@ includes some optional methods to enable its use with rRESPA.</p>
<hr class="docutils" />
</div>
<div class="section" id="region-styles">
<span id="mod-11"></span><h2>10.11. Region styles<a class="headerlink" href="#region-styles" title="Permalink to this headline"></a></h2>
<span id="mod-11"></span><h2>Region styles<a class="headerlink" href="#region-styles" title="Permalink to this headline"></a></h2>
<p>Classes that define geometric regions are derived from the Region
class. Regions are used elsewhere in LAMMPS to group atoms, delete
atoms to create a void, insert atoms in a specified region, etc. New
......@@ -921,7 +908,7 @@ class. See region.h for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="body-styles">
<span id="mod-12"></span><h2>10.12. Body styles<a class="headerlink" href="#body-styles" title="Permalink to this headline"></a></h2>
<span id="mod-12"></span><h2>Body styles<a class="headerlink" href="#body-styles" title="Permalink to this headline"></a></h2>
<p>Classes that define body particles are derived from the Body class.
Body particles can represent complex entities, such as surface meshes
of discrete points, collections of sub-particles, deformable objects,
......@@ -969,7 +956,7 @@ class. See body.h for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="thermodynamic-output-options">
<span id="mod-13"></span><h2>10.13. Thermodynamic output options<a class="headerlink" href="#thermodynamic-output-options" title="Permalink to this headline"></a></h2>
<span id="mod-13"></span><h2>Thermodynamic output options<a class="headerlink" href="#thermodynamic-output-options" title="Permalink to this headline"></a></h2>
<p>There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp.</p>
<p>There are two styles defined in thermo.cpp: &#8220;one&#8221; and &#8220;multi&#8221;. There
......@@ -993,7 +980,7 @@ by adding a new keyword to the thermo command.</p>
<hr class="docutils" />
</div>
<div class="section" id="variable-options">
<span id="mod-14"></span><h2>10.14. Variable options<a class="headerlink" href="#variable-options" title="Permalink to this headline"></a></h2>
<span id="mod-14"></span><h2>Variable options<a class="headerlink" href="#variable-options" title="Permalink to this headline"></a></h2>
<p>There is one class that computes and stores <a class="reference internal" href="variable.html"><em>variable</em></a>
information in LAMMPS; see the file variable.cpp. The value
associated with a variable can be periodically printed to the screen
......@@ -1027,7 +1014,7 @@ then be accessed by variables) was discussed
<a class="reference internal" href="Section_howto.html#compute"><span>here</span></a> on this page.</p>
</div>
<div class="section" id="submitting-new-features-for-inclusion-in-lammps">
<span id="mod-15"></span><h2>10.15. Submitting new features for inclusion in LAMMPS<a class="headerlink" href="#submitting-new-features-for-inclusion-in-lammps" title="Permalink to this headline"></a></h2>
<span id="mod-15"></span><h2>Submitting new features for inclusion in LAMMPS<a class="headerlink" href="#submitting-new-features-for-inclusion-in-lammps" title="Permalink to this headline"></a></h2>
<p>We encourage users to submit new features to <a class="reference external" href="http://lammps.sandia.gov/authors.html">the developers</a> that they add to
LAMMPS, especially if you think they will be of interest to other
users. If they are broadly useful we may add them as core files to
......@@ -1165,15 +1152,6 @@ feature.</p>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_python.html" class="btn btn-neutral float-right" title="11. Python interface to LAMMPS" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Section_tools.html" class="btn btn-neutral" title="9. Additional tools" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<hr/>
......
doc/Section_packages.html
+ 50
− 72
View file @ d205583a
......@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>4. Packages &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>Packages &mdash; LAMMPS 15 May 2015 version documentation</title>
......@@ -32,9 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="next" title="5. Accelerating LAMMPS performance" href="Section_accelerate.html"/>
<link rel="prev" title="3. Commands" href="Section_commands.html"/>
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
......@@ -73,45 +71,34 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<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="#user-packages">4.2. User packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-atc-package">4.3. USER-ATC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-awpmd-package">4.4. USER-AWPMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-cg-cmm-package">4.5. USER-CG-CMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-colvars-package">4.6. USER-COLVARS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-cuda-package">4.7. USER-CUDA package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-diffraction-package">4.8. USER-DIFFRACTION package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-drude-package">4.9. USER-DRUDE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-eff-package">4.10. USER-EFF package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-fep-package">4.11. USER-FEP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-intel-package">4.12. USER-INTEL package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-lb-package">4.13. USER-LB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-misc-package">4.14. USER-MISC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-molfile-package">4.15. USER-MOLFILE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-omp-package">4.16. USER-OMP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-phonon-package">4.17. USER-PHONON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-qmmm-package">4.18. USER-QMMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-qtb-package">4.19. USER-QTB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-reaxc-package">4.20. USER-REAXC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-sph-package">4.21. USER-SPH package</a></li>
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Packages</a><ul>
<li><a class="reference internal" href="#standard-packages">Standard packages</a></li>
<li><a class="reference internal" href="#user-packages">User packages</a></li>
<li><a class="reference internal" href="#user-atc-package">USER-ATC package</a></li>
<li><a class="reference internal" href="#user-awpmd-package">USER-AWPMD package</a></li>
<li><a class="reference internal" href="#user-cg-cmm-package">USER-CG-CMM package</a></li>
<li><a class="reference internal" href="#user-colvars-package">USER-COLVARS package</a></li>
<li><a class="reference internal" href="#user-cuda-package">USER-CUDA package</a></li>
<li><a class="reference internal" href="#user-diffraction-package">USER-DIFFRACTION package</a></li>
<li><a class="reference internal" href="#user-drude-package">USER-DRUDE package</a></li>
<li><a class="reference internal" href="#user-eff-package">USER-EFF package</a></li>
<li><a class="reference internal" href="#user-fep-package">USER-FEP package</a></li>
<li><a class="reference internal" href="#user-intel-package">USER-INTEL package</a></li>
<li><a class="reference internal" href="#user-lb-package">USER-LB package</a></li>
<li><a class="reference internal" href="#user-misc-package">USER-MISC package</a></li>
<li><a class="reference internal" href="#user-molfile-package">USER-MOLFILE package</a></li>
<li><a class="reference internal" href="#user-omp-package">USER-OMP package</a></li>
<li><a class="reference internal" href="#user-phonon-package">USER-PHONON package</a></li>
<li><a class="reference internal" href="#user-qmmm-package">USER-QMMM package</a></li>
<li><a class="reference internal" href="#user-qtb-package">USER-QTB package</a></li>
<li><a class="reference internal" href="#user-reaxc-package">USER-REAXC package</a></li>
<li><a class="reference internal" href="#user-sph-package">USER-SPH package</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
......@@ -134,7 +121,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>4. Packages</li>
<li>Packages</li>
<li class="wy-breadcrumbs-aside">
......@@ -149,7 +136,7 @@
<div itemprop="articleBody">
<div class="section" id="packages">
<h1>4. Packages<a class="headerlink" href="#packages" title="Permalink to this headline"></a></h1>
<h1>Packages<a class="headerlink" href="#packages" title="Permalink to this headline"></a></h1>
<p>This section gives a quick overview of the add-on packages that extend
LAMMPS functionality.</p>
<div class="line-block">
......@@ -170,7 +157,7 @@ between standard packages and user packages in LAMMPS.</p>
standard packages, just a one-line description is given. For user
packages, more details are provided.</p>
<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>
<span id="pkg-1"></span><h2>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:</p>
<table border="1" class="docutils">
<colgroup>
......@@ -552,7 +539,7 @@ info on where to download the library. <a class="reference internal" href="Sect
on how to build LAMMPS with both kinds of auxiliary libraries.</p>
</div>
<div class="section" id="user-packages">
<span id="pkg-2"></span><h2>4.2. User packages<a class="headerlink" href="#user-packages" title="Permalink to this headline"></a></h2>
<span id="pkg-2"></span><h2>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>
......@@ -876,7 +863,7 @@ below.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-atc-package">
<h2>4.3. USER-ATC package<a class="headerlink" href="#user-atc-package" title="Permalink to this headline"></a></h2>
<h2>USER-ATC package<a class="headerlink" href="#user-atc-package" title="Permalink to this headline"></a></h2>
<p>This package implements a &#8220;fix atc&#8221; command which can be used in a
LAMMPS input script. This fix can be employed to either do concurrent
coupling of MD with FE-based physics surrogates or on-the-fly
......@@ -896,7 +883,7 @@ you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-awpmd-package">
<h2>4.4. USER-AWPMD package<a class="headerlink" href="#user-awpmd-package" title="Permalink to this headline"></a></h2>
<h2>USER-AWPMD package<a class="headerlink" href="#user-awpmd-package" title="Permalink to this headline"></a></h2>
<p>This package contains a LAMMPS implementation of the Antisymmetrized
Wave Packet Molecular Dynamics (AWPMD) method.</p>
<p>See the doc page for the pair_style awpmd/cut command to get started.</p>
......@@ -911,7 +898,7 @@ have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-cg-cmm-package">
<h2>4.5. USER-CG-CMM package<a class="headerlink" href="#user-cg-cmm-package" title="Permalink to this headline"></a></h2>
<h2>USER-CG-CMM package<a class="headerlink" href="#user-cg-cmm-package" title="Permalink to this headline"></a></h2>
<p>This package implements 3 commands which can be used in a LAMMPS input
script:</p>
<ul class="simple">
......@@ -946,7 +933,7 @@ simulation systems.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-colvars-package">
<h2>4.6. USER-COLVARS package<a class="headerlink" href="#user-colvars-package" title="Permalink to this headline"></a></h2>
<h2>USER-COLVARS package<a class="headerlink" href="#user-colvars-package" title="Permalink to this headline"></a></h2>
<p>This package implements the &#8220;fix colvars&#8221; command which can be
used in a LAMMPS input script.</p>
<p>This fix allows to use &#8220;collective variables&#8221; to implement
......@@ -975,7 +962,7 @@ beta quality.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-cuda-package">
<h2>4.7. USER-CUDA package<a class="headerlink" href="#user-cuda-package" title="Permalink to this headline"></a></h2>
<h2>USER-CUDA package<a class="headerlink" href="#user-cuda-package" title="Permalink to this headline"></a></h2>
<p>This package provides acceleration of various LAMMPS pair styles, fix
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
GPUs.</p>
......@@ -993,7 +980,7 @@ tu-ilmenau.de). Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-diffraction-package">
<h2>4.8. USER-DIFFRACTION package<a class="headerlink" href="#user-diffraction-package" title="Permalink to this headline"></a></h2>
<h2>USER-DIFFRACTION package<a class="headerlink" href="#user-diffraction-package" title="Permalink to this headline"></a></h2>
<p>This package contains the commands neeed to calculate x-ray and
electron diffraction intensities based on kinematic diffraction
theory.</p>
......@@ -1009,7 +996,7 @@ Arkansas. Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-drude-package">
<h2>4.9. USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline"></a></h2>
<h2>USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline"></a></h2>
<p>This package implements methods for simulating polarizable systems
in LAMMPS using thermalized Drude oscillators.</p>
<p>See these doc pages and their related commands to get started:</p>
......@@ -1029,7 +1016,7 @@ Agilio Padua.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-eff-package">
<h2>4.10. USER-EFF package<a class="headerlink" href="#user-eff-package" title="Permalink to this headline"></a></h2>
<h2>USER-EFF package<a class="headerlink" href="#user-eff-package" title="Permalink to this headline"></a></h2>
<p>This package contains a LAMMPS implementation of the electron Force
Field (eFF) currently under development at Caltech, as described in
A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
......@@ -1063,7 +1050,7 @@ have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-fep-package">
<h2>4.11. USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline"></a></h2>
<h2>USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline"></a></h2>
<p>This package provides methods for performing free energy perturbation
simulations with soft-core pair potentials in LAMMPS.</p>
<p>See these doc pages and their related commands to get started:</p>
......@@ -1078,7 +1065,7 @@ Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-intel-package">
<h2>4.12. USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline"></a></h2>
<h2>USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline"></a></h2>
<p>This package provides options for performing neighbor list and
non-bonded force calculations in single, mixed, or double precision
and also a capability for accelerating calculations with an
......@@ -1090,7 +1077,7 @@ Intel(R) Xeon Phi(TM) coprocessor.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-lb-package">
<h2>4.13. USER-LB package<a class="headerlink" href="#user-lb-package" title="Permalink to this headline"></a></h2>
<h2>USER-LB package<a class="headerlink" href="#user-lb-package" title="Permalink to this headline"></a></h2>
<p>This package contains a LAMMPS implementation of a background
Lattice-Boltzmann fluid, which can be used to model MD particles
influenced by hydrodynamic forces.</p>
......@@ -1102,7 +1089,7 @@ Western Ontario. Contact them directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-misc-package">
<h2>4.14. USER-MISC package<a class="headerlink" href="#user-misc-package" title="Permalink to this headline"></a></h2>
<h2>USER-MISC package<a class="headerlink" href="#user-misc-package" title="Permalink to this headline"></a></h2>
<p>The files in this package are a potpourri of (mostly) unrelated
features contributed to LAMMPS by users. Each feature is a single
pair of files (<a href="#id3"><span class="problematic" id="id4">*</span></a>.cpp and <a href="#id5"><span class="problematic" id="id6">*</span></a>.h).</p>
......@@ -1119,7 +1106,7 @@ about the feature or its coding.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-molfile-package">
<h2>4.15. USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline"></a></h2>
<h2>USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline"></a></h2>
<p>This package contains a dump molfile command which uses molfile
plugins that are bundled with the
<a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a> molecular visualization and
......@@ -1138,7 +1125,7 @@ application itself.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-omp-package">
<h2>4.16. USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline"></a></h2>
<h2>USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline"></a></h2>
<p>This package provides OpenMP multi-threading support and
other optimizations of various LAMMPS pair styles, dihedral
styles, and fix styles.</p>
......@@ -1149,7 +1136,7 @@ styles, and fix styles.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-phonon-package">
<h2>4.17. USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline"></a></h2>
<h2>USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline"></a></h2>
<p>This package contains a fix phonon command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
relations, directly from molecular dynamics simulations.</p>
......@@ -1161,7 +1148,7 @@ if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-qmmm-package">
<h2>4.18. USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline"></a></h2>
<h2>USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline"></a></h2>
<p>This package provides a fix qmmm command which allows LAMMPS to be
used in a QM/MM simulation, currently only in combination with pw.x
code from the <a class="reference external" href="http://www.quantum-espresso.org">Quantum ESPRESSO</a> package.</p>
......@@ -1178,7 +1165,7 @@ without changes to LAMMPS itself.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-qtb-package">
<h2>4.19. USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline"></a></h2>
<h2>USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline"></a></h2>
<p>This package provides a self-consistent quantum treatment of the
vibrational modes in a classical molecular dynamics simulation. By
coupling the MD simulation to a colored thermostat, it introduces zero
......@@ -1200,7 +1187,7 @@ have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-reaxc-package">
<h2>4.20. USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline"></a></h2>
<h2>USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline"></a></h2>
<p>This package contains a implementation for LAMMPS of the ReaxFF force
field. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
......@@ -1228,7 +1215,7 @@ questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-sph-package">
<h2>4.21. USER-SPH package<a class="headerlink" href="#user-sph-package" title="Permalink to this headline"></a></h2>
<h2>USER-SPH package<a class="headerlink" href="#user-sph-package" title="Permalink to this headline"></a></h2>
<p>This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:</p>
<ul class="simple">
......@@ -1255,15 +1242,6 @@ you have questions.</p>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_accelerate.html" class="btn btn-neutral float-right" title="5. Accelerating LAMMPS performance" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Section_commands.html" class="btn btn-neutral" title="3. Commands" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<hr/>
......
doc/Section_perf.html
+ 8
− 30
View file @ d205583a
......@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>8. Performance &amp; scalability &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>Performance &amp; scalability &mdash; LAMMPS 15 May 2015 version documentation</title>
......@@ -32,9 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="next" title="9. Additional tools" href="Section_tools.html"/>
<link rel="prev" title="7. Example problems" href="Section_example.html"/>
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
......@@ -73,22 +71,11 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<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"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Performance &amp; scalability</a></li>
</ul>
</div>
</div>
......@@ -111,7 +98,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>8. Performance &amp; scalability</li>
<li>Performance &amp; scalability</li>
<li class="wy-breadcrumbs-aside">
......@@ -126,7 +113,7 @@
<div itemprop="articleBody">
<div class="section" id="performance-scalability">
<h1>8. Performance &amp; scalability<a class="headerlink" href="#performance-scalability" title="Permalink to this headline"></a></h1>
<h1>Performance &amp; scalability<a class="headerlink" href="#performance-scalability" title="Permalink to this headline"></a></h1>
<p>LAMMPS performance on several prototypical benchmarks and machines is
discussed on the Benchmarks page of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> where
CPU timings and parallel efficiencies are listed. Here, the
......@@ -225,15 +212,6 @@ on 1500 processors that ran at 85% parallel efficiency.</p>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_tools.html" class="btn btn-neutral float-right" title="9. Additional tools" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Section_example.html" class="btn btn-neutral" title="7. Example problems" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<hr/>
......
doc/Section_python.html
+ 34
− 56
View file @ d205583a
......@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>11. Python interface to LAMMPS &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>Python interface to LAMMPS &mdash; LAMMPS 15 May 2015 version documentation</title>
......@@ -32,9 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="next" title="12. Errors" href="Section_errors.html"/>
<link rel="prev" title="10. Modifying &amp; extending LAMMPS" href="Section_modify.html"/>
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
......@@ -73,37 +71,26 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<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"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">11. Python interface to LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
<li class="toctree-l2"><a class="reference internal" href="#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li>
<li class="toctree-l2"><a class="reference internal" href="#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="#extending-python-with-mpi-to-run-in-parallel">11.5. Extending Python with MPI to run in parallel</a></li>
<li class="toctree-l2"><a class="reference internal" href="#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#test-lammps-and-python-in-serial">11.6.1. <strong>Test LAMMPS and Python in serial:</strong></a></li>
<li class="toctree-l3"><a class="reference internal" href="#test-lammps-and-python-in-parallel">11.6.2. <strong>Test LAMMPS and Python in parallel:</strong></a></li>
<li class="toctree-l3"><a class="reference internal" href="#running-python-scripts">11.6.3. <strong>Running Python scripts:</strong></a></li>
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Python interface to LAMMPS</a><ul>
<li><a class="reference internal" href="#overview-of-running-lammps-from-python">Overview of running LAMMPS from Python</a></li>
<li><a class="reference internal" href="#overview-of-using-python-from-a-lammps-script">Overview of using Python from a LAMMPS script</a></li>
<li><a class="reference internal" href="#building-lammps-as-a-shared-library">Building LAMMPS as a shared library</a></li>
<li><a class="reference internal" href="#installing-the-python-wrapper-into-python">Installing the Python wrapper into Python</a></li>
<li><a class="reference internal" href="#extending-python-with-mpi-to-run-in-parallel">Extending Python with MPI to run in parallel</a></li>
<li><a class="reference internal" href="#testing-the-python-lammps-interface">Testing the Python-LAMMPS interface</a><ul>
<li><a class="reference internal" href="#test-lammps-and-python-in-serial"><strong>Test LAMMPS and Python in serial:</strong></a></li>
<li><a class="reference internal" href="#test-lammps-and-python-in-parallel"><strong>Test LAMMPS and Python in parallel:</strong></a></li>
<li><a class="reference internal" href="#running-python-scripts"><strong>Running Python scripts:</strong></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li>
<li><a class="reference internal" href="#using-lammps-from-python">Using LAMMPS from Python</a></li>
<li><a class="reference internal" href="#example-python-scripts-that-use-lammps">Example Python scripts that use LAMMPS</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
......@@ -126,7 +113,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>11. Python interface to LAMMPS</li>
<li>Python interface to LAMMPS</li>
<li class="wy-breadcrumbs-aside">
......@@ -141,7 +128,7 @@
<div itemprop="articleBody">
<div class="section" id="python-interface-to-lammps">
<h1>11. Python interface to LAMMPS<a class="headerlink" href="#python-interface-to-lammps" title="Permalink to this headline"></a></h1>
<h1>Python interface to LAMMPS<a class="headerlink" href="#python-interface-to-lammps" title="Permalink to this headline"></a></h1>
<p>LAMMPS can work together with Python in two ways. First, Python can
wrap LAMMPS through the <a class="reference internal" href="Section_howto.html#howto-19"><span>LAMMPS library interface</span></a>, so that a Python script can
create one or more instances of LAMMPS and launch one or more
......@@ -187,7 +174,7 @@ interesting Python functions that can be called from a LAMMPS input
script, that you think would be useful to other users, please <a class="reference external" href="http://lammps.sandia.gov/authors.html">email them to the developers</a>. We can
include them in the LAMMPS distribution.</p>
<div class="section" id="overview-of-running-lammps-from-python">
<span id="py-1"></span><h2>11.1. Overview of running LAMMPS from Python<a class="headerlink" href="#overview-of-running-lammps-from-python" title="Permalink to this headline"></a></h2>
<span id="py-1"></span><h2>Overview of running LAMMPS from Python<a class="headerlink" href="#overview-of-running-lammps-from-python" title="Permalink to this headline"></a></h2>
<p>The LAMMPS distribution includes a python directory with all you need
to run LAMMPS from Python. The python/lammps.py file wraps the LAMMPS
library interface, with one wrapper function per LAMMPS library
......@@ -227,7 +214,7 @@ check which version of Python you have installed, by simply typing
<hr class="docutils" />
</div>
<div class="section" id="overview-of-using-python-from-a-lammps-script">
<span id="py-2"></span><h2>11.2. Overview of using Python from a LAMMPS script<a class="headerlink" href="#overview-of-using-python-from-a-lammps-script" title="Permalink to this headline"></a></h2>
<span id="py-2"></span><h2>Overview of using Python from a LAMMPS script<a class="headerlink" href="#overview-of-using-python-from-a-lammps-script" title="Permalink to this headline"></a></h2>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">It is not currently possible to use the
......@@ -288,7 +275,7 @@ file and the shared library.</p>
<hr class="docutils" />
</div>
<div class="section" id="building-lammps-as-a-shared-library">
<span id="py-3"></span><h2>11.3. Building LAMMPS as a shared library<a class="headerlink" href="#building-lammps-as-a-shared-library" title="Permalink to this headline"></a></h2>
<span id="py-3"></span><h2>Building LAMMPS as a shared library<a class="headerlink" href="#building-lammps-as-a-shared-library" title="Permalink to this headline"></a></h2>
<p>Instructions on how to build LAMMPS as a shared library are given in
<a class="reference internal" href="Section_start.html#start-5"><span>Section_start 5</span></a>. A shared library is one
that is dynamically loadable, which is what Python requires to wrap
......@@ -310,7 +297,7 @@ system.</p>
<hr class="docutils" />
</div>
<div class="section" id="installing-the-python-wrapper-into-python">
<span id="py-4"></span><h2>11.4. Installing the Python wrapper into Python<a class="headerlink" href="#installing-the-python-wrapper-into-python" title="Permalink to this headline"></a></h2>
<span id="py-4"></span><h2>Installing the Python wrapper into Python<a class="headerlink" href="#installing-the-python-wrapper-into-python" title="Permalink to this headline"></a></h2>
<p>For Python to invoke LAMMPS, there are 2 files it needs to know about:</p>
<ul class="simple">
<li>python/lammps.py</li>
......@@ -372,7 +359,7 @@ environment variable as described above.</p>
<hr class="docutils" />
</div>
<div class="section" id="extending-python-with-mpi-to-run-in-parallel">
<span id="py-5"></span><h2>11.5. Extending Python with MPI to run in parallel<a class="headerlink" href="#extending-python-with-mpi-to-run-in-parallel" title="Permalink to this headline"></a></h2>
<span id="py-5"></span><h2>Extending Python with MPI to run in parallel<a class="headerlink" href="#extending-python-with-mpi-to-run-in-parallel" title="Permalink to this headline"></a></h2>
<p>If you wish to run LAMMPS in parallel from Python, you need to extend
your Python with an interface to MPI. This also allows you to
make MPI calls directly from Python in your script, if you desire.</p>
......@@ -458,7 +445,7 @@ the right one.</p>
<hr class="docutils" />
</div>
<div class="section" id="testing-the-python-lammps-interface">
<span id="py-6"></span><h2>11.6. Testing the Python-LAMMPS interface<a class="headerlink" href="#testing-the-python-lammps-interface" title="Permalink to this headline"></a></h2>
<span id="py-6"></span><h2>Testing the Python-LAMMPS interface<a class="headerlink" href="#testing-the-python-lammps-interface" title="Permalink to this headline"></a></h2>
<p>To test if LAMMPS is callable from Python, launch Python interactively
and type:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">lammps</span> <span class="kn">import</span> <span class="n">lammps</span>
......@@ -485,7 +472,7 @@ first importing from the lammps.py file:</p>
library and about insuring Python can find the necessary two files
it needs.</p>
<div class="section" id="test-lammps-and-python-in-serial">
<h3>11.6.1. <strong>Test LAMMPS and Python in serial:</strong><a class="headerlink" href="#test-lammps-and-python-in-serial" title="Permalink to this headline"></a></h3>
<h3><strong>Test LAMMPS and Python in serial:</strong><a class="headerlink" href="#test-lammps-and-python-in-serial" title="Permalink to this headline"></a></h3>
<p>To run a LAMMPS test in serial, type these lines into Python
interactively from the bench directory:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">lammps</span> <span class="kn">import</span> <span class="n">lammps</span>
......@@ -505,7 +492,7 @@ typed something like:</p>
</div>
</div>
<div class="section" id="test-lammps-and-python-in-parallel">
<h3>11.6.2. <strong>Test LAMMPS and Python in parallel:</strong><a class="headerlink" href="#test-lammps-and-python-in-parallel" title="Permalink to this headline"></a></h3>
<h3><strong>Test LAMMPS and Python in parallel:</strong><a class="headerlink" href="#test-lammps-and-python-in-parallel" title="Permalink to this headline"></a></h3>
<p>To run LAMMPS in parallel, assuming you have installed the
<a class="reference external" href="http://datamining.anu.edu.au/~ole/pypar">Pypar</a> package as discussed
above, create a test.py file containing these lines:</p>
......@@ -539,7 +526,7 @@ script should be pypar.finalize(), to insure MPI is shut down
correctly.</p>
</div>
<div class="section" id="running-python-scripts">
<h3>11.6.3. <strong>Running Python scripts:</strong><a class="headerlink" href="#running-python-scripts" title="Permalink to this headline"></a></h3>
<h3><strong>Running Python scripts:</strong><a class="headerlink" href="#running-python-scripts" title="Permalink to this headline"></a></h3>
<p>Note that any Python script (not just for LAMMPS) can be invoked in
one of several ways:</p>
<div class="highlight-python"><div class="highlight"><pre>% python foo.script
......@@ -566,7 +553,7 @@ Python on a single processor, not in parallel.</p>
</div>
</div>
<div class="section" id="using-lammps-from-python">
<span id="py-7"></span><h2>11.7. Using LAMMPS from Python<a class="headerlink" href="#using-lammps-from-python" title="Permalink to this headline"></a></h2>
<span id="py-7"></span><h2>Using LAMMPS from Python<a class="headerlink" href="#using-lammps-from-python" title="Permalink to this headline"></a></h2>
<p>As described above, the Python interface to LAMMPS consists of a
Python &#8220;lammps&#8221; module, the source code for which is in
python/lammps.py, which creates a &#8220;lammps&#8221; object, with a set of
......@@ -783,7 +770,7 @@ Python script. Isn&#8217;t ctypes amazing?</li>
</ul>
</div>
<div class="section" id="example-python-scripts-that-use-lammps">
<span id="py-8"></span><h2>11.8. Example Python scripts that use LAMMPS<a class="headerlink" href="#example-python-scripts-that-use-lammps" title="Permalink to this headline"></a></h2>
<span id="py-8"></span><h2>Example Python scripts that use LAMMPS<a class="headerlink" href="#example-python-scripts-that-use-lammps" title="Permalink to this headline"></a></h2>
<p>These are the Python scripts included as demos in the python/examples
directory of the LAMMPS distribution, to illustrate the kinds of
things that are possible when Python wraps LAMMPS. If you create your
......@@ -850,7 +837,7 @@ variables that have to match the VMD installation on your system.</p>
source code for individual scripts for comments about what they do.</p>
<p>Here are screenshots of the vizplotgui_tool.py script in action for
different visualization package options. Click to see larger images:</p>
<a data-lightbox="group-f968d92e-84e6-426c-9743-2b912364e267"
<a data-lightbox="group-18a49424-552b-4e40-84e6-3c68f302c35c"
href="_images/screenshot_gl.jpg"
class=""
title=""
......@@ -860,7 +847,7 @@ different visualization package options. Click to see larger images:</p>
width="25%"
height="auto"
alt=""/>
</a><a data-lightbox="group-35a178b2-c4be-409d-9395-728435f7f9a6"
</a><a data-lightbox="group-2b79ab21-07b7-47a3-81c3-94a3021a26e0"
href="_images/screenshot_atomeye.jpg"
class=""
title=""
......@@ -870,7 +857,7 @@ different visualization package options. Click to see larger images:</p>
width="25%"
height="auto"
alt=""/>
</a><a data-lightbox="group-5aa3c8f0-688f-42ab-9152-4b74f5a93c60"
</a><a data-lightbox="group-f4ded497-3be9-4ca3-99ca-0b3b2731bb5b"
href="_images/screenshot_pymol.jpg"
class=""
title=""
......@@ -880,7 +867,7 @@ different visualization package options. Click to see larger images:</p>
width="25%"
height="auto"
alt=""/>
</a><a data-lightbox="group-88f5e60c-df83-4a41-a12f-072e05d8edd0"
</a><a data-lightbox="group-0c7ab672-9c97-4a40-b3ac-1a55870e2905"
href="_images/screenshot_vmd.jpg"
class=""
title=""
......@@ -898,15 +885,6 @@ different visualization package options. Click to see larger images:</p>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_errors.html" class="btn btn-neutral float-right" title="12. Errors" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Section_modify.html" class="btn btn-neutral" title="10. Modifying &amp; extending LAMMPS" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<hr/>
......
doc/Section_start.html
+ 34
− 56
View file @ d205583a
......@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>2. Getting Started &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>Getting Started &mdash; LAMMPS 15 May 2015 version documentation</title>
......@@ -32,9 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="next" title="3. Commands" href="Section_commands.html"/>
<link rel="prev" title="1. Introduction" href="Section_intro.html"/>
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
......@@ -73,39 +71,28 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">2. Getting Started</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#what-s-in-the-lammps-distribution">2.1. What&#8217;s in the LAMMPS distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="#making-lammps">2.2. Making LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="#making-lammps-with-optional-packages">2.3. Making LAMMPS with optional packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="#building-lammps-via-the-make-py-script">2.4. Building LAMMPS via the Make.py script</a></li>
<li class="toctree-l2"><a class="reference internal" href="#building-lammps-as-a-library">2.5. Building LAMMPS as a library</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#static-library">2.5.1. <strong>Static library:</strong></a></li>
<li class="toctree-l3"><a class="reference internal" href="#shared-library">2.5.2. <strong>Shared library:</strong></a></li>
<li class="toctree-l3"><a class="reference internal" href="#additional-requirement-for-using-a-shared-library">2.5.3. <strong>Additional requirement for using a shared library:</strong></a></li>
<li class="toctree-l3"><a class="reference internal" href="#calling-the-lammps-library">2.5.4. <strong>Calling the LAMMPS library:</strong></a></li>
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Getting Started</a><ul>
<li><a class="reference internal" href="#what-s-in-the-lammps-distribution">What&#8217;s in the LAMMPS distribution</a></li>
<li><a class="reference internal" href="#making-lammps">Making LAMMPS</a></li>
<li><a class="reference internal" href="#making-lammps-with-optional-packages">Making LAMMPS with optional packages</a></li>
<li><a class="reference internal" href="#building-lammps-via-the-make-py-script">Building LAMMPS via the Make.py script</a></li>
<li><a class="reference internal" href="#building-lammps-as-a-library">Building LAMMPS as a library</a><ul>
<li><a class="reference internal" href="#static-library"><strong>Static library:</strong></a></li>
<li><a class="reference internal" href="#shared-library"><strong>Shared library:</strong></a></li>
<li><a class="reference internal" href="#additional-requirement-for-using-a-shared-library"><strong>Additional requirement for using a shared library:</strong></a></li>
<li><a class="reference internal" href="#calling-the-lammps-library"><strong>Calling the LAMMPS library:</strong></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#running-lammps">2.6. Running LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="#command-line-options">2.7. Command-line options</a></li>
<li class="toctree-l2"><a class="reference internal" href="#lammps-screen-output">2.8. LAMMPS screen output</a></li>
<li class="toctree-l2"><a class="reference internal" href="#tips-for-users-of-previous-lammps-versions">2.9. Tips for users of previous LAMMPS versions</a></li>
<li><a class="reference internal" href="#running-lammps">Running LAMMPS</a></li>
<li><a class="reference internal" href="#command-line-options">Command-line options</a></li>
<li><a class="reference internal" href="#lammps-screen-output">LAMMPS screen output</a></li>
<li><a class="reference internal" href="#tips-for-users-of-previous-lammps-versions">Tips for users of previous LAMMPS versions</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
......@@ -128,7 +115,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>2. Getting Started</li>
<li>Getting Started</li>
<li class="wy-breadcrumbs-aside">
......@@ -143,7 +130,7 @@
<div itemprop="articleBody">
<div class="section" id="getting-started">
<h1>2. Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline"></a></h1>
<h1>Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline"></a></h1>
<p>This section describes how to build and run LAMMPS, for both new and
experienced users.</p>
<div class="line-block">
......@@ -159,7 +146,7 @@ experienced users.</p>
<div class="line"><br /></div>
</div>
<div class="section" id="what-s-in-the-lammps-distribution">
<span id="start-1"></span><h2>2.1. What&#8217;s in the LAMMPS distribution<a class="headerlink" href="#what-s-in-the-lammps-distribution" title="Permalink to this headline"></a></h2>
<span id="start-1"></span><h2>What&#8217;s in the LAMMPS distribution<a class="headerlink" href="#what-s-in-the-lammps-distribution" title="Permalink to this headline"></a></h2>
<p>When you download a LAMMPS tarball you will need to unzip and untar
the downloaded file with the following commands, after placing the
tarball in an appropriate directory.</p>
......@@ -217,7 +204,7 @@ launch a LAMMPS Windows executable on a Windows box.</p>
<hr class="docutils" />
</div>
<div class="section" id="making-lammps">
<span id="start-2"></span><h2>2.2. Making LAMMPS<a class="headerlink" href="#making-lammps" title="Permalink to this headline"></a></h2>
<span id="start-2"></span><h2>Making LAMMPS<a class="headerlink" href="#making-lammps" title="Permalink to this headline"></a></h2>
<p>This section has the following sub-sections:</p>
<ul class="simple">
<li><a class="reference internal" href="#start-2-1"><span>Read this first</span></a></li>
......@@ -680,7 +667,7 @@ on both a basic build and a customized build with pacakges you select.</p>
<hr class="docutils" />
</div>
<div class="section" id="making-lammps-with-optional-packages">
<span id="start-3"></span><h2>2.3. Making LAMMPS with optional packages<a class="headerlink" href="#making-lammps-with-optional-packages" title="Permalink to this headline"></a></h2>
<span id="start-3"></span><h2>Making LAMMPS with optional packages<a class="headerlink" href="#making-lammps-with-optional-packages" title="Permalink to this headline"></a></h2>
<p>This section has the following sub-sections:</p>
<ul class="simple">
<li><a class="reference internal" href="#start-3-1"><span>Package basics</span></a></li>
......@@ -944,7 +931,7 @@ settings for CCFLAGS.</p>
<hr class="docutils" />
</div>
<div class="section" id="building-lammps-via-the-make-py-script">
<span id="start-4"></span><h2>2.4. Building LAMMPS via the Make.py script<a class="headerlink" href="#building-lammps-via-the-make-py-script" title="Permalink to this headline"></a></h2>
<span id="start-4"></span><h2>Building LAMMPS via the Make.py script<a class="headerlink" href="#building-lammps-via-the-make-py-script" title="Permalink to this headline"></a></h2>
<p>The src directory includes a Make.py script, written in Python, which
can be used to automate various steps of the build process. It is
particularly useful for working with the accelerator packages, as well
......@@ -1075,14 +1062,14 @@ and MPI options to use, via the &#8220;-cc&#8221; and &#8220;-mpi&#8221; switche
<hr class="docutils" />
</div>
<div class="section" id="building-lammps-as-a-library">
<span id="start-5"></span><h2>2.5. Building LAMMPS as a library<a class="headerlink" href="#building-lammps-as-a-library" title="Permalink to this headline"></a></h2>
<span id="start-5"></span><h2>Building LAMMPS as a library<a class="headerlink" href="#building-lammps-as-a-library" title="Permalink to this headline"></a></h2>
<p>LAMMPS can be built as either a static or shared library, which can
then be called from another application or a scripting language. See
<a class="reference internal" href="Section_howto.html#howto-10"><span>this section</span></a> for more info on coupling
LAMMPS to other codes. See <a class="reference internal" href="Section_python.html"><em>this section</em></a> for
more info on wrapping and running LAMMPS from Python.</p>
<div class="section" id="static-library">
<h3>2.5.1. <strong>Static library:</strong><a class="headerlink" href="#static-library" title="Permalink to this headline"></a></h3>
<h3><strong>Static library:</strong><a class="headerlink" href="#static-library" title="Permalink to this headline"></a></h3>
<p>To build LAMMPS as a static library (<a href="#id7"><span class="problematic" id="id8">*</span></a>.a file on Linux), type</p>
<div class="highlight-python"><div class="highlight"><pre>make foo mode=lib
</pre></div>
......@@ -1096,7 +1083,7 @@ link to. It will also create a soft link liblammps.a, which will
point to the most recently built static library.</p>
</div>
<div class="section" id="shared-library">
<h3>2.5.2. <strong>Shared library:</strong><a class="headerlink" href="#shared-library" title="Permalink to this headline"></a></h3>
<h3><strong>Shared library:</strong><a class="headerlink" href="#shared-library" title="Permalink to this headline"></a></h3>
<p>To build LAMMPS as a shared library (<a href="#id9"><span class="problematic" id="id10">*</span></a>.so file on Linux), which can be
dynamically loaded, e.g. from Python, type</p>
<div class="highlight-python"><div class="highlight"><pre>make foo mode=shlib
......@@ -1149,7 +1136,7 @@ you do not have write privileges for /usr/local/lib. The end result
should be the file /usr/local/lib/libmpich.so.</p>
</div>
<div class="section" id="additional-requirement-for-using-a-shared-library">
<h3>2.5.3. <strong>Additional requirement for using a shared library:</strong><a class="headerlink" href="#additional-requirement-for-using-a-shared-library" title="Permalink to this headline"></a></h3>
<h3><strong>Additional requirement for using a shared library:</strong><a class="headerlink" href="#additional-requirement-for-using-a-shared-library" title="Permalink to this headline"></a></h3>
<p>The operating system finds shared libraries to load at run-time using
the environment variable LD_LIBRARY_PATH. So you may wish to copy the
file src/liblammps.so or src/liblammps_g++.so (for example) to a place
......@@ -1164,7 +1151,7 @@ that use it.</p>
</div>
</div>
<div class="section" id="calling-the-lammps-library">
<h3>2.5.4. <strong>Calling the LAMMPS library:</strong><a class="headerlink" href="#calling-the-lammps-library" title="Permalink to this headline"></a></h3>
<h3><strong>Calling the LAMMPS library:</strong><a class="headerlink" href="#calling-the-lammps-library" title="Permalink to this headline"></a></h3>
<p>Either flavor of library (static or shared0 allows one or more LAMMPS
objects to be instantiated from the calling program.</p>
<p>When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS
......@@ -1187,7 +1174,7 @@ interface and how to extend it for your needs.</p>
</div>
</div>
<div class="section" id="running-lammps">
<span id="start-6"></span><h2>2.6. Running LAMMPS<a class="headerlink" href="#running-lammps" title="Permalink to this headline"></a></h2>
<span id="start-6"></span><h2>Running LAMMPS<a class="headerlink" href="#running-lammps" title="Permalink to this headline"></a></h2>
<p>By default, LAMMPS runs by reading commands from standard input. Thus
if you run the LAMMPS executable by itself, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">lmp_linux</span>
......@@ -1289,7 +1276,7 @@ more processors or setup a smaller problem.</p>
<hr class="docutils" />
</div>
<div class="section" id="command-line-options">
<span id="start-7"></span><h2>2.7. Command-line options<a class="headerlink" href="#command-line-options" title="Permalink to this headline"></a></h2>
<span id="start-7"></span><h2>Command-line options<a class="headerlink" href="#command-line-options" title="Permalink to this headline"></a></h2>
<p>At run time, LAMMPS recognizes several optional command-line switches
which may be used in any order. Either the full word or a one-or-two
letter abbreviation can be used:</p>
......@@ -1701,7 +1688,7 @@ negative numeric value. It is OK if the first value1 starts with a
<hr class="docutils" />
</div>
<div class="section" id="lammps-screen-output">
<span id="start-8"></span><h2>2.8. LAMMPS screen output<a class="headerlink" href="#lammps-screen-output" title="Permalink to this headline"></a></h2>
<span id="start-8"></span><h2>LAMMPS screen output<a class="headerlink" href="#lammps-screen-output" title="Permalink to this headline"></a></h2>
<p>As LAMMPS reads an input script, it prints information to both the
screen and a log file about significant actions it takes to setup a
simulation. When the simulation is ready to begin, LAMMPS performs
......@@ -1797,7 +1784,7 @@ communication, roughly 75% in the example above.</p>
<hr class="docutils" />
</div>
<div class="section" id="tips-for-users-of-previous-lammps-versions">
<span id="start-9"></span><h2>2.9. Tips for users of previous LAMMPS versions<a class="headerlink" href="#tips-for-users-of-previous-lammps-versions" title="Permalink to this headline"></a></h2>
<span id="start-9"></span><h2>Tips for users of previous LAMMPS versions<a class="headerlink" href="#tips-for-users-of-previous-lammps-versions" title="Permalink to this headline"></a></h2>
<p>The current C++ began with a complete rewrite of LAMMPS 2001, which
was written in F90. Features of earlier versions of LAMMPS are listed
in <a class="reference internal" href="Section_history.html"><em>Section_history</em></a>. The F90 and F77 versions
......@@ -1834,15 +1821,6 @@ close if you have setup the problem for both codes the same.</p>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_commands.html" class="btn btn-neutral float-right" title="3. Commands" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Section_intro.html" class="btn btn-neutral" title="1. Introduction" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<hr/>
......
doc/Section_tools.html
+ 70
− 92
View file @ d205583a
This diff is collapsed.
doc/_sources/Manual.txt
+ 3
− 3
View file @ d205583a
......@@ -71,7 +71,7 @@ it gives quick access to documentation for all LAMMPS commands.
.. toctree::
:maxdepth: 2
:numbered:
:numbered: // comment
Section_intro
Section_start
......@@ -91,8 +91,8 @@ it gives quick access to documentation for all LAMMPS commands.
Indices and tables
==================
* :ref:`genindex`
* :ref:`search`
* :ref:`genindex` // comment
* :ref:`search` // comment
.. raw:: html
......
doc/_sources/fix.txt
+ 1
− 1
View file @ d205583a
......@@ -177,7 +177,7 @@ in the fix section of :ref:`this page <cmd_5>`.
* :doc:`append/atoms <fix_append_atoms>` - append atoms to a running simulation
* :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
* :doc:`ave/atom <fix_ave_atom>` - compute per-atom time-averaged quantities
* :doc:`ave/correlate <fix_correlate_atom>` - compute/output time correlations
* :doc:`ave/correlate <fix_ave_correlate>` - compute/output time correlations
* :doc:`ave/histo <fix_ave_histo>` - compute/output time-averaged histograms
* :doc:`ave/spatial <fix_ave_spatial>` - compute/output time-averaged per-atom quantities by layer
* :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
......
doc/_sources/pair_hybrid.txt
+ 6
− 7
View file @ d205583a
......@@ -214,14 +214,13 @@ potentials.
Different force fields (e.g. CHARMM vs AMBER) may have different rules
for applying these factors to modulate the strength of pairwise
for applying weightings that change the strength of pairwise
interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4
neighbors in the molecular bond topology. Specific
:doc:`special_bonds <special_bonds>` settings can be assigned to
different pair hybrid sub-styles via the :doc:`pair_modify special <pair_modify>` special command, using its *pair* keyword
and optional *special* argument. This allows multiple force fields to
be used to a model a hybrid system. See the
:doc:`special_bonds <special_bonds>` doc page for details.
neighbors in the molecular bond topology, as normally set by the
:doc:`special_bonds <special_bonds>` command. Different weights can be
assigned to different pair hybrid sub-styles via the :doc:`pair_modify special <pair_modify>` command. This allows multiple force fields
to be used in a model of a hybrid system. See the
:doc:`pair_modify <pair_modify>` doc page for details.
The potential energy contribution to the overall system due to an
individual sub-style can be accessed and output via the :doc:`compute pair <compute_pair>` command.
......
doc/_sources/pair_modify.txt
+ 40
− 53
View file @ d205583a
......@@ -11,14 +11,14 @@ Syntax
pair_modify keyword values ...
* one or more keyword/value pairs may be listed
* keyword = *pair* or *shift* or *mix* or *table* or *table/disp* or *tabinner* or *tabinner/disp* or *tail* or *compute*
* keyword = *pair* or *special* or *shift* or *mix* or *table* or *table/disp* or *tabinner* or *tabinner/disp* or *tail* or *compute*
.. parsed-literal::
*pair* values = sub-style N special which w1 wt2 wt3
sub-style = sub-style of :doc:`pair hybrid <pair_hybrid>`
N = which instance of sub-style (only if sub-style is used multiple times)
special = optional if want to override :doc:`special_bonds <special_bonds>` settings for sub-style
which = *lj/coul* or *lj* or *coul*
*special* values = flavor w1 w2 w3
flavor = *lj/coul* or *lj* or *coul*
w1,w2,w3 = weights from 0.0 to 1.0 inclusive
*mix* value = *geometric* or *arithmetic* or *sixthpower*
*shift* value = *yes* or *no*
......@@ -50,15 +50,24 @@ Description
Modify the parameters of the currently defined pair style. Not all
parameters are relevant to all pair styles.
If used, the *pair* keyword and its optional *special* arguments must
appear first in the list of keywords. It can only be used with the
:doc:`hybrid and hybrid/overlay <pair_hybrid>` pair styles and when used
it means that all the following parameters will only be modified for
the specified sub-style. If the *pair* keyword is not used, and the
pair style is *hybrid* or *hybrid/overlay*, all the following
parameters keywords will be applied to all sub-styles. A more detailed
explanation of the *pair* keyword syntax, including its optional
*special* argument are given below.
If used, the *pair* keyword must appear first in the list of keywords.
It can only be used with the :doc:`hybrid and hybrid/overlay <pair_hybrid>` pair styles. It means that all the
following parameters will only be modified for the specified
sub-style. If the sub-style is defined multiple times, then an
additional numeric argument *N* must also be specified, which is a
number from 1 to M where M is the number of times the sub-style was
listed in the :doc:`pair_style hybrid <pair_hybrid>` command. The extra
number indicates which instance of the sub-style the remaining
keywords will be applied to. Note that if the *pair* keyword is not
used, and the pair style is *hybrid* or *hybrid/overlay*, then all the
specified keywords will be applied to all sub-styles.
If used, the *special* keyword must appear second in the list of
keywords, and must follow the *pair* keyword. Like the *pair*
keyword, it also can only be used with the :doc:`hybrid and hybrid/overlay <pair_hybrid>` pair styles. Its parameters are
similar to the :doc:`special_bonds <special_bonds>` command, and it
overrides the special_bond settings for the specified sub-style. More
details are given below.
The *mix* keyword affects pair coefficients for interactions between
atoms of type I and J, when I != J and the coefficients are not
......@@ -208,50 +217,28 @@ pair style be defined.
----------
Use of the pair keyword
-----------------------
If used, the *pair* keyword and its optional *special* arguments must
appear first in the list of keywords. It can only be used with the
:doc:`hybrid and hybrid/overlay <pair_hybrid>` pair styles and when used
it means that all the following parameters will only be modified for
the specified sub-style. If the *pair* keyword is not used, and the
pair style is *hybrid* or *hybrid/overlay*, all the following
parameters keywords will be applied to all sub-styles. A more detailed
explanation of the *pair* keyword syntax, including its optional
*special* argument are given below.
As mentioned above, the *pair* keyword can only be used with the
:doc:`hybrid and hybrid/overlay <pair_hybrid>` pair styles, and must
come first in the list of keywords. If used, the subsequent keywords
will only be applied to the specified sub-style. If the sub-style is
defined multiple times, then an additional numeric argument *N* must
also be specified, which is a number from 1 to M where M is the number
of times the sub-style was listed in the :doc:`pair_style hybrid <pair_hybrid>` command. The extra number indicates which
instance of the sub-style the pair_modify keywords will be applied to.
If the optional *special* argument is used, then the settings of the
:doc:`special_bonds <special_bonds>` command are overridden for the
specified sub-style. The *special* argument requires 4 additional
arguments: *which* and w1,w2,w3. These are analogous to arguments in
the :doc:`special_bonds <special_bonds>` command. The *which* argument
can be *lj* to change the Lennard-Jones settings, *coul* to change the
Coulombic settings, or *lj/coul* to change both to the same values.
The w1,w2,w3 arguments are numeric weights from 0.0 to 1.0 inclusive,
for the 1-2, 1-3, and 1-4 bond topology neighbors. For example, these
commands
Use of *special* keyword
^^^^^^^^^^^^^^^^^^^^^^^^
The *special* keyword requires 4 values similar to those specified
with the :doc:`special_bonds <special_bonds>` command, *flavor* and
w1,w2,w3. The *flavor* argument can be *lj* to change the
Lennard-Jones settings, *coul* to change the Coulombic settings, or
*lj/coul* to change both to the same set of 3 values. The w1,w2,w3
values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
1-3, and 1-4 bond topology neighbors. For example, these commands
.. parsed-literal::
special_bonds lj/coul 0.0 0.0 0.1
pair_hybrid lj/charmm/coul/charmm 8.0 10.0 lj/cut/coul/cut 10.0
pair_modify pair lj/charmm/coul/charmm special lj/coul 0.0 0.0 0.0
pair_modify pair lj/cut/coul/cut special lj 0.0 0.0 0.5
pair_modify pair lj/cut/coul/cut special coul 0.0 0.0 0.8333
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.8333
show how to use both the CHARMM and AMBER force fields in a single
simulation. The first pair modify command sets the special bonds to
CHARMM values (all 0.0). The latter 2 pair modify commands set the
CHARMM values (all 0.0). The last 2 pair modify commands set the
standard AMBER values for LJ and Coulombic weights.
.. warning::
......@@ -260,13 +247,13 @@ standard AMBER values for LJ and Coulombic weights.
:doc:`special_bonds <special_bonds>` command affect the construction of
neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
exclude those pairs from the neighbor list entirely. Weights of 1.0
store the neighbor with no weight flag applied. Neither of these
neighbor effects can be changed by setting a sub-style weight to a
store the neighbor with no weighting applied. The format of the
neighbor list cannot be changed by setting a sub-style weight to a
non-zero or non-one value. Thus an error is generated if the new
sub-style value is not 0.0 (or 1.0) and the global setting is 0.0 (or
sub-style value is not 0.0 (or 1.0) when the global setting is 0.0 (or
1.0). Note that as in the example above, the global factor can simply
be set a value other than 0.0 or 1.0, then overridden by any of the
sub-styles to a value that is 0.0 or 1.0.
sub-styles with a value that is 0.0 or 1.0.
----------
......
doc/accelerate_cuda.html
+ 7
− 15
View file @ d205583a
......@@ -71,22 +71,14 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<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"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">5.USER-CUDA package</a><ul>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
</ul>
</li>
</ul>
</div>
</div>
......
doc/accelerate_gpu.html
+ 7
− 15
View file @ d205583a
......@@ -71,22 +71,14 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<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"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">5.GPU package</a><ul>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
</ul>
</li>
</ul>
</div>
</div>
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment