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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>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<H1></H1><div class="section" id="lammps-documentation">
<h1>LAMMPS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline"></a></h1>
<div class="section" id="jul-2015-version">
<h2>27 Jul 2015 version<a class="headerlink" href="#jul-2015-version" title="Permalink to this headline"></a></h2>
</div>
<div class="section" id="version-info">
<h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline"></a></h2>
<p>The LAMMPS &#8220;version&#8221; is the date when it was released, such as 1 May
<HR>
<H1></H1>
<CENTER><H3>LAMMPS-ICMS Documentation
</H3></CENTER>
<CENTER><H4>4 Aug 2015 version
</H4></CENTER>
<H4>Version info:
</H4>
<P>The LAMMPS "version" is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on <a class="reference external" href="http://lammps.sandia.gov/bug.html">this page of the WWW site</a>. Each dated copy of LAMMPS contains all the
feature, we release it immediately, and post a notice on <A HREF = "http://lammps.sandia.gov/bug.html">this page of
the WWW site</A>. Each dated copy of LAMMPS contains all the
features and bug-fixes up to and including that version date. The
version date is printed to the screen and logfile every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page).</p>
the first page of the manual (this page).
</P>
<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.
<p>LAMMPS-ICMS is an experimental variant of LAMMPS with additional
features made available for testing before they will be submitted
@ -159,296 +55,437 @@ development will be halted except for important bugfixes until
all features of LAMMPS-ICMS fully compatible with the upstream
version or replaced by alternate implementations.
</p>
<LI>If you browse the HTML doc pages included in your tarball, they
describe the version you have.
<ul class="simple">
<li>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.</li>
<li>If you browse the HTML doc pages included in your tarball, they
describe the version you have.</li>
<li>The <a class="reference external" href="Manual.pdf">PDF file</a> on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don&#8217;t want
it to be part of every patch.</li>
<li>There is also a <a class="reference external" href="Developer.pdf">Developer.pdf</a> file in the doc
<LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of every patch.
<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS.</li>
</ul>
<p>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.</p>
<p>LAMMPS is a classical molecular dynamics simulation code designed to
LAMMPS.
</UL>
<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
</P>
<P>LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).</p>
<p>The primary developers of LAMMPS are <a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, Aidan
under the terms of the GNU Public License (GPL).
</P>
<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Aidan
Thompson, and Paul Crozier who can be contacted at
sjplimp,athomps,pscrozi at sandia.gov. The <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> at
<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a> has more information about the code and its
uses.</p>
<hr class="docutils" />
<p>The LAMMPS documentation is organized into the following sections. If
sjplimp,athomps,pscrozi at sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
http://lammps.sandia.gov has more information about the code and its
uses.
</P>
<HR>
<P>The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation.</p>
<p>Once you are familiar with LAMMPS, you may want to bookmark <a class="reference internal" href="Section_commands.html#comm"><span>this page</span></a> at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.</p>
<p><a class="reference external" href="Manual.pdf">PDF file</a> of the entire manual, generated by
<a class="reference external" href="http://freecode.com/projects/htmldoc">htmldoc</a></p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-features">1.2. LAMMPS features</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-non-features">1.3. LAMMPS non-features</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#open-source-distribution">1.4. Open source distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#what-s-in-the-lammps-distribution">2.1. What&#8217;s in the LAMMPS distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps">2.2. Making LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps-with-optional-packages">2.3. Making LAMMPS with optional packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-via-the-make-py-script">2.4. Building LAMMPS via the Make.py script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-as-a-library">2.5. Building LAMMPS as a library</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#running-lammps">2.6. Running LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#command-line-options">2.7. Command-line options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#lammps-screen-output">2.8. LAMMPS screen output</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#tips-for-users-of-previous-lammps-versions">2.9. Tips for users of previous LAMMPS versions</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#lammps-input-script">3.1. LAMMPS input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#parsing-rules">3.2. Parsing rules</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#input-script-structure">3.3. Input script structure</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#commands-listed-by-category">3.4. Commands listed by category</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#individual-commands">3.5. Individual commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#fix-styles">3.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#compute-styles">3.7. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#pair-style-potentials">3.8. Pair_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#bond-style-potentials">3.9. Bond_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#angle-style-potentials">3.10. Angle_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#improper-style-potentials">3.12. Improper_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_commands.html#kspace-solvers">3.13. Kspace solvers</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#standard-packages">4.1. Standard packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.2. User packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-atc-package">4.3. USER-ATC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-awpmd-package">4.4. USER-AWPMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cg-cmm-package">4.5. USER-CG-CMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.6. USER-COLVARS package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.7. USER-CUDA package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.8. USER-DIFFRACTION package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.9. USER-DRUDE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.10. USER-EFF package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.11. USER-FEP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.12. USER-INTEL package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.13. USER-LB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.14. USER-MISC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.15. USER-MOLFILE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.16. USER-OMP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.17. USER-PHONON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.18. USER-QMMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.19. USER-QTB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.20. USER-REAXC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.21. USER-SPH package</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#measuring-performance">5.1. Measuring performance</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#general-strategies">5.2. General strategies</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#restarting-a-simulation">6.1. Restarting a simulation</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#d-simulations">6.2. 2d simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#charmm-amber-and-dreiding-force-fields">6.3. CHARMM, AMBER, and DREIDING force fields</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#running-multiple-simulations-from-one-input-script">6.4. Running multiple simulations from one input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#granular-models">6.6. Granular models</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip3p-water-model">6.7. TIP3P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip4p-water-model">6.8. TIP4P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#spc-water-model">6.9. SPC water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#nemd-simulations">6.13. NEMD simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#finite-size-spherical-and-aspherical-particles">6.14. Finite-size spherical and aspherical particles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#output-from-lammps-thermo-dumps-computes-fixes-variables">6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#walls">6.17. Walls</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#elastic-constants">6.18. Elastic constants</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-viscosity">6.21. Calculating viscosity</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#using-chunks-to-calculate-system-properties">6.23. Using chunks to calculate system properties</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#setting-parameters-for-the-kspace-style-pppm-disp-command">6.24. Setting parameters for the <code class="docutils literal"><span class="pre">kspace_style</span> <span class="pre">pppm/disp</span></code> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#polarizable-models">6.25. Polarizable models</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#binary2txt-tool">9.2. binary2txt tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ch2lmp-tool">9.3. ch2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#chain-tool">9.4. chain tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#colvars-tools">9.5. colvars tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#createatoms-tool">9.6. createatoms tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#data2xmovie-tool">9.7. data2xmovie tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-database-tool">9.8. eam database tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-generate-tool">9.9. eam generate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eff-tool">9.10. eff tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#fep-tool">9.12. fep tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#i-pi-tool">9.13. i-pi tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ipp-tool">9.14. ipp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#kate-tool">9.15. kate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2arc-tool">9.16. lmp2arc tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#matlab-tool">9.19. matlab tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#micelle2d-tool">9.20. micelle2d tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#moltemplate-tool">9.21. moltemplate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#msi2lmp-tool">9.22. msi2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#phonon-tool">9.23. phonon tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#python-tool">9.26. python tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#reax-tool">9.27. reax tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#restart2data-tool">9.28. restart2data tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#vim-tool">9.29. vim tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmgrace-tool">9.30. xmgrace tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmovie-tool">9.31. xmovie tool</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#atom-styles">10.1. Atom styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#compute-styles">10.3. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-styles">10.4. Dump styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-custom-output-options">10.5. Dump custom output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#fix-styles">10.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#input-script-commands">10.7. Input script commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#kspace-computations">10.8. Kspace computations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#minimization-styles">10.9. Minimization styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#region-styles">10.11. Region styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#body-styles">10.12. Body styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#variable-options">10.14. Variable options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#extending-python-with-mpi-to-run-in-parallel">11.5. Extending Python with MPI to run in parallel</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#common-problems">12.1. Common problems</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#reporting-bugs">12.2. Reporting bugs</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error-warning-messages">12.3. Error &amp; warning messages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error">12.4. Errors:</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#warnings">12.5. Warnings:</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#coming-attractions">13.1. Coming attractions</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#past-versions">13.2. Past versions</a></li>
</ul>
</li>
</ul>
</div>
</div>
</div>
<div class="section" id="indices-and-tables">
<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline"></a></h1>
<ul class="simple">
<li><a class="reference internal" href="genindex.html"><span>Index</span></a></li>
<li><a class="reference internal" href="search.html"><span>Search Page</span></a></li>
</ul>
</BODY></div>
we can improve the LAMMPS documentation.
</P>
<P>Once you are familiar with LAMMPS, you may want to bookmark <A HREF = "Section_commands.html#comm">this
page</A> at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.
</P>
<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
<A HREF = "http://freecode.com/projects/htmldoc">htmldoc</A>
</P>
<P><!-- RST
</P>
<P>.. toctree::
:maxdepth: 2
:numbered: // comment
</P>
<P> Section_intro
Section_start
Section_commands
Section_packages
Section_accelerate
Section_howto
Section_example
Section_perf
Section_tools
Section_modify
Section_python
Section_errors
Section_history
</P>
<P>Indices and tables
==================
</P>
<P>* :ref:`genindex` // comment
* :ref:`search` // comment
</P>
<P>END_RST -->
</P>
<OL><LI><!-- HTML_ONLY -->
<A HREF = "Section_intro.html">Introduction</A>
<UL> 1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A>
<BR>
1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A>
<BR>
1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A>
<BR>
1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A>
<BR>
1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A>
<BR></UL>
<LI><A HREF = "Section_start.html">Getting started</A>
<UL> 2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A>
<BR>
2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A>
<BR>
2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A>
<BR>
2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS via the Make.py script</A>
<BR>
2.5 <A HREF = "Section_start.html#start_5">Building LAMMPS as a library</A>
<BR>
2.6 <A HREF = "Section_start.html#start_6">Running LAMMPS</A>
<BR>
2.7 <A HREF = "Section_start.html#start_7">Command-line options</A>
<BR>
2.8 <A HREF = "Section_start.html#start_8">Screen output</A>
<BR>
2.9 <A HREF = "Section_start.html#start_9">Tips for users of previous versions</A>
<BR></UL>
<LI><A HREF = "Section_commands.html">Commands</A>
<UL> 3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A>
<BR>
3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A>
<BR>
3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A>
<BR>
3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A>
<BR>
3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A>
<BR></UL>
<LI><A HREF = "Section_packages.html">Packages</A>
<UL> 4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A>
<BR>
4.2 <A HREF = "Section_packages.html#pkg_2">User packages</A>
<BR></UL>
<LI><A HREF = "Section_accelerate.html">Accelerating LAMMPS performance</A>
<UL> 5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A>
<BR>
5.2 <A HREF = "Section_accelerate.html#acc_2">Algorithms and code options to boost performace</A>
<BR>
5.3 <A HREF = "Section_accelerate.html#acc_3">Accelerator packages with optimized styles</A>
<BR>
<UL> 5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A>
<BR>
5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A>
<BR>
5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A>
<BR>
5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A>
<BR>
5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A>
<BR>
5.3.6 <A HREF = "accelerate_opt.html">OPT package</A>
<BR></UL>
5.4 <A HREF = "Section_accelerate.html#acc_4">Comparison of various accelerator packages</A>
<BR></UL>
<LI><A HREF = "Section_howto.html">How-to discussions</A>
<UL> 6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A>
<BR>
6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A>
<BR>
6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A>
<BR>
6.4 <A HREF = "Section_howto.html#howto_4">Running multiple simulations from one input script</A>
<BR>
6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A>
<BR>
6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A>
<BR>
6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A>
<BR>
6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A>
<BR>
6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A>
<BR>
6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A>
<BR>
6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A>
<BR>
6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A>
<BR>
6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A>
<BR>
6.14 <A HREF = "Section_howto.html#howto_14">Finite-size spherical and aspherical particles</A>
<BR>
6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A>
<BR>
6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A>
<BR>
6.17 <A HREF = "Section_howto.html#howto_17">Walls</A>
<BR>
6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A>
<BR>
6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A>
<BR>
6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A>
<BR>
6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A>
<BR>
6.22 <A HREF = "Section_howto.html#howto_22">Calculating a diffusion coefficient</A>
<BR>
6.23 <A HREF = "Section_howto.html#howto_23">Using chunks to calculate system properties</A>
<BR>
6.24 <A HREF = "Section_howto.html#howto_24">Setting parameters for pppm/disp</A>
<BR>
6.25 <A HREF = "Section_howto.html#howto_25">Polarizable models</A>
<BR>
6.26 <A HREF = "Section_howto.html#howto_26">Adiabatic core/shell model</A>
<BR>
6.27 <A HREF = "Section_howto.html#howto_27">Drude induced dipoles</A>
<BR></UL>
<LI><A HREF = "Section_example.html">Example problems</A>
<LI><A HREF = "Section_perf.html">Performance & scalability</A>
<LI><A HREF = "Section_tools.html">Additional tools</A>
<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A>
<UL> 10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A>
<BR>
10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A>
<BR>
10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A>
<BR>
10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A>
<BR>
10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A>
<BR>
10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A>
<BR>
10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A>
<BR>
10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A>
<BR>
10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A>
<BR>
10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A>
<BR>
10.11 <A HREF = "Section_modify.html#mod_11">Region styles</A>
<BR>
10.12 <A HREF = "Section_modify.html#mod_12">Body styles</A>
<BR>
10.13 <A HREF = "Section_modify.html#mod_13">Thermodynamic output options</A>
<BR>
10.14 <A HREF = "Section_modify.html#mod_14">Variable options</A>
<BR>
10.15 <A HREF = "Section_modify.html#mod_15">Submitting new features for inclusion in LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_python.html">Python interface</A>
<UL> 11.1 <A HREF = "Section_python.html#py_1">Overview of running LAMMPS from Python</A>
<BR>
11.2 <A HREF = "Section_python.html#py_2">Overview of using Python from a LAMMPS script</A>
<BR>
11.3 <A HREF = "Section_python.html#py_3">Building LAMMPS as a shared library</A>
<BR>
11.4 <A HREF = "Section_python.html#py_4">Installing the Python wrapper into Python</A>
<BR>
11.5 <A HREF = "Section_python.html#py_5">Extending Python with MPI to run in parallel</A>
<BR>
11.6 <A HREF = "Section_python.html#py_6">Testing the Python-LAMMPS interface</A>
<BR>
11.7 <A HREF = "py_7">Using LAMMPS from Python</A>
<BR>
11.8 <A HREF = "py_8">Example Python scripts that use LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_errors.html">Errors</A>
<UL> 12.1 <A HREF = "Section_errors.html#err_1">Common problems</A>
<BR>
12.2 <A HREF = "Section_errors.html#err_2">Reporting bugs</A>
<BR>
12.3 <A HREF = "Section_errors.html#err_3">Error & warning messages</A>
<BR></UL>
<LI><A HREF = "Section_history.html">Future and history</A>
<UL> 13.1 <A HREF = "Section_history.html#hist_1">Coming attractions</A>
<BR>
13.2 <A HREF = "Section_history.html#hist_2">Past versions</A>
<BR></UL>
</OL>
</div>
</div>
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10
doc/Manual.txt
View File

@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="27 Jul 2015 version">
<META NAME="docnumber" CONTENT="4 Aug 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<H1></H1>
LAMMPS-ICMS Documentation :c,h3
27 Jul 2015 version :c,h4
4 Aug 2015 version :c,h4
Version info: :h4
@ -100,7 +100,7 @@ it gives quick access to documentation for all LAMMPS commands.
.. toctree::
:maxdepth: 2
:numbered:
:numbered: // comment
Section_intro
Section_start
@ -120,8 +120,8 @@ it gives quick access to documentation for all LAMMPS commands.
Indices and tables
==================
* :ref:`genindex`
* :ref:`search`
* :ref:`genindex` // comment
* :ref:`search` // comment
END_RST -->

79
doc/Section_commands.html
View File

@ -758,12 +758,12 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
<a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="18%" />
<col width="15%" />
<col width="15%" />
<col width="20%" />
<col width="14%" />
<col width="22%" />
<col width="14%" />
<col width="17%" />
<col width="17%" />
<col width="18%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="fix_adapt_fep.html"><em>adapt/fep</em></a></td>
@ -806,14 +806,21 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
<td><a class="reference internal" href="fix_reaxc_species.html"><em>reax/c/species</em></a></td>
<td><a class="reference internal" href="fix_saed_vtk.html"><em>saed/vtk</em></a></td>
<td><a class="reference internal" href="fix_smd.html"><em>smd</em></a></td>
<td><a class="reference internal" href="fix_temp_rescale_eff.html"><em>temp/rescale/eff</em></a></td>
<td><a class="reference internal" href="fix_smd_adjust_dt.html"><em>smd/adjust/dt</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_ti_rs.html"><em>ti/rs</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="fix_smd_integrate_tlsph.html"><em>smd/integrate/tlsph</em></a></td>
<td><a class="reference internal" href="fix_smd_integrate_ulsph.html"><em>smd/integrate/ulsph</em></a></td>
<td><a class="reference internal" href="fix_smd_move_triangulated_surface.html"><em>smd/move/triangulated/surface</em></a></td>
<td><a class="reference internal" href="fix_smd_setvel.html"><em>smd/setvel</em></a></td>
<td><a class="reference internal" href="fix_smd_tlsph_reference_configuration.html"><em>smd/tlsph/reference/configuration</em></a></td>
<td><a class="reference internal" href="fix_smd_wall_surface.html"><em>smd/wall/surface</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_temp_rescale_eff.html"><em>temp/rescale/eff</em></a></td>
<td><a class="reference internal" href="fix_ti_rs.html"><em>ti/rs</em></a></td>
<td><a class="reference internal" href="fix_ti_spring.html"><em>ti/spring</em></a></td>
<td><a class="reference internal" href="fix_ttm.html"><em>ttm/mod</em></a></td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
</tr>
</tbody>
</table>
@ -920,12 +927,12 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
used if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="20%" />
<col width="17%" />
<col width="11%" />
<col width="16%" />
<col width="15%" />
<col width="18%" />
<col width="17%" />
<col width="20%" />
<col width="15%" />
<col width="19%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="compute_ackland_atom.html"><em>ackland/atom</em></a></td>
@ -938,16 +945,37 @@ used if <a class="reference internal" href="Section_start.html#start-3"><span>LA
<tr class="row-even"><td><a class="reference internal" href="compute_meso_rho_atom.html"><em>meso_rho/atom</em></a></td>
<td><a class="reference internal" href="compute_meso_t_atom.html"><em>meso_t/atom</em></a></td>
<td><a class="reference internal" href="compute_saed.html"><em>saed</em></a></td>
<td><a class="reference internal" href="compute_temp_drude.html"><em>temp/drude</em></a></td>
<td><a class="reference internal" href="compute_temp_eff.html"><em>temp/eff</em></a></td>
<td><a class="reference internal" href="compute_temp_deform_eff.html"><em>temp/deform/eff</em></a></td>
<td><a class="reference internal" href="compute_smd_contact_radius.html"><em>smd/contact/radius</em></a></td>
<td><a class="reference internal" href="compute_smd_damage.html"><em>smd/damage</em></a></td>
<td><a class="reference internal" href="compute_smd_hourglass_error.html"><em>smd/hourglass/error</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_temp_region_eff.html"><em>temp/region/eff</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="compute_smd_internal_energy.html"><em>smd/internal/energy</em></a></td>
<td><a class="reference internal" href="compute_smd_plastic_strain.html"><em>smd/plastic/strain</em></a></td>
<td><a class="reference internal" href="compute_smd_plastic_strain_rate.html"><em>smd/plastic/strain/rate</em></a></td>
<td><a class="reference internal" href="compute_smd_rho.html"><em>smd/rho</em></a></td>
<td><a class="reference internal" href="compute_smd_tlsph_defgrad.html"><em>smd/tlsph/defgrad</em></a></td>
<td><a class="reference internal" href="compute_smd_tlsph_dt.html"><em>smd/tlsph/dt</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_smd_tlsph_num_neighs.html"><em>smd/tlsph/num/neighs</em></a></td>
<td><a class="reference internal" href="compute_smd_tlsph_shape.html"><em>smd/tlsph/shape</em></a></td>
<td><a class="reference internal" href="compute_smd_tlsph_strain.html"><em>smd/tlsph/strain</em></a></td>
<td><a class="reference internal" href="compute_smd_tlsph_strain_rate.html"><em>smd/tlsph/strain/rate</em></a></td>
<td><a class="reference internal" href="compute_smd_tlsph_stress.html"><em>smd/tlsph/stress</em></a></td>
<td><a class="reference internal" href="compute_smd_triangle_mesh_vertices.html"><em>smd/triangle/mesh/vertices</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_smd_ulsph_num_neighs.html"><em>smd/ulsph/num/neighs</em></a></td>
<td><a class="reference internal" href="compute_smd_ulsph_strain.html"><em>smd/ulsph/strain</em></a></td>
<td><code class="xref doc docutils literal"><span class="pre">smd/ulsph/strain/rate</span></code></td>
<td><code class="xref doc docutils literal"><span class="pre">smd/ulpsh/stress</span></code></td>
<td><a class="reference internal" href="compute_smd_vol.html"><em>smd/vol</em></a></td>
<td><a class="reference internal" href="compute_temp_drude.html"><em>temp/drude</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_temp_eff.html"><em>temp/eff</em></a></td>
<td><a class="reference internal" href="compute_temp_deform_eff.html"><em>temp/deform/eff</em></a></td>
<td><a class="reference internal" href="compute_temp_region_eff.html"><em>temp/region/eff</em></a></td>
<td><a class="reference internal" href="compute_temp_rotate.html"><em>temp/rotate</em></a></td>
<td><a class="reference internal" href="compute_xrd.html"><em>xrd</em></a></td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
</tr>
</tbody>
</table>
@ -1110,10 +1138,10 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="27%" />
<col width="24%" />
<col width="24%" />
<col width="25%" />
<col width="29%" />
<col width="22%" />
<col width="24%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="pair_awpmd.html"><em>awpmd/cut</em></a></td>
@ -1144,19 +1172,24 @@ if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS
<tr class="row-even"><td><a class="reference internal" href="pair_meam_sw_spline.html"><em>meam/sw/spline</em></a></td>
<td><a class="reference internal" href="pair_quip.html"><em>quip</em></a></td>
<td><a class="reference internal" href="pair_reax_c.html"><em>reax/c</em></a></td>
<td><a class="reference internal" href="pair_smd_hertz.html"><em>smd/hertz</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_smd_tlsph.html"><em>smd/tlsph</em></a></td>
<td><a class="reference internal" href="pair_smd_triangulated_surface.html"><em>smd/triangulated/surface</em></a></td>
<td><a class="reference internal" href="pair_smd_ulsph.html"><em>smd/ulsph</em></a></td>
<td><a class="reference internal" href="pair_sph_heatconduction.html"><em>sph/heatconduction</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_sph_idealgas.html"><em>sph/idealgas</em></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_sph_idealgas.html"><em>sph/idealgas</em></a></td>
<td><a class="reference internal" href="pair_sph_lj.html"><em>sph/lj</em></a></td>
<td><a class="reference internal" href="pair_sph_rhosum.html"><em>sph/rhosum</em></a></td>
<td><a class="reference internal" href="pair_sph_taitwater.html"><em>sph/taitwater</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_sph_taitwater_morris.html"><em>sph/taitwater/morris</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="pair_sph_taitwater_morris.html"><em>sph/taitwater/morris</em></a></td>
<td><a class="reference internal" href="pair_srp.html"><em>srp</em></a></td>
<td><a class="reference internal" href="pair_tersoff.html"><em>tersoff/table (o)</em></a></td>
<td><a class="reference internal" href="pair_thole.html"><em>thole</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_soft.html"><em>tip4p/long/soft (o)</em></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_lj_soft.html"><em>tip4p/long/soft (o)</em></a></td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>

31
doc/Section_commands.txt
View File

@ -633,6 +633,13 @@ package"_Section_start.html#start_3.
"reax/c/species"_fix_reaxc_species.html,
"saed/vtk"_fix_saed_vtk.html,
"smd"_fix_smd.html,
"smd/adjust/dt"_fix_smd_adjust_dt.html,
"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html,
"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
"smd/setvel"_fix_smd_setvel.html,
"smd/tlsph/reference/configuration"_fix_smd_tlsph_reference_configuration.html,
"smd/wall/surface"_fix_smd_wall_surface.html,
"temp/rescale/eff"_fix_temp_rescale_eff.html,
"ti/rs"_fix_ti_rs.html,
"ti/spring"_fix_ti_spring.html,
@ -730,6 +737,26 @@ package"_Section_start.html#start_3.
"meso_rho/atom"_compute_meso_rho_atom.html,
"meso_t/atom"_compute_meso_t_atom.html,
"saed"_compute_saed.html,
"smd/contact/radius"_compute_smd_contact_radius.html,
"smd/damage"_compute_smd_damage.html,
"smd/hourglass/error"_compute_smd_hourglass_error.html,
"smd/internal/energy"_compute_smd_internal_energy.html,
"smd/plastic/strain"_compute_smd_plastic_strain.html,
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html,
"smd/rho"_compute_smd_rho.html,
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html,
"smd/tlsph/dt"_compute_smd_tlsph_dt.html,
"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html,
"smd/tlsph/shape"_compute_smd_tlsph_shape.html,
"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html,
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain/rate.html,
"smd/ulpsh/stress"_compute_smd_ulpsh_stress.html,
"smd/vol"_compute_smd_vol.html,
"temp/drude"_compute_temp_drude.html,
"temp/eff"_compute_temp_eff.html,
"temp/deform/eff"_compute_temp_deform_eff.html,
@ -884,6 +911,10 @@ package"_Section_start.html#start_3.
"meam/sw/spline"_pair_meam_sw_spline.html,
"quip"_pair_quip.html,
"reax/c"_pair_reax_c.html,
"smd/hertz"_pair_smd_hertz.html,
"smd/tlsph"_pair_smd_tlsph.html,
"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
"smd/ulsph"_pair_smd_ulsph.html,
"sph/heatconduction"_pair_sph_heatconduction.html,
"sph/idealgas"_pair_sph_idealgas.html,
"sph/lj"_pair_sph_lj.html,

39
doc/Section_packages.html
View File

@ -98,7 +98,8 @@
<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>
<li class="toctree-l2"><a class="reference internal" href="#user-smd-package">4.21. USER-SMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="#user-sph-package">4.22. 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>
@ -828,7 +829,21 @@ on how to build LAMMPS with both kinds of auxiliary libraries.</p>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-SPH</td>
<tr class="row-odd"><td>USER-SMD</td>
<td>smoothed Mach dynamics</td>
<td>Georg Ganzenmuller (EMI)</td>
<td><a class="reference external" href="USER/smd/SMD_user_guide.pdf">userguide.pdf</a></td>
<td>USER/smd</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-SPH</td>
<td>smoothed particle hydrodynamics</td>
<td>Georg Ganzenmuller (EMI)</td>
<td><a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">userguide.pdf</a></td>
@ -839,7 +854,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries.</p>
</ul>
</td>
</tr>
<tr class="row-even"><td>&nbsp;</td>
<tr class="row-odd"><td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
@ -881,7 +896,7 @@ See the src/package/Makefile.lammps file for info on where to download
the library. <a class="reference internal" href="Section_start.html#start-3-3"><span>Section start</span></a> of the
manual also gives details on how to build LAMMPS with both kinds of
auxiliary libraries.</p>
<p>More details on each package, from the USER-<a href="#id1"><span class="problematic" id="id2">*</span></a>/README file is given
<p>More details on each package, from the USER-<a href="#id2"><span class="problematic" id="id3">*</span></a>/README file is given
below.</p>
</div>
<hr class="docutils" />
@ -1115,7 +1130,7 @@ Western Ontario. Contact them directly if you have questions.</p>
<h2>4.14. 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>
pair of files (<a href="#id4"><span class="problematic" id="id5">*</span></a>.cpp and <a href="#id6"><span class="problematic" id="id7">*</span></a>.h).</p>
<p>More information about each feature can be found by reading its doc
page in the LAMMPS doc directory. The doc page which lists all LAMMPS
input script commands is as follows:</p>
@ -1237,8 +1252,20 @@ Aidan Thompson at Sandia (athomps at sandia.gov), if you have
questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-smd-package">
<h2>4.21. USER-SMD package<a class="headerlink" href="#user-smd-package" title="Permalink to this headline"></a></h2>
<p>This package implements smoothed Mach dynamics (SMD) in
LAMMPS. Currently, the package has the following features:</p>
<p>???</p>
<p>See the file doc/USER/smd/SPH_user_guide.pdf to get started.</p>
<p>There are example scripts for using this package in examples/USER/smd.</p>
<p>The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.</p>
</div>
<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>4.22. 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">

17
doc/Section_packages.txt
View File

@ -132,6 +132,7 @@ USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html,
USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix_qbmsst"_fix_qbmsst.html, qtb, -, -
USER-QUIP, QUIP/libatoms interface, Albert Bartok-Partay (U Cambridge), "pair_style quip"_pair_quip.html, USER/quip, -, lib/quip
USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, -
USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_USER/smd/SMD_user_guide.pdf, USER/smd, -, -
USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_USER/sph/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
:tb(ea=c)
@ -626,6 +627,22 @@ questions.
:line
USER-SMD package :h4
This package implements smoothed Mach dynamics (SMD) in
LAMMPS. Currently, the package has the following features:
???
See the file doc/USER/smd/SPH_user_guide.pdf to get started.
There are example scripts for using this package in examples/USER/smd.
The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.
USER-SPH package :h4
This package implements smoothed particle hydrodynamics (SPH) in

BIN
doc/USER/smd/SMD_user_guide.pdf Normal file
View File

Binary file not shown.

20
doc/atom_style.html
View File

@ -132,7 +132,7 @@
</pre></div>
</div>
<ul class="simple">
<li>style = <em>angle</em> or <em>atomic</em> or <em>body</em> or <em>bond</em> or <em>charge</em> or <em>dipole</em> or <em>electron</em> or <em>ellipsoid</em> or <em>full</em> or <em>line</em> or <em>meso</em> or <em>molecular</em> or <em>peri</em> or <em>sphere</em> or <em>tri</em> or <em>template</em> or <em>hybrid</em></li>
<li>style = <em>angle</em> or <em>atomic</em> or <em>body</em> or <em>bond</em> or <em>charge</em> or <em>dipole</em> or <em>electron</em> or <em>ellipsoid</em> or <em>full</em> or <em>line</em> or <em>meso</em> or <em>molecular</em> or <em>peri</em> or <em>smd</em> or <em>sphere</em> or <em>tri</em> or <em>template</em> or <em>hybrid</em></li>
</ul>
<pre class="literal-block">
args = none for any style except <em>body</em> and <em>hybrid</em>
@ -241,19 +241,23 @@ quantities.</p>
<td>mass, volume</td>
<td>mesocopic Peridynamic models</td>
</tr>
<tr class="row-even"><td><em>sphere</em></td>
<tr class="row-even"><td><em>smd</em></td>
<td>volume, kernel diameter, contact radius, mass</td>
<td>solid and fluid SPH particles</td>
</tr>
<tr class="row-odd"><td><em>sphere</em></td>
<td>diameter, mass, angular velocity</td>
<td>granular models</td>
</tr>
<tr class="row-odd"><td><em>template</em></td>
<tr class="row-even"><td><em>template</em></td>
<td>template index, template atom</td>
<td>small molecules with fixed topology</td>
</tr>
<tr class="row-even"><td><em>tri</em></td>
<tr class="row-odd"><td><em>tri</em></td>
<td>corner points, angular momentum</td>
<td>rigid bodies</td>
</tr>
<tr class="row-odd"><td><em>wavepacket</em></td>
<tr class="row-even"><td><em>wavepacket</em></td>
<td>charge, spin, eradius, etag, cs_re, cs_im</td>
<td>AWPMD</td>
</tr>
@ -293,6 +297,12 @@ per-particle mass and volume.</p>
<p>The <em>meso</em> style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (e), and heat capacity
(cv).</p>
<p>The <em>smd</em> style is for a general formulation of Smooth Particle
Hydrodynamics. Both fluids and solids can be modeled. Particles
store the mass and volume of an integration point, a kernel diameter
used for calculating the field variables (e.g. stress and deformation)
and a contact radius for calculating repulsive forces which prevent
individual physical bodies from penetretating each other.</p>
<p>The <em>wavepacket</em> style is similar to <em>electron</em>, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate

11
doc/atom_style.txt
View File

@ -14,7 +14,8 @@ atom_style style args :pre
style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
{electron} or {ellipsoid} or {full} or {line} or {meso} or \
{molecular} or {peri} or {sphere} or {tri} or {template} or {hybrid} :ulb,l
{molecular} or {peri} or {smd} or {sphere} or {tri} or \
{template} or {hybrid} :ulb,l
args = none for any style except {body} and {hybrid}
{body} args = bstyle bstyle-args
bstyle = style of body particles
@ -76,6 +77,7 @@ quantities.
{meso} | rho, e, cv | SPH particles |
{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
{peri} | mass, volume | mesocopic Peridynamic models |
{smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
{sphere} | diameter, mass, angular velocity | granular models |
{template} | template index, template atom | small molecules with fixed topology |
{tri} | corner points, angular momentum | rigid bodies |
@ -123,6 +125,13 @@ The {meso} style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (e), and heat capacity
(cv).
The {smd} style is for a general formulation of Smooth Particle
Hydrodynamics. Both fluids and solids can be modeled. Particles
store the mass and volume of an integration point, a kernel diameter
used for calculating the field variables (e.g. stress and deformation)
and a contact radius for calculating repulsive forces which prevent
individual physical bodies from penetretating each other.
The {wavepacket} style is similar to {electron}, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate

235
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@ -0,0 +1,235 @@
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<div class="section" id="compute-smd-contact-radius-command">
<span id="index-0"></span><h1>compute smd/contact_radius command<a class="headerlink" href="#compute-smd-contact-radius-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/contact_radius
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/contact_radius = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/contact_radius
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation which outputs the contact radius, i.e., the radius used to prevent particles from penetrating each other.
The contact radius is used only to prevent particles belonging to different physical bodies from penetrating each other. It is used by the contact pair styles,
e.g., smd/hertz and smd/tri_surface.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in
LAMMPS.</p>
<p>The value of the contact radius will be 0.0 for particles not in the
specified compute group.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of
LAMMPS output options.</p>
<p>The per-particle vector values will be in distance <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="dump.html"><em>dump custom</em></a> smd/hertz smd/tri_surface</p>
<p><strong>Default:</strong> none</p>
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/contact_radius command :h3
[Syntax:]
compute ID group-ID smd/contact_radius :pre
ID, group-ID are documented in "compute"_compute.html command
smd/contact_radius = style name of this compute command :ul
[Examples:]
compute 1 all smd/contact_radius :pre
[Description:]
Define a computation which outputs the contact radius, i.e., the radius used to prevent particles from penetrating each other.
The contact radius is used only to prevent particles belonging to different physical bodies from penetrating each other. It is used by the contact pair styles,
e.g., smd/hertz and smd/tri_surface.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in
LAMMPS.
The value of the contact radius will be 0.0 for particles not in the
specified compute group.
[Output info:]
This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-particle vector values will be in distance "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"dump custom"_dump.html smd/hertz smd/tri_surface
[Default:] none

232
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@ -0,0 +1,232 @@
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<div class="section" id="compute-smd-damage-command">
<span id="index-0"></span><h1>compute smd/damage command<a class="headerlink" href="#compute-smd-damage-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/damage
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/damage = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/damage
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that calculates the damage status of SPH particles
according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to use Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output Info:</strong></p>
<p>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>How-to discussions, section 6.15</span></a>
for an overview of LAMMPS output options.</p>
<p>The per-particle values are dimensionless an in the range of zero to one.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_smd_plastic_strain.html"><em>smd/plastic_strain</em></a>, <a class="reference internal" href="compute_smd_tlsph_stress.html"><em>smd/tlsph_stress</em></a></p>
<p><strong>Default:</strong> none</p>
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48
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@ -0,0 +1,48 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/damage command :h3
[Syntax:]
compute ID group-ID smd/damage :pre
ID, group-ID are documented in "compute"_compute.html command
smd/damage = style name of this compute command :ul
[Examples:]
compute 1 all smd/damage :pre
[Description:]
Define a computation that calculates the damage status of SPH particles
according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
[Output Info:]
This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
"How-to discussions, section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The per-particle values are dimensionless an in the range of zero to one.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
[Related commands:]
"smd/plastic_strain"_compute_smd_plastic_strain.html, "smd/tlsph_stress"_compute_smd_tlsph_stress.html
[Default:] none

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<div class="section" id="compute-smd-hourglass-error-command">
<span id="index-0"></span><h1>compute smd/hourglass_error command<a class="headerlink" href="#compute-smd-hourglass-error-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/hourglass_error
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/hourglass_error = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/hourglass_error
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation which outputs the error of the approximated
relative separation with respect to the actual relative separation of
the particles i and j. Ideally, if the deformation gradient is exact,
and there exists a unique mapping between all particles&#8217; positions
within the neighborhood of the central node and the deformation gradient,
the approximated relative separation will coincide with the actual relative
separation of the particles i and j in the deformed configuration.
This compute is only really useful for debugging the hourglass control mechanim which is part of the Total-Lagrangian SPH pair style.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to use Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output Info:</strong></p>
<p>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>How-to discussions, section 6.15</span></a>
for an overview of LAMMPS output options.</p>
<p>The per-particle vector values will are dimensionless. See <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info.</p>
<p>This quantity will be computed only for particles which interact with tlsph pair style.</p>
<p><strong>Related Commands:</strong></p>
<p><a class="reference internal" href="compute_smd_tlsph_defgrad.html"><em>smd/tlsph_defgrad</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/hourglass_error command :h3
[Syntax:]
compute ID group-ID smd/hourglass_error :pre
ID, group-ID are documented in "compute"_compute.html command
smd/hourglass_error = style name of this compute command :ul
[Examples:]
compute 1 all smd/hourglass_error :pre
[Description:]
Define a computation which outputs the error of the approximated
relative separation with respect to the actual relative separation of
the particles i and j. Ideally, if the deformation gradient is exact,
and there exists a unique mapping between all particles' positions
within the neighborhood of the central node and the deformation gradient,
the approximated relative separation will coincide with the actual relative
separation of the particles i and j in the deformed configuration.
This compute is only really useful for debugging the hourglass control mechanim which is part of the Total-Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
[Output Info:]
This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
"How-to discussions, section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The per-particle vector values will are dimensionless. See "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
This quantity will be computed only for particles which interact with tlsph pair style.
[Related Commands:]
"smd/tlsph_defgrad"_compute_smd_tlsph_defgrad.html
[Default:]

231
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<div class="section" id="compute-smd-internal-energy-command">
<span id="index-0"></span><h1>compute smd/internal_energy command<a class="headerlink" href="#compute-smd-internal-energy-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/internal_energy
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/smd/internal_energy = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/internal_energy
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation which outputs the per-particle enthalpy, i.e., the sum of potential energy and heat.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to use Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output Info:</strong></p>
<p>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>How-to discussions, section 6.15</span></a>
for an overview of LAMMPS output options.</p>
<p>The per-particle vector values will be given in <a class="reference internal" href="units.html"><em>units</em></a> of energy.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info. This compute can only be used for particles which interact via the
updated Lagrangian or total Lagrangian SPH pair styles.</p>
<p><strong>Related Commands:</strong></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/internal_energy command :h3
[Syntax:]
compute ID group-ID smd/internal_energy :pre
ID, group-ID are documented in "compute"_compute.html command
smd/smd/internal_energy = style name of this compute command :ul
[Examples:]
compute 1 all smd/internal_energy :pre
[Description:]
Define a computation which outputs the per-particle enthalpy, i.e., the sum of potential energy and heat.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
[Output Info:]
This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
"How-to discussions, section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The per-particle vector values will be given in "units"_units.html of energy.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info. This compute can only be used for particles which interact via the
updated Lagrangian or total Lagrangian SPH pair styles.
[Related Commands:]
[Default:]

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<div class="section" id="compute-smd-plastic-strain-command">
<span id="index-0"></span><h1>compute smd/plastic_strain command<a class="headerlink" href="#compute-smd-plastic-strain-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/plastic_strain
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/plastic_strain = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/plastic_strain
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that outputs the equivalent plastic strain per particle.
This command is only meaningful if a material model with plasticity is defined.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to use Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output Info:</strong></p>
<p>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>How-to discussions, section 6.15</span></a>
for an overview of LAMMPS output options.</p>
<p>The per-particle values will be given dimensionless. See <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info. This compute can only be used for particles which interact via the
updated Lagrangian or total Lagrangian SPH pair styles.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_smd_tlsph_strain.html"><em>smd/plastic_strain_rate</em></a>, <a class="reference internal" href="compute_smd_tlsph_strain_rate.html"><em>smd/tlsph_strain_rate</em></a>,
<a class="reference internal" href="compute_smd_tlsph_strain.html"><em>smd/tlsph_strain</em></a></p>
<p><strong>Default:</strong> none</p>
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/plastic_strain command :h3
[Syntax:]
compute ID group-ID smd/plastic_strain :pre
ID, group-ID are documented in "compute"_compute.html command
smd/plastic_strain = style name of this compute command :ul
[Examples:]
compute 1 all smd/plastic_strain :pre
[Description:]
Define a computation that outputs the equivalent plastic strain per particle.
This command is only meaningful if a material model with plasticity is defined.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
[Output Info:]
This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
"How-to discussions, section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The per-particle values will be given dimensionless. See "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info. This compute can only be used for particles which interact via the
updated Lagrangian or total Lagrangian SPH pair styles.
[Related commands:]
"smd/plastic_strain_rate"_compute_smd_tlsph_strain.html, "smd/tlsph_strain_rate"_compute_smd_tlsph_strain_rate.html,
"smd/tlsph_strain"_compute_smd_tlsph_strain.html
[Default:] none

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<div class="section" id="compute-smd-plastic-strain-rate-command">
<span id="index-0"></span><h1>compute smd/plastic_strain_rate command<a class="headerlink" href="#compute-smd-plastic-strain-rate-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/plastic_strain_rate
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/plastic_strain_rate = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/plastic_strain_rate
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that outputs the time rate of the equivalent plastic strain.
This command is only meaningful if a material model with plasticity is defined.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to use Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output Info:</strong></p>
<p>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>How-to discussions, section 6.15</span></a>
for an overview of LAMMPS output options.</p>
<p>The per-particle values will be given in <a class="reference internal" href="units.html"><em>units</em></a> of one over time.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info. This compute can only be used for particles which interact via the
updated Lagrangian or total Lagrangian SPH pair styles.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_smd_plastic_strain.html"><em>smd/plastic_strain</em></a>, <a class="reference internal" href="compute_smd_tlsph_strain_rate.html"><em>smd/tlsph_strain_rate</em></a>,
<a class="reference internal" href="compute_smd_tlsph_strain.html"><em>smd/tlsph_strain</em></a></p>
<p><strong>Default:</strong> none</p>
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/plastic_strain_rate command :h3
[Syntax:]
compute ID group-ID smd/plastic_strain_rate :pre
ID, group-ID are documented in "compute"_compute.html command
smd/plastic_strain_rate = style name of this compute command :ul
[Examples:]
compute 1 all smd/plastic_strain_rate :pre
[Description:]
Define a computation that outputs the time rate of the equivalent plastic strain.
This command is only meaningful if a material model with plasticity is defined.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
[Output Info:]
This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
"How-to discussions, section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The per-particle values will be given in "units"_units.html of one over time.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info. This compute can only be used for particles which interact via the
updated Lagrangian or total Lagrangian SPH pair styles.
[Related commands:]
"smd/plastic_strain"_compute_smd_plastic_strain.html, "smd/tlsph_strain_rate"_compute_smd_tlsph_strain_rate.html,
"smd/tlsph_strain"_compute_smd_tlsph_strain.html
[Default:] none

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<div class="section" id="compute-smd-rho-command">
<span id="index-0"></span><h1>compute smd/rho command<a class="headerlink" href="#compute-smd-rho-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/rho
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/rho = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/rho
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that calculates the per-particle mass density.
The mass density is the mass of a particle which is constant during
the course of a simulation, divided by its volume, which can change due to mechanical deformation.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to use Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>How-to discussions, section 6.15</span></a>
for an overview of LAMMPS output options.</p>
<p>The per-particle values will be in <a class="reference internal" href="units.html"><em>units</em></a> of mass over volume.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_smd_vol.html"><em>smd/vol</em></a></p>
<p><strong>Default:</strong> none</p>
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/rho command :h3
[Syntax:]
compute ID group-ID smd/rho :pre
ID, group-ID are documented in "compute"_compute.html command
smd/rho = style name of this compute command :ul
[Examples:]
compute 1 all smd/rho :pre
[Description:]
Define a computation that calculates the per-particle mass density.
The mass density is the mass of a particle which is constant during
the course of a simulation, divided by its volume, which can change due to mechanical deformation.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
[Output info:]
This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
"How-to discussions, section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The per-particle values will be in "units"_units.html of mass over volume.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
[Related commands:]
"smd/vol"_compute_smd_vol.html
[Default:] none

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@ -0,0 +1,236 @@
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<div class="section" id="compute-smd-tlsph-defgrad-command">
<span id="index-0"></span><h1>compute smd/tlsph_defgrad command<a class="headerlink" href="#compute-smd-tlsph-defgrad-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/tlsph_defgrad
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/tlsph_defgrad = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/tlsph_defgrad
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that calculates the deformation gradient.
It is only meaningful for particles which interact according to the Total-Lagrangian SPH pair style.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to use Smooth Mach Dynamics in
LAMMPS.</p>
<p><strong>Output info:</strong></p>
<p>This compute outputss a per-particle vector of vectors (tensors), which can be
accessed by any command that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>How-to discussions, section 6.15</span></a>
for an overview of LAMMPS output options.</p>
<p>The per-particle vector values will be given dimensionless. See <a class="reference internal" href="units.html"><em>units</em></a>.
The per-particle vector has 10 entries. The first nine entries correspond to the xx, xy, xz, yx, yy, yz, zx, zy, zz components
of the asymmetric deformation gradient tensor. The tenth entry is the determinant of the deformation gradient.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if LAMMPS was
built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info. TThis compute can only be used for particles which interact via the
total Lagrangian SPH pair style.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_smd_hourglass_error.html"><em>smd/hourglass_error</em></a></p>
<p><strong>Default:</strong> none</p>
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53
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/tlsph_defgrad command :h3
[Syntax:]
compute ID group-ID smd/tlsph_defgrad :pre
ID, group-ID are documented in "compute"_compute.html command
smd/tlsph_defgrad = style name of this compute command :ul
[Examples:]
compute 1 all smd/tlsph_defgrad :pre
[Description:]
Define a computation that calculates the deformation gradient.
It is only meaningful for particles which interact according to the Total-Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in
LAMMPS.
[Output info:]
This compute outputss a per-particle vector of vectors (tensors), which can be
accessed by any command that uses per-particle values from a compute as input. See
"How-to discussions, section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The per-particle vector values will be given dimensionless. See "units"_units.html.
The per-particle vector has 10 entries. The first nine entries correspond to the xx, xy, xz, yx, yy, yz, zx, zy, zz components
of the asymmetric deformation gradient tensor. The tenth entry is the determinant of the deformation gradient.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if LAMMPS was
built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info. TThis compute can only be used for particles which interact via the
total Lagrangian SPH pair style.
[Related commands:]
"smd/hourglass_error"_compute_smd_hourglass_error.html
[Default:] none

237
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@ -0,0 +1,237 @@
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<div class="section" id="compute-smd-tlsph-dt-command">
<span id="index-0"></span><h1>compute smd/tlsph_dt command<a class="headerlink" href="#compute-smd-tlsph-dt-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/tlsph_dt
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/tlsph_dt = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/tlsph_dt
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that outputs the CFL-stable time increment per particle.
This time increment is essentially given by the speed of sound, divided by the SPH smoothing length.
Because both the speed of sound and the smoothing length typically change during the course of a simulation,
the stable time increment needs to be recomputed every time step.
This calculation is performed automatically in the relevant SPH pair styles and this compute only serves to make the
stable time increment accessible for output purposes.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>How-to discussions, section 6.15</span></a>
for an overview of LAMMPS output options.</p>
<p>The per-particle values will be given in <a class="reference internal" href="units.html"><em>units</em></a> of time.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info.</p>
<p>This compute can only be used for particles interacting with the Total-Lagrangian SPH pair style.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="fix_smd_adjust_dt.html"><em>smd/adjust_dt</em></a></p>
<p><strong>Default:</strong> none</p>
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54
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@ -0,0 +1,54 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/tlsph_dt command :h3
[Syntax:]
compute ID group-ID smd/tlsph_dt :pre
ID, group-ID are documented in "compute"_compute.html command
smd/tlsph_dt = style name of this compute command :ul
[Examples:]
compute 1 all smd/tlsph_dt :pre
[Description:]
Define a computation that outputs the CFL-stable time increment per particle.
This time increment is essentially given by the speed of sound, divided by the SPH smoothing length.
Because both the speed of sound and the smoothing length typically change during the course of a simulation,
the stable time increment needs to be recomputed every time step.
This calculation is performed automatically in the relevant SPH pair styles and this compute only serves to make the
stable time increment accessible for output purposes.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
[Output info:]
This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
"How-to discussions, section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The per-particle values will be given in "units"_units.html of time.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
This compute can only be used for particles interacting with the Total-Lagrangian SPH pair style.
[Related commands:]
"smd/adjust_dt"_fix_smd_adjust_dt.html
[Default:] none

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<div class="section" id="compute-smd-tlsph-num-neighs-command">
<span id="index-0"></span><h1>compute smd/tlsph_num_neighs command<a class="headerlink" href="#compute-smd-tlsph-num-neighs-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/tlsph_num_neighs
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/tlsph_num_neighs = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/tlsph_num_neighs
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that calculates the number of particles
inside of the smoothing kernel radius for particles interacting via the Total-Lagrangian SPH pair style.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>How-to discussions, section 6.15</span></a>
for an overview of LAMMPS output options.</p>
<p>The per-particle values are dimensionless. See <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info.</p>
<p>This quantity will be computed only for particles which interact with the Total-Lagrangian pair style.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><code class="xref doc docutils literal"><span class="pre">smd/ulsph_num_neighs</span></code></p>
<p><strong>Default:</strong> none</p>
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/tlsph_num_neighs command :h3
[Syntax:]
compute ID group-ID smd/tlsph_num_neighs :pre
ID, group-ID are documented in "compute"_compute.html command
smd/tlsph_num_neighs = style name of this compute command :ul
[Examples:]
compute 1 all smd/tlsph_num_neighs :pre
[Description:]
Define a computation that calculates the number of particles
inside of the smoothing kernel radius for particles interacting via the Total-Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
[Output info:]
This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
"How-to discussions, section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The per-particle values are dimensionless. See "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
This quantity will be computed only for particles which interact with the Total-Lagrangian pair style.
[Related commands:]
"smd/ulsph_num_neighs"_compute_smd/ulsph_num_neighs.html
[Default:] none

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<div class="section" id="compute-smd-tlsph-shape-command">
<span id="index-0"></span><h1>compute smd/tlsph_shape command<a class="headerlink" href="#compute-smd-tlsph-shape-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/tlsph_shape
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/tlsph_shape = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/tlsph_shape
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that outputs the current shape of the volume associated with a particle as a rotated ellipsoid.
It is only meaningful for particles which interact according to the Total-Lagrangian SPH pair style.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to use Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-particle vector of vectors, which can be
accessed by any command that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>How-to discussions, section 6.15</span></a>
for an overview of LAMMPS output options.</p>
<p>The per-particle vector has 7 entries. The first three entries correspond to the lengths of the ellipsoid&#8217;s axes and have units of length.
These axis valus are computed as the contact radius times the xx, yy, or zz components of the Green-Lagrange strain tensor associated with the particle.
The next 4 values are quaternions (order: q, x, y, z) which describe the spatial rotation of the particle relative to its initial state.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if LAMMPS was
built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info.</p>
<p>This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_smd_contact_radius.html"><em>smd/contact_radius</em></a></p>
<p><strong>Default:</strong> none</p>
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52
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/tlsph_shape command :h3
[Syntax:]
compute ID group-ID smd/tlsph_shape :pre
ID, group-ID are documented in "compute"_compute.html command
smd/tlsph_shape = style name of this compute command :ul
[Examples:]
compute 1 all smd/tlsph_shape :pre
[Description:]
Define a computation that outputs the current shape of the volume associated with a particle as a rotated ellipsoid.
It is only meaningful for particles which interact according to the Total-Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
[Output info:]
This compute calculates a per-particle vector of vectors, which can be
accessed by any command that uses per-particle values from a compute as input. See
"How-to discussions, section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The per-particle vector has 7 entries. The first three entries correspond to the lengths of the ellipsoid's axes and have units of length.
These axis valus are computed as the contact radius times the xx, yy, or zz components of the Green-Lagrange strain tensor associated with the particle.
The next 4 values are quaternions (order: q, x, y, z) which describe the spatial rotation of the particle relative to its initial state.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if LAMMPS was
built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style.
[Related commands:]
"smd/contact_radius"_compute_smd_contact_radius.html
[Default:] none

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<div class="section" id="compute-smd-tlsph-strain-command">
<span id="index-0"></span><h1>compute smd/tlsph_strain command<a class="headerlink" href="#compute-smd-tlsph-strain-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/tlsph_strain
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/tlsph_strain = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/tlsph_strain
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that calculates the Green-Lagrange strain tensor for particles interacting via the Total-Lagrangian SPH pair style.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>How-to discussions, section 6.15</span></a></p>
<blockquote>
<div>for an overview of LAMMPS output options.</div></blockquote>
<p>The per-particle tensor values will be given dimensionless. See <a class="reference internal" href="units.html"><em>units</em></a>.</p>
<p>The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components
of the symmetric strain tensor.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info.</p>
<p>This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_smd_tlsph_strain_rate.html"><em>smd/tlsph_strain_rate</em></a>, <a class="reference internal" href="compute_smd_tlsph_stress.html"><em>smd/tlsph_stress</em></a></p>
<p><strong>Default:</strong> none</p>
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@ -0,0 +1,53 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/tlsph_strain command :h3
[Syntax:]
compute ID group-ID smd/tlsph_strain :pre
ID, group-ID are documented in "compute"_compute.html command
smd/tlsph_strain = style name of this compute command :ul
[Examples:]
compute 1 all smd/tlsph_strain :pre
[Description:]
Define a computation that calculates the Green-Lagrange strain tensor for particles interacting via the Total-Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
[Output info:]
This compute calculates a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
from a compute as input. See
"How-to discussions, section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The per-particle tensor values will be given dimensionless. See "units"_units.html.
The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components
of the symmetric strain tensor.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style.
[Related commands:]
"smd/tlsph_strain_rate"_compute_smd_tlsph_strain_rate.html, "smd/tlsph_stress"_compute_smd_tlsph_stress.html
[Default:] none

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<div class="section" id="compute-smd-tlsph-strain-rate-command">
<span id="index-0"></span><h1>compute smd/tlsph_strain_rate command<a class="headerlink" href="#compute-smd-tlsph-strain-rate-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/tlsph_strain_rate
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/tlsph_strain_rate = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/tlsph_strain_rate
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that calculates the rate of the strain tensor for particles interacting via the Total-Lagrangian SPH pair style.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-particle vector of vectors (tensors), which can be
accessed by any command that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>How-to discussions, section 6.15</span></a>
for an overview of LAMMPS output options.</p>
<p>The values will be given in <a class="reference internal" href="units.html"><em>units</em></a> of one over time.</p>
<p>The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components
of the symmetric strain rate tensor.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info.</p>
<p>This quantity will be computed only for particles which interact with Total-Lagrangian SPH pair style.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_smd_tlsph_strain.html"><em>smd/tlsph_strain</em></a>, <a class="reference internal" href="compute_smd_tlsph_stress.html"><em>smd/tlsph_stress</em></a></p>
<p><strong>Default:</strong> none</p>
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53
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/tlsph_strain_rate command :h3
[Syntax:]
compute ID group-ID smd/tlsph_strain_rate :pre
ID, group-ID are documented in "compute"_compute.html command
smd/tlsph_strain_rate = style name of this compute command :ul
[Examples:]
compute 1 all smd/tlsph_strain_rate :pre
[Description:]
Define a computation that calculates the rate of the strain tensor for particles interacting via the Total-Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
[Output info:]
This compute calculates a per-particle vector of vectors (tensors), which can be
accessed by any command that uses per-particle values from a compute as input. See
"How-to discussions, section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The values will be given in "units"_units.html of one over time.
The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components
of the symmetric strain rate tensor.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
This quantity will be computed only for particles which interact with Total-Lagrangian SPH pair style.
[Related commands:]
"smd/tlsph_strain"_compute_smd_tlsph_strain.html, "smd/tlsph_stress"_compute_smd_tlsph_stress.html
[Default:] none

235
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<div class="section" id="compute-smd-tlsph-stress-command">
<span id="index-0"></span><h1>compute smd/tlsph_stress command<a class="headerlink" href="#compute-smd-tlsph-stress-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/tlsph_stress
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/tlsph_stress = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/tlsph_stress
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that outputs the Cauchy stress tensor for particles interacting via the Total-Lagrangian SPH pair style.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-particle vector of vectors (tensors), which can be
accessed by any command that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>How-to discussions, section 6.15</span></a>
for an overview of LAMMPS output options.</p>
<p>The values will be given in <a class="reference internal" href="units.html"><em>units</em></a> of pressure.</p>
<p>The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz and yz components
of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the stress tensor, i.e.,
the von Mises equivalent stress.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info.</p>
<p>This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_smd_tlsph_strain.html"><em>smd/tlsph_strain</em></a>, <a class="reference internal" href="compute_smd_tlsph_strain_rate.html"><em>smd/tlsph_strain_rate</em></a></p>
<p><strong>Default:</strong> none</p>
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53
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View File

@ -0,0 +1,53 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/tlsph_stress command :h3
[Syntax:]
compute ID group-ID smd/tlsph_stress :pre
ID, group-ID are documented in "compute"_compute.html command
smd/tlsph_stress = style name of this compute command :ul
[Examples:]
compute 1 all smd/tlsph_stress :pre
[Description:]
Define a computation that outputs the Cauchy stress tensor for particles interacting via the Total-Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
[Output info:]
This compute calculates a per-particle vector of vectors (tensors), which can be
accessed by any command that uses per-particle values from a compute as input. See
"How-to discussions, section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The values will be given in "units"_units.html of pressure.
The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz and yz components
of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the stress tensor, i.e.,
the von Mises equivalent stress.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style.
[Related commands:]
"smd/tlsph_strain"_compute_smd_tlsph_strain.html, "smd/tlsph_strain_rate"_compute_smd_tlsph_strain_rate.html
[Default:] none

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<div class="section" id="compute-smd-triangle-mesh-vertices">
<h1>compute smd/triangle_mesh_vertices<a class="headerlink" href="#compute-smd-triangle-mesh-vertices" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/triangle_mesh_vertices
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/triangle_mesh_vertices = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/triangle_mesh_vertices
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that returns the coordinates of the vertices
corresponding to the triangle-elements of a mesh created by the <a href="#id4"><span class="problematic" id="id5">`fix smd/wall_surface &lt;ls_&gt;`_</span></a>.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output info:</strong></p>
<p>This compute returns a per-particle vector of vectors, which can be
accessed by any command that uses per-particle values from a compute as
input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>How-to discussions, section 6.15</span></a>
for an overview of LAMMPS output options.</p>
<p>The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and (x3/y3/z3) corresponding
to the first, second, and third vertex of each triangle.</p>
<p>It is only meaningful to use this compute for a group of particles which is created via the
<a href="#id6"><span class="problematic" id="id7">`fix smd/wall_surface &lt;ls_&gt;`_</span></a> command.</p>
<p>The output of this compute can be used with the dump2vtk_tris tool to generate a VTK representation of the
smd/wall_surace mesh for visualization purposes.</p>
<p>The values will be given in <a class="reference internal" href="units.html"><em>units</em></a> of distance.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="fix_smd_move_triangulated_surface.html"><em>smd/move_tri_surf</em></a>, <a href="#id8"><span class="problematic" id="id9">`smd/wall_surface &lt;ls_&gt;`_</span></a></p>
<p><strong>Default:</strong> none</p>
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59
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:link(ls,fix_smd_wall_surface.html)
:line
compute smd/triangle_mesh_vertices :h3
[Syntax:]
compute ID group-ID smd/triangle_mesh_vertices :pre
ID, group-ID are documented in "compute"_compute.html command
smd/triangle_mesh_vertices = style name of this compute command :ul
[Examples:]
compute 1 all smd/triangle_mesh_vertices :pre
[Description:]
Define a computation that returns the coordinates of the vertices
corresponding to the triangle-elements of a mesh created by the "fix smd/wall_surface"_ls.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
[Output info:]
This compute returns a per-particle vector of vectors, which can be
accessed by any command that uses per-particle values from a compute as
input. See "How-to discussions, section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and (x3/y3/z3) corresponding
to the first, second, and third vertex of each triangle.
It is only meaningful to use this compute for a group of particles which is created via the
"fix smd/wall_surface"_ls command.
The output of this compute can be used with the dump2vtk_tris tool to generate a VTK representation of the
smd/wall_surace mesh for visualization purposes.
The values will be given in "units"_units.html of distance.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
[Related commands:]
"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html, "smd/wall_surface"_ls
[Default:] none

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<div class="section" id="compute-smd-ulsph-num-neighs-command">
<span id="index-0"></span><h1>compute smd/ulsph_num_neighs command<a class="headerlink" href="#compute-smd-ulsph-num-neighs-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/ulsph_num_neighs
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/ulsph_num_neighs = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/ulsph_num_neighs
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that returns the number of neighbor particles
inside of the smoothing kernel radius for particles interacting via the updated Lagrangian SPH pair style.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output info:</strong></p>
<p>This compute returns a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of
LAMMPS output options.</p>
<p>The per-particle values will be given dimentionless, see <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-2"><span>Making LAMMPS</span></a>
section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p>smd/tlsph_num_neighs</p>
<p><strong>Default:</strong> none</p>
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/ulsph_num_neighs command :h3
[Syntax:]
compute ID group-ID smd/ulsph_num_neighs :pre
ID, group-ID are documented in "compute"_compute.html command
smd/ulsph_num_neighs = style name of this compute command :ul
[Examples:]
compute 1 all smd/ulsph_num_neighs :pre
[Description:]
Define a computation that returns the number of neighbor particles
inside of the smoothing kernel radius for particles interacting via the updated Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
[Output info:]
This compute returns a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-particle values will be given dimentionless, see "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_2
section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.
[Related commands:]
smd/tlsph_num_neighs
[Default:] none

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<div class="section" id="compute-smd-ulsph-strain-command">
<span id="index-0"></span><h1>compute smd/ulsph_strain command<a class="headerlink" href="#compute-smd-ulsph-strain-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/ulsph_strain
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/ulsph_strain = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/ulsph_strain
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that outputs the logarithmic strain tensor.
for particles interacting via the updated Lagrangian SPH pair style.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-particle tensor, which can be accessed by
any command that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of
LAMMPS output options.</p>
<p>The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components
of the symmetric strain rate tensor.</p>
<p>The per-particle tensor values will be given dimensionless, see <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p>smd/tlsph_strain</p>
<p><strong>Default:</strong> none</p>
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/ulsph_strain command :h3
[Syntax:]
compute ID group-ID smd/ulsph_strain :pre
ID, group-ID are documented in "compute"_compute.html command
smd/ulsph_strain = style name of this compute command :ul
[Examples:]
compute 1 all smd/ulsph_strain :pre
[Description:]
Define a computation that outputs the logarithmic strain tensor.
for particles interacting via the updated Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
[Output info:]
This compute calculates a per-particle tensor, which can be accessed by
any command that uses per-particle values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components
of the symmetric strain rate tensor.
The per-particle tensor values will be given dimensionless, see "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.
[Related commands:]
smd/tlsph_strain
[Default:] none

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<div class="section" id="compute-smd-ulsph-strain-rate-command">
<span id="index-0"></span><h1>compute smd/ulsph_strain_rate command<a class="headerlink" href="#compute-smd-ulsph-strain-rate-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/ulsph_strain_rate
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/ulsph_strain_rate = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/ulsph_strain_rate
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that outputs the rate of the logarithmic strain tensor
for particles interacting via the updated Lagrangian SPH pair style.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-particle vector of vectors (tensors), which
can be accessed by any command that uses per-particle values from a compute
as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of
LAMMPS output options.</p>
<p>The values will be given in <a class="reference internal" href="units.html"><em>units</em></a> of one over time.</p>
<p>The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components
of the symmetric strain rate tensor.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-2"><span>Making LAMMPS</span></a>
section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p>smd/utsph_strain_rate</p>
<p><strong>Default:</strong> none</p>
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52
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/ulsph_strain_rate command :h3
[Syntax:]
compute ID group-ID smd/ulsph_strain_rate :pre
ID, group-ID are documented in "compute"_compute.html command
smd/ulsph_strain_rate = style name of this compute command :ul
[Examples:]
compute 1 all smd/ulsph_strain_rate :pre
[Description:]
Define a computation that outputs the rate of the logarithmic strain tensor
for particles interacting via the updated Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
[Output info:]
This compute calculates a per-particle vector of vectors (tensors), which
can be accessed by any command that uses per-particle values from a compute
as input. See "Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The values will be given in "units"_units.html of one over time.
The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components
of the symmetric strain rate tensor.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_2
section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.
[Related commands:]
smd/utsph_strain_rate
[Default:] none

237
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@ -0,0 +1,237 @@
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<div class="section" id="compute-smd-ulsph-stress-command">
<span id="index-0"></span><h1>compute smd/ulsph_stress command<a class="headerlink" href="#compute-smd-ulsph-stress-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/ulsph_stress
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/ulsph_stress = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/ulsph_stress
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that outputs the Cauchy stress tensor.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a>
for an overview of LAMMPS output options.</p>
<p>The values will be given in <a class="reference internal" href="units.html"><em>units</em></a> of pressure.</p>
<p>The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz, yz components
of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the stress tensor, i.e.,
the von Mises equivalent stress.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<pre class="literal-block">
<a class="reference internal" href="compute_smd_ulsph_strain.html"><em>smd/ulsph_strain</em></a>, <a class="reference internal" href="compute_smd_ulsph_strain_rate.html"><em>smd/ulsph_strain_rate</em></a>
<a class="reference internal" href="compute_smd_tlsph_stress.html"><em>smd/tlsph_stress</em></a>
</pre>
<p><strong>Default:</strong> none</p>
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53
doc/compute_smd_ulsph_stress.txt Normal file
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@ -0,0 +1,53 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/ulsph_stress command :h3
[Syntax:]
compute ID group-ID smd/ulsph_stress :pre
ID, group-ID are documented in "compute"_compute.html command
smd/ulsph_stress = style name of this compute command :ul
[Examples:]
compute 1 all smd/ulsph_stress :pre
[Description:]
Define a computation that outputs the Cauchy stress tensor.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
[Output info:]
This compute calculates a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
from a compute as input. See "Section_howto 15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The values will be given in "units"_units.html of pressure.
The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz, yz components
of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the stress tensor, i.e.,
the von Mises equivalent stress.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.
[Related commands:]
"smd/ulsph_strain"_compute_smd_ulsph_strain.html, "smd/ulsph_strain_rate"_compute_smd_ulsph_strain_rate.html
"smd/tlsph_stress"_compute_smd_tlsph_stress.html :pre
[Default:] none

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<div class="section" id="compute-smd-vol-command">
<span id="index-0"></span><h1>compute smd/vol command<a class="headerlink" href="#compute-smd-vol-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID smd/vol
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>smd/vol = style name of this compute command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all smd/vol
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that provides the per-particle volume and the sum of the per-particle volumes of the
group for which the fix is defined.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in
LAMMPS.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span>How-to discussions, section 6.15</span></a>
for an overview of LAMMPS output options.</p>
<p>The per-particle vector values will be given in <a class="reference internal" href="units.html"><em>units</em></a> of volume.</p>
<p>Additionally, the compute returns a scalar, which is the sum of the per-particle volumes of the
group for which the fix is defined.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a></p>
<blockquote>
<div>section for more info.</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_smd_rho.html"><em>smd/rho</em></a></p>
<p><strong>Default:</strong> none</p>
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52
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@ -0,0 +1,52 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute smd/vol command :h3
[Syntax:]
compute ID group-ID smd/vol :pre
ID, group-ID are documented in "compute"_compute.html command
smd/vol = style name of this compute command :ul
[Examples:]
compute 1 all smd/vol :pre
[Description:]
Define a computation that provides the per-particle volume and the sum of the per-particle volumes of the
group for which the fix is defined.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in
LAMMPS.
[Output info:]
This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
"How-to discussions, section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The per-particle vector values will be given in "units"_units.html of volume.
Additionally, the compute returns a scalar, which is the sum of the per-particle volumes of the
group for which the fix is defined.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
[Related commands:]
"smd/rho"_compute_smd_rho.html
[Default:] none

15
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@ -438,8 +438,9 @@ package</A>.
<TR ALIGN="center"><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_lb_fluid.html">lb/fluid</A></TD><TD ><A HREF = "fix_lb_momentum.html">lb/momentum</A></TD><TD ><A HREF = "fix_lb_pc.html">lb/pc</A></TD><TD ><A HREF = "fix_lb_rigid_pc_sphere.html">lb/rigid/pc/sphere</A></TD><TD ><A HREF = "fix_lb_viscous.html">lb/viscous</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_meso.html">meso</A></TD><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_phonon.html">phonon</A></TD><TD ><A HREF = "fix_pimd.html">pimd</A></TD><TD ><A HREF = "fix_qbmsst.html">qbmsst</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_qtb.html">qtb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_saed_vtk.html">saed/vtk</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A></TD><TD ><A HREF = "fix_ttm.html">ttm/mod</A>
<TR ALIGN="center"><TD ><A HREF = "fix_qtb.html">qtb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_saed_vtk.html">saed/vtk</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_smd_adjust_dt.html">smd/adjust/dt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_smd_integrate_tlsph.html">smd/integrate/tlsph</A></TD><TD ><A HREF = "fix_smd_integrate_ulsph.html">smd/integrate/ulsph</A></TD><TD ><A HREF = "fix_smd_move_triangulated_surface.html">smd/move/triangulated/surface</A></TD><TD ><A HREF = "fix_smd_setvel.html">smd/setvel</A></TD><TD ><A HREF = "fix_smd_tlsph_reference_configuration.html">smd/tlsph/reference/configuration</A></TD><TD ><A HREF = "fix_smd_wall_surface.html">smd/wall/surface</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A></TD><TD ><A HREF = "fix_ttm.html">ttm/mod</A>
</TD></TR></TABLE></DIV>
<HR>
@ -474,8 +475,11 @@ package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_basal_atom.html">basal/atom</A></TD><TD ><A HREF = "compute_fep.html">fep</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_meso_e_atom.html">meso_e/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_meso_rho_atom.html">meso_rho/atom</A></TD><TD ><A HREF = "compute_meso_t_atom.html">meso_t/atom</A></TD><TD ><A HREF = "compute_saed.html">saed</A></TD><TD ><A HREF = "compute_temp_drude.html">temp/drude</A></TD><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A></TD><TD ><A HREF = "compute_xrd.html">xrd</A>
<TR ALIGN="center"><TD ><A HREF = "compute_meso_rho_atom.html">meso_rho/atom</A></TD><TD ><A HREF = "compute_meso_t_atom.html">meso_t/atom</A></TD><TD ><A HREF = "compute_saed.html">saed</A></TD><TD ><A HREF = "compute_smd_contact_radius.html">smd/contact/radius</A></TD><TD ><A HREF = "compute_smd_damage.html">smd/damage</A></TD><TD ><A HREF = "compute_smd_hourglass_error.html">smd/hourglass/error</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_internal_energy.html">smd/internal/energy</A></TD><TD ><A HREF = "compute_smd_plastic_strain.html">smd/plastic/strain</A></TD><TD ><A HREF = "compute_smd_plastic_strain_rate.html">smd/plastic/strain/rate</A></TD><TD ><A HREF = "compute_smd_rho.html">smd/rho</A></TD><TD ><A HREF = "compute_smd_tlsph_defgrad.html">smd/tlsph/defgrad</A></TD><TD ><A HREF = "compute_smd_tlsph_dt.html">smd/tlsph/dt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_tlsph_num_neighs.html">smd/tlsph/num/neighs</A></TD><TD ><A HREF = "compute_smd_tlsph_shape.html">smd/tlsph/shape</A></TD><TD ><A HREF = "compute_smd_tlsph_strain.html">smd/tlsph/strain</A></TD><TD ><A HREF = "compute_smd_tlsph_strain_rate.html">smd/tlsph/strain/rate</A></TD><TD ><A HREF = "compute_smd_tlsph_stress.html">smd/tlsph/stress</A></TD><TD ><A HREF = "compute_smd_triangle_mesh_vertices.html">smd/triangle/mesh/vertices</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_ulsph_num_neighs.html">smd/ulsph/num/neighs</A></TD><TD ><A HREF = "compute_smd_ulsph_strain.html">smd/ulsph/strain</A></TD><TD ><A HREF = "compute_smd_ulsph_strain/rate.html">smd/ulsph/strain/rate</A></TD><TD ><A HREF = "compute_smd_ulpsh_stress.html">smd/ulpsh/stress</A></TD><TD ><A HREF = "compute_smd_vol.html">smd/vol</A></TD><TD ><A HREF = "compute_temp_drude.html">temp/drude</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A></TD><TD ><A HREF = "compute_xrd.html">xrd</A>
</TD></TR></TABLE></DIV>
<HR>
@ -530,7 +534,8 @@ package</A>.
<TR ALIGN="center"><TD ><A HREF = "pair_list.html">list</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/cut/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/long/soft (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/sf (go)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/tip4p/long/soft (o)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk (gko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long (go)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm (o)</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf (o)</A></TD><TD ><A HREF = "pair_meam_spline.html">meam/spline</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_meam_sw_spline.html">meam/sw/spline</A></TD><TD ><A HREF = "pair_quip.html">quip</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD><TD ><A HREF = "pair_sph_heatconduction.html">sph/heatconduction</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_meam_sw_spline.html">meam/sw/spline</A></TD><TD ><A HREF = "pair_quip.html">quip</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD><TD ><A HREF = "pair_smd_hertz.html">smd/hertz</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_smd_tlsph.html">smd/tlsph</A></TD><TD ><A HREF = "pair_smd_triangulated_surface.html">smd/triangulated/surface</A></TD><TD ><A HREF = "pair_smd_ulsph.html">smd/ulsph</A></TD><TD ><A HREF = "pair_sph_heatconduction.html">sph/heatconduction</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sph_idealgas.html">sph/idealgas</A></TD><TD ><A HREF = "pair_sph_lj.html">sph/lj</A></TD><TD ><A HREF = "pair_sph_rhosum.html">sph/rhosum</A></TD><TD ><A HREF = "pair_sph_taitwater.html">sph/taitwater</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sph_taitwater_morris.html">sph/taitwater/morris</A></TD><TD ><A HREF = "pair_srp.html">srp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/table (o)</A></TD><TD ><A HREF = "pair_thole.html">thole</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft (o)</A>

17
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@ -140,6 +140,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries.
<TR ALIGN="center"><TD >USER-QTB</TD><TD > quantum nuclear effects</TD><TD > Yuan Shen (Stanford)</TD><TD > <A HREF = "fix_qtb.html">fix qtb</A> <A HREF = "fix_qbmsst.html">fix_qbmsst</A></TD><TD > qtb</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-QUIP</TD><TD > QUIP/libatoms interface</TD><TD > Albert Bartok-Partay (U Cambridge)</TD><TD > <A HREF = "pair_quip.html">pair_style quip</A></TD><TD > USER/quip</TD><TD > -</TD><TD > lib/quip</TD></TR>
<TR ALIGN="center"><TD >USER-REAXC</TD><TD > C version of ReaxFF</TD><TD > Metin Aktulga (LBNL)</TD><TD > <A HREF = "pair_reax_c.html">pair_style reaxc</A></TD><TD > reax</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-SMD</TD><TD > smoothed Mach dynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "USER/smd/SMD_user_guide.pdf">userguide.pdf</A></TD><TD > USER/smd</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-SPH</TD><TD > smoothed particle hydrodynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">userguide.pdf</A></TD><TD > USER/sph</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#sph">sph</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >
</TD></TR></TABLE></DIV>
@ -639,6 +640,22 @@ questions.
</P>
<HR>
<H4>USER-SMD package
</H4>
<P>This package implements smoothed Mach dynamics (SMD) in
LAMMPS. Currently, the package has the following features:
</P>
<P>???
</P>
<P>See the file doc/USER/smd/SPH_user_guide.pdf to get started.
</P>
<P>There are example scripts for using this package in examples/USER/smd.
</P>
<P>The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.
</P>
<H4>USER-SPH package
</H4>
<P>This package implements smoothed particle hydrodynamics (SPH) in

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@ -0,0 +1,59 @@
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<title>ATC: fix_modify AtC add_molecule</title>
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<h1><a class="anchor" id="man_add_molecule">fix_modify AtC add_molecule </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify_AtC add_molecule &lt;small|large&gt; &lt;TAG&gt; &lt;GROUP_NAME&gt; <br/>
</p>
<ul>
<li>small|large = can be small if molecule size &lt; cutoff radius, must be large otherwise <br/>
</li>
<li>&lt;TAG&gt; = tag for tracking a species <br/>
</li>
<li>&lt;GROUP_NAME&gt; = name of group that tracking will be applied to <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> group WATERGROUP type 1 2 </code> <br/>
<code> fix_modify AtC add_molecule small water WATERGROUP </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Associates a tag with all molecules corresponding to a specified group. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No defaults for this command. </p>
</div>
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<h1><a class="anchor" id="man_add_species">fix_modify AtC add_species </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify_AtC add_species &lt;TAG&gt; &lt;group|type&gt; &lt;ID&gt; <br/>
</p>
<ul>
<li>&lt;TAG&gt; = tag for tracking a species <br/>
</li>
<li>group|type = LAMMPS defined group or type of atoms <br/>
</li>
<li>&lt;ID&gt; = name of group or type number <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC add_species gold type 1 </code> <br/>
<code> group GOLDGROUP type 1 </code> <br/>
<code> fix_modify AtC add_species gold group GOLDGROUP </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Associates a tag with all atoms of a specified type or within a specified group. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No defaults for this command. </p>
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<h1><a class="anchor" id="man_atom_element_map">fix_modify AtC atom_element_map </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC atom_element_map &lt;eulerian|lagrangian&gt; &lt;frequency&gt; <br/>
</p>
<ul>
<li>frequency (int) : frequency of updating atom-to-continuum maps based on the current configuration - only for eulerian </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc atom_element_map eulerian 100 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Changes frame of reference from eulerian to lagrangian and sets the frequency for which the map from atoms to elements is reformed and all the attendant data is recalculated. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Cannot change map type after initialization. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>lagrangian </p>
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<h1><a class="anchor" id="man_atom_weight">fix_modify AtC atom_weight </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC atom_weight &lt;method&gt; &lt;arguments&gt;</p>
<ul>
<li>&lt;method&gt; = <br/>
value: atoms in specified group assigned constant value given <br/>
lattice: volume per atom for specified lattice type (e.g. fcc) and parameter <br/>
element: element volume divided among atoms within element <br/>
region: volume per atom determined based on the atom count in the MD regions and their volumes. Note: meaningful only if atoms completely fill all the regions. <br/>
group: volume per atom determined based on the atom count in a group and its volume<br/>
read_in: list of values for atoms are read-in from specified file <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc atom_weight constant myatoms 11.8 </code> <br/>
<code> fix_modify atc atom_weight lattice </code> <br/>
<code> fix_modify atc atom_weight read-in atm_wt_file.txt </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command for assigning the value of atomic weights used for atomic integration in atom-continuum coupled simulations. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Use of lattice option requires a lattice type and parameter is already specified. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>lattice </p>
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<h1><a class="anchor" id="man_atomic_charge">fix_modify AtC atomic_charge </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC &lt;include | omit&gt; atomic_charge</p>
<ul>
<li>&lt;include | omit&gt; = switch to activiate/deactiviate inclusion of intrinsic atomic charge in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc compute include atomic_charge </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Determines whether AtC tracks the total charge as a finite element field </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Required for: electrostatics </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>if the atom charge is defined, default is on, otherwise default is off </p>
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<h1><a class="anchor" id="man_boundary">fix_modify AtC boundary </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC boundary type &lt;atom-type-id&gt;</p>
<ul>
<li>&lt;atom-type-id&gt; = type id for atoms that represent a ficticious boundary internal to the FE mesh </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC boundary type ghost_atoms </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to define the atoms that represent the ficticious boundary internal to the FE mesh. For fully overlapped MD/FE domains with periodic boundary conditions no boundary atoms should be defined. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_boundary_dynamics">fix_modify AtC boundary_dynamics </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC boundary_dynamics &lt; on | damped_harmonic | prescribed | coupled | none &gt; [args] <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets different schemes for controlling boundary atoms. On will integrate the boundary atoms using the velocity-verlet algorithm. Damped harmonic uses a mass/spring/dashpot for the boundary atoms with added arguments of the damping and spring constants followed by the ratio of the boundary type mass to the desired mass. Prescribed forces the boundary atoms to follow the finite element displacement. Coupled does the same. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Boundary atoms must be specified. When using swaps between internal and boundary atoms, the initial configuration must have already correctly partitioned the two. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>prescribed on </p>
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<h1><a class="anchor" id="man_boundary_faceset">fix_modify AtC boundary_faceset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC boundary_faceset &lt;is | add&gt; [args] </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p>fix_modify AtC boundary_faceset is obndy </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>This command species the faceset name when using a faceset to compute the MD/FE boundary fluxes. The faceset must already exist. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>This is only valid when fe_md_boundary is set to faceset. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
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<h1><a class="anchor" id="man_boundary_integral">fix_modify AtC output boundary_integral </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC output boundary_integral [field] faceset [name]</p>
<ul>
<li>field (string) : name of hardy field</li>
<li>name (string) : name of faceset </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC output boundary_integral stress faceset loop1 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_consistent_fe_initialization">fix_modify AtC consistent_fe_initialization </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC consistent_fe_initialization &lt;on | off&gt;</p>
<ul>
<li>&lt;on|off&gt; = switch to activiate/deactiviate the intial setting of FE intrinsic field to match the projected MD field </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc consistent_fe_initialization on </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Determines whether AtC initializes FE intrinsic fields (e.g., temperature) to match the projected MD values. This is particularly useful for fully overlapping simulations. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Can be used with: thermal, two_temperature. Cannot be used with time filtering on. Does not include boundary nodes. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Default is off </p>
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<h1><a class="anchor" id="man_contour_integral">fix_modify AtC output contour_integral </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC output contour_integral [field] faceset [name] &lt;axis [x | y | z ]&gt;</p>
<ul>
<li>field (string) : name of hardy field</li>
<li>name (string) : name of faceset</li>
<li>axis (string) : x or y or z </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC output contour_integral stress faceset loop1 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_control">fix_modify AtC control </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control &lt;physics_type&gt; &lt;solution_parameter&gt; </p>
<p><br/>
</p>
<ul>
<li>physics_type (string) = thermal | momentum<br/>
</li>
<li>solution_parameter (string) = max_iterations | tolerance<br/>
</li>
</ul>
<p>fix_modify AtC transfer &lt;physics_type&gt; control max_iterations &lt;max_iterations&gt;<br/>
</p>
<ul>
<li>max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers<br/>
</li>
</ul>
<p>fix_modify AtC transfer &lt;physics_type&gt; control tolerance &lt;tolerance&gt; <br/>
</p>
<ul>
<li>tolerance (float) = relative tolerance to which matrix equations will be solved<br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC control thermal max_iterations 10 </code> <br/>
<code> fix_modify AtC control momentum tolerance 1.e-5 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets the numerical parameters for the matrix solvers used in the specified control algorithm. Many solution approaches require iterative solvers, and these methods enable users to provide the maximum number of iterations and the relative tolerance. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only for be used with specific controllers : thermal, momentum <br/>
They are ignored if a lumped solution is requested </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>max_iterations is the number of rows in the matrix<br/>
tolerance is 1.e-10 </p>
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<h1><a class="anchor" id="man_control_momentum">fix_modify AtC control momentum </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control momentum none <br/>
</p>
<p>fix_modify AtC control momentum rescale &lt;frequency&gt;<br/>
</p>
<ul>
<li>frequency (int) = time step frequency for applying displacement and velocity rescaling <br/>
</li>
</ul>
<p>fix_modify AtC control momentum glc_displacement <br/>
</p>
<p>fix_modify AtC control momentum glc_velocity <br/>
</p>
<p>fix_modify AtC control momentum hoover <br/>
</p>
<p>fix_modify AtC control momentum flux [faceset face_set_id, interpolate]</p>
<ul>
<li>face_set_id (string) = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation<br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p>fix_modify AtC control momentum glc_velocity <br/>
fix_modify AtC control momentum flux faceset bndy_faces <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only to be used with specific transfers : elastic <br/>
rescale not valid with time filtering activated </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_control_thermal">fix_modify AtC control thermal </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control thermal &lt;control_type&gt; &lt;optional_args&gt;</p>
<ul>
<li>control_type (string) = none | rescale | hoover | flux<br/>
</li>
</ul>
<p>fix_modify AtC control thermal rescale &lt;frequency&gt; <br/>
</p>
<ul>
<li>frequency (int) = time step frequency for applying velocity rescaling <br/>
</li>
</ul>
<p>fix_modify AtC control thermal hoover <br/>
</p>
<p>fix_modify AtC control thermal flux &lt;boundary_integration_type(optional)&gt; &lt;face_set_id(optional)&gt;<br/>
</p>
<ul>
<li>boundary_integration_type (string) = faceset | interpolate<br/>
</li>
<li>face_set_id (string), optional = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation, does not work with interpolate<br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC control thermal none </code> <br/>
<code> fix_modify AtC control thermal rescale 10 </code> <br/>
<code> fix_modify AtC control thermal hoover </code> <br/>
<code> fix_modify AtC control thermal flux </code> <br/>
<code> fix_modify AtC control thermal flux faceset bndy_faces </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets the energy exchange mechansim from the finite elements to the atoms, managed through a control algorithm. Rescale computes a scale factor for each atom to match the finite element temperature. Hoover is a Gaussian least-constraint isokinetic thermostat enforces that the nodal restricted atomic temperature matches the finite element temperature. Flux is a similar mode, but rather adds energy to the atoms based on conservation of energy. Hoover and flux allows the prescription of sources or fixed temperatures on the atoms. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux) <br/>
rescale not valid with time filtering activated </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none<br/>
rescale frequency is 1<br/>
flux boundary_integration_type is interpolate </p>
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<h1><a class="anchor" id="man_control_thermal_correction_max_iterations">fix_modify AtC control thermal correction_max_iterations </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control thermal correction_max_iterations &lt;max_iterations&gt;</p>
<ul>
<li>max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers<br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC control thermal correction_max_iterations 10 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets the maximum number of iterations to compute the 2nd order in time correction term for lambda with the fractional step method. The method uses the same tolerance as the controller's matrix solver. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only for use with thermal physics using the fractional step method. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>correction_max_iterations is 20 </p>
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<h1><a class="anchor" id="man_decomposition">fix_modify AtC decomposition </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC decomposition &lt;type&gt;</p>
<ul>
<li>&lt;type&gt; = <br/>
replicated_memory: nodal information replicated on each processor <br/>
distributed_memory: only owned nodal information on processor <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc decomposition distributed_memory </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command for assigning the distribution of work and memory for parallel runs. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>replicated_memory is appropriate for simulations were the number of nodes &lt;&lt; number of atoms </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>replicated_memory </p>
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<h1><a class="anchor" id="man_electron_integration">fix_modify AtC extrinsic electron_integration </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC extrinsic electron_integration &lt;integration_type&gt; &lt;num_subcyle_steps(optional)&gt; <br/>
</p>
<ul>
<li>integration_type (string) = explicit | implicit | steady <br/>
</li>
<li>num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC extrinsic electron_integration implicit </code> <br/>
<code> fix_modify AtC extrinsic electron_integration explicit 100 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Switches between integration scheme for the electron temperature. The number of subcyling steps used to integrate the electron temperature 1 LAMMPS timestep can be manually adjusted to capture fast electron dynamics.</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>For use only with two_temperature type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br/>
</p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>implicit<br/>
subcycle_steps = 1 </p>
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<h1><a class="anchor" id="man_equilibrium_start">fix_modify AtC equilibrium_start </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC equilibrium_start &lt;on|off&gt;</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc equilibrium_start on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only needed before filtering is begun</p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_time_filter.html">fix_modify AtC filter</a></p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>on </p>
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<h1><a class="anchor" id="man_extrinsic_exchange">fix_modify AtC extrinsic exchange </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC extrinsic exchange &lt;on|off&gt;</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC extrinsic exchange on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Switches energy exchange between the MD system and electron system on and off</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Only valid for use with two_temperature type of AtC fix.</p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a></p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>on </p>
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<h1><a class="anchor" id="man_fe_md_boundary">fix_modify AtC fe_md_boundary </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC fe_md_boundary &lt;faceset | interpolate | no_boundary&gt; [args] </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc fe_md_boundary interpolate </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Specifies different methods for computing fluxes between between the MD and FE integration regions. Faceset defines a faceset separating the MD and FE regions and uses finite element face quadrature to compute the flux. Interpolate uses a reconstruction scheme to approximate the flux, which is more robust but less accurate if the MD/FE boundary does correspond to a faceset. No boundary results in no fluxes between the systems being computed. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see for how to specify the faceset name. </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Interpolate. </p>
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<h1><a class="anchor" name="man_fem_mesh">fix_modify AtC fem create mesh</a></h1><h2><a class="anchor" name="syntax">
syntax</a></h2>
fix_modify AtC fem create mesh &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;<ul>
<li>nx ny nz = number of elements in x, y, z</li><li>region-id = id of region that is to be meshed</li><li>f p p = perioidicity flags for x, y, z </li></ul>
<h2><a class="anchor" name="examples">
examples</a></h2>
<code> fix_modify AtC fem create mesh 10 1 1 feRegion p p p </code> <h2><a class="anchor" name="description">
description</a></h2>
Creates a uniform mesh in a rectangular region <h2><a class="anchor" name="restrictions">
restrictions</a></h2>
creates only uniform rectangular grids in a rectangular region <h2><a class="anchor" name="related">
related</a></h2>
<h2><a class="anchor" name="default">
default</a></h2>
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<h1><a class="anchor" id="man_filter_scale">fix_modify AtC filter scale </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC filter scale &lt;scale&gt; <br/>
</p>
<ul>
<li>scale (real) = characteristic time scale of the filter <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC filter scale 10.0 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only for be used with specific transfers: thermal, two_temperature</p>
<h2><a class="anchor" id="related">
related</a></h2>
<p><a class="el" href="man_time_filter.html">fix_modify AtC filter</a> <a class="el" href="man_filter_type.html">fix_modify AtC filter type</a></p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>0. </p>
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<h1><a class="anchor" id="man_filter_type">fix_modify AtC filter type </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC filter type &lt;exponential | step | no_filter&gt; <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC filter type exponential </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Specifies the type of time filter used. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only for be used with specific transfers: thermal, two_temperature</p>
<h2><a class="anchor" id="related">
related</a></h2>
<p><a class="el" href="man_time_filter.html">fix_modify AtC filter</a> <a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a></p>
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default</a></h2>
<p>No default. </p>
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<h1><a class="anchor" id="man_fix_atc">fix atc command </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix &lt;fixID&gt; &lt;group&gt; atc &lt;type&gt; &lt;parameter_file&gt;</p>
<ul>
<li>fixID = name of fix</li>
<li>group = name of group fix is to be applied</li>
<li>type<br/>
= thermal : thermal coupling with fields: temperature <br/>
= two_temperature : electron-phonon coupling with field: temperature and electron_temperature <br/>
= hardy : on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) <br/>
= field : on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) <br/>
</li>
<li>parameter_file = name of the file with material parameters. <br/>
note: Neither hardy nor field requires a parameter file </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix AtC internal atc thermal Ar_thermal.dat </code> <br/>
<code> fix AtC internal atc two_temperature Ar_ttm.mat </code> <br/>
<code> fix AtC internal atc hardy </code> <br/>
<code> fix AtC internal atc field </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the /post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.</p>
<p>The following coupling example is typical, but non-exhaustive:<br/>
</p>
<p><code> # ... commands to create and initialize the MD system <br/>
</code></p>
<p><code> # initial fix to designate coupling type and group to apply it to <br/>
# tag group physics material_file <br/>
fix AtC internal atc thermal Ar_thermal.mat<br/>
<br/>
# create a uniform 12 x 2 x 2 mesh that covers region contain the group <br/>
# nx ny nz region periodicity <br/>
fix_modify AtC mesh create 12 2 2 mdRegion f p p<br/>
<br/>
# specify the control method for the type of coupling <br/>
# physics control_type <br/>
fix_modify AtC thermal control flux <br/>
<br/>
# specify the initial values for the empirical field "temperature" <br/>
# field node_group value <br/>
fix_modify AtC initial temperature all 30.<br/>
<br/>
# create an output stream for nodal fields <br/>
# filename output_frequency <br/>
fix_modify AtC output atc_fe_output 100<br/>
<br/>
</code></p>
<p><code> run 1000 <br/>
</code></p>
<p>likewise for this post-processing example: <br/>
</p>
<p><code> # ... commands to create and initialize the MD system <br/>
</code></p>
<p><code> # initial fix to designate post-processing and the group to apply it to <br/>
# no material file is allowed nor required <br/>
fix AtC internal atc hardy <br/>
<br/>
# for hardy fix, specific kernel function (function type and range) to # be used as a localization function <br/>
fix AtC kernel quartic_sphere 10.0 <br/>
<br/>
# create a uniform 1 x 1 x 1 mesh that covers region contain the group <br/>
# with periodicity this effectively creats a system average <br/>
fix_modify AtC mesh create 1 1 1 box p p p <br/>
<br/>
# change from default lagrangian map to eulerian <br/>
# refreshed every 100 steps <br/>
fix_modify AtC atom_element_map eulerian 100 <br/>
<br/>
# start with no field defined <br/>
# add mass density, potential energy density, stress and temperature <br/>
fix_modify AtC fields add density energy stress temperature <br/>
<br/>
# create an output stream for nodal fields <br/>
# filename output_frequency <br/>
fix_modify AtC output nvtFE 100 text <br/>
</code></p>
<p><code> run 1000 <br/>
</code></p>
<p>the mesh's linear interpolation functions can be used as the localization function <br/>
by using the field option: <br/>
</p>
<p><code> fix AtC internal atc field <br/>
<br/>
fix_modify AtC mesh create 1 1 1 box p p p <br/>
<br/>
... <br/>
<br/>
</code></p>
<p>Note coupling and post-processing can be combined in the same simulations using separate fixes. <br/>
For detailed exposition of the theory and algorithms please see:<br/>
</p>
<ul>
<li>Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, <em> An atomistic-to-continuum coupling method for heat transfer in solids. </em> Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351. <br/>
</li>
<li>Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, <em> Calculation of stress in atomistic simulation. </em> Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319. <br/>
</li>
<li>Zimmerman, JA; Jones, RE; Templeton, JA, <em> A material frame approach for evaluating continuum variables in atomistic simulations. </em> Journal of Computational Physics (2010), 229:2364. <br/>
</li>
<li>Templeton, JA; Jones, RE; Wagner, GJ, <em> Application of a field-based method to spatially varying thermal transport problems in molecular dynamics. </em> Modelling and Simulation in Materials Science and Engineering (2010), 18:085007. <br/>
</li>
<li>Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, <em> Electron transport enhanced molecular dynamics for metals and semi-metals. </em> International Journal for Numerical Methods in Engineering (2010), 83:940. <br/>
</li>
<li>Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, <em> A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling. </em> Journal of Chemical Theory and Computation (2011), 7:1736. <br/>
</li>
<li>Mandadapu, KK; Templeton, JA; Lee, JW, <em> Polarization as a field variable from molecular dynamics simulations. </em> Journal of Chemical Physics (2013), 139:054115. <br/>
</li>
</ul>
<p>Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes <em> The finite element method </em>, Dover 2003, for the basics of FE simulation.</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.</p>
<p>Currently,</p>
<ul>
<li>the coupling is restricted to thermal physics</li>
<li>the FE computations are done in serial on each processor.</li>
</ul>
<h2><a class="anchor" id="related">
related</a></h2>
<p>fix_modify commands for setup: <br/>
</p>
<ul>
<li><a class="el" href="man_mesh_create.html">fix_modify AtC mesh create</a></li>
<li><a class="el" href="man_mesh_quadrature.html">fix_modify AtC mesh quadrature</a></li>
<li><a class="el" href="man_mesh_read.html">fix_modify AtC mesh read</a></li>
<li><a class="el" href="man_mesh_write.html">fix_modify AtC mesh write</a></li>
<li><a class="el" href="man_mesh_create_nodeset.html">fix_modify AtC mesh create_nodeset</a></li>
<li><a class="el" href="man_mesh_add_to_nodeset.html">fix_modify AtC mesh add_to_nodeset</a></li>
<li><a class="el" href="man_mesh_create_faceset_box.html">fix_modify AtC mesh create_faceset box</a></li>
<li><a class="el" href="man_mesh_create_faceset_plane.html">fix_modify AtC mesh create_faceset plane</a></li>
<li><a class="el" href="man_mesh_create_elementset.html">fix_modify AtC mesh create_elementset</a></li>
<li><a class="el" href="man_mesh_delete_elements.html">fix_modify AtC mesh delete_elements</a></li>
<li><a class="el" href="man_mesh_nodeset_to_elementset.html">fix_modify AtC mesh nodeset_to_elementset</a></li>
<li><a class="el" href="man_boundary.html">fix_modify AtC boundary</a></li>
<li><a class="el" href="man_internal_quadrature.html">fix_modify AtC internal_quadrature</a></li>
<li><a class="el" href="man_thermal_time_integration.html">fix_modify AtC time_integration (thermal)</a></li>
<li><a class="el" href="man_momentum_time_integration.html">fix_modify AtC time_integration (momentum)</a></li>
<li><a class="el" href="man_electron_integration.html">fix_modify AtC extrinsic electron_integration</a></li>
<li><a class="el" href="man_internal_element_set.html">fix_modify AtC internal_element_set</a></li>
<li><a class="el" href="man_decomposition.html">fix_modify AtC decomposition</a></li>
</ul>
<p>fix_modify commands for boundary and initial conditions:<br/>
</p>
<ul>
<li><a class="el" href="man_initial.html">fix_modify AtC initial</a></li>
<li><a class="el" href="man_fix_nodes.html">fix_modify AtC fix</a></li>
<li><a class="el" href="man_unfix_nodes.html">fix_modify AtC unfix</a></li>
<li><a class="el" href="man_fix_flux.html">fix_modify AtC fix_flux</a></li>
<li><a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a></li>
<li><a class="el" href="man_source.html">fix_modify AtC source</a></li>
<li><a class="el" href="man_remove_source.html">fix_modify AtC remove_source</a></li>
</ul>
<p>fix_modify commands for control and filtering: <br/>
</p>
<ul>
<li><a class="el" href="man_control.html">fix_modify AtC control</a></li>
<li><a class="el" href="man_control_thermal.html">fix_modify AtC control thermal</a></li>
<li><a class="el" href="man_control_thermal_correction_max_iterations.html">fix_modify AtC control thermal correction_max_iterations</a></li>
<li><a class="el" href="man_control_momentum.html">fix_modify AtC control momentum</a></li>
<li><a class="el" href="man_localized_lambda.html">fix_modify AtC control localized_lambda</a></li>
<li><a class="el" href="man_lumped_lambda_solve.html">fix_modify AtC control lumped_lambda_solve</a></li>
<li><a class="el" href="man_mask_direction.html">fix_modify AtC control mask_direction</a></li>
<li><a class="el" href="man_time_filter.html">fix_modify AtC filter</a></li>
<li><a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a></li>
<li><a class="el" href="man_filter_type.html">fix_modify AtC filter type</a></li>
<li><a class="el" href="man_equilibrium_start.html">fix_modify AtC equilibrium_start</a></li>
<li><a class="el" href="man_extrinsic_exchange.html">fix_modify AtC extrinsic exchange</a></li>
<li><a class="el" href="man_poisson_solver.html">fix_modify AtC poisson_solver</a></li>
</ul>
<p>fix_modify commands for output: <br/>
</p>
<ul>
<li><a class="el" href="man_output.html">fix_modify AtC output</a></li>
<li><a class="el" href="man_output_nodeset.html">fix_modify AtC output nodeset</a></li>
<li><a class="el" href="man_output_elementset.html">fix_modify AtC output elementset</a></li>
<li><a class="el" href="man_boundary_integral.html">fix_modify AtC output boundary_integral</a></li>
<li><a class="el" href="man_contour_integral.html">fix_modify AtC output contour_integral</a></li>
<li><a class="el" href="man_mesh_output.html">fix_modify AtC mesh output</a></li>
<li><a class="el" href="man_write_restart.html">fix_modify AtC write_restart</a></li>
<li><a class="el" href="man_read_restart.html">fix_modify AtC read_restart</a></li>
</ul>
<p>fix_modify commands for post-processing: <br/>
</p>
<ul>
<li><a class="el" href="man_hardy_kernel.html">fix_modify AtC kernel</a></li>
<li><a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
<li><a class="el" href="man_hardy_gradients.html">fix_modify AtC gradients</a></li>
<li><a class="el" href="man_hardy_rates.html">fix_modify AtC rates</a></li>
<li><a class="el" href="man_hardy_computes.html">fix_modify AtC computes</a></li>
<li><a class="el" href="man_hardy_on_the_fly.html">fix_modify AtC on_the_fly</a></li>
<li><a class="el" href="man_pair_interactions.html">fix_modify AtC pair_interactions/bond_interactions</a></li>
<li><a class="el" href="man_sample_frequency.html">fix_modify AtC sample_frequency</a></li>
<li><a class="el" href="man_set.html">fix_modify AtC set</a></li>
</ul>
<p>miscellaneous fix_modify commands: <br/>
</p>
<ul>
<li><a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a></li>
<li><a class="el" href="man_atom_weight.html">fix_modify AtC atom_weight</a></li>
<li><a class="el" href="man_write_atom_weights.html">fix_modify AtC write_atom_weights</a></li>
<li><a class="el" href="man_reset_time.html">fix_modify AtC reset_time</a></li>
<li><a class="el" href="man_reset_atomic_reference_positions.html">fix_modify AtC reset_atomic_reference_positions</a></li>
<li><a class="el" href="man_fe_md_boundary.html">fix_modify AtC fe_md_boundary</a></li>
<li><a class="el" href="man_boundary_faceset.html">fix_modify AtC boundary_faceset</a></li>
<li><a class="el" href="man_consistent_fe_initialization.html">fix_modify AtC consistent_fe_initialization</a></li>
<li><a class="el" href="man_mass_matrix.html">fix_modify AtC mass_matrix</a></li>
<li><a class="el" href="man_material.html">fix_modify AtC material</a></li>
<li><a class="el" href="man_atomic_charge.html">fix_modify AtC atomic_charge</a></li>
<li><a class="el" href="man_source_integration.html">fix_modify AtC source_integration</a></li>
<li><a class="el" href="man_temperature_definition.html">fix_modify AtC temperature_definition</a></li>
<li><a class="el" href="man_track_displacement.html">fix_modify AtC track_displacement</a></li>
<li><a class="el" href="man_boundary_dynamics.html">fix_modify AtC boundary_dynamics</a></li>
<li><a class="el" href="man_add_species.html">fix_modify AtC add_species</a></li>
<li><a class="el" href="man_add_molecule.html">fix_modify AtC add_molecule</a></li>
<li><a class="el" href="man_remove_species.html">fix_modify AtC remove_species</a></li>
<li><a class="el" href="man_remove_molecule.html">fix_modify AtC remove_molecule</a></li>
</ul>
<p>Note: a set of example input files with the attendant material files are included with this package </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_fix_flux">fix_modify AtC fix_flux </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC fix_flux &lt;field&gt; &lt;face_set&gt; &lt;value | function&gt;</p>
<ul>
<li>&lt;field&gt; = field name valid for type of physics, temperature | electron_temperature</li>
<li>&lt;face_set&gt; = name of set of element faces </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc fix_flux temperature faceSet 10.0 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command for fixing normal fluxes e.g. heat_flux. This command only prescribes the normal component of the physical flux, e.g. heat (energy) flux. The units are in AtC units, i.e. derived from the LAMMPS length, time, and mass scales. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Only normal fluxes (Neumann data) can be prescribed. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
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<h1><a class="anchor" id="man_fix_nodes">fix_modify AtC fix </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC fix &lt;field&gt; &lt;nodeset&gt; &lt;constant | function&gt;</p>
<ul>
<li>&lt;field&gt; = field name valid for type of physics</li>
<li>&lt;nodeset&gt; = name of set of nodes to apply boundary condition</li>
<li>&lt;constant | function&gt; = value or name of function followed by its parameters </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC fix temperature groupNAME 10. </code> <br/>
<code> fix_modify AtC fix temperature groupNAME 0 0 0 10.0 0 0 1.0 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Creates a constraint on the values of the specified field at specified nodes. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>keyword 'all' reserved in nodeset name </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_unfix_nodes.html">fix_modify AtC unfix</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_hardy_computes">fix_modify AtC computes </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC computes &lt;add | delete&gt; [per-atom compute id] &lt;volume | number&gt; <br/>
</p>
<ul>
<li>add | delete (keyword) = add or delete the calculation of an equivalent continuum field for the specified per-atom compute as volume or number density quantity <br/>
</li>
<li>per-atom compute id = name/id for per-atom compute, fields can be calculated for all per-atom computes available from LAMMPS <br/>
</li>
<li>volume | number (keyword) = field created is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> compute virial all stress/atom </code> <br/>
<code> fix_modify AtC computes add virial volume </code> <br/>
<code> fix_modify AtC computes delete virial </code> <br/>
<br/>
<code> compute centrosymmetry all centro/atom </code> <br/>
<code> fix_modify AtC computes add centrosymmetry number </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Calculates continuum fields corresponding to specified per-atom computes created by LAMMPS <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br/>
Per-atom compute must be specified before corresponding continuum field can be requested <br/>
</p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>See manual page for compute </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No defaults exist for this command </p>
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<h1><a class="anchor" id="man_hardy_fields">fix_modify AtC fields </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC fields &lt;all | none&gt; <br/>
fix_modify AtC fields &lt;add | delete&gt; &lt;list_of_fields&gt; <br/>
</p>
<ul>
<li>all | none (keyword) = output all or no fields <br/>
</li>
<li>add | delete (keyword) = add or delete the listed output fields <br/>
</li>
<li>fields (keyword) = <br/>
density : mass per unit volume <br/>
displacement : displacement vector <br/>
momentum : momentum per unit volume <br/>
velocity : defined by momentum divided by density <br/>
projected_velocity : simple kernel estimation of atomic velocities <br/>
temperature : temperature derived from the relative atomic kinetic energy (as done by ) <br/>
kinetic_temperature : temperature derived from the full kinetic energy <br/>
number_density : simple kernel estimation of number of atoms per unit volume <br/>
stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis <br/>
transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis <br/>
heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian <br/>
potential_energy : potential energy per unit volume <br/>
kinetic_energy : kinetic energy per unit volume <br/>
thermal_energy : thermal energy (kinetic energy - continuum kinetic energy) per unit volume <br/>
internal_energy : total internal energy (potential + thermal) per unit volume <br/>
energy : total energy (potential + kinetic) per unit volume <br/>
number_density : number of atoms per unit volume <br/>
eshelby_stress: configurational stress (energy-momentum) tensor defined by Eshelby [References: Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335] <br/>
vacancy_concentration: volume fraction of vacancy content <br/>
type_concentration: volume fraction of a specific atom type <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC fields add velocity temperature </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Allows modification of the fields calculated and output by the transfer class. The commands are cumulative, e.g.<br/>
<code> fix_modify AtC fields none </code> <br/>
followed by <br/>
<code> fix_modify AtC fields add velocity temperature </code> <br/>
will only output the velocity and temperature fields. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix, see <a class="el" href="man_fix_atc.html">fix atc command</a>. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>See <a class="el" href="man_hardy_gradients.html">fix_modify AtC gradients</a> , <a class="el" href="man_hardy_rates.html">fix_modify AtC rates</a> and <a class="el" href="man_hardy_computes.html">fix_modify AtC computes</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>By default, no fields are output </p>
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<h1><a class="anchor" id="man_hardy_gradients">fix_modify AtC gradients </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC gradients &lt;add | delete&gt; &lt;list_of_fields&gt; <br/>
</p>
<ul>
<li>add | delete (keyword) = add or delete the calculation of gradients for the listed output fields <br/>
</li>
<li>fields (keyword) = <br/>
gradients can be calculated for all fields listed in <a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC gradients add temperature velocity stress </code> <br/>
<code> fix_modify AtC gradients delete velocity </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Requests calculation and ouput of gradients of the fields from the transfer class. These gradients will be with regard to spatial or material coordinate for eulerian or lagrangian analysis, respectively, as specified by atom_element_map (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ) </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No gradients are calculated by default </p>
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<h1><a class="anchor" id="man_hardy_kernel">fix_modify AtC kernel </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC kernel &lt;type&gt; &lt;parameters&gt;</p>
<ul>
<li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/>
</li>
<li>parameters :<br/>
step = radius (double) <br/>
cell = hx, hy, hz (double) or h (double) <br/>
cubic_bar = half-width (double) <br/>
cubic_cylinder = radius (double) <br/>
cubic_sphere = radius (double) <br/>
quartic_bar = half-width (double) <br/>
quartic_cylinder = radius (double) <br/>
quartic_sphere = radius (double) <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC kernel cell 1.0 1.0 1.0 </code> <br/>
<code> fix_modify AtC kernel quartic_sphere 10.0 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy AtC fix <br/>
For bar kernel types, half-width oriented along x-direction <br/>
For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/>
( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No default </p>
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<h1><a class="anchor" id="man_hardy_on_the_fly">fix_modify AtC on_the_fly </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC on_the_fly &lt;bond | kernel&gt; &lt;optional on | off&gt; <br/>
- bond | kernel (keyword) = specifies on-the-fly calculation of bond or kernel matrix elements <br/>
</p>
<ul>
<li>on | off (keyword) = activate or discontinue on-the-fly mode <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC on_the_fly bond on </code> <br/>
<code> fix_modify AtC on_the_fly kernel </code> <br/>
<code> fix_modify AtC on_the_fly kernel off </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Overrides normal mode of pre-calculating and storing bond pair-to-node a nd kernel atom-to-node matrices. If activated, will calculate elements of t hese matrices during repeated calls of field computations (i.e. "on-the-fly") and not store them for future use. <br/>
on flag is optional - if omitted, on_the_fly will be activated for the s pecified matrix. Can be deactivated using off flag. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>By default, on-the-fly calculation is not active (i.e. off). However, code does a memory allocation check to determine if it can store all needed bond and kernel matrix ele ments. If this allocation fails, on-the-fly is activated. <br/>
</p>
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<h1><a class="anchor" id="man_hardy_rates">fix_modify AtC rates </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC rates &lt;add | delete&gt; &lt;list_of_fields&gt; <br/>
</p>
<ul>
<li>add | delete (keyword) = add or delete the calculation of rates (time derivatives) for the listed output fields <br/>
</li>
<li>fields (keyword) = <br/>
rates can be calculated for all fields listed in <a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC rates add temperature velocity stress </code> <br/>
<code> fix_modify AtC rates delete stress </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Requests calculation and ouput of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No rates are calculated by default </p>
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<h1><a class="anchor" id="man_initial">fix_modify AtC initial </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC initial &lt;field&gt; &lt;nodeset&gt; &lt;constant | function&gt;</p>
<ul>
<li>&lt;field&gt; = field name valid for type of physics, temperature | electron_temperature</li>
<li>&lt;nodeset&gt; = name of set of nodes to apply initial condition</li>
<li>&lt;constant | function&gt; = value or name of function followed by its parameters </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc initial temperature groupNAME 10. </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets the initial values for the specified field at the specified nodes. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>keyword 'all' reserved in nodeset name </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_internal_atom_integrate">fix_modify AtC internal_atom_integrate </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC internal_atom_integrate &lt;on | off&gt; <code> fix_modify AtC internal_atom_integrate on </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Has AtC perform time integration for the atoms in the group on which it operates. This does not include boundary atoms. </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>on for coupling methods, off for post-processors off </p>
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<h1><a class="anchor" id="man_internal_element_set">fix_modify AtC internal_element_set </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC internal_element_set &lt;element-set-name&gt;</p>
<ul>
<li>&lt;element-set-name&gt; = name of element set defining internal region, or off </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC internal_element_set myElementSet </code> <code> fix_modify AtC internal_element_set off </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Enables AtC to base the region for internal atoms to be an element set. If no ghost atoms are used, all the AtC atoms must be constrained to remain in this element set by the user, e.g., with walls. If boundary atoms are used in conjunction with Eulerian atom maps AtC will partition all atoms of a boundary or internal type to be of type internal if they are in the internal region or to be of type boundary otherwise. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>If boundary atoms are used in conjunction with Eulerian atom maps, the Eulerian reset frequency must be an integer multiple of the Lammps reneighbor frequency </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see atom_element_map_type and boundary </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>off </p>
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<h1><a class="anchor" id="man_internal_quadrature">fix_modify AtC internal_quadrature </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify atc internal_quadrature &lt;on | off&gt; [region] </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc internal_quadrature off </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to use or not use atomic quadrature on internal elements fully filled with atoms. By turning the internal quadrature off these elements do not contribute to the governing PDE and the fields at the internal nodes follow the weighted averages of the atomic data. </p>
<h2><a class="anchor" id="optional">
optional</a></h2>
<p>Optional region tag specifies which finite element nodes will be treated as being within the MD region. This option is only valid with internal_quadrature off. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>on </p>
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<h1><a class="anchor" id="man_kernel_function">fix_modify AtC kernel </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC kernel &lt;type&gt; &lt;parameters&gt;</p>
<ul>
<li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/>
</li>
<li>parameters :<br/>
step = radius (double) <br/>
cell = hx, hy, hz (double) or h (double) <br/>
cubic_bar = half-width (double) <br/>
cubic_cylinder = radius (double) <br/>
cubic_sphere = radius (double) <br/>
quartic_bar = half-width (double) <br/>
quartic_cylinder = radius (double) <br/>
quartic_sphere = radius (double) <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p>fix_modify AtC kernel cell 1.0 1.0 1.0 fix_modify AtC kernel quartic_sphere 10.0 </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy AtC fix <br/>
For bar kernel types, half-width oriented along x-direction <br/>
For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/>
( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No default </p>
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<h1><a class="anchor" id="man_localized_lambda">fix_modify AtC control localized_lambda </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control localized_lambda &lt;on|off&gt; </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc control localized_lambda on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Turns on localization algorithms for control algorithms to restrict the influence of FE coupling or boundary conditions to a region near the boundary of the MD region. Control algorithms will not affect atoms in elements not possessing faces on the boundary of the region. Flux-based control is localized via row-sum lumping while quantity control is done by solving a truncated matrix equation. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Default is off. </p>
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<h1><a class="anchor" id="man_lumped_lambda_solve">fix_modify AtC control lumped_lambda_solve </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control lumped_lambda_solve &lt;on|off&gt; </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc control lumped_lambda_solve on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to use or not use lumped matrix for lambda solve </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
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default</a></h2>
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<h1><a class="anchor" id="man_mask_direction">fix_modify AtC control mask_direction </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control mask_direction &lt;direction&gt; &lt;on|off&gt; </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc control mask_direction 0 on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to mask out certain dimensions from the atomic regulator </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
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<h1><a class="anchor" id="man_mass_matrix">fix_modify AtC mass_matrix </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mass_matrix &lt;fe | md_fe&gt;</p>
<ul>
<li>&lt;fe | md_fe&gt; = activiate/deactiviate using the FE mass matrix in the MD region </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc mass_matrix fe </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Determines whether AtC uses the FE mass matrix based on Gaussian quadrature or based on atomic quadrature in the MD region. This is useful for fully overlapping simulations to improve efficiency. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Should not be used unless the FE region is contained within the MD region, otherwise the method will be unstable and inaccurate </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Default is off </p>
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<h1><a class="anchor" id="man_material">fix_modify AtC material </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC material [elementset_name] [material_id] <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC material gap_region 2</code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets the material model in elementset_name to be of type material_id. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>The element set must already be created and the material must be specified in the material file given the the atc fix on construction </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>All elements default to the first material in the material file. </p>
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<h1><a class="anchor" id="man_mesh_add_to_nodeset">fix_modify AtC mesh add_to_nodeset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh add_to_nodeset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
<ul>
<li>&lt;id&gt; = id of FE nodeset to be added to</li>
<li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains the desired nodes to be added </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh add_to_nodeset lbc -11.9 -11 -12 12 -12 12 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to add nodes to an already existing FE nodeset. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Coordinates are assumed to be in lattice units. </p>
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<h1><a class="anchor" id="man_mesh_create">fix_modify AtC mesh create </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh create &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt; <br/>
</p>
<ul>
<li>nx ny nz = number of elements in x, y, z</li>
<li>region-id = id of region that is to be meshed</li>
<li>f p p = periodicity flags for x, y, z </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh create 10 1 1 feRegion p p p </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Creates a uniform mesh in a rectangular region </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Creates only uniform rectangular grids in a rectangular region </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p><a class="el" href="man_mesh_quadrature.html">fix_modify AtC mesh quadrature</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>When created, mesh defaults to gauss2 (2-point Gaussian) quadrature. Use "mesh quadrature" command to change quadrature style. </p>
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<h1><a class="anchor" id="man_mesh_create_elementset">fix_modify AtC mesh create_elementset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC create_elementset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
<ul>
<li>&lt;id&gt; = id to assign to the collection of FE element</li>
<li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains only the desired elements </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to assign an id to a set of FE elements to be used subsequently in defining material and mesh-based operations. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Only viable for rectangular grids. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Coordinates are assumed to be in lattice units. </p>
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<h1><a class="anchor" id="man_mesh_create_faceset_box">fix_modify AtC mesh create_faceset box </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh create_faceset &lt;id&gt; box &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; &lt;in|out&gt; [units]</p>
<ul>
<li>&lt;id&gt; = id to assign to the collection of FE faces</li>
<li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that is coincident with the desired FE faces</li>
<li>&lt;in|out&gt; = "in" gives inner faces to the box, "out" gives the outer faces to the box</li>
<li>units = option to specify real as opposed to lattice units </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 out </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to assign an id to a set of FE faces. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Only viable for rectangular grids. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>The default options are units = lattice and the use of outer faces </p>
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<h1><a class="anchor" id="man_mesh_create_faceset_plane">fix_modify AtC mesh create_faceset plane </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh create_faceset &lt;id&gt; plane &lt;x|y|z&gt; &lt;val1&gt; &lt;x|y|z&gt; &lt;lval2&gt; &lt;uval2&gt; [units]</p>
<ul>
<li>&lt;id&gt; = id to assign to the collection of FE faces</li>
<li>&lt;x|y|z&gt; = coordinate directions that define plane on which faceset lies</li>
<li>&lt;val1&gt;,&lt;lval2&gt;,&lt;uval2&gt; = plane is specified as the x|y|z=val1 plane bounded by the segments x|y|z = [lval2,uval2]</li>
<li>units = option to specify real as opposed to lattice units </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh create_faceset xyplane plane y 0 x -4 0 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to assign an id to a set of FE faces. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Only viable for rectangular grids. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>The default option is units = lattice. </p>
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<h1><a class="anchor" id="man_mesh_create_nodeset">fix_modify AtC mesh create_nodeset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh create_nodeset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
<ul>
<li>&lt;id&gt; = id to assign to the collection of FE nodes</li>
<li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains only the desired nodes </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to assign an id to a set of FE nodes to be used subsequently in defining boundary conditions. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Coordinates are assumed to be in lattice units. </p>
</div>
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<h1><a class="anchor" id="man_mesh_delete_elements">fix_modify AtC mesh delete_elements </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh delete_elements &lt;element_set&gt;</p>
<ul>
<li>&lt;element_set&gt; = name of an element set </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC delete_elements gap </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Deletes a group of elements from the mesh. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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