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<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
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<link rel="next" title="1. Introduction" href="Section_intro.html"/>
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<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
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<script src="_static/js/modernizr.min.js"></script>
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@ -72,22 +71,16 @@
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<!-- Local TOC -->
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<div class="local-toc"><ul>
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<li><a class="reference internal" href="#">LAMMPS Documentation</a><ul>
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<li><a class="reference internal" href="#jul-2015-version">27 Jul 2015 version</a></li>
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<li><a class="reference internal" href="#version-info">Version info:</a></li>
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</ul>
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</li>
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<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
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</ul>
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</div>
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</div>
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@ -172,192 +165,13 @@ we can improve the LAMMPS documentation.</p>
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it gives quick access to documentation for all LAMMPS commands.</p>
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<p><a class="reference external" href="Manual.pdf">PDF file</a> of the entire manual, generated by
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<a class="reference external" href="http://freecode.com/projects/htmldoc">htmldoc</a></p>
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<div class="toctree-wrapper compound">
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-features">1.2. LAMMPS features</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-non-features">1.3. LAMMPS non-features</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#open-source-distribution">1.4. Open source distribution</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="Section_start.html#what-s-in-the-lammps-distribution">2.1. What’s in the LAMMPS distribution</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps">2.2. Making LAMMPS</a></li>
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<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>
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<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>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="Section_start.html#running-lammps">2.6. Running LAMMPS</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_start.html#command-line-options">2.7. Command-line options</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_start.html#lammps-screen-output">2.8. LAMMPS screen output</a></li>
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<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>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#lammps-input-script">3.1. LAMMPS input script</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#parsing-rules">3.2. Parsing rules</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#input-script-structure">3.3. Input script structure</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#commands-listed-by-category">3.4. Commands listed by category</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#individual-commands">3.5. Individual commands</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#fix-styles">3.6. Fix styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#compute-styles">3.7. Compute styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#pair-style-potentials">3.8. Pair_style potentials</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#bond-style-potentials">3.9. Bond_style potentials</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#angle-style-potentials">3.10. Angle_style potentials</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#improper-style-potentials">3.12. Improper_style potentials</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#kspace-solvers">3.13. Kspace solvers</a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#standard-packages">4.1. Standard packages</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.2. User packages</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-atc-package">4.3. USER-ATC package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-awpmd-package">4.4. USER-AWPMD package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cg-cmm-package">4.5. USER-CG-CMM package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.6. USER-COLVARS package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.7. USER-CUDA package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.8. USER-DIFFRACTION package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.9. USER-DRUDE package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.10. USER-EFF package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.11. USER-FEP package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.12. USER-INTEL package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.13. USER-LB package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.14. USER-MISC package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.15. USER-MOLFILE package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.16. USER-OMP package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.17. USER-PHONON package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.18. USER-QMMM package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.19. USER-QTB package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.20. USER-REAXC package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.21. USER-SPH package</a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#measuring-performance">5.1. Measuring performance</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#general-strategies">5.2. General strategies</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
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<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>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#restarting-a-simulation">6.1. Restarting a simulation</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#d-simulations">6.2. 2d simulations</a></li>
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<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>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#granular-models">6.6. Granular models</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip3p-water-model">6.7. TIP3P water model</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip4p-water-model">6.8. TIP4P water model</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#spc-water-model">6.9. SPC water model</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#nemd-simulations">6.13. NEMD simulations</a></li>
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<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>
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<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>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#walls">6.17. Walls</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#elastic-constants">6.18. Elastic constants</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-viscosity">6.21. Calculating viscosity</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
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<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>
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<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>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#polarizable-models">6.25. Polarizable models</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#binary2txt-tool">9.2. binary2txt tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ch2lmp-tool">9.3. ch2lmp tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#chain-tool">9.4. chain tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#colvars-tools">9.5. colvars tools</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#createatoms-tool">9.6. createatoms tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#data2xmovie-tool">9.7. data2xmovie tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-database-tool">9.8. eam database tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-generate-tool">9.9. eam generate tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eff-tool">9.10. eff tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#fep-tool">9.12. fep tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#i-pi-tool">9.13. i-pi tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ipp-tool">9.14. ipp tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#kate-tool">9.15. kate tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2arc-tool">9.16. lmp2arc tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#matlab-tool">9.19. matlab tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#micelle2d-tool">9.20. micelle2d tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#moltemplate-tool">9.21. moltemplate tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#msi2lmp-tool">9.22. msi2lmp tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#phonon-tool">9.23. phonon tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#python-tool">9.26. python tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#reax-tool">9.27. reax tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#restart2data-tool">9.28. restart2data tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#vim-tool">9.29. vim tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmgrace-tool">9.30. xmgrace tool</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmovie-tool">9.31. xmovie tool</a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & 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 & 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/>
|
||||
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@
|
|||
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>5. Accelerating LAMMPS performance — LAMMPS 15 May 2015 version documentation</title>
|
||||
<title>Accelerating LAMMPS performance — LAMMPS 15 May 2015 version documentation</title>
|
||||
|
||||
|
||||
|
||||
|
|
@ -32,9 +32,7 @@
|
|||
|
||||
|
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|
||||
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
|
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<link rel="next" title="6. How-to discussions" href="Section_howto.html"/>
|
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<link rel="prev" title="4. Packages" href="Section_packages.html"/>
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<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
|
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|
||||
|
||||
<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 & 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 & 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> »</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/>
|
||||
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@
|
|||
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>3. Commands — LAMMPS 15 May 2015 version documentation</title>
|
||||
<title>Commands — 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 & 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 & 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> »</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 “examples” 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’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’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/>
|
||||
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@
|
|||
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>12. Errors — LAMMPS 15 May 2015 version documentation</title>
|
||||
<title>Errors — 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 & 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 & 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 & 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 & 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> »</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 & warning messages<a class="headerlink" href="#error-warning-messages" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="err-3"></span><h2>Error & 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’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
|
||||
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|
@ -6299,15 +6286,6 @@ infinity.</dd>
|
|||
</div>
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<footer>
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||||
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||||
<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>
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||||
|
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</div>
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<title>7. Example problems — LAMMPS 15 May 2015 version documentation</title>
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<title>Example problems — LAMMPS 15 May 2015 version documentation</title>
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<link rel="prev" title="6. How-to discussions" href="Section_howto.html"/>
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<ul class="current">
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<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>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
|
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<li class="toctree-l1 current"><a class="current reference internal" href="">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
|
||||
<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 -->
|
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<div class="local-toc"><ul>
|
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<li><a class="reference internal" href="#">Example problems</a></li>
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</ul>
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</div>
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</div>
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<ul class="wy-breadcrumbs">
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<li><a href="Manual.html">Docs</a> »</li>
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<li>7. Example problems</li>
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<li>Example problems</li>
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<li class="wy-breadcrumbs-aside">
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<div itemprop="articleBody">
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<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">
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<a href="Section_perf.html" class="btn btn-neutral float-right" title="8. Performance & scalability" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
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|
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</div>
|
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<hr/>
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>13. Future and history — LAMMPS 15 May 2015 version documentation</title>
|
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<title>Future and history — LAMMPS 15 May 2015 version documentation</title>
|
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|
|||
|
||||
|
||||
|
||||
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
|
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<link rel="prev" title="12. Errors" href="Section_errors.html"/>
|
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<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
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|
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<script src="_static/js/modernizr.min.js"></script>
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<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 & 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 & 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>
|
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|
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|
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|
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|
|||
<ul class="wy-breadcrumbs">
|
||||
<li><a href="Manual.html">Docs</a> »</li>
|
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|
||||
<li>13. Future and history</li>
|
||||
<li>Future and history</li>
|
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<li class="wy-breadcrumbs-aside">
|
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|
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<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
|
||||
& 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">
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|
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|
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<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/>
|
||||
|
||||
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@ -8,7 +8,7 @@
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|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>6. How-to discussions — LAMMPS 15 May 2015 version documentation</title>
|
||||
<title>How-to discussions — LAMMPS 15 May 2015 version documentation</title>
|
||||
|
||||
|
||||
|
||||
|
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@ -32,9 +32,7 @@
|
|||
|
||||
|
||||
|
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<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
|
||||
<link rel="next" title="7. Example problems" href="Section_example.html"/>
|
||||
<link rel="prev" title="5. Accelerating LAMMPS performance" href="Section_accelerate.html"/>
|
||||
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
|
||||
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|
||||
<script src="_static/js/modernizr.min.js"></script>
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@ -73,77 +71,66 @@
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|
||||
|
||||
|
||||
<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 current"><a class="current reference internal" href="">6. How-to discussions</a><ul>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#restarting-a-simulation">6.1. Restarting a simulation</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#d-simulations">6.2. 2d simulations</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#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="#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="#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#granular-models">6.6. Granular models</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#tip3p-water-model">6.7. TIP3P water model</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#tip4p-water-model">6.8. TIP4P water model</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#spc-water-model">6.9. SPC water model</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#nemd-simulations">6.13. NEMD simulations</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#finite-size-spherical-and-aspherical-particles">6.14. Finite-size spherical and aspherical particles</a><ul>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#atom-styles">6.14.1. Atom styles</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#pair-potentials">6.14.2. Pair potentials</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#time-integration">6.14.3. Time integration</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#computes-thermodynamics-and-dump-output">6.14.4. Computes, thermodynamics, and dump output</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#rigid-bodies-composed-of-finite-size-particles">6.14.5. Rigid bodies composed of finite-size particles</a></li>
|
||||
<!-- Local TOC -->
|
||||
<div class="local-toc"><ul>
|
||||
<li><a class="reference internal" href="#">How-to discussions</a><ul>
|
||||
<li><a class="reference internal" href="#restarting-a-simulation">Restarting a simulation</a></li>
|
||||
<li><a class="reference internal" href="#d-simulations">2d simulations</a></li>
|
||||
<li><a class="reference internal" href="#charmm-amber-and-dreiding-force-fields">CHARMM, AMBER, and DREIDING force fields</a></li>
|
||||
<li><a class="reference internal" href="#running-multiple-simulations-from-one-input-script">Running multiple simulations from one input script</a></li>
|
||||
<li><a class="reference internal" href="#multi-replica-simulations">Multi-replica simulations</a></li>
|
||||
<li><a class="reference internal" href="#granular-models">Granular models</a></li>
|
||||
<li><a class="reference internal" href="#tip3p-water-model">TIP3P water model</a></li>
|
||||
<li><a class="reference internal" href="#tip4p-water-model">TIP4P water model</a></li>
|
||||
<li><a class="reference internal" href="#spc-water-model">SPC water model</a></li>
|
||||
<li><a class="reference internal" href="#coupling-lammps-to-other-codes">Coupling LAMMPS to other codes</a></li>
|
||||
<li><a class="reference internal" href="#visualizing-lammps-snapshots">Visualizing LAMMPS snapshots</a></li>
|
||||
<li><a class="reference internal" href="#triclinic-non-orthogonal-simulation-boxes">Triclinic (non-orthogonal) simulation boxes</a></li>
|
||||
<li><a class="reference internal" href="#nemd-simulations">NEMD simulations</a></li>
|
||||
<li><a class="reference internal" href="#finite-size-spherical-and-aspherical-particles">Finite-size spherical and aspherical particles</a><ul>
|
||||
<li><a class="reference internal" href="#atom-styles">Atom styles</a></li>
|
||||
<li><a class="reference internal" href="#pair-potentials">Pair potentials</a></li>
|
||||
<li><a class="reference internal" href="#time-integration">Time integration</a></li>
|
||||
<li><a class="reference internal" href="#computes-thermodynamics-and-dump-output">Computes, thermodynamics, and dump output</a></li>
|
||||
<li><a class="reference internal" href="#rigid-bodies-composed-of-finite-size-particles">Rigid bodies composed of finite-size particles</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#output-from-lammps-thermo-dumps-computes-fixes-variables">6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a><ul>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#global-per-atom-local-data">6.15.1. Global/per-atom/local data</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#scalar-vector-array-data">6.15.2. Scalar/vector/array data</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#thermodynamic-output">6.15.3. Thermodynamic output</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#dump-file-output">6.15.4. Dump file output</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#fixes-that-write-output-files">6.15.5. Fixes that write output files</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#computes-that-process-output-quantities">6.15.6. Computes that process output quantities</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#fixes-that-process-output-quantities">6.15.7. Fixes that process output quantities</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#computes-that-generate-values-to-output">6.15.8. Computes that generate values to output</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#fixes-that-generate-values-to-output">6.15.9. Fixes that generate values to output</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#variables-that-generate-values-to-output">6.15.10. Variables that generate values to output</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#summary-table-of-output-options-and-data-flow-between-commands">6.15.11. Summary table of output options and data flow between commands</a></li>
|
||||
<li><a class="reference internal" href="#output-from-lammps-thermo-dumps-computes-fixes-variables">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a><ul>
|
||||
<li><a class="reference internal" href="#global-per-atom-local-data">Global/per-atom/local data</a></li>
|
||||
<li><a class="reference internal" href="#scalar-vector-array-data">Scalar/vector/array data</a></li>
|
||||
<li><a class="reference internal" href="#thermodynamic-output">Thermodynamic output</a></li>
|
||||
<li><a class="reference internal" href="#dump-file-output">Dump file output</a></li>
|
||||
<li><a class="reference internal" href="#fixes-that-write-output-files">Fixes that write output files</a></li>
|
||||
<li><a class="reference internal" href="#computes-that-process-output-quantities">Computes that process output quantities</a></li>
|
||||
<li><a class="reference internal" href="#fixes-that-process-output-quantities">Fixes that process output quantities</a></li>
|
||||
<li><a class="reference internal" href="#computes-that-generate-values-to-output">Computes that generate values to output</a></li>
|
||||
<li><a class="reference internal" href="#fixes-that-generate-values-to-output">Fixes that generate values to output</a></li>
|
||||
<li><a class="reference internal" href="#variables-that-generate-values-to-output">Variables that generate values to output</a></li>
|
||||
<li><a class="reference internal" href="#summary-table-of-output-options-and-data-flow-between-commands">Summary table of output options and data flow between commands</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#walls">6.17. Walls</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#elastic-constants">6.18. Elastic constants</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#calculating-viscosity">6.21. Calculating viscosity</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#using-chunks-to-calculate-system-properties">6.23. Using chunks to calculate system properties</a><ul>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#compute-chunk-atom-command">6.23.1. Compute chunk/atom command:</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#fix-ave-chunk-command">6.23.2. Fix ave/chunk command:</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#compute-chunk-commands">6.23.3. Compute */chunk commands:</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#example-calculations-with-chunks">6.23.4. Example calculations with chunks</a></li>
|
||||
<li><a class="reference internal" href="#thermostatting-barostatting-and-computing-temperature">Thermostatting, barostatting, and computing temperature</a></li>
|
||||
<li><a class="reference internal" href="#walls">Walls</a></li>
|
||||
<li><a class="reference internal" href="#elastic-constants">Elastic constants</a></li>
|
||||
<li><a class="reference internal" href="#library-interface-to-lammps">Library interface to LAMMPS</a></li>
|
||||
<li><a class="reference internal" href="#calculating-thermal-conductivity">Calculating thermal conductivity</a></li>
|
||||
<li><a class="reference internal" href="#calculating-viscosity">Calculating viscosity</a></li>
|
||||
<li><a class="reference internal" href="#calculating-a-diffusion-coefficient">Calculating a diffusion coefficient</a></li>
|
||||
<li><a class="reference internal" href="#using-chunks-to-calculate-system-properties">Using chunks to calculate system properties</a><ul>
|
||||
<li><a class="reference internal" href="#compute-chunk-atom-command">Compute chunk/atom command:</a></li>
|
||||
<li><a class="reference internal" href="#fix-ave-chunk-command">Fix ave/chunk command:</a></li>
|
||||
<li><a class="reference internal" href="#compute-chunk-commands">Compute */chunk commands:</a></li>
|
||||
<li><a class="reference internal" href="#example-calculations-with-chunks">Example calculations with chunks</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#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="#polarizable-models">6.25. Polarizable models</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
|
||||
<li><a class="reference internal" href="#setting-parameters-for-the-kspace-style-pppm-disp-command">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><a class="reference internal" href="#polarizable-models">Polarizable models</a></li>
|
||||
<li><a class="reference internal" href="#adiabatic-core-shell-model">Adiabatic core/shell model</a></li>
|
||||
<li><a class="reference internal" href="#drude-induced-dipoles">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 & 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 & 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>
|
||||
|
|
@ -166,7 +153,7 @@
|
|||
<ul class="wy-breadcrumbs">
|
||||
<li><a href="Manual.html">Docs</a> »</li>
|
||||
|
||||
<li>6. How-to discussions</li>
|
||||
<li>How-to discussions</li>
|
||||
<li class="wy-breadcrumbs-aside">
|
||||
|
||||
|
||||
|
|
@ -181,7 +168,7 @@
|
|||
<div itemprop="articleBody">
|
||||
|
||||
<div class="section" id="how-to-discussions">
|
||||
<h1>6. How-to discussions<a class="headerlink" href="#how-to-discussions" title="Permalink to this headline">¶</a></h1>
|
||||
<h1>How-to discussions<a class="headerlink" href="#how-to-discussions" title="Permalink to this headline">¶</a></h1>
|
||||
<p>This section describes how to perform common tasks using LAMMPS.</p>
|
||||
<div class="line-block">
|
||||
<div class="line">6.1 <a class="reference internal" href="#howto-1"><span>Restarting a simulation</span></a></div>
|
||||
|
|
@ -217,7 +204,7 @@
|
|||
highlighted in <a class="reference internal" href="Section_example.html"><em>Section_example</em></a> also show how to
|
||||
setup and run various kinds of simulations.</p>
|
||||
<div class="section" id="restarting-a-simulation">
|
||||
<span id="howto-1"></span><h2>6.1. Restarting a simulation<a class="headerlink" href="#restarting-a-simulation" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-1"></span><h2>Restarting a simulation<a class="headerlink" href="#restarting-a-simulation" title="Permalink to this headline">¶</a></h2>
|
||||
<p>There are 3 ways to continue a long LAMMPS simulation. Multiple
|
||||
<a class="reference internal" href="run.html"><em>run</em></a> commands can be used in the same input script. Each
|
||||
run will continue from where the previous run left off. Or binary
|
||||
|
|
@ -310,7 +297,7 @@ but not in data files.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="d-simulations">
|
||||
<span id="howto-2"></span><h2>6.2. 2d simulations<a class="headerlink" href="#d-simulations" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-2"></span><h2>2d simulations<a class="headerlink" href="#d-simulations" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Use the <a class="reference internal" href="dimension.html"><em>dimension</em></a> command to specify a 2d simulation.</p>
|
||||
<p>Make the simulation box periodic in z via the <a class="reference internal" href="boundary.html"><em>boundary</em></a>
|
||||
command. This is the default.</p>
|
||||
|
|
@ -342,7 +329,7 @@ the same as in 3d.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="charmm-amber-and-dreiding-force-fields">
|
||||
<span id="howto-3"></span><h2>6.3. CHARMM, AMBER, and DREIDING force fields<a class="headerlink" href="#charmm-amber-and-dreiding-force-fields" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-3"></span><h2>CHARMM, AMBER, and DREIDING force fields<a class="headerlink" href="#charmm-amber-and-dreiding-force-fields" title="Permalink to this headline">¶</a></h2>
|
||||
<p>A force field has 2 parts: the formulas that define it and the
|
||||
coefficients used for a particular system. Here we only discuss
|
||||
formulas implemented in LAMMPS that correspond to formulas commonly
|
||||
|
|
@ -404,7 +391,7 @@ documentation for the formula it computes.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="running-multiple-simulations-from-one-input-script">
|
||||
<span id="howto-4"></span><h2>6.4. Running multiple simulations from one input script<a class="headerlink" href="#running-multiple-simulations-from-one-input-script" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-4"></span><h2>Running multiple simulations from one input script<a class="headerlink" href="#running-multiple-simulations-from-one-input-script" title="Permalink to this headline">¶</a></h2>
|
||||
<p>This can be done in several ways. See the documentation for
|
||||
individual commands for more details on how these examples work.</p>
|
||||
<p>If “multiple simulations” means continue a previous simulation for
|
||||
|
|
@ -487,7 +474,7 @@ the 4th simulation, and so forth, until all 8 were completed.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="multi-replica-simulations">
|
||||
<span id="howto-5"></span><h2>6.5. Multi-replica simulations<a class="headerlink" href="#multi-replica-simulations" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-5"></span><h2>Multi-replica simulations<a class="headerlink" href="#multi-replica-simulations" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Several commands in LAMMPS run mutli-replica simulations, meaning
|
||||
that multiple instances (replicas) of your simulation are run
|
||||
simultaneously, with small amounts of data exchanged between replicas
|
||||
|
|
@ -534,7 +521,7 @@ physical processors.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="granular-models">
|
||||
<span id="howto-6"></span><h2>6.6. Granular models<a class="headerlink" href="#granular-models" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-6"></span><h2>Granular models<a class="headerlink" href="#granular-models" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Granular system are composed of spherical particles with a diameter,
|
||||
as opposed to point particles. This means they have an angular
|
||||
velocity and torque can be imparted to them to cause them to rotate.</p>
|
||||
|
|
@ -575,7 +562,7 @@ computations between frozen atoms by using this command:</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="tip3p-water-model">
|
||||
<span id="howto-7"></span><h2>6.7. TIP3P water model<a class="headerlink" href="#tip3p-water-model" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-7"></span><h2>TIP3P water model<a class="headerlink" href="#tip3p-water-model" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The TIP3P water model as implemented in CHARMM
|
||||
<a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> specifies a 3-site rigid water molecule with
|
||||
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
|
||||
|
|
@ -627,7 +614,7 @@ details:</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="tip4p-water-model">
|
||||
<span id="howto-8"></span><h2>6.8. TIP4P water model<a class="headerlink" href="#tip4p-water-model" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-8"></span><h2>TIP4P water model<a class="headerlink" href="#tip4p-water-model" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The four-point TIP4P rigid water model extends the traditional
|
||||
three-point TIP3P model by adding an additional site, usually
|
||||
massless, where the charge associated with the oxygen atom is placed.
|
||||
|
|
@ -723,7 +710,7 @@ and Coulombic cutoffs are set in the <a class="reference internal" href="pair_lj
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="spc-water-model">
|
||||
<span id="howto-9"></span><h2>6.9. SPC water model<a class="headerlink" href="#spc-water-model" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-9"></span><h2>SPC water model<a class="headerlink" href="#spc-water-model" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The SPC water model specifies a 3-site rigid water molecule with
|
||||
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
|
||||
In LAMMPS the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command can be used to hold
|
||||
|
|
@ -762,7 +749,7 @@ the SPC and SPC/E models.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="coupling-lammps-to-other-codes">
|
||||
<span id="howto-10"></span><h2>6.10. Coupling LAMMPS to other codes<a class="headerlink" href="#coupling-lammps-to-other-codes" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-10"></span><h2>Coupling LAMMPS to other codes<a class="headerlink" href="#coupling-lammps-to-other-codes" title="Permalink to this headline">¶</a></h2>
|
||||
<p>LAMMPS is designed to allow it to be coupled to other codes. For
|
||||
example, a quantum mechanics code might compute forces on a subset of
|
||||
atoms and pass those forces to LAMMPS. Or a continuum finite element
|
||||
|
|
@ -843,7 +830,7 @@ instances of LAMMPS to perform different calculations.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="visualizing-lammps-snapshots">
|
||||
<span id="howto-11"></span><h2>6.11. Visualizing LAMMPS snapshots<a class="headerlink" href="#visualizing-lammps-snapshots" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-11"></span><h2>Visualizing LAMMPS snapshots<a class="headerlink" href="#visualizing-lammps-snapshots" title="Permalink to this headline">¶</a></h2>
|
||||
<p>LAMMPS itself does not do visualization, but snapshots from LAMMPS
|
||||
simulations can be visualized (and analyzed) in a variety of ways.</p>
|
||||
<p>LAMMPS snapshots are created by the <a class="reference internal" href="dump.html"><em>dump</em></a> command which can
|
||||
|
|
@ -886,7 +873,7 @@ See the <a class="reference internal" href="dump.html"><em>dump</em></a> command
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="triclinic-non-orthogonal-simulation-boxes">
|
||||
<span id="howto-12"></span><h2>6.12. Triclinic (non-orthogonal) simulation boxes<a class="headerlink" href="#triclinic-non-orthogonal-simulation-boxes" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-12"></span><h2>Triclinic (non-orthogonal) simulation boxes<a class="headerlink" href="#triclinic-non-orthogonal-simulation-boxes" title="Permalink to this headline">¶</a></h2>
|
||||
<p>By default, LAMMPS uses an orthogonal simulation box to encompass the
|
||||
particles. The <a class="reference internal" href="boundary.html"><em>boundary</em></a> command sets the boundary
|
||||
conditions of the box (periodic, non-periodic, etc). The orthogonal
|
||||
|
|
@ -1064,7 +1051,7 @@ on non-equilibrium MD (NEMD) simulations.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="nemd-simulations">
|
||||
<span id="howto-13"></span><h2>6.13. NEMD simulations<a class="headerlink" href="#nemd-simulations" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-13"></span><h2>NEMD simulations<a class="headerlink" href="#nemd-simulations" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Non-equilibrium molecular dynamics or NEMD simulations are typically
|
||||
used to measure a fluid’s rheological properties such as viscosity.
|
||||
In LAMMPS, such simulations can be performed by first setting up a
|
||||
|
|
@ -1094,7 +1081,7 @@ profile consistent with the applied shear strain rate.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="finite-size-spherical-and-aspherical-particles">
|
||||
<span id="howto-14"></span><h2>6.14. Finite-size spherical and aspherical particles<a class="headerlink" href="#finite-size-spherical-and-aspherical-particles" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-14"></span><h2>Finite-size spherical and aspherical particles<a class="headerlink" href="#finite-size-spherical-and-aspherical-particles" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Typical MD models treat atoms or particles as point masses. Sometimes
|
||||
it is desirable to have a model with finite-size particles such as
|
||||
spheroids or ellipsoids or generalized aspherical bodies. The
|
||||
|
|
@ -1114,7 +1101,7 @@ particles. The following aspects are discussed in turn:</p>
|
|||
colloid, dipole, ellipse, line, peri, pour, and tri directories of the
|
||||
<a class="reference internal" href="Section_example.html"><em>examples directory</em></a> in the LAMMPS distribution.</p>
|
||||
<div class="section" id="atom-styles">
|
||||
<h3>6.14.1. Atom styles<a class="headerlink" href="#atom-styles" title="Permalink to this headline">¶</a></h3>
|
||||
<h3>Atom styles<a class="headerlink" href="#atom-styles" title="Permalink to this headline">¶</a></h3>
|
||||
<p>There are several <a class="reference internal" href="atom_style.html"><em>atom styles</em></a> that allow for
|
||||
definition of finite-size particles: sphere, dipole, ellipsoid, line,
|
||||
tri, peri, and body.</p>
|
||||
|
|
@ -1184,7 +1171,7 @@ object. When temperature is computed, the correct degrees of freedom
|
|||
are used for rotation in a 2d versus 3d system.</p>
|
||||
</div>
|
||||
<div class="section" id="pair-potentials">
|
||||
<h3>6.14.2. Pair potentials<a class="headerlink" href="#pair-potentials" title="Permalink to this headline">¶</a></h3>
|
||||
<h3>Pair potentials<a class="headerlink" href="#pair-potentials" title="Permalink to this headline">¶</a></h3>
|
||||
<p>When a system with finite-size particles is defined, the particles
|
||||
will only rotate and experience torque if the force field computes
|
||||
such interactions. These are the various <a class="reference internal" href="pair_style.html"><em>pair styles</em></a> that generate torque:</p>
|
||||
|
|
@ -1211,7 +1198,7 @@ The line, tri, and body potentials are used with line segment,
|
|||
triangular, and body particles respectively.</p>
|
||||
</div>
|
||||
<div class="section" id="time-integration">
|
||||
<h3>6.14.3. Time integration<a class="headerlink" href="#time-integration" title="Permalink to this headline">¶</a></h3>
|
||||
<h3>Time integration<a class="headerlink" href="#time-integration" title="Permalink to this headline">¶</a></h3>
|
||||
<p>There are several fixes that perform time integration on finite-size
|
||||
spherical particles, meaning the integrators update the rotational
|
||||
orientation and angular velocity or angular momentum of the particles:</p>
|
||||
|
|
@ -1246,7 +1233,7 @@ integration fixes can only be used with <a class="reference internal" href="grou
|
|||
contain finite-size particles.</p>
|
||||
</div>
|
||||
<div class="section" id="computes-thermodynamics-and-dump-output">
|
||||
<h3>6.14.4. Computes, thermodynamics, and dump output<a class="headerlink" href="#computes-thermodynamics-and-dump-output" title="Permalink to this headline">¶</a></h3>
|
||||
<h3>Computes, thermodynamics, and dump output<a class="headerlink" href="#computes-thermodynamics-and-dump-output" title="Permalink to this headline">¶</a></h3>
|
||||
<p>There are several computes that calculate the temperature or
|
||||
rotational energy of spherical or ellipsoidal particles:</p>
|
||||
<ul class="simple">
|
||||
|
|
@ -1277,7 +1264,7 @@ corner-point coordinates (for line and tri particles), and
|
|||
sub-particle attributes of body particles.</p>
|
||||
</div>
|
||||
<div class="section" id="rigid-bodies-composed-of-finite-size-particles">
|
||||
<h3>6.14.5. Rigid bodies composed of finite-size particles<a class="headerlink" href="#rigid-bodies-composed-of-finite-size-particles" title="Permalink to this headline">¶</a></h3>
|
||||
<h3>Rigid bodies composed of finite-size particles<a class="headerlink" href="#rigid-bodies-composed-of-finite-size-particles" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command treats a collection of
|
||||
particles as a rigid body, computes its inertia tensor, sums the total
|
||||
force and torque on the rigid body each timestep due to forces on its
|
||||
|
|
@ -1306,7 +1293,7 @@ particles are computed via a command like <a class="reference internal" href="pa
|
|||
</div>
|
||||
</div>
|
||||
<div class="section" id="output-from-lammps-thermo-dumps-computes-fixes-variables">
|
||||
<span id="howto-15"></span><h2>6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)<a class="headerlink" href="#output-from-lammps-thermo-dumps-computes-fixes-variables" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-15"></span><h2>Output from LAMMPS (thermo, dumps, computes, fixes, variables)<a class="headerlink" href="#output-from-lammps-thermo-dumps-computes-fixes-variables" title="Permalink to this headline">¶</a></h2>
|
||||
<p>There are four basic kinds of LAMMPS output:</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference internal" href="thermo_style.html"><em>Thermodynamic output</em></a>, which is a list
|
||||
|
|
@ -1343,7 +1330,7 @@ to output and the kind of data they operate on and produce:</p>
|
|||
<li><a class="reference internal" href="#table"><span>Summary table of output options and data flow between commands</span></a></li>
|
||||
</ul>
|
||||
<div class="section" id="global-per-atom-local-data">
|
||||
<span id="global"></span><h3>6.15.1. Global/per-atom/local data<a class="headerlink" href="#global-per-atom-local-data" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="global"></span><h3>Global/per-atom/local data<a class="headerlink" href="#global-per-atom-local-data" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Various output-related commands work with three different styles of
|
||||
data: global, per-atom, or local. A global datum is one or more
|
||||
system-wide values, e.g. the temperature of the system. A per-atom
|
||||
|
|
@ -1353,7 +1340,7 @@ atoms it owns, but there may be zero or more per atom, e.g. a list of
|
|||
bond distances.</p>
|
||||
</div>
|
||||
<div class="section" id="scalar-vector-array-data">
|
||||
<span id="scalar"></span><h3>6.15.2. Scalar/vector/array data<a class="headerlink" href="#scalar-vector-array-data" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="scalar"></span><h3>Scalar/vector/array data<a class="headerlink" href="#scalar-vector-array-data" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Global, per-atom, and local datums can each come in three kinds: a
|
||||
single scalar value, a vector of values, or a 2d array of values. The
|
||||
doc page for a “compute” or “fix” or “variable” that generates data
|
||||
|
|
@ -1387,7 +1374,7 @@ scalar values as input can typically also process elements of a vector
|
|||
or array.</p>
|
||||
</div>
|
||||
<div class="section" id="thermodynamic-output">
|
||||
<span id="thermo"></span><h3>6.15.3. Thermodynamic output<a class="headerlink" href="#thermodynamic-output" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="thermo"></span><h3>Thermodynamic output<a class="headerlink" href="#thermodynamic-output" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The frequency and format of thermodynamic output is set by the
|
||||
<a class="reference internal" href="thermo.html"><em>thermo</em></a>, <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a>, and
|
||||
<a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a> commands. The
|
||||
|
|
@ -1411,7 +1398,7 @@ formula if desired, to make an extensive calculation produce an
|
|||
intensive result.</p>
|
||||
</div>
|
||||
<div class="section" id="dump-file-output">
|
||||
<span id="dump"></span><h3>6.15.4. Dump file output<a class="headerlink" href="#dump-file-output" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="dump"></span><h3>Dump file output<a class="headerlink" href="#dump-file-output" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Dump file output is specified by the <a class="reference internal" href="dump.html"><em>dump</em></a> and
|
||||
<a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> commands. There are several
|
||||
pre-defined formats (dump atom, dump xtc, etc).</p>
|
||||
|
|
@ -1432,7 +1419,7 @@ must generate local values for input to the <a class="reference internal" href="
|
|||
command.</p>
|
||||
</div>
|
||||
<div class="section" id="fixes-that-write-output-files">
|
||||
<span id="fixoutput"></span><h3>6.15.5. Fixes that write output files<a class="headerlink" href="#fixes-that-write-output-files" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="fixoutput"></span><h3>Fixes that write output files<a class="headerlink" href="#fixes-that-write-output-files" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Several fixes take various quantities as input and can write output
|
||||
files: <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>, <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a>, <a class="reference internal" href="fix_ave_histo.html"><em>fix ave/histo</em></a>,
|
||||
<a class="reference internal" href="fix_ave_correlate.html"><em>fix ave/correlate</em></a>, and <a class="reference internal" href="fix_print.html"><em>fix print</em></a>.</p>
|
||||
|
|
@ -1478,7 +1465,7 @@ command is a means to output a wide variety of quantities separate
|
|||
from normal thermodynamic or dump file output.</p>
|
||||
</div>
|
||||
<div class="section" id="computes-that-process-output-quantities">
|
||||
<span id="computeoutput"></span><h3>6.15.6. Computes that process output quantities<a class="headerlink" href="#computes-that-process-output-quantities" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="computeoutput"></span><h3>Computes that process output quantities<a class="headerlink" href="#computes-that-process-output-quantities" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The <a class="reference internal" href="compute_reduce.html"><em>compute reduce</em></a> and <a class="reference internal" href="compute_reduce.html"><em>compute reduce/region</em></a> commands take one or more per-atom
|
||||
or local vector quantities as inputs and “reduce” them (sum, min, max,
|
||||
ave) to scalar quantities. These are produced as output values which
|
||||
|
|
@ -1499,7 +1486,7 @@ are produced as output values which can be used as input to other
|
|||
output commands.</p>
|
||||
</div>
|
||||
<div class="section" id="fixes-that-process-output-quantities">
|
||||
<span id="id3"></span><h3>6.15.7. Fixes that process output quantities<a class="headerlink" href="#fixes-that-process-output-quantities" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="id3"></span><h3>Fixes that process output quantities<a class="headerlink" href="#fixes-that-process-output-quantities" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The <a class="reference internal" href="fix_vector.html"><em>fix vector</em></a> command can create global vectors as
|
||||
output from global scalars as input, accumulating them one element at
|
||||
a time.</p>
|
||||
|
|
@ -1519,7 +1506,7 @@ by a <a class="reference internal" href="fix.html"><em>fix</em></a>, or by an at
|
|||
The output of this fix can be used as input to other output commands.</p>
|
||||
</div>
|
||||
<div class="section" id="computes-that-generate-values-to-output">
|
||||
<span id="compute"></span><h3>6.15.8. Computes that generate values to output<a class="headerlink" href="#computes-that-generate-values-to-output" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="compute"></span><h3>Computes that generate values to output<a class="headerlink" href="#computes-that-generate-values-to-output" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Every <a class="reference internal" href="compute.html"><em>compute</em></a> in LAMMPS produces either global or
|
||||
per-atom or local values. The values can be scalars or vectors or
|
||||
arrays of data. These values can be output using the other commands
|
||||
|
|
@ -1529,7 +1516,7 @@ values have the word “atom” or “local” in their style na
|
|||
without the word “atom” or “local” produce global values.</p>
|
||||
</div>
|
||||
<div class="section" id="fixes-that-generate-values-to-output">
|
||||
<span id="fix"></span><h3>6.15.9. Fixes that generate values to output<a class="headerlink" href="#fixes-that-generate-values-to-output" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="fix"></span><h3>Fixes that generate values to output<a class="headerlink" href="#fixes-that-generate-values-to-output" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Some <a class="reference internal" href="fix.html"><em>fixes</em></a> in LAMMPS produces either global or per-atom or
|
||||
local values which can be accessed by other commands. The values can
|
||||
be scalars or vectors or arrays of data. These values can be output
|
||||
|
|
@ -1538,7 +1525,7 @@ each fix command tells whether it produces any output quantities and
|
|||
describes them.</p>
|
||||
</div>
|
||||
<div class="section" id="variables-that-generate-values-to-output">
|
||||
<span id="variable"></span><h3>6.15.10. Variables that generate values to output<a class="headerlink" href="#variables-that-generate-values-to-output" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="variable"></span><h3>Variables that generate values to output<a class="headerlink" href="#variables-that-generate-values-to-output" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Every <a class="reference internal" href="variable.html"><em>variables</em></a> defined in an input script generates
|
||||
either a global scalar value or a per-atom vector (only atom-style
|
||||
variables) when it is accessed. The formulas used to define equal-
|
||||
|
|
@ -1548,7 +1535,7 @@ and other variables. The values generated by variables can be output
|
|||
using the other commands described in this section.</p>
|
||||
</div>
|
||||
<div class="section" id="summary-table-of-output-options-and-data-flow-between-commands">
|
||||
<span id="table"></span><h3>6.15.11. Summary table of output options and data flow between commands<a class="headerlink" href="#summary-table-of-output-options-and-data-flow-between-commands" title="Permalink to this headline">¶</a></h3>
|
||||
<span id="table"></span><h3>Summary table of output options and data flow between commands<a class="headerlink" href="#summary-table-of-output-options-and-data-flow-between-commands" title="Permalink to this headline">¶</a></h3>
|
||||
<p>This table summarizes the various commands that can be used for
|
||||
generating output from LAMMPS. Each command produces output data of
|
||||
some kind and/or writes data to a file. Most of the commands can take
|
||||
|
|
@ -1680,7 +1667,7 @@ vector input could be a column of an array.</p>
|
|||
</div>
|
||||
</div>
|
||||
<div class="section" id="thermostatting-barostatting-and-computing-temperature">
|
||||
<span id="howto-16"></span><h2>6.16. Thermostatting, barostatting, and computing temperature<a class="headerlink" href="#thermostatting-barostatting-and-computing-temperature" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-16"></span><h2>Thermostatting, barostatting, and computing temperature<a class="headerlink" href="#thermostatting-barostatting-and-computing-temperature" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Thermostatting means controlling the temperature of particles in an MD
|
||||
simulation. Barostatting means controlling the pressure. Since the
|
||||
pressure includes a kinetic component due to particle velocities, both
|
||||
|
|
@ -1816,7 +1803,7 @@ thermodynamic output.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="walls">
|
||||
<span id="howto-17"></span><h2>6.17. Walls<a class="headerlink" href="#walls" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-17"></span><h2>Walls<a class="headerlink" href="#walls" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Walls in an MD simulation are typically used to bound particle motion,
|
||||
i.e. to serve as a boundary condition.</p>
|
||||
<p>Walls in LAMMPS can be of rough (made of particles) or idealized
|
||||
|
|
@ -1880,7 +1867,7 @@ frictional walls, as well as triangulated surfaces.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="elastic-constants">
|
||||
<span id="howto-18"></span><h2>6.18. Elastic constants<a class="headerlink" href="#elastic-constants" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-18"></span><h2>Elastic constants<a class="headerlink" href="#elastic-constants" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Elastic constants characterize the stiffness of a material. The formal
|
||||
definition is provided by the linear relation that holds between the
|
||||
stress and strain tensors in the limit of infinitesimal deformation.
|
||||
|
|
@ -1912,7 +1899,7 @@ converge and requires careful post-processing <a class="reference internal" href
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="library-interface-to-lammps">
|
||||
<span id="howto-19"></span><h2>6.19. Library interface to LAMMPS<a class="headerlink" href="#library-interface-to-lammps" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-19"></span><h2>Library interface to LAMMPS<a class="headerlink" href="#library-interface-to-lammps" title="Permalink to this headline">¶</a></h2>
|
||||
<p>As described in <a class="reference internal" href="Section_start.html#start-5"><span>Section_start 5</span></a>, LAMMPS
|
||||
can be built as a library, so that it can be called by another code,
|
||||
used in a <a class="reference internal" href="#howto-10"><span>coupled manner</span></a> with other
|
||||
|
|
@ -1987,7 +1974,7 @@ LAMMPS.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="calculating-thermal-conductivity">
|
||||
<span id="howto-20"></span><h2>6.20. Calculating thermal conductivity<a class="headerlink" href="#calculating-thermal-conductivity" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-20"></span><h2>Calculating thermal conductivity<a class="headerlink" href="#calculating-thermal-conductivity" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The thermal conductivity kappa of a material can be measured in at
|
||||
least 4 ways using various options in LAMMPS. See the examples/KAPPA
|
||||
directory for scripts that implement the 4 methods discussed here for
|
||||
|
|
@ -2041,7 +2028,7 @@ formalism.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="calculating-viscosity">
|
||||
<span id="howto-21"></span><h2>6.21. Calculating viscosity<a class="headerlink" href="#calculating-viscosity" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-21"></span><h2>Calculating viscosity<a class="headerlink" href="#calculating-viscosity" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The shear viscosity eta of a fluid can be measured in at least 4 ways
|
||||
using various options in LAMMPS. See the examples/VISCOSITY directory
|
||||
for scripts that implement the 4 methods discussed here for a simple
|
||||
|
|
@ -2162,7 +2149,7 @@ print "average viscosity: $v [Pa.s/** @ $T K, ${ndens} /A^3"
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="calculating-a-diffusion-coefficient">
|
||||
<span id="howto-22"></span><h2>6.22. Calculating a diffusion coefficient<a class="headerlink" href="#calculating-a-diffusion-coefficient" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-22"></span><h2>Calculating a diffusion coefficient<a class="headerlink" href="#calculating-a-diffusion-coefficient" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The diffusion coefficient D of a material can be measured in at least
|
||||
2 ways using various options in LAMMPS. See the examples/DIFFUSE
|
||||
directory for scripts that implement the 2 methods discussed here for
|
||||
|
|
@ -2184,7 +2171,7 @@ and thus extract D.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="using-chunks-to-calculate-system-properties">
|
||||
<span id="howto-23"></span><h2>6.23. Using chunks to calculate system properties<a class="headerlink" href="#using-chunks-to-calculate-system-properties" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-23"></span><h2>Using chunks to calculate system properties<a class="headerlink" href="#using-chunks-to-calculate-system-properties" title="Permalink to this headline">¶</a></h2>
|
||||
<p>In LAMMS, “chunks” are collections of atoms, as defined by the
|
||||
<a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command, which assigns
|
||||
each atom to a chunk ID (or to no chunk at all). The number of chunks
|
||||
|
|
@ -2201,7 +2188,7 @@ commands, to calculate various properties of a system:</p>
|
|||
overviewed. Then some examples are given of how to compute different
|
||||
properties with chunk commands.</p>
|
||||
<div class="section" id="compute-chunk-atom-command">
|
||||
<h3>6.23.1. Compute chunk/atom command:<a class="headerlink" href="#compute-chunk-atom-command" title="Permalink to this headline">¶</a></h3>
|
||||
<h3>Compute chunk/atom command:<a class="headerlink" href="#compute-chunk-atom-command" title="Permalink to this headline">¶</a></h3>
|
||||
<p>This compute can assign atoms to chunks of various styles. Only atoms
|
||||
in the specified group and optional specified region are assigned to a
|
||||
chunk. Here are some possible chunk definitions:</p>
|
||||
|
|
@ -2259,7 +2246,7 @@ the input script that uses a formula to generate a chunk ID for each
|
|||
atom.</p>
|
||||
</div>
|
||||
<div class="section" id="fix-ave-chunk-command">
|
||||
<h3>6.23.2. Fix ave/chunk command:<a class="headerlink" href="#fix-ave-chunk-command" title="Permalink to this headline">¶</a></h3>
|
||||
<h3>Fix ave/chunk command:<a class="headerlink" href="#fix-ave-chunk-command" title="Permalink to this headline">¶</a></h3>
|
||||
<p>This fix takes the ID of a <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command as input. For each chunk,
|
||||
it then sums one or more specified per-atom values over the atoms in
|
||||
each chunk. The per-atom values can be any atom property, such as
|
||||
|
|
@ -2273,7 +2260,7 @@ fix produces a global array as output with one row of values per
|
|||
chunk.</p>
|
||||
</div>
|
||||
<div class="section" id="compute-chunk-commands">
|
||||
<h3>6.23.3. Compute <a href="#id68"><span class="problematic" id="id69">*</span></a>/chunk commands:<a class="headerlink" href="#compute-chunk-commands" title="Permalink to this headline">¶</a></h3>
|
||||
<h3>Compute <a href="#id68"><span class="problematic" id="id69">*</span></a>/chunk commands:<a class="headerlink" href="#compute-chunk-commands" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Currently the following computes operate on chunks of atoms to produce
|
||||
per-chunk values.</p>
|
||||
<ul class="simple">
|
||||
|
|
@ -2310,7 +2297,7 @@ largest cluster or fastest diffusing molecule.</li>
|
|||
</ul>
|
||||
</div>
|
||||
<div class="section" id="example-calculations-with-chunks">
|
||||
<h3>6.23.4. Example calculations with chunks<a class="headerlink" href="#example-calculations-with-chunks" title="Permalink to this headline">¶</a></h3>
|
||||
<h3>Example calculations with chunks<a class="headerlink" href="#example-calculations-with-chunks" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Here are eaxmples using chunk commands to calculate various
|
||||
properties:</p>
|
||||
<ol class="arabic simple">
|
||||
|
|
@ -2359,7 +2346,7 @@ fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond igno
|
|||
</div>
|
||||
</div>
|
||||
<div class="section" id="setting-parameters-for-the-kspace-style-pppm-disp-command">
|
||||
<span id="howto-24"></span><h2>6.24. Setting parameters for the <a class="reference internal" href="kspace_style.html"><em>kspace_style pppm/disp</em></a> command<a class="headerlink" href="#setting-parameters-for-the-kspace-style-pppm-disp-command" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-24"></span><h2>Setting parameters for the <a class="reference internal" href="kspace_style.html"><em>kspace_style pppm/disp</em></a> command<a class="headerlink" href="#setting-parameters-for-the-kspace-style-pppm-disp-command" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The PPPM method computes interactions by splitting the pair potential
|
||||
into two parts, one of which is computed in a normal pairwise fashion,
|
||||
the so-called real-space part, and one of which is computed using the
|
||||
|
|
@ -2452,7 +2439,7 @@ to specify this command explicitly.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="polarizable-models">
|
||||
<span id="howto-25"></span><h2>6.25. Polarizable models<a class="headerlink" href="#polarizable-models" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-25"></span><h2>Polarizable models<a class="headerlink" href="#polarizable-models" title="Permalink to this headline">¶</a></h2>
|
||||
<p>In polarizable force fields the charge distributions in molecules and
|
||||
materials respond to their electrostatic environements. Polarizable
|
||||
systems can be simulated in LAMMPS using three methods:</p>
|
||||
|
|
@ -2522,7 +2509,7 @@ well.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="adiabatic-core-shell-model">
|
||||
<span id="howto-26"></span><h2>6.26. Adiabatic core/shell model<a class="headerlink" href="#adiabatic-core-shell-model" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-26"></span><h2>Adiabatic core/shell model<a class="headerlink" href="#adiabatic-core-shell-model" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The adiabatic core-shell model by <a class="reference internal" href="pair_cs.html#mitchellfinchham"><span>Mitchell and Finchham</span></a> is a simple method for adding
|
||||
polarizability to a system. In order to mimic the electron shell of
|
||||
an ion, a satellite particle is attached to it. This way the ions are
|
||||
|
|
@ -2700,7 +2687,7 @@ fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="drude-induced-dipoles">
|
||||
<span id="howto-27"></span><h2>6.27. Drude induced dipoles<a class="headerlink" href="#drude-induced-dipoles" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="howto-27"></span><h2>Drude induced dipoles<a class="headerlink" href="#drude-induced-dipoles" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The thermalized Drude model, similarly to the <a class="reference internal" href="#howto-26"><span>core-shell</span></a>
|
||||
model, representes induced dipoles by a pair of charges (the core atom
|
||||
and the Drude particle) connected by a harmonic spring. The Drude
|
||||
|
|
@ -2777,15 +2764,6 @@ Phys, 79, 926 (1983).</p>
|
|||
</div>
|
||||
<footer>
|
||||
|
||||
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
|
||||
|
||||
<a href="Section_example.html" class="btn btn-neutral float-right" title="7. Example problems" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
|
||||
|
||||
|
||||
<a href="Section_accelerate.html" class="btn btn-neutral" title="5. Accelerating LAMMPS performance" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<hr/>
|
||||
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@
|
|||
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>1. Introduction — LAMMPS 15 May 2015 version documentation</title>
|
||||
<title>Introduction — 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 & 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 & 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> »</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’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’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’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/>
|
||||
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@
|
|||
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||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>10. Modifying & extending LAMMPS — LAMMPS 15 May 2015 version documentation</title>
|
||||
<title>Modifying & extending LAMMPS — LAMMPS 15 May 2015 version documentation</title>
|
||||
|
||||
|
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|
||||
|
|
@ -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"/>
|
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<link rel="prev" title="9. Additional tools" href="Section_tools.html"/>
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|
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|
||||
<script src="_static/js/modernizr.min.js"></script>
|
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|
|
@ -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 & 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 & 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 & 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> »</li>
|
||||
|
||||
<li>10. Modifying & extending LAMMPS</li>
|
||||
<li>Modifying & 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 & extending LAMMPS<a class="headerlink" href="#modifying-extending-lammps" title="Permalink to this headline">¶</a></h1>
|
||||
<h1>Modifying & 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 “fix” 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 “command” 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: “one” and “multi”. 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/>
|
||||
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@
|
|||
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>4. Packages — LAMMPS 15 May 2015 version documentation</title>
|
||||
<title>Packages — 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 & 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 & 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> »</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 “fix atc” command which can be used in a
|
||||
LAMMPS input script. This fix can be employed to either do concurrent
|
||||
coupling of MD with FE-based physics surrogates or on-the-fly
|
||||
|
|
@ -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 “fix colvars” command which can be
|
||||
used in a LAMMPS input script.</p>
|
||||
<p>This fix allows to use “collective variables” 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>
|
||||
|
||||
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|
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|
||||
|
||||
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|
||||
|
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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|
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<title>8. Performance & scalability — LAMMPS 15 May 2015 version documentation</title>
|
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<title>Performance & scalability — LAMMPS 15 May 2015 version documentation</title>
|
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|||
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<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
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<link rel="next" title="9. Additional tools" href="Section_tools.html"/>
|
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<link rel="prev" title="7. Example problems" href="Section_example.html"/>
|
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<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
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|
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<script src="_static/js/modernizr.min.js"></script>
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<ul class="current">
|
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<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 & 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 & 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 & scalability</a></li>
|
||||
</ul>
|
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|
||||
</div>
|
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|
||||
|
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</div>
|
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|
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@ -111,7 +98,7 @@
|
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<ul class="wy-breadcrumbs">
|
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<li><a href="Manual.html">Docs</a> »</li>
|
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|
||||
<li>8. Performance & scalability</li>
|
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<li>Performance & scalability</li>
|
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<li class="wy-breadcrumbs-aside">
|
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|
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|
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|
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<div itemprop="articleBody">
|
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|
||||
<div class="section" id="performance-scalability">
|
||||
<h1>8. Performance & scalability<a class="headerlink" href="#performance-scalability" title="Permalink to this headline">¶</a></h1>
|
||||
<h1>Performance & 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>
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|
||||
|
||||
<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>
|
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|
||||
|
||||
<hr/>
|
||||
|
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|
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|
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@ -8,7 +8,7 @@
|
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|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>11. Python interface to LAMMPS — LAMMPS 15 May 2015 version documentation</title>
|
||||
<title>Python interface to LAMMPS — LAMMPS 15 May 2015 version documentation</title>
|
||||
|
||||
|
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|
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|
|||
|
||||
|
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<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 & extending LAMMPS" href="Section_modify.html"/>
|
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<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
|
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|
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|
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<script src="_static/js/modernizr.min.js"></script>
|
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|
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|
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|
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|
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|
||||
<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 & 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 & 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> »</li>
|
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|
||||
<li>11. Python interface to LAMMPS</li>
|
||||
<li>Python interface to LAMMPS</li>
|
||||
<li class="wy-breadcrumbs-aside">
|
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|
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|
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|
|
@ -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">>>> </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">>>> </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 “lammps” module, the source code for which is in
|
||||
python/lammps.py, which creates a “lammps” object, with a set of
|
||||
|
|
@ -783,7 +770,7 @@ Python script. Isn’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 & extending LAMMPS" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<hr/>
|
||||
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@
|
|||
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>2. Getting Started — LAMMPS 15 May 2015 version documentation</title>
|
||||
<title>Getting Started — 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’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’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 & 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 & 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> »</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’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’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 “-cc” and “-mpi” 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/>
|
||||
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@
|
|||
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>9. Additional tools — LAMMPS 15 May 2015 version documentation</title>
|
||||
<title>Additional tools — 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="10. Modifying & extending LAMMPS" href="Section_modify.html"/>
|
||||
<link rel="prev" title="8. Performance & scalability" href="Section_perf.html"/>
|
||||
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
|
||||
|
||||
|
||||
<script src="_static/js/modernizr.min.js"></script>
|
||||
|
|
@ -73,55 +71,44 @@
|
|||
|
||||
|
||||
|
||||
<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 & scalability</a></li>
|
||||
<li class="toctree-l1 current"><a class="current reference internal" href="">9. Additional tools</a><ul>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#amber2lmp-tool">9.1. amber2lmp tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#binary2txt-tool">9.2. binary2txt tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#ch2lmp-tool">9.3. ch2lmp tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#chain-tool">9.4. chain tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#colvars-tools">9.5. colvars tools</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#createatoms-tool">9.6. createatoms tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#data2xmovie-tool">9.7. data2xmovie tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#eam-database-tool">9.8. eam database tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#eam-generate-tool">9.9. eam generate tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#eff-tool">9.10. eff tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#emacs-tool">9.11. emacs tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#fep-tool">9.12. fep tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#i-pi-tool">9.13. i-pi tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#ipp-tool">9.14. ipp tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#kate-tool">9.15. kate tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#lmp2arc-tool">9.16. lmp2arc tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#matlab-tool">9.19. matlab tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#micelle2d-tool">9.20. micelle2d tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#moltemplate-tool">9.21. moltemplate tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#msi2lmp-tool">9.22. msi2lmp tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#phonon-tool">9.23. phonon tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#python-tool">9.26. python tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#reax-tool">9.27. reax tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#restart2data-tool">9.28. restart2data tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#vim-tool">9.29. vim tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#xmgrace-tool">9.30. xmgrace tool</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#xmovie-tool">9.31. xmovie tool</a></li>
|
||||
<!-- Local TOC -->
|
||||
<div class="local-toc"><ul>
|
||||
<li><a class="reference internal" href="#">Additional tools</a><ul>
|
||||
<li><a class="reference internal" href="#amber2lmp-tool">amber2lmp tool</a></li>
|
||||
<li><a class="reference internal" href="#binary2txt-tool">binary2txt tool</a></li>
|
||||
<li><a class="reference internal" href="#ch2lmp-tool">ch2lmp tool</a></li>
|
||||
<li><a class="reference internal" href="#chain-tool">chain tool</a></li>
|
||||
<li><a class="reference internal" href="#colvars-tools">colvars tools</a></li>
|
||||
<li><a class="reference internal" href="#createatoms-tool">createatoms tool</a></li>
|
||||
<li><a class="reference internal" href="#data2xmovie-tool">data2xmovie tool</a></li>
|
||||
<li><a class="reference internal" href="#eam-database-tool">eam database tool</a></li>
|
||||
<li><a class="reference internal" href="#eam-generate-tool">eam generate tool</a></li>
|
||||
<li><a class="reference internal" href="#eff-tool">eff tool</a></li>
|
||||
<li><a class="reference internal" href="#emacs-tool">emacs tool</a></li>
|
||||
<li><a class="reference internal" href="#fep-tool">fep tool</a></li>
|
||||
<li><a class="reference internal" href="#i-pi-tool">i-pi tool</a></li>
|
||||
<li><a class="reference internal" href="#ipp-tool">ipp tool</a></li>
|
||||
<li><a class="reference internal" href="#kate-tool">kate tool</a></li>
|
||||
<li><a class="reference internal" href="#lmp2arc-tool">lmp2arc tool</a></li>
|
||||
<li><a class="reference internal" href="#lmp2cfg-tool">lmp2cfg tool</a></li>
|
||||
<li><a class="reference internal" href="#lmp2vmd-tool">lmp2vmd tool</a></li>
|
||||
<li><a class="reference internal" href="#matlab-tool">matlab tool</a></li>
|
||||
<li><a class="reference internal" href="#micelle2d-tool">micelle2d tool</a></li>
|
||||
<li><a class="reference internal" href="#moltemplate-tool">moltemplate tool</a></li>
|
||||
<li><a class="reference internal" href="#msi2lmp-tool">msi2lmp tool</a></li>
|
||||
<li><a class="reference internal" href="#phonon-tool">phonon tool</a></li>
|
||||
<li><a class="reference internal" href="#polymer-bonding-tool">polymer bonding tool</a></li>
|
||||
<li><a class="reference internal" href="#pymol-asphere-tool">pymol_asphere tool</a></li>
|
||||
<li><a class="reference internal" href="#python-tool">python tool</a></li>
|
||||
<li><a class="reference internal" href="#reax-tool">reax tool</a></li>
|
||||
<li><a class="reference internal" href="#restart2data-tool">restart2data tool</a></li>
|
||||
<li><a class="reference internal" href="#vim-tool">vim tool</a></li>
|
||||
<li><a class="reference internal" href="#xmgrace-tool">xmgrace tool</a></li>
|
||||
<li><a class="reference internal" href="#xmovie-tool">xmovie tool</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & 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>
|
||||
|
|
@ -144,7 +131,7 @@
|
|||
<ul class="wy-breadcrumbs">
|
||||
<li><a href="Manual.html">Docs</a> »</li>
|
||||
|
||||
<li>9. Additional tools</li>
|
||||
<li>Additional tools</li>
|
||||
<li class="wy-breadcrumbs-aside">
|
||||
|
||||
|
||||
|
|
@ -159,7 +146,7 @@
|
|||
<div itemprop="articleBody">
|
||||
|
||||
<div class="section" id="additional-tools">
|
||||
<h1>9. Additional tools<a class="headerlink" href="#additional-tools" title="Permalink to this headline">¶</a></h1>
|
||||
<h1>Additional tools<a class="headerlink" href="#additional-tools" title="Permalink to this headline">¶</a></h1>
|
||||
<p>LAMMPS is designed to be a computational kernel for performing
|
||||
molecular dynamics computations. Additional pre- and post-processing
|
||||
steps are often necessary to setup and analyze a simulation. A few
|
||||
|
|
@ -216,7 +203,7 @@ own sub-directories with their own Makefiles.</p>
|
|||
</ul>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="amber2lmp-tool">
|
||||
<span id="amber"></span><h2>9.1. amber2lmp tool<a class="headerlink" href="#amber2lmp-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="amber"></span><h2>amber2lmp tool<a class="headerlink" href="#amber2lmp-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The amber2lmp sub-directory contains two Python scripts for converting
|
||||
files back-and-forth between the AMBER MD code and LAMMPS. See the
|
||||
README file in amber2lmp for more information.</p>
|
||||
|
|
@ -229,7 +216,7 @@ necessary modifications yourself.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="binary2txt-tool">
|
||||
<span id="binary"></span><h2>9.2. binary2txt tool<a class="headerlink" href="#binary2txt-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="binary"></span><h2>binary2txt tool<a class="headerlink" href="#binary2txt-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The file binary2txt.cpp converts one or more binary LAMMPS dump file
|
||||
into ASCII text files. The syntax for running the tool is</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>binary2txt file1 file2 ...
|
||||
|
|
@ -241,7 +228,7 @@ since binary files are not compatible across all platforms.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="ch2lmp-tool">
|
||||
<span id="charmm"></span><h2>9.3. ch2lmp tool<a class="headerlink" href="#ch2lmp-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="charmm"></span><h2>ch2lmp tool<a class="headerlink" href="#ch2lmp-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The ch2lmp sub-directory contains tools for converting files
|
||||
back-and-forth between the CHARMM MD code and LAMMPS.</p>
|
||||
<p>They are intended to make it easy to use CHARMM as a builder and as a
|
||||
|
|
@ -254,7 +241,7 @@ and Paul Crozier (pscrozi at sandia.gov) at Sandia.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="chain-tool">
|
||||
<span id="chain"></span><h2>9.4. chain tool<a class="headerlink" href="#chain-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="chain"></span><h2>chain tool<a class="headerlink" href="#chain-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The file chain.f creates a LAMMPS data file containing bead-spring
|
||||
polymer chains and/or monomer solvent atoms. It uses a text file
|
||||
containing chain definition parameters as an input. The created
|
||||
|
|
@ -270,7 +257,7 @@ system for the <a class="reference internal" href="Section_perf.html"><em>chain
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="colvars-tools">
|
||||
<span id="colvars"></span><h2>9.5. colvars tools<a class="headerlink" href="#colvars-tools" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="colvars"></span><h2>colvars tools<a class="headerlink" href="#colvars-tools" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The colvars directory contains a collection of tools for postprocessing
|
||||
data produced by the colvars collective variable library.
|
||||
To compile the tools, edit the makefile for your system and run “make”.</p>
|
||||
|
|
@ -288,7 +275,7 @@ gmail.com) at ICTP, Italy.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="createatoms-tool">
|
||||
<span id="create"></span><h2>9.6. createatoms tool<a class="headerlink" href="#createatoms-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="create"></span><h2>createatoms tool<a class="headerlink" href="#createatoms-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The tools/createatoms directory contains a Fortran program called
|
||||
createAtoms.f which can generate a variety of interesting crystal
|
||||
structures and geometries and output the resulting list of atom
|
||||
|
|
@ -298,7 +285,7 @@ coordinates in LAMMPS or other formats.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="data2xmovie-tool">
|
||||
<span id="data"></span><h2>9.7. data2xmovie tool<a class="headerlink" href="#data2xmovie-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="data"></span><h2>data2xmovie tool<a class="headerlink" href="#data2xmovie-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The file data2xmovie.c converts a LAMMPS data file into a snapshot
|
||||
suitable for visualizing with the <a class="reference internal" href="#xmovie"><span>xmovie</span></a> tool, as if it had
|
||||
been output with a dump command from LAMMPS itself. The syntax for
|
||||
|
|
@ -310,7 +297,7 @@ running the tool is</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="eam-database-tool">
|
||||
<span id="eamdb"></span><h2>9.8. eam database tool<a class="headerlink" href="#eam-database-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="eamdb"></span><h2>eam database tool<a class="headerlink" href="#eam-database-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The tools/eam_database directory contains a Fortran program that will
|
||||
generate EAM alloy setfl potential files for any combination of 16
|
||||
elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
|
||||
|
|
@ -322,7 +309,7 @@ and is based on his paper:</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="eam-generate-tool">
|
||||
<span id="eamgn"></span><h2>9.9. eam generate tool<a class="headerlink" href="#eam-generate-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="eamgn"></span><h2>eam generate tool<a class="headerlink" href="#eam-generate-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The tools/eam_generate directory contains several one-file C programs
|
||||
that convert an analytic formula into a tabulated <a class="reference internal" href="pair_eam.html"><em>embedded atom method (EAM)</em></a> setfl potential file. The potentials they
|
||||
produce are in the potentials directory, and can be used with the
|
||||
|
|
@ -332,7 +319,7 @@ produce are in the potentials directory, and can be used with the
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="eff-tool">
|
||||
<span id="eff"></span><h2>9.10. eff tool<a class="headerlink" href="#eff-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="eff"></span><h2>eff tool<a class="headerlink" href="#eff-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The tools/eff directory contains various scripts for generating
|
||||
structures and post-processing output for simulations using the
|
||||
electron force field (eFF).</p>
|
||||
|
|
@ -341,7 +328,7 @@ electron force field (eFF).</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="emacs-tool">
|
||||
<span id="emacs"></span><h2>9.11. emacs tool<a class="headerlink" href="#emacs-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="emacs"></span><h2>emacs tool<a class="headerlink" href="#emacs-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The tools/emacs directory contains a Lips add-on file for Emacs that
|
||||
enables a lammps-mode for editing of input scripts when using Emacs,
|
||||
with various highlighting options setup.</p>
|
||||
|
|
@ -350,7 +337,7 @@ with various highlighting options setup.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="fep-tool">
|
||||
<span id="fep"></span><h2>9.12. fep tool<a class="headerlink" href="#fep-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="fep"></span><h2>fep tool<a class="headerlink" href="#fep-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The tools/fep directory contains Python scripts useful for
|
||||
post-processing results from performing free-energy perturbation
|
||||
simulations using the USER-FEP package.</p>
|
||||
|
|
@ -360,7 +347,7 @@ Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="i-pi-tool">
|
||||
<span id="ipi"></span><h2>9.13. i-pi tool<a class="headerlink" href="#i-pi-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="ipi"></span><h2>i-pi tool<a class="headerlink" href="#i-pi-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The tools/i-pi directory contains a version of the i-PI package, with
|
||||
all the LAMMPS-unrelated files removed. It is provided so that it can
|
||||
be used with the <a class="reference internal" href="fix_ipi.html"><em>fix ipi</em></a> command to perform
|
||||
|
|
@ -374,7 +361,7 @@ calculations with LAMMPS.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="ipp-tool">
|
||||
<span id="ipp"></span><h2>9.14. ipp tool<a class="headerlink" href="#ipp-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="ipp"></span><h2>ipp tool<a class="headerlink" href="#ipp-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The tools/ipp directory contains a Perl script ipp which can be used
|
||||
to facilitate the creation of a complicated file (say, a lammps input
|
||||
script or tools/createatoms input file) using a template file.</p>
|
||||
|
|
@ -385,7 +372,7 @@ tools/createatoms tool’s input file.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="kate-tool">
|
||||
<span id="kate"></span><h2>9.15. kate tool<a class="headerlink" href="#kate-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="kate"></span><h2>kate tool<a class="headerlink" href="#kate-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The file in the tools/kate directory is an add-on to the Kate editor
|
||||
in the KDE suite that allow syntax highlighting of LAMMPS input
|
||||
scripts. See the README.txt file for details.</p>
|
||||
|
|
@ -394,7 +381,7 @@ scripts. See the README.txt file for details.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="lmp2arc-tool">
|
||||
<span id="arc"></span><h2>9.16. lmp2arc tool<a class="headerlink" href="#lmp2arc-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="arc"></span><h2>lmp2arc tool<a class="headerlink" href="#lmp2arc-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The lmp2arc sub-directory contains a tool for converting LAMMPS output
|
||||
files to the format for Accelrys’ Insight MD code (formerly
|
||||
MSI/Biosym and its Discover MD code). See the README file for more
|
||||
|
|
@ -407,7 +394,7 @@ Greathouse at Sandia (jagreat at sandia.gov).</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="lmp2cfg-tool">
|
||||
<span id="cfg"></span><h2>9.17. lmp2cfg tool<a class="headerlink" href="#lmp2cfg-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="cfg"></span><h2>lmp2cfg tool<a class="headerlink" href="#lmp2cfg-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The lmp2cfg sub-directory contains a tool for converting LAMMPS output
|
||||
files into a series of <a href="#id1"><span class="problematic" id="id2">*</span></a>.cfg files which can be read into the
|
||||
<a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualizer. See
|
||||
|
|
@ -416,7 +403,7 @@ the README file for more information.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="lmp2vmd-tool">
|
||||
<span id="vmd"></span><h2>9.18. lmp2vmd tool<a class="headerlink" href="#lmp2vmd-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="vmd"></span><h2>lmp2vmd tool<a class="headerlink" href="#lmp2vmd-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The lmp2vmd sub-directory contains a README.txt file that describes
|
||||
details of scripts and plugin support within the <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD package</a> for visualizing LAMMPS
|
||||
dump files.</p>
|
||||
|
|
@ -425,7 +412,7 @@ Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="matlab-tool">
|
||||
<span id="matlab"></span><h2>9.19. matlab tool<a class="headerlink" href="#matlab-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="matlab"></span><h2>matlab tool<a class="headerlink" href="#matlab-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The matlab sub-directory contains several <span class="xref std std-ref">MATLAB</span> scripts for
|
||||
post-processing LAMMPS output. The scripts include readers for log
|
||||
and dump files, a reader for EAM potential files, and a converter that
|
||||
|
|
@ -438,7 +425,7 @@ visualizer.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="micelle2d-tool">
|
||||
<span id="micelle"></span><h2>9.20. micelle2d tool<a class="headerlink" href="#micelle2d-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="micelle"></span><h2>micelle2d tool<a class="headerlink" href="#micelle2d-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The file micelle2d.f creates a LAMMPS data file containing short lipid
|
||||
chains in a monomer solution. It uses a text file containing lipid
|
||||
definition parameters as an input. The created molecules and solvent
|
||||
|
|
@ -454,7 +441,7 @@ definition file. This tool was used to create the system for the
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="moltemplate-tool">
|
||||
<span id="moltemplate"></span><h2>9.21. moltemplate tool<a class="headerlink" href="#moltemplate-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="moltemplate"></span><h2>moltemplate tool<a class="headerlink" href="#moltemplate-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The moltemplate sub-directory contains a Python-based tool for
|
||||
building molecular systems based on a text-file description, and
|
||||
creating LAMMPS data files that encode their molecular topology as
|
||||
|
|
@ -466,7 +453,7 @@ supports it. It has its own WWW page at
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="msi2lmp-tool">
|
||||
<span id="msi"></span><h2>9.22. msi2lmp tool<a class="headerlink" href="#msi2lmp-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="msi"></span><h2>msi2lmp tool<a class="headerlink" href="#msi2lmp-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The msi2lmp sub-directory contains a tool for creating LAMMPS input
|
||||
data files from Accelrys’ Insight MD code (formerly MSI/Biosym and
|
||||
its Discover MD code). See the README file for more information.</p>
|
||||
|
|
@ -479,7 +466,7 @@ experiment with it yourself.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="phonon-tool">
|
||||
<span id="phonon"></span><h2>9.23. phonon tool<a class="headerlink" href="#phonon-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="phonon"></span><h2>phonon tool<a class="headerlink" href="#phonon-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The phonon sub-directory contains a post-processing tool useful for
|
||||
analyzing the output of the <a class="reference internal" href="fix_phonon.html"><em>fix phonon</em></a> command in
|
||||
the USER-PHONON package.</p>
|
||||
|
|
@ -491,7 +478,7 @@ University.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="polymer-bonding-tool">
|
||||
<span id="polybond"></span><h2>9.24. polymer bonding tool<a class="headerlink" href="#polymer-bonding-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="polybond"></span><h2>polymer bonding tool<a class="headerlink" href="#polymer-bonding-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The polybond sub-directory contains a Python-based tool useful for
|
||||
performing “programmable polymer bonding”. The Python file
|
||||
lmpsdata.py provides a “Lmpsdata” class with various methods which can
|
||||
|
|
@ -502,7 +489,7 @@ complex bonding topologies.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="pymol-asphere-tool">
|
||||
<span id="pymol"></span><h2>9.25. pymol_asphere tool<a class="headerlink" href="#pymol-asphere-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="pymol"></span><h2>pymol_asphere tool<a class="headerlink" href="#pymol-asphere-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The pymol_asphere sub-directory contains a tool for converting a
|
||||
LAMMPS dump file that contains orientation info for ellipsoidal
|
||||
particles into an input file for the <span class="xref std std-ref">PyMol visualization package</span>.</p>
|
||||
|
|
@ -513,7 +500,7 @@ examples directory within pymol_asphere for more information.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="python-tool">
|
||||
<span id="pythontools"></span><h2>9.26. python tool<a class="headerlink" href="#python-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="pythontools"></span><h2>python tool<a class="headerlink" href="#python-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The python sub-directory contains several Python scripts
|
||||
that perform common LAMMPS post-processing tasks, such as:</p>
|
||||
<ul class="simple">
|
||||
|
|
@ -528,7 +515,7 @@ README for more info on Pizza.py and how to use these scripts.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="reax-tool">
|
||||
<span id="reax"></span><h2>9.27. reax tool<a class="headerlink" href="#reax-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="reax"></span><h2>reax tool<a class="headerlink" href="#reax-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The reax sub-directory contains stand-alond codes that can
|
||||
post-process the output of the <a class="reference internal" href="fix_reax_bonds.html"><em>fix reax/bonds</em></a>
|
||||
command from a LAMMPS simulation using <a class="reference internal" href="pair_reax.html"><em>ReaxFF</em></a>. See
|
||||
|
|
@ -537,7 +524,7 @@ the README.txt file for more info.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="restart2data-tool">
|
||||
<span id="restart"></span><h2>9.28. restart2data tool<a class="headerlink" href="#restart2data-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="restart"></span><h2>restart2data tool<a class="headerlink" href="#restart2data-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="admonition warning">
|
||||
<p class="first admonition-title">Warning</p>
|
||||
<p class="last">This tool is now obsolete and is not included in the
|
||||
|
|
@ -576,7 +563,7 @@ of files are written by LAMMPS, and how the files are named.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="vim-tool">
|
||||
<span id="vim"></span><h2>9.29. vim tool<a class="headerlink" href="#vim-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="vim"></span><h2>vim tool<a class="headerlink" href="#vim-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The files in the tools/vim directory are add-ons to the VIM editor
|
||||
that allow easier editing of LAMMPS input scripts. See the README.txt
|
||||
file for details.</p>
|
||||
|
|
@ -585,7 +572,7 @@ ziegenhain.com)</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="xmgrace-tool">
|
||||
<span id="xmgrace"></span><h2>9.30. xmgrace tool<a class="headerlink" href="#xmgrace-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="xmgrace"></span><h2>xmgrace tool<a class="headerlink" href="#xmgrace-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The files in the tools/xmgrace directory can be used to plot the
|
||||
thermodynamic data in LAMMPS log files via the xmgrace plotting
|
||||
package. There are several tools in the directory that can be used in
|
||||
|
|
@ -597,7 +584,7 @@ simulation.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="xmovie-tool">
|
||||
<span id="xmovie"></span><h2>9.31. xmovie tool<a class="headerlink" href="#xmovie-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="xmovie"></span><h2>xmovie tool<a class="headerlink" href="#xmovie-tool" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The xmovie tool is an X-based visualization package that can read
|
||||
LAMMPS dump files and animate them. It is in its own sub-directory
|
||||
with the tools directory. You may need to modify its Makefile so that
|
||||
|
|
@ -628,15 +615,6 @@ distributing his great tool!</p>
|
|||
</div>
|
||||
<footer>
|
||||
|
||||
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
|
||||
|
||||
<a href="Section_modify.html" class="btn btn-neutral float-right" title="10. Modifying & extending LAMMPS" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
|
||||
|
||||
|
||||
<a href="Section_perf.html" class="btn btn-neutral" title="8. Performance & scalability" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<hr/>
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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.
|
||||
|
|
|
|||
|
|
@ -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
|
||||
-----------------------
|
||||
Use of *special* 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
|
||||
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.
|
||||
|
||||
|
||||
----------
|
||||
|
|
|
|||
|
|
@ -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 & 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 & 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>
|
||||
|
|
|
|||
|
|
@ -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 & 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 & 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>
|
||||
|
|
|
|||
|
|
@ -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 & 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 & 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-INTEL package</a><ul>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -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 & 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 & 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.KOKKOS package</a><ul>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -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 & 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 & 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-OMP package</a><ul>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -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 & 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 & 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.OPT package</a><ul>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,20 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style charmm command</a></li>
|
||||
<li><a class="reference internal" href="#angle-style-charmm-kk-command">angle_style charmm/kk command</a></li>
|
||||
<li><a class="reference internal" href="#angle-style-charmm-omp-command">angle_style charmm/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style class2 command</a></li>
|
||||
<li><a class="reference internal" href="#angle-style-class2-omp-command">angle_style class2/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_coeff command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style cosine command</a></li>
|
||||
<li><a class="reference internal" href="#angle-style-cosine-omp-command">angle_style cosine/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style cosine/delta command</a></li>
|
||||
<li><a class="reference internal" href="#angle-style-cosine-delta-omp-command">angle_style cosine/delta/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style cosine/periodic command</a></li>
|
||||
<li><a class="reference internal" href="#angle-style-cosine-periodic-omp-command">angle_style cosine/periodic/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style cosine/shift command</a></li>
|
||||
<li><a class="reference internal" href="#angle-style-cosine-shift-omp-command">angle_style cosine/shift/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style cosine/shift/exp command</a></li>
|
||||
<li><a class="reference internal" href="#angle-style-cosine-shift-exp-omp-command">angle_style cosine/shift/exp/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style cosine/squared command</a></li>
|
||||
<li><a class="reference internal" href="#angle-style-cosine-squared-omp-command">angle_style cosine/squared/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style dipole command</a></li>
|
||||
<li><a class="reference internal" href="#angle-style-dipole-omp-command">angle_style dipole/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style fourier command</a></li>
|
||||
<li><a class="reference internal" href="#angle-style-fourier-omp-command">angle_style fourier/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style fourier/simple command</a></li>
|
||||
<li><a class="reference internal" href="#angle-style-fourier-simple-omp-command">angle_style fourier/simple/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,20 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style harmonic command</a></li>
|
||||
<li><a class="reference internal" href="#angle-style-harmonic-kk-command">angle_style harmonic/kk command</a></li>
|
||||
<li><a class="reference internal" href="#angle-style-harmonic-omp-command">angle_style harmonic/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style hybrid command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,17 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style none command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style quartic command</a></li>
|
||||
<li><a class="reference internal" href="#angle-style-quartic-omp-command">angle_style quartic/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style sdk command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
<li><a class="reference internal" href="#default">Default</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">angle_style table command</a></li>
|
||||
<li><a class="reference internal" href="#angle-style-table-omp-command">angle_style table/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">atom_modify command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#default">Default</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">atom_style command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
<li><a class="reference internal" href="#default">Default</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">balance command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
@ -264,7 +260,7 @@ the processor that owns them. The leftmost diagram is the default
|
|||
partitioning of the simulation box across processors (one sub-box for
|
||||
each of 16 processors); the middle diagram is after a “grid” method
|
||||
has been applied.</p>
|
||||
<a data-lightbox="group-33581b25-ff7a-4993-af10-3eb635606c51"
|
||||
<a data-lightbox="group-022505f1-dc20-4757-8079-1c46a98561c1"
|
||||
href="_images/balance_uniform.jpg"
|
||||
class=""
|
||||
title=""
|
||||
|
|
@ -274,7 +270,7 @@ has been applied.</p>
|
|||
width="25%"
|
||||
height="auto"
|
||||
alt=""/>
|
||||
</a><a data-lightbox="group-0707698a-5184-4a24-a0b3-55e008c10da2"
|
||||
</a><a data-lightbox="group-33c706ca-ec21-410d-8dea-549388d6ccd9"
|
||||
href="_images/balance_nonuniform.jpg"
|
||||
class=""
|
||||
title=""
|
||||
|
|
@ -284,7 +280,7 @@ has been applied.</p>
|
|||
width="25%"
|
||||
height="auto"
|
||||
alt=""/>
|
||||
</a><a data-lightbox="group-153ac620-167c-4887-8859-4d5f616526fe"
|
||||
</a><a data-lightbox="group-eb041c99-4215-4b9b-8dbd-437cfbda53dd"
|
||||
href="_images/balance_rcb.jpg"
|
||||
class=""
|
||||
title=""
|
||||
|
|
|
|||
|
|
@ -71,22 +71,11 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">Body particles</a></li>
|
||||
</ul>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">bond_style class2 command</a></li>
|
||||
<li><a class="reference internal" href="#bond-style-class2-omp-command">bond_style class2/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">bond_coeff command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,20 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">bond_style fene command</a></li>
|
||||
<li><a class="reference internal" href="#bond-style-fene-kk-command">bond_style fene/kk command</a></li>
|
||||
<li><a class="reference internal" href="#bond-style-fene-omp-command">bond_style fene/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">bond_style fene/expand command</a></li>
|
||||
<li><a class="reference internal" href="#bond-style-fene-expand-omp-command">bond_style fene/expand/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,20 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">bond_style harmonic command</a></li>
|
||||
<li><a class="reference internal" href="#bond-style-harmonic-kk-command">bond_style harmonic/kk command</a></li>
|
||||
<li><a class="reference internal" href="#bond-style-harmonic-omp-command">bond_style harmonic/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">bond_style harmonic/shift command</a></li>
|
||||
<li><a class="reference internal" href="#bond-style-harmonic-shift-omp-command">bond_style harmonic/shift/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">bond_style harmonic/shift/cut command</a></li>
|
||||
<li><a class="reference internal" href="#bond-style-harmonic-shift-cut-omp-command">bond_style harmonic/shift/cut/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">bond_style hybrid command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">bond_style morse command</a></li>
|
||||
<li><a class="reference internal" href="#bond-style-morse-omp-command">bond_style morse/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,17 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">bond_style none command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">bond_style nonlinear command</a></li>
|
||||
<li><a class="reference internal" href="#bond-style-nonlinear-omp-command">bond_style nonlinear/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">bond_style quartic command</a></li>
|
||||
<li><a class="reference internal" href="#bond-style-quartic-omp-command">bond_style quartic/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">bond_style command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
<li><a class="reference internal" href="#default">Default</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">bond_style table command</a></li>
|
||||
<li><a class="reference internal" href="#bond-style-table-omp-command">bond_style table/omp command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">boundary command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
<li><a class="reference internal" href="#default">Default</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
26
doc/box.html
26
doc/box.html
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">box command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#default">Default</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">change_box command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
<li><a class="reference internal" href="#default">Default</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,17 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">clear command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">comm_modify command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
<li><a class="reference internal" href="#default">Default</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
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|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">comm_style command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
<li><a class="reference internal" href="#default">Default</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute ackland/atom command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute angle/local command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute angmom/chunk command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute basal/atom command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute body/local command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute bond/local command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute centro/atom command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
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|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute chunk/atom command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
<li><a class="reference internal" href="#default">Default</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
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|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute cluster/atom command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute cna/atom command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute com command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute com/chunk command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute contact/atom command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute coord/atom command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute damage/atom command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
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|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute dihedral/local command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute dilatation/atom command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute displace/atom command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,17 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute erotate/asphere command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute erotate/rigid command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute erotate/sphere command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute erotate/sphere/atom command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute event/displace command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,19 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute fep command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
<li><a class="reference internal" href="#default">Default</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute group/group command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#default">Default</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute gyration command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,17 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute gyration/chunk command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute heat/flux command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute improper/local command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute inertia/chunk command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute ke command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -71,22 +71,18 @@
|
|||
|
||||
|
||||
|
||||
<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 & 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 & 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="#">compute ke/atom command</a><ul>
|
||||
<li><a class="reference internal" href="#syntax">Syntax</a></li>
|
||||
<li><a class="reference internal" href="#examples">Examples</a></li>
|
||||
<li><a class="reference internal" href="#description">Description</a></li>
|
||||
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
||||
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
|
||||
</ul>
|
||||
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
|
|
|
|||
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