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-<!-- HTML_ONLY -->
-<HEAD>
-<TITLE>LAMMPS-ICMS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="5 Oct 2015 version">
-<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
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-<CENTER><H3>LAMMPS-ICMS Documentation
-</H3></CENTER>
-<CENTER><H4>5 Oct 2015 version
-</H4></CENTER>
-<H4>Version info:
-</H4>
-<P>The LAMMPS "version" is the date when it was released, such as 1 May
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+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+</ul>
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+ <a href="Section_commands.html#comm">Commands</a>
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+
+ <div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
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+ <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+ <div itemprop="articleBody">
+
+ <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="aug-2015-version">
+<h2>10 Aug 2015 version<a class="headerlink" href="#aug-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 “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 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 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
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>
<P>LAMMPS-ICMS is an experimental variant of LAMMPS with additional
features made available for testing before they will be submitted
for inclusion into the official LAMMPS tree. The source code is
based on the official LAMMPS svn repository mirror at the Institute
for Computational Molecular Science at Temple University and generally
kept up-to-date as much as possible. Sometimes, e.g. when additional
development work is needed to adapt the upstream changes into
LAMMPS-ICMS it can take longer until synchronization; and occasionally,
e.g. in case of the rewrite of the multi-threading support, the
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>
<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.
<LI>If you browse the HTML doc pages included in your tarball, they
describe the version you have.
<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.
-</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.</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
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 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 class="reference external" 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 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
+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
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 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>
-
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-<!-- END_HTML_ONLY -->
-
-</BODY>
-
-</HTML>
+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’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-tool">2.4. Building LAMMPS via the Make.py tool</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#build-instructions-for-compress-package">4.2. Build instructions for COMPRESS package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-gpu-package">4.3. Build instructions for GPU package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kim-package">4.4. Build instructions for KIM package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kokkos-package">4.5. Build instructions for KOKKOS package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kspace-package">4.6. Build instructions for KSPACE package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-meam-package">4.7. Build instructions for MEAM package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-poems-package">4.8. Build instructions for POEMS package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-python-package">4.9. Build instructions for PYTHON package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-reax-package">4.10. Build instructions for REAX package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-voronoi-package">4.11. Build instructions for VORONOI package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-xtc-package">4.12. Build instructions for XTC package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.13. User packages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-atc-package">4.14. USER-ATC package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-awpmd-package">4.15. USER-AWPMD package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cg-cmm-package">4.16. USER-CG-CMM package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.17. USER-COLVARS package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.18. USER-CUDA package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.19. USER-DIFFRACTION package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.20. USER-DRUDE package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.21. USER-EFF package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.22. USER-FEP package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-h5md-package">4.23. USER-H5MD package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.24. USER-INTEL package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.25. USER-LB package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.26. USER-MISC package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.27. USER-MOLFILE package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.28. USER-OMP package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.29. USER-PHONON package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.30. USER-QMMM package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.31. USER-QTB package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.32. USER-REAXC package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smd-package">4.33. USER-SMD package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.34. 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 & 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 & extending LAMMPS</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#atom-styles">10.1. Atom styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#compute-styles">10.3. Compute styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-styles">10.4. Dump styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-custom-output-options">10.5. Dump custom output options</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#fix-styles">10.6. Fix styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#input-script-commands">10.7. Input script commands</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#kspace-computations">10.8. Kspace computations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#minimization-styles">10.9. Minimization styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#region-styles">10.11. Region styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#body-styles">10.12. Body styles</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#variable-options">10.14. Variable options</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#extending-python-with-mpi-to-run-in-parallel">11.5. Extending Python with MPI to run in parallel</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_python.html#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#common-problems">12.1. Common problems</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#reporting-bugs">12.2. Reporting bugs</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error-warning-messages">12.3. Error & warning messages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error">12.4. Errors:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#warnings">12.5. Warnings:</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="Section_history.html#coming-attractions">13.1. Coming attractions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_history.html#past-versions">13.2. Past versions</a></li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+</div>
+<div class="section" id="indices-and-tables">
+<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
+<ul class="simple">
+<li><a class="reference internal" href="genindex.html"><span>Index</span></a></li>
+<li><a class="reference internal" href="search.html"><span>Search Page</span></a></li>
+</ul>
+</BODY></div>
+
+
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+
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+
+ <a href="Section_intro.html" class="btn btn-neutral float-right" title="1. Introduction" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+
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+ </div>
+
+
+ <hr/>
+
+ <div role="contentinfo">
+ <p>
+ © Copyright .
+ </p>
+ </div>
+ Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
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+ var DOCUMENTATION_OPTIONS = {
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\ No newline at end of file
diff --git a/doc/Manual.html.html b/doc/Manual.html.html
index 25313b599..f76689504 100644
--- a/doc/Manual.html.html
+++ b/doc/Manual.html.html
@@ -1,318 +1,318 @@
<HTML>
<HTML>
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="25 Sep 2015 version">
+<META NAME="docnumber" CONTENT="22 Oct 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>
<BODY>
<!-- END_HTML_ONLY -->
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H1></H1>
<P><CENTER><H3>LAMMPS Documentation
</H3></CENTER>
-<CENTER><H4>25 Sep 2015 version
+<CENTER><H4>22 Oct 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 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>
<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.
</P>
<P><LI>If you browse the HTML doc pages included in your tarball, they
describe the version you have.
</P>
<P><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.
</P>
<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.
</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 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 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 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>
<!-- END_HTML_ONLY -->
</BODY>
</HTML>
</HTML>
diff --git a/doc/Manual.txt b/doc/Manual.txt
index 792972943..429e86719 100644
--- a/doc/Manual.txt
+++ b/doc/Manual.txt
@@ -1,319 +1,319 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="5 Oct 2015 version">
+<META NAME="docnumber" CONTENT="22 Oct 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>
<BODY>
<!-- END_HTML_ONLY -->
"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
<H1></H1>
LAMMPS-ICMS Documentation :c,h3
5 Oct 2015 version :c,h4
Version info: :h4
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 "this page of
the WWW site"_bug. 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).
LAMMPS-ICMS is an experimental variant of LAMMPS with additional
features made available for testing before they will be submitted
for inclusion into the official LAMMPS tree. The source code is
based on the official LAMMPS svn repository mirror at the Institute
for Computational Molecular Science at Temple University and generally
kept up-to-date as much as possible. Sometimes, e.g. when additional
development work is needed to adapt the upstream changes into
LAMMPS-ICMS it can take longer until synchronization; and occasionally,
e.g. in case of the rewrite of the multi-threading support, the
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.
If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of upstream LAMMPS, but may be
missing some new features in LAMMPS-ICMS. :ulb,l
If you browse the HTML doc pages included in your tarball, they
describe the version you have, however, not all new features in
LAMMPS-ICMS are documented immediately. :l
The "PDF file"_Manual.pdf 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. :l
There is also a "Developer.pdf"_Developer.pdf file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS. :ule,l
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
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).
The primary developers of LAMMPS are "Steve Plimpton"_sjp, Aidan
Thompson, and Paul Crozier who can be contacted at
sjplimp,athomps,pscrozi at sandia.gov. The "LAMMPS WWW Site"_lws at
http://lammps.sandia.gov has more information about the code and its
uses.
:link(bug,http://lammps.sandia.gov/bug.html)
:link(sjp,http://www.sandia.gov/~sjplimp)
:line
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.
Once you are familiar with LAMMPS, you may want to bookmark "this
page"_Section_commands.html#comm at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.
"PDF file"_Manual.pdf of the entire manual, generated by
"htmldoc"_http://freecode.com/projects/htmldoc
<!-- RST
.. toctree::
:maxdepth: 2
- :numbered: // comment
+ :numbered:
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
Indices and tables
==================
-* :ref:`genindex` // comment
-* :ref:`search` // comment
+* :ref:`genindex`
+* :ref:`search`
END_RST -->
<!-- HTML_ONLY -->
"Introduction"_Section_intro.html :olb,l
1.1 "What is LAMMPS"_intro_1 :ulb,b
1.2 "LAMMPS features"_intro_2 :b
1.3 "LAMMPS non-features"_intro_3 :b
1.4 "Open source distribution"_intro_4 :b
1.5 "Acknowledgments and citations"_intro_5 :ule,b
"Getting started"_Section_start.html :l
2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b
2.2 "Making LAMMPS"_start_2 :b
2.3 "Making LAMMPS with optional packages"_start_3 :b
2.4 "Building LAMMPS via the Make.py script"_start_4 :b
2.5 "Building LAMMPS as a library"_start_5 :b
2.6 "Running LAMMPS"_start_6 :b
2.7 "Command-line options"_start_7 :b
2.8 "Screen output"_start_8 :b
2.9 "Tips for users of previous versions"_start_9 :ule,b
"Commands"_Section_commands.html :l
3.1 "LAMMPS input script"_cmd_1 :ulb,b
3.2 "Parsing rules"_cmd_2 :b
3.3 "Input script structure"_cmd_3 :b
3.4 "Commands listed by category"_cmd_4 :b
3.5 "Commands listed alphabetically"_cmd_5 :ule,b
"Packages"_Section_packages.html :l
4.1 "Standard packages"_pkg_1 :ulb,b
4.2 "User packages"_pkg_2 :ule,b
"Accelerating LAMMPS performance"_Section_accelerate.html :l
5.1 "Measuring performance"_acc_1 :ulb,b
5.2 "Algorithms and code options to boost performace"_acc_2 :b
5.3 "Accelerator packages with optimized styles"_acc_3 :b
5.3.1 "USER-CUDA package"_accelerate_cuda.html :ulb,b
5.3.2 "GPU package"_accelerate_gpu.html :b
5.3.3 "USER-INTEL package"_accelerate_intel.html :b
5.3.4 "KOKKOS package"_accelerate_kokkos.html :b
5.3.5 "USER-OMP package"_accelerate_omp.html :b
5.3.6 "OPT package"_accelerate_opt.html :ule,b
5.4 "Comparison of various accelerator packages"_acc_4 :ule,b
"How-to discussions"_Section_howto.html :l
6.1 "Restarting a simulation"_howto_1 :ulb,b
6.2 "2d simulations"_howto_2 :b
6.3 "CHARMM and AMBER force fields"_howto_3 :b
6.4 "Running multiple simulations from one input script"_howto_4 :b
6.5 "Multi-replica simulations"_howto_5 :b
6.6 "Granular models"_howto_6 :b
6.7 "TIP3P water model"_howto_7 :b
6.8 "TIP4P water model"_howto_8 :b
6.9 "SPC water model"_howto_9 :b
6.10 "Coupling LAMMPS to other codes"_howto_10 :b
6.11 "Visualizing LAMMPS snapshots"_howto_11 :b
6.12 "Triclinic (non-orthogonal) simulation boxes"_howto_12 :b
6.13 "NEMD simulations"_howto_13 :b
6.14 "Finite-size spherical and aspherical particles"_howto_14 :b
6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_howto_15 :b
6.16 "Thermostatting, barostatting, and compute temperature"_howto_16 :b
6.17 "Walls"_howto_17 :b
6.18 "Elastic constants"_howto_18 :b
6.19 "Library interface to LAMMPS"_howto_19 :b
6.20 "Calculating thermal conductivity"_howto_20 :b
6.21 "Calculating viscosity"_howto_21 :b
6.22 "Calculating a diffusion coefficient"_howto_22 :b
6.23 "Using chunks to calculate system properties"_howto_23 :b
6.24 "Setting parameters for pppm/disp"_howto_24 :b
6.25 "Polarizable models"_howto_25 :b
6.26 "Adiabatic core/shell model"_howto_26 :b
6.27 "Drude induced dipoles"_howto_27 :ule,b
"Example problems"_Section_example.html :l
"Performance & scalability"_Section_perf.html :l
"Additional tools"_Section_tools.html :l
"Modifying & extending LAMMPS"_Section_modify.html :l
10.1 "Atom styles"_mod_1 :ulb,b
10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b
10.3 "Compute styles"_mod_3 :b
10.4 "Dump styles"_mod_4 :b
10.5 "Dump custom output options"_mod_5 :b
10.6 "Fix styles"_mod_6 :b
10.7 "Input script commands"_mod_7 :b
10.8 "Kspace computations"_mod_8 :b
10.9 "Minimization styles"_mod_9 :b
10.10 "Pairwise potentials"_mod_10 :b
10.11 "Region styles"_mod_11 :b
10.12 "Body styles"_mod_12 :b
10.13 "Thermodynamic output options"_mod_13 :b
10.14 "Variable options"_mod_14 :b
10.15 "Submitting new features for inclusion in LAMMPS"_mod_15 :ule,b
"Python interface"_Section_python.html :l
11.1 "Overview of running LAMMPS from Python"_py_1 :ulb,b
11.2 "Overview of using Python from a LAMMPS script"_py_2 :b
11.3 "Building LAMMPS as a shared library"_py_3 :b
11.4 "Installing the Python wrapper into Python"_py_4 :b
11.5 "Extending Python with MPI to run in parallel"_py_5 :b
11.6 "Testing the Python-LAMMPS interface"_py_6 :b
11.7 "Using LAMMPS from Python"_py_7 :b
11.8 "Example Python scripts that use LAMMPS"_py_8 :ule,b
"Errors"_Section_errors.html :l
12.1 "Common problems"_err_1 :ulb,b
12.2 "Reporting bugs"_err_2 :b
12.3 "Error & warning messages"_err_3 :ule,b
"Future and history"_Section_history.html :l
13.1 "Coming attractions"_hist_1 :ulb,b
13.2 "Past versions"_hist_2 :ule,b
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<div class="section" id="accelerating-lammps-performance">
<h1>5. Accelerating LAMMPS performance<a class="headerlink" href="#accelerating-lammps-performance" title="Permalink to this headline">¶</a></h1>
<p>This section describes various methods for improving LAMMPS
performance for different classes of problems running on different
kinds of machines.</p>
<p>There are two thrusts to the discussion that follows. The
first is using code options that implement alternate algorithms
that can speed-up a simulation. The second is to use one
of the several accelerator packages provided with LAMMPS that
contain code optimized for certain kinds of hardware, including
multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors.</p>
<ul class="simple">
<li>5.1 <a class="reference internal" href="#acc-1"><span>Measuring performance</span></a></li>
<li>5.2 <a class="reference internal" href="#acc-2"><span>Algorithms and code options to boost performace</span></a></li>
<li>5.3 <a class="reference internal" href="#acc-3"><span>Accelerator packages with optimized styles</span></a></li>
<li>5.3.1 <a class="reference internal" href="accelerate_cuda.html"><em>USER-CUDA package</em></a></li>
<li>5.3.2 <a class="reference internal" href="accelerate_gpu.html"><em>GPU package</em></a></li>
<li>5.3.3 <a class="reference internal" href="accelerate_intel.html"><em>USER-INTEL package</em></a></li>
<li>5.3.4 <a class="reference internal" href="accelerate_kokkos.html"><em>KOKKOS package</em></a></li>
<li>5.3.5 <a class="reference internal" href="accelerate_omp.html"><em>USER-OMP package</em></a></li>
<li>5.3.6 <a class="reference internal" href="accelerate_opt.html"><em>OPT package</em></a></li>
<li>5.4 <a class="reference internal" href="#acc-4"><span>Comparison of various accelerator packages</span></a></li>
</ul>
<p>The <a class="reference external" href="http://lammps.sandia.gov/bench.html">Benchmark page</a> of the LAMMPS
web site gives performance results for the various accelerator
packages discussed in Section 5.2, for several of the standard LAMMPS
benchmark problems, as a function of problem size and number of
compute nodes, on different hardware platforms.</p>
<div class="section" id="measuring-performance">
<span id="acc-1"></span><h2>5.1. Measuring performance<a class="headerlink" href="#measuring-performance" title="Permalink to this headline">¶</a></h2>
<p>Before trying to make your simulation run faster, you should
understand how it currently performs and where the bottlenecks are.</p>
<p>The best way to do this is run the your system (actual number of
atoms) for a modest number of timesteps (say 100 steps) on several
different processor counts, including a single processor if possible.
Do this for an equilibrium version of your system, so that the
100-step timings are representative of a much longer run. There is
typically no need to run for 1000s of timesteps to get accurate
timings; you can simply extrapolate from short runs.</p>
<p>For the set of runs, look at the timing data printed to the screen and
log file at the end of each LAMMPS run. <a class="reference internal" href="Section_start.html#start-8"><span>This section</span></a> of the manual has an overview.</p>
<p>Running on one (or a few processors) should give a good estimate of
the serial performance and what portions of the timestep are taking
the most time. Running the same problem on a few different processor
counts should give an estimate of parallel scalability. I.e. if the
simulation runs 16x faster on 16 processors, its 100% parallel
efficient; if it runs 8x faster on 16 processors, it’s 50% efficient.</p>
<p>The most important data to look at in the timing info is the timing
breakdown and relative percentages. For example, trying different
options for speeding up the long-range solvers will have little impact
if they only consume 10% of the run time. If the pairwise time is
dominating, you may want to look at GPU or OMP versions of the pair
style, as discussed below. Comparing how the percentages change as
you increase the processor count gives you a sense of how different
operations within the timestep are scaling. Note that if you are
running with a Kspace solver, there is additional output on the
breakdown of the Kspace time. For PPPM, this includes the fraction
spent on FFTs, which can be communication intensive.</p>
<p>Another important detail in the timing info are the histograms of
atoms counts and neighbor counts. If these vary widely across
processors, you have a load-imbalance issue. This often results in
inaccurate relative timing data, because processors have to wait when
communication occurs for other processors to catch up. Thus the
reported times for “Communication” or “Other” may be higher than they
really are, due to load-imbalance. If this is an issue, you can
uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
LAMMPS, to obtain synchronized timings.</p>
<hr class="docutils" />
</div>
<div class="section" id="general-strategies">
<span id="acc-2"></span><h2>5.2. General strategies<a class="headerlink" href="#general-strategies" title="Permalink to this headline">¶</a></h2>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">this section 5.2 is still a work in progress</p>
</div>
<p>Here is a list of general ideas for improving simulation performance.
Most of them are only applicable to certain models and certain
bottlenecks in the current performance, so let the timing data you
generate be your guide. It is hard, if not impossible, to predict how
much difference these options will make, since it is a function of
problem size, number of processors used, and your machine. There is
no substitute for identifying performance bottlenecks, and trying out
various options.</p>
<ul class="simple">
<li>rRESPA</li>
<li>2-FFT PPPM</li>
<li>Staggered PPPM</li>
<li>single vs double PPPM</li>
<li>partial charge PPPM</li>
<li>verlet/split run style</li>
<li>processor command for proc layout and numa layout</li>
<li>load-balancing: balance and fix balance</li>
</ul>
<p>2-FFT PPPM, also called <em>analytic differentiation</em> or <em>ad</em> PPPM, uses
2 FFTs instead of the 4 FFTs used by the default <em>ik differentiation</em>
PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
cost is the performance bottleneck (typically large problems running
on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.</p>
<p>Staggered PPPM performs calculations using two different meshes, one
shifted slightly with respect to the other. This can reduce force
aliasing errors and increase the accuracy of the method, but also
doubles the amount of work required. For high relative accuracy, using
staggered PPPM allows one to half the mesh size in each dimension as
compared to regular PPPM, which can give around a 4x speedup in the
kspace time. However, for low relative accuracy, using staggered PPPM
gives little benefit and can be up to 2x slower in the kspace
time. For example, the rhodopsin benchmark was run on a single
processor, and results for kspace time vs. relative accuracy for the
different methods are shown in the figure below. For this system,
staggered PPPM (using ik differentiation) becomes useful when using a
relative accuracy of slightly greater than 1e-5 and above.</p>
<img alt="_images/rhodo_staggered.jpg" class="align-center" src="_images/rhodo_staggered.jpg" />
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Using staggered PPPM may not give the same increase in
accuracy of energy and pressure as it does in forces, so some caution
must be used if energy and/or pressure are quantities of interest,
such as when using a barostat.</p>
</div>
<hr class="docutils" />
</div>
<div class="section" id="packages-with-optimized-styles">
<span id="acc-3"></span><h2>5.3. Packages with optimized styles<a class="headerlink" href="#packages-with-optimized-styles" title="Permalink to this headline">¶</a></h2>
<p>Accelerated versions of various <a class="reference internal" href="pair_style.html"><em>pair_style</em></a>,
<a class="reference internal" href="fix.html"><em>fixes</em></a>, <a class="reference internal" href="compute.html"><em>computes</em></a>, and other commands have
been added to LAMMPS, which will typically run faster than the
standard non-accelerated versions. Some require appropriate hardware
to be present on your system, e.g. GPUs or Intel Xeon Phi
coprocessors.</p>
<p>All of these commands are in packages provided with LAMMPS. An
-overview of packages is give in <a class="reference internal" href="Section_packages.html"><em>Section packages</em></a>. These are the accelerator packages
+overview of packages is give in <a class="reference internal" href="Section_packages.html"><em>Section packages</em></a>.</p>
+<p>These are the accelerator packages
currently in LAMMPS, either as standard or user packages:</p>
<table border="1" class="docutils">
<colgroup>
<col width="44%" />
<col width="56%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="accelerate_cuda.html"><em>USER-CUDA</em></a></td>
<td>for NVIDIA GPUs</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="accelerate_gpu.html"><em>GPU</em></a></td>
<td>for NVIDIA GPUs as well as OpenCL support</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="accelerate_intel.html"><em>USER-INTEL</em></a></td>
<td>for Intel CPUs and Intel Xeon Phi</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="accelerate_kokkos.html"><em>KOKKOS</em></a></td>
<td>for GPUs, Intel Xeon Phi, and OpenMP threading</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="accelerate_omp.html"><em>USER-OMP</em></a></td>
<td>for OpenMP threading</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="accelerate_opt.html"><em>OPT</em></a></td>
<td>generic CPU optimizations</td>
</tr>
</tbody>
</table>
+<p>Inverting this list, LAMMPS currently has acceleration support for
+three kinds of hardware, via the listed packages:</p>
+<table border="1" class="docutils">
+<colgroup>
+<col width="10%" />
+<col width="90%" />
+</colgroup>
+<tbody valign="top">
+<tr class="row-odd"><td>Many-core CPUs</td>
+<td><a class="reference internal" href="accelerate_intel.html"><em>USER-INTEL</em></a>, <a class="reference internal" href="accelerate_kokkos.html"><em>KOKKOS</em></a>, <a class="reference internal" href="accelerate_omp.html"><em>USER-OMP</em></a>, <a class="reference internal" href="accelerate_opt.html"><em>OPT</em></a> packages</td>
+</tr>
+<tr class="row-even"><td>NVIDIA GPUs</td>
+<td><a class="reference internal" href="accelerate_cuda.html"><em>USER-CUDA</em></a>, <a class="reference internal" href="accelerate_gpu.html"><em>GPU</em></a>, <a class="reference internal" href="accelerate_kokkos.html"><em>KOKKOS</em></a> packages</td>
+</tr>
+<tr class="row-odd"><td>Intel Phi</td>
+<td><a class="reference internal" href="accelerate_intel.html"><em>USER-INTEL</em></a>, <a class="reference internal" href="accelerate_kokkos.html"><em>KOKKOS</em></a> packages</td>
+</tr>
+</tbody>
+</table>
+<p>Which package is fastest for your hardware may depend on the size
+problem you are running and what commands (accelerated and
+non-accelerated) are invoked by your input script. While these doc
+pages include performance guidelines, there is no substitute for
+trying out the different packages appropriate to your hardware.</p>
<p>Any accelerated style has the same name as the corresponding standard
style, except that a suffix is appended. Otherwise, the syntax for
the command that uses the style is identical, their functionality is
the same, and the numerical results it produces should also be the
same, except for precision and round-off effects.</p>
<p>For example, all of these styles are accelerated variants of the
Lennard-Jones <a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut</em></a>:</p>
<ul class="simple">
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/cuda</em></a></li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/gpu</em></a></li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/intel</em></a></li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/kk</em></a></li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/omp</em></a></li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/opt</em></a></li>
</ul>
<p>To see what accelerate styles are currently available, see
<a class="reference internal" href="Section_commands.html#cmd-5"><span>Section_commands 5</span></a> of the manual. The
doc pages for individual commands (e.g. <a class="reference internal" href="pair_lj.html"><em>pair lj/cut</em></a> or
<a class="reference internal" href="fix_nve.html"><em>fix nve</em></a>) also list any accelerated variants available
for that style.</p>
<p>To use an accelerator package in LAMMPS, and one or more of the styles
it provides, follow these general steps. Details vary from package to
package and are explained in the individual accelerator doc pages,
listed above:</p>
<table border="1" class="docutils">
<colgroup>
<col width="26%" />
<col width="74%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>build the accelerator library</td>
<td>only for USER-CUDA and GPU packages</td>
</tr>
<tr class="row-even"><td>install the accelerator package</td>
<td>make yes-opt, make yes-user-intel, etc</td>
</tr>
</tbody>
</table>
<div class="line-block">
<div class="line">install the accelerator package | make yes-opt, make yes-user-intel, etc |</div>
</div>
<blockquote>
-<div>only for USER-INTEL, KOKKOS, USER-OMP packages |</div></blockquote>
+<div>only for USER-INTEL, KOKKOS, USER-OMP, OPT packages |</div></blockquote>
<table border="1" class="docutils">
<colgroup>
<col width="26%" />
<col width="74%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>re-build LAMMPS</td>
<td>make machine</td>
</tr>
-<tr class="row-even"><td>run a LAMMPS simulation</td>
-<td>lmp_machine < in.script</td>
-</tr>
</tbody>
</table>
<div class="line-block">
-<div class="line">run a LAMMPS simulation | lmp_machine < in.script |</div>
+<div class="line">re-build LAMMPS | make machine |</div>
</div>
<blockquote>
+<div>mpirun -np 32 lmp_machine -in in.script |</div></blockquote>
+<blockquote>
<div>only for USER-CUDA and KOKKOS packages |</div></blockquote>
<blockquote>
<div><a class="reference internal" href="package.html"><em>package</em></a> command, <br>
only if defaults need to be changed |</div></blockquote>
<blockquote>
<div><a class="reference internal" href="suffix.html"><em>suffix</em></a> command |</div></blockquote>
<table border="1" class="docutils">
<colgroup>
</colgroup>
<tbody valign="top">
</tbody>
</table>
-<p>The first 4 steps can be done as a single command, using the
-src/Make.py tool. The Make.py tool is discussed in <a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a> of the manual, and its use is
+<p>Note that the first 4 steps can be done as a single command, using the
+src/Make.py tool. This tool is discussed in <a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a> of the manual, and its use is
illustrated in the individual accelerator sections. Typically these
steps only need to be done once, to create an executable that uses one
or more accelerator packages.</p>
<p>The last 4 steps can all be done from the command-line when LAMMPS is
launched, without changing your input script, as illustrated in the
individual accelerator sections. Or you can add
<a class="reference internal" href="package.html"><em>package</em></a> and <a class="reference internal" href="suffix.html"><em>suffix</em></a> commands to your input
script.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">With a few exceptions, you can build a single LAMMPS
-executable with all its accelerator packages installed. Note that the
-USER-INTEL and KOKKOS packages require you to choose one of their
-options when building. I.e. CPU or Phi for USER-INTEL. OpenMP, Cuda,
-or Phi for KOKKOS. Here are the exceptions; you cannot build a single
-executable with:</p>
+executable with all its accelerator packages installed. Note however
+that the USER-INTEL and KOKKOS packages require you to choose one of
+their hardware options when building for a specific platform.
+I.e. CPU or Phi option for the USER-INTEL package. Or the OpenMP,
+Cuda, or Phi option for the KOKKOS package.</p>
</div>
+<p>These are the exceptions. You cannot build a single executable with:</p>
<ul class="simple">
<li>both the USER-INTEL Phi and KOKKOS Phi options</li>
<li>the USER-INTEL Phi or Kokkos Phi option, and either the USER-CUDA or GPU packages</li>
</ul>
<p>See the examples/accelerate/README and make.list files for sample
Make.py commands that build LAMMPS with any or all of the accelerator
packages. As an example, here is a command that builds with all the
GPU related packages installed (USER-CUDA, GPU, KOKKOS with Cuda),
including settings to build the needed auxiliary USER-CUDA and GPU
libraries for Kepler GPUs:</p>
<pre class="literal-block">
Make.py -j 16 -p omp gpu cuda kokkos -cc nvcc wrap=mpi -cuda mode=double arch=35 -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi
</pre>
<p>The examples/accelerate directory also has input scripts that can be
used with all of the accelerator packages. See its README file for
details.</p>
<p>Likewise, the bench directory has FERMI and KEPLER and PHI
sub-directories with Make.py commands and input scripts for using all
the accelerator packages on various machines. See the README files in
those dirs.</p>
<p>As mentioned above, the <a class="reference external" href="http://lammps.sandia.gov/bench.html">Benchmark page</a> of the LAMMPS web site gives
performance results for the various accelerator packages for several
of the standard LAMMPS benchmark problems, as a function of problem
size and number of compute nodes, on different hardware platforms.</p>
<p>Here is a brief summary of what the various packages provide. Details
are in the individual accelerator sections.</p>
<ul class="simple">
<li>Styles with a “cuda” or “gpu” suffix are part of the USER-CUDA or GPU
packages, and can be run on NVIDIA GPUs. The speed-up on a GPU
depends on a variety of factors, discussed in the accelerator
sections.</li>
<li>Styles with an “intel” suffix are part of the USER-INTEL
package. These styles support vectorized single and mixed precision
calculations, in addition to full double precision. In extreme cases,
this can provide speedups over 3.5x on CPUs. The package also
supports acceleration in “offload” mode to Intel(R) Xeon Phi(TM)
coprocessors. This can result in additional speedup over 2x depending
on the hardware configuration.</li>
<li>Styles with a “kk” suffix are part of the KOKKOS package, and can be
run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
Xeon Phi in “native” mode. The speed-up depends on a variety of
factors, as discussed on the KOKKOS accelerator page.</li>
<li>Styles with an “omp” suffix are part of the USER-OMP package and allow
a pair-style to be run in multi-threaded mode using OpenMP. This can
be useful on nodes with high-core counts when using less MPI processes
than cores is advantageous, e.g. when running with PPPM so that FFTs
are run on fewer MPI processors or when the many MPI tasks would
overload the available bandwidth for communication.</li>
<li>Styles with an “opt” suffix are part of the OPT package and typically
speed-up the pairwise calculations of your simulation by 5-25% on a
CPU.</li>
</ul>
<p>The individual accelerator package doc pages explain:</p>
<ul class="simple">
<li>what hardware and software the accelerated package requires</li>
<li>how to build LAMMPS with the accelerated package</li>
<li>how to run with the accelerated package either via command-line switches or modifying the input script</li>
<li>speed-ups to expect</li>
<li>guidelines for best performance</li>
<li>restrictions</li>
</ul>
<hr class="docutils" />
</div>
<div class="section" id="comparison-of-various-accelerator-packages">
<span id="acc-4"></span><h2>5.4. Comparison of various accelerator packages<a class="headerlink" href="#comparison-of-various-accelerator-packages" title="Permalink to this headline">¶</a></h2>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">this section still needs to be re-worked with additional KOKKOS
and USER-INTEL information.</p>
</div>
<p>The next section compares and contrasts the various accelerator
options, since there are multiple ways to perform OpenMP threading,
run on GPUs, and run on Intel Xeon Phi coprocessors.</p>
<p>All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
hardware, but they do it in different ways.</p>
<p>As a consequence, for a particular simulation on specific hardware,
one package may be faster than the other. We give guidelines below,
but the best way to determine which package is faster for your input
script is to try both of them on your machine. See the benchmarking
section below for examples where this has been done.</p>
<p><strong>Guidelines for using each package optimally:</strong></p>
<ul class="simple">
<li>The GPU package allows you to assign multiple CPUs (cores) to a single
GPU (a common configuration for “hybrid” nodes that contain multicore
CPU(s) and GPU(s)) and works effectively in this mode. The USER-CUDA
package does not allow this; you can only use one CPU per GPU.</li>
<li>The GPU package moves per-atom data (coordinates, forces)
back-and-forth between the CPU and GPU every timestep. The USER-CUDA
package only does this on timesteps when a CPU calculation is required
(e.g. to invoke a fix or compute that is non-GPU-ized). Hence, if you
can formulate your input script to only use GPU-ized fixes and
computes, and avoid doing I/O too often (thermo output, dump file
snapshots, restart files), then the data transfer cost of the
USER-CUDA package can be very low, causing it to run faster than the
GPU package.</li>
<li>The GPU package is often faster than the USER-CUDA package, if the
-number of atoms per GPU is “small”. The crossover point, in terms of
+number of atoms per GPU is smaller. The crossover point, in terms of
atoms/GPU at which the USER-CUDA package becomes faster depends
strongly on the pair style. For example, for a simple Lennard Jones
system the crossover (in single precision) is often about 50K-100K
atoms per GPU. When performing double precision calculations the
crossover point can be significantly smaller.</li>
<li>Both packages compute bonded interactions (bonds, angles, etc) on the
CPU. This means a model with bonds will force the USER-CUDA package
to transfer per-atom data back-and-forth between the CPU and GPU every
timestep. If the GPU package is running with several MPI processes
assigned to one GPU, the cost of computing the bonded interactions is
spread across more CPUs and hence the GPU package can run faster.</li>
<li>When using the GPU package with multiple CPUs assigned to one GPU, its
performance depends to some extent on high bandwidth between the CPUs
and the GPU. Hence its performance is affected if full 16 PCIe lanes
are not available for each GPU. In HPC environments this can be the
case if S2050/70 servers are used, where two devices generally share
one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide
full 16 lanes to each of the PCIe 2.0 16x slots.</li>
</ul>
<p><strong>Differences between the two packages:</strong></p>
<ul class="simple">
<li>The GPU package accelerates only pair force, neighbor list, and PPPM
calculations. The USER-CUDA package currently supports a wider range
of pair styles and can also accelerate many fix styles and some
compute styles, as well as neighbor list and PPPM calculations.</li>
<li>The USER-CUDA package does not support acceleration for minimization.</li>
<li>The USER-CUDA package does not support hybrid pair styles.</li>
<li>The USER-CUDA package can order atoms in the neighbor list differently
from run to run resulting in a different order for force accumulation.</li>
<li>The USER-CUDA package has a limit on the number of atom types that can be
used in a simulation.</li>
<li>The GPU package requires neighbor lists to be built on the CPU when using
exclusion lists or a triclinic simulation box.</li>
<li>The GPU package uses more GPU memory than the USER-CUDA package. This
is generally not a problem since typical runs are computation-limited
rather than memory-limited.</li>
</ul>
<div class="section" id="examples">
<h3>5.4.1. Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
<p>The LAMMPS distribution has two directories with sample input scripts
for the GPU and USER-CUDA packages.</p>
<ul class="simple">
<li>lammps/examples/gpu = GPU package files</li>
<li>lammps/examples/USER/cuda = USER-CUDA package files</li>
</ul>
<p>These contain input scripts for identical systems, so they can be used
to benchmark the performance of both packages on your system.</p>
</div>
</div>
</div>
</div>
</div>
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\ No newline at end of file
diff --git a/doc/Section_accelerate.txt b/doc/Section_accelerate.txt
index ac9b8563d..d5c5dede3 100644
--- a/doc/Section_accelerate.txt
+++ b/doc/Section_accelerate.txt
@@ -1,397 +1,415 @@
"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_howto.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
5. Accelerating LAMMPS performance :h3
This section describes various methods for improving LAMMPS
performance for different classes of problems running on different
kinds of machines.
There are two thrusts to the discussion that follows. The
first is using code options that implement alternate algorithms
that can speed-up a simulation. The second is to use one
of the several accelerator packages provided with LAMMPS that
contain code optimized for certain kinds of hardware, including
multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors.
5.1 "Measuring performance"_#acc_1 :ulb,l
5.2 "Algorithms and code options to boost performace"_#acc_2 :l
5.3 "Accelerator packages with optimized styles"_#acc_3 :l
5.3.1 "USER-CUDA package"_accelerate_cuda.html :ulb,l
5.3.2 "GPU package"_accelerate_gpu.html :l
5.3.3 "USER-INTEL package"_accelerate_intel.html :l
5.3.4 "KOKKOS package"_accelerate_kokkos.html :l
5.3.5 "USER-OMP package"_accelerate_omp.html :l
5.3.6 "OPT package"_accelerate_opt.html :l,ule
5.4 "Comparison of various accelerator packages"_#acc_4 :l,ule
The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS
web site gives performance results for the various accelerator
packages discussed in Section 5.2, for several of the standard LAMMPS
benchmark problems, as a function of problem size and number of
compute nodes, on different hardware platforms.
:line
:line
5.1 Measuring performance :h4,link(acc_1)
Before trying to make your simulation run faster, you should
understand how it currently performs and where the bottlenecks are.
The best way to do this is run the your system (actual number of
atoms) for a modest number of timesteps (say 100 steps) on several
different processor counts, including a single processor if possible.
Do this for an equilibrium version of your system, so that the
100-step timings are representative of a much longer run. There is
typically no need to run for 1000s of timesteps to get accurate
timings; you can simply extrapolate from short runs.
For the set of runs, look at the timing data printed to the screen and
log file at the end of each LAMMPS run. "This
section"_Section_start.html#start_8 of the manual has an overview.
Running on one (or a few processors) should give a good estimate of
the serial performance and what portions of the timestep are taking
the most time. Running the same problem on a few different processor
counts should give an estimate of parallel scalability. I.e. if the
simulation runs 16x faster on 16 processors, its 100% parallel
efficient; if it runs 8x faster on 16 processors, it's 50% efficient.
The most important data to look at in the timing info is the timing
breakdown and relative percentages. For example, trying different
options for speeding up the long-range solvers will have little impact
if they only consume 10% of the run time. If the pairwise time is
dominating, you may want to look at GPU or OMP versions of the pair
style, as discussed below. Comparing how the percentages change as
you increase the processor count gives you a sense of how different
operations within the timestep are scaling. Note that if you are
running with a Kspace solver, there is additional output on the
breakdown of the Kspace time. For PPPM, this includes the fraction
spent on FFTs, which can be communication intensive.
Another important detail in the timing info are the histograms of
atoms counts and neighbor counts. If these vary widely across
processors, you have a load-imbalance issue. This often results in
inaccurate relative timing data, because processors have to wait when
communication occurs for other processors to catch up. Thus the
reported times for "Communication" or "Other" may be higher than they
really are, due to load-imbalance. If this is an issue, you can
uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
LAMMPS, to obtain synchronized timings.
:line
5.2 General strategies :h4,link(acc_2)
NOTE: this section 5.2 is still a work in progress
Here is a list of general ideas for improving simulation performance.
Most of them are only applicable to certain models and certain
bottlenecks in the current performance, so let the timing data you
generate be your guide. It is hard, if not impossible, to predict how
much difference these options will make, since it is a function of
problem size, number of processors used, and your machine. There is
no substitute for identifying performance bottlenecks, and trying out
various options.
rRESPA
2-FFT PPPM
Staggered PPPM
single vs double PPPM
partial charge PPPM
verlet/split run style
processor command for proc layout and numa layout
load-balancing: balance and fix balance :ul
2-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, uses
2 FFTs instead of the 4 FFTs used by the default {ik differentiation}
PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
cost is the performance bottleneck (typically large problems running
on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.
Staggered PPPM performs calculations using two different meshes, one
shifted slightly with respect to the other. This can reduce force
aliasing errors and increase the accuracy of the method, but also
doubles the amount of work required. For high relative accuracy, using
staggered PPPM allows one to half the mesh size in each dimension as
compared to regular PPPM, which can give around a 4x speedup in the
kspace time. However, for low relative accuracy, using staggered PPPM
gives little benefit and can be up to 2x slower in the kspace
time. For example, the rhodopsin benchmark was run on a single
processor, and results for kspace time vs. relative accuracy for the
different methods are shown in the figure below. For this system,
staggered PPPM (using ik differentiation) becomes useful when using a
relative accuracy of slightly greater than 1e-5 and above.
:c,image(JPG/rhodo_staggered.jpg)
IMPORTANT NOTE: Using staggered PPPM may not give the same increase in
accuracy of energy and pressure as it does in forces, so some caution
must be used if energy and/or pressure are quantities of interest,
such as when using a barostat.
:line
5.3 Packages with optimized styles :h4,link(acc_3)
Accelerated versions of various "pair_style"_pair_style.html,
"fixes"_fix.html, "computes"_compute.html, and other commands have
been added to LAMMPS, which will typically run faster than the
standard non-accelerated versions. Some require appropriate hardware
to be present on your system, e.g. GPUs or Intel Xeon Phi
coprocessors.
All of these commands are in packages provided with LAMMPS. An
overview of packages is give in "Section
-packages"_Section_packages.html. These are the accelerator packages
+packages"_Section_packages.html.
+
+These are the accelerator packages
currently in LAMMPS, either as standard or user packages:
"USER-CUDA"_accelerate_cuda.html : for NVIDIA GPUs
"GPU"_accelerate_gpu.html : for NVIDIA GPUs as well as OpenCL support
"USER-INTEL"_accelerate_intel.html : for Intel CPUs and Intel Xeon Phi
"KOKKOS"_accelerate_kokkos.html : for GPUs, Intel Xeon Phi, and OpenMP threading
"USER-OMP"_accelerate_omp.html : for OpenMP threading
"OPT"_accelerate_opt.html : generic CPU optimizations :tb(s=:)
+Inverting this list, LAMMPS currently has acceleration support for
+three kinds of hardware, via the listed packages:
+
+Many-core CPUs : "USER-INTEL"_accelerate_intel.html, "KOKKOS"_accelerate_kokkos.html, "USER-OMP"_accelerate_omp.html, "OPT"_accelerate_opt.html packages
+NVIDIA GPUs : "USER-CUDA"_accelerate_cuda.html, "GPU"_accelerate_gpu.html, "KOKKOS"_accelerate_kokkos.html packages
+Intel Phi : "USER-INTEL"_accelerate_intel.html, "KOKKOS"_accelerate_kokkos.html packages :tb(s=:)
+
+Which package is fastest for your hardware may depend on the size
+problem you are running and what commands (accelerated and
+non-accelerated) are invoked by your input script. While these doc
+pages include performance guidelines, there is no substitute for
+trying out the different packages appropriate to your hardware.
+
Any accelerated style has the same name as the corresponding standard
style, except that a suffix is appended. Otherwise, the syntax for
the command that uses the style is identical, their functionality is
the same, and the numerical results it produces should also be the
same, except for precision and round-off effects.
For example, all of these styles are accelerated variants of the
Lennard-Jones "pair_style lj/cut"_pair_lj.html:
"pair_style lj/cut/cuda"_pair_lj.html
"pair_style lj/cut/gpu"_pair_lj.html
"pair_style lj/cut/intel"_pair_lj.html
"pair_style lj/cut/kk"_pair_lj.html
"pair_style lj/cut/omp"_pair_lj.html
"pair_style lj/cut/opt"_pair_lj.html :ul
To see what accelerate styles are currently available, see
"Section_commands 5"_Section_commands.html#cmd_5 of the manual. The
doc pages for individual commands (e.g. "pair lj/cut"_pair_lj.html or
"fix nve"_fix_nve.html) also list any accelerated variants available
for that style.
To use an accelerator package in LAMMPS, and one or more of the styles
it provides, follow these general steps. Details vary from package to
package and are explained in the individual accelerator doc pages,
listed above:
build the accelerator library |
only for USER-CUDA and GPU packages |
install the accelerator package |
make yes-opt, make yes-user-intel, etc |
add compile/link flags to Makefile.machine |
in src/MAKE, <br>
- only for USER-INTEL, KOKKOS, USER-OMP packages |
+ only for USER-INTEL, KOKKOS, USER-OMP, OPT packages |
re-build LAMMPS |
make machine |
run a LAMMPS simulation |
- lmp_machine < in.script |
+ lmp_machine < in.script <br>
+ mpirun -np 32 lmp_machine -in in.script |
enable the accelerator package |
via "-c on" and "-k on" "command-line switches"_Section_start.html#start_7, <br>
only for USER-CUDA and KOKKOS packages |
set any needed options for the package |
via "-pk" "command-line switch"_Section_start.html#start_7 or
"package"_package.html command, <br>
only if defaults need to be changed |
use accelerated styles in your input script |
via "-sf" "command-line switch"_Section_start.html#start_7 or
"suffix"_suffix.html command :tb(c=2,s=|)
-The first 4 steps can be done as a single command, using the
-src/Make.py tool. The Make.py tool is discussed in "Section
+Note that the first 4 steps can be done as a single command, using the
+src/Make.py tool. This tool is discussed in "Section
2.4"_Section_start.html#start_4 of the manual, and its use is
illustrated in the individual accelerator sections. Typically these
steps only need to be done once, to create an executable that uses one
or more accelerator packages.
The last 4 steps can all be done from the command-line when LAMMPS is
launched, without changing your input script, as illustrated in the
individual accelerator sections. Or you can add
"package"_package.html and "suffix"_suffix.html commands to your input
script.
IMPORTANT NOTE: With a few exceptions, you can build a single LAMMPS
-executable with all its accelerator packages installed. Note that the
-USER-INTEL and KOKKOS packages require you to choose one of their
-options when building. I.e. CPU or Phi for USER-INTEL. OpenMP, Cuda,
-or Phi for KOKKOS. Here are the exceptions; you cannot build a single
-executable with:
+executable with all its accelerator packages installed. Note however
+that the USER-INTEL and KOKKOS packages require you to choose one of
+their hardware options when building for a specific platform.
+I.e. CPU or Phi option for the USER-INTEL package. Or the OpenMP,
+Cuda, or Phi option for the KOKKOS package.
+
+These are the exceptions. You cannot build a single executable with:
both the USER-INTEL Phi and KOKKOS Phi options
the USER-INTEL Phi or Kokkos Phi option, and either the USER-CUDA or GPU packages :ul
See the examples/accelerate/README and make.list files for sample
Make.py commands that build LAMMPS with any or all of the accelerator
packages. As an example, here is a command that builds with all the
GPU related packages installed (USER-CUDA, GPU, KOKKOS with Cuda),
including settings to build the needed auxiliary USER-CUDA and GPU
libraries for Kepler GPUs:
Make.py -j 16 -p omp gpu cuda kokkos -cc nvcc wrap=mpi \
-cuda mode=double arch=35 -gpu mode=double arch=35 \\
-kokkos cuda arch=35 lib-all file mpi :pre
The examples/accelerate directory also has input scripts that can be
used with all of the accelerator packages. See its README file for
details.
Likewise, the bench directory has FERMI and KEPLER and PHI
sub-directories with Make.py commands and input scripts for using all
the accelerator packages on various machines. See the README files in
those dirs.
As mentioned above, the "Benchmark
page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives
performance results for the various accelerator packages for several
of the standard LAMMPS benchmark problems, as a function of problem
size and number of compute nodes, on different hardware platforms.
Here is a brief summary of what the various packages provide. Details
are in the individual accelerator sections.
Styles with a "cuda" or "gpu" suffix are part of the USER-CUDA or GPU
packages, and can be run on NVIDIA GPUs. The speed-up on a GPU
depends on a variety of factors, discussed in the accelerator
sections. :ulb,l
Styles with an "intel" suffix are part of the USER-INTEL
package. These styles support vectorized single and mixed precision
calculations, in addition to full double precision. In extreme cases,
this can provide speedups over 3.5x on CPUs. The package also
supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
coprocessors. This can result in additional speedup over 2x depending
on the hardware configuration. :l
Styles with a "kk" suffix are part of the KOKKOS package, and can be
run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
Xeon Phi in "native" mode. The speed-up depends on a variety of
factors, as discussed on the KOKKOS accelerator page. :l
Styles with an "omp" suffix are part of the USER-OMP package and allow
a pair-style to be run in multi-threaded mode using OpenMP. This can
be useful on nodes with high-core counts when using less MPI processes
than cores is advantageous, e.g. when running with PPPM so that FFTs
are run on fewer MPI processors or when the many MPI tasks would
overload the available bandwidth for communication. :l
Styles with an "opt" suffix are part of the OPT package and typically
speed-up the pairwise calculations of your simulation by 5-25% on a
CPU. :l,ule
The individual accelerator package doc pages explain:
what hardware and software the accelerated package requires
how to build LAMMPS with the accelerated package
how to run with the accelerated package either via command-line switches or modifying the input script
speed-ups to expect
guidelines for best performance
restrictions :ul
:line
5.4 Comparison of various accelerator packages :h4,link(acc_4)
NOTE: this section still needs to be re-worked with additional KOKKOS
and USER-INTEL information.
The next section compares and contrasts the various accelerator
options, since there are multiple ways to perform OpenMP threading,
run on GPUs, and run on Intel Xeon Phi coprocessors.
All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
hardware, but they do it in different ways.
As a consequence, for a particular simulation on specific hardware,
one package may be faster than the other. We give guidelines below,
but the best way to determine which package is faster for your input
script is to try both of them on your machine. See the benchmarking
section below for examples where this has been done.
[Guidelines for using each package optimally:]
The GPU package allows you to assign multiple CPUs (cores) to a single
GPU (a common configuration for "hybrid" nodes that contain multicore
CPU(s) and GPU(s)) and works effectively in this mode. The USER-CUDA
package does not allow this; you can only use one CPU per GPU. :ulb,l
The GPU package moves per-atom data (coordinates, forces)
back-and-forth between the CPU and GPU every timestep. The USER-CUDA
package only does this on timesteps when a CPU calculation is required
(e.g. to invoke a fix or compute that is non-GPU-ized). Hence, if you
can formulate your input script to only use GPU-ized fixes and
computes, and avoid doing I/O too often (thermo output, dump file
snapshots, restart files), then the data transfer cost of the
USER-CUDA package can be very low, causing it to run faster than the
GPU package. :l
The GPU package is often faster than the USER-CUDA package, if the
-number of atoms per GPU is "small". The crossover point, in terms of
+number of atoms per GPU is smaller. The crossover point, in terms of
atoms/GPU at which the USER-CUDA package becomes faster depends
strongly on the pair style. For example, for a simple Lennard Jones
system the crossover (in single precision) is often about 50K-100K
atoms per GPU. When performing double precision calculations the
crossover point can be significantly smaller. :l
Both packages compute bonded interactions (bonds, angles, etc) on the
CPU. This means a model with bonds will force the USER-CUDA package
to transfer per-atom data back-and-forth between the CPU and GPU every
timestep. If the GPU package is running with several MPI processes
assigned to one GPU, the cost of computing the bonded interactions is
spread across more CPUs and hence the GPU package can run faster. :l
When using the GPU package with multiple CPUs assigned to one GPU, its
performance depends to some extent on high bandwidth between the CPUs
and the GPU. Hence its performance is affected if full 16 PCIe lanes
are not available for each GPU. In HPC environments this can be the
case if S2050/70 servers are used, where two devices generally share
one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide
full 16 lanes to each of the PCIe 2.0 16x slots. :l,ule
[Differences between the two packages:]
The GPU package accelerates only pair force, neighbor list, and PPPM
calculations. The USER-CUDA package currently supports a wider range
of pair styles and can also accelerate many fix styles and some
compute styles, as well as neighbor list and PPPM calculations. :ulb,l
The USER-CUDA package does not support acceleration for minimization. :l
The USER-CUDA package does not support hybrid pair styles. :l
The USER-CUDA package can order atoms in the neighbor list differently
from run to run resulting in a different order for force accumulation. :l
The USER-CUDA package has a limit on the number of atom types that can be
used in a simulation. :l
The GPU package requires neighbor lists to be built on the CPU when using
exclusion lists or a triclinic simulation box. :l
The GPU package uses more GPU memory than the USER-CUDA package. This
is generally not a problem since typical runs are computation-limited
rather than memory-limited. :l,ule
[Examples:]
The LAMMPS distribution has two directories with sample input scripts
for the GPU and USER-CUDA packages.
lammps/examples/gpu = GPU package files
lammps/examples/USER/cuda = USER-CUDA package files :ul
These contain input scripts for identical systems, so they can be used
to benchmark the performance of both packages on your system.
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">3. Commands</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#lammps-input-script">3.1. LAMMPS input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="#parsing-rules">3.2. Parsing rules</a></li>
<li class="toctree-l2"><a class="reference internal" href="#input-script-structure">3.3. Input script structure</a></li>
<li class="toctree-l2"><a class="reference internal" href="#commands-listed-by-category">3.4. Commands listed by category</a></li>
<li class="toctree-l2"><a class="reference internal" href="#individual-commands">3.5. Individual commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="#fix-styles">3.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#compute-styles">3.7. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="#pair-style-potentials">3.8. Pair_style potentials</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#angle-style-potentials">3.10. Angle_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#dihedral-style-potentials">3.11. Dihedral_style potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="#improper-style-potentials">3.12. Improper_style potentials</a></li>
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<div class="section" id="commands">
<h1>3. Commands<a class="headerlink" href="#commands" title="Permalink to this headline">¶</a></h1>
<p>This section describes how a LAMMPS input script is formatted and the
input script commands used to define a LAMMPS simulation.</p>
<div class="line-block">
<div class="line">3.1 <a class="reference internal" href="#cmd-1"><span>LAMMPS input script</span></a></div>
<div class="line">3.2 <a class="reference internal" href="#cmd-2"><span>Parsing rules</span></a></div>
<div class="line">3.3 <a class="reference internal" href="#cmd-3"><span>Input script structure</span></a></div>
<div class="line">3.4 <a class="reference internal" href="#cmd-4"><span>Commands listed by category</span></a></div>
<div class="line">3.5 <a class="reference internal" href="#cmd-5"><span>Commands listed alphabetically</span></a></div>
<div class="line"><br /></div>
</div>
<div class="section" id="lammps-input-script">
<span id="cmd-1"></span><h2>3.1. LAMMPS input script<a class="headerlink" href="#lammps-input-script" title="Permalink to this headline">¶</a></h2>
<p>LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
command causes LAMMPS to take some action. It may set an internal
variable, read in a file, or run a simulation. Most commands have
default settings, which means you only need to use the command if you
wish to change the default.</p>
<p>In many cases, the ordering of commands in an input script is not
important. However the following rules apply:</p>
<p>(1) LAMMPS does not read your entire input script and then perform a
simulation with all the settings. Rather, the input script is read
one line at a time and each command takes effect when it is read.
Thus this sequence of commands:</p>
<div class="highlight-python"><div class="highlight"><pre>timestep 0.5
run 100
run 100
</pre></div>
</div>
<p>does something different than this sequence:</p>
<div class="highlight-python"><div class="highlight"><pre>run 100
timestep 0.5
run 100
</pre></div>
</div>
<p>In the first case, the specified timestep (0.5 fmsec) is used for two
simulations of 100 timesteps each. In the 2nd case, the default
timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
fmsec timestep is used for the 2nd one.</p>
<p>(2) Some commands are only valid when they follow other commands. For
example you cannot set the temperature of a group of atoms until atoms
have been defined and a group command is used to define which atoms
belong to the group.</p>
<p>(3) Sometimes command B will use values that can be set by command A.
This means command A must precede command B in the input script if it
is to have the desired effect. For example, the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command initializes the system by setting
up the simulation box and assigning atoms to processors. If default
values are not desired, the <a class="reference internal" href="processors.html"><em>processors</em></a> and
<a class="reference internal" href="boundary.html"><em>boundary</em></a> commands need to be used before read_data to
tell LAMMPS how to map processors to the simulation box.</p>
<p>Many input script errors are detected by LAMMPS and an ERROR or
WARNING message is printed. <a class="reference internal" href="Section_errors.html"><em>This section</em></a> gives
more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used.</p>
<hr class="docutils" />
</div>
<div class="section" id="parsing-rules">
<span id="cmd-2"></span><h2>3.2. Parsing rules<a class="headerlink" href="#parsing-rules" title="Permalink to this headline">¶</a></h2>
<p>Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
are specified command arguments. Upper case letters may be used in
file names or user-chosen ID strings.</p>
<p>Here is how each line in the input script is parsed by LAMMPS:</p>
<p>(1) If the last printable character on the line is a “&” character,
the command is assumed to continue on the next line. The next line is
concatenated to the previous line by removing the “&” character and
line break. This allows long commands to be continued across two or
more lines. See the discussion of triple quotes in (6) for how to
continue a command across multiple line without using “&” characters.</p>
<p>(2) All characters from the first “#” character onward are treated as
comment and discarded. See an exception in (6). Note that a
comment after a trailing “&” character will prevent the command from
continuing on the next line. Also note that for multi-line commands a
single leading “#” will comment out the entire command.</p>
<p>(3) The line is searched repeatedly for $ characters, which indicate
variables that are replaced with a text string. See an exception in
(6).</p>
<p>If the $ is followed by curly brackets, then the variable name is the
text inside the curly brackets. If no curly brackets follow the $,
then the variable name is the single character immediately following
the $. Thus ${myTemp} and $x refer to variable names “myTemp” and
“x”.</p>
<p>How the variable is converted to a text string depends on what style
of variable it is; see the <a class="reference external" href="variable">variable</a> doc page for details.
It can be a variable that stores multiple text strings, and return one
of them. The returned text string can be multiple “words” (space
separated) which will then be interpreted as multiple arguments in the
input command. The variable can also store a numeric formula which
will be evaluated and its numeric result returned as a string.</p>
<p>As a special case, if the $ is followed by parenthesis, then the text
inside the parenthesis is treated as an “immediate” variable and
evaluated as an <a class="reference internal" href="variable.html"><em>equal-style variable</em></a>. This is a way
to use numeric formulas in an input script without having to assign
them to variable names. For example, these 3 input script lines:</p>
<div class="highlight-python"><div class="highlight"><pre>variable X equal (xlo+xhi)/2+sqrt(v_area)
region 1 block $X 2 INF INF EDGE EDGE
variable X delete
</pre></div>
</div>
<p>can be replaced by</p>
<div class="highlight-python"><div class="highlight"><pre>region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
</pre></div>
</div>
<p>so that you do not have to define (or discard) a temporary variable X.</p>
<p>Note that neither the curly-bracket or immediate form of variables can
contain nested $ characters for other variables to substitute for.
Thus you cannot do this:</p>
<div class="highlight-python"><div class="highlight"><pre>variable a equal 2
variable b2 equal 4
print "B2 = ${b$a}"
</pre></div>
</div>
<p>Nor can you specify this $($x-1.0) for an immediate variable, but
you could use $(v_x-1.0), since the latter is valid syntax for an
<a class="reference internal" href="variable.html"><em>equal-style variable</em></a>.</p>
<p>See the <a class="reference internal" href="variable.html"><em>variable</em></a> command for more details of how
strings are assigned to variables and evaluated, and how they can be
used in input script commands.</p>
<p>(4) The line is broken into “words” separated by whitespace (tabs,
spaces). Note that words can thus contain letters, digits,
underscores, or punctuation characters.</p>
<p>(5) The first word is the command name. All successive words in the
line are arguments.</p>
<p>(6) If you want text with spaces to be treated as a single argument,
it can be enclosed in either single or double or triple quotes. A
long single argument enclosed in single or double quotes can span
multiple lines if the “&” character is used, as described above. When
the lines are concatenated together (and the “&” characters and line
breaks removed), the text will become a single line. If you want
multiple lines of an argument to retain their line breaks, the text
can be enclosed in triple quotes, in which case “&” characters are not
needed. For example:</p>
<div class="highlight-python"><div class="highlight"><pre>print "Volume = $v"
print 'Volume = $v'
if "${steps} > 1000" then quit
variable a string "red green blue &
purple orange cyan"
print """
System volume = $v
System temperature = $t
"""
</pre></div>
</div>
<p>In each case, the single, double, or triple quotes are removed when
the single argument they enclose is stored internally.</p>
<p>See the <a class="reference internal" href="dump_modify.html"><em>dump modify format</em></a>, <a class="reference internal" href="print.html"><em>print</em></a>,
<a class="reference internal" href="if.html"><em>if</em></a>, and <a class="reference internal" href="python.html"><em>python</em></a> commands for examples.</p>
<p>A “#” or “$” character that is between quotes will not be treated as a
comment indicator in (2) or substituted for as a variable in (3).</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If the argument is itself a command that requires a
quoted argument (e.g. using a <a class="reference internal" href="print.html"><em>print</em></a> command as part of an
<a class="reference internal" href="if.html"><em>if</em></a> or <a class="reference internal" href="run.html"><em>run every</em></a> command), then single, double, or
triple quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.</p>
</div>
<hr class="docutils" />
</div>
<div class="section" id="input-script-structure">
<span id="cmd-3"></span><h2>3.3. Input script structure<a class="headerlink" href="#input-script-structure" title="Permalink to this headline">¶</a></h2>
<p>This section describes the structure of a typical LAMMPS input script.
The “examples” directory in the LAMMPS distribution contains many
sample input scripts; the corresponding problems are discussed in
<a class="reference internal" href="Section_example.html"><em>Section_example</em></a>, and animated on the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>
<p>A LAMMPS input script typically has 4 parts:</p>
<ol class="arabic simple">
<li>Initialization</li>
<li>Atom definition</li>
<li>Settings</li>
<li>Run a simulation</li>
</ol>
<p>The last 2 parts can be repeated as many times as desired. I.e. run a
simulation, change some settings, run some more, etc. Each of the 4
parts is now described in more detail. Remember that almost all the
commands need only be used if a non-default value is desired.</p>
<ol class="arabic simple">
<li>Initialization</li>
</ol>
<p>Set parameters that need to be defined before atoms are created or
read-in from a file.</p>
<p>The relevant commands are <a class="reference internal" href="units.html"><em>units</em></a>,
<a class="reference internal" href="dimension.html"><em>dimension</em></a>, <a class="reference internal" href="newton.html"><em>newton</em></a>,
<a class="reference internal" href="processors.html"><em>processors</em></a>, <a class="reference internal" href="boundary.html"><em>boundary</em></a>,
<a class="reference internal" href="atom_style.html"><em>atom_style</em></a>, <a class="reference internal" href="atom_modify.html"><em>atom_modify</em></a>.</p>
<p>If force-field parameters appear in the files that will be read, these
commands tell LAMMPS what kinds of force fields are being used:
<a class="reference internal" href="pair_style.html"><em>pair_style</em></a>, <a class="reference internal" href="bond_style.html"><em>bond_style</em></a>,
<a class="reference internal" href="angle_style.html"><em>angle_style</em></a>, <a class="reference internal" href="dihedral_style.html"><em>dihedral_style</em></a>,
<a class="reference internal" href="improper_style.html"><em>improper_style</em></a>.</p>
<ol class="arabic simple" start="2">
<li>Atom definition</li>
</ol>
<p>There are 3 ways to define atoms in LAMMPS. Read them in from a data
or restart file via the <a class="reference internal" href="read_data.html"><em>read_data</em></a> or
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands. These files can contain
molecular topology information. Or create atoms on a lattice (with no
molecular topology), using these commands: <a class="reference internal" href="lattice.html"><em>lattice</em></a>,
<a class="reference internal" href="region.html"><em>region</em></a>, <a class="reference internal" href="create_box.html"><em>create_box</em></a>,
<a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a>. The entire set of atoms can be
duplicated to make a larger simulation using the
<a class="reference internal" href="replicate.html"><em>replicate</em></a> command.</p>
<ol class="arabic simple" start="3">
<li>Settings</li>
</ol>
<p>Once atoms and molecular topology are defined, a variety of settings
can be specified: force field coefficients, simulation parameters,
output options, etc.</p>
<p>Force field coefficients are set by these commands (they can also be
set in the read-in files): <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>,
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>,
<a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a>,
<a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a>,
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a>, <a class="reference internal" href="dielectric.html"><em>dielectric</em></a>,
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a>.</p>
<p>Various simulation parameters are set by these commands:
<a class="reference internal" href="neighbor.html"><em>neighbor</em></a>, <a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a>,
<a class="reference internal" href="group.html"><em>group</em></a>, <a class="reference internal" href="timestep.html"><em>timestep</em></a>,
<a class="reference internal" href="reset_timestep.html"><em>reset_timestep</em></a>, <a class="reference internal" href="run_style.html"><em>run_style</em></a>,
<a class="reference internal" href="min_style.html"><em>min_style</em></a>, <a class="reference internal" href="min_modify.html"><em>min_modify</em></a>.</p>
<p>Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The <a class="reference internal" href="fix.html"><em>fix</em></a> command comes in many flavors.</p>
<p>Various computations can be specified for execution during a
simulation using the <a class="reference internal" href="compute.html"><em>compute</em></a>,
<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a>, and <a class="reference internal" href="variable.html"><em>variable</em></a>
commands.</p>
<p>Output options are set by the <a class="reference internal" href="thermo.html"><em>thermo</em></a>, <a class="reference internal" href="dump.html"><em>dump</em></a>,
and <a class="reference internal" href="restart.html"><em>restart</em></a> commands.</p>
<ol class="arabic simple" start="4">
<li>Run a simulation</li>
</ol>
<p>A molecular dynamics simulation is run using the <a class="reference internal" href="run.html"><em>run</em></a>
command. Energy minimization (molecular statics) is performed using
the <a class="reference internal" href="minimize.html"><em>minimize</em></a> command. A parallel tempering
(replica-exchange) simulation can be run using the
<a class="reference internal" href="temper.html"><em>temper</em></a> command.</p>
<hr class="docutils" />
</div>
<div class="section" id="commands-listed-by-category">
<span id="cmd-4"></span><h2>3.4. Commands listed by category<a class="headerlink" href="#commands-listed-by-category" title="Permalink to this headline">¶</a></h2>
<p>This section lists all LAMMPS commands, grouped by category. The
<a class="reference internal" href="#cmd-5"><span>next section</span></a> lists the same commands alphabetically. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command’s documentation.</p>
<p>Initialization:</p>
<p><a class="reference internal" href="atom_modify.html"><em>atom_modify</em></a>, <a class="reference internal" href="atom_style.html"><em>atom_style</em></a>,
<a class="reference internal" href="boundary.html"><em>boundary</em></a>, <a class="reference internal" href="dimension.html"><em>dimension</em></a>,
<a class="reference internal" href="newton.html"><em>newton</em></a>, <a class="reference internal" href="processors.html"><em>processors</em></a>, <a class="reference internal" href="units.html"><em>units</em></a></p>
<p>Atom definition:</p>
<p><a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a>, <a class="reference internal" href="create_box.html"><em>create_box</em></a>,
<a class="reference internal" href="lattice.html"><em>lattice</em></a>, <a class="reference internal" href="read_data.html"><em>read_data</em></a>,
<a class="reference internal" href="read_dump.html"><em>read_dump</em></a>, <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>,
<a class="reference internal" href="region.html"><em>region</em></a>, <a class="reference internal" href="replicate.html"><em>replicate</em></a></p>
<p>Force fields:</p>
<p><a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>, <a class="reference internal" href="angle_style.html"><em>angle_style</em></a>,
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>, <a class="reference internal" href="bond_style.html"><em>bond_style</em></a>,
<a class="reference internal" href="dielectric.html"><em>dielectric</em></a>, <a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a>,
<a class="reference internal" href="dihedral_style.html"><em>dihedral_style</em></a>,
<a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a>,
<a class="reference internal" href="improper_style.html"><em>improper_style</em></a>,
<a class="reference internal" href="kspace_modify.html"><em>kspace_modify</em></a>, <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a>,
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>,
<a class="reference internal" href="pair_style.html"><em>pair_style</em></a>, <a class="reference internal" href="pair_write.html"><em>pair_write</em></a>,
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a></p>
<p>Settings:</p>
<p><a class="reference internal" href="comm_style.html"><em>comm_style</em></a>, <a class="reference internal" href="group.html"><em>group</em></a>, <a class="reference internal" href="mass.html"><em>mass</em></a>,
<a class="reference internal" href="min_modify.html"><em>min_modify</em></a>, <a class="reference internal" href="min_style.html"><em>min_style</em></a>,
<a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a>, <a class="reference internal" href="neighbor.html"><em>neighbor</em></a>,
<a class="reference internal" href="reset_timestep.html"><em>reset_timestep</em></a>, <a class="reference internal" href="run_style.html"><em>run_style</em></a>,
<a class="reference internal" href="set.html"><em>set</em></a>, <a class="reference internal" href="timestep.html"><em>timestep</em></a>, <a class="reference internal" href="velocity.html"><em>velocity</em></a></p>
<p>Fixes:</p>
<p><a class="reference internal" href="fix.html"><em>fix</em></a>, <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a>, <a class="reference internal" href="unfix.html"><em>unfix</em></a></p>
<p>Computes:</p>
<p><a class="reference internal" href="compute.html"><em>compute</em></a>, <a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a>,
<a class="reference internal" href="uncompute.html"><em>uncompute</em></a></p>
<p>Output:</p>
<p><a class="reference internal" href="dump.html"><em>dump</em></a>, <a class="reference internal" href="dump_image.html"><em>dump image</em></a>,
<a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a>, <a class="reference internal" href="dump_image.html"><em>dump movie</em></a>,
<a class="reference internal" href="restart.html"><em>restart</em></a>, <a class="reference internal" href="thermo.html"><em>thermo</em></a>,
<a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a>, <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a>,
<a class="reference internal" href="undump.html"><em>undump</em></a>, <a class="reference internal" href="write_data.html"><em>write_data</em></a>,
<a class="reference internal" href="write_dump.html"><em>write_dump</em></a>, <a class="reference internal" href="write_restart.html"><em>write_restart</em></a></p>
<p>Actions:</p>
<p><a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a>,
<a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a>, <a class="reference internal" href="change_box.html"><em>change_box</em></a>,
<a class="reference internal" href="minimize.html"><em>minimize</em></a>, <a class="reference internal" href="neb.html"><em>neb</em></a> <a class="reference internal" href="prd.html"><em>prd</em></a>,
<a class="reference internal" href="rerun.html"><em>rerun</em></a>, <a class="reference internal" href="run.html"><em>run</em></a>, <a class="reference internal" href="temper.html"><em>temper</em></a></p>
<p>Miscellaneous:</p>
<p><a class="reference internal" href="clear.html"><em>clear</em></a>, <a class="reference internal" href="echo.html"><em>echo</em></a>, <a class="reference internal" href="if.html"><em>if</em></a>,
<a class="reference internal" href="include.html"><em>include</em></a>, <a class="reference internal" href="jump.html"><em>jump</em></a>, <a class="reference internal" href="label.html"><em>label</em></a>,
<a class="reference internal" href="log.html"><em>log</em></a>, <a class="reference internal" href="next.html"><em>next</em></a>, <a class="reference internal" href="print.html"><em>print</em></a>,
<a class="reference internal" href="shell.html"><em>shell</em></a>, <a class="reference internal" href="variable.html"><em>variable</em></a></p>
<hr class="docutils" />
</div>
<div class="section" id="individual-commands">
<span id="comm"></span><span id="cmd-5"></span><h2>3.5. Individual commands<a class="headerlink" href="#individual-commands" title="Permalink to this headline">¶</a></h2>
<p>This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The <a class="reference internal" href="#cmd-4"><span>previous section</span></a> lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command’s documentation.</p>
<table border="1" class="docutils">
<colgroup>
<col width="17%" />
<col width="15%" />
<col width="17%" />
<col width="17%" />
<col width="17%" />
<col width="17%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a></td>
<td><a class="reference internal" href="angle_style.html"><em>angle_style</em></a></td>
<td><a class="reference internal" href="atom_modify.html"><em>atom_modify</em></a></td>
<td><a class="reference internal" href="atom_style.html"><em>atom_style</em></a></td>
<td><a class="reference internal" href="balance.html"><em>balance</em></a></td>
<td><a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="bond_style.html"><em>bond_style</em></a></td>
<td><a class="reference internal" href="boundary.html"><em>boundary</em></a></td>
<td><a class="reference internal" href="box.html"><em>box</em></a></td>
<td><a class="reference internal" href="change_box.html"><em>change_box</em></a></td>
<td><a class="reference internal" href="clear.html"><em>clear</em></a></td>
<td><a class="reference internal" href="comm_modify.html"><em>comm_modify</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="comm_style.html"><em>comm_style</em></a></td>
<td><a class="reference internal" href="compute.html"><em>compute</em></a></td>
<td><a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a></td>
<td><a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a></td>
<td><a class="reference internal" href="create_bonds.html"><em>create_bonds</em></a></td>
<td><a class="reference internal" href="create_box.html"><em>create_box</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a></td>
<td><a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a></td>
<td><a class="reference internal" href="dielectric.html"><em>dielectric</em></a></td>
<td><a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a></td>
<td><a class="reference internal" href="dihedral_style.html"><em>dihedral_style</em></a></td>
<td><a class="reference internal" href="dimension.html"><em>dimension</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a></td>
<td><a class="reference internal" href="dump.html"><em>dump</em></a></td>
<td><a class="reference internal" href="dump_image.html"><em>dump image</em></a></td>
<td><a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a></td>
<td><a class="reference internal" href="dump_image.html"><em>dump movie</em></a></td>
<td><a class="reference internal" href="echo.html"><em>echo</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix.html"><em>fix</em></a></td>
<td><a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a></td>
<td><a class="reference internal" href="group.html"><em>group</em></a></td>
<td><a class="reference internal" href="if.html"><em>if</em></a></td>
<td><a class="reference internal" href="info.html"><em>info</em></a></td>
<td><a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="improper_style.html"><em>improper_style</em></a></td>
<td><a class="reference internal" href="include.html"><em>include</em></a></td>
<td><a class="reference internal" href="jump.html"><em>jump</em></a></td>
<td><a class="reference internal" href="kspace_modify.html"><em>kspace_modify</em></a></td>
<td><a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a></td>
<td><a class="reference internal" href="label.html"><em>label</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="lattice.html"><em>lattice</em></a></td>
<td><a class="reference internal" href="log.html"><em>log</em></a></td>
<td><a class="reference internal" href="mass.html"><em>mass</em></a></td>
<td><a class="reference internal" href="minimize.html"><em>minimize</em></a></td>
<td><a class="reference internal" href="min_modify.html"><em>min_modify</em></a></td>
<td><a class="reference internal" href="min_style.html"><em>min_style</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="molecule.html"><em>molecule</em></a></td>
<td><a class="reference internal" href="neb.html"><em>neb</em></a></td>
<td><a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a></td>
<td><a class="reference internal" href="neighbor.html"><em>neighbor</em></a></td>
<td><a class="reference internal" href="newton.html"><em>newton</em></a></td>
<td><a class="reference internal" href="next.html"><em>next</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="package.html"><em>package</em></a></td>
<td><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></td>
<td><a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a></td>
<td><a class="reference internal" href="pair_style.html"><em>pair_style</em></a></td>
<td><a class="reference internal" href="pair_write.html"><em>pair_write</em></a></td>
<td><a class="reference internal" href="partition.html"><em>partition</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="prd.html"><em>prd</em></a></td>
<td><a class="reference internal" href="print.html"><em>print</em></a></td>
<td><a class="reference internal" href="processors.html"><em>processors</em></a></td>
<td><a class="reference internal" href="python.html"><em>python</em></a></td>
<td><a class="reference internal" href="quit.html"><em>quit</em></a></td>
<td><a class="reference internal" href="read_data.html"><em>read_data</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="read_dump.html"><em>read_dump</em></a></td>
<td><a class="reference internal" href="read_restart.html"><em>read_restart</em></a></td>
<td><a class="reference internal" href="region.html"><em>region</em></a></td>
<td><a class="reference internal" href="replicate.html"><em>replicate</em></a></td>
<td><a class="reference internal" href="rerun.html"><em>rerun</em></a></td>
<td><a class="reference internal" href="reset_timestep.html"><em>reset_timestep</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="restart.html"><em>restart</em></a></td>
<td><a class="reference internal" href="run.html"><em>run</em></a></td>
<td><a class="reference internal" href="run_style.html"><em>run_style</em></a></td>
<td><a class="reference internal" href="set.html"><em>set</em></a></td>
<td><a class="reference internal" href="shell.html"><em>shell</em></a></td>
<td><a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="suffix.html"><em>suffix</em></a></td>
<td><a class="reference internal" href="tad.html"><em>tad</em></a></td>
<td><a class="reference internal" href="temper.html"><em>temper</em></a></td>
<td><a class="reference internal" href="thermo.html"><em>thermo</em></a></td>
<td><a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a></td>
<td><a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="timer.html"><em>timer</em></a></td>
<td><a class="reference internal" href="timestep.html"><em>timestep</em></a></td>
<td><a class="reference internal" href="uncompute.html"><em>uncompute</em></a></td>
<td><a class="reference internal" href="undump.html"><em>undump</em></a></td>
<td><a class="reference internal" href="unfix.html"><em>unfix</em></a></td>
<td><a class="reference internal" href="units.html"><em>units</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="variable.html"><em>variable</em></a></td>
<td><a class="reference internal" href="velocity.html"><em>velocity</em></a></td>
<td><a class="reference internal" href="write_data.html"><em>write_data</em></a></td>
<td><a class="reference internal" href="write_dump.html"><em>write_dump</em></a></td>
<td><a class="reference internal" href="write_restart.html"><em>write_restart</em></a></td>
<td> </td>
</tr>
</tbody>
</table>
<p>These are additional commands in USER packages, which can be 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="100%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="group2ndx.html"><em>group2ndx</em></a></td>
</tr>
</tbody>
</table>
</div>
<hr class="docutils" />
<div class="section" id="fix-styles">
<h2>3.6. Fix styles<a class="headerlink" href="#fix-styles" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="fix.html"><em>fix</em></a> command for one-line descriptions of each style
or click on the style itself for a full description. Some of the
styles have accelerated versions, which can be used if LAMMPS is built
with the <a class="reference internal" href="Section_accelerate.html"><em>appropriate accelerated package</em></a>.
This is indicated by additional letters in parenthesis: c = USER-CUDA,
g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="16%" />
<col width="11%" />
<col width="12%" />
<col width="13%" />
<col width="10%" />
<col width="11%" />
<col width="15%" />
<col width="12%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="fix_adapt.html"><em>adapt</em></a></td>
<td><a class="reference internal" href="fix_addforce.html"><em>addforce (c)</em></a></td>
<td><a class="reference internal" href="fix_append_atoms.html"><em>append/atoms</em></a></td>
<td><a class="reference internal" href="fix_atom_swap.html"><em>atom/swap</em></a></td>
<td><a class="reference internal" href="fix_aveforce.html"><em>aveforce (c)</em></a></td>
<td><a class="reference internal" href="fix_ave_atom.html"><em>ave/atom</em></a></td>
<td><a class="reference internal" href="fix_ave_chunk.html"><em>ave/chunk</em></a></td>
<td><a class="reference internal" href="fix_ave_correlate.html"><em>ave/correlate</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_ave_histo.html"><em>ave/histo</em></a></td>
<td><a class="reference internal" href="fix_ave_histo.html"><em>ave/histo/weight</em></a></td>
<td><a class="reference internal" href="fix_ave_spatial.html"><em>ave/spatial</em></a></td>
<td><a class="reference internal" href="fix_ave_time.html"><em>ave/time</em></a></td>
<td><a class="reference internal" href="fix_balance.html"><em>balance</em></a></td>
<td><a class="reference internal" href="fix_bond_break.html"><em>bond/break</em></a></td>
<td><a class="reference internal" href="fix_bond_create.html"><em>bond/create</em></a></td>
<td><a class="reference internal" href="fix_bond_swap.html"><em>bond/swap</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_box_relax.html"><em>box/relax</em></a></td>
<td><a class="reference internal" href="fix_deform.html"><em>deform (k)</em></a></td>
<td><a class="reference internal" href="fix_deposit.html"><em>deposit</em></a></td>
<td><a class="reference internal" href="fix_drag.html"><em>drag</em></a></td>
<td><a class="reference internal" href="fix_dt_reset.html"><em>dt/reset</em></a></td>
<td><a class="reference internal" href="fix_efield.html"><em>efield</em></a></td>
<td><a class="reference internal" href="fix_enforce2d.html"><em>enforce2d (c)</em></a></td>
<td><a class="reference internal" href="fix_evaporate.html"><em>evaporate</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_external.html"><em>external</em></a></td>
<td><a class="reference internal" href="fix_freeze.html"><em>freeze (c)</em></a></td>
<td><a class="reference internal" href="fix_gcmc.html"><em>gcmc</em></a></td>
<td><a class="reference internal" href="fix_gld.html"><em>gld</em></a></td>
<td><a class="reference internal" href="fix_gravity.html"><em>gravity (co)</em></a></td>
<td><a class="reference internal" href="fix_heat.html"><em>heat</em></a></td>
<td><a class="reference internal" href="fix_indent.html"><em>indent</em></a></td>
<td><a class="reference internal" href="fix_langevin.html"><em>langevin (k)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_lineforce.html"><em>lineforce</em></a></td>
<td><a class="reference internal" href="fix_momentum.html"><em>momentum</em></a></td>
<td><a class="reference internal" href="fix_move.html"><em>move</em></a></td>
<td><a class="reference internal" href="fix_msst.html"><em>msst</em></a></td>
<td><a class="reference internal" href="fix_neb.html"><em>neb</em></a></td>
<td><a class="reference internal" href="fix_nh.html"><em>nph (ko)</em></a></td>
<td><a class="reference internal" href="fix_nphug.html"><em>nphug (o)</em></a></td>
<td><a class="reference internal" href="fix_nph_asphere.html"><em>nph/asphere (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_nph_sphere.html"><em>nph/sphere (o)</em></a></td>
<td><a class="reference internal" href="fix_nh.html"><em>npt (cko)</em></a></td>
<td><a class="reference internal" href="fix_npt_asphere.html"><em>npt/asphere (o)</em></a></td>
<td><a class="reference internal" href="fix_npt_sphere.html"><em>npt/sphere (o)</em></a></td>
<td><a class="reference internal" href="fix_nve.html"><em>nve (cko)</em></a></td>
<td><a class="reference internal" href="fix_nve_asphere.html"><em>nve/asphere</em></a></td>
<td><a class="reference internal" href="fix_nve_asphere_noforce.html"><em>nve/asphere/noforce</em></a></td>
<td><a class="reference internal" href="fix_nve_body.html"><em>nve/body</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_nve_limit.html"><em>nve/limit</em></a></td>
<td><a class="reference internal" href="fix_nve_line.html"><em>nve/line</em></a></td>
<td><a class="reference internal" href="fix_nve_noforce.html"><em>nve/noforce</em></a></td>
<td><a class="reference internal" href="fix_nve_sphere.html"><em>nve/sphere (o)</em></a></td>
<td><a class="reference internal" href="fix_nve_tri.html"><em>nve/tri</em></a></td>
<td><a class="reference internal" href="fix_nh.html"><em>nvt (cko)</em></a></td>
<td><a class="reference internal" href="fix_nvt_asphere.html"><em>nvt/asphere (o)</em></a></td>
<td><a class="reference internal" href="fix_nvt_sllod.html"><em>nvt/sllod (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_nvt_sphere.html"><em>nvt/sphere (o)</em></a></td>
<td><a class="reference internal" href="fix_oneway.html"><em>oneway</em></a></td>
<td><a class="reference internal" href="fix_orient_fcc.html"><em>orient/fcc</em></a></td>
<td><a class="reference internal" href="fix_planeforce.html"><em>planeforce</em></a></td>
<td><a class="reference internal" href="fix_poems.html"><em>poems</em></a></td>
<td><a class="reference internal" href="fix_pour.html"><em>pour</em></a></td>
<td><a class="reference internal" href="fix_press_berendsen.html"><em>press/berendsen</em></a></td>
<td><a class="reference internal" href="fix_print.html"><em>print</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_property_atom.html"><em>property/atom</em></a></td>
<td><a class="reference internal" href="fix_qeq_comb.html"><em>qeq/comb (o)</em></a></td>
<td><a class="reference internal" href="fix_qeq.html"><em>qeq/dynamic</em></a></td>
<td><a class="reference internal" href="fix_qeq.html"><em>qeq/point</em></a></td>
<td><a class="reference internal" href="fix_qeq.html"><em>qeq/shielded</em></a></td>
<td><a class="reference internal" href="fix_qeq.html"><em>qeq/slater</em></a></td>
<td><a class="reference internal" href="fix_reax_bonds.html"><em>reax/bonds</em></a></td>
<td><a class="reference internal" href="fix_recenter.html"><em>recenter</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_restrain.html"><em>restrain</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/nph (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/npt (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/nve (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/nvt (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/small (o)</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/small/nph</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_rigid.html"><em>rigid/small/npt</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/small/nve</em></a></td>
<td><a class="reference internal" href="fix_rigid.html"><em>rigid/small/nvt</em></a></td>
<td><a class="reference internal" href="fix_setforce.html"><em>setforce (c)</em></a></td>
<td><a class="reference internal" href="fix_shake.html"><em>shake (c)</em></a></td>
<td><a class="reference internal" href="fix_spring.html"><em>spring</em></a></td>
<td><a class="reference internal" href="fix_spring_rg.html"><em>spring/rg</em></a></td>
<td><a class="reference internal" href="fix_spring_self.html"><em>spring/self</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_srd.html"><em>srd</em></a></td>
<td><a class="reference internal" href="fix_store_force.html"><em>store/force</em></a></td>
<td><a class="reference internal" href="fix_store_state.html"><em>store/state</em></a></td>
<td><a class="reference internal" href="fix_temp_berendsen.html"><em>temp/berendsen (c)</em></a></td>
<td><a class="reference internal" href="fix_temp_csvr.html"><em>temp/csld</em></a></td>
<td><a class="reference internal" href="fix_temp_csvr.html"><em>temp/csvr</em></a></td>
<td><a class="reference internal" href="fix_temp_rescale.html"><em>temp/rescale (c)</em></a></td>
<td><a class="reference internal" href="fix_tfmc.html"><em>tfmc</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_thermal_conductivity.html"><em>thermal/conductivity</em></a></td>
<td><a class="reference internal" href="fix_tmd.html"><em>tmd</em></a></td>
<td><a class="reference internal" href="fix_ttm.html"><em>ttm</em></a></td>
<td><a class="reference internal" href="fix_tune_kspace.html"><em>tune/kspace</em></a></td>
<td><a class="reference internal" href="fix_vector.html"><em>vector</em></a></td>
<td><a class="reference internal" href="fix_viscosity.html"><em>viscosity</em></a></td>
<td><a class="reference internal" href="fix_viscous.html"><em>viscous (c)</em></a></td>
<td><a class="reference internal" href="fix_wall.html"><em>wall/colloid</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_wall_gran.html"><em>wall/gran</em></a></td>
<td><a class="reference internal" href="fix_wall.html"><em>wall/harmonic</em></a></td>
<td><a class="reference internal" href="fix_wall.html"><em>wall/lj1043</em></a></td>
<td><a class="reference internal" href="fix_wall.html"><em>wall/lj126</em></a></td>
<td><a class="reference internal" href="fix_wall.html"><em>wall/lj93</em></a></td>
<td><a class="reference internal" href="fix_wall_piston.html"><em>wall/piston</em></a></td>
<td><a class="reference internal" href="fix_wall_reflect.html"><em>wall/reflect (k)</em></a></td>
<td><a class="reference internal" href="fix_wall_region.html"><em>wall/region</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_wall_srd.html"><em>wall/srd</em></a></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p>These are additional fix styles in USER packages, which can be 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="14%" />
<col width="15%" />
<col width="15%" />
<col width="20%" />
<col width="14%" />
<col width="22%" />
-<col width="14%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="fix_adapt_fep.html"><em>adapt/fep</em></a></td>
<td><a class="reference internal" href="fix_addtorque.html"><em>addtorque</em></a></td>
<td><a class="reference internal" href="fix_atc.html"><em>atc</em></a></td>
+<td><a class="reference internal" href="fix_ave_correlate_long.html"><em>ave/correlate/long</em></a></td>
<td><a class="reference internal" href="fix_ave_spatial_sphere.html"><em>ave/spatial/sphere</em></a></td>
<td><a class="reference internal" href="fix_drude.html"><em>drude</em></a></td>
-<td><a class="reference internal" href="fix_drude_transform.html"><em>drude/transform/direct</em></a></td>
</tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_drude_transform.html"><em>drude/transform/reverse</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_drude_transform.html"><em>drude/transform/direct</em></a></td>
+<td><a class="reference internal" href="fix_drude_transform.html"><em>drude/transform/reverse</em></a></td>
<td><a class="reference internal" href="fix_colvars.html"><em>colvars</em></a></td>
<td><a class="reference internal" href="fix_gle.html"><em>gle</em></a></td>
<td><a class="reference internal" href="fix_imd.html"><em>imd</em></a></td>
<td><a class="reference internal" href="fix_ipi.html"><em>ipi</em></a></td>
-<td><a class="reference internal" href="fix_langevin_drude.html"><em>langevin/drude</em></a></td>
</tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_langevin_eff.html"><em>langevin/eff</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_langevin_drude.html"><em>langevin/drude</em></a></td>
+<td><a class="reference internal" href="fix_langevin_eff.html"><em>langevin/eff</em></a></td>
<td><a class="reference internal" href="fix_lb_fluid.html"><em>lb/fluid</em></a></td>
<td><a class="reference internal" href="fix_lb_momentum.html"><em>lb/momentum</em></a></td>
<td><a class="reference internal" href="fix_lb_pc.html"><em>lb/pc</em></a></td>
<td><a class="reference internal" href="fix_lb_rigid_pc_sphere.html"><em>lb/rigid/pc/sphere</em></a></td>
-<td><a class="reference internal" href="fix_lb_viscous.html"><em>lb/viscous</em></a></td>
</tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_meso.html"><em>meso</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_lb_viscous.html"><em>lb/viscous</em></a></td>
+<td><a class="reference internal" href="fix_meso.html"><em>meso</em></a></td>
<td><a class="reference internal" href="fix_meso_stationary.html"><em>meso/stationary</em></a></td>
<td><a class="reference internal" href="fix_nh_eff.html"><em>nph/eff</em></a></td>
<td><a class="reference internal" href="fix_nh_eff.html"><em>npt/eff</em></a></td>
<td><a class="reference internal" href="fix_nve_eff.html"><em>nve/eff</em></a></td>
-<td><a class="reference internal" href="fix_nh_eff.html"><em>nvt/eff</em></a></td>
</tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_nvt_sllod_eff.html"><em>nvt/sllod/eff</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_nh_eff.html"><em>nvt/eff</em></a></td>
+<td><a class="reference internal" href="fix_nvt_sllod_eff.html"><em>nvt/sllod/eff</em></a></td>
<td><a class="reference internal" href="fix_phonon.html"><em>phonon</em></a></td>
<td><a class="reference internal" href="fix_pimd.html"><em>pimd</em></a></td>
<td><a class="reference internal" href="fix_qbmsst.html"><em>qbmsst</em></a></td>
<td><a class="reference internal" href="fix_qeq_reax.html"><em>qeq/reax</em></a></td>
-<td><a class="reference internal" href="fix_qmmm.html"><em>qmmm</em></a></td>
</tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_qtb.html"><em>qtb</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_qmmm.html"><em>qmmm</em></a></td>
+<td><a class="reference internal" href="fix_qtb.html"><em>qtb</em></a></td>
<td><a class="reference internal" href="fix_reax_bonds.html"><em>reax/c/bonds</em></a></td>
<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_smd_adjust_dt.html"><em>smd/adjust/dt</em></a></td>
</tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_smd_integrate_tlsph.html"><em>smd/integrate/tlsph</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_smd_adjust_dt.html"><em>smd/adjust/dt</em></a></td>
+<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>
+<tr class="row-even"><td><a class="reference internal" href="fix_smd_wall_surface.html"><em>smd/wall/surface</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_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> </td>
-<td> </td>
</tr>
</tbody>
</table>
</div>
<hr class="docutils" />
<div class="section" id="compute-styles">
<h2>3.7. Compute styles<a class="headerlink" href="#compute-styles" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="compute.html"><em>compute</em></a> command for one-line descriptions of
each style or click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
is built with the <a class="reference internal" href="Section_accelerate.html"><em>appropriate accelerated package</em></a>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="16%" />
<col width="19%" />
<col width="17%" />
<col width="15%" />
<col width="17%" />
<col width="16%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="compute_angle_local.html"><em>angle/local</em></a></td>
<td><a class="reference internal" href="compute_angmom_chunk.html"><em>angmom/chunk</em></a></td>
<td><a class="reference internal" href="compute_body_local.html"><em>body/local</em></a></td>
<td><a class="reference internal" href="compute_bond_local.html"><em>bond/local</em></a></td>
<td><a class="reference internal" href="compute_centro_atom.html"><em>centro/atom</em></a></td>
<td><a class="reference internal" href="compute_chunk_atom.html"><em>chunk/atom</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_cluster_atom.html"><em>cluster/atom</em></a></td>
<td><a class="reference internal" href="compute_cna_atom.html"><em>cna/atom</em></a></td>
<td><a class="reference internal" href="compute_com.html"><em>com</em></a></td>
<td><a class="reference internal" href="compute_com_chunk.html"><em>com/chunk</em></a></td>
<td><a class="reference internal" href="compute_contact_atom.html"><em>contact/atom</em></a></td>
<td><a class="reference internal" href="compute_coord_atom.html"><em>coord/atom</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_damage_atom.html"><em>damage/atom</em></a></td>
<td><a class="reference internal" href="compute_dihedral_local.html"><em>dihedral/local</em></a></td>
<td><a class="reference internal" href="compute_dilatation_atom.html"><em>dilatation/atom</em></a></td>
<td><a class="reference internal" href="compute_displace_atom.html"><em>displace/atom</em></a></td>
<td><a class="reference internal" href="compute_erotate_asphere.html"><em>erotate/asphere</em></a></td>
<td><a class="reference internal" href="compute_erotate_rigid.html"><em>erotate/rigid</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_erotate_sphere.html"><em>erotate/sphere</em></a></td>
<td><a class="reference internal" href="compute_erotate_sphere_atom.html"><em>erotate/sphere/atom</em></a></td>
<td><a class="reference internal" href="compute_event_displace.html"><em>event/displace</em></a></td>
<td><a class="reference internal" href="compute_group_group.html"><em>group/group</em></a></td>
<td><a class="reference internal" href="compute_gyration.html"><em>gyration</em></a></td>
<td><a class="reference internal" href="compute_gyration_chunk.html"><em>gyration/chunk</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_heat_flux.html"><em>heat/flux</em></a></td>
<td><a class="reference internal" href="compute_improper_local.html"><em>improper/local</em></a></td>
<td><a class="reference internal" href="compute_inertia_chunk.html"><em>inertia/chunk</em></a></td>
<td><a class="reference internal" href="compute_ke.html"><em>ke</em></a></td>
<td><a class="reference internal" href="compute_ke_atom.html"><em>ke/atom</em></a></td>
<td><a class="reference internal" href="compute_ke_rigid.html"><em>ke/rigid</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_msd.html"><em>msd</em></a></td>
<td><a class="reference internal" href="compute_msd_chunk.html"><em>msd/chunk</em></a></td>
<td><a class="reference internal" href="compute_msd_nongauss.html"><em>msd/nongauss</em></a></td>
<td><a class="reference internal" href="compute_omega_chunk.html"><em>omega/chunk</em></a></td>
<td><a class="reference internal" href="compute_pair.html"><em>pair</em></a></td>
<td><a class="reference internal" href="compute_pair_local.html"><em>pair/local</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_pe.html"><em>pe (c)</em></a></td>
<td><a class="reference internal" href="compute_pe_atom.html"><em>pe/atom</em></a></td>
<td><a class="reference internal" href="compute_plasticity_atom.html"><em>plasticity/atom</em></a></td>
<td><a class="reference internal" href="compute_pressure.html"><em>pressure (c)</em></a></td>
<td><a class="reference internal" href="compute_property_atom.html"><em>property/atom</em></a></td>
<td><a class="reference internal" href="compute_property_local.html"><em>property/local</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_property_chunk.html"><em>property/chunk</em></a></td>
<td><a class="reference internal" href="compute_rdf.html"><em>rdf</em></a></td>
<td><a class="reference internal" href="compute_reduce.html"><em>reduce</em></a></td>
<td><a class="reference internal" href="compute_reduce.html"><em>reduce/region</em></a></td>
<td><a class="reference internal" href="compute_slice.html"><em>slice</em></a></td>
<td><a class="reference internal" href="compute_sna_atom.html"><em>sna/atom</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_sna_atom.html"><em>snad/atom</em></a></td>
<td><a class="reference internal" href="compute_sna_atom.html"><em>snav/atom</em></a></td>
<td><a class="reference internal" href="compute_stress_atom.html"><em>stress/atom</em></a></td>
<td><a class="reference internal" href="compute_temp.html"><em>temp (ck)</em></a></td>
<td><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a></td>
<td><a class="reference internal" href="compute_temp_com.html"><em>temp/com</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_temp_chunk.html"><em>temp/chunk</em></a></td>
<td><a class="reference internal" href="compute_temp_deform.html"><em>temp/deform</em></a></td>
<td><a class="reference internal" href="compute_temp_partial.html"><em>temp/partial (c)</em></a></td>
<td><a class="reference internal" href="compute_temp_profile.html"><em>temp/profile</em></a></td>
<td><a class="reference internal" href="compute_temp_ramp.html"><em>temp/ramp</em></a></td>
<td><a class="reference internal" href="compute_temp_region.html"><em>temp/region</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_temp_sphere.html"><em>temp/sphere</em></a></td>
<td><a class="reference internal" href="compute_ti.html"><em>ti</em></a></td>
<td><a class="reference internal" href="compute_torque_chunk.html"><em>torque/chunk</em></a></td>
<td><a class="reference internal" href="compute_vacf.html"><em>vacf</em></a></td>
<td><a class="reference internal" href="compute_vcm_chunk.html"><em>vcm/chunk</em></a></td>
<td><a class="reference internal" href="compute_voronoi_atom.html"><em>voronoi/atom</em></a></td>
</tr>
</tbody>
</table>
<p>These are additional compute styles in USER packages, which can be
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="17%" />
<col width="15%" />
<col width="19%" />
<col width="16%" />
<col width="15%" />
<col width="18%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="compute_ackland_atom.html"><em>ackland/atom</em></a></td>
<td><a class="reference internal" href="compute_basal_atom.html"><em>basal/atom</em></a></td>
<td><a class="reference internal" href="compute_fep.html"><em>fep</em></a></td>
<td><a class="reference internal" href="compute_tally.html"><em>force/tally</em></a></td>
<td><a class="reference internal" href="compute_tally.html"><em>heat/flux/tally</em></a></td>
<td><a class="reference internal" href="compute_ke_eff.html"><em>ke/eff</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_ke_atom_eff.html"><em>ke/atom/eff</em></a></td>
<td><a class="reference internal" href="compute_meso_e_atom.html"><em>meso_e/atom</em></a></td>
<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_tally.html"><em>pe/tally</em></a></td>
<td><a class="reference internal" href="compute_saed.html"><em>saed</em></a></td>
</tr>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><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>
<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><a class="reference internal" href="compute_smd_ulsph_strain_rate.html"><em>smd/ulsph/strain/rate</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_smd_ulsph_stress.html"><em>smd/ulsph/stress</em></a></td>
<td><a class="reference internal" href="compute_smd_vol.html"><em>smd/vol</em></a></td>
<td><a class="reference internal" href="compute_tally.html"><em>stress/tally</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>
</tr>
<tr class="row-odd"><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> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
</div>
<hr class="docutils" />
<div class="section" id="pair-style-potentials">
<h2>3.8. Pair_style potentials<a class="headerlink" href="#pair-style-potentials" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command for an overview of pair
potentials. Click on the style itself for a full description. Many
of the styles have accelerated versions, which can be used if LAMMPS
is built with the <a class="reference internal" href="Section_accelerate.html"><em>appropriate accelerated package</em></a>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="24%" />
<col width="25%" />
<col width="27%" />
<col width="24%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="pair_none.html"><em>none</em></a></td>
<td><a class="reference internal" href="pair_hybrid.html"><em>hybrid</em></a></td>
<td><a class="reference internal" href="pair_hybrid.html"><em>hybrid/overlay</em></a></td>
<td><a class="reference internal" href="pair_adp.html"><em>adp (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_airebo.html"><em>airebo (o)</em></a></td>
<td><a class="reference internal" href="pair_beck.html"><em>beck (go)</em></a></td>
<td><a class="reference internal" href="pair_body.html"><em>body</em></a></td>
<td><a class="reference internal" href="pair_bop.html"><em>bop</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_born.html"><em>born (go)</em></a></td>
<td><a class="reference internal" href="pair_born.html"><em>born/coul/long (cgo)</em></a></td>
<td><a class="reference internal" href="pair_born.html"><em>born/coul/long/cs</em></a></td>
<td><a class="reference internal" href="pair_born.html"><em>born/coul/msm (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_born.html"><em>born/coul/wolf (go)</em></a></td>
<td><a class="reference internal" href="pair_brownian.html"><em>brownian (o)</em></a></td>
<td><a class="reference internal" href="pair_brownian.html"><em>brownian/poly (o)</em></a></td>
<td><a class="reference internal" href="pair_buck.html"><em>buck (cgko)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_buck.html"><em>buck/coul/cut (cgko)</em></a></td>
<td><a class="reference internal" href="pair_buck.html"><em>buck/coul/long (cgko)</em></a></td>
<td><a class="reference internal" href="pair_buck.html"><em>buck/coul/long/cs</em></a></td>
<td><a class="reference internal" href="pair_buck.html"><em>buck/coul/msm (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_buck_long.html"><em>buck/long/coul/long (o)</em></a></td>
<td><a class="reference internal" href="pair_colloid.html"><em>colloid (go)</em></a></td>
<td><a class="reference internal" href="pair_comb.html"><em>comb (o)</em></a></td>
<td><a class="reference internal" href="pair_comb.html"><em>comb3</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><em>coul/cut (gko)</em></a></td>
<td><a class="reference internal" href="pair_coul.html"><em>coul/debye (gko)</em></a></td>
<td><a class="reference internal" href="pair_coul.html"><em>coul/dsf (gko)</em></a></td>
<td><a class="reference internal" href="pair_coul.html"><em>coul/long (gko)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_coul.html"><em>coul/long/cs</em></a></td>
<td><a class="reference internal" href="pair_coul.html"><em>coul/msm</em></a></td>
<td><a class="reference internal" href="pair_coul.html"><em>coul/streitz</em></a></td>
<td><a class="reference internal" href="pair_coul.html"><em>coul/wolf (ko)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_dpd.html"><em>dpd (o)</em></a></td>
<td><a class="reference internal" href="pair_dpd.html"><em>dpd/tstat (o)</em></a></td>
<td><a class="reference internal" href="pair_dsmc.html"><em>dsmc</em></a></td>
<td><a class="reference internal" href="pair_eam.html"><em>eam (cgkot)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_eam.html"><em>eam/alloy (cgkot)</em></a></td>
<td><a class="reference internal" href="pair_eam.html"><em>eam/fs (cgkot)</em></a></td>
<td><a class="reference internal" href="pair_eim.html"><em>eim (o)</em></a></td>
<td><a class="reference internal" href="pair_gauss.html"><em>gauss (go)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_gayberne.html"><em>gayberne (gio)</em></a></td>
<td><a class="reference internal" href="pair_gran.html"><em>gran/hertz/history (o)</em></a></td>
<td><a class="reference internal" href="pair_gran.html"><em>gran/hooke (co)</em></a></td>
<td><a class="reference internal" href="pair_gran.html"><em>gran/hooke/history (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_hbond_dreiding.html"><em>hbond/dreiding/lj (o)</em></a></td>
<td><a class="reference internal" href="pair_hbond_dreiding.html"><em>hbond/dreiding/morse (o)</em></a></td>
<td><a class="reference internal" href="pair_kim.html"><em>kim</em></a></td>
<td><a class="reference internal" href="pair_lcbop.html"><em>lcbop</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_line_lj.html"><em>line/lj (o)</em></a></td>
<td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/charmm (cko)</em></a></td>
<td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/charmm/implicit (cko)</em></a></td>
<td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/long (cgiko)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/msm</em></a></td>
<td><a class="reference internal" href="pair_class2.html"><em>lj/class2 (cgko)</em></a></td>
<td><a class="reference internal" href="pair_class2.html"><em>lj/class2/coul/cut (cko)</em></a></td>
<td><a class="reference internal" href="pair_class2.html"><em>lj/class2/coul/long (cgko)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_cubic.html"><em>lj/cubic (go)</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut (cgikot)</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/cut (cgko)</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/debye (cgko)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/dsf (gko)</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/long (cgikot)</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/long/cs</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/msm (go)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_dipole.html"><em>lj/cut/dipole/cut (go)</em></a></td>
<td><a class="reference internal" href="pair_dipole.html"><em>lj/cut/dipole/long</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/tip4p/cut (o)</em></a></td>
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/tip4p/long (ot)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj_expand.html"><em>lj/expand (cgko)</em></a></td>
<td><a class="reference internal" href="pair_gromacs.html"><em>lj/gromacs (cgko)</em></a></td>
<td><a class="reference internal" href="pair_gromacs.html"><em>lj/gromacs/coul/gromacs (cko)</em></a></td>
<td><a class="reference internal" href="pair_lj_long.html"><em>lj/long/coul/long (o)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_dipole.html"><em>lj/long/dipole/long</em></a></td>
<td><a class="reference internal" href="pair_lj_long.html"><em>lj/long/tip4p/long</em></a></td>
<td><a class="reference internal" href="pair_lj_smooth.html"><em>lj/smooth (co)</em></a></td>
<td><a class="reference internal" href="pair_lj_smooth_linear.html"><em>lj/smooth/linear (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj96.html"><em>lj96/cut (cgo)</em></a></td>
<td><a class="reference internal" href="pair_lubricate.html"><em>lubricate (o)</em></a></td>
<td><a class="reference internal" href="pair_lubricate.html"><em>lubricate/poly (o)</em></a></td>
<td><a class="reference internal" href="pair_lubricateU.html"><em>lubricateU</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lubricateU.html"><em>lubricateU/poly</em></a></td>
<td><a class="reference internal" href="pair_meam.html"><em>meam (o)</em></a></td>
<td><a class="reference internal" href="pair_mie.html"><em>mie/cut (o)</em></a></td>
<td><a class="reference internal" href="pair_morse.html"><em>morse (cgot)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_nb3b_harmonic.html"><em>nb3b/harmonic (o)</em></a></td>
<td><a class="reference internal" href="pair_nm.html"><em>nm/cut (o)</em></a></td>
<td><a class="reference internal" href="pair_nm.html"><em>nm/cut/coul/cut (o)</em></a></td>
<td><a class="reference internal" href="pair_nm.html"><em>nm/cut/coul/long (o)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_peri.html"><em>peri/eps</em></a></td>
<td><a class="reference internal" href="pair_peri.html"><em>peri/lps (o)</em></a></td>
<td><a class="reference internal" href="pair_peri.html"><em>peri/pmb (o)</em></a></td>
<td><a class="reference internal" href="pair_peri.html"><em>peri/ves</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_polymorphic.html"><em>polymorphic</em></a></td>
<td><a class="reference internal" href="pair_reax.html"><em>reax</em></a></td>
<td><a class="reference internal" href="pair_airebo.html"><em>rebo (o)</em></a></td>
<td><a class="reference internal" href="pair_resquared.html"><em>resquared (go)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_snap.html"><em>snap</em></a></td>
<td><a class="reference internal" href="pair_soft.html"><em>soft (go)</em></a></td>
<td><a class="reference internal" href="pair_sw.html"><em>sw (cgkio)</em></a></td>
<td><a class="reference internal" href="pair_table.html"><em>table (gko)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_tersoff.html"><em>tersoff (cgko)</em></a></td>
<td><a class="reference internal" href="pair_tersoff_mod.html"><em>tersoff/mod (ko)</em></a></td>
<td><a class="reference internal" href="pair_tersoff_zbl.html"><em>tersoff/zbl (ko)</em></a></td>
<td><a class="reference internal" href="pair_coul.html"><em>tip4p/cut (o)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><em>tip4p/long (o)</em></a></td>
<td><a class="reference internal" href="pair_tri_lj.html"><em>tri/lj (o)</em></a></td>
+<td><a class="reference internal" href="pair_vashishta.html"><em>vashishta (o)</em></a></td>
<td><a class="reference internal" href="pair_yukawa.html"><em>yukawa (go)</em></a></td>
-<td><a class="reference internal" href="pair_yukawa_colloid.html"><em>yukawa/colloid (go)</em></a></td>
</tr>
-<tr class="row-even"><td><a class="reference internal" href="pair_zbl.html"><em>zbl (go)</em></a></td>
-<td> </td>
+<tr class="row-even"><td><a class="reference internal" href="pair_yukawa_colloid.html"><em>yukawa/colloid (go)</em></a></td>
+<td><a class="reference internal" href="pair_zbl.html"><em>zbl (go)</em></a></td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p>These are additional pair styles in USER packages, which can be 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="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>
<td><a class="reference internal" href="pair_lj_soft.html"><em>coul/cut/soft (o)</em></a></td>
<td><a class="reference internal" href="pair_coul_diel.html"><em>coul/diel (o)</em></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><em>coul/long/soft (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_eam.html"><em>eam/cd (o)</em></a></td>
<td><a class="reference internal" href="pair_edip.html"><em>edip (o)</em></a></td>
<td><a class="reference internal" href="pair_eff.html"><em>eff/cut</em></a></td>
<td><a class="reference internal" href="pair_gauss.html"><em>gauss/cut</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_list.html"><em>list</em></a></td>
<td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/long/soft (o)</em></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/coul/cut/soft (o)</em></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/coul/long/soft (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_dipole.html"><em>lj/cut/dipole/sf (go)</em></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/soft (o)</em></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/tip4p/long/soft (o)</em></a></td>
<td><a class="reference internal" href="pair_sdk.html"><em>lj/sdk (gko)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_sdk.html"><em>lj/sdk/coul/long (go)</em></a></td>
<td><a class="reference internal" href="pair_sdk.html"><em>lj/sdk/coul/msm (o)</em></a></td>
<td><a class="reference internal" href="pair_lj_sf.html"><em>lj/sf (o)</em></a></td>
<td><a class="reference internal" href="pair_meam_spline.html"><em>meam/spline</em></a></td>
</tr>
<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-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-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-even"><td><a class="reference internal" href="pair_lj_soft.html"><em>tip4p/long/soft (o)</em></a></td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
</div>
<hr class="docutils" />
<div class="section" id="bond-style-potentials">
<h2>3.9. Bond_style potentials<a class="headerlink" href="#bond-style-potentials" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="bond_style.html"><em>bond_style</em></a> command for an overview of bond
potentials. Click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
is built with the <a class="reference internal" href="Section_accelerate.html"><em>appropriate accelerated package</em></a>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="28%" />
<col width="25%" />
<col width="22%" />
<col width="25%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="bond_none.html"><em>none</em></a></td>
<td><a class="reference internal" href="bond_hybrid.html"><em>hybrid</em></a></td>
<td><a class="reference internal" href="bond_class2.html"><em>class2 (o)</em></a></td>
<td><a class="reference internal" href="bond_fene.html"><em>fene (ko)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="bond_fene_expand.html"><em>fene/expand (o)</em></a></td>
<td><a class="reference internal" href="bond_harmonic.html"><em>harmonic (ko)</em></a></td>
<td><a class="reference internal" href="bond_morse.html"><em>morse (o)</em></a></td>
<td><a class="reference internal" href="bond_nonlinear.html"><em>nonlinear (o)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="bond_quartic.html"><em>quartic (o)</em></a></td>
<td><a class="reference internal" href="bond_table.html"><em>table (o)</em></a></td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p>These are additional bond styles in USER packages, which can be 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="46%" />
<col width="54%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="bond_harmonic_shift.html"><em>harmonic/shift (o)</em></a></td>
<td><a class="reference internal" href="bond_harmonic_shift_cut.html"><em>harmonic/shift/cut (o)</em></a></td>
</tr>
</tbody>
</table>
</div>
<hr class="docutils" />
<div class="section" id="angle-style-potentials">
<h2>3.10. Angle_style potentials<a class="headerlink" href="#angle-style-potentials" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="angle_style.html"><em>angle_style</em></a> command for an overview of
angle potentials. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
LAMMPS is built with the <a class="reference internal" href="Section_accelerate.html"><em>appropriate accelerated package</em></a>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="21%" />
<col width="25%" />
<col width="28%" />
<col width="27%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="angle_none.html"><em>none</em></a></td>
<td><a class="reference internal" href="angle_hybrid.html"><em>hybrid</em></a></td>
<td><a class="reference internal" href="angle_charmm.html"><em>charmm (ko)</em></a></td>
<td><a class="reference internal" href="angle_class2.html"><em>class2 (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="angle_cosine.html"><em>cosine (o)</em></a></td>
<td><a class="reference internal" href="angle_cosine_delta.html"><em>cosine/delta (o)</em></a></td>
<td><a class="reference internal" href="angle_cosine_periodic.html"><em>cosine/periodic (o)</em></a></td>
<td><a class="reference internal" href="angle_cosine_squared.html"><em>cosine/squared (o)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="angle_harmonic.html"><em>harmonic (ko)</em></a></td>
<td><a class="reference internal" href="angle_table.html"><em>table (o)</em></a></td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p>These are additional angle styles in USER packages, which can be 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="29%" />
<col width="31%" />
<col width="20%" />
<col width="21%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="angle_cosine_shift.html"><em>cosine/shift (o)</em></a></td>
<td><a class="reference internal" href="angle_cosine_shift_exp.html"><em>cosine/shift/exp (o)</em></a></td>
<td><a class="reference internal" href="angle_dipole.html"><em>dipole (o)</em></a></td>
<td><a class="reference internal" href="angle_fourier.html"><em>fourier (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="angle_fourier_simple.html"><em>fourier/simple (o)</em></a></td>
<td><a class="reference internal" href="angle_quartic.html"><em>quartic (o)</em></a></td>
<td><a class="reference internal" href="angle_sdk.html"><em>sdk</em></a></td>
<td> </td>
</tr>
</tbody>
</table>
</div>
<hr class="docutils" />
<div class="section" id="dihedral-style-potentials">
<h2>3.11. Dihedral_style potentials<a class="headerlink" href="#dihedral-style-potentials" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="dihedral_style.html"><em>dihedral_style</em></a> command for an overview
of dihedral potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
be used if LAMMPS is built with the <a class="reference internal" href="Section_accelerate.html"><em>appropriate accelerated package</em></a>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="25%" />
<col width="21%" />
<col width="32%" />
<col width="22%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="dihedral_none.html"><em>none</em></a></td>
<td><a class="reference internal" href="dihedral_hybrid.html"><em>hybrid</em></a></td>
<td><a class="reference internal" href="dihedral_charmm.html"><em>charmm (ko)</em></a></td>
<td><a class="reference internal" href="dihedral_class2.html"><em>class2 (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="dihedral_harmonic.html"><em>harmonic (o)</em></a></td>
<td><a class="reference internal" href="dihedral_helix.html"><em>helix (o)</em></a></td>
<td><a class="reference internal" href="dihedral_multi_harmonic.html"><em>multi/harmonic (o)</em></a></td>
<td><a class="reference internal" href="dihedral_opls.html"><em>opls (ko)</em></a></td>
</tr>
</tbody>
</table>
<p>These are additional dihedral styles in USER packages, which can be
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="31%" />
<col width="21%" />
<col width="24%" />
<col width="24%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="dihedral_cosine_shift_exp.html"><em>cosine/shift/exp (o)</em></a></td>
<td><a class="reference internal" href="dihedral_fourier.html"><em>fourier (o)</em></a></td>
<td><a class="reference internal" href="dihedral_nharmonic.html"><em>nharmonic (o)</em></a></td>
<td><a class="reference internal" href="dihedral_quadratic.html"><em>quadratic (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="dihedral_table.html"><em>table (o)</em></a></td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
</div>
<hr class="docutils" />
<div class="section" id="improper-style-potentials">
<h2>3.12. Improper_style potentials<a class="headerlink" href="#improper-style-potentials" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="improper_style.html"><em>improper_style</em></a> command for an overview
of improper potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
be used if LAMMPS is built with the <a class="reference internal" href="Section_accelerate.html"><em>appropriate accelerated package</em></a>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="27%" />
<col width="27%" />
<col width="24%" />
<col width="22%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="improper_none.html"><em>none</em></a></td>
<td><a class="reference internal" href="improper_hybrid.html"><em>hybrid</em></a></td>
<td><a class="reference internal" href="improper_class2.html"><em>class2 (o)</em></a></td>
<td><a class="reference internal" href="improper_cvff.html"><em>cvff (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="improper_harmonic.html"><em>harmonic (ko)</em></a></td>
<td><a class="reference internal" href="improper_umbrella.html"><em>umbrella (o)</em></a></td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p>These are additional improper styles in USER packages, which can be
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="33%" />
<col width="36%" />
<col width="31%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="improper_cossq.html"><em>cossq (o)</em></a></td>
<td><a class="reference internal" href="improper_fourier.html"><em>fourier (o)</em></a></td>
<td><a class="reference internal" href="improper_ring.html"><em>ring (o)</em></a></td>
</tr>
</tbody>
</table>
</div>
<hr class="docutils" />
<div class="section" id="kspace-solvers">
<h2>3.13. Kspace solvers<a class="headerlink" href="#kspace-solvers" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command for an overview of
Kspace solvers. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
LAMMPS is built with the <a class="reference internal" href="Section_accelerate.html"><em>appropriate accelerated package</em></a>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="26%" />
<col width="24%" />
<col width="23%" />
<col width="27%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="kspace_style.html"><em>ewald (o)</em></a></td>
<td><a class="reference internal" href="kspace_style.html"><em>ewald/disp</em></a></td>
<td><a class="reference internal" href="kspace_style.html"><em>msm (o)</em></a></td>
<td><a class="reference internal" href="kspace_style.html"><em>msm/cg (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="kspace_style.html"><em>pppm (cgo)</em></a></td>
<td><a class="reference internal" href="kspace_style.html"><em>pppm/cg (o)</em></a></td>
<td><a class="reference internal" href="kspace_style.html"><em>pppm/disp</em></a></td>
<td><a class="reference internal" href="kspace_style.html"><em>pppm/disp/tip4p</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="kspace_style.html"><em>pppm/tip4p (o)</em></a></td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
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diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index 16fc3bb4a..c5aad509a 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -1,1078 +1,1079 @@
"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_packages.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
3. Commands :h3
This section describes how a LAMMPS input script is formatted and the
input script commands used to define a LAMMPS simulation.
3.1 "LAMMPS input script"_#cmd_1
3.2 "Parsing rules"_#cmd_2
3.3 "Input script structure"_#cmd_3
3.4 "Commands listed by category"_#cmd_4
3.5 "Commands listed alphabetically"_#cmd_5 :all(b)
:line
:line
3.1 LAMMPS input script :link(cmd_1),h4
LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
command causes LAMMPS to take some action. It may set an internal
variable, read in a file, or run a simulation. Most commands have
default settings, which means you only need to use the command if you
wish to change the default.
In many cases, the ordering of commands in an input script is not
important. However the following rules apply:
(1) LAMMPS does not read your entire input script and then perform a
simulation with all the settings. Rather, the input script is read
one line at a time and each command takes effect when it is read.
Thus this sequence of commands:
timestep 0.5
run 100
run 100 :pre
does something different than this sequence:
run 100
timestep 0.5
run 100 :pre
In the first case, the specified timestep (0.5 fmsec) is used for two
simulations of 100 timesteps each. In the 2nd case, the default
timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
fmsec timestep is used for the 2nd one.
(2) Some commands are only valid when they follow other commands. For
example you cannot set the temperature of a group of atoms until atoms
have been defined and a group command is used to define which atoms
belong to the group.
(3) Sometimes command B will use values that can be set by command A.
This means command A must precede command B in the input script if it
is to have the desired effect. For example, the
"read_data"_read_data.html command initializes the system by setting
up the simulation box and assigning atoms to processors. If default
values are not desired, the "processors"_processors.html and
"boundary"_boundary.html commands need to be used before read_data to
tell LAMMPS how to map processors to the simulation box.
Many input script errors are detected by LAMMPS and an ERROR or
WARNING message is printed. "This section"_Section_errors.html gives
more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used.
:line
3.2 Parsing rules :link(cmd_2),h4
Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
are specified command arguments. Upper case letters may be used in
file names or user-chosen ID strings.
Here is how each line in the input script is parsed by LAMMPS:
(1) If the last printable character on the line is a "&" character,
the command is assumed to continue on the next line. The next line is
concatenated to the previous line by removing the "&" character and
line break. This allows long commands to be continued across two or
more lines. See the discussion of triple quotes in (6) for how to
continue a command across multiple line without using "&" characters.
(2) All characters from the first "#" character onward are treated as
comment and discarded. See an exception in (6). Note that a
comment after a trailing "&" character will prevent the command from
continuing on the next line. Also note that for multi-line commands a
single leading "#" will comment out the entire command.
(3) The line is searched repeatedly for $ characters, which indicate
variables that are replaced with a text string. See an exception in
(6).
If the $ is followed by curly brackets, then the variable name is the
text inside the curly brackets. If no curly brackets follow the $,
then the variable name is the single character immediately following
the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and
"x".
How the variable is converted to a text string depends on what style
of variable it is; see the "variable"_variable doc page for details.
It can be a variable that stores multiple text strings, and return one
of them. The returned text string can be multiple "words" (space
separated) which will then be interpreted as multiple arguments in the
input command. The variable can also store a numeric formula which
will be evaluated and its numeric result returned as a string.
As a special case, if the $ is followed by parenthesis, then the text
inside the parenthesis is treated as an "immediate" variable and
evaluated as an "equal-style variable"_variable.html. This is a way
to use numeric formulas in an input script without having to assign
them to variable names. For example, these 3 input script lines:
variable X equal (xlo+xhi)/2+sqrt(v_area)
region 1 block $X 2 INF INF EDGE EDGE
variable X delete :pre
can be replaced by
region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
so that you do not have to define (or discard) a temporary variable X.
Note that neither the curly-bracket or immediate form of variables can
contain nested $ characters for other variables to substitute for.
Thus you cannot do this:
variable a equal 2
variable b2 equal 4
print "B2 = $\{b$a\}" :pre
Nor can you specify this $($x-1.0) for an immediate variable, but
you could use $(v_x-1.0), since the latter is valid syntax for an
"equal-style variable"_variable.html.
See the "variable"_variable.html command for more details of how
strings are assigned to variables and evaluated, and how they can be
used in input script commands.
(4) The line is broken into "words" separated by whitespace (tabs,
spaces). Note that words can thus contain letters, digits,
underscores, or punctuation characters.
(5) The first word is the command name. All successive words in the
line are arguments.
(6) If you want text with spaces to be treated as a single argument,
it can be enclosed in either single or double or triple quotes. A
long single argument enclosed in single or double quotes can span
multiple lines if the "&" character is used, as described above. When
the lines are concatenated together (and the "&" characters and line
breaks removed), the text will become a single line. If you want
multiple lines of an argument to retain their line breaks, the text
can be enclosed in triple quotes, in which case "&" characters are not
needed. For example:
print "Volume = $v"
print 'Volume = $v'
if "$\{steps\} > 1000" then quit
variable a string "red green blue &
purple orange cyan"
print """
System volume = $v
System temperature = $t
""" :pre
In each case, the single, double, or triple quotes are removed when
the single argument they enclose is stored internally.
See the "dump modify format"_dump_modify.html, "print"_print.html,
"if"_if.html, and "python"_python.html commands for examples.
A "#" or "$" character that is between quotes will not be treated as a
comment indicator in (2) or substituted for as a variable in (3).
IMPORTANT NOTE: If the argument is itself a command that requires a
quoted argument (e.g. using a "print"_print.html command as part of an
"if"_if.html or "run every"_run.html command), then single, double, or
triple quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.
:line
3.3 Input script structure :h4,link(cmd_3)
This section describes the structure of a typical LAMMPS input script.
The "examples" directory in the LAMMPS distribution contains many
sample input scripts; the corresponding problems are discussed in
"Section_example"_Section_example.html, and animated on the "LAMMPS
WWW Site"_lws.
A LAMMPS input script typically has 4 parts:
Initialization
Atom definition
Settings
Run a simulation :ol
The last 2 parts can be repeated as many times as desired. I.e. run a
simulation, change some settings, run some more, etc. Each of the 4
parts is now described in more detail. Remember that almost all the
commands need only be used if a non-default value is desired.
(1) Initialization
Set parameters that need to be defined before atoms are created or
read-in from a file.
The relevant commands are "units"_units.html,
"dimension"_dimension.html, "newton"_newton.html,
"processors"_processors.html, "boundary"_boundary.html,
"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
If force-field parameters appear in the files that will be read, these
commands tell LAMMPS what kinds of force fields are being used:
"pair_style"_pair_style.html, "bond_style"_bond_style.html,
"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
"improper_style"_improper_style.html.
(2) Atom definition
There are 3 ways to define atoms in LAMMPS. Read them in from a data
or restart file via the "read_data"_read_data.html or
"read_restart"_read_restart.html commands. These files can contain
molecular topology information. Or create atoms on a lattice (with no
molecular topology), using these commands: "lattice"_lattice.html,
"region"_region.html, "create_box"_create_box.html,
"create_atoms"_create_atoms.html. The entire set of atoms can be
duplicated to make a larger simulation using the
"replicate"_replicate.html command.
(3) Settings
Once atoms and molecular topology are defined, a variety of settings
can be specified: force field coefficients, simulation parameters,
output options, etc.
Force field coefficients are set by these commands (they can also be
set in the read-in files): "pair_coeff"_pair_coeff.html,
"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
"dihedral_coeff"_dihedral_coeff.html,
"improper_coeff"_improper_coeff.html,
"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
"special_bonds"_special_bonds.html.
Various simulation parameters are set by these commands:
"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
"group"_group.html, "timestep"_timestep.html,
"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
"min_style"_min_style.html, "min_modify"_min_modify.html.
Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The "fix"_fix.html command comes in many flavors.
Various computations can be specified for execution during a
simulation using the "compute"_compute.html,
"compute_modify"_compute_modify.html, and "variable"_variable.html
commands.
Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
and "restart"_restart.html commands.
(4) Run a simulation
A molecular dynamics simulation is run using the "run"_run.html
command. Energy minimization (molecular statics) is performed using
the "minimize"_minimize.html command. A parallel tempering
(replica-exchange) simulation can be run using the
"temper"_temper.html command.
:line
3.4 Commands listed by category :link(cmd_4),h4
This section lists all LAMMPS commands, grouped by category. The
"next section"_#cmd_5 lists the same commands alphabetically. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
Initialization:
"atom_modify"_atom_modify.html, "atom_style"_atom_style.html,
"boundary"_boundary.html, "dimension"_dimension.html,
"newton"_newton.html, "processors"_processors.html, "units"_units.html
Atom definition:
"create_atoms"_create_atoms.html, "create_box"_create_box.html,
"lattice"_lattice.html, "read_data"_read_data.html,
"read_dump"_read_dump.html, "read_restart"_read_restart.html,
"region"_region.html, "replicate"_replicate.html
Force fields:
"angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html,
"bond_coeff"_bond_coeff.html, "bond_style"_bond_style.html,
"dielectric"_dielectric.html, "dihedral_coeff"_dihedral_coeff.html,
"dihedral_style"_dihedral_style.html,
"improper_coeff"_improper_coeff.html,
"improper_style"_improper_style.html,
"kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html,
"pair_coeff"_pair_coeff.html, "pair_modify"_pair_modify.html,
"pair_style"_pair_style.html, "pair_write"_pair_write.html,
"special_bonds"_special_bonds.html
Settings:
"comm_style"_comm_style.html, "group"_group.html, "mass"_mass.html,
"min_modify"_min_modify.html, "min_style"_min_style.html,
"neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html,
"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
"set"_set.html, "timestep"_timestep.html, "velocity"_velocity.html
Fixes:
"fix"_fix.html, "fix_modify"_fix_modify.html, "unfix"_unfix.html
Computes:
"compute"_compute.html, "compute_modify"_compute_modify.html,
"uncompute"_uncompute.html
Output:
"dump"_dump.html, "dump image"_dump_image.html,
"dump_modify"_dump_modify.html, "dump movie"_dump_image.html,
"restart"_restart.html, "thermo"_thermo.html,
"thermo_modify"_thermo_modify.html, "thermo_style"_thermo_style.html,
"undump"_undump.html, "write_data"_write_data.html,
"write_dump"_write_dump.html, "write_restart"_write_restart.html
Actions:
"delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html,
"displace_atoms"_displace_atoms.html, "change_box"_change_box.html,
"minimize"_minimize.html, "neb"_neb.html "prd"_prd.html,
"rerun"_rerun.html, "run"_run.html, "temper"_temper.html
Miscellaneous:
"clear"_clear.html, "echo"_echo.html, "if"_if.html,
"include"_include.html, "jump"_jump.html, "label"_label.html,
"log"_log.html, "next"_next.html, "print"_print.html,
"shell"_shell.html, "variable"_variable.html
:line
3.5 Individual commands :h4,link(cmd_5),link(comm)
This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The "previous
section"_#cmd_4 lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
"angle_coeff"_angle_coeff.html,
"angle_style"_angle_style.html,
"atom_modify"_atom_modify.html,
"atom_style"_atom_style.html,
"balance"_balance.html,
"bond_coeff"_bond_coeff.html,
"bond_style"_bond_style.html,
"boundary"_boundary.html,
"box"_box.html,
"change_box"_change_box.html,
"clear"_clear.html,
"comm_modify"_comm_modify.html,
"comm_style"_comm_style.html,
"compute"_compute.html,
"compute_modify"_compute_modify.html,
"create_atoms"_create_atoms.html,
"create_bonds"_create_bonds.html,
"create_box"_create_box.html,
"delete_atoms"_delete_atoms.html,
"delete_bonds"_delete_bonds.html,
"dielectric"_dielectric.html,
"dihedral_coeff"_dihedral_coeff.html,
"dihedral_style"_dihedral_style.html,
"dimension"_dimension.html,
"displace_atoms"_displace_atoms.html,
"dump"_dump.html,
"dump image"_dump_image.html,
"dump_modify"_dump_modify.html,
"dump movie"_dump_image.html,
"echo"_echo.html,
"fix"_fix.html,
"fix_modify"_fix_modify.html,
"group"_group.html,
"if"_if.html,
"info"_info.html,
"improper_coeff"_improper_coeff.html,
"improper_style"_improper_style.html,
"include"_include.html,
"jump"_jump.html,
"kspace_modify"_kspace_modify.html,
"kspace_style"_kspace_style.html,
"label"_label.html,
"lattice"_lattice.html,
"log"_log.html,
"mass"_mass.html,
"minimize"_minimize.html,
"min_modify"_min_modify.html,
"min_style"_min_style.html,
"molecule"_molecule.html,
"neb"_neb.html,
"neigh_modify"_neigh_modify.html,
"neighbor"_neighbor.html,
"newton"_newton.html,
"next"_next.html,
"package"_package.html,
"pair_coeff"_pair_coeff.html,
"pair_modify"_pair_modify.html,
"pair_style"_pair_style.html,
"pair_write"_pair_write.html,
"partition"_partition.html,
"prd"_prd.html,
"print"_print.html,
"processors"_processors.html,
"python"_python.html,
"quit"_quit.html,
"read_data"_read_data.html,
"read_dump"_read_dump.html,
"read_restart"_read_restart.html,
"region"_region.html,
"replicate"_replicate.html,
"rerun"_rerun.html,
"reset_timestep"_reset_timestep.html,
"restart"_restart.html,
"run"_run.html,
"run_style"_run_style.html,
"set"_set.html,
"shell"_shell.html,
"special_bonds"_special_bonds.html,
"suffix"_suffix.html,
"tad"_tad.html,
"temper"_temper.html,
"thermo"_thermo.html,
"thermo_modify"_thermo_modify.html,
"thermo_style"_thermo_style.html,
"timer"_timer.html,
"timestep"_timestep.html,
"uncompute"_uncompute.html,
"undump"_undump.html,
"unfix"_unfix.html,
"units"_units.html,
"variable"_variable.html,
"velocity"_velocity.html,
"write_data"_write_data.html,
"write_dump"_write_dump.html,
"write_restart"_write_restart.html :tb(c=6,ea=c)
These are additional commands in USER packages, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"group2ndx"_group2ndx.html :tb(c=1,ea=c)
:line
Fix styles :h4
See the "fix"_fix.html command for one-line descriptions of each style
or click on the style itself for a full description. Some of the
styles have accelerated versions, which can be used if LAMMPS is built
with the "appropriate accelerated package"_Section_accelerate.html.
This is indicated by additional letters in parenthesis: c = USER-CUDA,
g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"adapt"_fix_adapt.html,
"addforce (c)"_fix_addforce.html,
"append/atoms"_fix_append_atoms.html,
"atom/swap"_fix_atom_swap.html,
"aveforce (c)"_fix_aveforce.html,
"ave/atom"_fix_ave_atom.html,
"ave/chunk"_fix_ave_chunk.html,
"ave/correlate"_fix_ave_correlate.html,
"ave/histo"_fix_ave_histo.html,
"ave/histo/weight"_fix_ave_histo.html,
"ave/spatial"_fix_ave_spatial.html,
"ave/time"_fix_ave_time.html,
"balance"_fix_balance.html,
"bond/break"_fix_bond_break.html,
"bond/create"_fix_bond_create.html,
"bond/swap"_fix_bond_swap.html,
"box/relax"_fix_box_relax.html,
"deform (k)"_fix_deform.html,
"deposit"_fix_deposit.html,
"drag"_fix_drag.html,
"dt/reset"_fix_dt_reset.html,
"efield"_fix_efield.html,
"enforce2d (c)"_fix_enforce2d.html,
"evaporate"_fix_evaporate.html,
"external"_fix_external.html,
"freeze (c)"_fix_freeze.html,
"gcmc"_fix_gcmc.html,
"gld"_fix_gld.html,
"gravity (co)"_fix_gravity.html,
"heat"_fix_heat.html,
"indent"_fix_indent.html,
"langevin (k)"_fix_langevin.html,
"lineforce"_fix_lineforce.html,
"momentum"_fix_momentum.html,
"move"_fix_move.html,
"msst"_fix_msst.html,
"neb"_fix_neb.html,
"nph (ko)"_fix_nh.html,
"nphug (o)"_fix_nphug.html,
"nph/asphere (o)"_fix_nph_asphere.html,
"nph/sphere (o)"_fix_nph_sphere.html,
"npt (cko)"_fix_nh.html,
"npt/asphere (o)"_fix_npt_asphere.html,
"npt/sphere (o)"_fix_npt_sphere.html,
"nve (cko)"_fix_nve.html,
"nve/asphere"_fix_nve_asphere.html,
"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
"nve/body"_fix_nve_body.html,
"nve/limit"_fix_nve_limit.html,
"nve/line"_fix_nve_line.html,
"nve/noforce"_fix_nve_noforce.html,
"nve/sphere (o)"_fix_nve_sphere.html,
"nve/tri"_fix_nve_tri.html,
"nvt (cko)"_fix_nh.html,
"nvt/asphere (o)"_fix_nvt_asphere.html,
"nvt/sllod (o)"_fix_nvt_sllod.html,
"nvt/sphere (o)"_fix_nvt_sphere.html,
"oneway"_fix_oneway.html,
"orient/fcc"_fix_orient_fcc.html,
"planeforce"_fix_planeforce.html,
"poems"_fix_poems.html,
"pour"_fix_pour.html,
"press/berendsen"_fix_press_berendsen.html,
"print"_fix_print.html,
"property/atom"_fix_property_atom.html,
"qeq/comb (o)"_fix_qeq_comb.html,
"qeq/dynamic"_fix_qeq.html,
"qeq/point"_fix_qeq.html,
"qeq/shielded"_fix_qeq.html,
"qeq/slater"_fix_qeq.html,
"recenter"_fix_recenter.html,
"restrain"_fix_restrain.html,
"rigid (o)"_fix_rigid.html,
"rigid/nph (o)"_fix_rigid.html,
"rigid/npt (o)"_fix_rigid.html,
"rigid/nve (o)"_fix_rigid.html,
"rigid/nvt (o)"_fix_rigid.html,
"rigid/small (o)"_fix_rigid.html,
"rigid/small/nph"_fix_rigid.html,
"rigid/small/npt"_fix_rigid.html,
"rigid/small/nve"_fix_rigid.html,
"rigid/small/nvt"_fix_rigid.html,
"setforce (c)"_fix_setforce.html,
"shake (c)"_fix_shake.html,
"spring"_fix_spring.html,
"spring/rg"_fix_spring_rg.html,
"spring/self"_fix_spring_self.html,
"srd"_fix_srd.html,
"store/force"_fix_store_force.html,
"store/state"_fix_store_state.html,
"temp/berendsen (c)"_fix_temp_berendsen.html,
"temp/csld"_fix_temp_csvr.html,
"temp/csvr"_fix_temp_csvr.html,
"temp/rescale (c)"_fix_temp_rescale.html,
"tfmc"_fix_tfmc.html,
"thermal/conductivity"_fix_thermal_conductivity.html,
"tmd"_fix_tmd.html,
"ttm"_fix_ttm.html,
"tune/kspace"_fix_tune_kspace.html,
"vector"_fix_vector.html,
"viscosity"_fix_viscosity.html,
"viscous (c)"_fix_viscous.html,
"wall/colloid"_fix_wall.html,
"wall/gran"_fix_wall_gran.html,
"wall/harmonic"_fix_wall.html,
"wall/lj1043"_fix_wall.html,
"wall/lj126"_fix_wall.html,
"wall/lj93"_fix_wall.html,
"wall/piston"_fix_wall_piston.html,
"wall/reflect (k)"_fix_wall_reflect.html,
"wall/region"_fix_wall_region.html,
"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
These are additional fix styles in USER packages, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"adapt/fep"_fix_adapt_fep.html,
"addtorque"_fix_addtorque.html,
"atc"_fix_atc.html,
+"ave/correlate/long"_fix_ave_correlate_long.html,
"ave/spatial/sphere"_fix_ave_spatial_sphere.html,
"drude"_fix_drude.html,
"drude/transform/direct"_fix_drude_transform.html,
"drude/transform/reverse"_fix_drude_transform.html,
"colvars"_fix_colvars.html,
"gle"_fix_gle.html,
"imd"_fix_imd.html,
"ipi"_fix_ipi.html,
"langevin/drude"_fix_langevin_drude.html,
"langevin/eff"_fix_langevin_eff.html,
"lb/fluid"_fix_lb_fluid.html,
"lb/momentum"_fix_lb_momentum.html,
"lb/pc"_fix_lb_pc.html,
"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
"lb/viscous"_fix_lb_viscous.html,
"meso"_fix_meso.html,
"meso/stationary"_fix_meso_stationary.html,
"nph/eff"_fix_nh_eff.html,
"npt/eff"_fix_nh_eff.html,
"nve/eff"_fix_nve_eff.html,
"nvt/eff"_fix_nh_eff.html,
"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
"phonon"_fix_phonon.html,
"pimd"_fix_pimd.html,
"qbmsst"_fix_qbmsst.html,
"qeq/reax"_fix_qeq_reax.html,
"qmmm"_fix_qmmm.html,
"qtb"_fix_qtb.html,
"reax/c/bonds"_fix_reaxc_bonds.html,
"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,
"ttm/mod"_fix_ttm.html :tb(c=6,ea=c)
:line
Compute styles :h4
See the "compute"_compute.html command for one-line descriptions of
each style or click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"angle/local"_compute_angle_local.html,
"angmom/chunk"_compute_angmom_chunk.html,
"body/local"_compute_body_local.html,
"bond/local"_compute_bond_local.html,
"centro/atom"_compute_centro_atom.html,
"chunk/atom"_compute_chunk_atom.html,
"cluster/atom"_compute_cluster_atom.html,
"cna/atom"_compute_cna_atom.html,
"com"_compute_com.html,
"com/chunk"_compute_com_chunk.html,
"contact/atom"_compute_contact_atom.html,
"coord/atom"_compute_coord_atom.html,
"damage/atom"_compute_damage_atom.html,
"dihedral/local"_compute_dihedral_local.html,
"dilatation/atom"_compute_dilatation_atom.html,
"displace/atom"_compute_displace_atom.html,
"erotate/asphere"_compute_erotate_asphere.html,
"erotate/rigid"_compute_erotate_rigid.html,
"erotate/sphere"_compute_erotate_sphere.html,
"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
"event/displace"_compute_event_displace.html,
"group/group"_compute_group_group.html,
"gyration"_compute_gyration.html,
"gyration/chunk"_compute_gyration_chunk.html,
"heat/flux"_compute_heat_flux.html,
"improper/local"_compute_improper_local.html,
"inertia/chunk"_compute_inertia_chunk.html,
"ke"_compute_ke.html,
"ke/atom"_compute_ke_atom.html,
"ke/rigid"_compute_ke_rigid.html,
"msd"_compute_msd.html,
"msd/chunk"_compute_msd_chunk.html,
"msd/nongauss"_compute_msd_nongauss.html,
"omega/chunk"_compute_omega_chunk.html,
"pair"_compute_pair.html,
"pair/local"_compute_pair_local.html,
"pe (c)"_compute_pe.html,
"pe/atom"_compute_pe_atom.html,
"plasticity/atom"_compute_plasticity_atom.html,
"pressure (c)"_compute_pressure.html,
"property/atom"_compute_property_atom.html,
"property/local"_compute_property_local.html,
"property/chunk"_compute_property_chunk.html,
"rdf"_compute_rdf.html,
"reduce"_compute_reduce.html,
"reduce/region"_compute_reduce.html,
"slice"_compute_slice.html,
"sna/atom"_compute_sna_atom.html,
"snad/atom"_compute_sna_atom.html,
"snav/atom"_compute_sna_atom.html,
"stress/atom"_compute_stress_atom.html,
"temp (ck)"_compute_temp.html,
"temp/asphere"_compute_temp_asphere.html,
"temp/com"_compute_temp_com.html,
"temp/chunk"_compute_temp_chunk.html,
"temp/deform"_compute_temp_deform.html,
"temp/partial (c)"_compute_temp_partial.html,
"temp/profile"_compute_temp_profile.html,
"temp/ramp"_compute_temp_ramp.html,
"temp/region"_compute_temp_region.html,
"temp/sphere"_compute_temp_sphere.html,
"ti"_compute_ti.html,
"torque/chunk"_compute_torque_chunk.html,
"vacf"_compute_vacf.html,
"vcm/chunk"_compute_vcm_chunk.html,
"voronoi/atom"_compute_voronoi_atom.html :tb(c=6,ea=c)
These are additional compute styles in USER packages, which can be
used if "LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"ackland/atom"_compute_ackland_atom.html,
"basal/atom"_compute_basal_atom.html,
"fep"_compute_fep.html,
"force/tally"_compute_tally.html,
"heat/flux/tally"_compute_tally.html,
"ke/eff"_compute_ke_eff.html,
"ke/atom/eff"_compute_ke_atom_eff.html,
"meso_e/atom"_compute_meso_e_atom.html,
"meso_rho/atom"_compute_meso_rho_atom.html,
"meso_t/atom"_compute_meso_t_atom.html,
"pe/tally"_compute_tally.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/ulsph/stress"_compute_smd_ulsph_stress.html,
"smd/vol"_compute_smd_vol.html,
"stress/tally"_compute_tally.html,
"temp/drude"_compute_temp_drude.html,
"temp/eff"_compute_temp_eff.html,
"temp/deform/eff"_compute_temp_deform_eff.html,
"temp/region/eff"_compute_temp_region_eff.html,
"temp/rotate"_compute_temp_rotate.html,
"xrd"_compute_xrd.html :tb(c=6,ea=c)
:line
Pair_style potentials :h4
See the "pair_style"_pair_style.html command for an overview of pair
potentials. Click on the style itself for a full description. Many
of the styles have accelerated versions, which can be used if LAMMPS
is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"none"_pair_none.html,
"hybrid"_pair_hybrid.html,
"hybrid/overlay"_pair_hybrid.html,
"adp (o)"_pair_adp.html,
"airebo (o)"_pair_airebo.html,
"beck (go)"_pair_beck.html,
"body"_pair_body.html,
"bop"_pair_bop.html,
"born (go)"_pair_born.html,
"born/coul/long (cgo)"_pair_born.html,
"born/coul/long/cs"_pair_born.html,
"born/coul/msm (o)"_pair_born.html,
"born/coul/wolf (go)"_pair_born.html,
"brownian (o)"_pair_brownian.html,
"brownian/poly (o)"_pair_brownian.html,
"buck (cgko)"_pair_buck.html,
"buck/coul/cut (cgko)"_pair_buck.html,
"buck/coul/long (cgko)"_pair_buck.html,
"buck/coul/long/cs"_pair_buck.html,
"buck/coul/msm (o)"_pair_buck.html,
"buck/long/coul/long (o)"_pair_buck_long.html,
"colloid (go)"_pair_colloid.html,
"comb (o)"_pair_comb.html,
"comb3"_pair_comb.html,
"coul/cut (gko)"_pair_coul.html,
"coul/debye (gko)"_pair_coul.html,
"coul/dsf (gko)"_pair_coul.html,
"coul/long (gko)"_pair_coul.html,
"coul/long/cs"_pair_coul.html,
"coul/msm"_pair_coul.html,
"coul/streitz"_pair_coul.html,
"coul/wolf (ko)"_pair_coul.html,
"dpd (o)"_pair_dpd.html,
"dpd/tstat (o)"_pair_dpd.html,
"dsmc"_pair_dsmc.html,
"eam (cgkot)"_pair_eam.html,
"eam/alloy (cgkot)"_pair_eam.html,
"eam/fs (cgkot)"_pair_eam.html,
"eim (o)"_pair_eim.html,
"gauss (go)"_pair_gauss.html,
"gayberne (gio)"_pair_gayberne.html,
"gran/hertz/history (o)"_pair_gran.html,
"gran/hooke (co)"_pair_gran.html,
"gran/hooke/history (o)"_pair_gran.html,
"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
"kim"_pair_kim.html,
"lcbop"_pair_lcbop.html,
"line/lj (o)"_pair_line_lj.html,
"lj/charmm/coul/charmm (cko)"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit (cko)"_pair_charmm.html,
"lj/charmm/coul/long (cgiko)"_pair_charmm.html,
"lj/charmm/coul/msm"_pair_charmm.html,
"lj/class2 (cgko)"_pair_class2.html,
"lj/class2/coul/cut (cko)"_pair_class2.html,
"lj/class2/coul/long (cgko)"_pair_class2.html,
"lj/cubic (go)"_pair_lj_cubic.html,
"lj/cut (cgikot)"_pair_lj.html,
"lj/cut/coul/cut (cgko)"_pair_lj.html,
"lj/cut/coul/debye (cgko)"_pair_lj.html,
"lj/cut/coul/dsf (gko)"_pair_lj.html,
"lj/cut/coul/long (cgikot)"_pair_lj.html,
"lj/cut/coul/long/cs"_pair_lj.html,
"lj/cut/coul/msm (go)"_pair_lj.html,
"lj/cut/dipole/cut (go)"_pair_dipole.html,
"lj/cut/dipole/long"_pair_dipole.html,
"lj/cut/tip4p/cut (o)"_pair_lj.html,
"lj/cut/tip4p/long (ot)"_pair_lj.html,
"lj/expand (cgko)"_pair_lj_expand.html,
"lj/gromacs (cgko)"_pair_gromacs.html,
"lj/gromacs/coul/gromacs (cko)"_pair_gromacs.html,
"lj/long/coul/long (o)"_pair_lj_long.html,
"lj/long/dipole/long"_pair_dipole.html,
"lj/long/tip4p/long"_pair_lj_long.html,
"lj/smooth (co)"_pair_lj_smooth.html,
"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
"lj96/cut (cgo)"_pair_lj96.html,
"lubricate (o)"_pair_lubricate.html,
"lubricate/poly (o)"_pair_lubricate.html,
"lubricateU"_pair_lubricateU.html,
"lubricateU/poly"_pair_lubricateU.html,
"meam (o)"_pair_meam.html,
"mie/cut (o)"_pair_mie.html,
"morse (cgot)"_pair_morse.html,
"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
"nm/cut (o)"_pair_nm.html,
"nm/cut/coul/cut (o)"_pair_nm.html,
"nm/cut/coul/long (o)"_pair_nm.html,
"peri/eps"_pair_peri.html,
"peri/lps (o)"_pair_peri.html,
"peri/pmb (o)"_pair_peri.html,
"peri/ves"_pair_peri.html,
"polymorphic"_pair_polymorphic.html,
"rebo (o)"_pair_airebo.html,
"resquared (go)"_pair_resquared.html,
"snap"_pair_snap.html,
"soft (go)"_pair_soft.html,
"sw (cgkio)"_pair_sw.html,
"table (gko)"_pair_table.html,
"tersoff (cgko)"_pair_tersoff.html,
"tersoff/mod (ko)"_pair_tersoff_mod.html,
"tersoff/zbl (ko)"_pair_tersoff_zbl.html,
"tip4p/cut (o)"_pair_coul.html,
"tip4p/long (o)"_pair_coul.html,
"tri/lj (o)"_pair_tri_lj.html,
-"vashishta"_pair_vashishta.html,
+"vashishta (o)"_pair_vashishta.html,
"yukawa (go)"_pair_yukawa.html,
"yukawa/colloid (go)"_pair_yukawa_colloid.html,
"zbl (go)"_pair_zbl.html :tb(c=4,ea=c)
These are additional pair styles in USER packages, which can be used
if "LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"awpmd/cut"_pair_awpmd.html,
"coul/cut/soft (o)"_pair_lj_soft.html,
"coul/diel (o)"_pair_coul_diel.html,
"coul/long/soft (o)"_pair_lj_soft.html,
"eam/cd (o)"_pair_eam.html,
"edip (o)"_pair_edip.html,
"eff/cut"_pair_eff.html,
"gauss/cut"_pair_gauss.html,
"list"_pair_list.html,
"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
"lj/cut/dipole/sf (go)"_pair_dipole.html,
"lj/cut/soft (o)"_pair_lj_soft.html,
"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
"lj/sdk (gko)"_pair_sdk.html,
"lj/sdk/coul/long (go)"_pair_sdk.html,
"lj/sdk/coul/msm (o)"_pair_sdk.html,
"lj/sf (o)"_pair_lj_sf.html,
"meam/spline"_pair_meam_spline.html,
"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,
"sph/rhosum"_pair_sph_rhosum.html,
"sph/taitwater"_pair_sph_taitwater.html,
"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
"srp"_pair_srp.html,
"tersoff/table (o)"_pair_tersoff.html,
"thole"_pair_thole.html,
"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
:line
Bond_style potentials :h4
See the "bond_style"_bond_style.html command for an overview of bond
potentials. Click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"none"_bond_none.html,
"hybrid"_bond_hybrid.html,
"class2 (o)"_bond_class2.html,
"fene (ko)"_bond_fene.html,
"fene/expand (o)"_bond_fene_expand.html,
"harmonic (ko)"_bond_harmonic.html,
"morse (o)"_bond_morse.html,
"nonlinear (o)"_bond_nonlinear.html,
"quartic (o)"_bond_quartic.html,
"table (o)"_bond_table.html :tb(c=4,ea=c)
These are additional bond styles in USER packages, which can be used
if "LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"harmonic/shift (o)"_bond_harmonic_shift.html,
"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html :tb(c=4,ea=c)
:line
Angle_style potentials :h4
See the "angle_style"_angle_style.html command for an overview of
angle potentials. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
LAMMPS is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"none"_angle_none.html,
"hybrid"_angle_hybrid.html,
"charmm (ko)"_angle_charmm.html,
"class2 (o)"_angle_class2.html,
"cosine (o)"_angle_cosine.html,
"cosine/delta (o)"_angle_cosine_delta.html,
"cosine/periodic (o)"_angle_cosine_periodic.html,
"cosine/squared (o)"_angle_cosine_squared.html,
"harmonic (ko)"_angle_harmonic.html,
"table (o)"_angle_table.html :tb(c=4,ea=c)
These are additional angle styles in USER packages, which can be used
if "LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"cosine/shift (o)"_angle_cosine_shift.html,
"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
"dipole (o)"_angle_dipole.html,
"fourier (o)"_angle_fourier.html,
"fourier/simple (o)"_angle_fourier_simple.html,
"quartic (o)"_angle_quartic.html,
"sdk"_angle_sdk.html :tb(c=4,ea=c)
:line
Dihedral_style potentials :h4
See the "dihedral_style"_dihedral_style.html command for an overview
of dihedral potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
be used if LAMMPS is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"none"_dihedral_none.html,
"hybrid"_dihedral_hybrid.html,
"charmm (ko)"_dihedral_charmm.html,
"class2 (o)"_dihedral_class2.html,
"harmonic (o)"_dihedral_harmonic.html,
"helix (o)"_dihedral_helix.html,
"multi/harmonic (o)"_dihedral_multi_harmonic.html,
"opls (ko)"_dihedral_opls.html :tb(c=4,ea=c)
These are additional dihedral styles in USER packages, which can be
used if "LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
"fourier (o)"_dihedral_fourier.html,
"nharmonic (o)"_dihedral_nharmonic.html,
"quadratic (o)"_dihedral_quadratic.html,
"table (o)"_dihedral_table.html :tb(c=4,ea=c)
:line
Improper_style potentials :h4
See the "improper_style"_improper_style.html command for an overview
of improper potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
be used if LAMMPS is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"none"_improper_none.html,
"hybrid"_improper_hybrid.html,
"class2 (o)"_improper_class2.html,
"cvff (o)"_improper_cvff.html,
"harmonic (ko)"_improper_harmonic.html,
"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
These are additional improper styles in USER packages, which can be
used if "LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"cossq (o)"_improper_cossq.html,
"fourier (o)"_improper_fourier.html,
"ring (o)"_improper_ring.html :tb(c=4,ea=c)
:line
Kspace solvers :h4
See the "kspace_style"_kspace_style.html command for an overview of
Kspace solvers. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
LAMMPS is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"ewald (o)"_kspace_style.html,
"ewald/disp"_kspace_style.html,
"msm (o)"_kspace_style.html,
"msm/cg (o)"_kspace_style.html,
"pppm (cgo)"_kspace_style.html,
"pppm/cg (o)"_kspace_style.html,
"pppm/disp"_kspace_style.html,
"pppm/disp/tip4p"_kspace_style.html,
"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
diff --git a/doc/Section_example.html b/doc/Section_example.html
index 9a9441679..779318d58 100644
--- a/doc/Section_example.html
+++ b/doc/Section_example.html
@@ -1,130 +1,401 @@
-<HTML>
-<CENTER><A HREF = "Section_howto.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_perf.html">Next Section</A>
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-<H3>7. Example problems
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-<P>The LAMMPS distribution includes an examples sub-directory with
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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 current"><a class="current reference internal" href="">7. Example problems</a></li>
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+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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+ <div class="section" id="example-problems">
+<h1>7. Example problems<a class="headerlink" href="#example-problems" title="Permalink to this headline">¶</a></h1>
+<p>The LAMMPS distribution includes an examples sub-directory with
several sample problems. Each problem is in a sub-directory of its
own. Most are 2d models so that they run quickly, requiring at most a
couple of minutes to run on a desktop machine. Each problem has an
input script (in.*) and produces a log file (log.*) and dump file
(dump.*) when it runs. Some use a data file (data.*) of initial
coordinates as additional input. A few sample log file outputs on
different machines and different numbers of processors are included in
the directories to compare your answers to. E.g. a log file like
-log.crack.foo.P means it ran on P processors of machine "foo".
-</P>
-<P>For examples that use input data files, many of them were produced by
-<A HREF = "http://pizza.sandia.gov">Pizza.py</A> or setup tools described in the
-<A HREF = "Section_tools.html">Additional Tools</A> section of the LAMMPS
-documentation and provided with the LAMMPS distribution.
-</P>
-<P>If you uncomment the <A HREF = "dump.html">dump</A> command in the input script, a
+log.crack.foo.P means it ran on P processors of machine “foo”.</p>
+<p>For examples that use input data files, many of them were produced by
+<a class="reference external" href="http://pizza.sandia.gov">Pizza.py</a> or setup tools described in the
+<a class="reference internal" href="Section_tools.html"><em>Additional Tools</em></a> section of the LAMMPS
+documentation and provided with the LAMMPS distribution.</p>
+<p>If you uncomment the <a class="reference internal" href="dump.html"><em>dump</em></a> command in the input script, a
text dump file will be produced, which can be animated by various
-<A HREF = "http://lammps.sandia.gov/viz.html">visualization programs</A>. It can
-also be animated using the xmovie tool described in the <A HREF = "Section_tools.html">Additional
-Tools</A> section of the LAMMPS documentation.
-</P>
-<P>If you uncomment the <A HREF = "dump.html">dump image</A> command in the input
+<a class="reference external" href="http://lammps.sandia.gov/viz.html">visualization programs</a>. It can
+also be animated using the xmovie tool described in the <a class="reference internal" href="Section_tools.html"><em>Additional Tools</em></a> section of the LAMMPS documentation.</p>
+<p>If you uncomment the <a class="reference internal" href="dump.html"><em>dump image</em></a> command in the input
script, and assuming you have built LAMMPS with a JPG library, JPG
snapshot images will be produced when the simulation runs. They can
be quickly post-processed into a movie using commands described on the
-<A HREF = "dump_image.html">dump image</A> doc page.
-</P>
-<P>Animations of many of these examples can be viewed on the Movies
-section of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
-</P>
-<P>These are the sample problems in the examples sub-directories:
-</P>
-<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
-<TR><TD >balance</TD><TD > dynamic load balancing, 2d system</TD></TR>
-<TR><TD >body</TD><TD > body particles, 2d system</TD></TR>
-<TR><TD >colloid</TD><TD > big colloid particles in a small particle solvent, 2d system</TD></TR>
-<TR><TD >comb</TD><TD > models using the COMB potential</TD></TR>
-<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
-<TR><TD >cuda</TD><TD > use of the USER-CUDA package for GPU acceleration</TD></TR>
-<TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR>
-<TR><TD >dreiding</TD><TD > methanol via Dreiding FF</TD></TR>
-<TR><TD >eim</TD><TD > NaCl using the EIM potential</TD></TR>
-<TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR>
-<TR><TD >flow</TD><TD > Couette and Poiseuille flow in a 2d channel</TD></TR>
-<TR><TD >friction</TD><TD > frictional contact of spherical asperities between 2d surfaces</TD></TR>
-<TR><TD >gpu</TD><TD > use of the GPU package for GPU acceleration</TD></TR>
-<TR><TD >hugoniostat</TD><TD > Hugoniostat shock dynamics</TD></TR>
-<TR><TD >indent</TD><TD > spherical indenter into a 2d solid</TD></TR>
-<TR><TD >intel</TD><TD > use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor</TD></TR>
-<TR><TD >kim</TD><TD > use of potentials in Knowledge Base for Interatomic Models (KIM)</TD></TR>
-<TR><TD >line</TD><TD > line segment particles in 2d rigid bodies</TD></TR>
-<TR><TD >meam</TD><TD > MEAM test for SiC and shear (same as shear examples)</TD></TR>
-<TR><TD >melt</TD><TD > rapid melt of 3d LJ system</TD></TR>
-<TR><TD >micelle</TD><TD > self-assembly of small lipid-like molecules into 2d bilayers</TD></TR>
-<TR><TD >min</TD><TD > energy minimization of 2d LJ melt</TD></TR>
-<TR><TD >msst</TD><TD > MSST shock dynamics</TD></TR>
-<TR><TD >nb3b</TD><TD > use of nonbonded 3-body harmonic pair style</TD></TR>
-<TR><TD >neb</TD><TD > nudged elastic band (NEB) calculation for barrier finding</TD></TR>
-<TR><TD >nemd</TD><TD > non-equilibrium MD of 2d sheared system</TD></TR>
-<TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
-<TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR>
-<TR><TD >peri</TD><TD > Peridynamic model of cylinder impacted by indenter</TD></TR>
-<TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR>
-<TR><TD >prd</TD><TD > parallel replica dynamics of vacancy diffusion in bulk Si</TD></TR>
-<TR><TD >qeq</TD><TD > use of the QEQ pacakge for charge equilibration</TD></TR>
-<TR><TD >reax</TD><TD > RDX and TATB models using the ReaxFF</TD></TR>
-<TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR>
-<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void</TD></TR>
-<TR><TD >snap</TD><TD > NVE dynamics for BCC tantalum crystal using SNAP potential</TD></TR>
-<TR><TD >srd</TD><TD > stochastic rotation dynamics (SRD) particles as solvent</TD></TR>
-<TR><TD >tad</TD><TD > temperature-accelerated dynamics of vacancy diffusion in bulk Si</TD></TR>
-<TR><TD >tri</TD><TD > triangular particles in rigid bodies
-</TD></TR></TABLE></DIV>
-
-<P>Here is how you might run and visualize one of the sample problems:
-</P>
-<PRE>cd indent
+<a class="reference internal" href="dump_image.html"><em>dump image</em></a> doc page.</p>
+<p>Animations of many of these examples can be viewed on the Movies
+section of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>
+<p>These are the sample problems in the examples sub-directories:</p>
+<table border="1" class="docutils">
+<colgroup>
+<col width="15%" />
+<col width="85%" />
+</colgroup>
+<tbody valign="top">
+<tr class="row-odd"><td>balance</td>
+<td>dynamic load balancing, 2d system</td>
+</tr>
+<tr class="row-even"><td>body</td>
+<td>body particles, 2d system</td>
+</tr>
+<tr class="row-odd"><td>colloid</td>
+<td>big colloid particles in a small particle solvent, 2d system</td>
+</tr>
+<tr class="row-even"><td>comb</td>
+<td>models using the COMB potential</td>
+</tr>
+<tr class="row-odd"><td>crack</td>
+<td>crack propagation in a 2d solid</td>
+</tr>
+<tr class="row-even"><td>cuda</td>
+<td>use of the USER-CUDA package for GPU acceleration</td>
+</tr>
+<tr class="row-odd"><td>dipole</td>
+<td>point dipolar particles, 2d system</td>
+</tr>
+<tr class="row-even"><td>dreiding</td>
+<td>methanol via Dreiding FF</td>
+</tr>
+<tr class="row-odd"><td>eim</td>
+<td>NaCl using the EIM potential</td>
+</tr>
+<tr class="row-even"><td>ellipse</td>
+<td>ellipsoidal particles in spherical solvent, 2d system</td>
+</tr>
+<tr class="row-odd"><td>flow</td>
+<td>Couette and Poiseuille flow in a 2d channel</td>
+</tr>
+<tr class="row-even"><td>friction</td>
+<td>frictional contact of spherical asperities between 2d surfaces</td>
+</tr>
+<tr class="row-odd"><td>gpu</td>
+<td>use of the GPU package for GPU acceleration</td>
+</tr>
+<tr class="row-even"><td>hugoniostat</td>
+<td>Hugoniostat shock dynamics</td>
+</tr>
+<tr class="row-odd"><td>indent</td>
+<td>spherical indenter into a 2d solid</td>
+</tr>
+<tr class="row-even"><td>intel</td>
+<td>use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor</td>
+</tr>
+<tr class="row-odd"><td>kim</td>
+<td>use of potentials in Knowledge Base for Interatomic Models (KIM)</td>
+</tr>
+<tr class="row-even"><td>line</td>
+<td>line segment particles in 2d rigid bodies</td>
+</tr>
+<tr class="row-odd"><td>meam</td>
+<td>MEAM test for SiC and shear (same as shear examples)</td>
+</tr>
+<tr class="row-even"><td>melt</td>
+<td>rapid melt of 3d LJ system</td>
+</tr>
+<tr class="row-odd"><td>micelle</td>
+<td>self-assembly of small lipid-like molecules into 2d bilayers</td>
+</tr>
+<tr class="row-even"><td>min</td>
+<td>energy minimization of 2d LJ melt</td>
+</tr>
+<tr class="row-odd"><td>msst</td>
+<td>MSST shock dynamics</td>
+</tr>
+<tr class="row-even"><td>nb3b</td>
+<td>use of nonbonded 3-body harmonic pair style</td>
+</tr>
+<tr class="row-odd"><td>neb</td>
+<td>nudged elastic band (NEB) calculation for barrier finding</td>
+</tr>
+<tr class="row-even"><td>nemd</td>
+<td>non-equilibrium MD of 2d sheared system</td>
+</tr>
+<tr class="row-odd"><td>obstacle</td>
+<td>flow around two voids in a 2d channel</td>
+</tr>
+<tr class="row-even"><td>peptide</td>
+<td>dynamics of a small solvated peptide chain (5-mer)</td>
+</tr>
+<tr class="row-odd"><td>peri</td>
+<td>Peridynamic model of cylinder impacted by indenter</td>
+</tr>
+<tr class="row-even"><td>pour</td>
+<td>pouring of granular particles into a 3d box, then chute flow</td>
+</tr>
+<tr class="row-odd"><td>prd</td>
+<td>parallel replica dynamics of vacancy diffusion in bulk Si</td>
+</tr>
+<tr class="row-even"><td>qeq</td>
+<td>use of the QEQ pacakge for charge equilibration</td>
+</tr>
+<tr class="row-odd"><td>reax</td>
+<td>RDX and TATB models using the ReaxFF</td>
+</tr>
+<tr class="row-even"><td>rigid</td>
+<td>rigid bodies modeled as independent or coupled</td>
+</tr>
+<tr class="row-odd"><td>shear</td>
+<td>sideways shear applied to 2d solid, with and without a void</td>
+</tr>
+<tr class="row-even"><td>snap</td>
+<td>NVE dynamics for BCC tantalum crystal using SNAP potential</td>
+</tr>
+<tr class="row-odd"><td>srd</td>
+<td>stochastic rotation dynamics (SRD) particles as solvent</td>
+</tr>
+<tr class="row-even"><td>tad</td>
+<td>temperature-accelerated dynamics of vacancy diffusion in bulk Si</td>
+</tr>
+<tr class="row-odd"><td>tri</td>
+<td>triangular particles in rigid bodies</td>
+</tr>
+</tbody>
+</table>
+<p>vashishta: models using the Vashishta potential</p>
+<p>Here is how you might run and visualize one of the sample problems:</p>
+<div class="highlight-python"><div class="highlight"><pre>cd indent
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
-lmp_linux -in in.indent # run the problem
-</PRE>
-<P>Running the simulation produces the files <I>dump.indent</I> and
-<I>log.lammps</I>. You can visualize the dump file as follows:
-</P>
-<PRE>../../tools/xmovie/xmovie -scale dump.indent
-</PRE>
-<P>If you uncomment the <A HREF = "dump_image.html">dump image</A> line(s) in the input
+lmp_linux -in in.indent # run the problem
+</pre></div>
+</div>
+<p>Running the simulation produces the files <em>dump.indent</em> and
+<em>log.lammps</em>. You can visualize the dump file as follows:</p>
+<div class="highlight-python"><div class="highlight"><pre>../../tools/xmovie/xmovie -scale dump.indent
+</pre></div>
+</div>
+<p>If you uncomment the <a class="reference internal" href="dump_image.html"><em>dump image</em></a> line(s) in the input
script a series of JPG images will be produced by the run. These can
be viewed individually or turned into a movie or animated by tools
like ImageMagick or QuickTime or various Windows-based tools. See the
-<A HREF = "dump_image.html">dump image</A> doc page for more details. E.g. this
+<a class="reference internal" href="dump_image.html"><em>dump image</em></a> doc page for more details. E.g. this
Imagemagick command would create a GIF file suitable for viewing in a
-browser.
-</P>
-<PRE>% convert -loop 1 *.jpg foo.gif
-</PRE>
-<HR>
-
-<P>There is also a COUPLE directory with examples of how to use LAMMPS as
+browser.</p>
+<div class="highlight-python"><div class="highlight"><pre>% convert -loop 1 *.jpg foo.gif
+</pre></div>
+</div>
+<hr class="docutils" />
+<p>There is also a COUPLE directory with examples of how to use LAMMPS as
a library, either by itself or in tandem with another code or library.
-See the COUPLE/README file to get started.
-</P>
-<P>There is also an ELASTIC directory with an example script for
+See the COUPLE/README file to get started.</p>
+<p>There is also an ELASTIC directory with an example script for
computing elastic constants at zero temperature, using an Si example. See
-the ELASTIC/in.elastic file for more info.
-</P>
-<P>There is also an ELASTIC_T directory with an example script for
+the ELASTIC/in.elastic file for more info.</p>
+<p>There is also an ELASTIC_T directory with an example script for
computing elastic constants at finite temperature, using an Si example. See
-the ELASTIC_T/in.elastic file for more info.
-</P>
-<P>There is also a USER directory which contains subdirectories of
+the ELASTIC_T/in.elastic file for more info.</p>
+<p>There is also a USER directory which contains subdirectories of
user-provided examples for user packages. See the README files in
those directories for more info. See the
-<A HREF = "Section_start.html">Section_start.html</A> file for more info about user
-packages.
-</P>
-</HTML>
+<a class="reference internal" href="Section_start.html"><em>Section_start.html</em></a> file for more info about user
+packages.</p>
+</div>
+
+
+ </div>
+ </div>
+ <footer>
+
+ <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
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<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">6. How-to discussions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#restarting-a-simulation">6.1. Restarting a simulation</a></li>
<li class="toctree-l2"><a class="reference internal" href="#d-simulations">6.2. 2d simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#charmm-amber-and-dreiding-force-fields">6.3. CHARMM, AMBER, and DREIDING force fields</a></li>
<li class="toctree-l2"><a class="reference internal" href="#running-multiple-simulations-from-one-input-script">6.4. Running multiple simulations from one input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#granular-models">6.6. Granular models</a></li>
<li class="toctree-l2"><a class="reference internal" href="#tip3p-water-model">6.7. TIP3P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="#tip4p-water-model">6.8. TIP4P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="#spc-water-model">6.9. SPC water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li>
<li class="toctree-l2"><a class="reference internal" href="#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
<li class="toctree-l2"><a class="reference internal" href="#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li>
<li class="toctree-l2"><a class="reference internal" href="#nemd-simulations">6.13. NEMD simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#finite-size-spherical-and-aspherical-particles">6.14. Finite-size spherical and aspherical particles</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#atom-styles">6.14.1. Atom styles</a></li>
<li class="toctree-l3"><a class="reference internal" href="#pair-potentials">6.14.2. Pair potentials</a></li>
<li class="toctree-l3"><a class="reference internal" href="#time-integration">6.14.3. Time integration</a></li>
<li class="toctree-l3"><a class="reference internal" href="#computes-thermodynamics-and-dump-output">6.14.4. Computes, thermodynamics, and dump output</a></li>
<li class="toctree-l3"><a class="reference internal" href="#rigid-bodies-composed-of-finite-size-particles">6.14.5. Rigid bodies composed of finite-size particles</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#output-from-lammps-thermo-dumps-computes-fixes-variables">6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#global-per-atom-local-data">6.15.1. Global/per-atom/local data</a></li>
<li class="toctree-l3"><a class="reference internal" href="#scalar-vector-array-data">6.15.2. Scalar/vector/array data</a></li>
<li class="toctree-l3"><a class="reference internal" href="#thermodynamic-output">6.15.3. Thermodynamic output</a></li>
<li class="toctree-l3"><a class="reference internal" href="#dump-file-output">6.15.4. Dump file output</a></li>
<li class="toctree-l3"><a class="reference internal" href="#fixes-that-write-output-files">6.15.5. Fixes that write output files</a></li>
<li class="toctree-l3"><a class="reference internal" href="#computes-that-process-output-quantities">6.15.6. Computes that process output quantities</a></li>
<li class="toctree-l3"><a class="reference internal" href="#fixes-that-process-output-quantities">6.15.7. Fixes that process output quantities</a></li>
<li class="toctree-l3"><a class="reference internal" href="#computes-that-generate-values-to-output">6.15.8. Computes that generate values to output</a></li>
<li class="toctree-l3"><a class="reference internal" href="#fixes-that-generate-values-to-output">6.15.9. Fixes that generate values to output</a></li>
<li class="toctree-l3"><a class="reference internal" href="#variables-that-generate-values-to-output">6.15.10. Variables that generate values to output</a></li>
<li class="toctree-l3"><a class="reference internal" href="#summary-table-of-output-options-and-data-flow-between-commands">6.15.11. Summary table of output options and data flow between commands</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li>
<li class="toctree-l2"><a class="reference internal" href="#walls">6.17. Walls</a></li>
<li class="toctree-l2"><a class="reference internal" href="#elastic-constants">6.18. Elastic constants</a></li>
<li class="toctree-l2"><a class="reference internal" href="#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
<li class="toctree-l2"><a class="reference internal" href="#calculating-viscosity">6.21. Calculating viscosity</a></li>
<li class="toctree-l2"><a class="reference internal" href="#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
<li class="toctree-l2"><a class="reference internal" href="#using-chunks-to-calculate-system-properties">6.23. Using chunks to calculate system properties</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#compute-chunk-atom-command">6.23.1. Compute chunk/atom command:</a></li>
<li class="toctree-l3"><a class="reference internal" href="#fix-ave-chunk-command">6.23.2. Fix ave/chunk command:</a></li>
<li class="toctree-l3"><a class="reference internal" href="#compute-chunk-commands">6.23.3. Compute */chunk commands:</a></li>
<li class="toctree-l3"><a class="reference internal" href="#example-calculations-with-chunks">6.23.4. Example calculations with chunks</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#setting-parameters-for-the-kspace-style-pppm-disp-command">6.24. Setting parameters for the <code class="docutils literal"><span class="pre">kspace_style</span> <span class="pre">pppm/disp</span></code> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="#polarizable-models">6.25. Polarizable models</a></li>
<li class="toctree-l2"><a class="reference internal" href="#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
<li class="toctree-l2"><a class="reference internal" href="#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
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<div class="section" id="how-to-discussions">
<h1>6. How-to discussions<a class="headerlink" href="#how-to-discussions" title="Permalink to this headline">¶</a></h1>
<p>This section describes how to perform common tasks using LAMMPS.</p>
<div class="line-block">
<div class="line">6.1 <a class="reference internal" href="#howto-1"><span>Restarting a simulation</span></a></div>
<div class="line">6.2 <a class="reference internal" href="#howto-2"><span>2d simulations</span></a></div>
<div class="line">6.3 <a class="reference internal" href="#howto-3"><span>CHARMM, AMBER, and DREIDING force fields</span></a></div>
<div class="line">6.4 <a class="reference internal" href="#howto-4"><span>Running multiple simulations from one input script</span></a></div>
<div class="line">6.5 <a class="reference internal" href="#howto-5"><span>Multi-replica simulations</span></a></div>
<div class="line">6.6 <a class="reference internal" href="#howto-6"><span>Granular models</span></a></div>
<div class="line">6.7 <a class="reference internal" href="#howto-7"><span>TIP3P water model</span></a></div>
<div class="line">6.8 <a class="reference internal" href="#howto-8"><span>TIP4P water model</span></a></div>
<div class="line">6.9 <a class="reference internal" href="#howto-9"><span>SPC water model</span></a></div>
<div class="line">6.10 <a class="reference internal" href="#howto-10"><span>Coupling LAMMPS to other codes</span></a></div>
<div class="line">6.11 <a class="reference internal" href="#howto-11"><span>Visualizing LAMMPS snapshots</span></a></div>
<div class="line">6.12 <a class="reference internal" href="#howto-12"><span>Triclinic (non-orthogonal) simulation boxes</span></a></div>
<div class="line">6.13 <a class="reference internal" href="#howto-13"><span>NEMD simulations</span></a></div>
<div class="line">6.14 <a class="reference internal" href="#howto-14"><span>Finite-size spherical and aspherical particles</span></a></div>
<div class="line">6.15 <a class="reference internal" href="#howto-15"><span>Output from LAMMPS (thermo, dumps, computes, fixes, variables)</span></a></div>
<div class="line">6.16 <a class="reference internal" href="#howto-16"><span>Thermostatting, barostatting and computing temperature</span></a></div>
<div class="line">6.17 <a class="reference internal" href="#howto-17"><span>Walls</span></a></div>
<div class="line">6.18 <a class="reference internal" href="#howto-18"><span>Elastic constants</span></a></div>
<div class="line">6.19 <a class="reference internal" href="#howto-19"><span>Library interface to LAMMPS</span></a></div>
<div class="line">6.20 <a class="reference internal" href="#howto-20"><span>Calculating thermal conductivity</span></a></div>
<div class="line">6.21 <a class="reference internal" href="#howto-21"><span>Calculating viscosity</span></a></div>
<div class="line">6.22 <a class="reference internal" href="#howto-22"><span>Calculating a diffusion coefficient</span></a></div>
<div class="line">6.23 <a class="reference internal" href="#howto-23"><span>Using chunks to calculate system properties</span></a></div>
<div class="line">6.24 <a class="reference internal" href="#howto-24"><span>Setting parameters for the kspace_style pppm/disp command</span></a></div>
<div class="line">6.25 <a class="reference internal" href="#howto-25"><span>Polarizable models</span></a></div>
<div class="line">6.26 <a class="reference internal" href="#howto-26"><span>Adiabatic core/shell model</span></a></div>
<div class="line">6.27 <a class="reference internal" href="#howto-27"><span>Drude induced dipoles</span></a></div>
<div class="line"><br /></div>
</div>
<p>The example input scripts included in the LAMMPS distribution and
highlighted in <a class="reference internal" href="Section_example.html"><em>Section_example</em></a> also show how to
setup and run various kinds of simulations.</p>
<div class="section" id="restarting-a-simulation">
<span id="howto-1"></span><h2>6.1. Restarting a simulation<a class="headerlink" href="#restarting-a-simulation" title="Permalink to this headline">¶</a></h2>
<p>There are 3 ways to continue a long LAMMPS simulation. Multiple
<a class="reference internal" href="run.html"><em>run</em></a> commands can be used in the same input script. Each
run will continue from where the previous run left off. Or binary
restart files can be saved to disk using the <a class="reference internal" href="restart.html"><em>restart</em></a>
command. At a later time, these binary files can be read via a
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command in a new script. Or they can
be converted to text data files using the <a class="reference internal" href="Section_start.html#start-7"><span>-r command-line switch</span></a> and read by a
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command in a new script.</p>
<p>Here we give examples of 2 scripts that read either a binary restart
file or a converted data file and then issue a new run command to
continue where the previous run left off. They illustrate what
settings must be made in the new script. Details are discussed in the
documentation for the <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> and
<a class="reference internal" href="read_data.html"><em>read_data</em></a> commands.</p>
<p>Look at the <em>in.chain</em> input script provided in the <em>bench</em> directory
of the LAMMPS distribution to see the original script that these 2
scripts are based on. If that script had the line</p>
<div class="highlight-python"><div class="highlight"><pre>restart 50 tmp.restart
</pre></div>
</div>
<p>added to it, it would produce 2 binary restart files (tmp.restart.50
and tmp.restart.100) as it ran.</p>
<p>This script could be used to read the 1st restart file and re-run the
last 50 timesteps:</p>
<div class="highlight-python"><div class="highlight"><pre>read_restart tmp.restart.50
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>neighbor 0.4 bin
neigh_modify every 1 delay 1
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>timestep 0.012
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>run 50
</pre></div>
</div>
<p>Note that the following commands do not need to be repeated because
their settings are included in the restart file: <em>units, atom_style,
special_bonds, pair_style, bond_style</em>. However these commands do
need to be used, since their settings are not in the restart file:
<em>neighbor, fix, timestep</em>.</p>
<p>If you actually use this script to perform a restarted run, you will
notice that the thermodynamic data match at step 50 (if you also put a
“thermo 50” command in the original script), but do not match at step
100. This is because the <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a> command
uses random numbers in a way that does not allow for perfect restarts.</p>
<p>As an alternate approach, the restart file could be converted to a data
file as follows:</p>
<div class="highlight-python"><div class="highlight"><pre>lmp_g++ -r tmp.restart.50 tmp.restart.data
</pre></div>
</div>
<p>Then, this script could be used to re-run the last 50 steps:</p>
<div class="highlight-python"><div class="highlight"><pre>units lj
atom_style bond
pair_style lj/cut 1.12
pair_modify shift yes
bond_style fene
special_bonds 0.0 1.0 1.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>read_data tmp.restart.data
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>neighbor 0.4 bin
neigh_modify every 1 delay 1
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>timestep 0.012
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>reset_timestep 50
run 50
</pre></div>
</div>
<p>Note that nearly all the settings specified in the original <em>in.chain</em>
script must be repeated, except the <em>pair_coeff</em> and <em>bond_coeff</em>
commands since the new data file lists the force field coefficients.
Also, the <a class="reference internal" href="reset_timestep.html"><em>reset_timestep</em></a> command is used to tell
LAMMPS the current timestep. This value is stored in restart files,
but not in data files.</p>
<hr class="docutils" />
</div>
<div class="section" id="d-simulations">
<span id="howto-2"></span><h2>6.2. 2d simulations<a class="headerlink" href="#d-simulations" title="Permalink to this headline">¶</a></h2>
<p>Use the <a class="reference internal" href="dimension.html"><em>dimension</em></a> command to specify a 2d simulation.</p>
<p>Make the simulation box periodic in z via the <a class="reference internal" href="boundary.html"><em>boundary</em></a>
command. This is the default.</p>
<p>If using the <a class="reference internal" href="create_box.html"><em>create box</em></a> command to define a
simulation box, set the z dimensions narrow, but finite, so that the
create_atoms command will tile the 3d simulation box with a single z
plane of atoms - e.g.</p>
<pre class="literal-block">
<a class="reference internal" href="create_box.html"><em>create box</em></a> 1 -10 10 -10 10 -0.25 0.25
</pre>
<p>If using the <a class="reference internal" href="read_data.html"><em>read data</em></a> command to read in a file of
atom coordinates, set the “zlo zhi” values to be finite but narrow,
similar to the create_box command settings just described. For each
atom in the file, assign a z coordinate so it falls inside the
z-boundaries of the box - e.g. 0.0.</p>
<p>Use the <a class="reference internal" href="fix_enforce2d.html"><em>fix enforce2d</em></a> command as the last
defined fix to insure that the z-components of velocities and forces
are zeroed out every timestep. The reason to make it the last fix is
so that any forces induced by other fixes will be zeroed out.</p>
<p>Many of the example input scripts included in the LAMMPS distribution
are for 2d models.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Some models in LAMMPS treat particles as finite-size
spheres, as opposed to point particles. In 2d, the particles will
still be spheres, not disks, meaning their moment of inertia will be
the same as in 3d.</p>
</div>
<hr class="docutils" />
</div>
<div class="section" id="charmm-amber-and-dreiding-force-fields">
<span id="howto-3"></span><h2>6.3. CHARMM, AMBER, and DREIDING force fields<a class="headerlink" href="#charmm-amber-and-dreiding-force-fields" title="Permalink to this headline">¶</a></h2>
<p>A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
formulas implemented in LAMMPS that correspond to formulas commonly
used in the CHARMM, AMBER, and DREIDING force fields. Setting
coefficients is done in the input data file via the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command or in the input script with
commands like <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> or
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>. See <a class="reference internal" href="Section_tools.html"><em>Section_tools</em></a>
for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input.</p>
<p>See <a class="reference internal" href="#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
field. See <a class="reference internal" href="#cornell"><span>(Cornell)</span></a> for a description of the AMBER force
field.</p>
<p>These style choices compute force field formulas that are consistent
with common options in CHARMM or AMBER. See each command’s
documentation for the formula it computes.</p>
<ul class="simple">
<li><a class="reference internal" href="bond_harmonic.html"><em>bond_style</em></a> harmonic</li>
<li><a class="reference internal" href="angle_charmm.html"><em>angle_style</em></a> charmm</li>
<li><a class="reference internal" href="dihedral_charmm.html"><em>dihedral_style</em></a> charmm</li>
<li><a class="reference internal" href="pair_charmm.html"><em>pair_style</em></a> lj/charmm/coul/charmm</li>
<li><a class="reference internal" href="pair_charmm.html"><em>pair_style</em></a> lj/charmm/coul/charmm/implicit</li>
<li><a class="reference internal" href="pair_charmm.html"><em>pair_style</em></a> lj/charmm/coul/long</li>
<li><a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> charmm</li>
<li><a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> amber</li>
</ul>
<p>DREIDING is a generic force field developed by the <a class="reference external" href="http://www.wag.caltech.edu">Goddard group</a> at Caltech and is useful for
predicting structures and dynamics of organic, biological and
main-group inorganic molecules. The philosophy in DREIDING is to use
general force constants and geometry parameters based on simple
hybridization considerations, rather than individual force constants
and geometric parameters that depend on the particular combinations of
atoms involved in the bond, angle, or torsion terms. DREIDING has an
<a class="reference internal" href="pair_hbond_dreiding.html"><em>explicit hydrogen bond term</em></a> to describe
interactions involving a hydrogen atom on very electronegative atoms
(N, O, F).</p>
<p>See <a class="reference internal" href="#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field</p>
<p>These style choices compute force field formulas that are consistent
with the DREIDING force field. See each command’s
documentation for the formula it computes.</p>
<ul class="simple">
<li><a class="reference internal" href="bond_harmonic.html"><em>bond_style</em></a> harmonic</li>
<li><a class="reference internal" href="bond_morse.html"><em>bond_style</em></a> morse</li>
<li><a class="reference internal" href="angle_harmonic.html"><em>angle_style</em></a> harmonic</li>
<li><a class="reference internal" href="angle_cosine.html"><em>angle_style</em></a> cosine</li>
<li><a class="reference internal" href="angle_cosine_periodic.html"><em>angle_style</em></a> cosine/periodic</li>
<li><a class="reference internal" href="dihedral_charmm.html"><em>dihedral_style</em></a> charmm</li>
<li><a class="reference internal" href="improper_umbrella.html"><em>improper_style</em></a> umbrella</li>
<li><a class="reference internal" href="pair_buck.html"><em>pair_style</em></a> buck</li>
<li><a class="reference internal" href="pair_buck.html"><em>pair_style</em></a> buck/coul/cut</li>
<li><a class="reference internal" href="pair_buck.html"><em>pair_style</em></a> buck/coul/long</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style</em></a> lj/cut</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style</em></a> lj/cut/coul/cut</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style</em></a> lj/cut/coul/long</li>
<li><a class="reference internal" href="pair_hbond_dreiding.html"><em>pair_style</em></a> hbond/dreiding/lj</li>
<li><a class="reference internal" href="pair_hbond_dreiding.html"><em>pair_style</em></a> hbond/dreiding/morse</li>
<li><a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> dreiding</li>
</ul>
<hr class="docutils" />
</div>
<div class="section" id="running-multiple-simulations-from-one-input-script">
<span id="howto-4"></span><h2>6.4. Running multiple simulations from one input script<a class="headerlink" href="#running-multiple-simulations-from-one-input-script" title="Permalink to this headline">¶</a></h2>
<p>This can be done in several ways. See the documentation for
individual commands for more details on how these examples work.</p>
<p>If “multiple simulations” means continue a previous simulation for
more timesteps, then you simply use the <a class="reference internal" href="run.html"><em>run</em></a> command
multiple times. For example, this script</p>
<div class="highlight-python"><div class="highlight"><pre>units lj
atom_style atomic
read_data data.lj
run 10000
run 10000
run 10000
run 10000
run 10000
</pre></div>
</div>
<p>would run 5 successive simulations of the same system for a total of
50,000 timesteps.</p>
<p>If you wish to run totally different simulations, one after the other,
the <a class="reference internal" href="clear.html"><em>clear</em></a> command can be used in between them to
re-initialize LAMMPS. For example, this script</p>
<div class="highlight-python"><div class="highlight"><pre>units lj
atom_style atomic
read_data data.lj
run 10000
clear
units lj
atom_style atomic
read_data data.lj.new
run 10000
</pre></div>
</div>
<p>would run 2 independent simulations, one after the other.</p>
<p>For large numbers of independent simulations, you can use
<a class="reference internal" href="variable.html"><em>variables</em></a> and the <a class="reference internal" href="next.html"><em>next</em></a> and
<a class="reference internal" href="jump.html"><em>jump</em></a> commands to loop over the same input script
multiple times with different settings. For example, this
script, named in.polymer</p>
<div class="highlight-python"><div class="highlight"><pre>variable d index run1 run2 run3 run4 run5 run6 run7 run8
shell cd $d
read_data data.polymer
run 10000
shell cd ..
clear
next d
jump in.polymer
</pre></div>
</div>
<p>would run 8 simulations in different directories, using a data.polymer
file in each directory. The same concept could be used to run the
same system at 8 different temperatures, using a temperature variable
and storing the output in different log and dump files, for example</p>
<div class="highlight-python"><div class="highlight"><pre>variable a loop 8
variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
log log.$a
read data.polymer
velocity all create $t 352839
fix 1 all nvt $t $t 100.0
dump 1 all atom 1000 dump.$a
run 100000
clear
next t
next a
jump in.polymer
</pre></div>
</div>
<p>All of the above examples work whether you are running on 1 or
multiple processors, but assumed you are running LAMMPS on a single
partition of processors. LAMMPS can be run on multiple partitions via
the “-partition” command-line switch as described in <a class="reference internal" href="Section_start.html#start-7"><span>this section</span></a> of the manual.</p>
<p>In the last 2 examples, if LAMMPS were run on 3 partitions, the same
scripts could be used if the “index” and “loop” variables were
replaced with <em>universe</em>-style variables, as described in the
<a class="reference internal" href="variable.html"><em>variable</em></a> command. Also, the “next t” and “next a”
commands would need to be replaced with a single “next a t” command.
With these modifications, the 8 simulations of each script would run
on the 3 partitions one after the other until all were finished.
Initially, 3 simulations would be started simultaneously, one on each
partition. When one finished, that partition would then start
the 4th simulation, and so forth, until all 8 were completed.</p>
<hr class="docutils" />
</div>
<div class="section" id="multi-replica-simulations">
<span id="howto-5"></span><h2>6.5. Multi-replica simulations<a class="headerlink" href="#multi-replica-simulations" title="Permalink to this headline">¶</a></h2>
<p>Several commands in LAMMPS run mutli-replica simulations, meaning
that multiple instances (replicas) of your simulation are run
simultaneously, with small amounts of data exchanged between replicas
periodically.</p>
<p>These are the relevant commands:</p>
<ul class="simple">
<li><a class="reference internal" href="neb.html"><em>neb</em></a> for nudged elastic band calculations</li>
<li><a class="reference internal" href="prd.html"><em>prd</em></a> for parallel replica dynamics</li>
<li><a class="reference internal" href="tad.html"><em>tad</em></a> for temperature accelerated dynamics</li>
<li><a class="reference internal" href="temper.html"><em>temper</em></a> for parallel tempering</li>
<li><a class="reference internal" href="fix_pimd.html"><em>fix pimd</em></a> for path-integral molecular dynamics (PIMD)</li>
</ul>
<p>NEB is a method for finding transition states and barrier energies.
PRD and TAD are methods for performing accelerated dynamics to find
and perform infrequent events. Parallel tempering or replica exchange
runs different replicas at a series of temperature to facilitate
rare-event sampling.</p>
<p>These commands can only be used if LAMMPS was built with the REPLICA
package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
for more info on packages.</p>
<p>PIMD runs different replicas whose individual particles are coupled
together by springs to model a system or ring-polymers.</p>
<p>This commands can only be used if LAMMPS was built with the USER-MISC
package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
for more info on packages.</p>
<p>In all these cases, you must run with one or more processors per
replica. The processors assigned to each replica are determined at
run-time by using the <a class="reference internal" href="Section_start.html#start-7"><span>-partition command-line switch</span></a> to launch LAMMPS on multiple
partitions, which in this context are the same as replicas. E.g.
these commands:</p>
<div class="highlight-python"><div class="highlight"><pre>mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
mpirun -np 8 lmp_linux -partition 8x1 -in in.neb
</pre></div>
</div>
<p>would each run 8 replicas, on either 16 or 8 processors. Note the use
of the <a class="reference internal" href="Section_start.html#start-7"><span>-in command-line switch</span></a> to specify
the input script which is required when running in multi-replica mode.</p>
<p>Also note that with MPI installed on a machine (e.g. your desktop),
you can run on more (virtual) processors than you have physical
processors. Thus the above commands could be run on a
single-processor (or few-processor) desktop so that you can run
a multi-replica simulation on more replicas than you have
physical processors.</p>
<hr class="docutils" />
</div>
<div class="section" id="granular-models">
<span id="howto-6"></span><h2>6.6. Granular models<a class="headerlink" href="#granular-models" title="Permalink to this headline">¶</a></h2>
<p>Granular system are composed of spherical particles with a diameter,
as opposed to point particles. This means they have an angular
velocity and torque can be imparted to them to cause them to rotate.</p>
<p>To run a simulation of a granular model, you will want to use
the following commands:</p>
<ul class="simple">
<li><a class="reference internal" href="atom_style.html"><em>atom_style sphere</em></a></li>
<li><a class="reference internal" href="fix_nve_sphere.html"><em>fix nve/sphere</em></a></li>
<li><a class="reference internal" href="fix_gravity.html"><em>fix gravity</em></a></li>
</ul>
<p>This compute</p>
<ul class="simple">
<li><a class="reference internal" href="compute_erotate_sphere.html"><em>compute erotate/sphere</em></a></li>
</ul>
<p>calculates rotational kinetic energy which can be <a class="reference internal" href="#howto-15"><span>output with thermodynamic info</span></a>.</p>
<p>Use one of these 3 pair potentials, which compute forces and torques
between interacting pairs of particles:</p>
<ul class="simple">
<li><a class="reference internal" href="pair_style.html"><em>pair_style</em></a> gran/history</li>
<li><a class="reference internal" href="pair_style.html"><em>pair_style</em></a> gran/no_history</li>
<li><a class="reference internal" href="pair_style.html"><em>pair_style</em></a> gran/hertzian</li>
</ul>
<p>These commands implement fix options specific to granular systems:</p>
<ul class="simple">
<li><a class="reference internal" href="fix_freeze.html"><em>fix freeze</em></a></li>
<li><a class="reference internal" href="fix_pour.html"><em>fix pour</em></a></li>
<li><a class="reference internal" href="fix_viscous.html"><em>fix viscous</em></a></li>
<li><a class="reference internal" href="fix_wall_gran.html"><em>fix wall/gran</em></a></li>
</ul>
<p>The fix style <em>freeze</em> zeroes both the force and torque of frozen
atoms, and should be used for granular system instead of the fix style
<em>setforce</em>.</p>
<p>For computational efficiency, you can eliminate needless pairwise
computations between frozen atoms by using this command:</p>
<ul class="simple">
<li><a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a> exclude</li>
</ul>
<hr class="docutils" />
</div>
<div class="section" id="tip3p-water-model">
<span id="howto-7"></span><h2>6.7. TIP3P water model<a class="headerlink" href="#tip3p-water-model" title="Permalink to this headline">¶</a></h2>
<p>The TIP3P water model as implemented in CHARMM
<a class="reference internal" href="#mackerell"><span>(MacKerell)</span></a> specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
<em>harmonic</em> and an angle style of <em>harmonic</em> or <em>charmm</em> should also be
used.</p>
<p>These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
cutoff. The K values can be used if a flexible TIP3P model (without
fix shake) is desired. If the LJ epsilon and sigma for HH and OH are
set to 0.0, it corresponds to the original 1983 TIP3P model
-<a class="reference internal" href="pair_lj.html#jorgensen"><span>(Jorgensen)</span></a>.</p>
+<a class="reference internal" href="#jorgensen"><span>(Jorgensen)</span></a>.</p>
<div class="line-block">
<div class="line">O mass = 15.9994</div>
<div class="line">H mass = 1.008</div>
<div class="line">O charge = -0.834</div>
<div class="line">H charge = 0.417</div>
<div class="line">LJ epsilon of OO = 0.1521</div>
<div class="line">LJ sigma of OO = 3.1507</div>
<div class="line">LJ epsilon of HH = 0.0460</div>
<div class="line">LJ sigma of HH = 0.4000</div>
<div class="line">LJ epsilon of OH = 0.0836</div>
<div class="line">LJ sigma of OH = 1.7753</div>
<div class="line">K of OH bond = 450</div>
<div class="line">r0 of OH bond = 0.9572</div>
<div class="line">K of HOH angle = 55</div>
<div class="line">theta of HOH angle = 104.52</div>
<div class="line"><br /></div>
</div>
<p>These are the parameters to use for TIP3P with a long-range Coulombic
solver (e.g. Ewald or PPPM in LAMMPS), see <a class="reference internal" href="#price"><span>(Price)</span></a> for
details:</p>
<div class="line-block">
<div class="line">O mass = 15.9994</div>
<div class="line">H mass = 1.008</div>
<div class="line">O charge = -0.830</div>
<div class="line">H charge = 0.415</div>
<div class="line">LJ epsilon of OO = 0.102</div>
<div class="line">LJ sigma of OO = 3.188</div>
<div class="line">LJ epsilon, sigma of OH, HH = 0.0</div>
<div class="line">K of OH bond = 450</div>
<div class="line">r0 of OH bond = 0.9572</div>
<div class="line">K of HOH angle = 55</div>
<div class="line">theta of HOH angle = 104.52</div>
<div class="line"><br /></div>
</div>
<p>Wikipedia also has a nice article on <a class="reference external" href="http://en.wikipedia.org/wiki/Water_model">water models</a>.</p>
<hr class="docutils" />
</div>
<div class="section" id="tip4p-water-model">
<span id="howto-8"></span><h2>6.8. TIP4P water model<a class="headerlink" href="#tip4p-water-model" title="Permalink to this headline">¶</a></h2>
<p>The four-point TIP4P rigid water model extends the traditional
three-point TIP3P model by adding an additional site, usually
massless, where the charge associated with the oxygen atom is placed.
This site M is located at a fixed distance away from the oxygen along
the bisector of the HOH bond angle. A bond style of <em>harmonic</em> and an
angle style of <em>harmonic</em> or <em>charmm</em> should also be used.</p>
<p>A TIP4P model is run with LAMMPS using either this command
for a cutoff model:</p>
<p><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/tip4p/cut</em></a></p>
<p>or these two commands for a long-range model:</p>
<ul class="simple">
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/tip4p/long</em></a></li>
<li><a class="reference internal" href="kspace_style.html"><em>kspace_style pppm/tip4p</em></a></li>
</ul>
<p>For both models, the bond lengths and bond angles should be held fixed
using the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command.</p>
<p>These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP4P model with a cutoff
-<a class="reference internal" href="pair_lj.html#jorgensen"><span>(Jorgensen)</span></a>. Note that the OM distance is specified in
+<a class="reference internal" href="#jorgensen"><span>(Jorgensen)</span></a>. Note that the OM distance is specified in
the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command, not as part of the pair
coefficients.</p>
<div class="line-block">
<div class="line">O mass = 15.9994</div>
<div class="line">H mass = 1.008</div>
<div class="line">O charge = -1.040</div>
<div class="line">H charge = 0.520</div>
<div class="line">r0 of OH bond = 0.9572</div>
<div class="line">theta of HOH angle = 104.52</div>
<div class="line">OM distance = 0.15</div>
<div class="line">LJ epsilon of O-O = 0.1550</div>
<div class="line">LJ sigma of O-O = 3.1536</div>
<div class="line">LJ epsilon, sigma of OH, HH = 0.0</div>
<div class="line">Coulombic cutoff = 8.5</div>
<div class="line"><br /></div>
</div>
<p>For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
<a class="reference external" href="http://dx.doi.org/10.1063/1.1931662">http://dx.doi.org/10.1063/1.1931662</a>) these values can be used:</p>
<div class="line-block">
<div class="line">O mass = 15.9994</div>
<div class="line">H mass = 1.008</div>
<div class="line">O charge = -1.1794</div>
<div class="line">H charge = 0.5897</div>
<div class="line">r0 of OH bond = 0.9572</div>
<div class="line">theta of HOH angle = 104.52</div>
<div class="line">OM distance = 0.1577</div>
<div class="line">LJ epsilon of O-O = 0.21084</div>
<div class="line">LJ sigma of O-O = 3.1668</div>
<div class="line">LJ epsilon, sigma of OH, HH = 0.0</div>
<div class="line">Coulombic cutoff = 8.5</div>
<div class="line"><br /></div>
</div>
<p>For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
<a class="reference external" href="http://dx.doi.org/10.1063/1.2121687">http://dx.doi.org/10.1063/1.2121687</a>), these values can be used:</p>
<div class="line-block">
<div class="line">O mass = 15.9994</div>
<div class="line">H mass = 1.008</div>
<div class="line">O charge = -1.1128</div>
<div class="line">H charge = 0.5564</div>
<div class="line">r0 of OH bond = 0.9572</div>
<div class="line">theta of HOH angle = 104.52</div>
<div class="line">OM distance = 0.1546</div>
<div class="line">LJ epsilon of O-O = 0.1852</div>
<div class="line">LJ sigma of O-O = 3.1589</div>
<div class="line">LJ epsilon, sigma of OH, HH = 0.0</div>
<div class="line">Coulombic cutoff = 8.5</div>
<div class="line"><br /></div>
</div>
<p>These are the parameters to use for TIP4P with a long-range Coulombic
solver (e.g. Ewald or PPPM in LAMMPS):</p>
<div class="line-block">
<div class="line">O mass = 15.9994</div>
<div class="line">H mass = 1.008</div>
<div class="line">O charge = -1.0484</div>
<div class="line">H charge = 0.5242</div>
<div class="line">r0 of OH bond = 0.9572</div>
<div class="line">theta of HOH angle = 104.52</div>
<div class="line">OM distance = 0.1250</div>
<div class="line">LJ epsilon of O-O = 0.16275</div>
<div class="line">LJ sigma of O-O = 3.16435</div>
<div class="line">LJ epsilon, sigma of OH, HH = 0.0</div>
<div class="line"><br /></div>
</div>
<p>Note that the when using the TIP4P pair style, the neighobr list
cutoff for Coulomb interactions is effectively extended by a distance
2 * (OM distance), to account for the offset distance of the
fictitious charges on O atoms in water molecules. Thus it is
typically best in an efficiency sense to use a LJ cutoff >= Coulomb
cutoff + 2*(OM distance), to shrink the size of the neighbor list.
This leads to slightly larger cost for the long-range calculation, so
you can test the trade-off for your model. The OM distance and the LJ
and Coulombic cutoffs are set in the <a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/tip4p/long</em></a> command.</p>
<p>Wikipedia also has a nice article on <a class="reference external" href="http://en.wikipedia.org/wiki/Water_model">water models</a>.</p>
<hr class="docutils" />
</div>
<div class="section" id="spc-water-model">
<span id="howto-9"></span><h2>6.9. SPC water model<a class="headerlink" href="#spc-water-model" title="Permalink to this headline">¶</a></h2>
<p>The SPC water model specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
<em>harmonic</em> and an angle style of <em>harmonic</em> or <em>charmm</em> should also be
used.</p>
<p>These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid SPC model.</p>
<div class="line-block">
<div class="line">O mass = 15.9994</div>
<div class="line">H mass = 1.008</div>
<div class="line">O charge = -0.820</div>
<div class="line">H charge = 0.410</div>
<div class="line">LJ epsilon of OO = 0.1553</div>
<div class="line">LJ sigma of OO = 3.166</div>
<div class="line">LJ epsilon, sigma of OH, HH = 0.0</div>
<div class="line">r0 of OH bond = 1.0</div>
<div class="line">theta of HOH angle = 109.47</div>
<div class="line"><br /></div>
</div>
<p>Note that as originally proposed, the SPC model was run with a 9
Angstrom cutoff for both LJ and Coulommbic terms. It can also be used
with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
any of the parameters above, though it becomes a different model in
that mode of usage.</p>
<p>The SPC/E (extended) water model is the same, except
the partial charge assignemnts change:</p>
<div class="line-block">
<div class="line">O charge = -0.8476</div>
<div class="line">H charge = 0.4238</div>
<div class="line"><br /></div>
</div>
<p>See the <a class="reference internal" href="#berendsen"><span>(Berendsen)</span></a> reference for more details on both
the SPC and SPC/E models.</p>
<p>Wikipedia also has a nice article on <a class="reference external" href="http://en.wikipedia.org/wiki/Water_model">water models</a>.</p>
<hr class="docutils" />
</div>
<div class="section" id="coupling-lammps-to-other-codes">
<span id="howto-10"></span><h2>6.10. Coupling LAMMPS to other codes<a class="headerlink" href="#coupling-lammps-to-other-codes" title="Permalink to this headline">¶</a></h2>
<p>LAMMPS is designed to allow it to be coupled to other codes. For
example, a quantum mechanics code might compute forces on a subset of
atoms and pass those forces to LAMMPS. Or a continuum finite element
(FE) simulation might use atom positions as boundary conditions on FE
nodal points, compute a FE solution, and return interpolated forces on
MD atoms.</p>
<p>LAMMPS can be coupled to other codes in at least 3 ways. Each has
advantages and disadvantages, which you’ll have to think about in the
context of your application.</p>
<p>(1) Define a new <a class="reference internal" href="fix.html"><em>fix</em></a> command that calls the other code. In
this scenario, LAMMPS is the driver code. During its timestepping,
the fix is invoked, and can make library calls to the other code,
which has been linked to LAMMPS as a library. This is the way the
<a class="reference external" href="http://www.rpi.edu/~anderk5/lab">POEMS</a> package that performs constrained rigid-body motion on
groups of atoms is hooked to LAMMPS. See the
<a class="reference internal" href="fix_poems.html"><em>fix_poems</em></a> command for more details. See <a class="reference internal" href="Section_modify.html"><em>this section</em></a> of the documentation for info on how to add
a new fix to LAMMPS.</p>
<p>(2) Define a new LAMMPS command that calls the other code. This is
conceptually similar to method (1), but in this case LAMMPS and the
other code are on a more equal footing. Note that now the other code
is not called during the timestepping of a LAMMPS run, but between
runs. The LAMMPS input script can be used to alternate LAMMPS runs
with calls to the other code, invoked via the new command. The
<a class="reference internal" href="run.html"><em>run</em></a> command facilitates this with its <em>every</em> option, which
makes it easy to run a few steps, invoke the command, run a few steps,
invoke the command, etc.</p>
<p>In this scenario, the other code can be called as a library, as in
(1), or it could be a stand-alone code, invoked by a system() call
made by the command (assuming your parallel machine allows one or more
processors to start up another program). In the latter case the
stand-alone code could communicate with LAMMPS thru files that the
command writes and reads.</p>
<p>See <a class="reference internal" href="Section_modify.html"><em>Section_modify</em></a> of the documentation for how
to add a new command to LAMMPS.</p>
<p>(3) Use LAMMPS as a library called by another code. In this case the
other code is the driver and calls LAMMPS as needed. Or a wrapper
code could link and call both LAMMPS and another code as libraries.
Again, the <a class="reference internal" href="run.html"><em>run</em></a> command has options that allow it to be
invoked with minimal overhead (no setup or clean-up) if you wish to do
multiple short runs, driven by another program.</p>
<p>Examples of driver codes that call LAMMPS as a library are included in
the examples/COUPLE directory of the LAMMPS distribution; see
examples/COUPLE/README for more details:</p>
<ul class="simple">
<li>simple: simple driver programs in C++ and C which invoke LAMMPS as a
library</li>
<li>lammps_quest: coupling of LAMMPS and <a class="reference external" href="http://dft.sandia.gov/Quest">Quest</a>, to run classical
MD with quantum forces calculated by a density functional code</li>
<li>lammps_spparks: coupling of LAMMPS and <a class="reference external" href="http://www.sandia.gov/~sjplimp/spparks.html">SPPARKS</a>, to couple
a kinetic Monte Carlo model for grain growth using MD to calculate
strain induced across grain boundaries</li>
</ul>
<p><a class="reference internal" href="Section_start.html#start-5"><span>This section</span></a> of the documentation
describes how to build LAMMPS as a library. Once this is done, you
can interface with LAMMPS either via C++, C, Fortran, or Python (or
any other language that supports a vanilla C-like interface). For
example, from C++ you could create one (or more) “instances” of
LAMMPS, pass it an input script to process, or execute individual
commands, all by invoking the correct class methods in LAMMPS. From C
or Fortran you can make function calls to do the same things. See
<a class="reference internal" href="Section_python.html"><em>Section_python</em></a> of the manual for a description
of the Python wrapper provided with LAMMPS that operates through the
LAMMPS library interface.</p>
<p>The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See <a class="reference internal" href="#howto-19"><span>Section_howto 19</span></a> of the
manual for a description of the interface and how to extend it for
your needs.</p>
<p>Note that the lammps_open() function that creates an instance of
LAMMPS takes an MPI communicator as an argument. This means that
instance of LAMMPS will run on the set of processors in the
communicator. Thus the calling code can run LAMMPS on all or a subset
of processors. For example, a wrapper script might decide to
alternate between LAMMPS and another code, allowing them both to run
on all the processors. Or it might allocate half the processors to
LAMMPS and half to the other code and run both codes simultaneously
before syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.</p>
<hr class="docutils" />
</div>
<div class="section" id="visualizing-lammps-snapshots">
<span id="howto-11"></span><h2>6.11. Visualizing LAMMPS snapshots<a class="headerlink" href="#visualizing-lammps-snapshots" title="Permalink to this headline">¶</a></h2>
<p>LAMMPS itself does not do visualization, but snapshots from LAMMPS
simulations can be visualized (and analyzed) in a variety of ways.</p>
<p>LAMMPS snapshots are created by the <a class="reference internal" href="dump.html"><em>dump</em></a> command which can
create files in several formats. The native LAMMPS dump format is a
text file (see “dump atom” or “dump custom”) which can be visualized
by the <a class="reference internal" href="Section_tools.html#xmovie"><span>xmovie</span></a> program, included with the
LAMMPS package. This produces simple, fast 2d projections of 3d
systems, and can be useful for rapid debugging of simulation geometry
and atom trajectories.</p>
<p>Several programs included with LAMMPS as auxiliary tools can convert
native LAMMPS dump files to other formats. See the
<a class="reference internal" href="Section_tools.html"><em>Section_tools</em></a> doc page for details. The first is
the <a class="reference internal" href="Section_tools.html#charmm"><span>ch2lmp tool</span></a>, which contains a
lammps2pdb Perl script which converts LAMMPS dump files into PDB
files. The second is the <a class="reference internal" href="Section_tools.html#arc"><span>lmp2arc tool</span></a> which
converts LAMMPS dump files into Accelrys’ Insight MD program files.
The third is the <a class="reference internal" href="Section_tools.html#cfg"><span>lmp2cfg tool</span></a> which converts
LAMMPS dump files into CFG files which can be read into the
<a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualizer.</p>
<p>A Python-based toolkit distributed by our group can read native LAMMPS
dump files, including custom dump files with additional columns of
user-specified atom information, and convert them to various formats
or pipe them into visualization software directly. See the <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py WWW site</a> for details. Specifically, Pizza.py can convert
LAMMPS dump files into PDB, XYZ, <a class="reference external" href="http://www.ensight.com">Ensight</a>, and VTK formats.
Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
RasMol visualization programs. Pizza.py has tools that do interactive
3d OpenGL visualization and one that creates SVG images of dump file
snapshots.</p>
<p>LAMMPS can create XYZ files directly (via “dump xyz”) which is a
simple text-based file format used by many visualization programs
including <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a>.</p>
<p>LAMMPS can create DCD files directly (via “dump dcd”) which can be
read by <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a> in conjunction with a CHARMM PSF file. Using this
form of output avoids the need to convert LAMMPS snapshots to PDB
files. See the <a class="reference internal" href="dump.html"><em>dump</em></a> command for more information on DCD
files.</p>
<p>LAMMPS can create XTC files directly (via “dump xtc”) which is GROMACS
file format which can also be read by <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a> for visualization.
See the <a class="reference internal" href="dump.html"><em>dump</em></a> command for more information on XTC files.</p>
<hr class="docutils" />
</div>
<div class="section" id="triclinic-non-orthogonal-simulation-boxes">
<span id="howto-12"></span><h2>6.12. Triclinic (non-orthogonal) simulation boxes<a class="headerlink" href="#triclinic-non-orthogonal-simulation-boxes" title="Permalink to this headline">¶</a></h2>
<p>By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The <a class="reference internal" href="boundary.html"><em>boundary</em></a> command sets the boundary
conditions of the box (periodic, non-periodic, etc). The orthogonal
box has its “origin” at (xlo,ylo,zlo) and is defined by 3 edge vectors
starting from the origin given by <strong>a</strong> = (xhi-xlo,0,0); <strong>b</strong> =
(0,yhi-ylo,0); <strong>c</strong> = (0,0,zhi-zlo). The 6 parameters
(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box
is created, e.g. by the <a class="reference internal" href="create_box.html"><em>create_box</em></a> or
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands. Additionally, LAMMPS defines box size parameters lx,ly,lz
where lx = xhi-xlo, and similarly in the y and z dimensions. The 6
parameters, as well as lx,ly,lz, can be output via the <a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> command.</p>
<p>LAMMPS also allows simulations to be performed in triclinic
(non-orthogonal) simulation boxes shaped as a parallelepiped with
triclinic symmetry. The parallelepiped has its “origin” at
(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the
origin given by <strong>a</strong> = (xhi-xlo,0,0); <strong>b</strong> = (xy,yhi-ylo,0); <strong>c</strong> =
(xz,yz,zhi-zlo). <em>xy,xz,yz</em> can be 0.0 or positive or negative values
and are called “tilt factors” because they are the amount of
displacement applied to faces of an originally orthogonal box to
transform it into the parallelepiped. In LAMMPS the triclinic
simulation box edge vectors <strong>a</strong>, <strong>b</strong>, and <strong>c</strong> cannot be arbitrary
vectors. As indicated, <strong>a</strong> must lie on the positive x axis. <strong>b</strong> must
lie in the xy plane, with strictly positive y component. <strong>c</strong> may have
any orientation with strictly positive z component. The requirement
that <strong>a</strong>, <strong>b</strong>, and <strong>c</strong> have strictly positive x, y, and z components,
respectively, ensures that <strong>a</strong>, <strong>b</strong>, and <strong>c</strong> form a complete
right-handed basis. These restrictions impose no loss of generality,
since it is possible to rotate/invert any set of 3 crystal basis
vectors so that they conform to the restrictions.</p>
<p>For example, assume that the 3 vectors <strong>A</strong>,**B**,**C** are the edge
vectors of a general parallelepiped, where there is no restriction on
<strong>A</strong>,**B**,**C** other than they form a complete right-handed basis i.e.
<strong>A</strong> x <strong>B</strong> . <strong>C</strong> > 0. The equivalent LAMMPS <strong>a</strong>,**b**,**c** are a linear
rotation of <strong>A</strong>, <strong>B</strong>, and <strong>C</strong> and can be computed as follows:</p>
<img alt="_images/transform.jpg" class="align-center" src="_images/transform.jpg" />
<p>where A = <a href="#id73"><span class="problematic" id="id74">|**A**|</span></a> indicates the scalar length of <strong>A</strong>. The ^ hat symbol
indicates the corresponding unit vector. <em>beta</em> and <em>gamma</em> are angles
between the vectors described below. Note that by construction,
<strong>a</strong>, <strong>b</strong>, and <strong>c</strong> have strictly positive x, y, and z components, respectively.
If it should happen that
<strong>A</strong>, <strong>B</strong>, and <strong>C</strong> form a left-handed basis, then the above equations
are not valid for <strong>c</strong>. In this case, it is necessary
to first apply an inversion. This can be achieved
by interchanging two basis vectors or by changing the sign of one of them.</p>
<p>For consistency, the same rotation/inversion applied to the basis vectors
must also be applied to atom positions, velocities,
and any other vector quantities.
This can be conveniently achieved by first converting to
fractional coordinates in the
old basis and then converting to distance coordinates in the new basis.
The transformation is given by the following equation:</p>
<img alt="_images/rotate.jpg" class="align-center" src="_images/rotate.jpg" />
<p>where <em>V</em> is the volume of the box, <strong>X</strong> is the original vector quantity and
<strong>x</strong> is the vector in the LAMMPS basis.</p>
<p>There is no requirement that a triclinic box be periodic in any
dimension, though it typically should be in at least the 2nd dimension
of the tilt (y in xy) if you want to enforce a shift in periodic
boundary conditions across that boundary. Some commands that work
with triclinic boxes, e.g. the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> and <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> commands, require periodicity or non-shrink-wrap
boundary conditions in specific dimensions. See the command doc pages
for details.</p>
<p>The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
time the simluation box is created. This happens in one of 3 ways.
If the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command is used with a region of
style <em>prism</em>, then a triclinic box is setup. See the
<a class="reference internal" href="region.html"><em>region</em></a> command for details. If the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command is used to define the simulation
box, and the header of the data file contains a line with the “xy xz
yz” keyword, then a triclinic box is setup. See the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command for details. Finally, if the
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command reads a restart file which
was written from a simulation using a triclinic box, then a triclinic
box will be setup for the restarted simulation.</p>
<p>Note that you can define a triclinic box with all 3 tilt factors =
0.0, so that it is initially orthogonal. This is necessary if the box
will become non-orthogonal, e.g. due to the <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> or
<a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> commands. Alternatively, you can use the
<a class="reference internal" href="change_box.html"><em>change_box</em></a> command to convert a simulation box from
orthogonal to triclinic and vice versa.</p>
<p>As with orthogonal boxes, LAMMPS defines triclinic box size parameters
lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions.
The 9 parameters, as well as lx,ly,lz, can be output via the
<a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> command.</p>
<p>To avoid extremely tilted boxes (which would be computationally
inefficient), LAMMPS normally requires that no tilt factor can skew
the box more than half the distance of the parallel box length, which
is the 1st dimension in the tilt factor (x for xz). This is required
both when the simulation box is created, e.g. via the
<a class="reference internal" href="create_box.html"><em>create_box</em></a> or <a class="reference internal" href="read_data.html"><em>read_data</em></a> commands,
as well as when the box shape changes dynamically during a simulation,
e.g. via the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> or <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a>
commands.</p>
<p>For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
the xy tilt factor must be between -5 and 5. Similarly, both xz and
yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is
not a limitation, since if the maximum tilt factor is 5 (as in this
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
... are geometrically all equivalent. If the box tilt exceeds this
limit during a dynamics run (e.g. via the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a>
command), then the box is “flipped” to an equivalent shape with a tilt
factor within the bounds, so the run can continue. See the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> doc page for further details.</p>
<p>One exception to this rule is if the 1st dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this
mode, if you tilt the system to extreme angles, the simulation will
simply become inefficient, due to the highly skewed simulation box.</p>
<p>The limitation on not creating a simulation box with a tilt factor
skewing the box more than half the distance of the parallel box length
can be overridden via the <a class="reference internal" href="box.html"><em>box</em></a> command. Setting the <em>tilt</em>
keyword to <em>large</em> allows any tilt factors to be specified.</p>
<p>Box flips that may occur using the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> or
<a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> commands can be turned off using the <em>flip no</em>
option with either of the commands.</p>
<p>Note that if a simulation box has a large tilt factor, LAMMPS will run
less efficiently, due to the large volume of communication needed to
acquire ghost atoms around a processor’s irregular-shaped sub-domain.
For extreme values of tilt, LAMMPS may also lose atoms and generate an
error.</p>
<p>Triclinic crystal structures are often defined using three lattice
constants <em>a</em>, <em>b</em>, and <em>c</em>, and three angles <em>alpha</em>, <em>beta</em> and
<em>gamma</em>. Note that in this nomenclature, the a, b, and c lattice
constants are the scalar lengths of the edge vectors <strong>a</strong>, <strong>b</strong>, and <strong>c</strong>
defined above. The relationship between these 6 quantities
(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) =
(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:</p>
<img alt="_images/box.jpg" class="align-center" src="_images/box.jpg" />
<p>The inverse relationship can be written as follows:</p>
<img alt="_images/box_inverse.jpg" class="align-center" src="_images/box_inverse.jpg" />
<p>The values of <em>a</em>, <em>b</em>, <em>c</em> , <em>alpha</em>, <em>beta</em> , and <em>gamma</em> can be printed
out or accessed by computes using the
<a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> keywords
<em>cella</em>, <em>cellb</em>, <em>cellc</em>, <em>cellalpha</em>, <em>cellbeta</em>, <em>cellgamma</em>,
respectively.</p>
<p>As discussed on the <a class="reference internal" href="dump.html"><em>dump</em></a> command doc page, when the BOX
BOUNDS for a snapshot is written to a dump file for a triclinic box,
an orthogonal bounding box which encloses the triclinic simulation box
is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
box, formatted as follows:</p>
<div class="highlight-python"><div class="highlight"><pre>ITEM: BOX BOUNDS xy xz yz
xlo_bound xhi_bound xy
ylo_bound yhi_bound xz
zlo_bound zhi_bound yz
</pre></div>
</div>
<p>This bounding box is convenient for many visualization programs and is
calculated from the 9 triclinic box parameters
(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">xlo_bound</span> <span class="o">=</span> <span class="n">xlo</span> <span class="o">+</span> <span class="n">MIN</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">xy</span><span class="p">,</span><span class="n">xz</span><span class="p">,</span><span class="n">xy</span><span class="o">+</span><span class="n">xz</span><span class="p">)</span>
<span class="n">xhi_bound</span> <span class="o">=</span> <span class="n">xhi</span> <span class="o">+</span> <span class="n">MAX</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">xy</span><span class="p">,</span><span class="n">xz</span><span class="p">,</span><span class="n">xy</span><span class="o">+</span><span class="n">xz</span><span class="p">)</span>
<span class="n">ylo_bound</span> <span class="o">=</span> <span class="n">ylo</span> <span class="o">+</span> <span class="n">MIN</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">yz</span><span class="p">)</span>
<span class="n">yhi_bound</span> <span class="o">=</span> <span class="n">yhi</span> <span class="o">+</span> <span class="n">MAX</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">yz</span><span class="p">)</span>
<span class="n">zlo_bound</span> <span class="o">=</span> <span class="n">zlo</span>
<span class="n">zhi_bound</span> <span class="o">=</span> <span class="n">zhi</span>
</pre></div>
</div>
<p>These formulas can be inverted if you need to convert the bounding box
back into the triclinic box parameters, e.g. xlo = xlo_bound -
MIN(0.0,xy,xz,xy+xz).</p>
<p>One use of triclinic simulation boxes is to model solid-state crystals
with triclinic symmetry. The <a class="reference internal" href="lattice.html"><em>lattice</em></a> command can be
used with non-orthogonal basis vectors to define a lattice that will
tile a triclinic simulation box via the
<a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a> command.</p>
<p>A second use is to run Parinello-Rahman dyanamics via the <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> command, which will adjust the xy, xz, yz tilt
factors to compensate for off-diagonal components of the pressure
tensor. The analalog for an <a class="reference internal" href="minimize.html"><em>energy minimization</em></a> is
the <a class="reference internal" href="fix_box_relax.html"><em>fix box/relax</em></a> command.</p>
<p>A third use is to shear a bulk solid to study the response of the
material. The <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> command can be used for
this purpose. It allows dynamic control of the xy, xz, yz tilt
factors as a simulation runs. This is discussed in the next section
on non-equilibrium MD (NEMD) simulations.</p>
<hr class="docutils" />
</div>
<div class="section" id="nemd-simulations">
<span id="howto-13"></span><h2>6.13. NEMD simulations<a class="headerlink" href="#nemd-simulations" title="Permalink to this headline">¶</a></h2>
<p>Non-equilibrium molecular dynamics or NEMD simulations are typically
used to measure a fluid’s rheological properties such as viscosity.
In LAMMPS, such simulations can be performed by first setting up a
non-orthogonal simulation box (see the preceding Howto section).</p>
<p>A shear strain can be applied to the simulation box at a desired
strain rate by using the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> command. The
<a class="reference internal" href="fix_nvt_sllod.html"><em>fix nvt/sllod</em></a> command can be used to thermostat
the sheared fluid and integrate the SLLOD equations of motion for the
system. Fix nvt/sllod uses <a class="reference internal" href="compute_temp_deform.html"><em>compute temp/deform</em></a> to compute a thermal temperature
by subtracting out the streaming velocity of the shearing atoms. The
velocity profile or other properties of the fluid can be monitored via
the <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a> command.</p>
<p>As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by
LAMMPS for computational efficiency to be 1/2 of the parallel box
length. However, <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> can continuously strain
a box by an arbitrary amount. As discussed in the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> command, when the tilt value reaches a limit,
the box is flipped to the opposite limit which is an equivalent tiling
of periodic space. The strain rate can then continue to change as
before. In a long NEMD simulation these box re-shaping events may
occur many times.</p>
<p>In a NEMD simulation, the “remap” option of <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> should be set to “remap v”, since that is what
<a class="reference internal" href="fix_nvt_sllod.html"><em>fix nvt/sllod</em></a> assumes to generate a velocity
profile consistent with the applied shear strain rate.</p>
<p>An alternative method for calculating viscosities is provided via the
<a class="reference internal" href="fix_viscosity.html"><em>fix viscosity</em></a> command.</p>
<hr class="docutils" />
</div>
<div class="section" id="finite-size-spherical-and-aspherical-particles">
<span id="howto-14"></span><h2>6.14. Finite-size spherical and aspherical particles<a class="headerlink" href="#finite-size-spherical-and-aspherical-particles" title="Permalink to this headline">¶</a></h2>
<p>Typical MD models treat atoms or particles as point masses. Sometimes
it is desirable to have a model with finite-size particles such as
spheroids or ellipsoids or generalized aspherical bodies. The
difference is that such particles have a moment of inertia, rotational
energy, and angular momentum. Rotation is induced by torque coming
from interactions with other particles.</p>
<p>LAMMPS has several options for running simulations with these kinds of
particles. The following aspects are discussed in turn:</p>
<ul class="simple">
<li>atom styles</li>
<li>pair potentials</li>
<li>time integration</li>
<li>computes, thermodynamics, and dump output</li>
<li>rigid bodies composed of finite-size particles</li>
</ul>
<p>Example input scripts for these kinds of models are in the body,
colloid, dipole, ellipse, line, peri, pour, and tri directories of the
<a class="reference internal" href="Section_example.html"><em>examples directory</em></a> in the LAMMPS distribution.</p>
<div class="section" id="atom-styles">
<h3>6.14.1. Atom styles<a class="headerlink" href="#atom-styles" title="Permalink to this headline">¶</a></h3>
<p>There are several <a class="reference internal" href="atom_style.html"><em>atom styles</em></a> that allow for
definition of finite-size particles: sphere, dipole, ellipsoid, line,
tri, peri, and body.</p>
<p>The sphere style defines particles that are spheriods and each
particle can have a unique diameter and mass (or density). These
particles store an angular velocity (omega) and can be acted upon by
torque. The “set” command can be used to modify the diameter and mass
of individual particles, after then are created.</p>
<p>The dipole style does not actually define finite-size particles, but
is often used in conjunction with spherical particles, via a command
like</p>
<div class="highlight-python"><div class="highlight"><pre>atom_style hybrid sphere dipole
</pre></div>
</div>
<p>This is because when dipoles interact with each other, they induce
torques, and a particle must be finite-size (i.e. have a moment of
inertia) in order to respond and rotate. See the <a class="reference internal" href="atom_style.html"><em>atom_style dipole</em></a> command for details. The “set” command can be
used to modify the orientation and length of the dipole moment of
individual particles, after then are created.</p>
<p>The ellipsoid style defines particles that are ellipsoids and thus can
be aspherical. Each particle has a shape, specified by 3 diameters,
and mass (or density). These particles store an angular momentum and
their orientation (quaternion), and can be acted upon by torque. They
do not store an angular velocity (omega), which can be in a different
direction than angular momentum, rather they compute it as needed.
The “set” command can be used to modify the diameter, orientation, and
mass of individual particles, after then are created. It also has a
brief explanation of what quaternions are.</p>
<p>The line style defines line segment particles with two end points and
a mass (or density). They can be used in 2d simulations, and they can
be joined together to form rigid bodies which represent arbitrary
polygons.</p>
<p>The tri style defines triangular particles with three corner points
and a mass (or density). They can be used in 3d simulations, and they
can be joined together to form rigid bodies which represent arbitrary
particles with a triangulated surface.</p>
<p>The peri style is used with <a class="reference internal" href="pair_peri.html"><em>Peridynamic models</em></a> and
defines particles as having a volume, that is used internally in the
<a class="reference internal" href="pair_peri.html"><em>pair_style peri</em></a> potentials.</p>
<p>The body style allows for definition of particles which can represent
complex entities, such as surface meshes of discrete points,
collections of sub-particles, deformable objects, etc. The body style
is discussed in more detail on the <a class="reference internal" href="body.html"><em>body</em></a> doc page.</p>
<p>Note that if one of these atom styles is used (or multiple styles via
the <a class="reference internal" href="atom_style.html"><em>atom_style hybrid</em></a> command), not all particles in
the system are required to be finite-size or aspherical.</p>
<p>For example, in the ellipsoid style, if the 3 shape parameters are set
to the same value, the particle will be a sphere rather than an
ellipsoid. If the 3 shape parameters are all set to 0.0 or if the
diameter is set to 0.0, it will be a point particle. In the line or
tri style, if the lineflag or triflag is specified as 0, then it
will be a point particle.</p>
<p>Some of the pair styles used to compute pairwise interactions between
finite-size particles also compute the correct interaction with point
particles as well, e.g. the interaction between a point particle and a
finite-size particle or between two point particles. If necessary,
<a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> can be used to insure the correct
interactions are computed for the appropriate style of interactions.
Likewise, using groups to partition particles (ellipsoids versus
spheres versus point particles) will allow you to use the appropriate
time integrators and temperature computations for each class of
particles. See the doc pages for various commands for details.</p>
<p>Also note that for <a class="reference internal" href="dimension.html"><em>2d simulations</em></a>, atom styles sphere
and ellipsoid still use 3d particles, rather than as circular disks or
ellipses. This means they have the same moment of inertia as the 3d
object. When temperature is computed, the correct degrees of freedom
are used for rotation in a 2d versus 3d system.</p>
</div>
<div class="section" id="pair-potentials">
<h3>6.14.2. Pair potentials<a class="headerlink" href="#pair-potentials" title="Permalink to this headline">¶</a></h3>
<p>When a system with finite-size particles is defined, the particles
will only rotate and experience torque if the force field computes
such interactions. These are the various <a class="reference internal" href="pair_style.html"><em>pair styles</em></a> that generate torque:</p>
<ul class="simple">
<li><a class="reference internal" href="pair_gran.html"><em>pair_style gran/history</em></a></li>
<li><a class="reference internal" href="pair_gran.html"><em>pair_style gran/hertzian</em></a></li>
<li><a class="reference internal" href="pair_gran.html"><em>pair_style gran/no_history</em></a></li>
<li><a class="reference internal" href="pair_dipole.html"><em>pair_style dipole/cut</em></a></li>
<li><a class="reference internal" href="pair_gayberne.html"><em>pair_style gayberne</em></a></li>
<li><a class="reference internal" href="pair_resquared.html"><em>pair_style resquared</em></a></li>
<li><a class="reference internal" href="pair_brownian.html"><em>pair_style brownian</em></a></li>
<li><a class="reference internal" href="pair_lubricate.html"><em>pair_style lubricate</em></a></li>
<li><a class="reference internal" href="pair_line_lj.html"><em>pair_style line/lj</em></a></li>
<li><a class="reference internal" href="pair_tri_lj.html"><em>pair_style tri/lj</em></a></li>
<li><a class="reference internal" href="pair_body.html"><em>pair_style body</em></a></li>
</ul>
<p>The granular pair styles are used with spherical particles. The
dipole pair style is used with the dipole atom style, which could be
applied to spherical or ellipsoidal particles. The GayBerne and
REsquared potentials require ellipsoidal particles, though they will
also work if the 3 shape parameters are the same (a sphere). The
Brownian and lubrication potentials are used with spherical particles.
The line, tri, and body potentials are used with line segment,
triangular, and body particles respectively.</p>
</div>
<div class="section" id="time-integration">
<h3>6.14.3. Time integration<a class="headerlink" href="#time-integration" title="Permalink to this headline">¶</a></h3>
<p>There are several fixes that perform time integration on finite-size
spherical particles, meaning the integrators update the rotational
orientation and angular velocity or angular momentum of the particles:</p>
<ul class="simple">
<li><a class="reference internal" href="fix_nve_sphere.html"><em>fix nve/sphere</em></a></li>
<li><a class="reference internal" href="fix_nvt_sphere.html"><em>fix nvt/sphere</em></a></li>
<li><a class="reference internal" href="fix_npt_sphere.html"><em>fix npt/sphere</em></a></li>
</ul>
<p>Likewise, there are 3 fixes that perform time integration on
ellipsoidal particles:</p>
<ul class="simple">
<li><a class="reference internal" href="fix_nve_asphere.html"><em>fix nve/asphere</em></a></li>
<li><a class="reference internal" href="fix_nvt_asphere.html"><em>fix nvt/asphere</em></a></li>
<li><a class="reference internal" href="fix_npt_asphere.html"><em>fix npt/asphere</em></a></li>
</ul>
<p>The advantage of these fixes is that those which thermostat the
particles include the rotational degrees of freedom in the temperature
calculation and thermostatting. The <a class="reference external" href="fix_langevin">fix langevin</a>
command can also be used with its <em>omgea</em> or <em>angmom</em> options to
thermostat the rotational degrees of freedom for spherical or
ellipsoidal particles. Other thermostatting fixes only operate on the
translational kinetic energy of finite-size particles.</p>
<p>These fixes perform constant NVE time integration on line segment,
triangular, and body particles:</p>
<ul class="simple">
<li><a class="reference internal" href="fix_nve_line.html"><em>fix nve/line</em></a></li>
<li><a class="reference internal" href="fix_nve_tri.html"><em>fix nve/tri</em></a></li>
<li><a class="reference internal" href="fix_nve_body.html"><em>fix nve/body</em></a></li>
</ul>
<p>Note that for mixtures of point and finite-size particles, these
integration fixes can only be used with <a class="reference internal" href="group.html"><em>groups</em></a> which
contain finite-size particles.</p>
</div>
<div class="section" id="computes-thermodynamics-and-dump-output">
<h3>6.14.4. Computes, thermodynamics, and dump output<a class="headerlink" href="#computes-thermodynamics-and-dump-output" title="Permalink to this headline">¶</a></h3>
<p>There are several computes that calculate the temperature or
rotational energy of spherical or ellipsoidal particles:</p>
<ul class="simple">
<li><a class="reference internal" href="compute_temp_sphere.html"><em>compute temp/sphere</em></a></li>
<li><a class="reference internal" href="compute_temp_asphere.html"><em>compute temp/asphere</em></a></li>
<li><a class="reference internal" href="compute_erotate_sphere.html"><em>compute erotate/sphere</em></a></li>
<li><a class="reference internal" href="compute_erotate_asphere.html"><em>compute erotate/asphere</em></a></li>
</ul>
<p>These include rotational degrees of freedom in their computation. If
you wish the thermodynamic output of temperature or pressure to use
one of these computes (e.g. for a system entirely composed of
finite-size particles), then the compute can be defined and the
<a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a> command used. Note that by default
thermodynamic quantities will be calculated with a temperature that
only includes translational degrees of freedom. See the
<a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command for details.</p>
<p>These commands can be used to output various attributes of finite-size
particles:</p>
<ul class="simple">
<li><a class="reference internal" href="dump.html"><em>dump custom</em></a></li>
<li><a class="reference internal" href="compute_property_atom.html"><em>compute property/atom</em></a></li>
<li><a class="reference internal" href="dump.html"><em>dump local</em></a></li>
<li><a class="reference internal" href="compute_body_local.html"><em>compute body/local</em></a></li>
</ul>
<p>Attributes include the dipole moment, the angular velocity, the
angular momentum, the quaternion, the torque, the end-point and
corner-point coordinates (for line and tri particles), and
sub-particle attributes of body particles.</p>
</div>
<div class="section" id="rigid-bodies-composed-of-finite-size-particles">
<h3>6.14.5. Rigid bodies composed of finite-size particles<a class="headerlink" href="#rigid-bodies-composed-of-finite-size-particles" title="Permalink to this headline">¶</a></h3>
<p>The <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command treats a collection of
particles as a rigid body, computes its inertia tensor, sums the total
force and torque on the rigid body each timestep due to forces on its
constituent particles, and integrates the motion of the rigid body.</p>
<p>If any of the constituent particles of a rigid body are finite-size
particles (spheres or ellipsoids or line segments or triangles), then
their contribution to the inertia tensor of the body is different than
if they were point particles. This means the rotational dynamics of
the rigid body will be different. Thus a model of a dimer is
different if the dimer consists of two point masses versus two
spheroids, even if the two particles have the same mass. Finite-size
particles that experience torque due to their interaction with other
particles will also impart that torque to a rigid body they are part
of.</p>
<p>See the “fix rigid” command for example of complex rigid-body models
it is possible to define in LAMMPS.</p>
<p>Note that the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command can also be used to
treat 2, 3, or 4 particles as a rigid body, but it always assumes the
particles are point masses.</p>
<p>Also note that body particles cannot be modeled with the <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command. Body particles are treated by LAMMPS
as single particles, though they can store internal state, such as a
list of sub-particles. Individual body partices are typically treated
as rigid bodies, and their motion integrated with a command like <a class="reference internal" href="fix_nve_body.html"><em>fix nve/body</em></a>. Interactions between pairs of body
particles are computed via a command like <a class="reference internal" href="pair_body.html"><em>pair_style body</em></a>.</p>
<hr class="docutils" />
</div>
</div>
<div class="section" id="output-from-lammps-thermo-dumps-computes-fixes-variables">
<span id="howto-15"></span><h2>6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)<a class="headerlink" href="#output-from-lammps-thermo-dumps-computes-fixes-variables" title="Permalink to this headline">¶</a></h2>
<p>There are four basic kinds of LAMMPS output:</p>
<ul class="simple">
<li><a class="reference internal" href="thermo_style.html"><em>Thermodynamic output</em></a>, which is a list
of quantities printed every few timesteps to the screen and logfile.</li>
<li><a class="reference internal" href="dump.html"><em>Dump files</em></a>, which contain snapshots of atoms and various
per-atom values and are written at a specified frequency.</li>
<li>Certain fixes can output user-specified quantities to files: <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a> for time averaging, <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a> for spatial averaging, and <a class="reference internal" href="fix_print.html"><em>fix print</em></a> for single-line output of
<a class="reference internal" href="variable.html"><em>variables</em></a>. Fix print can also output to the
screen.</li>
<li><a class="reference internal" href="restart.html"><em>Restart files</em></a>.</li>
</ul>
<p>A simulation prints one set of thermodynamic output and (optionally)
restart files. It can generate any number of dump files and fix
output files, depending on what <a class="reference internal" href="dump.html"><em>dump</em></a> and <a class="reference internal" href="fix.html"><em>fix</em></a>
commands you specify.</p>
<p>As discussed below, LAMMPS gives you a variety of ways to determine
what quantities are computed and printed when the thermodynamics,
dump, or fix commands listed above perform output. Throughout this
discussion, note that users can also <a class="reference internal" href="Section_modify.html"><em>add their own computes and fixes to LAMMPS</em></a> which can then generate values that can
then be output with these commands.</p>
<p>The following sub-sections discuss different LAMMPS command related
to output and the kind of data they operate on and produce:</p>
<ul class="simple">
<li><a class="reference internal" href="#global"><span>Global/per-atom/local data</span></a></li>
<li><a class="reference internal" href="#scalar"><span>Scalar/vector/array data</span></a></li>
<li><a class="reference internal" href="#thermo"><span>Thermodynamic output</span></a></li>
<li><a class="reference internal" href="#dump"><span>Dump file output</span></a></li>
<li><span class="xref std std-ref">Fixes that write output files</span></li>
<li><a class="reference internal" href="#computeoutput"><span>Computes that process output quantities</span></a></li>
<li><span class="xref std std-ref">Fixes that process output quantities</span></li>
<li><a class="reference internal" href="#compute"><span>Computes that generate values to output</span></a></li>
<li><a class="reference internal" href="#fix"><span>Fixes that generate values to output</span></a></li>
<li><a class="reference internal" href="#variable"><span>Variables that generate values to output</span></a></li>
<li><a class="reference internal" href="#table"><span>Summary table of output options and data flow between commands</span></a></li>
</ul>
<div class="section" id="global-per-atom-local-data">
<span id="global"></span><h3>6.15.1. Global/per-atom/local data<a class="headerlink" href="#global-per-atom-local-data" title="Permalink to this headline">¶</a></h3>
<p>Various output-related commands work with three different styles of
data: global, per-atom, or local. A global datum is one or more
system-wide values, e.g. the temperature of the system. A per-atom
datum is one or more values per atom, e.g. the kinetic energy of each
atom. Local datums are calculated by each processor based on the
atoms it owns, but there may be zero or more per atom, e.g. a list of
bond distances.</p>
</div>
<div class="section" id="scalar-vector-array-data">
<span id="scalar"></span><h3>6.15.2. Scalar/vector/array data<a class="headerlink" href="#scalar-vector-array-data" title="Permalink to this headline">¶</a></h3>
<p>Global, per-atom, and local datums can each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The
doc page for a “compute” or “fix” or “variable” that generates data
will specify both the style and kind of data it produces, e.g. a
per-atom vector.</p>
<p>When a quantity is accessed, as in many of the output commands
discussed below, it can be referenced via the following bracket
notation, where ID in this case is the ID of a compute. The leading
“<a href="#id75"><span class="problematic" id="id76">c_</span></a>” would be replaced by “<a href="#id77"><span class="problematic" id="id78">f_</span></a>” for a fix, or “<a href="#id79"><span class="problematic" id="id80">v_</span></a>” for a variable:</p>
<table border="1" class="docutils">
<colgroup>
<col width="21%" />
<col width="79%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>c_ID</td>
<td>entire scalar, vector, or array</td>
</tr>
<tr class="row-even"><td>c_ID[I]</td>
<td>one element of vector, one column of array</td>
</tr>
<tr class="row-odd"><td>c_ID[I][J]</td>
<td>one element of array</td>
</tr>
</tbody>
</table>
<p>In other words, using one bracket reduces the dimension of the data
once (vector -> scalar, array -> vector). Using two brackets reduces
the dimension twice (array -> scalar). Thus a command that uses
scalar values as input can typically also process elements of a vector
or array.</p>
</div>
<div class="section" id="thermodynamic-output">
<span id="thermo"></span><h3>6.15.3. Thermodynamic output<a class="headerlink" href="#thermodynamic-output" title="Permalink to this headline">¶</a></h3>
<p>The frequency and format of thermodynamic output is set by the
<a class="reference internal" href="thermo.html"><em>thermo</em></a>, <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a>, and
<a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a> commands. The
<a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command also specifies what values
are calculated and written out. Pre-defined keywords can be specified
(e.g. press, etotal, etc). Three additional kinds of keywords can
also be specified (c_ID, f_ID, v_name), where a <a class="reference internal" href="compute.html"><em>compute</em></a>
or <a class="reference internal" href="fix.html"><em>fix</em></a> or <a class="reference internal" href="variable.html"><em>variable</em></a> provides the value to be
output. In each case, the compute, fix, or variable must generate
global values for input to the <a class="reference internal" href="dump.html"><em>thermo_style custom</em></a>
command.</p>
<p>Note that thermodynamic output values can be “extensive” or
“intensive”. The former scale with the number of atoms in the system
(e.g. total energy), the latter do not (e.g. temperature). The
setting for <a class="reference internal" href="thermo_modify.html"><em>thermo_modify norm</em></a> determines whether
extensive quantities are normalized or not. Computes and fixes
produce either extensive or intensive values; see their individual doc
pages for details. <a class="reference internal" href="variable.html"><em>Equal-style variables</em></a> produce only
intensive values; you can include a division by “natoms” in the
formula if desired, to make an extensive calculation produce an
intensive result.</p>
</div>
<div class="section" id="dump-file-output">
<span id="dump"></span><h3>6.15.4. Dump file output<a class="headerlink" href="#dump-file-output" title="Permalink to this headline">¶</a></h3>
<p>Dump file output is specified by the <a class="reference internal" href="dump.html"><em>dump</em></a> and
<a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> commands. There are several
pre-defined formats (dump atom, dump xtc, etc).</p>
<p>There is also a <a class="reference internal" href="dump.html"><em>dump custom</em></a> format where the user
specifies what values are output with each atom. Pre-defined atom
attributes can be specified (id, x, fx, etc). Three additional kinds
of keywords can also be specified (c_ID, f_ID, v_name), where a
<a class="reference internal" href="compute.html"><em>compute</em></a> or <a class="reference internal" href="fix.html"><em>fix</em></a> or <a class="reference internal" href="variable.html"><em>variable</em></a>
provides the values to be output. In each case, the compute, fix, or
variable must generate per-atom values for input to the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command.</p>
<p>There is also a <a class="reference internal" href="dump.html"><em>dump local</em></a> format where the user specifies
what local values to output. A pre-defined index keyword can be
specified to enumuerate the local values. Two additional kinds of
keywords can also be specified (c_ID, f_ID), where a
<a class="reference internal" href="compute.html"><em>compute</em></a> or <a class="reference internal" href="fix.html"><em>fix</em></a> or <a class="reference internal" href="variable.html"><em>variable</em></a>
provides the values to be output. In each case, the compute or fix
must generate local values for input to the <a class="reference internal" href="dump.html"><em>dump local</em></a>
command.</p>
</div>
<div class="section" id="fixes-that-write-output-files">
<span id="fixoutput"></span><h3>6.15.5. Fixes that write output files<a class="headerlink" href="#fixes-that-write-output-files" title="Permalink to this headline">¶</a></h3>
<p>Several fixes take various quantities as input and can write output
files: <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>, <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a>, <a class="reference internal" href="fix_ave_histo.html"><em>fix ave/histo</em></a>,
<a class="reference internal" href="fix_ave_correlate.html"><em>fix ave/correlate</em></a>, and <a class="reference internal" href="fix_print.html"><em>fix print</em></a>.</p>
<p>The <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a> command enables direct output to
a file and/or time-averaging of global scalars or vectors. The user
specifies one or more quantities as input. These can be global
<a class="reference internal" href="compute.html"><em>compute</em></a> values, global <a class="reference internal" href="fix.html"><em>fix</em></a> values, or
<a class="reference internal" href="variable.html"><em>variables</em></a> of any style except the atom style which
produces per-atom values. Since a variable can refer to keywords used
by the <a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> command (like temp or
press) and individual per-atom values, a wide variety of quantities
can be time averaged and/or output in this way. If the inputs are one
or more scalar values, then the fix generate a global scalar or vector
of output. If the inputs are one or more vector values, then the fix
generates a global vector or array of output. The time-averaged
output of this fix can also be used as input to other output commands.</p>
<p>The <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a> command enables direct
output to a file of spatial-averaged per-atom quantities like those
output in dump files, within 1d layers of the simulation box. The
per-atom quantities can be atom density (mass or number) or atom
attributes such as position, velocity, force. They can also be
per-atom quantities calculated by a <a class="reference internal" href="compute.html"><em>compute</em></a>, by a
<a class="reference internal" href="fix.html"><em>fix</em></a>, or by an atom-style <a class="reference internal" href="variable.html"><em>variable</em></a>. The
spatial-averaged output of this fix can also be used as input to other
output commands.</p>
<p>The <a class="reference internal" href="fix_ave_histo.html"><em>fix ave/histo</em></a> command enables direct output
to a file of histogrammed quantities, which can be global or per-atom
or local quantities. The histogram output of this fix can also be
used as input to other output commands.</p>
<p>The <a class="reference internal" href="fix_ave_correlate.html"><em>fix ave/correlate</em></a> command enables direct
output to a file of time-correlated quantities, which can be global
scalars. The correlation matrix output of this fix can also be used
as input to other output commands.</p>
<p>The <a class="reference internal" href="fix_print.html"><em>fix print</em></a> command can generate a line of output
written to the screen and log file or to a separate file, periodically
during a running simulation. The line can contain one or more
<a class="reference internal" href="variable.html"><em>variable</em></a> values for any style variable except the atom
style). As explained above, variables themselves can contain
references to global values generated by <a class="reference internal" href="thermo_style.html"><em>thermodynamic keywords</em></a>, <a class="reference internal" href="compute.html"><em>computes</em></a>,
<a class="reference internal" href="fix.html"><em>fixes</em></a>, or other <a class="reference internal" href="variable.html"><em>variables</em></a>, or to per-atom
values for a specific atom. Thus the <a class="reference internal" href="fix_print.html"><em>fix print</em></a>
command is a means to output a wide variety of quantities separate
from normal thermodynamic or dump file output.</p>
</div>
<div class="section" id="computes-that-process-output-quantities">
<span id="computeoutput"></span><h3>6.15.6. Computes that process output quantities<a class="headerlink" href="#computes-that-process-output-quantities" title="Permalink to this headline">¶</a></h3>
<p>The <a class="reference internal" href="compute_reduce.html"><em>compute reduce</em></a> and <a class="reference internal" href="compute_reduce.html"><em>compute reduce/region</em></a> commands take one or more per-atom
or local vector quantities as inputs and “reduce” them (sum, min, max,
ave) to scalar quantities. These are produced as output values which
can be used as input to other output commands.</p>
<p>The <a class="reference internal" href="compute_slice.html"><em>compute slice</em></a> command take one or more global
vector or array quantities as inputs and extracts a subset of their
values to create a new vector or array. These are produced as output
values which can be used as input to other output commands.</p>
<p>The <a class="reference internal" href="compute_property_atom.html"><em>compute property/atom</em></a> command takes a
list of one or more pre-defined atom attributes (id, x, fx, etc) and
stores the values in a per-atom vector or array. These are produced
as output values which can be used as input to other output commands.
The list of atom attributes is the same as for the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command.</p>
<p>The <a class="reference internal" href="compute_property_local.html"><em>compute property/local</em></a> command takes
a list of one or more pre-defined local attributes (bond info, angle
info, etc) and stores the values in a local vector or array. These
are produced as output values which can be used as input to other
output commands.</p>
</div>
<div class="section" id="fixes-that-process-output-quantities">
<span id="id3"></span><h3>6.15.7. Fixes that process output quantities<a class="headerlink" href="#fixes-that-process-output-quantities" title="Permalink to this headline">¶</a></h3>
<p>The <a class="reference internal" href="fix_vector.html"><em>fix vector</em></a> command can create global vectors as
output from global scalars as input, accumulating them one element at
a time.</p>
<p>The <a class="reference internal" href="fix_ave_atom.html"><em>fix ave/atom</em></a> command performs time-averaging
of per-atom vectors. The per-atom quantities can be atom attributes
such as position, velocity, force. They can also be per-atom
quantities calculated by a <a class="reference internal" href="compute.html"><em>compute</em></a>, by a
<a class="reference internal" href="fix.html"><em>fix</em></a>, or by an atom-style <a class="reference internal" href="variable.html"><em>variable</em></a>. The
time-averaged per-atom output of this fix can be used as input to
other output commands.</p>
<p>The <a class="reference internal" href="fix_store_state.html"><em>fix store/state</em></a> command can archive one or
more per-atom attributes at a particular time, so that the old values
can be used in a future calculation or output. The list of atom
attributes is the same as for the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command,
including per-atom quantities calculated by a <a class="reference internal" href="compute.html"><em>compute</em></a>,
by a <a class="reference internal" href="fix.html"><em>fix</em></a>, or by an atom-style <a class="reference internal" href="variable.html"><em>variable</em></a>.
The output of this fix can be used as input to other output commands.</p>
</div>
<div class="section" id="computes-that-generate-values-to-output">
<span id="compute"></span><h3>6.15.8. Computes that generate values to output<a class="headerlink" href="#computes-that-generate-values-to-output" title="Permalink to this headline">¶</a></h3>
<p>Every <a class="reference internal" href="compute.html"><em>compute</em></a> in LAMMPS produces either global or
per-atom or local values. The values can be scalars or vectors or
arrays of data. These values can be output using the other commands
described in this section. The doc page for each compute command
describes what it produces. Computes that produce per-atom or local
values have the word “atom” or “local” in their style name. Computes
without the word “atom” or “local” produce global values.</p>
</div>
<div class="section" id="fixes-that-generate-values-to-output">
<span id="fix"></span><h3>6.15.9. Fixes that generate values to output<a class="headerlink" href="#fixes-that-generate-values-to-output" title="Permalink to this headline">¶</a></h3>
<p>Some <a class="reference internal" href="fix.html"><em>fixes</em></a> in LAMMPS produces either global or per-atom or
local values which can be accessed by other commands. The values can
be scalars or vectors or arrays of data. These values can be output
using the other commands described in this section. The doc page for
each fix command tells whether it produces any output quantities and
describes them.</p>
</div>
<div class="section" id="variables-that-generate-values-to-output">
<span id="variable"></span><h3>6.15.10. Variables that generate values to output<a class="headerlink" href="#variables-that-generate-values-to-output" title="Permalink to this headline">¶</a></h3>
<p>Every <a class="reference internal" href="variable.html"><em>variables</em></a> defined in an input script generates
either a global scalar value or a per-atom vector (only atom-style
variables) when it is accessed. The formulas used to define equal-
and atom-style variables can contain references to the thermodynamic
keywords and to global and per-atom data generated by computes, fixes,
and other variables. The values generated by variables can be output
using the other commands described in this section.</p>
</div>
<div class="section" id="summary-table-of-output-options-and-data-flow-between-commands">
<span id="table"></span><h3>6.15.11. Summary table of output options and data flow between commands<a class="headerlink" href="#summary-table-of-output-options-and-data-flow-between-commands" title="Permalink to this headline">¶</a></h3>
<p>This table summarizes the various commands that can be used for
generating output from LAMMPS. Each command produces output data of
some kind and/or writes data to a file. Most of the commands can take
data from other commands as input. Thus you can link many of these
commands together in pipeline form, where data produced by one command
is used as input to another command and eventually written to the
screen or to a file. Note that to hook two commands together the
output and input data types must match, e.g. global/per-atom/local
data and scalar/vector/array data.</p>
<p>Also note that, as described above, when a command takes a scalar as
input, that could be an element of a vector or array. Likewise a
vector input could be a column of an array.</p>
<table border="1" class="docutils">
<colgroup>
<col width="39%" />
<col width="30%" />
<col width="30%" />
<col width="1%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>Command</td>
<td>Input</td>
<td>Output</td>
<td> </td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a></td>
<td>global scalars</td>
<td>screen, log file</td>
<td> </td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="dump.html"><em>dump custom</em></a></td>
<td>per-atom vectors</td>
<td>dump file</td>
<td> </td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="dump.html"><em>dump local</em></a></td>
<td>local vectors</td>
<td>dump file</td>
<td> </td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_print.html"><em>fix print</em></a></td>
<td>global scalar from variable</td>
<td>screen, file</td>
<td> </td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="print.html"><em>print</em></a></td>
<td>global scalar from variable</td>
<td>screen</td>
<td> </td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute.html"><em>computes</em></a></td>
<td>N/A</td>
<td>global/per-atom/local scalar/vector/array</td>
<td> </td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix.html"><em>fixes</em></a></td>
<td>N/A</td>
<td>global/per-atom/local scalar/vector/array</td>
<td> </td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="variable.html"><em>variables</em></a></td>
<td>global scalars, per-atom vectors</td>
<td>global scalar, per-atom vector</td>
<td> </td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_reduce.html"><em>compute reduce</em></a></td>
<td>per-atom/local vectors</td>
<td>global scalar/vector</td>
<td> </td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_slice.html"><em>compute slice</em></a></td>
<td>global vectors/arrays</td>
<td>global vector/array</td>
<td> </td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_property_atom.html"><em>compute property/atom</em></a></td>
<td>per-atom vectors</td>
<td>per-atom vector/array</td>
<td> </td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_property_local.html"><em>compute property/local</em></a></td>
<td>local vectors</td>
<td>local vector/array</td>
<td> </td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_vector.html"><em>fix vector</em></a></td>
<td>global scalars</td>
<td>global vector</td>
<td> </td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_ave_atom.html"><em>fix ave/atom</em></a></td>
<td>per-atom vectors</td>
<td>per-atom vector/array</td>
<td> </td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a></td>
<td>global scalars/vectors</td>
<td>global scalar/vector/array, file</td>
<td> </td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a></td>
<td>per-atom vectors</td>
<td>global array, file</td>
<td> </td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_ave_histo.html"><em>fix ave/histo</em></a></td>
<td>global/per-atom/local scalars and vectors</td>
<td>global array, file</td>
<td> </td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_ave_correlate.html"><em>fix ave/correlate</em></a></td>
<td>global scalars</td>
<td>global array, file</td>
<td> </td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_store_state.html"><em>fix store/state</em></a></td>
<td>per-atom vectors</td>
<td>per-atom vector/array</td>
<td> </td>
</tr>
<tr class="row-odd"><td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<hr class="docutils" />
</div>
</div>
<div class="section" id="thermostatting-barostatting-and-computing-temperature">
<span id="howto-16"></span><h2>6.16. Thermostatting, barostatting, and computing temperature<a class="headerlink" href="#thermostatting-barostatting-and-computing-temperature" title="Permalink to this headline">¶</a></h2>
<p>Thermostatting means controlling the temperature of particles in an MD
simulation. Barostatting means controlling the pressure. Since the
pressure includes a kinetic component due to particle velocities, both
these operations require calculation of the temperature. Typically a
target temperature (T) and/or pressure (P) is specified by the user,
and the thermostat or barostat attempts to equilibrate the system to
the requested T and/or P.</p>
<p>Temperature is computed as kinetic energy divided by some number of
degrees of freedom (and the Boltzmann constant). Since kinetic energy
is a function of particle velocity, there is often a need to
distinguish between a particle’s advection velocity (due to some
aggregate motiion of particles) and its thermal velocity. The sum of
the two is the particle’s total velocity, but the latter is often what
is wanted to compute a temperature.</p>
<p>LAMMPS has several options for computing temperatures, any of which
can be used in thermostatting and barostatting. These <a class="reference internal" href="compute.html"><em>compute commands</em></a> calculate temperature, and the <a class="reference internal" href="compute_pressure.html"><em>compute pressure</em></a> command calculates pressure.</p>
<ul class="simple">
<li><a class="reference internal" href="compute_temp.html"><em>compute temp</em></a></li>
<li><a class="reference internal" href="compute_temp_sphere.html"><em>compute temp/sphere</em></a></li>
<li><a class="reference internal" href="compute_temp_asphere.html"><em>compute temp/asphere</em></a></li>
<li><a class="reference internal" href="compute_temp_com.html"><em>compute temp/com</em></a></li>
<li><a class="reference internal" href="compute_temp_deform.html"><em>compute temp/deform</em></a></li>
<li><a class="reference internal" href="compute_temp_partial.html"><em>compute temp/partial</em></a></li>
<li><a class="reference internal" href="compute_temp_profile.html"><em>compute temp/profile</em></a></li>
<li><a class="reference internal" href="compute_temp_ramp.html"><em>compute temp/ramp</em></a></li>
<li><a class="reference internal" href="compute_temp_region.html"><em>compute temp/region</em></a></li>
</ul>
<p>All but the first 3 calculate velocity biases directly (e.g. advection
velocities) that are removed when computing the thermal temperature.
<a class="reference internal" href="compute_temp_sphere.html"><em>Compute temp/sphere</em></a> and <a class="reference internal" href="compute_temp_asphere.html"><em>compute temp/asphere</em></a> compute kinetic energy for
finite-size particles that includes rotational degrees of freedom.
They both allow for velocity biases indirectly, via an optional extra
argument, another temperature compute that subtracts a velocity bias.
This allows the translational velocity of spherical or aspherical
particles to be adjusted in prescribed ways.</p>
<p>Thermostatting in LAMMPS is performed by <a class="reference internal" href="fix.html"><em>fixes</em></a>, or in one
case by a pair style. Several thermostatting fixes are available:
Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling
(temp/rescale). Dissipative particle dynamics (DPD) thermostatting
can be invoked via the <em>dpd/tstat</em> pair style:</p>
<ul class="simple">
<li><a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a></li>
<li><a class="reference internal" href="fix_nvt_sphere.html"><em>fix nvt/sphere</em></a></li>
<li><a class="reference internal" href="fix_nvt_asphere.html"><em>fix nvt/asphere</em></a></li>
<li><a class="reference internal" href="fix_nvt_sllod.html"><em>fix nvt/sllod</em></a></li>
<li><a class="reference internal" href="fix_temp_berendsen.html"><em>fix temp/berendsen</em></a></li>
<li><a class="reference internal" href="fix_temp_csvr.html"><em>fix temp/csvr</em></a></li>
<li><a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a></li>
<li><a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a></li>
<li><a class="reference internal" href="pair_dpd.html"><em>pair_style dpd/tstat</em></a></li>
</ul>
<p><a class="reference internal" href="fix_nh.html"><em>Fix nvt</em></a> only thermostats the translational velocity of
particles. <a class="reference internal" href="fix_nvt_sllod.html"><em>Fix nvt/sllod</em></a> also does this, except
that it subtracts out a velocity bias due to a deforming box and
integrates the SLLOD equations of motion. See the <a class="reference internal" href="#howto-13"><span>NEMD simulations</span></a> section of this page for further details. <a class="reference internal" href="fix_nvt_sphere.html"><em>Fix nvt/sphere</em></a> and <a class="reference internal" href="fix_nvt_asphere.html"><em>fix nvt/asphere</em></a> thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
particles.</p>
<p>DPD thermostatting alters pairwise interactions in a manner analagous
to the per-particle thermostatting of <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a>.</p>
<p>Any of the thermostatting fixes can use temperature computes that
remove bias which has two effects. First, the current calculated
temperature, which is compared to the requested target temperature, is
caluclated with the velocity bias removed. Second, the thermostat
adjusts only the thermal temperature component of the particle’s
velocities, which are the velocities with the bias removed. The
removed bias is then added back to the adjusted velocities. See the
doc pages for the individual fixes and for the
<a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> command for instructions on how to assign
a temperature compute to a thermostatting fix. For example, you can
apply a thermostat to only the x and z components of velocity by using
it in conjunction with <a class="reference internal" href="compute_temp_partial.html"><em>compute temp/partial</em></a>. Of you could thermostat only
the thermal temperature of a streaming flow of particles without
affecting the streaming velocity, by using <a class="reference internal" href="compute_temp_profile.html"><em>compute temp/profile</em></a>.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Only the nvt fixes perform time integration, meaning
they update the velocities and positions of particles due to forces
and velocities respectively. The other thermostat fixes only adjust
velocities; they do NOT perform time integration updates. Thus they
should be used in conjunction with a constant NVE integration fix such
as these:</p>
</div>
<ul class="simple">
<li><a class="reference internal" href="fix_nve.html"><em>fix nve</em></a></li>
<li><a class="reference internal" href="fix_nve_sphere.html"><em>fix nve/sphere</em></a></li>
<li><a class="reference internal" href="fix_nve_asphere.html"><em>fix nve/asphere</em></a></li>
</ul>
<p>Barostatting in LAMMPS is also performed by <a class="reference internal" href="fix.html"><em>fixes</em></a>. Two
barosttating methods are currently available: Nose-Hoover (npt and
nph) and Berendsen:</p>
<ul class="simple">
<li><a class="reference internal" href="fix_nh.html"><em>fix npt</em></a></li>
<li><a class="reference internal" href="fix_npt_sphere.html"><em>fix npt/sphere</em></a></li>
<li><a class="reference internal" href="fix_npt_asphere.html"><em>fix npt/asphere</em></a></li>
<li><a class="reference internal" href="fix_nh.html"><em>fix nph</em></a></li>
<li><a class="reference internal" href="fix_press_berendsen.html"><em>fix press/berendsen</em></a></li>
</ul>
<p>The <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> commands include a Nose-Hoover thermostat
and barostat. <a class="reference internal" href="fix_nh.html"><em>Fix nph</em></a> is just a Nose/Hoover barostat;
it does no thermostatting. Both <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a> and <a class="reference internal" href="fix_press_berendsen.html"><em>fix press/bernendsen</em></a> can be used in conjunction
with any of the thermostatting fixes.</p>
<p>As with the thermostats, <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> and <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a> only use translational motion of the particles in
computing T and P and performing thermo/barostatting. <a class="reference internal" href="fix_npt_sphere.html"><em>Fix npt/sphere</em></a> and <a class="reference internal" href="fix_npt_asphere.html"><em>fix npt/asphere</em></a> thermo/barostat using not only
translation velocities but also rotational velocities for spherical
and aspherical particles.</p>
<p>All of the barostatting fixes use the <a class="reference internal" href="compute_pressure.html"><em>compute pressure</em></a> compute to calculate a current
pressure. By default, this compute is created with a simple <a class="reference internal" href="compute_temp.html"><em>compute temp</em></a> (see the last argument of the <a class="reference internal" href="compute_pressure.html"><em>compute pressure</em></a> command), which is used to calculated
the kinetic componenet of the pressure. The barostatting fixes can
also use temperature computes that remove bias for the purpose of
computing the kinetic componenet which contributes to the current
pressure. See the doc pages for the individual fixes and for the
<a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> command for instructions on how to assign
a temperature or pressure compute to a barostatting fix.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">As with the thermostats, the Nose/Hoover methods (<a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> and <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a>) perform time
integration. <a class="reference internal" href="fix_press_berendsen.html"><em>Fix press/berendsen</em></a> does NOT,
so it should be used with one of the constant NVE fixes or with one of
the NVT fixes.</p>
</div>
<p>Finally, thermodynamic output, which can be setup via the
<a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command, often includes temperature
and pressure values. As explained on the doc page for the
<a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command, the default T and P are
setup by the thermo command itself. They are NOT the ones associated
with any thermostatting or barostatting fix you have defined or with
any compute that calculates a temperature or pressure. Thus if you
want to view these values of T and P, you need to specify them
explicitly via a <a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> command. Or
you can use the <a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a> command to
re-define what temperature or pressure compute is used for default
thermodynamic output.</p>
<hr class="docutils" />
</div>
<div class="section" id="walls">
<span id="howto-17"></span><h2>6.17. Walls<a class="headerlink" href="#walls" title="Permalink to this headline">¶</a></h2>
<p>Walls in an MD simulation are typically used to bound particle motion,
i.e. to serve as a boundary condition.</p>
<p>Walls in LAMMPS can be of rough (made of particles) or idealized
surfaces. Ideal walls can be smooth, generating forces only in the
normal direction, or frictional, generating forces also in the
tangential direction.</p>
<p>Rough walls, built of particles, can be created in various ways. The
particles themselves can be generated like any other particle, via the
<a class="reference internal" href="lattice.html"><em>lattice</em></a> and <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a> commands,
or read in via the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command.</p>
<p>Their motion can be constrained by many different commands, so that
they do not move at all, move together as a group at constant velocity
or in response to a net force acting on them, move in a prescribed
fashion (e.g. rotate around a point), etc. Note that if a time
integration fix like <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> or <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>
is not used with the group that contains wall particles, their
positions and velocities will not be updated.</p>
<ul class="simple">
<li><a class="reference internal" href="fix_aveforce.html"><em>fix aveforce</em></a> - set force on particles to average value, so they move together</li>
<li><a class="reference internal" href="fix_setforce.html"><em>fix setforce</em></a> - set force on particles to a value, e.g. 0.0</li>
<li><a class="reference internal" href="fix_freeze.html"><em>fix freeze</em></a> - freeze particles for use as granular walls</li>
<li><a class="reference internal" href="fix_nve_noforce.html"><em>fix nve/noforce</em></a> - advect particles by their velocity, but without force</li>
<li><a class="reference internal" href="fix_move.html"><em>fix move</em></a> - prescribe motion of particles by a linear velocity, oscillation, rotation, variable</li>
</ul>
<p>The <a class="reference internal" href="fix_move.html"><em>fix move</em></a> command offers the most generality, since
the motion of individual particles can be specified with
<a class="reference internal" href="variable.html"><em>variable</em></a> formula which depends on time and/or the
particle position.</p>
<p>For rough walls, it may be useful to turn off pairwise interactions
between wall particles via the <a class="reference internal" href="neigh_modify.html"><em>neigh_modify exclude</em></a> command.</p>
<p>Rough walls can also be created by specifying frozen particles that do
not move and do not interact with mobile particles, and then tethering
other particles to the fixed particles, via a <a class="reference internal" href="bond_style.html"><em>bond</em></a>.
The bonded particles do interact with other mobile particles.</p>
<p>Idealized walls can be specified via several fix commands. <a class="reference internal" href="fix_wall_gran.html"><em>Fix wall/gran</em></a> creates frictional walls for use with
granular particles; all the other commands create smooth walls.</p>
<ul class="simple">
<li><a class="reference internal" href="fix_wall_reflect.html"><em>fix wall/reflect</em></a> - reflective flat walls</li>
<li><a class="reference internal" href="fix_wall.html"><em>fix wall/lj93</em></a> - flat walls, with Lennard-Jones 9/3 potential</li>
<li><a class="reference internal" href="fix_wall.html"><em>fix wall/lj126</em></a> - flat walls, with Lennard-Jones 12/6 potential</li>
<li><a class="reference internal" href="fix_wall.html"><em>fix wall/colloid</em></a> - flat walls, with <a class="reference internal" href="pair_colloid.html"><em>pair_style colloid</em></a> potential</li>
<li><a class="reference internal" href="fix_wall.html"><em>fix wall/harmonic</em></a> - flat walls, with repulsive harmonic spring potential</li>
<li><a class="reference internal" href="fix_wall_region.html"><em>fix wall/region</em></a> - use region surface as wall</li>
<li><a class="reference internal" href="fix_wall_gran.html"><em>fix wall/gran</em></a> - flat or curved walls with <a class="reference internal" href="pair_gran.html"><em>pair_style granular</em></a> potential</li>
</ul>
<p>The <em>lj93</em>, <em>lj126</em>, <em>colloid</em>, and <em>harmonic</em> styles all allow the
flat walls to move with a constant velocity, or oscillate in time.
The <a class="reference internal" href="fix_wall_region.html"><em>fix wall/region</em></a> command offers the most
generality, since the region surface is treated as a wall, and the
geometry of the region can be a simple primitive volume (e.g. a
sphere, or cube, or plane), or a complex volume made from the union
and intersection of primitive volumes. <a class="reference internal" href="region.html"><em>Regions</em></a> can also
specify a volume “interior” or “exterior” to the specified primitive
shape or <em>union</em> or <em>intersection</em>. <a class="reference internal" href="region.html"><em>Regions</em></a> can also be
“dynamic” meaning they move with constant velocity, oscillate, or
rotate.</p>
<p>The only frictional idealized walls currently in LAMMPS are flat or
curved surfaces specified by the <a class="reference internal" href="fix_wall_gran.html"><em>fix wall/gran</em></a>
command. At some point we plan to allow regoin surfaces to be used as
frictional walls, as well as triangulated surfaces.</p>
<hr class="docutils" />
</div>
<div class="section" id="elastic-constants">
<span id="howto-18"></span><h2>6.18. Elastic constants<a class="headerlink" href="#elastic-constants" title="Permalink to this headline">¶</a></h2>
<p>Elastic constants characterize the stiffness of a material. The formal
definition is provided by the linear relation that holds between the
stress and strain tensors in the limit of infinitesimal deformation.
In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where
the repeated indices imply summation. s_ij are the elements of the
symmetric stress tensor. e_kl are the elements of the symmetric strain
tensor. C_ijkl are the elements of the fourth rank tensor of elastic
constants. In three dimensions, this tensor has 3^4=81 elements. Using
Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij
is now the derivative of s_i w.r.t. e_j. Because s_i is itself a
derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
most 7*6/2 = 21 distinct elements.</p>
<p>At zero temperature, it is easy to estimate these derivatives by
deforming the simulation box in one of the six directions using the
<a class="reference internal" href="change_box.html"><em>change_box</em></a> command and measuring the change in the
stress tensor. A general-purpose script that does this is given in the
examples/elastic directory described in <a class="reference internal" href="Section_example.html"><em>this section</em></a>.</p>
<p>Calculating elastic constants at finite temperature is more
challenging, because it is necessary to run a simulation that perfoms
time averages of differential properties. One way to do this is to
measure the change in average stress tensor in an NVT simulations when
the cell volume undergoes a finite deformation. In order to balance
the systematic and statistical errors in this method, the magnitude of
the deformation must be chosen judiciously, and care must be taken to
fully equilibrate the deformed cell before sampling the stress
tensor. Another approach is to sample the triclinic cell fluctuations
that occur in an NPT simulation. This method can also be slow to
converge and requires careful post-processing <a class="reference internal" href="#shinoda"><span>(Shinoda)</span></a></p>
<hr class="docutils" />
</div>
<div class="section" id="library-interface-to-lammps">
<span id="howto-19"></span><h2>6.19. Library interface to LAMMPS<a class="headerlink" href="#library-interface-to-lammps" title="Permalink to this headline">¶</a></h2>
<p>As described in <a class="reference internal" href="Section_start.html#start-5"><span>Section_start 5</span></a>, LAMMPS
can be built as a library, so that it can be called by another code,
used in a <a class="reference internal" href="#howto-10"><span>coupled manner</span></a> with other
codes, or driven through a <a class="reference internal" href="Section_python.html"><em>Python interface</em></a>.</p>
<p>All of these methodologies use a C-style interface to LAMMPS that is
provided in the files src/library.cpp and src/library.h. The
functions therein have a C-style argument list, but contain C++ code
you could write yourself in a C++ application that was invoking LAMMPS
directly. The C++ code in the functions illustrates how to invoke
internal LAMMPS operations. Note that LAMMPS classes are defined
within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
application.</p>
<p>Library.cpp contains these 5 basic functions:</p>
<div class="highlight-python"><div class="highlight"><pre>void lammps_open(int, char **, MPI_Comm, void **)
void lammps_close(void *)
int lammps_version(void *)
void lammps_file(void *, char *)
char *lammps_command(void *, char *)
</pre></div>
</div>
<p>The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were <a class="reference internal" href="Section_start.html#start-7"><span>command-line arguments</span></a> when LAMMPS is run in
stand-alone mode from the command line, and a MPI communicator for
LAMMPS to run under. It returns a ptr to the LAMMPS object that is
created, and which is used in subsequent library calls. The
lammps_open() function can be called multiple times, to create
multiple instances of LAMMPS.</p>
<p>LAMMPS will run on the set of processors in the communicator. This
means the calling code can run LAMMPS on all or a subset of
processors. For example, a wrapper script might decide to alternate
between LAMMPS and another code, allowing them both to run on all the
processors. Or it might allocate half the processors to LAMMPS and
half to the other code and run both codes simultaneously before
syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.</p>
<p>The lammps_close() function is used to shut down an instance of LAMMPS
and free all its memory.</p>
<p>The lammps_version() function can be used to determined the specific
version of the underlying LAMMPS code. This is particularly useful
when loading LAMMPS as a shared library via dlopen(). The code using
the library interface can than use this information to adapt to
changes to the LAMMPS command syntax between versions. The returned
LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
20150902) that grows with every new LAMMPS version.</p>
<p>The lammps_file() and lammps_command() functions are used to pass a
file or string to LAMMPS as if it were an input script or single
command in an input script. Thus the calling code can read or
generate a series of LAMMPS commands one line at a time and pass it
thru the library interface to setup a problem and then run it,
interleaving the lammps_command() calls with other calls to extract
information from LAMMPS, perform its own operations, or call another
code’s library.</p>
<p>Other useful functions are also included in library.cpp. For example:</p>
<div class="highlight-python"><div class="highlight"><pre>void *lammps_extract_global(void *, char *)
void *lammps_extract_atom(void *, char *)
void *lammps_extract_compute(void *, char *, int, int)
void *lammps_extract_fix(void *, char *, int, int, int, int)
void *lammps_extract_variable(void *, char *, char *)
int lammps_set_variable(void *, char *, char *)
int lammps_get_natoms(void *)
void lammps_get_coords(void *, double *)
void lammps_put_coords(void *, double *)
</pre></div>
</div>
<p>These can extract various global or per-atom quantities from LAMMPS as
well as values calculated by a compute, fix, or variable. The
“set_variable” function can set an existing string-style variable to a
new value, so that subsequent LAMMPS commands can access the variable.
The “get” and “put” operations can retrieve and reset atom
coordinates. See the library.cpp file and its associated header file
library.h for details.</p>
<p>The key idea of the library interface is that you can write any
functions you wish to define how your code talks to LAMMPS and add
them to src/library.cpp and src/library.h, as well as to the <a class="reference internal" href="Section_python.html"><em>Python interface</em></a>. The routines you add can access or
change any LAMMPS data you wish. The examples/COUPLE and python
directories have example C++ and C and Python codes which show how a
driver code can link to LAMMPS as a library, run LAMMPS on a subset of
processors, grab data from LAMMPS, change it, and put it back into
LAMMPS.</p>
<hr class="docutils" />
</div>
<div class="section" id="calculating-thermal-conductivity">
<span id="howto-20"></span><h2>6.20. Calculating thermal conductivity<a class="headerlink" href="#calculating-thermal-conductivity" title="Permalink to this headline">¶</a></h2>
<p>The thermal conductivity kappa of a material can be measured in at
least 4 ways using various options in LAMMPS. See the examples/KAPPA
directory for scripts that implement the 4 methods discussed here for
a simple Lennard-Jones fluid model. Also, see <a class="reference internal" href="#howto-21"><span>this section</span></a> of the manual for an analogous
discussion for viscosity.</p>
<p>The thermal conducitivity tensor kappa is a measure of the propensity
of a material to transmit heat energy in a diffusive manner as given
by Fourier’s law</p>
<p>J = -kappa grad(T)</p>
<p>where J is the heat flux in units of energy per area per time and
grad(T) is the spatial gradient of temperature. The thermal
conductivity thus has units of energy per distance per time per degree
K and is often approximated as an isotropic quantity, i.e. as a
scalar.</p>
<p>The first method is to setup two thermostatted regions at opposite
ends of a simulation box, or one in the middle and one at the end of a
periodic box. By holding the two regions at different temperatures
with a <a class="reference internal" href="#howto-13"><span>thermostatting fix</span></a>, the energy
added to the hot region should equal the energy subtracted from the
cold region and be proportional to the heat flux moving between the
regions. See the paper by <a class="reference internal" href="#ikeshoji"><span>Ikeshoji and Hafskjold</span></a> for
details of this idea. Note that thermostatting fixes such as <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a>, and <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a> store the cumulative energy they
add/subtract.</p>
<p>Alternatively, as a second method, the <a class="reference internal" href="fix_heat.html"><em>fix heat</em></a>
command can used in place of thermostats on each of two regions to
add/subtract specified amounts of energy to both regions. In both
cases, the resulting temperatures of the two regions can be monitored
with the “compute temp/region” command and the temperature profile of
the intermediate region can be monitored with the <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a> and <a class="reference internal" href="compute_ke_atom.html"><em>compute ke/atom</em></a> commands.</p>
<p>The third method is to perform a reverse non-equilibrium MD simulation
using the <a class="reference internal" href="fix_thermal_conductivity.html"><em>fix thermal/conductivity</em></a>
command which implements the rNEMD algorithm of Muller-Plathe.
Kinetic energy is swapped between atoms in two different layers of the
simulation box. This induces a temperature gradient between the two
layers which can be monitored with the <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a> and <a class="reference internal" href="compute_ke_atom.html"><em>compute ke/atom</em></a> commands. The fix tallies the
cumulative energy transfer that it performs. See the <a class="reference internal" href="fix_thermal_conductivity.html"><em>fix thermal/conductivity</em></a> command for
details.</p>
<p>The fourth method is based on the Green-Kubo (GK) formula which
relates the ensemble average of the auto-correlation of the heat flux
to kappa. The heat flux can be calculated from the fluctuations of
per-atom potential and kinetic energies and per-atom stress tensor in
a steady-state equilibrated simulation. This is in contrast to the
two preceding non-equilibrium methods, where energy flows continuously
between hot and cold regions of the simulation box.</p>
<p>The <a class="reference internal" href="compute_heat_flux.html"><em>compute heat/flux</em></a> command can calculate
the needed heat flux and describes how to implement the Green_Kubo
formalism using additional LAMMPS commands, such as the <a class="reference internal" href="fix_ave_correlate.html"><em>fix ave/correlate</em></a> command to calculate the needed
auto-correlation. See the doc page for the <a class="reference internal" href="compute_heat_flux.html"><em>compute heat/flux</em></a> command for an example input script
that calculates the thermal conductivity of solid Ar via the GK
formalism.</p>
<hr class="docutils" />
</div>
<div class="section" id="calculating-viscosity">
<span id="howto-21"></span><h2>6.21. Calculating viscosity<a class="headerlink" href="#calculating-viscosity" title="Permalink to this headline">¶</a></h2>
<p>The shear viscosity eta of a fluid can be measured in at least 4 ways
using various options in LAMMPS. See the examples/VISCOSITY directory
for scripts that implement the 4 methods discussed here for a simple
Lennard-Jones fluid model. Also, see <a class="reference internal" href="#howto-20"><span>this section</span></a> of the manual for an analogous
discussion for thermal conductivity.</p>
<p>Eta is a measure of the propensity of a fluid to transmit momentum in
a direction perpendicular to the direction of velocity or momentum
flow. Alternatively it is the resistance the fluid has to being
sheared. It is given by</p>
<p>J = -eta grad(Vstream)</p>
<p>where J is the momentum flux in units of momentum per area per time.
and grad(Vstream) is the spatial gradient of the velocity of the fluid
moving in another direction, normal to the area through which the
momentum flows. Viscosity thus has units of pressure-time.</p>
<p>The first method is to perform a non-equlibrium MD (NEMD) simulation
by shearing the simulation box via the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a>
command, and using the <a class="reference internal" href="fix_nvt_sllod.html"><em>fix nvt/sllod</em></a> command to
thermostat the fluid via the SLLOD equations of motion.
Alternatively, as a second method, one or more moving walls can be
used to shear the fluid in between them, again with some kind of
thermostat that modifies only the thermal (non-shearing) components of
velocity to prevent the fluid from heating up.</p>
<p>In both cases, the velocity profile setup in the fluid by this
procedure can be monitored by the <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a> command, which determines
grad(Vstream) in the equation above. E.g. the derivative in the
y-direction of the Vx component of fluid motion or grad(Vstream) =
dVx/dy. The Pxy off-diagonal component of the pressure or stress
tensor, as calculated by the <a class="reference internal" href="compute_pressure.html"><em>compute pressure</em></a>
command, can also be monitored, which is the J term in the equation
above. See <a class="reference internal" href="#howto-13"><span>this section</span></a> of the manual
for details on NEMD simulations.</p>
<p>The third method is to perform a reverse non-equilibrium MD simulation
using the <a class="reference internal" href="fix_viscosity.html"><em>fix viscosity</em></a> command which implements
the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is
swapped between atoms in two different layers of the simulation box in
a different dimension. This induces a velocity gradient which can be
monitored with the <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a> command.
The fix tallies the cummulative momentum transfer that it performs.
See the <a class="reference internal" href="fix_viscosity.html"><em>fix viscosity</em></a> command for details.</p>
<p>The fourth method is based on the Green-Kubo (GK) formula which
relates the ensemble average of the auto-correlation of the
stress/pressure tensor to eta. This can be done in a steady-state
equilibrated simulation which is in contrast to the two preceding
non-equilibrium methods, where momentum flows continuously through the
simulation box.</p>
<p>Here is an example input script that calculates the viscosity of
liquid Ar via the GK formalism:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># Sample LAMMPS input script for viscosity of liquid Ar</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>units real
variable T equal 86.4956
variable V equal vol
variable dt equal 4.0
variable p equal 400 # correlation length
variable s equal 5 # sample interval
variable d equal $p*$s # dump interval
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># convert from LAMMPS real units to SI</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>variable kB equal 1.3806504e-23 # [J/K/** Boltzmann
variable atm2Pa equal 101325.0
variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15
variable convert equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m}
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># setup problem</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>dimension 3
boundary p p p
lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region box block 0 4 0 4 0 4
create_box 1 box
create_atoms 1 box
mass 1 39.948
pair_style lj/cut 13.0
pair_coeff * * 0.2381 3.405
timestep ${dt}
thermo $d
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># equilibration and thermalization</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>velocity all create $T 102486 mom yes rot yes dist gaussian
fix NVT all nvt temp $T $T 10 drag 0.2
run 8000
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># viscosity calculation, switch to NVE if desired</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="c">#unfix NVT</span>
<span class="c">#fix NVE all nve</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>reset_timestep 0
variable pxy equal pxy
variable pxz equal pxz
variable pyz equal pyz
fix SS all ave/correlate $s $p $d &
v_pxy v_pxz v_pyz type auto file S0St.dat ave running
variable scale equal ${convert}/(${kB}*$T)*$V*$s*${dt}
variable v11 equal trap(f_SS[3])*${scale}
variable v22 equal trap(f_SS[4])*${scale}
variable v33 equal trap(f_SS[5])*${scale}
thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
run 100000
variable v equal (v_v11+v_v22+v_v33)/3.0
variable ndens equal count(all)/vol
print "average viscosity: $v [Pa.s/** @ $T K, ${ndens} /A^3"
</pre></div>
</div>
<hr class="docutils" />
</div>
<div class="section" id="calculating-a-diffusion-coefficient">
<span id="howto-22"></span><h2>6.22. Calculating a diffusion coefficient<a class="headerlink" href="#calculating-a-diffusion-coefficient" title="Permalink to this headline">¶</a></h2>
<p>The diffusion coefficient D of a material can be measured in at least
2 ways using various options in LAMMPS. See the examples/DIFFUSE
directory for scripts that implement the 2 methods discussed here for
a simple Lennard-Jones fluid model.</p>
<p>The first method is to measure the mean-squared displacement (MSD) of
the system, via the <a class="reference internal" href="compute_msd.html"><em>compute msd</em></a> command. The slope
of the MSD versus time is proportional to the diffusion coefficient.
The instantaneous MSD values can be accumulated in a vector via the
<a class="reference internal" href="fix_vector.html"><em>fix vector</em></a> command, and a line fit to the vector to
compute its slope via the <a class="reference internal" href="variable.html"><em>variable slope</em></a> function, and
thus extract D.</p>
<p>The second method is to measure the velocity auto-correlation function
(VACF) of the system, via the <a class="reference internal" href="compute_vacf.html"><em>compute vacf</em></a>
command. The time-integral of the VACF is proportional to the
diffusion coefficient. The instantaneous VACF values can be
accumulated in a vector via the <a class="reference internal" href="fix_vector.html"><em>fix vector</em></a> command,
and time integrated via the <a class="reference internal" href="variable.html"><em>variable trap</em></a> function,
and thus extract D.</p>
<hr class="docutils" />
</div>
<div class="section" id="using-chunks-to-calculate-system-properties">
<span id="howto-23"></span><h2>6.23. Using chunks to calculate system properties<a class="headerlink" href="#using-chunks-to-calculate-system-properties" title="Permalink to this headline">¶</a></h2>
<p>In LAMMS, “chunks” are collections of atoms, as defined by the
<a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command, which assigns
each atom to a chunk ID (or to no chunk at all). The number of chunks
and the assignment of chunk IDs to atoms can be static or change over
time. Examples of “chunks” are molecules or spatial bins or atoms
with similar values (e.g. coordination number or potential energy).</p>
<p>The per-atom chunk IDs can be used as input to two other kinds of
commands, to calculate various properties of a system:</p>
<ul class="simple">
<li><a class="reference internal" href="fix_ave_chunk.html"><em>fix ave/chunk</em></a></li>
<li>any of the <a class="reference internal" href="compute.html"><em>compute */chunk</em></a> commands</li>
</ul>
<p>Here, each of the 3 kinds of chunk-related commands is briefly
overviewed. Then some examples are given of how to compute different
properties with chunk commands.</p>
<div class="section" id="compute-chunk-atom-command">
<h3>6.23.1. Compute chunk/atom command:<a class="headerlink" href="#compute-chunk-atom-command" title="Permalink to this headline">¶</a></h3>
<p>This compute can assign atoms to chunks of various styles. Only atoms
in the specified group and optional specified region are assigned to a
chunk. Here are some possible chunk definitions:</p>
<table border="1" class="docutils">
<colgroup>
<col width="31%" />
<col width="69%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>atoms in same molecule</td>
<td>chunk ID = molecule ID</td>
</tr>
<tr class="row-even"><td>atoms of same atom type</td>
<td>chunk ID = atom type</td>
</tr>
<tr class="row-odd"><td>all atoms with same atom property (charge, radius, etc)</td>
<td>chunk ID = output of compute property/atom</td>
</tr>
<tr class="row-even"><td>atoms in same cluster</td>
<td>chunk ID = output of <a class="reference internal" href="compute_cluster_atom.html"><em>compute cluster/atom</em></a> command</td>
</tr>
<tr class="row-odd"><td>atoms in same spatial bin</td>
<td>chunk ID = bin ID</td>
</tr>
<tr class="row-even"><td>atoms in same rigid body</td>
<td>chunk ID = molecule ID used to define rigid bodies</td>
</tr>
<tr class="row-odd"><td>atoms with similar potential energy</td>
<td>chunk ID = output of <a class="reference internal" href="compute_pe_atom.html"><em>compute pe/atom</em></a></td>
</tr>
<tr class="row-even"><td>atoms with same local defect structure</td>
<td>chunk ID = output of <a class="reference internal" href="compute_centro_atom.html"><em>compute centro/atom</em></a> or <a class="reference internal" href="compute_coord_atom.html"><em>compute coord/atom</em></a> command</td>
</tr>
</tbody>
</table>
<p>Note that chunk IDs are integer values, so for atom properties or
computes that produce a floating point value, they will be truncated
to an integer. You could also use the compute in a variable that
scales the floating point value to spread it across multiple intergers.</p>
<p>Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
pencils, 3d bins = boxes, spherical bins, cylindrical bins.</p>
<p>This compute also calculates the number of chunks <em>Nchunk</em>, which is
used by other commands to tally per-chunk data. <em>Nchunk</em> can be a
static value or change over time (e.g. the number of clusters). The
chunk ID for an individual atom can also be static (e.g. a molecule
ID), or dynamic (e.g. what spatial bin an atom is in as it moves).</p>
<p>Note that this compute allows the per-atom output of other
<a class="reference internal" href="compute.html"><em>computes</em></a>, <a class="reference internal" href="fix.html"><em>fixes</em></a>, and
<a class="reference internal" href="variable.html"><em>variables</em></a> to be used to define chunk IDs for each
atom. This means you can write your own compute or fix to output a
per-atom quantity to use as chunk ID. See
<a class="reference internal" href="Section_modify.html"><em>Section_modify</em></a> of the documentation for how to
do this. You can also define a <a class="reference internal" href="variable.html"><em>per-atom variable</em></a> in
the input script that uses a formula to generate a chunk ID for each
atom.</p>
</div>
<div class="section" id="fix-ave-chunk-command">
<h3>6.23.2. Fix ave/chunk command:<a class="headerlink" href="#fix-ave-chunk-command" title="Permalink to this headline">¶</a></h3>
<p>This fix takes the ID of a <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command as input. For each chunk,
it then sums one or more specified per-atom values over the atoms in
each chunk. The per-atom values can be any atom property, such as
velocity, force, charge, potential energy, kinetic energy, stress,
etc. Additional keywords are defined for per-chunk properties like
density and temperature. More generally any per-atom value generated
by other <a class="reference internal" href="compute.html"><em>computes</em></a>, <a class="reference internal" href="fix.html"><em>fixes</em></a>, and <a class="reference internal" href="variable.html"><em>per-atom variables</em></a>, can be summed over atoms in each chunk.</p>
<p>Similar to other averaging fixes, this fix allows the summed per-chunk
values to be time-averaged in various ways, and output to a file. The
fix produces a global array as output with one row of values per
chunk.</p>
</div>
<div class="section" id="compute-chunk-commands">
<h3>6.23.3. Compute <a href="#id70"><span class="problematic" id="id71">*</span></a>/chunk commands:<a class="headerlink" href="#compute-chunk-commands" title="Permalink to this headline">¶</a></h3>
<p>Currently the following computes operate on chunks of atoms to produce
per-chunk values.</p>
<ul class="simple">
<li><a class="reference internal" href="compute_com_chunk.html"><em>compute com/chunk</em></a></li>
<li><a class="reference internal" href="compute_gyration_chunk.html"><em>compute gyration/chunk</em></a></li>
<li><a class="reference internal" href="compute_inertia_chunk.html"><em>compute inertia/chunk</em></a></li>
<li><a class="reference internal" href="compute_msd_chunk.html"><em>compute msd/chunk</em></a></li>
<li><a class="reference internal" href="compute_property_chunk.html"><em>compute property/chunk</em></a></li>
<li><a class="reference internal" href="compute_temp_chunk.html"><em>compute temp/chunk</em></a></li>
<li><a class="reference internal" href="compute_vcm_chunk.html"><em>compute torque/chunk</em></a></li>
<li><a class="reference internal" href="compute_vcm_chunk.html"><em>compute vcm/chunk</em></a></li>
</ul>
<p>They each take the ID of a <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command as input. As their names
indicate, they calculate the center-of-mass, radius of gyration,
moments of inertia, mean-squared displacement, temperature, torque,
and velocity of center-of-mass for each chunk of atoms. The <a class="reference internal" href="compute_property_chunk.html"><em>compute property/chunk</em></a> command can tally the
count of atoms in each chunk and extract other per-chunk properties.</p>
<p>The reason these various calculations are not part of the <a class="reference internal" href="fix_ave_chunk.html"><em>fix ave/chunk command</em></a>, is that each requires a more
complicated operation than simply summing and averaging over per-atom
values in each chunk. For example, many of them require calculation
of a center of mass, which requires summing mass*position over the
atoms and then dividing by summed mass.</p>
<p>All of these computes produce a global vector or global array as
output, wih one or more values per chunk. They can be used
in various ways:</p>
<ul class="simple">
<li>As input to the <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a> command, which can
write the values to a file and optionally time average them.</li>
<li>As input to the <a class="reference internal" href="fix_ave_histo.html"><em>fix ave/histo</em></a> command to
histogram values across chunks. E.g. a histogram of cluster sizes or
molecule diffusion rates.</li>
<li>As input to special functions of <a class="reference internal" href="variable.html"><em>equal-style variables</em></a>, like sum() and max(). E.g. to find the
largest cluster or fastest diffusing molecule.</li>
</ul>
</div>
<div class="section" id="example-calculations-with-chunks">
<h3>6.23.4. Example calculations with chunks<a class="headerlink" href="#example-calculations-with-chunks" title="Permalink to this headline">¶</a></h3>
<p>Here are eaxmples using chunk commands to calculate various
properties:</p>
<ol class="arabic simple">
<li>Average velocity in each of 1000 2d spatial bins:</li>
</ol>
<div class="highlight-python"><div class="highlight"><pre>compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out
</pre></div>
</div>
<p>(2) Temperature in each spatial bin, after subtracting a flow
velocity:</p>
<div class="highlight-python"><div class="highlight"><pre>compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
compute vbias all temp/profile 1 0 0 y 10
fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out
</pre></div>
</div>
<ol class="arabic simple" start="3">
<li>Center of mass of each molecule:</li>
</ol>
<div class="highlight-python"><div class="highlight"><pre>compute cc1 all chunk/atom molecule
compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</pre></div>
</div>
<ol class="arabic simple" start="4">
<li>Total force on each molecule and ave/max across all molecules:</li>
</ol>
<div class="highlight-python"><div class="highlight"><pre>compute cc1 all chunk/atom molecule
fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
variable xave equal ave(f_1**2**)
variable xmax equal max(f_1**2**)
thermo 1000
thermo_style custom step temp v_xave v_xmax
</pre></div>
</div>
<ol class="arabic simple" start="5">
<li>Histogram of cluster sizes:</li>
</ol>
<div class="highlight-python"><div class="highlight"><pre>compute cluster all cluster/atom 1.0
compute cc1 all chunk/atom c_cluster compress yes
compute size all property/chunk cc1 count
fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
</pre></div>
</div>
<hr class="docutils" />
</div>
</div>
<div class="section" id="setting-parameters-for-the-kspace-style-pppm-disp-command">
<span id="howto-24"></span><h2>6.24. Setting parameters for the <a class="reference internal" href="kspace_style.html"><em>kspace_style pppm/disp</em></a> command<a class="headerlink" href="#setting-parameters-for-the-kspace-style-pppm-disp-command" title="Permalink to this headline">¶</a></h2>
<p>The PPPM method computes interactions by splitting the pair potential
into two parts, one of which is computed in a normal pairwise fashion,
the so-called real-space part, and one of which is computed using the
Fourier transform, the so called reciprocal-space or kspace part. For
both parts, the potential is not computed exactly but is approximated.
Thus, there is an error in both parts of the computation, the
real-space and the kspace error. The just mentioned facts are true
both for the PPPM for Coulomb as well as dispersion interactions. The
deciding difference - and also the reason why the parameters for
pppm/disp have to be selected with more care - is the impact of the
errors on the results: The kspace error of the PPPM for Coulomb and
dispersion interaction and the real-space error of the PPPM for
Coulomb interaction have the character of noise. In contrast, the
real-space error of the PPPM for dispersion has a clear physical
interpretation: the underprediction of cohesion. As a consequence, the
real-space error has a much stronger effect than the kspace error on
simulation results for pppm/disp. Parameters must thus be chosen in a
way that this error is much smaller than the kspace error.</p>
<p>When using pppm/disp and not making any specifications on the PPPM
parameters via the kspace modify command, parameters will be tuned
such that the real-space error and the kspace error are equal. This
will result in simulations that are either inaccurate or slow, both of
which is not desirable. For selecting parameters for the pppm/disp
that provide fast and accurate simulations, there are two approaches,
which both have their up- and downsides.</p>
<p>The first approach is to set desired real-space an kspace accuracies
via the <em>kspace_modify force/disp/real</em> and <em>kspace_modify
force/disp/kspace</em> commands. Note that the accuracies have to be
specified in force units and are thus dependend on the chosen unit
settings. For real units, 0.0001 and 0.002 seem to provide reasonable
accurate and efficient computations for the real-space and kspace
accuracies. 0.002 and 0.05 work well for most systems using lj
units. PPPM parameters will be generated based on the desired
accuracies. The upside of this approach is that it usually provides a
good set of parameters and will work for both the <em>kspace_modify diff
ad</em> and <em>kspace_modify diff ik</em> options. The downside of the method
is that setting the PPPM parameters will take some time during the
initialization of the simulation.</p>
<p>The second approach is to set the parameters for the pppm/disp
explicitly using the <em>kspace_modify mesh/disp</em>, <em>kspace_modify
order/disp</em>, and <em>kspace_modify gewald/disp</em> commands. This approach
requires a more experienced user who understands well the impact of
the choice of parameters on the simulation accuracy and
performance. This approach provides a fast initialization of the
simulation. However, it is sensitive to errors: A combination of
parameters that will perform well for one system might result in
far-from-optimal conditions for other simulations. For example,
parametes that provide accurate and fast computations for
all-atomistic force fields can provide insufficient accuracy or
united-atomistic force fields (which is related to that the latter
typically have larger dispersion coefficients).</p>
<p>To avoid inaccurate or inefficient simulations, the pppm/disp stops
simulations with an error message if no action is taken to control the
PPPM parameters. If the automatic parameter generation is desired and
real-space and kspace accuracies are desired to be equal, this error
message can be suppressed using the <em>kspace_modify disp/auto yes</em>
command.</p>
<p>A reasonable approach that combines the upsides of both methods is to
make the first run using the <em>kspace_modify force/disp/real</em> and
<em>kspace_modify force/disp/kspace</em> commands, write down the PPPM
parameters from the outut, and specify these parameters using the
second approach in subsequent runs (which have the same composition,
force field, and approximately the same volume).</p>
<p>Concerning the performance of the pppm/disp there are two more things
to consider. The first is that when using the pppm/disp, the cutoff
parameter does no longer affect the accuracy of the simulation
(subject to that gewald/disp is adjusted when changing the cutoff).
The performance can thus be increased by examining different values
for the cutoff parameter. A lower bound for the cutoff is only set by
the truncation error of the repulsive term of pair potentials.</p>
<p>The second is that the mixing rule of the pair style has an impact on
the computation time when using the pppm/disp. Fastest computations
are achieved when using the geometric mixing rule. Using the
arithmetic mixing rule substantially increases the computational cost.
The computational overhead can be reduced using the <em>kspace_modify
mix/disp geom</em> and <em>kspace_modify splittol</em> commands. The first
command simply enforces geometric mixing of the dispersion
coeffiecients in kspace computations. This introduces some error in
the computations but will also significantly speed-up the
simulations. The second keyword sets the accuracy with which the
dispersion coefficients are approximated using a matrix factorization
approach. This may result in better accuracy then using the first
command, but will usually also not provide an equally good increase of
efficiency.</p>
<p>Finally, pppm/disp can also be used when no mixing rules apply.
This can be achieved using the <em>kspace_modify mix/disp none</em> command.
Note that the code does not check automatically whether any mixing
rule is fulfilled. If mixing rules do not apply, the user will have
to specify this command explicitly.</p>
<hr class="docutils" />
</div>
<div class="section" id="polarizable-models">
<span id="howto-25"></span><h2>6.25. Polarizable models<a class="headerlink" href="#polarizable-models" title="Permalink to this headline">¶</a></h2>
<p>In polarizable force fields the charge distributions in molecules and
materials respond to their electrostatic environements. Polarizable
systems can be simulated in LAMMPS using three methods:</p>
<ul class="simple">
<li>the fluctuating charge method, implemented in the <a class="reference internal" href="fix_qeq.html"><em>QEQ</em></a>
package,</li>
<li>the adiabatic core-shell method, implemented in the
<a class="reference internal" href="#howto-26"><span>CORESHELL</span></a> package,</li>
<li>the thermalized Drude dipole method, implemented in the
<a class="reference internal" href="#howto-27"><span>USER-DRUDE</span></a> package.</li>
</ul>
<p>The fluctuating charge method calculates instantaneous charges on
interacting atoms based on the electronegativity equalization
principle. It is implemented in the <a class="reference internal" href="fix_qeq.html"><em>fix qeq</em></a> which is
available in several variants. It is a relatively efficient technique
since no additional particles are introduced. This method allows for
charge transfer between molecules or atom groups. However, because the
charges are located at the interaction sites, off-plane components of
polarization cannot be represented in planar molecules or atom groups.</p>
<p>The two other methods share the same basic idea: polarizable atoms are
split into one core atom and one satellite particle (called shell or
Drude particle) attached to it by a harmonic spring. Both atoms bear
a charge and they represent collectively an induced electric dipole.
These techniques are computationally more expensive than the QEq
method because of additional particles and bonds. These two
charge-on-spring methods differ in certain features, with the
core-shell model being normally used for ionic/crystalline materials,
whereas the so-called Drude model is normally used for molecular
systems and fluid states.</p>
<p>The core-shell model is applicable to crystalline materials where the
high symmetry around each site leads to stable trajectories of the
core-shell pairs. However, bonded atoms in molecules can be so close
that a core would interact too strongly or even capture the Drude
particle of a neighbor. The Drude dipole model is relatively more
complex in order to remediate this and other issues. Specifically, the
Drude model includes specific thermostating of the core-Drude pairs
and short-range damping of the induced dipoles.</p>
<p>The three polarization methods can be implemented through a
self-consistent calculation of charges or induced dipoles at each
timestep. In the fluctuating charge scheme this is done by the matrix
inversion method in <a class="reference internal" href="fix_qeq.html"><em>fix qeq/point</em></a>, but for core-shell
or Drude-dipoles the relaxed-dipoles technique would require an slow
iterative procedure. These self-consistent solutions yield accurate
trajectories since the additional degrees of freedom representing
polarization are massless. An alternative is to attribute a mass to
the additional degrees of freedom and perform time integration using
an extended Lagrangian technique. For the fluctuating charge scheme
this is done by <a class="reference internal" href="fix_qeq.html"><em>fix qeq/dynamic</em></a>, and for the
charge-on-spring models by the methods outlined in the next two
sections. The assignment of masses to the additional degrees of
freedom can lead to unphysical trajectories if care is not exerted in
choosing the parameters of the poarizable models and the simulation
conditions.</p>
<p>In the core-shell model the vibration of the shells is kept faster
than the ionic vibrations to mimic the fast response of the
polarizable electrons. But in molecular systems thermalizing the
core-Drude pairs at temperatures comparable to the rest of the
simulation leads to several problems (kinetic energy transfer, too
short a timestep, etc.) In order to avoid these problems the relative
motion of the Drude particles with respect to their cores is kept
“cold” so the vibration of the core-Drude pairs is very slow,
approaching the self-consistent regime. In both models the
temperature is regulated using the velocities of the center of mass of
core+shell (or Drude) pairs, but in the Drude model the actual
relative core-Drude particle motion is thermostated separately as
well.</p>
<hr class="docutils" />
</div>
<div class="section" id="adiabatic-core-shell-model">
<span id="howto-26"></span><h2>6.26. Adiabatic core/shell model<a class="headerlink" href="#adiabatic-core-shell-model" title="Permalink to this headline">¶</a></h2>
<p>The adiabatic core-shell model by <a class="reference internal" href="compute_temp_cs.html#mitchellfinchham"><span>Mitchell and Finchham</span></a> is a simple method for adding
polarizability to a system. In order to mimic the electron shell of
an ion, a satellite particle is attached to it. This way the ions are
split into a core and a shell where the latter is meant to react to
the electrostatic environment inducing polarizability.</p>
<p>Technically, shells are attached to the cores by a spring force f =
k*r where k is a parametrized spring constant and r is the distance
between the core and the shell. The charges of the core and the shell
-add up to the ion charge, thus q(ion) = q(core) + q(shell). In a
+add up to the ion charge, thus q(ion) = q(core) + q(shell). This
+setup introduces the ion polarizability (alpha) given by
+alpha = q(shell)^2 / k. In a
similar fashion the mass of the ion is distributed on the core and the
shell with the core having the larger mass.</p>
<p>To run this model in LAMMPS, <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> <em>full</em> can
be used since atom charge and bonds are needed. Each kind of
core/shell pair requires two atom types and a bond type. The core and
shell of a core/shell pair should be bonded to each other with a
harmonic bond that provides the spring force. For example, a data file
for NaCl, as found in examples/coreshell, has this format:</p>
<div class="highlight-python"><div class="highlight"><pre>432 atoms # core and shell atoms
216 bonds # number of core/shell springs
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>4 atom types # 2 cores and 2 shells for Na and Cl
2 bond types
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>0.0 24.09597 xlo xhi
0.0 24.09597 ylo yhi
0.0 24.09597 zlo zhi
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="n">Masses</span> <span class="c"># core/shell mass ratio = 0.1</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>1 20.690784 # Na core
2 31.90500 # Cl core
3 2.298976 # Na shell
4 3.54500 # Cl shell
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="n">Atoms</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1
2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1
3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2
4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2
(...)
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="n">Bonds</span> <span class="c"># Bond topology for spring forces</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>1 2 1 2 # spring for core/shell pair 1
2 2 3 4 # spring for core/shell pair 2
(...)
</pre></div>
</div>
<p>Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
defined between the shells. Coulombic interactions are defined
between all cores and shells. If desired, additional bonds can be
specified between cores.</p>
<p>The <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command should be used to
turn-off the Coulombic interaction within core/shell pairs, since that
interaction is set by the bond spring. This is done using the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command with a 1-2 weight = 0.0,
which is the default value. It needs to be considered whether one has
to adjust the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> weighting according
to the molecular topology since the interactions of the shells are
bypassed over an extra bond.</p>
<p>Note that this core/shell implementation does not require all ions to
be polarized. One can mix core/shell pairs and ions without a
satellite particle if desired.</p>
<p>Since the core/shell model permits distances of r = 0.0 between the
core and shell, a pair style with a “cs” suffix needs to be used to
-implement a valid long-rangeCoulombic correction. Several such pair
+implement a valid long-range Coulombic correction. Several such pair
styles are provided in the CORESHELL package. See <a class="reference internal" href="pair_cs.html"><em>this doc page</em></a> for details. All of the core/shell enabled pair
styles require the use of a long-range Coulombic solver, as specified
by the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command. Either the PPPM or
Ewald solvers can be used.</p>
<p>For the NaCL example problem, these pair style and bond style settings
are used:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style born/coul/long/cs 20.0 20.0
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0
</pre></div>
</div>
<p>When running dynamics with the adiabatic core/shell model, the
following issues should be considered. Since the relative motion of
the core and shell particles corresponds to the polarization, typical
-thermostats can alter the polarization behaviour, meaining the shell
-will not react freely to its electrostatic environment. Therefore
+thermostats can alter the polarization behaviour, meaning the shell
+will not react freely to its electrostatic environment. This is
+critical during the equilibration of the system. Therefore
it’s typically desirable to decouple the relative motion of the
core/shell pair, which is an imaginary degree of freedom, from the
real physical system. To do that, the <a class="reference internal" href="compute_temp_cs.html"><em>compute temp/cs</em></a> command can be used, in conjunction with
any of the thermostat fixes, such as <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a> or <a class="reference external" href="fix_langevin">fix langevin</a>. This compute uses the center-of-mass velocity
of the core/shell pairs to calculate a temperature, and insures that
velocity is what is rescaled for thermostatting purposes. This
compute also works for a system with both core/shell pairs and
non-polarized ions (ions without an attached satellite particle). The
<a class="reference internal" href="compute_temp_cs.html"><em>compute temp/cs</em></a> command requires input of two
groups, one for the core atoms, another for the shell atoms.
Non-polarized ions which might also be included in the treated system
should not be included into either of these groups, they are taken
into account by the <em>group-ID</em> (2nd argument) of the compute. The
groups can be defined using the <a class="reference internal" href="group.html"><em>group *type*</em></a> command.
Note that to perform thermostatting using this definition of
temperature, the <a class="reference internal" href="fix_modify.html"><em>fix modify temp</em></a> command should be
-used to assign the comptue to the thermostat fix. Likewise the
+used to assign the compute to the thermostat fix. Likewise the
<a class="reference internal" href="thermo_modify.html"><em>thermo_modify temp</em></a> command can be used to make
this temperature be output for the overall system.</p>
<p>For the NaCl example, this can be done as follows:</p>
<div class="highlight-python"><div class="highlight"><pre>group cores type 1 2
group shells type 3 4
compute CSequ all temp/cs cores shells
fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system
fix thermostatequ all nve # integrator as needed for the berendsen thermostat
fix_modify thermoberendsen temp CSequ
thermo_modify temp CSequ # output of center-of-mass derived temperature
</pre></div>
</div>
+<p>If <a class="reference internal" href="compute_temp_cs.html"><em>compute temp/cs</em></a> is used, the decoupled
+relative motion of the core and the shell should in theory be
+stable. However numerical fluctuation can introduce a small
+momentum to the system, which is noticable over long trajectories.
+Therefore it is recomendable to use the <a class="reference internal" href="fix_momentum.html"><em>fix momentum</em></a> command in combination with <a class="reference internal" href="compute_temp_cs.html"><em>compute temp/cs</em></a> when equilibrating the system to
+prevent any drift.</p>
<p>When intializing the velocities of a system with core/shell pairs, it
is also desirable to not introduce energy into the relative motion of
the core/shell particles, but only assign a center-of-mass velocity to
the pairs. This can be done by using the <em>bias</em> keyword of the
<a class="reference internal" href="velocity.html"><em>velocity create</em></a> command and assigning the <a class="reference internal" href="compute_temp_cs.html"><em>compute temp/cs</em></a> command to the <em>temp</em> keyword of the
<a class="reference internal" href="velocity.html"><em>velocity</em></a> commmand, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>velocity all create 1427 134 bias yes temp CSequ
velocity all scale 1427 temp CSequ
</pre></div>
</div>
<p>It is important to note that the polarizability of the core/shell
pairs is based on their relative motion. Therefore the choice of
spring force and mass ratio need to ensure much faster relative motion
of the 2 atoms within the core/shell pair than their center-of-mass
velocity. This allow the shells to effectively react instantaneously
to the electrostatic environment. This fast movement also limits the
timestep size that can be used.</p>
-<p>Additionally, the mass mismatch of the core and shell particles means
-that only a small amount of energy is transfered to the decoupled
-imaginary degrees of freedom. However, this transfer will typically
-lead to a a small drift in total energy over time. This internal
-energy can be monitored using the <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> and <a class="reference internal" href="compute_temp_chunk.html"><em>compute temp/chunk</em></a> commands. The internal kinetic
+<p>The primary literature of the adiabatic core/shell model suggests that
+the fast relative motion of the core/shell pairs only allows negligible
+energy transfer to the environment. Therefore it is not intended to
+decouple the core/shell degree of freedom from the physical system
+during production runs. In other words, the <a class="reference internal" href="compute_temp_cs.html"><em>compute temp/cs</em></a> command should not be used during
+production runs and is only required during equilibration. This way one
+is consistent with literature (based on the code packages DL_POLY or
+GULP for instance).</p>
+<p>The mentioned energy transfer will typically lead to a a small drift
+in total energy over time. This internal energy can be monitored
+using the <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> and <a class="reference internal" href="compute_temp_chunk.html"><em>compute temp/chunk</em></a> commands. The internal kinetic
energies of each core/shell pair can then be summed using the sum()
special function of the <a class="reference internal" href="variable.html"><em>variable</em></a> command. Or they can
be time/averaged and output using the <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>
command. To use these commands, each core/shell pair must be defined
as a “chunk”. If each core/shell pair is defined as its own molecule,
the molecule ID can be used to define the chunks. If cores are bonded
to each other to form larger molecules, the chunks can be identified
by the <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> via assigning a
core/shell ID to each atom using a special field in the data file read
by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command. This field can then be
accessed by the <a class="reference internal" href="compute_property_atom.html"><em>compute property/atom</em></a>
command, to use as input to the <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command to define the core/shell
pairs as chunks.</p>
<p>For example,</p>
<div class="highlight-python"><div class="highlight"><pre>fix csinfo all property/atom i_CSID # property/atom command
read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file
compute prop all property/atom i_CSID
compute cs_chunk all chunk/atom c_prop
compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
</pre></div>
</div>
<p>The additional section in the date file would be formatted like this:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">CS</span><span class="o">-</span><span class="n">Info</span> <span class="c"># header of additional section</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>1 1 # column 1 = atom ID, column 2 = core/shell ID
2 1
3 2
4 2
5 3
6 3
7 4
8 4
(...)
</pre></div>
</div>
<hr class="docutils" />
</div>
<div class="section" id="drude-induced-dipoles">
<span id="howto-27"></span><h2>6.27. Drude induced dipoles<a class="headerlink" href="#drude-induced-dipoles" title="Permalink to this headline">¶</a></h2>
<p>The thermalized Drude model, similarly to the <a class="reference internal" href="#howto-26"><span>core-shell</span></a>
model, representes induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems
(<a class="reference internal" href="#lamoureux"><span>Lamoureux and Roux</span></a>):</p>
<ul class="simple">
<li>Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced
coordinates of the Drude particles with respect to their cores. This
makes the trajectory close to that of relaxed induced dipoles.</li>
<li>Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle
pair represents a single (polarizable) atom, so the special screening
factors in a covalent structure should be the same for the core and
the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4
special neighbor relations from their respective cores.</li>
<li>Stabilization of the interactions between induced dipoles. Drude
dipoles on covalently bonded atoms interact too strongly due to the
short distances, so an atom may capture the Drude particle of a
neighbor, or the induced dipoles within the same molecule may align
too much. To avoid this, damping at short range can be done by Thole
functions (for which there are physical grounds). This Thole damping
is applied to the point charges composing the induced dipole (the
charge of the Drude particle and the opposite charge on the core, not
to the total charge of the core atom).</li>
</ul>
<p>A detailed tutorial covering the usage of Drude induced dipoles in
LAMMPS is <a class="reference internal" href="tutorial_drude.html"><em>available here</em></a>.</p>
<p>As with the core-shell model, the cores and Drude particles should
appear in the data file as standard atoms. The same holds for the
springs between them, which are described by standard harmonic bonds.
The nature of the atoms (core, Drude particle or non-polarizable) is
specified via the <a class="reference internal" href="fix_drude.html"><em>fix drude</em></a> command. The special
list of neighbors is automatically refactored to account for the
equivalence of core and Drude particles as regards special 1-2 to 1-4
screening. It may be necessary to use the <em>extra</em> keyword of the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command. If using <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a>, make sure no Drude particle is in this fix
group.</p>
<p>There are two ways to thermostat the Drude particles at a low
temperature: use either <a class="reference internal" href="fix_langevin_drude.html"><em>fix langevin/drude</em></a>
for a Langevin thermostat, or <a class="reference internal" href="fix_drude_transform.html"><em>fix drude/transform/*</em></a> for a Nose-Hoover
thermostat. The former requires use of the command <a class="reference internal" href="comm_modify.html"><em>comm_modify vel yes</em></a>. The latter requires two separate integration
fixes like <em>nvt</em> or <em>npt</em>. The correct temperatures of the reduced
degrees of freedom can be calculated using the <a class="reference internal" href="compute_temp_drude.html"><em>compute temp/drude</em></a>. This requires also to use the
command <em>comm_modify vel yes</em>.</p>
<p>Short-range damping of the induced dipole interactions can be achieved
using Thole functions through the the <a class="reference internal" href="pair_thole.html"><em>pair style thole</em></a> in <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a>
with a Coulomb pair style. It may be useful to use <em>coul/long/cs</em> or
similar from the CORESHELL package if the core and Drude particle come
too close, which can cause numerical issues.</p>
<p id="berendsen"><strong>(Berendsen)</strong> Berendsen, Grigera, Straatsma, J Phys Chem, 91,
6269-6271 (1987).</p>
<p id="cornell"><strong>(Cornell)</strong> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).</p>
<p id="horn"><strong>(Horn)</strong> Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon,
J Chem Phys, 120, 9665 (2004).</p>
<p id="ikeshoji"><strong>(Ikeshoji)</strong> Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
(1994).</p>
<p id="mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</p>
<p id="mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).</p>
<p id="jorgensen"><strong>(Jorgensen)</strong> Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).</p>
<p id="price"><strong>(Price)</strong> Price and Brooks, J Chem Phys, 121, 10096 (2004).</p>
<p id="shinoda"><strong>(Shinoda)</strong> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).</p>
<p id="mitchellfinchham"><strong>(Mitchell and Finchham)</strong> Mitchell, Finchham, J Phys Condensed Matter,
5, 1031-1038 (1993).</p>
<p id="lamoureux"><strong>(Lamoureux and Roux)</strong> G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)</p>
</div>
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diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt
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"Previous Section"_Section_accelerate.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_example.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
6. How-to discussions :h3
This section describes how to perform common tasks using LAMMPS.
6.1 "Restarting a simulation"_#howto_1
6.2 "2d simulations"_#howto_2
6.3 "CHARMM, AMBER, and DREIDING force fields"_#howto_3
6.4 "Running multiple simulations from one input script"_#howto_4
6.5 "Multi-replica simulations"_#howto_5
6.6 "Granular models"_#howto_6
6.7 "TIP3P water model"_#howto_7
6.8 "TIP4P water model"_#howto_8
6.9 "SPC water model"_#howto_9
6.10 "Coupling LAMMPS to other codes"_#howto_10
6.11 "Visualizing LAMMPS snapshots"_#howto_11
6.12 "Triclinic (non-orthogonal) simulation boxes"_#howto_12
6.13 "NEMD simulations"_#howto_13
6.14 "Finite-size spherical and aspherical particles"_#howto_14
6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#howto_15
6.16 "Thermostatting, barostatting and computing temperature"_#howto_16
6.17 "Walls"_#howto_17
6.18 "Elastic constants"_#howto_18
6.19 "Library interface to LAMMPS"_#howto_19
6.20 "Calculating thermal conductivity"_#howto_20
6.21 "Calculating viscosity"_#howto_21
6.22 "Calculating a diffusion coefficient"_#howto_22
6.23 "Using chunks to calculate system properties"_#howto_23
6.24 "Setting parameters for the kspace_style pppm/disp command"_#howto_24
6.25 "Polarizable models"_#howto_25
6.26 "Adiabatic core/shell model"_#howto_26
6.27 "Drude induced dipoles"_#howto_27 :all(b)
The example input scripts included in the LAMMPS distribution and
highlighted in "Section_example"_Section_example.html also show how to
setup and run various kinds of simulations.
:line
:line
6.1 Restarting a simulation :link(howto_1),h4
There are 3 ways to continue a long LAMMPS simulation. Multiple
"run"_run.html commands can be used in the same input script. Each
run will continue from where the previous run left off. Or binary
restart files can be saved to disk using the "restart"_restart.html
command. At a later time, these binary files can be read via a
"read_restart"_read_restart.html command in a new script. Or they can
be converted to text data files using the "-r command-line
switch"_Section_start.html#start_7 and read by a
"read_data"_read_data.html command in a new script.
Here we give examples of 2 scripts that read either a binary restart
file or a converted data file and then issue a new run command to
continue where the previous run left off. They illustrate what
settings must be made in the new script. Details are discussed in the
documentation for the "read_restart"_read_restart.html and
"read_data"_read_data.html commands.
Look at the {in.chain} input script provided in the {bench} directory
of the LAMMPS distribution to see the original script that these 2
scripts are based on. If that script had the line
restart 50 tmp.restart :pre
added to it, it would produce 2 binary restart files (tmp.restart.50
and tmp.restart.100) as it ran.
This script could be used to read the 1st restart file and re-run the
last 50 timesteps:
read_restart tmp.restart.50 :pre
neighbor 0.4 bin
neigh_modify every 1 delay 1 :pre
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297 :pre
timestep 0.012 :pre
run 50 :pre
Note that the following commands do not need to be repeated because
their settings are included in the restart file: {units, atom_style,
special_bonds, pair_style, bond_style}. However these commands do
need to be used, since their settings are not in the restart file:
{neighbor, fix, timestep}.
If you actually use this script to perform a restarted run, you will
notice that the thermodynamic data match at step 50 (if you also put a
"thermo 50" command in the original script), but do not match at step
100. This is because the "fix langevin"_fix_langevin.html command
uses random numbers in a way that does not allow for perfect restarts.
As an alternate approach, the restart file could be converted to a data
file as follows:
lmp_g++ -r tmp.restart.50 tmp.restart.data :pre
Then, this script could be used to re-run the last 50 steps:
units lj
atom_style bond
pair_style lj/cut 1.12
pair_modify shift yes
bond_style fene
special_bonds 0.0 1.0 1.0 :pre
read_data tmp.restart.data :pre
neighbor 0.4 bin
neigh_modify every 1 delay 1 :pre
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297 :pre
timestep 0.012 :pre
reset_timestep 50
run 50 :pre
Note that nearly all the settings specified in the original {in.chain}
script must be repeated, except the {pair_coeff} and {bond_coeff}
commands since the new data file lists the force field coefficients.
Also, the "reset_timestep"_reset_timestep.html command is used to tell
LAMMPS the current timestep. This value is stored in restart files,
but not in data files.
:line
6.2 2d simulations :link(howto_2),h4
Use the "dimension"_dimension.html command to specify a 2d simulation.
Make the simulation box periodic in z via the "boundary"_boundary.html
command. This is the default.
If using the "create box"_create_box.html command to define a
simulation box, set the z dimensions narrow, but finite, so that the
create_atoms command will tile the 3d simulation box with a single z
plane of atoms - e.g.
"create box"_create_box.html 1 -10 10 -10 10 -0.25 0.25 :pre
If using the "read data"_read_data.html command to read in a file of
atom coordinates, set the "zlo zhi" values to be finite but narrow,
similar to the create_box command settings just described. For each
atom in the file, assign a z coordinate so it falls inside the
z-boundaries of the box - e.g. 0.0.
Use the "fix enforce2d"_fix_enforce2d.html command as the last
defined fix to insure that the z-components of velocities and forces
are zeroed out every timestep. The reason to make it the last fix is
so that any forces induced by other fixes will be zeroed out.
Many of the example input scripts included in the LAMMPS distribution
are for 2d models.
IMPORTANT NOTE: Some models in LAMMPS treat particles as finite-size
spheres, as opposed to point particles. In 2d, the particles will
still be spheres, not disks, meaning their moment of inertia will be
the same as in 3d.
:line
6.3 CHARMM, AMBER, and DREIDING force fields :link(howto_3),h4
A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
formulas implemented in LAMMPS that correspond to formulas commonly
used in the CHARMM, AMBER, and DREIDING force fields. Setting
coefficients is done in the input data file via the
"read_data"_read_data.html command or in the input script with
commands like "pair_coeff"_pair_coeff.html or
"bond_coeff"_bond_coeff.html. See "Section_tools"_Section_tools.html
for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input.
See "(MacKerell)"_#MacKerell for a description of the CHARMM force
field. See "(Cornell)"_#Cornell for a description of the AMBER force
field.
:link(charmm,http://www.scripps.edu/brooks)
:link(amber,http://amber.scripps.edu)
These style choices compute force field formulas that are consistent
with common options in CHARMM or AMBER. See each command's
documentation for the formula it computes.
"bond_style"_bond_harmonic.html harmonic
"angle_style"_angle_charmm.html charmm
"dihedral_style"_dihedral_charmm.html charmm
"pair_style"_pair_charmm.html lj/charmm/coul/charmm
"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit
"pair_style"_pair_charmm.html lj/charmm/coul/long :ul
"special_bonds"_special_bonds.html charmm
"special_bonds"_special_bonds.html amber :ul
DREIDING is a generic force field developed by the "Goddard
group"_http://www.wag.caltech.edu at Caltech and is useful for
predicting structures and dynamics of organic, biological and
main-group inorganic molecules. The philosophy in DREIDING is to use
general force constants and geometry parameters based on simple
hybridization considerations, rather than individual force constants
and geometric parameters that depend on the particular combinations of
atoms involved in the bond, angle, or torsion terms. DREIDING has an
"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe
interactions involving a hydrogen atom on very electronegative atoms
(N, O, F).
See "(Mayo)"_#Mayo for a description of the DREIDING force field
These style choices compute force field formulas that are consistent
with the DREIDING force field. See each command's
documentation for the formula it computes.
"bond_style"_bond_harmonic.html harmonic
"bond_style"_bond_morse.html morse :ul
"angle_style"_angle_harmonic.html harmonic
"angle_style"_angle_cosine.html cosine
"angle_style"_angle_cosine_periodic.html cosine/periodic :ul
"dihedral_style"_dihedral_charmm.html charmm
"improper_style"_improper_umbrella.html umbrella :ul
"pair_style"_pair_buck.html buck
"pair_style"_pair_buck.html buck/coul/cut
"pair_style"_pair_buck.html buck/coul/long
"pair_style"_pair_lj.html lj/cut
"pair_style"_pair_lj.html lj/cut/coul/cut
"pair_style"_pair_lj.html lj/cut/coul/long :ul
"pair_style"_pair_hbond_dreiding.html hbond/dreiding/lj
"pair_style"_pair_hbond_dreiding.html hbond/dreiding/morse :ul
"special_bonds"_special_bonds.html dreiding :ul
:line
6.4 Running multiple simulations from one input script :link(howto_4),h4
This can be done in several ways. See the documentation for
individual commands for more details on how these examples work.
If "multiple simulations" means continue a previous simulation for
more timesteps, then you simply use the "run"_run.html command
multiple times. For example, this script
units lj
atom_style atomic
read_data data.lj
run 10000
run 10000
run 10000
run 10000
run 10000 :pre
would run 5 successive simulations of the same system for a total of
50,000 timesteps.
If you wish to run totally different simulations, one after the other,
the "clear"_clear.html command can be used in between them to
re-initialize LAMMPS. For example, this script
units lj
atom_style atomic
read_data data.lj
run 10000
clear
units lj
atom_style atomic
read_data data.lj.new
run 10000 :pre
would run 2 independent simulations, one after the other.
For large numbers of independent simulations, you can use
"variables"_variable.html and the "next"_next.html and
"jump"_jump.html commands to loop over the same input script
multiple times with different settings. For example, this
script, named in.polymer
variable d index run1 run2 run3 run4 run5 run6 run7 run8
shell cd $d
read_data data.polymer
run 10000
shell cd ..
clear
next d
jump in.polymer :pre
would run 8 simulations in different directories, using a data.polymer
file in each directory. The same concept could be used to run the
same system at 8 different temperatures, using a temperature variable
and storing the output in different log and dump files, for example
variable a loop 8
variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
log log.$a
read data.polymer
velocity all create $t 352839
fix 1 all nvt $t $t 100.0
dump 1 all atom 1000 dump.$a
run 100000
clear
next t
next a
jump in.polymer :pre
All of the above examples work whether you are running on 1 or
multiple processors, but assumed you are running LAMMPS on a single
partition of processors. LAMMPS can be run on multiple partitions via
the "-partition" command-line switch as described in "this
section"_Section_start.html#start_7 of the manual.
In the last 2 examples, if LAMMPS were run on 3 partitions, the same
scripts could be used if the "index" and "loop" variables were
replaced with {universe}-style variables, as described in the
"variable"_variable.html command. Also, the "next t" and "next a"
commands would need to be replaced with a single "next a t" command.
With these modifications, the 8 simulations of each script would run
on the 3 partitions one after the other until all were finished.
Initially, 3 simulations would be started simultaneously, one on each
partition. When one finished, that partition would then start
the 4th simulation, and so forth, until all 8 were completed.
:line
6.5 Multi-replica simulations :link(howto_5),h4
Several commands in LAMMPS run mutli-replica simulations, meaning
that multiple instances (replicas) of your simulation are run
simultaneously, with small amounts of data exchanged between replicas
periodically.
These are the relevant commands:
"neb"_neb.html for nudged elastic band calculations
"prd"_prd.html for parallel replica dynamics
"tad"_tad.html for temperature accelerated dynamics
"temper"_temper.html for parallel tempering
"fix pimd"_fix_pimd.html for path-integral molecular dynamics (PIMD) :ul
NEB is a method for finding transition states and barrier energies.
PRD and TAD are methods for performing accelerated dynamics to find
and perform infrequent events. Parallel tempering or replica exchange
runs different replicas at a series of temperature to facilitate
rare-event sampling.
These commands can only be used if LAMMPS was built with the REPLICA
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
PIMD runs different replicas whose individual particles are coupled
together by springs to model a system or ring-polymers.
This commands can only be used if LAMMPS was built with the USER-MISC
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
In all these cases, you must run with one or more processors per
replica. The processors assigned to each replica are determined at
run-time by using the "-partition command-line
switch"_Section_start.html#start_7 to launch LAMMPS on multiple
partitions, which in this context are the same as replicas. E.g.
these commands:
mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre
would each run 8 replicas, on either 16 or 8 processors. Note the use
of the "-in command-line switch"_Section_start.html#start_7 to specify
the input script which is required when running in multi-replica mode.
Also note that with MPI installed on a machine (e.g. your desktop),
you can run on more (virtual) processors than you have physical
processors. Thus the above commands could be run on a
single-processor (or few-processor) desktop so that you can run
a multi-replica simulation on more replicas than you have
physical processors.
:line
6.6 Granular models :link(howto_6),h4
Granular system are composed of spherical particles with a diameter,
as opposed to point particles. This means they have an angular
velocity and torque can be imparted to them to cause them to rotate.
To run a simulation of a granular model, you will want to use
the following commands:
"atom_style sphere"_atom_style.html
"fix nve/sphere"_fix_nve_sphere.html
"fix gravity"_fix_gravity.html :ul
This compute
"compute erotate/sphere"_compute_erotate_sphere.html :ul
calculates rotational kinetic energy which can be "output with
thermodynamic info"_Section_howto.html#howto_15.
Use one of these 3 pair potentials, which compute forces and torques
between interacting pairs of particles:
"pair_style"_pair_style.html gran/history
"pair_style"_pair_style.html gran/no_history
"pair_style"_pair_style.html gran/hertzian :ul
These commands implement fix options specific to granular systems:
"fix freeze"_fix_freeze.html
"fix pour"_fix_pour.html
"fix viscous"_fix_viscous.html
"fix wall/gran"_fix_wall_gran.html :ul
The fix style {freeze} zeroes both the force and torque of frozen
atoms, and should be used for granular system instead of the fix style
{setforce}.
For computational efficiency, you can eliminate needless pairwise
computations between frozen atoms by using this command:
"neigh_modify"_neigh_modify.html exclude :ul
:line
6.7 TIP3P water model :link(howto_7),h4
The TIP3P water model as implemented in CHARMM
"(MacKerell)"_#MacKerell specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
{harmonic} and an angle style of {harmonic} or {charmm} should also be
used.
These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
cutoff. The K values can be used if a flexible TIP3P model (without
fix shake) is desired. If the LJ epsilon and sigma for HH and OH are
set to 0.0, it corresponds to the original 1983 TIP3P model
"(Jorgensen)"_#Jorgensen.
O mass = 15.9994
H mass = 1.008
O charge = -0.834
H charge = 0.417
LJ epsilon of OO = 0.1521
LJ sigma of OO = 3.1507
LJ epsilon of HH = 0.0460
LJ sigma of HH = 0.4000
LJ epsilon of OH = 0.0836
LJ sigma of OH = 1.7753
K of OH bond = 450
r0 of OH bond = 0.9572
K of HOH angle = 55
theta of HOH angle = 104.52 :all(b),p
These are the parameters to use for TIP3P with a long-range Coulombic
solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price for
details:
O mass = 15.9994
H mass = 1.008
O charge = -0.830
H charge = 0.415
LJ epsilon of OO = 0.102
LJ sigma of OO = 3.188
LJ epsilon, sigma of OH, HH = 0.0
K of OH bond = 450
r0 of OH bond = 0.9572
K of HOH angle = 55
theta of HOH angle = 104.52 :all(b),p
Wikipedia also has a nice article on "water
models"_http://en.wikipedia.org/wiki/Water_model.
:line
6.8 TIP4P water model :link(howto_8),h4
The four-point TIP4P rigid water model extends the traditional
three-point TIP3P model by adding an additional site, usually
massless, where the charge associated with the oxygen atom is placed.
This site M is located at a fixed distance away from the oxygen along
the bisector of the HOH bond angle. A bond style of {harmonic} and an
angle style of {harmonic} or {charmm} should also be used.
A TIP4P model is run with LAMMPS using either this command
for a cutoff model:
"pair_style lj/cut/tip4p/cut"_pair_lj.html
or these two commands for a long-range model:
"pair_style lj/cut/tip4p/long"_pair_lj.html
"kspace_style pppm/tip4p"_kspace_style.html :ul
For both models, the bond lengths and bond angles should be held fixed
using the "fix shake"_fix_shake.html command.
These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP4P model with a cutoff
"(Jorgensen)"_#Jorgensen. Note that the OM distance is specified in
the "pair_style"_pair_style.html command, not as part of the pair
coefficients.
O mass = 15.9994
H mass = 1.008
O charge = -1.040
H charge = 0.520
r0 of OH bond = 0.9572
theta of HOH angle = 104.52
OM distance = 0.15
LJ epsilon of O-O = 0.1550
LJ sigma of O-O = 3.1536
LJ epsilon, sigma of OH, HH = 0.0
Coulombic cutoff = 8.5 :all(b),p
For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
http://dx.doi.org/10.1063/1.1931662) these values can be used:
O mass = 15.9994
H mass = 1.008
O charge = -1.1794
H charge = 0.5897
r0 of OH bond = 0.9572
theta of HOH angle = 104.52
OM distance = 0.1577
LJ epsilon of O-O = 0.21084
LJ sigma of O-O = 3.1668
LJ epsilon, sigma of OH, HH = 0.0
Coulombic cutoff = 8.5 :all(b),p
For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
http://dx.doi.org/10.1063/1.2121687), these values can be used:
O mass = 15.9994
H mass = 1.008
O charge = -1.1128
H charge = 0.5564
r0 of OH bond = 0.9572
theta of HOH angle = 104.52
OM distance = 0.1546
LJ epsilon of O-O = 0.1852
LJ sigma of O-O = 3.1589
LJ epsilon, sigma of OH, HH = 0.0
Coulombic cutoff = 8.5 :all(b),p
These are the parameters to use for TIP4P with a long-range Coulombic
solver (e.g. Ewald or PPPM in LAMMPS):
O mass = 15.9994
H mass = 1.008
O charge = -1.0484
H charge = 0.5242
r0 of OH bond = 0.9572
theta of HOH angle = 104.52
OM distance = 0.1250
LJ epsilon of O-O = 0.16275
LJ sigma of O-O = 3.16435
LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
Note that the when using the TIP4P pair style, the neighobr list
cutoff for Coulomb interactions is effectively extended by a distance
2 * (OM distance), to account for the offset distance of the
fictitious charges on O atoms in water molecules. Thus it is
typically best in an efficiency sense to use a LJ cutoff >= Coulomb
cutoff + 2*(OM distance), to shrink the size of the neighbor list.
This leads to slightly larger cost for the long-range calculation, so
you can test the trade-off for your model. The OM distance and the LJ
and Coulombic cutoffs are set in the "pair_style
lj/cut/tip4p/long"_pair_lj.html command.
Wikipedia also has a nice article on "water
models"_http://en.wikipedia.org/wiki/Water_model.
:line
6.9 SPC water model :link(howto_9),h4
The SPC water model specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
{harmonic} and an angle style of {harmonic} or {charmm} should also be
used.
These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid SPC model.
O mass = 15.9994
H mass = 1.008
O charge = -0.820
H charge = 0.410
LJ epsilon of OO = 0.1553
LJ sigma of OO = 3.166
LJ epsilon, sigma of OH, HH = 0.0
r0 of OH bond = 1.0
theta of HOH angle = 109.47 :all(b),p
Note that as originally proposed, the SPC model was run with a 9
Angstrom cutoff for both LJ and Coulommbic terms. It can also be used
with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
any of the parameters above, though it becomes a different model in
that mode of usage.
The SPC/E (extended) water model is the same, except
the partial charge assignemnts change:
O charge = -0.8476
H charge = 0.4238 :all(b),p
See the "(Berendsen)"_#Berendsen reference for more details on both
the SPC and SPC/E models.
Wikipedia also has a nice article on "water
models"_http://en.wikipedia.org/wiki/Water_model.
:line
6.10 Coupling LAMMPS to other codes :link(howto_10),h4
LAMMPS is designed to allow it to be coupled to other codes. For
example, a quantum mechanics code might compute forces on a subset of
atoms and pass those forces to LAMMPS. Or a continuum finite element
(FE) simulation might use atom positions as boundary conditions on FE
nodal points, compute a FE solution, and return interpolated forces on
MD atoms.
LAMMPS can be coupled to other codes in at least 3 ways. Each has
advantages and disadvantages, which you'll have to think about in the
context of your application.
(1) Define a new "fix"_fix.html command that calls the other code. In
this scenario, LAMMPS is the driver code. During its timestepping,
the fix is invoked, and can make library calls to the other code,
which has been linked to LAMMPS as a library. This is the way the
"POEMS"_poems package that performs constrained rigid-body motion on
groups of atoms is hooked to LAMMPS. See the
"fix_poems"_fix_poems.html command for more details. See "this
section"_Section_modify.html of the documentation for info on how to add
a new fix to LAMMPS.
:link(poems,http://www.rpi.edu/~anderk5/lab)
(2) Define a new LAMMPS command that calls the other code. This is
conceptually similar to method (1), but in this case LAMMPS and the
other code are on a more equal footing. Note that now the other code
is not called during the timestepping of a LAMMPS run, but between
runs. The LAMMPS input script can be used to alternate LAMMPS runs
with calls to the other code, invoked via the new command. The
"run"_run.html command facilitates this with its {every} option, which
makes it easy to run a few steps, invoke the command, run a few steps,
invoke the command, etc.
In this scenario, the other code can be called as a library, as in
(1), or it could be a stand-alone code, invoked by a system() call
made by the command (assuming your parallel machine allows one or more
processors to start up another program). In the latter case the
stand-alone code could communicate with LAMMPS thru files that the
command writes and reads.
See "Section_modify"_Section_modify.html of the documentation for how
to add a new command to LAMMPS.
(3) Use LAMMPS as a library called by another code. In this case the
other code is the driver and calls LAMMPS as needed. Or a wrapper
code could link and call both LAMMPS and another code as libraries.
Again, the "run"_run.html command has options that allow it to be
invoked with minimal overhead (no setup or clean-up) if you wish to do
multiple short runs, driven by another program.
Examples of driver codes that call LAMMPS as a library are included in
the examples/COUPLE directory of the LAMMPS distribution; see
examples/COUPLE/README for more details:
simple: simple driver programs in C++ and C which invoke LAMMPS as a
library :ulb,l
lammps_quest: coupling of LAMMPS and "Quest"_quest, to run classical
MD with quantum forces calculated by a density functional code :l
lammps_spparks: coupling of LAMMPS and "SPPARKS"_spparks, to couple
a kinetic Monte Carlo model for grain growth using MD to calculate
strain induced across grain boundaries :l,ule
:link(quest,http://dft.sandia.gov/Quest)
:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html)
"This section"_Section_start.html#start_5 of the documentation
describes how to build LAMMPS as a library. Once this is done, you
can interface with LAMMPS either via C++, C, Fortran, or Python (or
any other language that supports a vanilla C-like interface). For
example, from C++ you could create one (or more) "instances" of
LAMMPS, pass it an input script to process, or execute individual
commands, all by invoking the correct class methods in LAMMPS. From C
or Fortran you can make function calls to do the same things. See
"Section_python"_Section_python.html of the manual for a description
of the Python wrapper provided with LAMMPS that operates through the
LAMMPS library interface.
The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See "Section_howto 19"_Section_howto.html#howto_19 of the
manual for a description of the interface and how to extend it for
your needs.
Note that the lammps_open() function that creates an instance of
LAMMPS takes an MPI communicator as an argument. This means that
instance of LAMMPS will run on the set of processors in the
communicator. Thus the calling code can run LAMMPS on all or a subset
of processors. For example, a wrapper script might decide to
alternate between LAMMPS and another code, allowing them both to run
on all the processors. Or it might allocate half the processors to
LAMMPS and half to the other code and run both codes simultaneously
before syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.
:line
6.11 Visualizing LAMMPS snapshots :link(howto_11),h4
LAMMPS itself does not do visualization, but snapshots from LAMMPS
simulations can be visualized (and analyzed) in a variety of ways.
LAMMPS snapshots are created by the "dump"_dump.html command which can
create files in several formats. The native LAMMPS dump format is a
text file (see "dump atom" or "dump custom") which can be visualized
by the "xmovie"_Section_tools.html#xmovie program, included with the
LAMMPS package. This produces simple, fast 2d projections of 3d
systems, and can be useful for rapid debugging of simulation geometry
and atom trajectories.
Several programs included with LAMMPS as auxiliary tools can convert
native LAMMPS dump files to other formats. See the
"Section_tools"_Section_tools.html doc page for details. The first is
the "ch2lmp tool"_Section_tools.html#charmm, which contains a
lammps2pdb Perl script which converts LAMMPS dump files into PDB
files. The second is the "lmp2arc tool"_Section_tools.html#arc which
converts LAMMPS dump files into Accelrys' Insight MD program files.
The third is the "lmp2cfg tool"_Section_tools.html#cfg which converts
LAMMPS dump files into CFG files which can be read into the
"AtomEye"_atomeye visualizer.
A Python-based toolkit distributed by our group can read native LAMMPS
dump files, including custom dump files with additional columns of
user-specified atom information, and convert them to various formats
or pipe them into visualization software directly. See the "Pizza.py
WWW site"_pizza for details. Specifically, Pizza.py can convert
LAMMPS dump files into PDB, XYZ, "Ensight"_ensight, and VTK formats.
Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
RasMol visualization programs. Pizza.py has tools that do interactive
3d OpenGL visualization and one that creates SVG images of dump file
snapshots.
LAMMPS can create XYZ files directly (via "dump xyz") which is a
simple text-based file format used by many visualization programs
including "VMD"_vmd.
LAMMPS can create DCD files directly (via "dump dcd") which can be
read by "VMD"_vmd in conjunction with a CHARMM PSF file. Using this
form of output avoids the need to convert LAMMPS snapshots to PDB
files. See the "dump"_dump.html command for more information on DCD
files.
LAMMPS can create XTC files directly (via "dump xtc") which is GROMACS
file format which can also be read by "VMD"_vmd for visualization.
See the "dump"_dump.html command for more information on XTC files.
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
:link(vmd,http://www.ks.uiuc.edu/Research/vmd)
:link(ensight,http://www.ensight.com)
:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
:line
6.12 Triclinic (non-orthogonal) simulation boxes :link(howto_12),h4
By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The "boundary"_boundary.html command sets the boundary
conditions of the box (periodic, non-periodic, etc). The orthogonal
box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
starting from the origin given by [a] = (xhi-xlo,0,0); [b] =
(0,yhi-ylo,0); [c] = (0,0,zhi-zlo). The 6 parameters
(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box
is created, e.g. by the "create_box"_create_box.html or
"read_data"_read_data.html or "read_restart"_read_restart.html
commands. Additionally, LAMMPS defines box size parameters lx,ly,lz
where lx = xhi-xlo, and similarly in the y and z dimensions. The 6
parameters, as well as lx,ly,lz, can be output via the "thermo_style
custom"_thermo_style.html command.
LAMMPS also allows simulations to be performed in triclinic
(non-orthogonal) simulation boxes shaped as a parallelepiped with
triclinic symmetry. The parallelepiped has its "origin" at
(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the
origin given by [a] = (xhi-xlo,0,0); [b] = (xy,yhi-ylo,0); [c] =
(xz,yz,zhi-zlo). {xy,xz,yz} can be 0.0 or positive or negative values
and are called "tilt factors" because they are the amount of
displacement applied to faces of an originally orthogonal box to
transform it into the parallelepiped. In LAMMPS the triclinic
simulation box edge vectors [a], [b], and [c] cannot be arbitrary
vectors. As indicated, [a] must lie on the positive x axis. [b] must
lie in the xy plane, with strictly positive y component. [c] may have
any orientation with strictly positive z component. The requirement
that [a], [b], and [c] have strictly positive x, y, and z components,
respectively, ensures that [a], [b], and [c] form a complete
right-handed basis. These restrictions impose no loss of generality,
since it is possible to rotate/invert any set of 3 crystal basis
vectors so that they conform to the restrictions.
For example, assume that the 3 vectors [A],[B],[C] are the edge
vectors of a general parallelepiped, where there is no restriction on
[A],[B],[C] other than they form a complete right-handed basis i.e.
[A] x [B] . [C] > 0. The equivalent LAMMPS [a],[b],[c] are a linear
rotation of [A], [B], and [C] and can be computed as follows:
:c,image(Eqs/transform.jpg)
where A = |[A]| indicates the scalar length of [A]. The ^ hat symbol
indicates the corresponding unit vector. {beta} and {gamma} are angles
between the vectors described below. Note that by construction,
[a], [b], and [c] have strictly positive x, y, and z components, respectively.
If it should happen that
[A], [B], and [C] form a left-handed basis, then the above equations
are not valid for [c]. In this case, it is necessary
to first apply an inversion. This can be achieved
by interchanging two basis vectors or by changing the sign of one of them.
For consistency, the same rotation/inversion applied to the basis vectors
must also be applied to atom positions, velocities,
and any other vector quantities.
This can be conveniently achieved by first converting to
fractional coordinates in the
old basis and then converting to distance coordinates in the new basis.
The transformation is given by the following equation:
:c,image(Eqs/rotate.jpg)
where {V} is the volume of the box, [X] is the original vector quantity and
[x] is the vector in the LAMMPS basis.
There is no requirement that a triclinic box be periodic in any
dimension, though it typically should be in at least the 2nd dimension
of the tilt (y in xy) if you want to enforce a shift in periodic
boundary conditions across that boundary. Some commands that work
with triclinic boxes, e.g. the "fix deform"_fix_deform.html and "fix
npt"_fix_nh.html commands, require periodicity or non-shrink-wrap
boundary conditions in specific dimensions. See the command doc pages
for details.
The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
time the simluation box is created. This happens in one of 3 ways.
If the "create_box"_create_box.html command is used with a region of
style {prism}, then a triclinic box is setup. See the
"region"_region.html command for details. If the
"read_data"_read_data.html command is used to define the simulation
box, and the header of the data file contains a line with the "xy xz
yz" keyword, then a triclinic box is setup. See the
"read_data"_read_data.html command for details. Finally, if the
"read_restart"_read_restart.html command reads a restart file which
was written from a simulation using a triclinic box, then a triclinic
box will be setup for the restarted simulation.
Note that you can define a triclinic box with all 3 tilt factors =
0.0, so that it is initially orthogonal. This is necessary if the box
will become non-orthogonal, e.g. due to the "fix npt"_fix_nh.html or
"fix deform"_fix_deform.html commands. Alternatively, you can use the
"change_box"_change_box.html command to convert a simulation box from
orthogonal to triclinic and vice versa.
As with orthogonal boxes, LAMMPS defines triclinic box size parameters
lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions.
The 9 parameters, as well as lx,ly,lz, can be output via the
"thermo_style custom"_thermo_style.html command.
To avoid extremely tilted boxes (which would be computationally
inefficient), LAMMPS normally requires that no tilt factor can skew
the box more than half the distance of the parallel box length, which
is the 1st dimension in the tilt factor (x for xz). This is required
both when the simulation box is created, e.g. via the
"create_box"_create_box.html or "read_data"_read_data.html commands,
as well as when the box shape changes dynamically during a simulation,
e.g. via the "fix deform"_fix_deform.html or "fix npt"_fix_nh.html
commands.
For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
the xy tilt factor must be between -5 and 5. Similarly, both xz and
yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is
not a limitation, since if the maximum tilt factor is 5 (as in this
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
... are geometrically all equivalent. If the box tilt exceeds this
limit during a dynamics run (e.g. via the "fix deform"_fix_deform.html
command), then the box is "flipped" to an equivalent shape with a tilt
factor within the bounds, so the run can continue. See the "fix
deform"_fix_deform.html doc page for further details.
One exception to this rule is if the 1st dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this
mode, if you tilt the system to extreme angles, the simulation will
simply become inefficient, due to the highly skewed simulation box.
The limitation on not creating a simulation box with a tilt factor
skewing the box more than half the distance of the parallel box length
can be overridden via the "box"_box.html command. Setting the {tilt}
keyword to {large} allows any tilt factors to be specified.
Box flips that may occur using the "fix deform"_fix_deform.html or
"fix npt"_fix_nh.html commands can be turned off using the {flip no}
option with either of the commands.
Note that if a simulation box has a large tilt factor, LAMMPS will run
less efficiently, due to the large volume of communication needed to
acquire ghost atoms around a processor's irregular-shaped sub-domain.
For extreme values of tilt, LAMMPS may also lose atoms and generate an
error.
Triclinic crystal structures are often defined using three lattice
constants {a}, {b}, and {c}, and three angles {alpha}, {beta} and
{gamma}. Note that in this nomenclature, the a, b, and c lattice
constants are the scalar lengths of the edge vectors [a], [b], and [c]
defined above. The relationship between these 6 quantities
(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) =
(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
:c,image(Eqs/box.jpg)
The inverse relationship can be written as follows:
:c,image(Eqs/box_inverse.jpg)
The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed
out or accessed by computes using the
"thermo_style custom"_thermo_style.html keywords
{cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma},
respectively.
As discussed on the "dump"_dump.html command doc page, when the BOX
BOUNDS for a snapshot is written to a dump file for a triclinic box,
an orthogonal bounding box which encloses the triclinic simulation box
is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
box, formatted as follows:
ITEM: BOX BOUNDS xy xz yz
xlo_bound xhi_bound xy
ylo_bound yhi_bound xz
zlo_bound zhi_bound yz :pre
This bounding box is convenient for many visualization programs and is
calculated from the 9 triclinic box parameters
(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:
xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
ylo_bound = ylo + MIN(0.0,yz)
yhi_bound = yhi + MAX(0.0,yz)
zlo_bound = zlo
zhi_bound = zhi :pre
These formulas can be inverted if you need to convert the bounding box
back into the triclinic box parameters, e.g. xlo = xlo_bound -
MIN(0.0,xy,xz,xy+xz).
One use of triclinic simulation boxes is to model solid-state crystals
with triclinic symmetry. The "lattice"_lattice.html command can be
used with non-orthogonal basis vectors to define a lattice that will
tile a triclinic simulation box via the
"create_atoms"_create_atoms.html command.
A second use is to run Parinello-Rahman dyanamics via the "fix
npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt
factors to compensate for off-diagonal components of the pressure
tensor. The analalog for an "energy minimization"_minimize.html is
the "fix box/relax"_fix_box_relax.html command.
A third use is to shear a bulk solid to study the response of the
material. The "fix deform"_fix_deform.html command can be used for
this purpose. It allows dynamic control of the xy, xz, yz tilt
factors as a simulation runs. This is discussed in the next section
on non-equilibrium MD (NEMD) simulations.
:line
6.13 NEMD simulations :link(howto_13),h4
Non-equilibrium molecular dynamics or NEMD simulations are typically
used to measure a fluid's rheological properties such as viscosity.
In LAMMPS, such simulations can be performed by first setting up a
non-orthogonal simulation box (see the preceding Howto section).
A shear strain can be applied to the simulation box at a desired
strain rate by using the "fix deform"_fix_deform.html command. The
"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat
the sheared fluid and integrate the SLLOD equations of motion for the
system. Fix nvt/sllod uses "compute
temp/deform"_compute_temp_deform.html to compute a thermal temperature
by subtracting out the streaming velocity of the shearing atoms. The
velocity profile or other properties of the fluid can be monitored via
the "fix ave/spatial"_fix_ave_spatial.html command.
As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by
LAMMPS for computational efficiency to be 1/2 of the parallel box
length. However, "fix deform"_fix_deform.html can continuously strain
a box by an arbitrary amount. As discussed in the "fix
deform"_fix_deform.html command, when the tilt value reaches a limit,
the box is flipped to the opposite limit which is an equivalent tiling
of periodic space. The strain rate can then continue to change as
before. In a long NEMD simulation these box re-shaping events may
occur many times.
In a NEMD simulation, the "remap" option of "fix
deform"_fix_deform.html should be set to "remap v", since that is what
"fix nvt/sllod"_fix_nvt_sllod.html assumes to generate a velocity
profile consistent with the applied shear strain rate.
An alternative method for calculating viscosities is provided via the
"fix viscosity"_fix_viscosity.html command.
:line
6.14 Finite-size spherical and aspherical particles :link(howto_14),h4
Typical MD models treat atoms or particles as point masses. Sometimes
it is desirable to have a model with finite-size particles such as
spheroids or ellipsoids or generalized aspherical bodies. The
difference is that such particles have a moment of inertia, rotational
energy, and angular momentum. Rotation is induced by torque coming
from interactions with other particles.
LAMMPS has several options for running simulations with these kinds of
particles. The following aspects are discussed in turn:
atom styles
pair potentials
time integration
computes, thermodynamics, and dump output
rigid bodies composed of finite-size particles :ul
Example input scripts for these kinds of models are in the body,
colloid, dipole, ellipse, line, peri, pour, and tri directories of the
"examples directory"_Section_example.html in the LAMMPS distribution.
Atom styles :h5
There are several "atom styles"_atom_style.html that allow for
definition of finite-size particles: sphere, dipole, ellipsoid, line,
tri, peri, and body.
The sphere style defines particles that are spheriods and each
particle can have a unique diameter and mass (or density). These
particles store an angular velocity (omega) and can be acted upon by
torque. The "set" command can be used to modify the diameter and mass
of individual particles, after then are created.
The dipole style does not actually define finite-size particles, but
is often used in conjunction with spherical particles, via a command
like
atom_style hybrid sphere dipole :pre
This is because when dipoles interact with each other, they induce
torques, and a particle must be finite-size (i.e. have a moment of
inertia) in order to respond and rotate. See the "atom_style
dipole"_atom_style.html command for details. The "set" command can be
used to modify the orientation and length of the dipole moment of
individual particles, after then are created.
The ellipsoid style defines particles that are ellipsoids and thus can
be aspherical. Each particle has a shape, specified by 3 diameters,
and mass (or density). These particles store an angular momentum and
their orientation (quaternion), and can be acted upon by torque. They
do not store an angular velocity (omega), which can be in a different
direction than angular momentum, rather they compute it as needed.
The "set" command can be used to modify the diameter, orientation, and
mass of individual particles, after then are created. It also has a
brief explanation of what quaternions are.
The line style defines line segment particles with two end points and
a mass (or density). They can be used in 2d simulations, and they can
be joined together to form rigid bodies which represent arbitrary
polygons.
The tri style defines triangular particles with three corner points
and a mass (or density). They can be used in 3d simulations, and they
can be joined together to form rigid bodies which represent arbitrary
particles with a triangulated surface.
The peri style is used with "Peridynamic models"_pair_peri.html and
defines particles as having a volume, that is used internally in the
"pair_style peri"_pair_peri.html potentials.
The body style allows for definition of particles which can represent
complex entities, such as surface meshes of discrete points,
collections of sub-particles, deformable objects, etc. The body style
is discussed in more detail on the "body"_body.html doc page.
Note that if one of these atom styles is used (or multiple styles via
the "atom_style hybrid"_atom_style.html command), not all particles in
the system are required to be finite-size or aspherical.
For example, in the ellipsoid style, if the 3 shape parameters are set
to the same value, the particle will be a sphere rather than an
ellipsoid. If the 3 shape parameters are all set to 0.0 or if the
diameter is set to 0.0, it will be a point particle. In the line or
tri style, if the lineflag or triflag is specified as 0, then it
will be a point particle.
Some of the pair styles used to compute pairwise interactions between
finite-size particles also compute the correct interaction with point
particles as well, e.g. the interaction between a point particle and a
finite-size particle or between two point particles. If necessary,
"pair_style hybrid"_pair_hybrid.html can be used to insure the correct
interactions are computed for the appropriate style of interactions.
Likewise, using groups to partition particles (ellipsoids versus
spheres versus point particles) will allow you to use the appropriate
time integrators and temperature computations for each class of
particles. See the doc pages for various commands for details.
Also note that for "2d simulations"_dimension.html, atom styles sphere
and ellipsoid still use 3d particles, rather than as circular disks or
ellipses. This means they have the same moment of inertia as the 3d
object. When temperature is computed, the correct degrees of freedom
are used for rotation in a 2d versus 3d system.
Pair potentials :h5
When a system with finite-size particles is defined, the particles
will only rotate and experience torque if the force field computes
such interactions. These are the various "pair
styles"_pair_style.html that generate torque:
"pair_style gran/history"_pair_gran.html
"pair_style gran/hertzian"_pair_gran.html
"pair_style gran/no_history"_pair_gran.html
"pair_style dipole/cut"_pair_dipole.html
"pair_style gayberne"_pair_gayberne.html
"pair_style resquared"_pair_resquared.html
"pair_style brownian"_pair_brownian.html
"pair_style lubricate"_pair_lubricate.html
"pair_style line/lj"_pair_line_lj.html
"pair_style tri/lj"_pair_tri_lj.html
"pair_style body"_pair_body.html :ul
The granular pair styles are used with spherical particles. The
dipole pair style is used with the dipole atom style, which could be
applied to spherical or ellipsoidal particles. The GayBerne and
REsquared potentials require ellipsoidal particles, though they will
also work if the 3 shape parameters are the same (a sphere). The
Brownian and lubrication potentials are used with spherical particles.
The line, tri, and body potentials are used with line segment,
triangular, and body particles respectively.
Time integration :h5
There are several fixes that perform time integration on finite-size
spherical particles, meaning the integrators update the rotational
orientation and angular velocity or angular momentum of the particles:
"fix nve/sphere"_fix_nve_sphere.html
"fix nvt/sphere"_fix_nvt_sphere.html
"fix npt/sphere"_fix_npt_sphere.html :ul
Likewise, there are 3 fixes that perform time integration on
ellipsoidal particles:
"fix nve/asphere"_fix_nve_asphere.html
"fix nvt/asphere"_fix_nvt_asphere.html
"fix npt/asphere"_fix_npt_asphere.html :ul
The advantage of these fixes is that those which thermostat the
particles include the rotational degrees of freedom in the temperature
calculation and thermostatting. The "fix langevin"_fix_langevin
command can also be used with its {omgea} or {angmom} options to
thermostat the rotational degrees of freedom for spherical or
ellipsoidal particles. Other thermostatting fixes only operate on the
translational kinetic energy of finite-size particles.
These fixes perform constant NVE time integration on line segment,
triangular, and body particles:
"fix nve/line"_fix_nve_line.html
"fix nve/tri"_fix_nve_tri.html
"fix nve/body"_fix_nve_body.html :ul
Note that for mixtures of point and finite-size particles, these
integration fixes can only be used with "groups"_group.html which
contain finite-size particles.
Computes, thermodynamics, and dump output :h5
There are several computes that calculate the temperature or
rotational energy of spherical or ellipsoidal particles:
"compute temp/sphere"_compute_temp_sphere.html
"compute temp/asphere"_compute_temp_asphere.html
"compute erotate/sphere"_compute_erotate_sphere.html
"compute erotate/asphere"_compute_erotate_asphere.html :ul
These include rotational degrees of freedom in their computation. If
you wish the thermodynamic output of temperature or pressure to use
one of these computes (e.g. for a system entirely composed of
finite-size particles), then the compute can be defined and the
"thermo_modify"_thermo_modify.html command used. Note that by default
thermodynamic quantities will be calculated with a temperature that
only includes translational degrees of freedom. See the
"thermo_style"_thermo_style.html command for details.
These commands can be used to output various attributes of finite-size
particles:
"dump custom"_dump.html
"compute property/atom"_compute_property_atom.html
"dump local"_dump.html
"compute body/local"_compute_body_local.html :ul
Attributes include the dipole moment, the angular velocity, the
angular momentum, the quaternion, the torque, the end-point and
corner-point coordinates (for line and tri particles), and
sub-particle attributes of body particles.
Rigid bodies composed of finite-size particles :h5
The "fix rigid"_fix_rigid.html command treats a collection of
particles as a rigid body, computes its inertia tensor, sums the total
force and torque on the rigid body each timestep due to forces on its
constituent particles, and integrates the motion of the rigid body.
If any of the constituent particles of a rigid body are finite-size
particles (spheres or ellipsoids or line segments or triangles), then
their contribution to the inertia tensor of the body is different than
if they were point particles. This means the rotational dynamics of
the rigid body will be different. Thus a model of a dimer is
different if the dimer consists of two point masses versus two
spheroids, even if the two particles have the same mass. Finite-size
particles that experience torque due to their interaction with other
particles will also impart that torque to a rigid body they are part
of.
See the "fix rigid" command for example of complex rigid-body models
it is possible to define in LAMMPS.
Note that the "fix shake"_fix_shake.html command can also be used to
treat 2, 3, or 4 particles as a rigid body, but it always assumes the
particles are point masses.
Also note that body particles cannot be modeled with the "fix
rigid"_fix_rigid.html command. Body particles are treated by LAMMPS
as single particles, though they can store internal state, such as a
list of sub-particles. Individual body partices are typically treated
as rigid bodies, and their motion integrated with a command like "fix
nve/body"_fix_nve_body.html. Interactions between pairs of body
particles are computed via a command like "pair_style
body"_pair_body.html.
:line
6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables) :link(howto_15),h4
There are four basic kinds of LAMMPS output:
"Thermodynamic output"_thermo_style.html, which is a list
of quantities printed every few timesteps to the screen and logfile. :ulb,l
"Dump files"_dump.html, which contain snapshots of atoms and various
per-atom values and are written at a specified frequency. :l
Certain fixes can output user-specified quantities to files: "fix
ave/time"_fix_ave_time.html for time averaging, "fix
ave/spatial"_fix_ave_spatial.html for spatial averaging, and "fix
print"_fix_print.html for single-line output of
"variables"_variable.html. Fix print can also output to the
screen. :l
"Restart files"_restart.html. :l,ule
A simulation prints one set of thermodynamic output and (optionally)
restart files. It can generate any number of dump files and fix
output files, depending on what "dump"_dump.html and "fix"_fix.html
commands you specify.
As discussed below, LAMMPS gives you a variety of ways to determine
what quantities are computed and printed when the thermodynamics,
dump, or fix commands listed above perform output. Throughout this
discussion, note that users can also "add their own computes and fixes
to LAMMPS"_Section_modify.html which can then generate values that can
then be output with these commands.
The following sub-sections discuss different LAMMPS command related
to output and the kind of data they operate on and produce:
"Global/per-atom/local data"_#global
"Scalar/vector/array data"_#scalar
"Thermodynamic output"_#thermo
"Dump file output"_#dump
"Fixes that write output files"_#fixoutput
"Computes that process output quantities"_#computeoutput
"Fixes that process output quantities"_#fixoutput
"Computes that generate values to output"_#compute
"Fixes that generate values to output"_#fix
"Variables that generate values to output"_#variable
"Summary table of output options and data flow between commands"_#table :ul
Global/per-atom/local data :h5,link(global)
Various output-related commands work with three different styles of
data: global, per-atom, or local. A global datum is one or more
system-wide values, e.g. the temperature of the system. A per-atom
datum is one or more values per atom, e.g. the kinetic energy of each
atom. Local datums are calculated by each processor based on the
atoms it owns, but there may be zero or more per atom, e.g. a list of
bond distances.
Scalar/vector/array data :h5,link(scalar)
Global, per-atom, and local datums can each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The
doc page for a "compute" or "fix" or "variable" that generates data
will specify both the style and kind of data it produces, e.g. a
per-atom vector.
When a quantity is accessed, as in many of the output commands
discussed below, it can be referenced via the following bracket
notation, where ID in this case is the ID of a compute. The leading
"c_" would be replaced by "f_" for a fix, or "v_" for a variable:
c_ID | entire scalar, vector, or array
c_ID\[I\] | one element of vector, one column of array
c_ID\[I\]\[J\] | one element of array :tb(s=|)
In other words, using one bracket reduces the dimension of the data
once (vector -> scalar, array -> vector). Using two brackets reduces
the dimension twice (array -> scalar). Thus a command that uses
scalar values as input can typically also process elements of a vector
or array.
Thermodynamic output :h5,link(thermo)
The frequency and format of thermodynamic output is set by the
"thermo"_thermo.html, "thermo_style"_thermo_style.html, and
"thermo_modify"_thermo_modify.html commands. The
"thermo_style"_thermo_style.html command also specifies what values
are calculated and written out. Pre-defined keywords can be specified
(e.g. press, etotal, etc). Three additional kinds of keywords can
also be specified (c_ID, f_ID, v_name), where a "compute"_compute.html
or "fix"_fix.html or "variable"_variable.html provides the value to be
output. In each case, the compute, fix, or variable must generate
global values for input to the "thermo_style custom"_dump.html
command.
Note that thermodynamic output values can be "extensive" or
"intensive". The former scale with the number of atoms in the system
(e.g. total energy), the latter do not (e.g. temperature). The
setting for "thermo_modify norm"_thermo_modify.html determines whether
extensive quantities are normalized or not. Computes and fixes
produce either extensive or intensive values; see their individual doc
pages for details. "Equal-style variables"_variable.html produce only
intensive values; you can include a division by "natoms" in the
formula if desired, to make an extensive calculation produce an
intensive result.
Dump file output :h5,link(dump)
Dump file output is specified by the "dump"_dump.html and
"dump_modify"_dump_modify.html commands. There are several
pre-defined formats (dump atom, dump xtc, etc).
There is also a "dump custom"_dump.html format where the user
specifies what values are output with each atom. Pre-defined atom
attributes can be specified (id, x, fx, etc). Three additional kinds
of keywords can also be specified (c_ID, f_ID, v_name), where a
"compute"_compute.html or "fix"_fix.html or "variable"_variable.html
provides the values to be output. In each case, the compute, fix, or
variable must generate per-atom values for input to the "dump
custom"_dump.html command.
There is also a "dump local"_dump.html format where the user specifies
what local values to output. A pre-defined index keyword can be
specified to enumuerate the local values. Two additional kinds of
keywords can also be specified (c_ID, f_ID), where a
"compute"_compute.html or "fix"_fix.html or "variable"_variable.html
provides the values to be output. In each case, the compute or fix
must generate local values for input to the "dump local"_dump.html
command.
Fixes that write output files :h5,link(fixoutput)
Several fixes take various quantities as input and can write output
files: "fix ave/time"_fix_ave_time.html, "fix
ave/spatial"_fix_ave_spatial.html, "fix ave/histo"_fix_ave_histo.html,
"fix ave/correlate"_fix_ave_correlate.html, and "fix
print"_fix_print.html.
The "fix ave/time"_fix_ave_time.html command enables direct output to
a file and/or time-averaging of global scalars or vectors. The user
specifies one or more quantities as input. These can be global
"compute"_compute.html values, global "fix"_fix.html values, or
"variables"_variable.html of any style except the atom style which
produces per-atom values. Since a variable can refer to keywords used
by the "thermo_style custom"_thermo_style.html command (like temp or
press) and individual per-atom values, a wide variety of quantities
can be time averaged and/or output in this way. If the inputs are one
or more scalar values, then the fix generate a global scalar or vector
of output. If the inputs are one or more vector values, then the fix
generates a global vector or array of output. The time-averaged
output of this fix can also be used as input to other output commands.
The "fix ave/spatial"_fix_ave_spatial.html command enables direct
output to a file of spatial-averaged per-atom quantities like those
output in dump files, within 1d layers of the simulation box. The
per-atom quantities can be atom density (mass or number) or atom
attributes such as position, velocity, force. They can also be
per-atom quantities calculated by a "compute"_compute.html, by a
"fix"_fix.html, or by an atom-style "variable"_variable.html. The
spatial-averaged output of this fix can also be used as input to other
output commands.
The "fix ave/histo"_fix_ave_histo.html command enables direct output
to a file of histogrammed quantities, which can be global or per-atom
or local quantities. The histogram output of this fix can also be
used as input to other output commands.
The "fix ave/correlate"_fix_ave_correlate.html command enables direct
output to a file of time-correlated quantities, which can be global
scalars. The correlation matrix output of this fix can also be used
as input to other output commands.
The "fix print"_fix_print.html command can generate a line of output
written to the screen and log file or to a separate file, periodically
during a running simulation. The line can contain one or more
"variable"_variable.html values for any style variable except the atom
style). As explained above, variables themselves can contain
references to global values generated by "thermodynamic
keywords"_thermo_style.html, "computes"_compute.html,
"fixes"_fix.html, or other "variables"_variable.html, or to per-atom
values for a specific atom. Thus the "fix print"_fix_print.html
command is a means to output a wide variety of quantities separate
from normal thermodynamic or dump file output.
Computes that process output quantities :h5,link(computeoutput)
The "compute reduce"_compute_reduce.html and "compute
reduce/region"_compute_reduce.html commands take one or more per-atom
or local vector quantities as inputs and "reduce" them (sum, min, max,
ave) to scalar quantities. These are produced as output values which
can be used as input to other output commands.
The "compute slice"_compute_slice.html command take one or more global
vector or array quantities as inputs and extracts a subset of their
values to create a new vector or array. These are produced as output
values which can be used as input to other output commands.
The "compute property/atom"_compute_property_atom.html command takes a
list of one or more pre-defined atom attributes (id, x, fx, etc) and
stores the values in a per-atom vector or array. These are produced
as output values which can be used as input to other output commands.
The list of atom attributes is the same as for the "dump
custom"_dump.html command.
The "compute property/local"_compute_property_local.html command takes
a list of one or more pre-defined local attributes (bond info, angle
info, etc) and stores the values in a local vector or array. These
are produced as output values which can be used as input to other
output commands.
Fixes that process output quantities :h5,link(fixoutput)
The "fix vector"_fix_vector.html command can create global vectors as
output from global scalars as input, accumulating them one element at
a time.
The "fix ave/atom"_fix_ave_atom.html command performs time-averaging
of per-atom vectors. The per-atom quantities can be atom attributes
such as position, velocity, force. They can also be per-atom
quantities calculated by a "compute"_compute.html, by a
"fix"_fix.html, or by an atom-style "variable"_variable.html. The
time-averaged per-atom output of this fix can be used as input to
other output commands.
The "fix store/state"_fix_store_state.html command can archive one or
more per-atom attributes at a particular time, so that the old values
can be used in a future calculation or output. The list of atom
attributes is the same as for the "dump custom"_dump.html command,
including per-atom quantities calculated by a "compute"_compute.html,
by a "fix"_fix.html, or by an atom-style "variable"_variable.html.
The output of this fix can be used as input to other output commands.
Computes that generate values to output :h5,link(compute)
Every "compute"_compute.html in LAMMPS produces either global or
per-atom or local values. The values can be scalars or vectors or
arrays of data. These values can be output using the other commands
described in this section. The doc page for each compute command
describes what it produces. Computes that produce per-atom or local
values have the word "atom" or "local" in their style name. Computes
without the word "atom" or "local" produce global values.
Fixes that generate values to output :h5,link(fix)
Some "fixes"_fix.html in LAMMPS produces either global or per-atom or
local values which can be accessed by other commands. The values can
be scalars or vectors or arrays of data. These values can be output
using the other commands described in this section. The doc page for
each fix command tells whether it produces any output quantities and
describes them.
Variables that generate values to output :h5,link(variable)
Every "variables"_variable.html defined in an input script generates
either a global scalar value or a per-atom vector (only atom-style
variables) when it is accessed. The formulas used to define equal-
and atom-style variables can contain references to the thermodynamic
keywords and to global and per-atom data generated by computes, fixes,
and other variables. The values generated by variables can be output
using the other commands described in this section.
Summary table of output options and data flow between commands :h5,link(table)
This table summarizes the various commands that can be used for
generating output from LAMMPS. Each command produces output data of
some kind and/or writes data to a file. Most of the commands can take
data from other commands as input. Thus you can link many of these
commands together in pipeline form, where data produced by one command
is used as input to another command and eventually written to the
screen or to a file. Note that to hook two commands together the
output and input data types must match, e.g. global/per-atom/local
data and scalar/vector/array data.
Also note that, as described above, when a command takes a scalar as
input, that could be an element of a vector or array. Likewise a
vector input could be a column of an array.
Command: Input: Output:
"thermo_style custom"_thermo_style.html: global scalars: screen, log file:
"dump custom"_dump.html: per-atom vectors: dump file:
"dump local"_dump.html: local vectors: dump file:
"fix print"_fix_print.html: global scalar from variable: screen, file:
"print"_print.html: global scalar from variable: screen:
"computes"_compute.html: N/A: global/per-atom/local scalar/vector/array:
"fixes"_fix.html: N/A: global/per-atom/local scalar/vector/array:
"variables"_variable.html: global scalars, per-atom vectors: global scalar, per-atom vector:
"compute reduce"_compute_reduce.html: per-atom/local vectors: global scalar/vector:
"compute slice"_compute_slice.html: global vectors/arrays: global vector/array:
"compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array:
"compute property/local"_compute_property_local.html: local vectors: local vector/array:
"fix vector"_fix_vector.html: global scalars: global vector:
"fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array:
"fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file:
"fix ave/spatial"_fix_ave_spatial.html: per-atom vectors: global array, file:
"fix ave/histo"_fix_ave_histo.html: global/per-atom/local scalars and vectors: global array, file:
"fix ave/correlate"_fix_ave_correlate.html: global scalars: global array, file:
"fix store/state"_fix_store_state.html: per-atom vectors: per-atom vector/array:
:tb(s=:)
:line
6.16 Thermostatting, barostatting, and computing temperature :link(howto_16),h4
Thermostatting means controlling the temperature of particles in an MD
simulation. Barostatting means controlling the pressure. Since the
pressure includes a kinetic component due to particle velocities, both
these operations require calculation of the temperature. Typically a
target temperature (T) and/or pressure (P) is specified by the user,
and the thermostat or barostat attempts to equilibrate the system to
the requested T and/or P.
Temperature is computed as kinetic energy divided by some number of
degrees of freedom (and the Boltzmann constant). Since kinetic energy
is a function of particle velocity, there is often a need to
distinguish between a particle's advection velocity (due to some
aggregate motiion of particles) and its thermal velocity. The sum of
the two is the particle's total velocity, but the latter is often what
is wanted to compute a temperature.
LAMMPS has several options for computing temperatures, any of which
can be used in thermostatting and barostatting. These "compute
commands"_compute.html calculate temperature, and the "compute
pressure"_compute_pressure.html command calculates pressure.
"compute temp"_compute_temp.html
"compute temp/sphere"_compute_temp_sphere.html
"compute temp/asphere"_compute_temp_asphere.html
"compute temp/com"_compute_temp_com.html
"compute temp/deform"_compute_temp_deform.html
"compute temp/partial"_compute_temp_partial.html
"compute temp/profile"_compute_temp_profile.html
"compute temp/ramp"_compute_temp_ramp.html
"compute temp/region"_compute_temp_region.html :ul
All but the first 3 calculate velocity biases directly (e.g. advection
velocities) that are removed when computing the thermal temperature.
"Compute temp/sphere"_compute_temp_sphere.html and "compute
temp/asphere"_compute_temp_asphere.html compute kinetic energy for
finite-size particles that includes rotational degrees of freedom.
They both allow for velocity biases indirectly, via an optional extra
argument, another temperature compute that subtracts a velocity bias.
This allows the translational velocity of spherical or aspherical
particles to be adjusted in prescribed ways.
Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one
case by a pair style. Several thermostatting fixes are available:
Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling
(temp/rescale). Dissipative particle dynamics (DPD) thermostatting
can be invoked via the {dpd/tstat} pair style:
"fix nvt"_fix_nh.html
"fix nvt/sphere"_fix_nvt_sphere.html
"fix nvt/asphere"_fix_nvt_asphere.html
"fix nvt/sllod"_fix_nvt_sllod.html
"fix temp/berendsen"_fix_temp_berendsen.html
"fix temp/csvr"_fix_temp_csvr.html
"fix langevin"_fix_langevin.html
"fix temp/rescale"_fix_temp_rescale.html
"pair_style dpd/tstat"_pair_dpd.html :ul
"Fix nvt"_fix_nh.html only thermostats the translational velocity of
particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except
that it subtracts out a velocity bias due to a deforming box and
integrates the SLLOD equations of motion. See the "NEMD
simulations"_#howto_13 section of this page for further details. "Fix
nvt/sphere"_fix_nvt_sphere.html and "fix
nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
particles.
DPD thermostatting alters pairwise interactions in a manner analagous
to the per-particle thermostatting of "fix
langevin"_fix_langevin.html.
Any of the thermostatting fixes can use temperature computes that
remove bias which has two effects. First, the current calculated
temperature, which is compared to the requested target temperature, is
caluclated with the velocity bias removed. Second, the thermostat
adjusts only the thermal temperature component of the particle's
velocities, which are the velocities with the bias removed. The
removed bias is then added back to the adjusted velocities. See the
doc pages for the individual fixes and for the
"fix_modify"_fix_modify.html command for instructions on how to assign
a temperature compute to a thermostatting fix. For example, you can
apply a thermostat to only the x and z components of velocity by using
it in conjunction with "compute
temp/partial"_compute_temp_partial.html. Of you could thermostat only
the thermal temperature of a streaming flow of particles without
affecting the streaming velocity, by using "compute
temp/profile"_compute_temp_profile.html.
IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
they update the velocities and positions of particles due to forces
and velocities respectively. The other thermostat fixes only adjust
velocities; they do NOT perform time integration updates. Thus they
should be used in conjunction with a constant NVE integration fix such
as these:
"fix nve"_fix_nve.html
"fix nve/sphere"_fix_nve_sphere.html
"fix nve/asphere"_fix_nve_asphere.html :ul
Barostatting in LAMMPS is also performed by "fixes"_fix.html. Two
barosttating methods are currently available: Nose-Hoover (npt and
nph) and Berendsen:
"fix npt"_fix_nh.html
"fix npt/sphere"_fix_npt_sphere.html
"fix npt/asphere"_fix_npt_asphere.html
"fix nph"_fix_nh.html
"fix press/berendsen"_fix_press_berendsen.html :ul
The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat
and barostat. "Fix nph"_fix_nh.html is just a Nose/Hoover barostat;
it does no thermostatting. Both "fix nph"_fix_nh.html and "fix
press/bernendsen"_fix_press_berendsen.html can be used in conjunction
with any of the thermostatting fixes.
As with the thermostats, "fix npt"_fix_nh.html and "fix
nph"_fix_nh.html only use translational motion of the particles in
computing T and P and performing thermo/barostatting. "Fix
npt/sphere"_fix_npt_sphere.html and "fix
npt/asphere"_fix_npt_asphere.html thermo/barostat using not only
translation velocities but also rotational velocities for spherical
and aspherical particles.
All of the barostatting fixes use the "compute
pressure"_compute_pressure.html compute to calculate a current
pressure. By default, this compute is created with a simple "compute
temp"_compute_temp.html (see the last argument of the "compute
pressure"_compute_pressure.html command), which is used to calculated
the kinetic componenet of the pressure. The barostatting fixes can
also use temperature computes that remove bias for the purpose of
computing the kinetic componenet which contributes to the current
pressure. See the doc pages for the individual fixes and for the
"fix_modify"_fix_modify.html command for instructions on how to assign
a temperature or pressure compute to a barostatting fix.
IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods ("fix
npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time
integration. "Fix press/berendsen"_fix_press_berendsen.html does NOT,
so it should be used with one of the constant NVE fixes or with one of
the NVT fixes.
Finally, thermodynamic output, which can be setup via the
"thermo_style"_thermo_style.html command, often includes temperature
and pressure values. As explained on the doc page for the
"thermo_style"_thermo_style.html command, the default T and P are
setup by the thermo command itself. They are NOT the ones associated
with any thermostatting or barostatting fix you have defined or with
any compute that calculates a temperature or pressure. Thus if you
want to view these values of T and P, you need to specify them
explicitly via a "thermo_style custom"_thermo_style.html command. Or
you can use the "thermo_modify"_thermo_modify.html command to
re-define what temperature or pressure compute is used for default
thermodynamic output.
:line
6.17 Walls :link(howto_17),h4
Walls in an MD simulation are typically used to bound particle motion,
i.e. to serve as a boundary condition.
Walls in LAMMPS can be of rough (made of particles) or idealized
surfaces. Ideal walls can be smooth, generating forces only in the
normal direction, or frictional, generating forces also in the
tangential direction.
Rough walls, built of particles, can be created in various ways. The
particles themselves can be generated like any other particle, via the
"lattice"_lattice.html and "create_atoms"_create_atoms.html commands,
or read in via the "read_data"_read_data.html command.
Their motion can be constrained by many different commands, so that
they do not move at all, move together as a group at constant velocity
or in response to a net force acting on them, move in a prescribed
fashion (e.g. rotate around a point), etc. Note that if a time
integration fix like "fix nve"_fix_nve.html or "fix nvt"_fix_nh.html
is not used with the group that contains wall particles, their
positions and velocities will not be updated.
"fix aveforce"_fix_aveforce.html - set force on particles to average value, so they move together
"fix setforce"_fix_setforce.html - set force on particles to a value, e.g. 0.0
"fix freeze"_fix_freeze.html - freeze particles for use as granular walls
"fix nve/noforce"_fix_nve_noforce.html - advect particles by their velocity, but without force
"fix move"_fix_move.html - prescribe motion of particles by a linear velocity, oscillation, rotation, variable :ul
The "fix move"_fix_move.html command offers the most generality, since
the motion of individual particles can be specified with
"variable"_variable.html formula which depends on time and/or the
particle position.
For rough walls, it may be useful to turn off pairwise interactions
between wall particles via the "neigh_modify
exclude"_neigh_modify.html command.
Rough walls can also be created by specifying frozen particles that do
not move and do not interact with mobile particles, and then tethering
other particles to the fixed particles, via a "bond"_bond_style.html.
The bonded particles do interact with other mobile particles.
Idealized walls can be specified via several fix commands. "Fix
wall/gran"_fix_wall_gran.html creates frictional walls for use with
granular particles; all the other commands create smooth walls.
"fix wall/reflect"_fix_wall_reflect.html - reflective flat walls
"fix wall/lj93"_fix_wall.html - flat walls, with Lennard-Jones 9/3 potential
"fix wall/lj126"_fix_wall.html - flat walls, with Lennard-Jones 12/6 potential
"fix wall/colloid"_fix_wall.html - flat walls, with "pair_style colloid"_pair_colloid.html potential
"fix wall/harmonic"_fix_wall.html - flat walls, with repulsive harmonic spring potential
"fix wall/region"_fix_wall_region.html - use region surface as wall
"fix wall/gran"_fix_wall_gran.html - flat or curved walls with "pair_style granular"_pair_gran.html potential :ul
The {lj93}, {lj126}, {colloid}, and {harmonic} styles all allow the
flat walls to move with a constant velocity, or oscillate in time.
The "fix wall/region"_fix_wall_region.html command offers the most
generality, since the region surface is treated as a wall, and the
geometry of the region can be a simple primitive volume (e.g. a
sphere, or cube, or plane), or a complex volume made from the union
and intersection of primitive volumes. "Regions"_region.html can also
specify a volume "interior" or "exterior" to the specified primitive
shape or {union} or {intersection}. "Regions"_region.html can also be
"dynamic" meaning they move with constant velocity, oscillate, or
rotate.
The only frictional idealized walls currently in LAMMPS are flat or
curved surfaces specified by the "fix wall/gran"_fix_wall_gran.html
command. At some point we plan to allow regoin surfaces to be used as
frictional walls, as well as triangulated surfaces.
:line
6.18 Elastic constants :link(howto_18),h4
Elastic constants characterize the stiffness of a material. The formal
definition is provided by the linear relation that holds between the
stress and strain tensors in the limit of infinitesimal deformation.
In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where
the repeated indices imply summation. s_ij are the elements of the
symmetric stress tensor. e_kl are the elements of the symmetric strain
tensor. C_ijkl are the elements of the fourth rank tensor of elastic
constants. In three dimensions, this tensor has 3^4=81 elements. Using
Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij
is now the derivative of s_i w.r.t. e_j. Because s_i is itself a
derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
most 7*6/2 = 21 distinct elements.
At zero temperature, it is easy to estimate these derivatives by
deforming the simulation box in one of the six directions using the
"change_box"_change_box.html command and measuring the change in the
stress tensor. A general-purpose script that does this is given in the
examples/elastic directory described in "this
section"_Section_example.html.
Calculating elastic constants at finite temperature is more
challenging, because it is necessary to run a simulation that perfoms
time averages of differential properties. One way to do this is to
measure the change in average stress tensor in an NVT simulations when
the cell volume undergoes a finite deformation. In order to balance
the systematic and statistical errors in this method, the magnitude of
the deformation must be chosen judiciously, and care must be taken to
fully equilibrate the deformed cell before sampling the stress
tensor. Another approach is to sample the triclinic cell fluctuations
that occur in an NPT simulation. This method can also be slow to
converge and requires careful post-processing "(Shinoda)"_#Shinoda
:line
6.19 Library interface to LAMMPS :link(howto_19),h4
As described in "Section_start 5"_Section_start.html#start_5, LAMMPS
can be built as a library, so that it can be called by another code,
used in a "coupled manner"_Section_howto.html#howto_10 with other
codes, or driven through a "Python interface"_Section_python.html.
All of these methodologies use a C-style interface to LAMMPS that is
provided in the files src/library.cpp and src/library.h. The
functions therein have a C-style argument list, but contain C++ code
you could write yourself in a C++ application that was invoking LAMMPS
directly. The C++ code in the functions illustrates how to invoke
internal LAMMPS operations. Note that LAMMPS classes are defined
within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
application.
Library.cpp contains these 5 basic functions:
void lammps_open(int, char **, MPI_Comm, void **)
void lammps_close(void *)
int lammps_version(void *)
void lammps_file(void *, char *)
char *lammps_command(void *, char *) :pre
The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were "command-line
arguments"_Section_start.html#start_7 when LAMMPS is run in
stand-alone mode from the command line, and a MPI communicator for
LAMMPS to run under. It returns a ptr to the LAMMPS object that is
created, and which is used in subsequent library calls. The
lammps_open() function can be called multiple times, to create
multiple instances of LAMMPS.
LAMMPS will run on the set of processors in the communicator. This
means the calling code can run LAMMPS on all or a subset of
processors. For example, a wrapper script might decide to alternate
between LAMMPS and another code, allowing them both to run on all the
processors. Or it might allocate half the processors to LAMMPS and
half to the other code and run both codes simultaneously before
syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.
The lammps_close() function is used to shut down an instance of LAMMPS
and free all its memory.
The lammps_version() function can be used to determined the specific
version of the underlying LAMMPS code. This is particularly useful
when loading LAMMPS as a shared library via dlopen(). The code using
the library interface can than use this information to adapt to
changes to the LAMMPS command syntax between versions. The returned
LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
20150902) that grows with every new LAMMPS version.
The lammps_file() and lammps_command() functions are used to pass a
file or string to LAMMPS as if it were an input script or single
command in an input script. Thus the calling code can read or
generate a series of LAMMPS commands one line at a time and pass it
thru the library interface to setup a problem and then run it,
interleaving the lammps_command() calls with other calls to extract
information from LAMMPS, perform its own operations, or call another
code's library.
Other useful functions are also included in library.cpp. For example:
void *lammps_extract_global(void *, char *)
void *lammps_extract_atom(void *, char *)
void *lammps_extract_compute(void *, char *, int, int)
void *lammps_extract_fix(void *, char *, int, int, int, int)
void *lammps_extract_variable(void *, char *, char *)
int lammps_set_variable(void *, char *, char *)
int lammps_get_natoms(void *)
void lammps_get_coords(void *, double *)
void lammps_put_coords(void *, double *) :pre
These can extract various global or per-atom quantities from LAMMPS as
well as values calculated by a compute, fix, or variable. The
"set_variable" function can set an existing string-style variable to a
new value, so that subsequent LAMMPS commands can access the variable.
The "get" and "put" operations can retrieve and reset atom
coordinates. See the library.cpp file and its associated header file
library.h for details.
The key idea of the library interface is that you can write any
functions you wish to define how your code talks to LAMMPS and add
them to src/library.cpp and src/library.h, as well as to the "Python
interface"_Section_python.html. The routines you add can access or
change any LAMMPS data you wish. The examples/COUPLE and python
directories have example C++ and C and Python codes which show how a
driver code can link to LAMMPS as a library, run LAMMPS on a subset of
processors, grab data from LAMMPS, change it, and put it back into
LAMMPS.
:line
6.20 Calculating thermal conductivity :link(howto_20),h4
The thermal conductivity kappa of a material can be measured in at
least 4 ways using various options in LAMMPS. See the examples/KAPPA
directory for scripts that implement the 4 methods discussed here for
a simple Lennard-Jones fluid model. Also, see "this
section"_Section_howto.html#howto_21 of the manual for an analogous
discussion for viscosity.
The thermal conducitivity tensor kappa is a measure of the propensity
of a material to transmit heat energy in a diffusive manner as given
by Fourier's law
J = -kappa grad(T)
where J is the heat flux in units of energy per area per time and
grad(T) is the spatial gradient of temperature. The thermal
conductivity thus has units of energy per distance per time per degree
K and is often approximated as an isotropic quantity, i.e. as a
scalar.
The first method is to setup two thermostatted regions at opposite
ends of a simulation box, or one in the middle and one at the end of a
periodic box. By holding the two regions at different temperatures
with a "thermostatting fix"_Section_howto.html#howto_13, the energy
added to the hot region should equal the energy subtracted from the
cold region and be proportional to the heat flux moving between the
regions. See the paper by "Ikeshoji and Hafskjold"_#Ikeshoji for
details of this idea. Note that thermostatting fixes such as "fix
nvt"_fix_nh.html, "fix langevin"_fix_langevin.html, and "fix
temp/rescale"_fix_temp_rescale.html store the cumulative energy they
add/subtract.
Alternatively, as a second method, the "fix heat"_fix_heat.html
command can used in place of thermostats on each of two regions to
add/subtract specified amounts of energy to both regions. In both
cases, the resulting temperatures of the two regions can be monitored
with the "compute temp/region" command and the temperature profile of
the intermediate region can be monitored with the "fix
ave/spatial"_fix_ave_spatial.html and "compute
ke/atom"_compute_ke_atom.html commands.
The third method is to perform a reverse non-equilibrium MD simulation
using the "fix thermal/conductivity"_fix_thermal_conductivity.html
command which implements the rNEMD algorithm of Muller-Plathe.
Kinetic energy is swapped between atoms in two different layers of the
simulation box. This induces a temperature gradient between the two
layers which can be monitored with the "fix
ave/spatial"_fix_ave_spatial.html and "compute
ke/atom"_compute_ke_atom.html commands. The fix tallies the
cumulative energy transfer that it performs. See the "fix
thermal/conductivity"_fix_thermal_conductivity.html command for
details.
The fourth method is based on the Green-Kubo (GK) formula which
relates the ensemble average of the auto-correlation of the heat flux
to kappa. The heat flux can be calculated from the fluctuations of
per-atom potential and kinetic energies and per-atom stress tensor in
a steady-state equilibrated simulation. This is in contrast to the
two preceding non-equilibrium methods, where energy flows continuously
between hot and cold regions of the simulation box.
The "compute heat/flux"_compute_heat_flux.html command can calculate
the needed heat flux and describes how to implement the Green_Kubo
formalism using additional LAMMPS commands, such as the "fix
ave/correlate"_fix_ave_correlate.html command to calculate the needed
auto-correlation. See the doc page for the "compute
heat/flux"_compute_heat_flux.html command for an example input script
that calculates the thermal conductivity of solid Ar via the GK
formalism.
:line
6.21 Calculating viscosity :link(howto_21),h4
The shear viscosity eta of a fluid can be measured in at least 4 ways
using various options in LAMMPS. See the examples/VISCOSITY directory
for scripts that implement the 4 methods discussed here for a simple
Lennard-Jones fluid model. Also, see "this
section"_Section_howto.html#howto_20 of the manual for an analogous
discussion for thermal conductivity.
Eta is a measure of the propensity of a fluid to transmit momentum in
a direction perpendicular to the direction of velocity or momentum
flow. Alternatively it is the resistance the fluid has to being
sheared. It is given by
J = -eta grad(Vstream)
where J is the momentum flux in units of momentum per area per time.
and grad(Vstream) is the spatial gradient of the velocity of the fluid
moving in another direction, normal to the area through which the
momentum flows. Viscosity thus has units of pressure-time.
The first method is to perform a non-equlibrium MD (NEMD) simulation
by shearing the simulation box via the "fix deform"_fix_deform.html
command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to
thermostat the fluid via the SLLOD equations of motion.
Alternatively, as a second method, one or more moving walls can be
used to shear the fluid in between them, again with some kind of
thermostat that modifies only the thermal (non-shearing) components of
velocity to prevent the fluid from heating up.
In both cases, the velocity profile setup in the fluid by this
procedure can be monitored by the "fix
ave/spatial"_fix_ave_spatial.html command, which determines
grad(Vstream) in the equation above. E.g. the derivative in the
y-direction of the Vx component of fluid motion or grad(Vstream) =
dVx/dy. The Pxy off-diagonal component of the pressure or stress
tensor, as calculated by the "compute pressure"_compute_pressure.html
command, can also be monitored, which is the J term in the equation
above. See "this section"_Section_howto.html#howto_13 of the manual
for details on NEMD simulations.
The third method is to perform a reverse non-equilibrium MD simulation
using the "fix viscosity"_fix_viscosity.html command which implements
the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is
swapped between atoms in two different layers of the simulation box in
a different dimension. This induces a velocity gradient which can be
monitored with the "fix ave/spatial"_fix_ave_spatial.html command.
The fix tallies the cummulative momentum transfer that it performs.
See the "fix viscosity"_fix_viscosity.html command for details.
The fourth method is based on the Green-Kubo (GK) formula which
relates the ensemble average of the auto-correlation of the
stress/pressure tensor to eta. This can be done in a steady-state
equilibrated simulation which is in contrast to the two preceding
non-equilibrium methods, where momentum flows continuously through the
simulation box.
Here is an example input script that calculates the viscosity of
liquid Ar via the GK formalism:
# Sample LAMMPS input script for viscosity of liquid Ar :pre
units real
variable T equal 86.4956
variable V equal vol
variable dt equal 4.0
variable p equal 400 # correlation length
variable s equal 5 # sample interval
variable d equal $p*$s # dump interval :pre
# convert from LAMMPS real units to SI :pre
variable kB equal 1.3806504e-23 # \[J/K/] Boltzmann
variable atm2Pa equal 101325.0
variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15
variable convert equal $\{atm2Pa\}*$\{atm2Pa\}*$\{fs2s\}*$\{A2m\}*$\{A2m\}*$\{A2m\} :pre
# setup problem :pre
dimension 3
boundary p p p
lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region box block 0 4 0 4 0 4
create_box 1 box
create_atoms 1 box
mass 1 39.948
pair_style lj/cut 13.0
pair_coeff * * 0.2381 3.405
timestep $\{dt\}
thermo $d :pre
# equilibration and thermalization :pre
velocity all create $T 102486 mom yes rot yes dist gaussian
fix NVT all nvt temp $T $T 10 drag 0.2
run 8000 :pre
# viscosity calculation, switch to NVE if desired :pre
#unfix NVT
#fix NVE all nve :pre
reset_timestep 0
variable pxy equal pxy
variable pxz equal pxz
variable pyz equal pyz
fix SS all ave/correlate $s $p $d &
v_pxy v_pxz v_pyz type auto file S0St.dat ave running
variable scale equal $\{convert\}/($\{kB\}*$T)*$V*$s*$\{dt\}
variable v11 equal trap(f_SS\[3\])*$\{scale\}
variable v22 equal trap(f_SS\[4\])*$\{scale\}
variable v33 equal trap(f_SS\[5\])*$\{scale\}
thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
run 100000
variable v equal (v_v11+v_v22+v_v33)/3.0
variable ndens equal count(all)/vol
print "average viscosity: $v \[Pa.s/] @ $T K, $\{ndens\} /A^3" :pre
:line
6.22 Calculating a diffusion coefficient :link(howto_22),h4
The diffusion coefficient D of a material can be measured in at least
2 ways using various options in LAMMPS. See the examples/DIFFUSE
directory for scripts that implement the 2 methods discussed here for
a simple Lennard-Jones fluid model.
The first method is to measure the mean-squared displacement (MSD) of
the system, via the "compute msd"_compute_msd.html command. The slope
of the MSD versus time is proportional to the diffusion coefficient.
The instantaneous MSD values can be accumulated in a vector via the
"fix vector"_fix_vector.html command, and a line fit to the vector to
compute its slope via the "variable slope"_variable.html function, and
thus extract D.
The second method is to measure the velocity auto-correlation function
(VACF) of the system, via the "compute vacf"_compute_vacf.html
command. The time-integral of the VACF is proportional to the
diffusion coefficient. The instantaneous VACF values can be
accumulated in a vector via the "fix vector"_fix_vector.html command,
and time integrated via the "variable trap"_variable.html function,
and thus extract D.
:line
6.23 Using chunks to calculate system properties :link(howto_23),h4
In LAMMS, "chunks" are collections of atoms, as defined by the
"compute chunk/atom"_compute_chunk_atom.html command, which assigns
each atom to a chunk ID (or to no chunk at all). The number of chunks
and the assignment of chunk IDs to atoms can be static or change over
time. Examples of "chunks" are molecules or spatial bins or atoms
with similar values (e.g. coordination number or potential energy).
The per-atom chunk IDs can be used as input to two other kinds of
commands, to calculate various properties of a system:
"fix ave/chunk"_fix_ave_chunk.html
any of the "compute */chunk"_compute.html commands :ul
Here, each of the 3 kinds of chunk-related commands is briefly
overviewed. Then some examples are given of how to compute different
properties with chunk commands.
Compute chunk/atom command: :h5
This compute can assign atoms to chunks of various styles. Only atoms
in the specified group and optional specified region are assigned to a
chunk. Here are some possible chunk definitions:
atoms in same molecule | chunk ID = molecule ID |
atoms of same atom type | chunk ID = atom type |
all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom |
atoms in same cluster | chunk ID = output of "compute cluster/atom"_compute_cluster_atom.html command |
atoms in same spatial bin | chunk ID = bin ID |
atoms in same rigid body | chunk ID = molecule ID used to define rigid bodies |
atoms with similar potential energy | chunk ID = output of "compute pe/atom"_compute_pe_atom.html |
atoms with same local defect structure | chunk ID = output of "compute centro/atom"_compute_centro_atom.html or "compute coord/atom"_compute_coord_atom.html command :tb(s=|,c=2)
Note that chunk IDs are integer values, so for atom properties or
computes that produce a floating point value, they will be truncated
to an integer. You could also use the compute in a variable that
scales the floating point value to spread it across multiple intergers.
Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
pencils, 3d bins = boxes, spherical bins, cylindrical bins.
This compute also calculates the number of chunks {Nchunk}, which is
used by other commands to tally per-chunk data. {Nchunk} can be a
static value or change over time (e.g. the number of clusters). The
chunk ID for an individual atom can also be static (e.g. a molecule
ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
Note that this compute allows the per-atom output of other
"computes"_compute.html, "fixes"_fix.html, and
"variables"_variable.html to be used to define chunk IDs for each
atom. This means you can write your own compute or fix to output a
per-atom quantity to use as chunk ID. See
"Section_modify"_Section_modify.html of the documentation for how to
do this. You can also define a "per-atom variable"_variable.html in
the input script that uses a formula to generate a chunk ID for each
atom.
Fix ave/chunk command: :h5
This fix takes the ID of a "compute
chunk/atom"_compute_chunk_atom.html command as input. For each chunk,
it then sums one or more specified per-atom values over the atoms in
each chunk. The per-atom values can be any atom property, such as
velocity, force, charge, potential energy, kinetic energy, stress,
etc. Additional keywords are defined for per-chunk properties like
density and temperature. More generally any per-atom value generated
by other "computes"_compute.html, "fixes"_fix.html, and "per-atom
variables"_variable.html, can be summed over atoms in each chunk.
Similar to other averaging fixes, this fix allows the summed per-chunk
values to be time-averaged in various ways, and output to a file. The
fix produces a global array as output with one row of values per
chunk.
Compute */chunk commands: :h5
Currently the following computes operate on chunks of atoms to produce
per-chunk values.
"compute com/chunk"_compute_com_chunk.html
"compute gyration/chunk"_compute_gyration_chunk.html
"compute inertia/chunk"_compute_inertia_chunk.html
"compute msd/chunk"_compute_msd_chunk.html
"compute property/chunk"_compute_property_chunk.html
"compute temp/chunk"_compute_temp_chunk.html
"compute torque/chunk"_compute_vcm_chunk.html
"compute vcm/chunk"_compute_vcm_chunk.html :ul
They each take the ID of a "compute
chunk/atom"_compute_chunk_atom.html command as input. As their names
indicate, they calculate the center-of-mass, radius of gyration,
moments of inertia, mean-squared displacement, temperature, torque,
and velocity of center-of-mass for each chunk of atoms. The "compute
property/chunk"_compute_property_chunk.html command can tally the
count of atoms in each chunk and extract other per-chunk properties.
The reason these various calculations are not part of the "fix
ave/chunk command"_fix_ave_chunk.html, is that each requires a more
complicated operation than simply summing and averaging over per-atom
values in each chunk. For example, many of them require calculation
of a center of mass, which requires summing mass*position over the
atoms and then dividing by summed mass.
All of these computes produce a global vector or global array as
output, wih one or more values per chunk. They can be used
in various ways:
As input to the "fix ave/time"_fix_ave_time.html command, which can
write the values to a file and optionally time average them. :ulb,l
As input to the "fix ave/histo"_fix_ave_histo.html command to
histogram values across chunks. E.g. a histogram of cluster sizes or
molecule diffusion rates. :l
As input to special functions of "equal-style
variables"_variable.html, like sum() and max(). E.g. to find the
largest cluster or fastest diffusing molecule. :l,ule
Example calculations with chunks :h5
Here are eaxmples using chunk commands to calculate various
properties:
(1) Average velocity in each of 1000 2d spatial bins:
compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out :pre
(2) Temperature in each spatial bin, after subtracting a flow
velocity:
compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
compute vbias all temp/profile 1 0 0 y 10
fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out :pre
(3) Center of mass of each molecule:
compute cc1 all chunk/atom molecule
compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre
(4) Total force on each molecule and ave/max across all molecules:
compute cc1 all chunk/atom molecule
fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
variable xave equal ave(f_1[2])
variable xmax equal max(f_1[2])
thermo 1000
thermo_style custom step temp v_xave v_xmax :pre
(5) Histogram of cluster sizes:
compute cluster all cluster/atom 1.0
compute cc1 all chunk/atom c_cluster compress yes
compute size all property/chunk cc1 count
fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre
:line
6.24 Setting parameters for the "kspace_style pppm/disp"_kspace_style.html command :link(howto_24),h4
The PPPM method computes interactions by splitting the pair potential
into two parts, one of which is computed in a normal pairwise fashion,
the so-called real-space part, and one of which is computed using the
Fourier transform, the so called reciprocal-space or kspace part. For
both parts, the potential is not computed exactly but is approximated.
Thus, there is an error in both parts of the computation, the
real-space and the kspace error. The just mentioned facts are true
both for the PPPM for Coulomb as well as dispersion interactions. The
deciding difference - and also the reason why the parameters for
pppm/disp have to be selected with more care - is the impact of the
errors on the results: The kspace error of the PPPM for Coulomb and
dispersion interaction and the real-space error of the PPPM for
Coulomb interaction have the character of noise. In contrast, the
real-space error of the PPPM for dispersion has a clear physical
interpretation: the underprediction of cohesion. As a consequence, the
real-space error has a much stronger effect than the kspace error on
simulation results for pppm/disp. Parameters must thus be chosen in a
way that this error is much smaller than the kspace error.
When using pppm/disp and not making any specifications on the PPPM
parameters via the kspace modify command, parameters will be tuned
such that the real-space error and the kspace error are equal. This
will result in simulations that are either inaccurate or slow, both of
which is not desirable. For selecting parameters for the pppm/disp
that provide fast and accurate simulations, there are two approaches,
which both have their up- and downsides.
The first approach is to set desired real-space an kspace accuracies
via the {kspace_modify force/disp/real} and {kspace_modify
force/disp/kspace} commands. Note that the accuracies have to be
specified in force units and are thus dependend on the chosen unit
settings. For real units, 0.0001 and 0.002 seem to provide reasonable
accurate and efficient computations for the real-space and kspace
accuracies. 0.002 and 0.05 work well for most systems using lj
units. PPPM parameters will be generated based on the desired
accuracies. The upside of this approach is that it usually provides a
good set of parameters and will work for both the {kspace_modify diff
ad} and {kspace_modify diff ik} options. The downside of the method
is that setting the PPPM parameters will take some time during the
initialization of the simulation.
The second approach is to set the parameters for the pppm/disp
explicitly using the {kspace_modify mesh/disp}, {kspace_modify
order/disp}, and {kspace_modify gewald/disp} commands. This approach
requires a more experienced user who understands well the impact of
the choice of parameters on the simulation accuracy and
performance. This approach provides a fast initialization of the
simulation. However, it is sensitive to errors: A combination of
parameters that will perform well for one system might result in
far-from-optimal conditions for other simulations. For example,
parametes that provide accurate and fast computations for
all-atomistic force fields can provide insufficient accuracy or
united-atomistic force fields (which is related to that the latter
typically have larger dispersion coefficients).
To avoid inaccurate or inefficient simulations, the pppm/disp stops
simulations with an error message if no action is taken to control the
PPPM parameters. If the automatic parameter generation is desired and
real-space and kspace accuracies are desired to be equal, this error
message can be suppressed using the {kspace_modify disp/auto yes}
command.
A reasonable approach that combines the upsides of both methods is to
make the first run using the {kspace_modify force/disp/real} and
{kspace_modify force/disp/kspace} commands, write down the PPPM
parameters from the outut, and specify these parameters using the
second approach in subsequent runs (which have the same composition,
force field, and approximately the same volume).
Concerning the performance of the pppm/disp there are two more things
to consider. The first is that when using the pppm/disp, the cutoff
parameter does no longer affect the accuracy of the simulation
(subject to that gewald/disp is adjusted when changing the cutoff).
The performance can thus be increased by examining different values
for the cutoff parameter. A lower bound for the cutoff is only set by
the truncation error of the repulsive term of pair potentials.
The second is that the mixing rule of the pair style has an impact on
the computation time when using the pppm/disp. Fastest computations
are achieved when using the geometric mixing rule. Using the
arithmetic mixing rule substantially increases the computational cost.
The computational overhead can be reduced using the {kspace_modify
mix/disp geom} and {kspace_modify splittol} commands. The first
command simply enforces geometric mixing of the dispersion
coeffiecients in kspace computations. This introduces some error in
the computations but will also significantly speed-up the
simulations. The second keyword sets the accuracy with which the
dispersion coefficients are approximated using a matrix factorization
approach. This may result in better accuracy then using the first
command, but will usually also not provide an equally good increase of
efficiency.
Finally, pppm/disp can also be used when no mixing rules apply.
This can be achieved using the {kspace_modify mix/disp none} command.
Note that the code does not check automatically whether any mixing
rule is fulfilled. If mixing rules do not apply, the user will have
to specify this command explicitly.
:line
6.25 Polarizable models :link(howto_25),h4
In polarizable force fields the charge distributions in molecules and
materials respond to their electrostatic environements. Polarizable
systems can be simulated in LAMMPS using three methods:
the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html
package, :ulb,l
the adiabatic core-shell method, implemented in the
"CORESHELL"_#howto_26 package, :l
the thermalized Drude dipole method, implemented in the
"USER-DRUDE"_#howto_27 package. :l,ule
The fluctuating charge method calculates instantaneous charges on
interacting atoms based on the electronegativity equalization
principle. It is implemented in the "fix qeq"_fix_qeq.html which is
available in several variants. It is a relatively efficient technique
since no additional particles are introduced. This method allows for
charge transfer between molecules or atom groups. However, because the
charges are located at the interaction sites, off-plane components of
polarization cannot be represented in planar molecules or atom groups.
The two other methods share the same basic idea: polarizable atoms are
split into one core atom and one satellite particle (called shell or
Drude particle) attached to it by a harmonic spring. Both atoms bear
a charge and they represent collectively an induced electric dipole.
These techniques are computationally more expensive than the QEq
method because of additional particles and bonds. These two
charge-on-spring methods differ in certain features, with the
core-shell model being normally used for ionic/crystalline materials,
whereas the so-called Drude model is normally used for molecular
systems and fluid states.
The core-shell model is applicable to crystalline materials where the
high symmetry around each site leads to stable trajectories of the
core-shell pairs. However, bonded atoms in molecules can be so close
that a core would interact too strongly or even capture the Drude
particle of a neighbor. The Drude dipole model is relatively more
complex in order to remediate this and other issues. Specifically, the
Drude model includes specific thermostating of the core-Drude pairs
and short-range damping of the induced dipoles.
The three polarization methods can be implemented through a
self-consistent calculation of charges or induced dipoles at each
timestep. In the fluctuating charge scheme this is done by the matrix
inversion method in "fix qeq/point"_fix_qeq.html, but for core-shell
or Drude-dipoles the relaxed-dipoles technique would require an slow
iterative procedure. These self-consistent solutions yield accurate
trajectories since the additional degrees of freedom representing
polarization are massless. An alternative is to attribute a mass to
the additional degrees of freedom and perform time integration using
an extended Lagrangian technique. For the fluctuating charge scheme
this is done by "fix qeq/dynamic"_fix_qeq.html, and for the
charge-on-spring models by the methods outlined in the next two
sections. The assignment of masses to the additional degrees of
freedom can lead to unphysical trajectories if care is not exerted in
choosing the parameters of the poarizable models and the simulation
conditions.
In the core-shell model the vibration of the shells is kept faster
than the ionic vibrations to mimic the fast response of the
polarizable electrons. But in molecular systems thermalizing the
core-Drude pairs at temperatures comparable to the rest of the
simulation leads to several problems (kinetic energy transfer, too
short a timestep, etc.) In order to avoid these problems the relative
motion of the Drude particles with respect to their cores is kept
"cold" so the vibration of the core-Drude pairs is very slow,
approaching the self-consistent regime. In both models the
temperature is regulated using the velocities of the center of mass of
core+shell (or Drude) pairs, but in the Drude model the actual
relative core-Drude particle motion is thermostated separately as
well.
:line
6.26 Adiabatic core/shell model :link(howto_26),h4
The adiabatic core-shell model by "Mitchell and
Finchham"_#MitchellFinchham is a simple method for adding
polarizability to a system. In order to mimic the electron shell of
an ion, a satellite particle is attached to it. This way the ions are
split into a core and a shell where the latter is meant to react to
the electrostatic environment inducing polarizability.
Technically, shells are attached to the cores by a spring force f =
k*r where k is a parametrized spring constant and r is the distance
between the core and the shell. The charges of the core and the shell
-add up to the ion charge, thus q(ion) = q(core) + q(shell). In a
+add up to the ion charge, thus q(ion) = q(core) + q(shell). This
+setup introduces the ion polarizability (alpha) given by
+alpha = q(shell)^2 / k. In a
similar fashion the mass of the ion is distributed on the core and the
shell with the core having the larger mass.
To run this model in LAMMPS, "atom_style"_atom_style.html {full} can
be used since atom charge and bonds are needed. Each kind of
core/shell pair requires two atom types and a bond type. The core and
shell of a core/shell pair should be bonded to each other with a
harmonic bond that provides the spring force. For example, a data file
for NaCl, as found in examples/coreshell, has this format:
432 atoms # core and shell atoms
216 bonds # number of core/shell springs :pre
4 atom types # 2 cores and 2 shells for Na and Cl
2 bond types :pre
0.0 24.09597 xlo xhi
0.0 24.09597 ylo yhi
0.0 24.09597 zlo zhi :pre
Masses # core/shell mass ratio = 0.1 :pre
1 20.690784 # Na core
2 31.90500 # Cl core
3 2.298976 # Na shell
4 3.54500 # Cl shell :pre
Atoms :pre
1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1
2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1
3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2
4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2
(...) :pre
Bonds # Bond topology for spring forces :pre
1 2 1 2 # spring for core/shell pair 1
2 2 3 4 # spring for core/shell pair 2
(...) :pre
Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
defined between the shells. Coulombic interactions are defined
between all cores and shells. If desired, additional bonds can be
-specified between cores.
+specified between cores.
The "special_bonds"_special_bonds.html command should be used to
turn-off the Coulombic interaction within core/shell pairs, since that
interaction is set by the bond spring. This is done using the
"special_bonds"_special_bonds.html command with a 1-2 weight = 0.0,
which is the default value. It needs to be considered whether one has
to adjust the "special_bonds"_special_bonds.html weighting according
to the molecular topology since the interactions of the shells are
bypassed over an extra bond.
Note that this core/shell implementation does not require all ions to
be polarized. One can mix core/shell pairs and ions without a
satellite particle if desired.
Since the core/shell model permits distances of r = 0.0 between the
core and shell, a pair style with a "cs" suffix needs to be used to
-implement a valid long-rangeCoulombic correction. Several such pair
+implement a valid long-range Coulombic correction. Several such pair
styles are provided in the CORESHELL package. See "this doc
page"_pair_cs.html for details. All of the core/shell enabled pair
styles require the use of a long-range Coulombic solver, as specified
by the "kspace_style"_kspace_style.html command. Either the PPPM or
Ewald solvers can be used.
For the NaCL example problem, these pair style and bond style settings
are used:
pair_style born/coul/long/cs 20.0 20.0
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl :pre
bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0 :pre
When running dynamics with the adiabatic core/shell model, the
following issues should be considered. Since the relative motion of
the core and shell particles corresponds to the polarization, typical
-thermostats can alter the polarization behaviour, meaining the shell
-will not react freely to its electrostatic environment. Therefore
+thermostats can alter the polarization behaviour, meaning the shell
+will not react freely to its electrostatic environment. This is
+critical during the equilibration of the system. Therefore
it's typically desirable to decouple the relative motion of the
core/shell pair, which is an imaginary degree of freedom, from the
real physical system. To do that, the "compute
temp/cs"_compute_temp_cs.html command can be used, in conjunction with
any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix
langevin"_fix_langevin. This compute uses the center-of-mass velocity
of the core/shell pairs to calculate a temperature, and insures that
velocity is what is rescaled for thermostatting purposes. This
compute also works for a system with both core/shell pairs and
non-polarized ions (ions without an attached satellite particle). The
"compute temp/cs"_compute_temp_cs.html command requires input of two
groups, one for the core atoms, another for the shell atoms.
Non-polarized ions which might also be included in the treated system
should not be included into either of these groups, they are taken
into account by the {group-ID} (2nd argument) of the compute. The
groups can be defined using the "group {type}"_group.html command.
Note that to perform thermostatting using this definition of
temperature, the "fix modify temp"_fix_modify.html command should be
-used to assign the comptue to the thermostat fix. Likewise the
+used to assign the compute to the thermostat fix. Likewise the
"thermo_modify temp"_thermo_modify.html command can be used to make
-this temperature be output for the overall system.
+this temperature be output for the overall system.
For the NaCl example, this can be done as follows:
group cores type 1 2
group shells type 3 4
compute CSequ all temp/cs cores shells
fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system
fix thermostatequ all nve # integrator as needed for the berendsen thermostat
fix_modify thermoberendsen temp CSequ
thermo_modify temp CSequ # output of center-of-mass derived temperature :pre
+If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
+relative motion of the core and the shell should in theory be
+stable. However numerical fluctuation can introduce a small
+momentum to the system, which is noticable over long trajectories.
+Therefore it is recomendable to use the "fix
+momentum"_fix_momentum.html command in combination with "compute
+temp/cs"_compute_temp_cs.html when equilibrating the system to
+prevent any drift.
+
When intializing the velocities of a system with core/shell pairs, it
is also desirable to not introduce energy into the relative motion of
the core/shell particles, but only assign a center-of-mass velocity to
the pairs. This can be done by using the {bias} keyword of the
"velocity create"_velocity.html command and assigning the "compute
temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
"velocity"_velocity.html commmand, e.g.
velocity all create 1427 134 bias yes temp CSequ
velocity all scale 1427 temp CSequ :pre
It is important to note that the polarizability of the core/shell
pairs is based on their relative motion. Therefore the choice of
spring force and mass ratio need to ensure much faster relative motion
of the 2 atoms within the core/shell pair than their center-of-mass
velocity. This allow the shells to effectively react instantaneously
to the electrostatic environment. This fast movement also limits the
timestep size that can be used.
-Additionally, the mass mismatch of the core and shell particles means
-that only a small amount of energy is transfered to the decoupled
-imaginary degrees of freedom. However, this transfer will typically
-lead to a a small drift in total energy over time. This internal
-energy can be monitored using the "compute
-chunk/atom"_compute_chunk_atom.html and "compute
+The primary literature of the adiabatic core/shell model suggests that
+the fast relative motion of the core/shell pairs only allows negligible
+energy transfer to the environment. Therefore it is not intended to
+decouple the core/shell degree of freedom from the physical system
+during production runs. In other words, the "compute
+temp/cs"_compute_temp_cs.html command should not be used during
+production runs and is only required during equilibration. This way one
+is consistent with literature (based on the code packages DL_POLY or
+GULP for instance).
+
+The mentioned energy transfer will typically lead to a a small drift
+in total energy over time. This internal energy can be monitored
+using the "compute chunk/atom"_compute_chunk_atom.html and "compute
temp/chunk"_compute_temp_chunk.html commands. The internal kinetic
energies of each core/shell pair can then be summed using the sum()
special function of the "variable"_variable.html command. Or they can
be time/averaged and output using the "fix ave/time"_fix_ave_time.html
command. To use these commands, each core/shell pair must be defined
as a "chunk". If each core/shell pair is defined as its own molecule,
the molecule ID can be used to define the chunks. If cores are bonded
to each other to form larger molecules, the chunks can be identified
by the "fix property/atom"_fix_property_atom.html via assigning a
core/shell ID to each atom using a special field in the data file read
by the "read_data"_read_data.html command. This field can then be
accessed by the "compute property/atom"_compute_property_atom.html
command, to use as input to the "compute
chunk/atom"_compute_chunk_atom.html command to define the core/shell
pairs as chunks.
For example,
fix csinfo all property/atom i_CSID # property/atom command
read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file
compute prop all property/atom i_CSID
compute cs_chunk all chunk/atom c_prop
compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre
The additional section in the date file would be formatted like this:
CS-Info # header of additional section :pre
1 1 # column 1 = atom ID, column 2 = core/shell ID
2 1
3 2
4 2
5 3
6 3
7 4
8 4
(...) :pre
:line
6.27 Drude induced dipoles :link(howto_27),h4
The thermalized Drude model, similarly to the "core-shell"_#howto_26
model, representes induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems
("Lamoureux and Roux"_#Lamoureux):
Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced
coordinates of the Drude particles with respect to their cores. This
makes the trajectory close to that of relaxed induced dipoles. :ulb,l
Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle
pair represents a single (polarizable) atom, so the special screening
factors in a covalent structure should be the same for the core and
the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4
special neighbor relations from their respective cores. :l
Stabilization of the interactions between induced dipoles. Drude
dipoles on covalently bonded atoms interact too strongly due to the
short distances, so an atom may capture the Drude particle of a
neighbor, or the induced dipoles within the same molecule may align
too much. To avoid this, damping at short range can be done by Thole
functions (for which there are physical grounds). This Thole damping
is applied to the point charges composing the induced dipole (the
charge of the Drude particle and the opposite charge on the core, not
to the total charge of the core atom). :l,ule
A detailed tutorial covering the usage of Drude induced dipoles in
LAMMPS is "available here"_tutorial_drude.html.
As with the core-shell model, the cores and Drude particles should
appear in the data file as standard atoms. The same holds for the
springs between them, which are described by standard harmonic bonds.
The nature of the atoms (core, Drude particle or non-polarizable) is
specified via the "fix drude"_fix_drude.html command. The special
list of neighbors is automatically refactored to account for the
equivalence of core and Drude particles as regards special 1-2 to 1-4
screening. It may be necessary to use the {extra} keyword of the
"special_bonds"_special_bonds.html command. If using "fix
shake"_fix_shake.html, make sure no Drude particle is in this fix
group.
There are two ways to thermostat the Drude particles at a low
temperature: use either "fix langevin/drude"_fix_langevin_drude.html
for a Langevin thermostat, or "fix
drude/transform/*"_fix_drude_transform.html for a Nose-Hoover
thermostat. The former requires use of the command "comm_modify vel
yes"_comm_modify.html. The latter requires two separate integration
fixes like {nvt} or {npt}. The correct temperatures of the reduced
degrees of freedom can be calculated using the "compute
temp/drude"_compute_temp_drude.html. This requires also to use the
command {comm_modify vel yes}.
Short-range damping of the induced dipole interactions can be achieved
using Thole functions through the the "pair style
thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
with a Coulomb pair style. It may be useful to use {coul/long/cs} or
similar from the CORESHELL package if the core and Drude particle come
too close, which can cause numerical issues.
:line
:line
:link(Berendsen)
[(Berendsen)] Berendsen, Grigera, Straatsma, J Phys Chem, 91,
6269-6271 (1987).
:link(Cornell)
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
:link(Horn)
[(Horn)] Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon,
J Chem Phys, 120, 9665 (2004).
:link(Ikeshoji)
[(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
(1994).
:link(MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
:link(Mayo)
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
:link(Jorgensen)
[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
:link(Price)
[(Price)] Price and Brooks, J Chem Phys, 121, 10096 (2004).
:link(Shinoda)
[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
:link(MitchellFinchham)
[(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
5, 1031-1038 (1993).
:link(Lamoureux)
[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
diff --git a/doc/Section_packages.html b/doc/Section_packages.html
index e66095d9b..eaa221f45 100644
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<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">4. Packages</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#standard-packages">4.1. Standard packages</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-packages">4.2. User packages</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-atc-package">4.3. USER-ATC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-awpmd-package">4.4. USER-AWPMD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-cg-cmm-package">4.5. USER-CG-CMM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-colvars-package">4.6. USER-COLVARS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-cuda-package">4.7. USER-CUDA package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-diffraction-package">4.8. USER-DIFFRACTION package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-drude-package">4.9. USER-DRUDE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-eff-package">4.10. USER-EFF package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-fep-package">4.11. USER-FEP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-h5md-package">4.12. USER-H5MD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-intel-package">4.13. USER-INTEL package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-lb-package">4.14. USER-LB package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-misc-package">4.15. USER-MISC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-molfile-package">4.16. USER-MOLFILE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-omp-package">4.17. USER-OMP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-phonon-package">4.18. USER-PHONON package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-qmmm-package">4.19. USER-QMMM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-qtb-package">4.20. USER-QTB package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-reaxc-package">4.21. USER-REAXC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-smd-package">4.22. USER-SMD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-sph-package">4.23. USER-SPH package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-compress-package">4.2. Build instructions for COMPRESS package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-gpu-package">4.3. Build instructions for GPU package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-kim-package">4.4. Build instructions for KIM package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-kokkos-package">4.5. Build instructions for KOKKOS package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-kspace-package">4.6. Build instructions for KSPACE package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-meam-package">4.7. Build instructions for MEAM package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-poems-package">4.8. Build instructions for POEMS package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-python-package">4.9. Build instructions for PYTHON package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-reax-package">4.10. Build instructions for REAX package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-voronoi-package">4.11. Build instructions for VORONOI package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-xtc-package">4.12. Build instructions for XTC package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-packages">4.13. User packages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-atc-package">4.14. USER-ATC package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-awpmd-package">4.15. USER-AWPMD package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-cg-cmm-package">4.16. USER-CG-CMM package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-colvars-package">4.17. USER-COLVARS package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-cuda-package">4.18. USER-CUDA package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-diffraction-package">4.19. USER-DIFFRACTION package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-drude-package">4.20. USER-DRUDE package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-eff-package">4.21. USER-EFF package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-fep-package">4.22. USER-FEP package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-h5md-package">4.23. USER-H5MD package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-intel-package">4.24. USER-INTEL package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-lb-package">4.25. USER-LB package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-misc-package">4.26. USER-MISC package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-molfile-package">4.27. USER-MOLFILE package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-omp-package">4.28. USER-OMP package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-phonon-package">4.29. USER-PHONON package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-qmmm-package">4.30. USER-QMMM package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-qtb-package">4.31. USER-QTB package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-reaxc-package">4.32. USER-REAXC package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-smd-package">4.33. USER-SMD package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#user-sph-package">4.34. USER-SPH package</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<div class="section" id="packages">
<h1>4. Packages<a class="headerlink" href="#packages" title="Permalink to this headline">¶</a></h1>
<p>This section gives a quick overview of the add-on packages that extend
LAMMPS functionality.</p>
<div class="line-block">
<div class="line">4.1 <a class="reference internal" href="#pkg-1"><span>Standard packages</span></a></div>
<div class="line">4.2 <a class="reference internal" href="#pkg-2"><span>User packages</span></a></div>
<div class="line"><br /></div>
</div>
<p>LAMMPS includes many optional packages, which are groups of files that
enable a specific set of features. For example, force fields for
molecular systems or granular systems are in packages. You can see
the list of all packages by typing “make package” from within the src
directory of the LAMMPS distribution.</p>
<p>See <a class="reference internal" href="Section_start.html#start-3"><span>Section_start 3</span></a> of the manual for
details on how to include/exclude specific packages as part of the
LAMMPS build process, and for more details about the differences
-between standard packages and user packages in LAMMPS.</p>
-<p>Below, the packages currently availabe in LAMMPS are listed. For
-standard packages, just a one-line description is given. For user
-packages, more details are provided.</p>
+between standard packages and user packages.</p>
+<p>Unless otherwise noted below, every package is independent of all the
+others. I.e. any package can be included or excluded in a LAMMPS
+build, independent of all other packages. However, note that some
+packages include commands derived from commands in other packages. If
+the other package is not installed, the derived command from the new
+package will also not be installed when you include the new one.
+E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package
+will not be installed as part of the USER-OMP package if the KSPACE
+package is not also installed, since it contains the pair
+lj/cut/coul/long command. If you later install the KSPACE pacakge and
+the USER-OMP package is already installed, both the pair
+lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.</p>
+<p>The two tables below list currently available packages in LAMMPS, with
+a one-line descriptions of each. The sections below give a few more
+details, including instructions for building LAMMPS with the package,
+either via the make command or the Make.py tool described in <a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a>.</p>
<div class="section" id="standard-packages">
<span id="pkg-1"></span><h2>4.1. Standard packages<a class="headerlink" href="#standard-packages" title="Permalink to this headline">¶</a></h2>
-<p>The current list of standard packages is as follows:</p>
+<p>The current list of standard packages is as follows.</p>
<table border="1" class="docutils">
<colgroup>
<col width="7%" />
<col width="23%" />
<col width="24%" />
<col width="32%" />
<col width="7%" />
<col width="7%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>Package</td>
<td>Description</td>
<td>Author(s)</td>
<td>Doc page</td>
<td>Example</td>
<td>Library</td>
</tr>
<tr class="row-even"><td>ASPHERE</td>
<td>aspherical particles</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="Section_howto.html#howto-14"><span>Section_howto 6.14</span></a></td>
<td>ellipse</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>BODY</td>
<td>body-style particles</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="body.html"><em>body</em></a></td>
<td>body</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>CLASS2</td>
<td>class 2 force fields</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="pair_class2.html"><em>pair_style lj/class2</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>COLLOID</td>
<td>colloidal particles</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="atom_style.html"><em>atom_style colloid</em></a></td>
<td>colloid</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>COMPRESS</td>
<td>I/O compression</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="dump.html"><em>dump */gz</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>CORESHELL</td>
<td>adiabatic core/shell model</td>
<td>Hendrik Heenen (Technical U of Munich)</td>
<td><a class="reference internal" href="Section_howto.html#howto-25"><span>Section_howto 6.25</span></a></td>
<td>coreshell</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>DIPOLE</td>
<td>point dipole particles</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="pair_dipole.html"><em>pair_style dipole/cut</em></a></td>
<td>dipole</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>FLD</td>
<td>Fast Lubrication Dynamics</td>
<td>Kumar & Bybee & Higdon (1)</td>
<td><a class="reference internal" href="pair_lubricateU.html"><em>pair_style lubricateU</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>GPU</td>
<td>GPU-enabled styles</td>
<td>Mike Brown (ORNL)</td>
<td><a class="reference internal" href="accelerate_gpu.html"><em>Section accelerate</em></a></td>
<td>gpu</td>
<td>lib/gpu</td>
</tr>
<tr class="row-odd"><td>GRANULAR</td>
<td>granular systems</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="Section_howto.html#howto-6"><span>Section_howto 6.6</span></a></td>
<td>pour</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>KIM</td>
<td>openKIM potentials</td>
<td>Smirichinski & Elliot & Tadmor (3)</td>
<td><a class="reference internal" href="pair_kim.html"><em>pair_style kim</em></a></td>
<td>kim</td>
<td>KIM</td>
</tr>
<tr class="row-odd"><td>KOKKOS</td>
<td>Kokkos-enabled styles</td>
<td>Trott & Edwards (4)</td>
<td><a class="reference internal" href="accelerate_kokkos.html"><em>Section_accelerate</em></a></td>
<td>kokkos</td>
<td>lib/kokkos</td>
</tr>
<tr class="row-even"><td>KSPACE</td>
<td>long-range Coulombic solvers</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a></td>
<td>peptide</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>MANYBODY</td>
<td>many-body potentials</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="pair_tersoff.html"><em>pair_style tersoff</em></a></td>
<td>shear</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>MEAM</td>
<td>modified EAM potential</td>
<td>Greg Wagner (Sandia)</td>
<td><a class="reference internal" href="pair_meam.html"><em>pair_style meam</em></a></td>
<td>meam</td>
<td>lib/meam</td>
</tr>
<tr class="row-odd"><td>MC</td>
<td>Monte Carlo options</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="fix_gcmc.html"><em>fix gcmc</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>MOLECULE</td>
<td>molecular system force fields</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="Section_howto.html#howto-3"><span>Section_howto 6.3</span></a></td>
<td>peptide</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>OPT</td>
<td>optimized pair styles</td>
<td>Fischer & Richie & Natoli (2)</td>
<td><a class="reference internal" href="accelerate_opt.html"><em>Section accelerate</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>PERI</td>
<td>Peridynamics models</td>
<td>Mike Parks (Sandia)</td>
<td><a class="reference internal" href="pair_peri.html"><em>pair_style peri</em></a></td>
<td>peri</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>POEMS</td>
<td>coupled rigid body motion</td>
<td>Rudra Mukherjee (JPL)</td>
<td><a class="reference internal" href="fix_poems.html"><em>fix poems</em></a></td>
<td>rigid</td>
<td>lib/poems</td>
</tr>
<tr class="row-even"><td>PYTHON</td>
<td>embed Python code in an input script</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="python.html"><em>python</em></a></td>
<td>python</td>
<td>lib/python</td>
</tr>
<tr class="row-odd"><td>REAX</td>
<td>ReaxFF potential</td>
<td>Aidan Thompson (Sandia)</td>
<td><a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a></td>
<td>reax</td>
<td>lib/reax</td>
</tr>
<tr class="row-even"><td>REPLICA</td>
<td>multi-replica methods</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="Section_howto.html#howto-5"><span>Section_howto 6.5</span></a></td>
<td>tad</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>RIGID</td>
<td>rigid bodies</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a></td>
<td>rigid</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>SHOCK</td>
<td>shock loading methods</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="fix_msst.html"><em>fix msst</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>SNAP</td>
<td>quantum-fit potential</td>
<td>Aidan Thompson (Sandia)</td>
<td><a class="reference internal" href="pair_snap.html"><em>pair snap</em></a></td>
<td>snap</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>SRD</td>
<td>stochastic rotation dynamics</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="fix_srd.html"><em>fix srd</em></a></td>
<td>srd</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>VORONOI</td>
<td>Voronoi tesselations</td>
<td>Daniel Schwen (LANL)</td>
<td><a class="reference internal" href="compute_voronoi_atom.html"><em>compute voronoi/atom</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>Voro++</td>
</tr>
<tr class="row-even"><td>XTC</td>
<td>dumps in XTC format</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="dump.html"><em>dump</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p>The “Authors” column lists a name(s) if a specific person is
-responible for creating and maintaining the package.</p>
+responible for creating and maintaining the package.
+More details on
+multiple authors are give below.</p>
<p>(1) The FLD package was created by Amit Kumar and Michael Bybee from
Jonathan Higdon’s group at UIUC.</p>
<p>(2) The OPT package was created by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technolgy).</p>
<p>(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
and Ellad Tadmor (U Minn).</p>
<p>(4) The KOKKOS package was created primarily by Christian Trott
(Sandia). It uses the Kokkos library which was developed by Carter
Edwards, Christian, and collaborators at Sandia.</p>
<p>The “Doc page” column links to either a portion of the
<a class="reference internal" href="Section_howto.html"><em>Section_howto</em></a> of the manual, or an input script
command implemented as part of the package.</p>
<p>The “Example” column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. “peptide” refers to the examples/peptide directory.</p>
<p>The “Library” column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See the src/package/README or 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>Except where explained below, all of these packages can be installed,
+and LAMMPS re-built, by issuing these commands from the src dir.</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-package
+make machine
+or
+Make.py -p package -a machine
+</pre></div>
+</div>
+<p>To un-install the package and re-build LAMMPS without it:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-package
+make machine
+or
+Make.py -p ^package -a machine
+</pre></div>
+</div>
+<p>“Package” is the name of the package in lower-case letters,
+e.g. asphere or rigid, and “machine” is the build target, e.g. mpi or
+serial.</p>
+</div>
+<div class="section" id="build-instructions-for-compress-package">
+<h2>4.2. Build instructions for COMPRESS package<a class="headerlink" href="#build-instructions-for-compress-package" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="build-instructions-for-gpu-package">
+<h2>4.3. Build instructions for GPU package<a class="headerlink" href="#build-instructions-for-gpu-package" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="build-instructions-for-kim-package">
+<h2>4.4. Build instructions for KIM package<a class="headerlink" href="#build-instructions-for-kim-package" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="build-instructions-for-kokkos-package">
+<h2>4.5. Build instructions for KOKKOS package<a class="headerlink" href="#build-instructions-for-kokkos-package" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="build-instructions-for-kspace-package">
+<h2>4.6. Build instructions for KSPACE package<a class="headerlink" href="#build-instructions-for-kspace-package" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="build-instructions-for-meam-package">
+<h2>4.7. Build instructions for MEAM package<a class="headerlink" href="#build-instructions-for-meam-package" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="build-instructions-for-poems-package">
+<h2>4.8. Build instructions for POEMS package<a class="headerlink" href="#build-instructions-for-poems-package" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="build-instructions-for-python-package">
+<h2>4.9. Build instructions for PYTHON package<a class="headerlink" href="#build-instructions-for-python-package" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="build-instructions-for-reax-package">
+<h2>4.10. Build instructions for REAX package<a class="headerlink" href="#build-instructions-for-reax-package" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="build-instructions-for-voronoi-package">
+<h2>4.11. Build instructions for VORONOI package<a class="headerlink" href="#build-instructions-for-voronoi-package" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="build-instructions-for-xtc-package">
+<h2>4.12. Build instructions for XTC package<a class="headerlink" href="#build-instructions-for-xtc-package" title="Permalink to this headline">¶</a></h2>
+<hr class="docutils" />
</div>
<div class="section" id="user-packages">
-<span id="pkg-2"></span><h2>4.2. User packages<a class="headerlink" href="#user-packages" title="Permalink to this headline">¶</a></h2>
+<span id="pkg-2"></span><h2>4.13. User packages<a class="headerlink" href="#user-packages" title="Permalink to this headline">¶</a></h2>
<p>The current list of user-contributed packages is as follows:</p>
<table border="1" class="docutils">
<colgroup>
<col width="8%" />
<col width="21%" />
<col width="22%" />
<col width="25%" />
<col width="8%" />
<col width="10%" />
<col width="6%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>Package</td>
<td>Description</td>
<td>Author(s)</td>
<td>Doc page</td>
<td>Example</td>
<td>Pic/movie</td>
<td>Library</td>
</tr>
<tr class="row-even"><td>USER-ATC</td>
<td>atom-to-continuum coupling</td>
<td>Jones & Templeton & Zimmerman (1)</td>
<td><a class="reference internal" href="fix_atc.html"><em>fix atc</em></a></td>
<td>USER/atc</td>
<td><a class="reference external" href="http://lammps.sandia.gov/pictures.html#atc">atc</a></td>
<td>lib/atc</td>
</tr>
<tr class="row-odd"><td>USER-AWPMD</td>
<td>wave-packet MD</td>
<td>Ilya Valuev (JIHT)</td>
<td><a class="reference internal" href="pair_awpmd.html"><em>pair_style awpmd/cut</em></a></td>
<td>USER/awpmd</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>lib/awpmd</td>
</tr>
<tr class="row-even"><td>USER-CG-CMM</td>
<td>coarse-graining model</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="pair_sdk.html"><em>pair_style lj/sdk</em></a></td>
<td>USER/cg-cmm</td>
<td><a class="reference external" href="http://lammps.sandia.gov/pictures.html#cg">cg</a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-COLVARS</td>
<td>collective variables</td>
<td>Fiorin & Henin & Kohlmeyer (2)</td>
<td><a class="reference internal" href="fix_colvars.html"><em>fix colvars</em></a></td>
<td>USER/colvars</td>
<td><a class="reference external" href="colvars">colvars</a></td>
<td>lib/colvars</td>
</tr>
<tr class="row-even"><td>USER-CUDA</td>
<td>NVIDIA GPU styles</td>
<td>Christian Trott (U Tech Ilmenau)</td>
<td><a class="reference internal" href="accelerate_cuda.html"><em>Section accelerate</em></a></td>
<td>USER/cuda</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>lib/cuda</td>
</tr>
<tr class="row-odd"><td>USER-DIFFRACTION</td>
<td>virutal x-ray and electron diffraction</td>
<td>Shawn Coleman (ARL)</td>
<td><a class="reference internal" href="compute_xrd.html"><em>compute xrd</em></a></td>
<td>USER/diffraction</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-DRUDE</td>
<td>Drude oscillators</td>
<td>Dequidt & Devemy & Padua (3)</td>
<td><a class="reference internal" href="tutorial_drude.html"><em>tutorial</em></a></td>
<td>USER/drude</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-EFF</td>
<td>electron force field</td>
<td>Andres Jaramillo-Botero (Caltech)</td>
<td><a class="reference internal" href="pair_eff.html"><em>pair_style eff/cut</em></a></td>
<td>USER/eff</td>
<td><a class="reference external" href="http://lammps.sandia.gov/movies.html#eff">eff</a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-FEP</td>
<td>free energy perturbation</td>
<td>Agilio Padua (U Blaise Pascal Clermont-Ferrand)</td>
<td><a class="reference internal" href="compute_fep.html"><em>compute fep</em></a></td>
<td>USER/fep</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-H5MD</td>
<td>dump output via HDF5</td>
<td>Pierre de Buyl (KU Leuven)</td>
<td><a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>lib/h5md</td>
</tr>
<tr class="row-even"><td>USER-INTEL</td>
<td>Vectorized CPU and Intel(R) coprocessor styles</td>
<td><ol class="first last upperalpha simple" start="23">
<li>Michael Brown (Intel)</li>
</ol>
</td>
<td><a class="reference internal" href="accelerate_intel.html"><em>Section accelerate</em></a></td>
<td>examples/intel</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-LB</td>
<td>Lattice Boltzmann fluid</td>
<td>Colin Denniston (U Western Ontario)</td>
<td><a class="reference internal" href="fix_lb_fluid.html"><em>fix lb/fluid</em></a></td>
<td>USER/lb</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-MISC</td>
<td>single-file contributions</td>
<td>USER-MISC/README</td>
<td>USER-MISC/README</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-MOLFILE</td>
<td><a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a> molfile plug-ins</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="dump_molfile.html"><em>dump molfile</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>VMD-MOLFILE</td>
</tr>
<tr class="row-even"><td>USER-OMP</td>
<td>OpenMP threaded styles</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="accelerate_omp.html"><em>Section accelerate</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-PHONON</td>
<td>phonon dynamical matrix</td>
<td>Ling-Ti Kong (Shanghai Jiao Tong U)</td>
<td><a class="reference internal" href="fix_phonon.html"><em>fix phonon</em></a></td>
<td>USER/phonon</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-QMMM</td>
<td>QM/MM coupling</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="fix_qmmm.html"><em>fix qmmm</em></a></td>
<td>USER/qmmm</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>lib/qmmm</td>
</tr>
<tr class="row-odd"><td>USER-QTB</td>
<td>quantum nuclear effects</td>
<td>Yuan Shen (Stanford)</td>
<td><a class="reference internal" href="fix_qtb.html"><em>fix qtb</em></a> <a class="reference internal" href="fix_qbmsst.html"><em>fix_qbmsst</em></a></td>
<td>qtb</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-QUIP</td>
<td>QUIP/libatoms interface</td>
<td>Albert Bartok-Partay (U Cambridge)</td>
<td><a class="reference internal" href="pair_quip.html"><em>pair_style quip</em></a></td>
<td>USER/quip</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>lib/quip</td>
</tr>
<tr class="row-odd"><td>USER-REAXC</td>
<td>C version of ReaxFF</td>
<td>Metin Aktulga (LBNL)</td>
<td><a class="reference internal" href="pair_reax_c.html"><em>pair_style reaxc</em></a></td>
<td>reax</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-SMD</td>
<td>smoothed Mach dynamics</td>
<td>Georg Ganzenmuller (EMI)</td>
<td><a class="reference external" href="PDF/SMD_LAMMPS_userguide.pdf">userguide.pdf</a></td>
<td>USER/smd</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td>USER-SPH</td>
<td>smoothed particle hydrodynamics</td>
<td>Georg Ganzenmuller (EMI)</td>
<td><a class="reference external" href="PDF/SPH_LAMMPS_userguide.pdf">userguide.pdf</a></td>
<td>USER/sph</td>
<td><a class="reference external" href="http://lammps.sandia.gov/movies.html#sph">sph</a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td>USER-TALLY</td>
<td>Pairwise tallied computes</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><code class="xref doc docutils literal"><span class="pre">compute</span></code></td>
<td>USER/tally</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p>The “Authors” column lists a name(s) if a specific person is
responible for creating and maintaining the package.</p>
-<p>If the Library is not listed as lib/package, then it is a third-party
-library not included in the LAMMPS distribution. See the
-src/package/Makefile.lammps file for info on where to download the
-library from.</p>
-<p>(2) The ATC package was created by Reese Jones, Jeremy Templeton, and
+<p>(1) The ATC package was created by Reese Jones, Jeremy Templeton, and
Jon Zimmerman (Sandia).</p>
<p>(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
the colvars module library written by Giacomo Fiorin (Temple U) and
Jerome Henin (LISM, Marseille, France).</p>
<p>(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal
Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
(U Blaise Pascal).</p>
+<p>If the Library is not listed as lib/package, then it is a third-party
+library not included in the LAMMPS distribution. See the
+src/package/Makefile.lammps file for info on where to download the
+library from.</p>
<p>The “Doc page” column links to either a portion of the
<a class="reference internal" href="Section_howto.html"><em>Section_howto</em></a> of the manual, or an input script
command implemented as part of the package, or to additional
-documentation provided witht he package.</p>
+documentation provided within the package.</p>
<p>The “Example” column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. “peptide” refers to the examples/peptide directory. USER/cuda
refers to the examples/USER/cuda directory.</p>
<p>The “Library” column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See 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="#id2"><span class="problematic" id="id3">*</span></a>/README file is given
-below.</p>
+<p>Except where explained below, all of these packages can be installed,
+and LAMMPS re-built, by issuing these commands from the src dir.</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-user-package
+make machine
+or
+Make.py -p package -a machine
+</pre></div>
+</div>
+<p>To un-install the package and re-build LAMMPS without it:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-user-package
+make machine
+or
+Make.py -p ^package -a machine
+</pre></div>
+</div>
+<p>“Package” is the name of the package (in this case without the user
+prefix) in lower-case letters, e.g. drude or phonon, and “machine” is
+the build target, e.g. mpi or serial.</p>
</div>
-<hr class="docutils" />
<div class="section" id="user-atc-package">
-<h2>4.3. USER-ATC package<a class="headerlink" href="#user-atc-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.14. USER-ATC package<a class="headerlink" href="#user-atc-package" title="Permalink to this headline">¶</a></h2>
<p>This package implements a “fix atc” command which can be used in a
LAMMPS input script. This fix can be employed to either do concurrent
coupling of MD with FE-based physics surrogates or on-the-fly
post-processing of atomic information to continuum fields.</p>
<p>See the doc page for the fix atc command to get started. At the
bottom of the doc page are many links to additional documentation
contained in the doc/USER/atc directory.</p>
<p>There are example scripts for using this package in examples/USER/atc.</p>
<p>This package uses an external library in lib/atc which must be
compiled before making LAMMPS. See the lib/atc/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.</p>
<p>The primary people who created this package are Reese Jones (rjones at
sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-awpmd-package">
-<h2>4.4. USER-AWPMD package<a class="headerlink" href="#user-awpmd-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.15. USER-AWPMD package<a class="headerlink" href="#user-awpmd-package" title="Permalink to this headline">¶</a></h2>
<p>This package contains a LAMMPS implementation of the Antisymmetrized
Wave Packet Molecular Dynamics (AWPMD) method.</p>
<p>See the doc page for the pair_style awpmd/cut command to get started.</p>
<p>There are example scripts for using this package in examples/USER/awpmd.</p>
<p>This package uses an external library in lib/awpmd which must be
compiled before making LAMMPS. See the lib/awpmd/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.</p>
<p>The person who created this package is Ilya Valuev at the JIHT in
Russia (valuev at physik.hu-berlin.de). Contact him directly if you
have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-cg-cmm-package">
-<h2>4.5. USER-CG-CMM package<a class="headerlink" href="#user-cg-cmm-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.16. USER-CG-CMM package<a class="headerlink" href="#user-cg-cmm-package" title="Permalink to this headline">¶</a></h2>
<p>This package implements 3 commands which can be used in a LAMMPS input
script:</p>
<ul class="simple">
<li>pair_style lj/sdk</li>
<li>pair_style lj/sdk/coul/long</li>
<li>angle_style sdk</li>
</ul>
<p>These styles allow coarse grained MD simulations with the
parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
(SDK), with extensions to simulate ionic liquids, electrolytes, lipids
and charged amino acids.</p>
<p>See the doc pages for these commands for details.</p>
<p>There are example scripts for using this package in
examples/USER/cg-cmm.</p>
<p>This is the second generation implementation reducing the the clutter
of the previous version. For many systems with electrostatics, it will
be faster to use pair_style hybrid/overlay with lj/sdk and coul/long
instead of the combined lj/sdk/coul/long style. since the number of
charged atom types is usually small. For any other coulomb
interactions this is now required. To exploit this property, the use
of the kspace_style pppm/cg is recommended over regular pppm. For all
new styles, input file backward compatibility is provided. The old
implementation is still available through appending the /old
suffix. These will be discontinued and removed after the new
implementation has been fully validated.</p>
<p>The current version of this package should be considered beta
quality. The CG potentials work correctly for “normal” situations, but
have not been testing with all kinds of potential parameters and
simulation systems.</p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-colvars-package">
-<h2>4.6. USER-COLVARS package<a class="headerlink" href="#user-colvars-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.17. USER-COLVARS package<a class="headerlink" href="#user-colvars-package" title="Permalink to this headline">¶</a></h2>
<p>This package implements the “fix colvars” command which can be
used in a LAMMPS input script.</p>
<p>This fix allows to use “collective variables” to implement
Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
Sampling and Restraints. This code consists of two parts:</p>
<ul class="simple">
<li>A portable collective variable module library written and maintained</li>
<li>by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and</li>
<li>Jerome Henin (LISM, CNRS, Marseille, France). This code is located in</li>
<li>the directory lib/colvars and needs to be compiled first. The colvars</li>
<li>fix and an interface layer, exchanges information between LAMMPS and</li>
<li>the collective variable module.</li>
</ul>
<p>See the doc page of <a class="reference internal" href="fix_colvars.html"><em>fix colvars</em></a> for more details.</p>
<p>There are example scripts for using this package in
examples/USER/colvars</p>
<p>This is a very new interface that does not yet support all
features in the module and will see future optimizations
and improvements. The colvars module library is also available
in NAMD has been thoroughly used and tested there. Bugs and
problems are likely due to the interface layers code.
Thus the current version of this package should be considered
beta quality.</p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-cuda-package">
-<h2>4.7. USER-CUDA package<a class="headerlink" href="#user-cuda-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.18. USER-CUDA package<a class="headerlink" href="#user-cuda-package" title="Permalink to this headline">¶</a></h2>
<p>This package provides acceleration of various LAMMPS pair styles, fix
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
GPUs.</p>
<p>See this section of the manual to get started:</p>
<p><span class="xref std std-ref">Section_accelerate</span></p>
<p>There are example scripts for using this package in
examples/USER/cuda.</p>
<p>This package uses an external library in lib/cuda which must be
compiled before making LAMMPS. See the lib/cuda/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.</p>
<p>The person who created this package is Christian Trott at the
University of Technology Ilmenau, Germany (christian.trott at
tu-ilmenau.de). Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-diffraction-package">
-<h2>4.8. USER-DIFFRACTION package<a class="headerlink" href="#user-diffraction-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.19. USER-DIFFRACTION package<a class="headerlink" href="#user-diffraction-package" title="Permalink to this headline">¶</a></h2>
<p>This package contains the commands neeed to calculate x-ray and
electron diffraction intensities based on kinematic diffraction
theory.</p>
<p>See these doc pages and their related commands to get started:</p>
<ul class="simple">
<li><a class="reference internal" href="compute_xrd.html"><em>compute xrd</em></a></li>
<li><a class="reference internal" href="compute_saed.html"><em>compute saed</em></a></li>
<li><a class="reference internal" href="fix_saed_vtk.html"><em>fix saed/vtk</em></a></li>
</ul>
<p>The person who created this package is Shawn P. Coleman
(shawn.p.coleman8.ctr at mail.mil) while at the University of
Arkansas. Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-drude-package">
-<h2>4.9. USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.20. USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline">¶</a></h2>
<p>This package implements methods for simulating polarizable systems
in LAMMPS using thermalized Drude oscillators.</p>
<p>See these doc pages and their related commands to get started:</p>
<ul class="simple">
<li><a class="reference internal" href="tutorial_drude.html"><em>Drude tutorial</em></a></li>
<li><a class="reference internal" href="fix_drude.html"><em>fix drude</em></a></li>
<li><a class="reference internal" href="compute_temp_drude.html"><em>compute temp/drude</em></a></li>
<li><a class="reference internal" href="fix_langevin_drude.html"><em>fix langevin/drude</em></a></li>
<li><a class="reference internal" href="fix_drude_transform.html"><em>fix drude/transform/...</em></a></li>
<li><a class="reference internal" href="pair_thole.html"><em>pair thole</em></a></li>
</ul>
<p>There are auxiliary tools for using this package in tools/drude.</p>
<p>The person who created this package is Alain Dequidt at Universite
Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
Contact him directly if you have questions. Co-authors: Julien Devemy,
Agilio Padua.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-eff-package">
-<h2>4.10. USER-EFF package<a class="headerlink" href="#user-eff-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.21. USER-EFF package<a class="headerlink" href="#user-eff-package" title="Permalink to this headline">¶</a></h2>
<p>This package contains a LAMMPS implementation of the electron Force
Field (eFF) currently under development at Caltech, as described in
A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
2010. The eFF potential was first introduced by Su and Goddard, in
2007.</p>
<p>eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
structure methods to describe atomic structure, bonding, and chemistry
in materials, and of plasma methods to describe nonequilibrium
dynamics of large systems with a large number of highly excited
electrons. We classify it as a mixed QM-classical approach rather than
a conventional force field method, which introduces QM-based terms (a
spin-dependent repulsion term to account for the Pauli exclusion
principle and the electron wavefunction kinetic energy associated with
the Heisenberg principle) that reduce, along with classical
electrostatic terms between nuclei and electrons, to the sum of a set
of effective pairwise potentials. This makes eFF uniquely suited to
simulate materials over a wide range of temperatures and pressures
where electronically excited and ionized states of matter can occur
and coexist.</p>
<p>The necessary customizations to the LAMMPS core are in place to
enable the correct handling of explicit electron properties during
minimization and dynamics.</p>
<p>See the doc page for the pair_style eff/cut command to get started.</p>
<p>There are example scripts for using this package in
examples/USER/eff.</p>
<p>There are auxiliary tools for using this package in tools/eff.</p>
<p>The person who created this package is Andres Jaramillo-Botero at
CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-fep-package">
-<h2>4.11. USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.22. USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline">¶</a></h2>
<p>This package provides methods for performing free energy perturbation
simulations with soft-core pair potentials in LAMMPS.</p>
<p>See these doc pages and their related commands to get started:</p>
<ul class="simple">
<li><a class="reference internal" href="fix_adapt_fep.html"><em>fix adapt/fep</em></a></li>
<li><a class="reference internal" href="compute_fep.html"><em>compute fep</em></a></li>
<li><a class="reference internal" href="pair_lj_soft.html"><em>soft pair styles</em></a></li>
</ul>
<p>The person who created this package is Agilio Padua at Universite
Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-h5md-package">
-<h2>4.12. USER-H5MD package<a class="headerlink" href="#user-h5md-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.23. USER-H5MD package<a class="headerlink" href="#user-h5md-package" title="Permalink to this headline">¶</a></h2>
<p>This package contains a <a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a> command for
performing a dump of atom properties in HDF5 format. <a class="reference external" href="http://www.hdfgroup.org/HDF5/">HDF5 files</a> are binary, portable and self-describing and can be
examined and used by a variety of auxiliary tools. The output HDF5
files are structured in a format called H5MD, which was designed to
store molecular data, and can be used and produced by various MD and
MD-related codes. The <code class="xref doc docutils literal"><span class="pre">dump</span> <span class="pre">h5md</span></code> command gives a
citation to a paper describing the format.</p>
<p>The person who created this package and the underlying H5MD format is
Pierre de Buyl at KU Leuven (see <a class="reference external" href="http://pdebuyl.be">http://pdebuyl.be</a>). Contact him
directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-intel-package">
-<h2>4.13. USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.24. USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline">¶</a></h2>
<p>This package provides options for performing neighbor list and
non-bonded force calculations in single, mixed, or double precision
and also a capability for accelerating calculations with an
Intel(R) Xeon Phi(TM) coprocessor.</p>
<p>See this section of the manual to get started:</p>
<p><span class="xref std std-ref">Section_accelerate</span></p>
<p>The person who created this package is W. Michael Brown at Intel
(michael.w.brown at intel.com). Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-lb-package">
-<h2>4.14. USER-LB package<a class="headerlink" href="#user-lb-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.25. USER-LB package<a class="headerlink" href="#user-lb-package" title="Permalink to this headline">¶</a></h2>
<p>This package contains a LAMMPS implementation of a background
Lattice-Boltzmann fluid, which can be used to model MD particles
influenced by hydrodynamic forces.</p>
<p>See this doc page and its related commands to get started:</p>
<p><a class="reference internal" href="fix_lb_fluid.html"><em>fix lb/fluid</em></a></p>
<p>The people who created this package are Frances Mackay (fmackay at
uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
Western Ontario. Contact them directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-misc-package">
-<h2>4.15. USER-MISC package<a class="headerlink" href="#user-misc-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.26. 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="#id4"><span class="problematic" id="id5">*</span></a>.cpp and <a href="#id6"><span class="problematic" id="id7">*</span></a>.h).</p>
+pair of files (<a href="#id2"><span class="problematic" id="id3">*</span></a>.cpp and <a href="#id4"><span class="problematic" id="id5">*</span></a>.h).</p>
<p>More information about each feature can be found by reading its doc
page in the LAMMPS doc directory. The doc page which lists all LAMMPS
input script commands is as follows:</p>
<p><a class="reference internal" href="Section_commands.html#cmd-5"><span>Section_commands</span></a></p>
<p>User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections.</p>
<p>The list of features and author of each is given in the
src/USER-MISC/README file.</p>
<p>You should contact the author directly if you have specific questions
about the feature or its coding.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-molfile-package">
-<h2>4.16. USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.27. USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline">¶</a></h2>
<p>This package contains a dump molfile command which uses molfile
plugins that are bundled with the
<a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a> molecular visualization and
analysis program, to enable LAMMPS to dump its information in formats
compatible with various molecular simulation tools.</p>
<p>The package only provides the interface code, not the plugins. These
can be obtained from a VMD installation which has to match the
platform that you are using to compile LAMMPS for. By adding plugins
to VMD, support for new file formats can be added to LAMMPS (or VMD or
other programs that use them) without having to recompile the
application itself.</p>
<p>See this doc page to get started:</p>
<p><span class="xref std std-ref">dump molfile</span></p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-omp-package">
-<h2>4.17. USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.28. USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline">¶</a></h2>
<p>This package provides OpenMP multi-threading support and
other optimizations of various LAMMPS pair styles, dihedral
styles, and fix styles.</p>
<p>See this section of the manual to get started:</p>
<p><span class="xref std std-ref">Section_accelerate</span></p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-phonon-package">
-<h2>4.18. USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.29. USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline">¶</a></h2>
<p>This package contains a fix phonon command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
relations, directly from molecular dynamics simulations.</p>
<p>See this doc page to get started:</p>
<p><a class="reference internal" href="fix_phonon.html"><em>fix phonon</em></a></p>
<p>The person who created this package is Ling-Ti Kong (konglt at
sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly
if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-qmmm-package">
-<h2>4.19. USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.30. USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline">¶</a></h2>
<p>This package provides a fix qmmm command which allows LAMMPS to be
used in a QM/MM simulation, currently only in combination with pw.x
code from the <a class="reference external" href="http://www.quantum-espresso.org">Quantum ESPRESSO</a> package.</p>
<p>The current implementation only supports an ONIOM style mechanical
coupling to the Quantum ESPRESSO plane wave DFT package.
Electrostatic coupling is in preparation and the interface has been
written in a manner that coupling to other QM codes should be possible
without changes to LAMMPS itself.</p>
<p>See this doc page to get started:</p>
<p><a class="reference internal" href="fix_qmmm.html"><em>fix qmmm</em></a></p>
<p>as well as the lib/qmmm/README file.</p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-qtb-package">
-<h2>4.20. USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.31. USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline">¶</a></h2>
<p>This package provides a self-consistent quantum treatment of the
vibrational modes in a classical molecular dynamics simulation. By
coupling the MD simulation to a colored thermostat, it introduces zero
point energy into the system, alter the energy power spectrum and the
heat capacity towards their quantum nature. This package could be of
interest if one wants to model systems at temperatures lower than
their classical limits or when temperatures ramp up across the
classical limits in the simulation.</p>
<p>See these two doc pages to get started:</p>
<p><a class="reference internal" href="fix_qtb.html"><em>fix qtb</em></a> provides quantum nulcear correction through a
colored thermostat and can be used with other time integration schemes
like <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> or <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a>.</p>
<p><a class="reference internal" href="fix_qbmsst.html"><em>fix qbmsst</em></a> enables quantum nuclear correction of a
multi-scale shock technique simulation by coupling the quantum thermal
bath with the shocked system.</p>
<p>The person who created this package is Yuan Shen (sy0302 at
stanford.edu) at Stanford University. Contact him directly if you
have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-reaxc-package">
-<h2>4.21. USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.32. USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline">¶</a></h2>
<p>This package contains a implementation for LAMMPS of the ReaxFF force
field. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. It was originally developed by Adri van Duin and the Goddard
group at CalTech.</p>
<p>The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
C, should give identical or very similar results to pair_style reax,
which is a ReaxFF implementation on top of a Fortran library, a
version of which library was originally authored by Adri van Duin.</p>
<p>The reax/c version should be somewhat faster and more scalable,
particularly with respect to the charge equilibration calculation. It
should also be easier to build and use since there are no complicating
issues with Fortran memory allocation or linking to a Fortran library.</p>
<p>For technical details about this implemention of ReaxFF, see
this paper:</p>
<p>Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011).</p>
<p>See the doc page for the pair_style reax/c command for details
of how to use it in LAMMPS.</p>
<p>The person who created this package is Hasan Metin Aktulga (hmaktulga
at lbl.gov), while at Purdue University. Contact him directly, or
Aidan Thompson at Sandia (athomps at sandia.gov), if you have
questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-smd-package">
-<h2>4.22. USER-SMD package<a class="headerlink" href="#user-smd-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.33. 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>
<ul class="simple">
<li>Does liquids via traditional Smooth Particle Hydrodynamics (SPH)</li>
<li>Also solves solids mechanics problems via a state of the art
stabilized meshless method with hourglass control.</li>
<li>Can specify hydrostatic interactions independently from material
strength models, i.e. pressure and deviatoric stresses are separated.</li>
<li>Many material models available (Johnson-Cook, plasticity with
hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
material models.</li>
<li>Rigid boundary conditions (walls) can be loaded as surface geometries
-from <a href="#id9"><span class="problematic" id="id10">*</span></a>.STL files.</li>
+from <a href="#id7"><span class="problematic" id="id8">*</span></a>.STL files.</li>
</ul>
<p>See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.</p>
<p>There are example scripts for using this package in examples/USER/smd.</p>
<p>The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.</p>
</div>
<div class="section" id="user-sph-package">
-<h2>4.23. USER-SPH package<a class="headerlink" href="#user-sph-package" title="Permalink to this headline">¶</a></h2>
+<h2>4.34. 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">
<li>Tait, ideal gas, Lennard-Jones equation of states, full support for
complete (i.e. internal-energy dependent) equations of state</li>
<li>Plain or Monaghans XSPH integration of the equations of motion</li>
<li>Density continuity or density summation to propagate the density field</li>
<li>Commands to set internal energy and density of particles from the
input script</li>
<li>Output commands to access internal energy and density for dumping and
thermo output</li>
</ul>
<p>See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.</p>
<p>There are example scripts for using this package in examples/USER/sph.</p>
<p>The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.</p>
</div>
</div>
</div>
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\ No newline at end of file
diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt
index 01190f4a0..cfc879fb2 100644
--- a/doc/Section_packages.txt
+++ b/doc/Section_packages.txt
@@ -1,705 +1,803 @@
"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_accelerate.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
4. Packages :h3
This section gives a quick overview of the add-on packages that extend
LAMMPS functionality.
4.1 "Standard packages"_#pkg_1
4.2 "User packages"_#pkg_2 :all(b)
LAMMPS includes many optional packages, which are groups of files that
enable a specific set of features. For example, force fields for
molecular systems or granular systems are in packages. You can see
the list of all packages by typing "make package" from within the src
directory of the LAMMPS distribution.
See "Section_start 3"_Section_start.html#start_3 of the manual for
details on how to include/exclude specific packages as part of the
LAMMPS build process, and for more details about the differences
-between standard packages and user packages in LAMMPS.
-
-Below, the packages currently availabe in LAMMPS are listed. For
-standard packages, just a one-line description is given. For user
-packages, more details are provided.
+between standard packages and user packages.
+
+Unless otherwise noted below, every package is independent of all the
+others. I.e. any package can be included or excluded in a LAMMPS
+build, independent of all other packages. However, note that some
+packages include commands derived from commands in other packages. If
+the other package is not installed, the derived command from the new
+package will also not be installed when you include the new one.
+E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package
+will not be installed as part of the USER-OMP package if the KSPACE
+package is not also installed, since it contains the pair
+lj/cut/coul/long command. If you later install the KSPACE pacakge and
+the USER-OMP package is already installed, both the pair
+lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.
+
+The two tables below list currently available packages in LAMMPS, with
+a one-line descriptions of each. The sections below give a few more
+details, including instructions for building LAMMPS with the package,
+either via the make command or the Make.py tool described in "Section
+2.4"_Section_start.html#start_4.
:line
:line
4.1 Standard packages :h4,link(pkg_1)
-The current list of standard packages is as follows:
+The current list of standard packages is as follows.
Package, Description, Author(s), Doc page, Example, Library
ASPHERE, aspherical particles, -, "Section_howto 6.14"_Section_howto.html#howto_14, ellipse, -
BODY, body-style particles, -, "body"_body.html, body, -
CLASS2, class 2 force fields, -, "pair_style lj/class2"_pair_class2.html, -, -
COLLOID, colloidal particles, -, "atom_style colloid"_atom_style.html, colloid, -
COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, -
CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section_howto 6.25"_Section_howto.html#howto_25, coreshell, -
DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -
FLD, Fast Lubrication Dynamics, Kumar & Bybee & Higdon (1), "pair_style lubricateU"_pair_lubricateU.html, -, -
GPU, GPU-enabled styles, Mike Brown (ORNL), "Section accelerate"_accelerate_gpu.html, gpu, lib/gpu
GRANULAR, granular systems, -, "Section_howto 6.6"_Section_howto.html#howto_6, pour, -
KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM
KOKKOS, Kokkos-enabled styles, Trott & Edwards (4), "Section_accelerate"_accelerate_kokkos.html, kokkos, lib/kokkos
KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
MOLECULE, molecular system force fields, -, "Section_howto 6.3"_Section_howto.html#howto_3, peptide, -
OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section accelerate"_accelerate_opt.html, -, -
PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
REPLICA, multi-replica methods, -, "Section_howto 6.5"_Section_howto.html#howto_5, tad, -
RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
SNAP, quantum-fit potential, Aidan Thompson (Sandia), "pair snap"_pair_snap.html, snap, -
SRD, stochastic rotation dynamics, -, "fix srd"_fix_srd.html, srd, -
VORONOI, Voronoi tesselations, Daniel Schwen (LANL), "compute voronoi/atom"_compute_voronoi_atom.html, -, Voro++
XTC, dumps in XTC format, -, "dump"_dump.html, -, -
:tb(ea=c)
The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
+More details on
+multiple authors are give below.
(1) The FLD package was created by Amit Kumar and Michael Bybee from
Jonathan Higdon's group at UIUC.
(2) The OPT package was created by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technolgy).
(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
and Ellad Tadmor (U Minn).
(4) The KOKKOS package was created primarily by Christian Trott
(Sandia). It uses the Kokkos library which was developed by Carter
Edwards, Christian, and collaborators at Sandia.
The "Doc page" column links to either a portion of the
"Section_howto"_Section_howto.html of the manual, or an input script
command implemented as part of the package.
The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory.
The "Library" column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See the src/package/README or src/package/Makefile.lammps file for
info on where to download the library. "Section
start"_Section_start.html#start_3_3 of the manual also gives details
on how to build LAMMPS with both kinds of auxiliary libraries.
+Except where explained below, all of these packages can be installed,
+and LAMMPS re-built, by issuing these commands from the src dir.
+
+make yes-package
+make machine
+or
+Make.py -p package -a machine :pre
+
+To un-install the package and re-build LAMMPS without it:
+
+make no-package
+make machine
+or
+Make.py -p ^package -a machine :pre
+
+"Package" is the name of the package in lower-case letters,
+e.g. asphere or rigid, and "machine" is the build target, e.g. mpi or
+serial.
+
+:line
+:line
+
+Build instructions for COMPRESS package :h4
+
+:line
+
+Build instructions for GPU package :h4
+
+:line
+
+Build instructions for KIM package :h4
+
+:line
+
+Build instructions for KOKKOS package :h4
+
+:line
+
+Build instructions for KSPACE package :h4
+
+:line
+
+Build instructions for MEAM package :h4
+
+:line
+
+Build instructions for POEMS package :h4
+
+:line
+
+Build instructions for PYTHON package :h4
+
+:line
+
+Build instructions for REAX package :h4
+
+:line
+
+Build instructions for VORONOI package :h4
+
+:line
+
+Build instructions for XTC package :h4
+
:line
:line
4.2 User packages :h4,link(pkg_2)
The current list of user-contributed packages is as follows:
Package, Description, Author(s), Doc page, Example, Pic/movie, Library
USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda
USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
USER-DRUDE, Drude oscillators, Dequidt & Devemy & Padua (3), "tutorial"_tutorial_drude.html, USER/drude, -, -
USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md
USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, -
USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, -
USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
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"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, -
USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute <...>/tally"_compute_tally.html, USER/tally, -, -
:tb(ea=c)
:link(atc,http://lammps.sandia.gov/pictures.html#atc)
:link(cg,http://lammps.sandia.gov/pictures.html#cg)
:link(eff,http://lammps.sandia.gov/movies.html#eff)
:link(sph,http://lammps.sandia.gov/movies.html#sph)
:link(VMD,http://www.ks.uiuc.edu/Research/vmd)
The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
-If the Library is not listed as lib/package, then it is a third-party
-library not included in the LAMMPS distribution. See the
-src/package/Makefile.lammps file for info on where to download the
-library from.
-
-(2) The ATC package was created by Reese Jones, Jeremy Templeton, and
+(1) The ATC package was created by Reese Jones, Jeremy Templeton, and
Jon Zimmerman (Sandia).
(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
the colvars module library written by Giacomo Fiorin (Temple U) and
Jerome Henin (LISM, Marseille, France).
(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal
Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
(U Blaise Pascal).
+If the Library is not listed as lib/package, then it is a third-party
+library not included in the LAMMPS distribution. See the
+src/package/Makefile.lammps file for info on where to download the
+library from.
+
The "Doc page" column links to either a portion of the
"Section_howto"_Section_howto.html of the manual, or an input script
command implemented as part of the package, or to additional
-documentation provided witht he package.
+documentation provided within the package.
The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory. USER/cuda
refers to the examples/USER/cuda directory.
The "Library" column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See the src/package/Makefile.lammps file for info on where to download
the library. "Section start"_Section_start.html#start_3_3 of the
manual also gives details on how to build LAMMPS with both kinds of
auxiliary libraries.
-More details on each package, from the USER-*/README file is given
-below.
+Except where explained below, all of these packages can be installed,
+and LAMMPS re-built, by issuing these commands from the src dir.
+
+make yes-user-package
+make machine
+or
+Make.py -p package -a machine :pre
+
+To un-install the package and re-build LAMMPS without it:
+make no-user-package
+make machine
+or
+Make.py -p ^package -a machine :pre
+
+"Package" is the name of the package (in this case without the user
+prefix) in lower-case letters, e.g. drude or phonon, and "machine" is
+the build target, e.g. mpi or serial.
+
+:line
:line
USER-ATC package :h4
This package implements a "fix atc" command which can be used in a
LAMMPS input script. This fix can be employed to either do concurrent
coupling of MD with FE-based physics surrogates or on-the-fly
post-processing of atomic information to continuum fields.
See the doc page for the fix atc command to get started. At the
bottom of the doc page are many links to additional documentation
contained in the doc/USER/atc directory.
There are example scripts for using this package in examples/USER/atc.
This package uses an external library in lib/atc which must be
compiled before making LAMMPS. See the lib/atc/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
The primary people who created this package are Reese Jones (rjones at
sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
you have questions.
:line
USER-AWPMD package :h4
This package contains a LAMMPS implementation of the Antisymmetrized
Wave Packet Molecular Dynamics (AWPMD) method.
See the doc page for the pair_style awpmd/cut command to get started.
There are example scripts for using this package in examples/USER/awpmd.
This package uses an external library in lib/awpmd which must be
compiled before making LAMMPS. See the lib/awpmd/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
The person who created this package is Ilya Valuev at the JIHT in
Russia (valuev at physik.hu-berlin.de). Contact him directly if you
have questions.
:line
USER-CG-CMM package :h4
This package implements 3 commands which can be used in a LAMMPS input
script:
pair_style lj/sdk
pair_style lj/sdk/coul/long
angle_style sdk :ul
These styles allow coarse grained MD simulations with the
parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
(SDK), with extensions to simulate ionic liquids, electrolytes, lipids
and charged amino acids.
See the doc pages for these commands for details.
There are example scripts for using this package in
examples/USER/cg-cmm.
This is the second generation implementation reducing the the clutter
of the previous version. For many systems with electrostatics, it will
be faster to use pair_style hybrid/overlay with lj/sdk and coul/long
instead of the combined lj/sdk/coul/long style. since the number of
charged atom types is usually small. For any other coulomb
interactions this is now required. To exploit this property, the use
of the kspace_style pppm/cg is recommended over regular pppm. For all
new styles, input file backward compatibility is provided. The old
implementation is still available through appending the /old
suffix. These will be discontinued and removed after the new
implementation has been fully validated.
The current version of this package should be considered beta
quality. The CG potentials work correctly for "normal" situations, but
have not been testing with all kinds of potential parameters and
simulation systems.
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
:line
USER-COLVARS package :h4
This package implements the "fix colvars" command which can be
used in a LAMMPS input script.
This fix allows to use "collective variables" to implement
Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
Sampling and Restraints. This code consists of two parts:
A portable collective variable module library written and maintained
by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
Jerome Henin (LISM, CNRS, Marseille, France). This code is located in
the directory lib/colvars and needs to be compiled first. The colvars
fix and an interface layer, exchanges information between LAMMPS and
the collective variable module. :ul
See the doc page of "fix colvars"_fix_colvars.html for more details.
There are example scripts for using this package in
examples/USER/colvars
This is a very new interface that does not yet support all
features in the module and will see future optimizations
and improvements. The colvars module library is also available
in NAMD has been thoroughly used and tested there. Bugs and
problems are likely due to the interface layers code.
Thus the current version of this package should be considered
beta quality.
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
:line
USER-CUDA package :h4
This package provides acceleration of various LAMMPS pair styles, fix
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
GPUs.
See this section of the manual to get started:
"Section_accelerate"_Section_accelerate.html#acc_7
There are example scripts for using this package in
examples/USER/cuda.
This package uses an external library in lib/cuda which must be
compiled before making LAMMPS. See the lib/cuda/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
The person who created this package is Christian Trott at the
University of Technology Ilmenau, Germany (christian.trott at
tu-ilmenau.de). Contact him directly if you have questions.
:line
USER-DIFFRACTION package :h4
This package contains the commands neeed to calculate x-ray and
electron diffraction intensities based on kinematic diffraction
theory.
See these doc pages and their related commands to get started:
"compute xrd"_compute_xrd.html
"compute saed"_compute_saed.html
"fix saed/vtk"_fix_saed_vtk.html :ul
The person who created this package is Shawn P. Coleman
(shawn.p.coleman8.ctr at mail.mil) while at the University of
Arkansas. Contact him directly if you have questions.
:line
USER-DRUDE package :h4
This package implements methods for simulating polarizable systems
in LAMMPS using thermalized Drude oscillators.
See these doc pages and their related commands to get started:
"Drude tutorial"_tutorial_drude.html
"fix drude"_fix_drude.html
"compute temp/drude"_compute_temp_drude.html
"fix langevin/drude"_fix_langevin_drude.html
"fix drude/transform/..."_fix_drude_transform.html
"pair thole"_pair_thole.html :ul
There are auxiliary tools for using this package in tools/drude.
The person who created this package is Alain Dequidt at Universite
Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
Contact him directly if you have questions. Co-authors: Julien Devemy,
Agilio Padua.
:line
USER-EFF package :h4
This package contains a LAMMPS implementation of the electron Force
Field (eFF) currently under development at Caltech, as described in
A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
2010. The eFF potential was first introduced by Su and Goddard, in
2007.
eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
structure methods to describe atomic structure, bonding, and chemistry
in materials, and of plasma methods to describe nonequilibrium
dynamics of large systems with a large number of highly excited
electrons. We classify it as a mixed QM-classical approach rather than
a conventional force field method, which introduces QM-based terms (a
spin-dependent repulsion term to account for the Pauli exclusion
principle and the electron wavefunction kinetic energy associated with
the Heisenberg principle) that reduce, along with classical
electrostatic terms between nuclei and electrons, to the sum of a set
of effective pairwise potentials. This makes eFF uniquely suited to
simulate materials over a wide range of temperatures and pressures
where electronically excited and ionized states of matter can occur
and coexist.
The necessary customizations to the LAMMPS core are in place to
enable the correct handling of explicit electron properties during
minimization and dynamics.
See the doc page for the pair_style eff/cut command to get started.
There are example scripts for using this package in
examples/USER/eff.
There are auxiliary tools for using this package in tools/eff.
The person who created this package is Andres Jaramillo-Botero at
CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
have questions.
:line
USER-FEP package :h4
This package provides methods for performing free energy perturbation
simulations with soft-core pair potentials in LAMMPS.
See these doc pages and their related commands to get started:
"fix adapt/fep"_fix_adapt_fep.html
"compute fep"_compute_fep.html
"soft pair styles"_pair_lj_soft.html :ul
The person who created this package is Agilio Padua at Universite
Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
Contact him directly if you have questions.
:line
USER-H5MD package :h4
This package contains a "dump h5md"_dump_h5md.html command for
performing a dump of atom properties in HDF5 format. "HDF5
files"_HDF5 are binary, portable and self-describing and can be
examined and used by a variety of auxiliary tools. The output HDF5
files are structured in a format called H5MD, which was designed to
store molecular data, and can be used and produced by various MD and
MD-related codes. The "dump h5md"_doc/dump_h5md.html command gives a
citation to a paper describing the format.
:link(HDF5,http://www.hdfgroup.org/HDF5/)
The person who created this package and the underlying H5MD format is
Pierre de Buyl at KU Leuven (see http://pdebuyl.be). Contact him
directly if you have questions.
:line
USER-INTEL package :h4
This package provides options for performing neighbor list and
non-bonded force calculations in single, mixed, or double precision
and also a capability for accelerating calculations with an
Intel(R) Xeon Phi(TM) coprocessor.
See this section of the manual to get started:
"Section_accelerate"_Section_accelerate.html#acc_9
The person who created this package is W. Michael Brown at Intel
(michael.w.brown at intel.com). Contact him directly if you have questions.
:line
USER-LB package :h4
This package contains a LAMMPS implementation of a background
Lattice-Boltzmann fluid, which can be used to model MD particles
influenced by hydrodynamic forces.
See this doc page and its related commands to get started:
"fix lb/fluid"_fix_lb_fluid.html
The people who created this package are Frances Mackay (fmackay at
uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
Western Ontario. Contact them directly if you have questions.
:line
USER-MISC package :h4
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 (*.cpp and *.h).
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:
"Section_commands"_Section_commands.html#cmd_5
User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections.
The list of features and author of each is given in the
src/USER-MISC/README file.
You should contact the author directly if you have specific questions
about the feature or its coding.
:line
USER-MOLFILE package :h4
This package contains a dump molfile command which uses molfile
plugins that are bundled with the
"VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
analysis program, to enable LAMMPS to dump its information in formats
compatible with various molecular simulation tools.
The package only provides the interface code, not the plugins. These
can be obtained from a VMD installation which has to match the
platform that you are using to compile LAMMPS for. By adding plugins
to VMD, support for new file formats can be added to LAMMPS (or VMD or
other programs that use them) without having to recompile the
application itself.
See this doc page to get started:
"dump molfile"_dump_molfile.html#acc_5
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
:line
USER-OMP package :h4
This package provides OpenMP multi-threading support and
other optimizations of various LAMMPS pair styles, dihedral
styles, and fix styles.
See this section of the manual to get started:
"Section_accelerate"_Section_accelerate.html#acc_5
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
:line
USER-PHONON package :h4
This package contains a fix phonon command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
relations, directly from molecular dynamics simulations.
See this doc page to get started:
"fix phonon"_fix_phonon.html
The person who created this package is Ling-Ti Kong (konglt at
sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly
if you have questions.
:line
USER-QMMM package :h4
This package provides a fix qmmm command which allows LAMMPS to be
used in a QM/MM simulation, currently only in combination with pw.x
code from the "Quantum ESPRESSO"_espresso package.
:link(espresso,http://www.quantum-espresso.org)
The current implementation only supports an ONIOM style mechanical
coupling to the Quantum ESPRESSO plane wave DFT package.
Electrostatic coupling is in preparation and the interface has been
written in a manner that coupling to other QM codes should be possible
without changes to LAMMPS itself.
See this doc page to get started:
"fix qmmm"_fix_qmmm.html
as well as the lib/qmmm/README file.
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
:line
USER-QTB package :h4
This package provides a self-consistent quantum treatment of the
vibrational modes in a classical molecular dynamics simulation. By
coupling the MD simulation to a colored thermostat, it introduces zero
point energy into the system, alter the energy power spectrum and the
heat capacity towards their quantum nature. This package could be of
interest if one wants to model systems at temperatures lower than
their classical limits or when temperatures ramp up across the
classical limits in the simulation.
See these two doc pages to get started:
"fix qtb"_fix_qtb.html provides quantum nulcear correction through a
colored thermostat and can be used with other time integration schemes
like "fix nve"_fix_nve.html or "fix nph"_fix_nh.html.
"fix qbmsst"_fix_qbmsst.html enables quantum nuclear correction of a
multi-scale shock technique simulation by coupling the quantum thermal
bath with the shocked system.
The person who created this package is Yuan Shen (sy0302 at
stanford.edu) at Stanford University. Contact him directly if you
have questions.
:line
USER-REAXC package :h4
This package contains a implementation for LAMMPS of the ReaxFF force
field. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. It was originally developed by Adri van Duin and the Goddard
group at CalTech.
The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
C, should give identical or very similar results to pair_style reax,
which is a ReaxFF implementation on top of a Fortran library, a
version of which library was originally authored by Adri van Duin.
The reax/c version should be somewhat faster and more scalable,
particularly with respect to the charge equilibration calculation. It
should also be easier to build and use since there are no complicating
issues with Fortran memory allocation or linking to a Fortran library.
For technical details about this implemention of ReaxFF, see
this paper:
Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011).
See the doc page for the pair_style reax/c command for details
of how to use it in LAMMPS.
The person who created this package is Hasan Metin Aktulga (hmaktulga
at lbl.gov), while at Purdue University. Contact him directly, or
Aidan Thompson at Sandia (athomps at sandia.gov), if you have
questions.
:line
USER-SMD package :h4
This package implements smoothed Mach dynamics (SMD) in
LAMMPS. Currently, the package has the following features:
* Does liquids via traditional Smooth Particle Hydrodynamics (SPH)
* Also solves solids mechanics problems via a state of the art
stabilized meshless method with hourglass control.
* Can specify hydrostatic interactions independently from material
strength models, i.e. pressure and deviatoric stresses are separated.
* Many material models available (Johnson-Cook, plasticity with
hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
material models.
* Rigid boundary conditions (walls) can be loaded as surface geometries
from *.STL files.
See the file doc/PDF/SMD_LAMMPS_userguide.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
LAMMPS. Currently, the package has the following features:
* Tait, ideal gas, Lennard-Jones equation of states, full support for
complete (i.e. internal-energy dependent) equations of state
* Plain or Monaghans XSPH integration of the equations of motion
* Density continuity or density summation to propagate the density field
* Commands to set internal energy and density of particles from the
input script
* Output commands to access internal energy and density for dumping and
thermo output
See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.
There are example scripts for using this package in examples/USER/sph.
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.
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">2. Getting Started</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#what-s-in-the-lammps-distribution">2.1. What’s in the LAMMPS distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="#making-lammps">2.2. Making LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="#making-lammps-with-optional-packages">2.3. Making LAMMPS with optional packages</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#building-lammps-via-the-make-py-script">2.4. Building LAMMPS via the Make.py script</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#building-lammps-via-the-make-py-tool">2.4. Building LAMMPS via the Make.py tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#building-lammps-as-a-library">2.5. Building LAMMPS as a library</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#static-library">2.5.1. <strong>Static library:</strong></a></li>
<li class="toctree-l3"><a class="reference internal" href="#shared-library">2.5.2. <strong>Shared library:</strong></a></li>
<li class="toctree-l3"><a class="reference internal" href="#additional-requirement-for-using-a-shared-library">2.5.3. <strong>Additional requirement for using a shared library:</strong></a></li>
<li class="toctree-l3"><a class="reference internal" href="#calling-the-lammps-library">2.5.4. <strong>Calling the LAMMPS library:</strong></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#running-lammps">2.6. Running LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="#command-line-options">2.7. Command-line options</a></li>
<li class="toctree-l2"><a class="reference internal" href="#lammps-screen-output">2.8. LAMMPS screen output</a></li>
<li class="toctree-l2"><a class="reference internal" href="#tips-for-users-of-previous-lammps-versions">2.9. Tips for users of previous LAMMPS versions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<div class="section" id="getting-started">
<h1>2. Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h1>
<p>This section describes how to build and run LAMMPS, for both new and
experienced users.</p>
<div class="line-block">
<div class="line">2.1 <a class="reference internal" href="#start-1"><span>What’s in the LAMMPS distribution</span></a></div>
<div class="line">2.2 <a class="reference internal" href="#start-2"><span>Making LAMMPS</span></a></div>
<div class="line">2.3 <a class="reference internal" href="#start-3"><span>Making LAMMPS with optional packages</span></a></div>
<div class="line">2.4 <a class="reference internal" href="#start-4"><span>Building LAMMPS via the Make.py script</span></a></div>
<div class="line">2.5 <a class="reference internal" href="#start-5"><span>Building LAMMPS as a library</span></a></div>
<div class="line">2.6 <a class="reference internal" href="#start-6"><span>Running LAMMPS</span></a></div>
<div class="line">2.7 <a class="reference internal" href="#start-7"><span>Command-line options</span></a></div>
<div class="line">2.8 <a class="reference internal" href="#start-8"><span>Screen output</span></a></div>
<div class="line">2.9 <a class="reference internal" href="#start-9"><span>Tips for users of previous versions</span></a></div>
<div class="line"><br /></div>
</div>
<div class="section" id="what-s-in-the-lammps-distribution">
<span id="start-1"></span><h2>2.1. What’s in the LAMMPS distribution<a class="headerlink" href="#what-s-in-the-lammps-distribution" title="Permalink to this headline">¶</a></h2>
<p>When you download a LAMMPS tarball you will need to unzip and untar
the downloaded file with the following commands, after placing the
tarball in an appropriate directory.</p>
<div class="highlight-python"><div class="highlight"><pre>gunzip lammps*.tar.gz
tar xvf lammps*.tar
</pre></div>
</div>
<p>This will create a LAMMPS directory containing two files and several
sub-directories:</p>
<table border="1" class="docutils">
<colgroup>
<col width="21%" />
<col width="79%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>README</td>
<td>text file</td>
</tr>
<tr class="row-even"><td>LICENSE</td>
<td>the GNU General Public License (GPL)</td>
</tr>
<tr class="row-odd"><td>bench</td>
<td>benchmark problems</td>
</tr>
<tr class="row-even"><td>doc</td>
<td>documentation</td>
</tr>
<tr class="row-odd"><td>examples</td>
<td>simple test problems</td>
</tr>
<tr class="row-even"><td>potentials</td>
<td>embedded atom method (EAM) potential files</td>
</tr>
<tr class="row-odd"><td>src</td>
<td>source files</td>
</tr>
<tr class="row-even"><td>tools</td>
<td>pre- and post-processing tools</td>
</tr>
</tbody>
</table>
<p>Note that the <a class="reference external" href="download">download page</a> also has links to download
Windows exectubles and installers, as well as pre-built executables
for a few specific Linux distributions. It also has instructions for
how to download/install LAMMPS for Macs (via Homebrew), and to
download and update LAMMPS from SVN and Git repositories, which gives
you the same files that are in the download tarball.</p>
<p>The Windows and Linux executables for serial or parallel only include
certain packages and bug-fixes/upgrades listed on <a class="reference external" href="http://lammps.sandia.gov/bug.html">this page</a> up to a certain date, as
stated on the download page. If you want an executable with
non-included packages or that is more current, then you’ll need to
build LAMMPS yourself, as discussed in the next section.</p>
<p>Skip to the <a class="reference internal" href="#start-6"><span>Running LAMMPS</span></a> sections for info on how to
launch a LAMMPS Windows executable on a Windows box.</p>
<hr class="docutils" />
</div>
<div class="section" id="making-lammps">
<span id="start-2"></span><h2>2.2. Making LAMMPS<a class="headerlink" href="#making-lammps" title="Permalink to this headline">¶</a></h2>
<p>This section has the following sub-sections:</p>
<ul class="simple">
<li><a class="reference internal" href="#start-2-1"><span>Read this first</span></a></li>
<li><a class="reference internal" href="#start-2-2"><span>Steps to build a LAMMPS executable</span></a></li>
<li><a class="reference internal" href="#start-2-3"><span>Common errors that can occur when making LAMMPS</span></a></li>
<li><a class="reference internal" href="#start-2-4"><span>Additional build tips</span></a></li>
<li><a class="reference internal" href="#start-2-5"><span>Building for a Mac</span></a></li>
<li><a class="reference internal" href="#start-2-6"><span>Building for Windows</span></a></li>
</ul>
<hr class="docutils" />
<p id="start-2-1"><strong>*Read this first:*</strong></p>
<p>If you want to avoid building LAMMPS yourself, read the preceeding
section about options available for downloading and installing
executables. Details are discussed on the <a class="reference external" href="download">download</a> page.</p>
<p>Building LAMMPS can be simple or not-so-simple. If all you need are
the default packages installed in LAMMPS, and MPI is already installed
on your machine, or you just want to run LAMMPS in serial, then you
can typically use the Makefile.mpi or Makefile.serial files in
src/MAKE by typing one of these lines (from the src dir):</p>
<div class="highlight-python"><div class="highlight"><pre>make mpi
make serial
</pre></div>
</div>
<p>Note that on a facility supercomputer, there are often “modules”
loaded in your environment that provide the compilers and MPI you
should use. In this case, the “mpicxx” compile/link command in
Makefile.mpi should just work by accessing those modules.</p>
<p>It may be the case that one of the other Makefile.machine files in the
src/MAKE sub-directories is a better match to your system (type “make”
to see a list), you can use it as-is by typing (for example):</p>
<div class="highlight-python"><div class="highlight"><pre>make stampede
</pre></div>
</div>
<p>If any of these builds (with an existing Makefile.machine) works on
your system, then you’re done!</p>
<p>If you want to do one of the following:</p>
<ul class="simple">
<li>use optional LAMMPS features that require additional libraries</li>
<li>use optional packages that require additional libraries</li>
<li>use optional accelerator packages that require special compiler/linker settings</li>
<li>run on a specialized platform that has its own compilers, settings, or other libs to use</li>
</ul>
<p>then building LAMMPS is more complicated. You may need to find where
auxiliary libraries exist on your machine or install them if they
don’t. You may need to build additional libraries that are part of
the LAMMPS package, before building LAMMPS. You may need to edit a
Makefile.machine file to make it compatible with your system.</p>
<p>Note that there is a Make.py tool in the src directory that automates
several of these steps, but you still have to know what you are doing.
<a class="reference internal" href="#start-4"><span>Section 2.4</span></a> below describes the tool. It is a convenient
way to work with installing/un-installing various packages, the
Makefile.machine changes required by some packages, and the auxiliary
libraries some of them use.</p>
<p>Please read the following sections carefully. If you are not
comfortable with makefiles, or building codes on a Unix platform, or
running an MPI job on your machine, please find a local expert to help
you. Many compilation, linking, and run problems that users have are
often not really LAMMPS issues - they are peculiar to the user’s
system, compilers, libraries, etc. Such questions are better answered
by a local expert.</p>
<p>If you have a build problem that you are convinced is a LAMMPS issue
(e.g. the compiler complains about a line of LAMMPS source code), then
please post the issue to the <a class="reference external" href="http://lammps.sandia.gov/mail.html">LAMMPS mail list</a>.</p>
<p>If you succeed in building LAMMPS on a new kind of machine, for which
there isn’t a similar machine Makefile included in the
src/MAKE/MACHINES directory, then send it to the developers and we can
include it in the LAMMPS distribution.</p>
<hr class="docutils" />
<p id="start-2-2"><strong>*Steps to build a LAMMPS executable:*</strong></p>
<p><strong>Step 0</strong></p>
<p>The src directory contains the C++ source and header files for LAMMPS.
It also contains a top-level Makefile and a MAKE sub-directory with
low-level Makefile.* files for many systems and machines. See the
src/MAKE/README file for a quick overview of what files are available
and what sub-directories they are in.</p>
<p>The src/MAKE dir has a few files that should work as-is on many
platforms. The src/MAKE/OPTIONS dir has more that invoke additional
compiler, MPI, and other setting options commonly used by LAMMPS, to
illustrate their syntax. The src/MAKE/MACHINES dir has many more that
have been tweaked or optimized for specific machines. These files are
all good starting points if you find you need to change them for your
machine. Put any file you edit into the src/MAKE/MINE directory and
it will be never be touched by any LAMMPS updates.</p>
<p>>From within the src directory, type “make” or “gmake”. You should see
a list of available choices from src/MAKE and all of its
sub-directories. If one of those has the options you want or is the
machine you want, you can type a command like:</p>
<div class="highlight-python"><div class="highlight"><pre>make mpi
or
make serial_icc
or
gmake mac
</pre></div>
</div>
<p>Note that the corresponding Makefile.machine can exist in src/MAKE or
any of its sub-directories. If a file with the same name appears in
multiple places (not a good idea), the order they are used is as
follows: src/MAKE/MINE, src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES.
This gives preference to a file you have created/edited and put in
src/MAKE/MINE.</p>
<p>Note that on a multi-processor or multi-core platform you can launch a
parallel make, by using the “-j” switch with the make command, which
will build LAMMPS more quickly.</p>
<p>If you get no errors and an executable like lmp_mpi or lmp_g++_serial
or lmp_mac is produced, then you’re done; it’s your lucky day.</p>
<p>Note that by default only a few of LAMMPS optional packages are
installed. To build LAMMPS with optional packages, see <a class="reference internal" href="#start-3"><span>this section</span></a> below.</p>
<p><strong>Step 1</strong></p>
<p>If Step 0 did not work, you will need to create a low-level Makefile
for your machine, like Makefile.foo. You should make a copy of an
existing Makefile.* in src/MAKE or one of its sub-directories as a
starting point. The only portions of the file you need to edit are
the first line, the “compiler/linker settings” section, and the
“LAMMPS-specific settings” section. When it works, put the edited
file in src/MAKE/MINE and it will not be altered by any future LAMMPS
updates.</p>
<p><strong>Step 2</strong></p>
<p>Change the first line of Makefile.foo to list the word “foo” after the
“#”, and whatever other options it will set. This is the line you
will see if you just type “make”.</p>
<p><strong>Step 3</strong></p>
<p>The “compiler/linker settings” section lists compiler and linker
settings for your C++ compiler, including optimization flags. You can
use g++, the open-source GNU compiler, which is available on all Unix
systems. You can also use mpicxx which will typically be available if
MPI is installed on your system, though you should check which actual
compiler it wraps. Vendor compilers often produce faster code. On
boxes with Intel CPUs, we suggest using the Intel icc compiler, which
can be downloaded from <a class="reference external" href="http://www.intel.com/software/products/noncom">Intel’s compiler site</a>.</p>
<p>If building a C++ code on your machine requires additional libraries,
then you should list them as part of the LIB variable. You should
not need to do this if you use mpicxx.</p>
<p>The DEPFLAGS setting is what triggers the C++ compiler to create a
dependency list for a source file. This speeds re-compilation when
source (<em>.cpp) or header (</em>.h) files are edited. Some compilers do
not support dependency file creation, or may use a different switch
than -D. GNU g++ and Intel icc works with -D. If your compiler can’t
create dependency files, then you’ll need to create a Makefile.foo
patterned after Makefile.storm, which uses different rules that do not
involve dependency files. Note that when you build LAMMPS for the
first time on a new platform, a long list of <a href="#id1"><span class="problematic" id="id2">*</span></a>.d files will be printed
out rapidly. This is not an error; it is the Makefile doing its
normal creation of dependencies.</p>
<p><strong>Step 4</strong></p>
<p>The “system-specific settings” section has several parts. Note that
if you change any -D setting in this section, you should do a full
re-compile, after typing “make clean” (which will describe different
clean options).</p>
<p>The LMP_INC variable is used to include options that turn on ifdefs
within the LAMMPS code. The options that are currently recogized are:</p>
<ul class="simple">
<li>-DLAMMPS_GZIP</li>
<li>-DLAMMPS_JPEG</li>
<li>-DLAMMPS_PNG</li>
<li>-DLAMMPS_FFMPEG</li>
<li>-DLAMMPS_MEMALIGN</li>
<li>-DLAMMPS_XDR</li>
<li>-DLAMMPS_SMALLBIG</li>
<li>-DLAMMPS_BIGBIG</li>
<li>-DLAMMPS_SMALLSMALL</li>
<li>-DLAMMPS_LONGLONG_TO_LONG</li>
<li>-DPACK_ARRAY</li>
<li>-DPACK_POINTER</li>
<li>-DPACK_MEMCPY</li>
</ul>
<p>The read_data and dump commands will read/write gzipped files if you
compile with -DLAMMPS_GZIP. It requires that your machine supports
the “popen()” function in the standard runtime library and that a gzip
executable can be found by LAMMPS during a run.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">on some clusters with high-speed networks, using the
fork() library calls (required by popen()) can interfere with the fast
communication library and lead to simulations using compressed output
or input to hang or crash. For selected operations, compressed file
I/O is also available using a compression library instead, which are
provided in the COMPRESS package. From more details about compiling
LAMMPS with packages, please see below.</p>
</div>
<p>If you use -DLAMMPS_JPEG, the <a class="reference internal" href="dump_image.html"><em>dump image</em></a> command
will be able to write out JPEG image files. For JPEG files, you must
also link LAMMPS with a JPEG library, as described below. If you use
-DLAMMPS_PNG, the <a class="reference internal" href="dump.html"><em>dump image</em></a> command will be able to write
out PNG image files. For PNG files, you must also link LAMMPS with a
PNG library, as described below. If neither of those two defines are
used, LAMMPS will only be able to write out uncompressed PPM image
files.</p>
<p>If you use -DLAMMPS_FFMPEG, the <a class="reference internal" href="dump_image.html"><em>dump movie</em></a> command
will be available to support on-the-fly generation of rendered movies
the need to store intermediate image files. It requires that your
machines supports the “popen” function in the standard runtime library
and that an FFmpeg executable can be found by LAMMPS during the run.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Similar to the note above, this option can conflict
with high-speed networks, because it uses popen().</p>
</div>
<p>Using -DLAMMPS_MEMALIGN=<bytes> enables the use of the
posix_memalign() call instead of malloc() when large chunks or memory
are allocated by LAMMPS. This can help to make more efficient use of
vector instructions of modern CPUS, since dynamically allocated memory
has to be aligned on larger than default byte boundaries (e.g. 16
bytes instead of 8 bytes on x86 type platforms) for optimal
performance.</p>
<p>If you use -DLAMMPS_XDR, the build will include XDR compatibility
files for doing particle dumps in XTC format. This is only necessary
if your platform does have its own XDR files available. See the
Restrictions section of the <a class="reference internal" href="dump.html"><em>dump</em></a> command for details.</p>
<p>Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, -D-
DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These
settings refer to use of 4-byte (small) vs 8-byte (big) integers
within LAMMPS, as specified in src/lmptype.h. The only reason to use
the BIGBIG setting is to enable simulation of huge molecular systems
(which store bond topology info) with more than 2 billion atoms, or to
track the image flags of moving atoms that wrap around a periodic box
more than 512 times. Normally, the only reason to use SMALLSMALL is
if your machine does not support 64-bit integers, though you can use
SMALLSMALL setting if you are running in serial or on a desktop
machine or small cluster where you will never run large systems or for
long time (more than 2 billion atoms, more than 2 billion timesteps).
See the <a class="reference internal" href="#start-2-4"><span>Additional build tips</span></a> section below for more
details on these settings.</p>
<p>Note that two packages, USER-ATC and USER-CUDA are not currently
compatible with -DLAMMPS_BIGBIG. Also the GPU package requires the
lib/gpu library to be compiled with the same setting, or the link will
fail.</p>
<p>The -DLAMMPS_LONGLONG_TO_LONG setting may be needed if your system or
MPI version does not recognize “long long” data types. In this case a
“long” data type is likely already 64-bits, in which case this setting
will convert to that data type.</p>
<p>Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY
options can make for faster parallel FFTs (in the PPPM solver) on some
platforms. The -DPACK_ARRAY setting is the default. See the
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command for info about PPPM. See
Step 6 below for info about building LAMMPS with an FFT library.</p>
<p><strong>Step 5</strong></p>
<p>The 3 MPI variables are used to specify an MPI library to build LAMMPS
with. Note that you do not need to set these if you use the MPI
compiler mpicxx for your CC and LINK setting in the section above.
The MPI wrapper knows where to find the needed files.</p>
<p>If you want LAMMPS to run in parallel, you must have an MPI library
installed on your platform. If MPI is installed on your system in the
usual place (under /usr/local), you also may not need to specify these
3 variables, assuming /usr/local is in your path. On some large
parallel machines which use “modules” for their compile/link
environements, you may simply need to include the correct module in
your build environment, before building LAMMPS. Or the parallel
machine may have a vendor-provided MPI which the compiler has no
trouble finding.</p>
<p>Failing this, these 3 variables can be used to specify where the mpi.h
file (MPI_INC) and the MPI library file (MPI_PATH) are found and the
name of the library file (MPI_LIB).</p>
<p>If you are installing MPI yourself, we recommend Argonne’s MPICH2
or OpenMPI. MPICH can be downloaded from the <a class="reference external" href="http://www.mcs.anl.gov/research/projects/mpich2/">Argonne MPI site</a>. OpenMPI can
be downloaded from the <a class="reference external" href="http://www.open-mpi.org">OpenMPI site</a>.
Other MPI packages should also work. If you are running on a big
parallel platform, your system people or the vendor should have
already installed a version of MPI, which is likely to be faster
than a self-installed MPICH or OpenMPI, so find out how to build
and link with it. If you use MPICH or OpenMPI, you will have to
configure and build it for your platform. The MPI configure script
should have compiler options to enable you to use the same compiler
you are using for the LAMMPS build, which can avoid problems that can
arise when linking LAMMPS to the MPI library.</p>
<p>If you just want to run LAMMPS on a single processor, you can use the
dummy MPI library provided in src/STUBS, since you don’t need a true
MPI library installed on your system. See src/MAKE/Makefile.serial
for how to specify the 3 MPI variables in this case. You will also
need to build the STUBS library for your platform before making LAMMPS
itself. Note that if you are building with src/MAKE/Makefile.serial,
e.g. by typing “make serial”, then the STUBS library is built for you.</p>
<p>To build the STUBS library from the src directory, type “make
mpi-stubs”, or from the src/STUBS dir, type “make”. This should
create a libmpi_stubs.a file suitable for linking to LAMMPS. If the
build fails, you will need to edit the STUBS/Makefile for your
platform.</p>
<p>The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime()
that calls gettimeofday() . If your system doesn’t support
gettimeofday() , you’ll need to insert code to call another timer.
Note that the ANSI-standard function clock() rolls over after an hour
or so, and is therefore insufficient for timing long LAMMPS
simulations.</p>
<p><strong>Step 6</strong></p>
<p>The 3 FFT variables allow you to specify an FFT library which LAMMPS
uses (for performing 1d FFTs) when running the particle-particle
particle-mesh (PPPM) option for long-range Coulombics via the
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command.</p>
<p>LAMMPS supports various open-source or vendor-supplied FFT libraries
for this purpose. If you leave these 3 variables blank, LAMMPS will
use the open-source <a class="reference external" href="http://kissfft.sf.net">KISS FFT library</a>, which is
included in the LAMMPS distribution. This library is portable to all
platforms and for typical LAMMPS simulations is almost as fast as FFTW
or vendor optimized libraries. If you are not including the KSPACE
package in your build, you can also leave the 3 variables blank.</p>
<p>Otherwise, select which kinds of FFTs to use as part of the FFT_INC
setting by a switch of the form -DFFT_XXX. Recommended values for XXX
are: MKL, SCSL, FFTW2, and FFTW3. Legacy options are: INTEL, SGI,
ACML, and T3E. For backward compatability, using -DFFT_FFTW will use
the FFTW2 library. Using -DFFT_NONE will use the KISS library
described above.</p>
<p>You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
so the compiler and linker can find the needed FFT header and library
files. Note that on some large parallel machines which use “modules”
for their compile/link environements, you may simply need to include
the correct module in your build environment. Or the parallel machine
may have a vendor-provided FFT library which the compiler has no
trouble finding.</p>
<p>FFTW is a fast, portable library that should also work on any
platform. You can download it from
<a class="reference external" href="http://www.fftw.org">www.fftw.org</a>. Both the legacy version 2.1.X and
the newer 3.X versions are supported as -DFFT_FFTW2 or -DFFT_FFTW3.
Building FFTW for your box should be as simple as ./configure; make.
Note that on some platforms FFTW2 has been pre-installed, and uses
renamed files indicating the precision it was compiled with,
e.g. sfftw.h, or dfftw.h instead of fftw.h. In this case, you can
specify an additional define variable for FFT_INC called -DFFTW_SIZE,
which will select the correct include file. In this case, for FFT_LIB
you must also manually specify the correct library, namely -lsfftw or
-ldfftw.</p>
<p>The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
use single-precision FFTs with PPPM, which can speed-up long-range
calulations, particularly in parallel or on GPUs. Fourier transform
and related PPPM operations are somewhat insensitive to floating point
truncation errors and thus do not always need to be performed in
double precision. Using the -DFFT_SINGLE setting trades off a little
accuracy for reduced memory use and parallel communication costs for
transposing 3d FFT data. Note that single precision FFTs have only
been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.</p>
<p><strong>Step 7</strong></p>
<p>The 3 JPG variables allow you to specify a JPEG and/or PNG library
which LAMMPS uses when writing out JPEG or PNG files via the <a class="reference internal" href="dump_image.html"><em>dump image</em></a> command. These can be left blank if you do not
use the -DLAMMPS_JPEG or -DLAMMPS_PNG switches discussed above in Step
4, since in that case JPEG/PNG output will be disabled.</p>
<p>A standard JPEG library usually goes by the name libjpeg.a or
libjpeg.so and has an associated header file jpeglib.h. Whichever
JPEG library you have on your platform, you’ll need to set the
appropriate JPG_INC, JPG_PATH, and JPG_LIB variables, so that the
compiler and linker can find it.</p>
<p>A standard PNG library usually goes by the name libpng.a or libpng.so
and has an associated header file png.h. Whichever PNG library you
have on your platform, you’ll need to set the appropriate JPG_INC,
JPG_PATH, and JPG_LIB variables, so that the compiler and linker can
find it.</p>
<p>As before, if these header and library files are in the usual place on
your machine, you may not need to set these variables.</p>
<p><strong>Step 8</strong></p>
<p>Note that by default only a few of LAMMPS optional packages are
installed. To build LAMMPS with optional packages, see <a class="reference internal" href="#start-3"><span>this section</span></a> below, before proceeding to Step 9.</p>
<p><strong>Step 9</strong></p>
<p>That’s it. Once you have a correct Makefile.foo, and you have
pre-built any other needed libraries (e.g. MPI, FFT, etc) all you need
to do from the src directory is type something like this:</p>
<div class="highlight-python"><div class="highlight"><pre>make foo
or
gmake foo
</pre></div>
</div>
<p>You should get the executable lmp_foo when the build is complete.</p>
<hr class="docutils" />
<p id="start-2-3"><strong>*Errors that can occur when making LAMMPS:*</strong></p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If an error occurs when building LAMMPS, the compiler
or linker will state very explicitly what the problem is. The error
message should give you a hint as to which of the steps above has
failed, and what you need to do in order to fix it. Building a code
with a Makefile is a very logical process. The compiler and linker
need to find the appropriate files and those files need to be
compatible with LAMMPS source files. When a make fails, there is
usually a very simple reason, which you or a local expert will need to
fix.</p>
</div>
<p>Here are two non-obvious errors that can occur:</p>
<p>(1) If the make command breaks immediately with errors that indicate
it can’t find files with a “*” in their names, this can be because
your machine’s native make doesn’t support wildcard expansion in a
makefile. Try gmake instead of make. If that doesn’t work, try using
a -f switch with your make command to use a pre-generated
Makefile.list which explicitly lists all the needed files, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>make makelist
make -f Makefile.list linux
gmake -f Makefile.list mac
</pre></div>
</div>
<p>The first “make” command will create a current Makefile.list with all
the file names in your src dir. The 2nd “make” command (make or
gmake) will use it to build LAMMPS. Note that you should
include/exclude any desired optional packages before using the “make
makelist” command.</p>
<p>(2) If you get an error that says something like ‘identifier “atoll”
is undefined’, then your machine does not support “long long”
integers. Try using the -DLAMMPS_LONGLONG_TO_LONG setting described
above in Step 4.</p>
<hr class="docutils" />
<p id="start-2-4"><strong>*Additional build tips:*</strong></p>
<ol class="arabic simple">
<li>Building LAMMPS for multiple platforms.</li>
</ol>
<p>You can make LAMMPS for multiple platforms from the same src
directory. Each target creates its own object sub-directory called
Obj_target where it stores the system-specific <a href="#id3"><span class="problematic" id="id4">*</span></a>.o files.</p>
<ol class="arabic simple" start="2">
<li>Cleaning up.</li>
</ol>
<p>Typing “make clean-all” or “make clean-machine” will delete <a href="#id5"><span class="problematic" id="id6">*</span></a>.o object
files created when LAMMPS is built, for either all builds or for a
particular machine.</p>
<p>(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL</p>
<p>As explained above, any of these 3 settings can be specified on the
LMP_INC line in your low-level src/MAKE/Makefile.foo.</p>
<p>The default is -DLAMMPS_SMALLBIG which allows for systems with up to
2^63 atoms and 2^63 timesteps (about 9e18). The atom limit is for
atomic systems which do not store bond topology info and thus do not
require atom IDs. If you use atom IDs for atomic systems (which is
the default) or if you use a molecular model, which stores bond
topology info and thus requires atom IDs, the limit is 2^31 atoms
(about 2 billion). This is because the IDs are stored in 32-bit
integers.</p>
<p>Likewise, with this setting, the 3 image flags for each atom (see the
<a class="reference internal" href="dump.html"><em>dump</em></a> doc page for a discussion) are stored in a 32-bit
integer, which means the atoms can only wrap around a periodic box (in
each dimension) at most 512 times. If atoms move through the periodic
box more than this many times, the image flags will “roll over”,
e.g. from 511 to -512, which can cause diagnostics like the
mean-squared displacement, as calculated by the <a class="reference internal" href="compute_msd.html"><em>compute msd</em></a> command, to be faulty.</p>
<p>To allow for larger atomic systems with atom IDs or larger molecular
systems or larger image flags, compile with -DLAMMPS_BIGBIG. This
stores atom IDs and image flags in 64-bit integers. This enables
atomic or molecular systems with atom IDS of up to 2^63 atoms (about
9e18). And image flags will not “roll over” until they reach 2^20 =
1048576.</p>
<p>If your system does not support 8-byte integers, you will need to
compile with the -DLAMMPS_SMALLSMALL setting. This will restrict the
total number of atoms (for atomic or molecular systems) and timesteps
to 2^31 (about 2 billion). Image flags will roll over at 2^9 = 512.</p>
<p>Note that in src/lmptype.h there are definitions of all these data
types as well as the MPI data types associated with them. The MPI
types need to be consistent with the associated C data types, or else
LAMMPS will generate a run-time error. As far as we know, the
settings defined in src/lmptype.h are portable and work on every
current system.</p>
<p>In all cases, the size of problem that can be run on a per-processor
basis is limited by 4-byte integer storage to 2^31 atoms per processor
(about 2 billion). This should not normally be a limitation since such
a problem would have a huge per-processor memory footprint due to
neighbor lists and would run very slowly in terms of CPU secs/timestep.</p>
<hr class="docutils" />
<p id="start-2-5"><strong>*Building for a Mac:*</strong></p>
<p>OS X is BSD Unix, so it should just work. See the
src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.</p>
<hr class="docutils" />
<p id="start-2-6"><strong>*Building for Windows:*</strong></p>
<p>The LAMMPS download page has an option to download both a serial and
parallel pre-built Windows executable. See the <a class="reference internal" href="#start-6"><span>Running LAMMPS</span></a> section for instructions on running these executables
on a Windows box.</p>
<p>The pre-built executables hosted on the <a class="reference external" href="http://lammps.sandia.gov/download.html">LAMMPS download page</a> are built with a subset
of the available packages; see the download page for the list. These
are single executable files. No examples or documentation in
included. You will need to download the full source code package to
obtain those.</p>
<p>As an alternative, you can download “daily builds” (and some older
versions) of the installer packages from
<a class="reference external" href="http://rpm.lammps.org/windows.html">rpm.lammps.org/windows.html</a>.
These executables are built with most optional packages and the
download includes documentation, some tools and most examples.</p>
<p>If you want a Windows version with specific packages included and
excluded, you can build it yourself.</p>
<p>One way to do this is install and use cygwin to build LAMMPS with a
standard unix style make program, just as you would on a Linux box;
see src/MAKE/MACHINES/Makefile.cygwin.</p>
-<p>The other way to do this is using Visual Studio and project files.
-See the src/WINDOWS directory and its README.txt file for instructions
-on both a basic build and a customized build with pacakges you select.</p>
<hr class="docutils" />
</div>
<div class="section" id="making-lammps-with-optional-packages">
<span id="start-3"></span><h2>2.3. Making LAMMPS with optional packages<a class="headerlink" href="#making-lammps-with-optional-packages" title="Permalink to this headline">¶</a></h2>
<p>This section has the following sub-sections:</p>
<ul class="simple">
<li><a class="reference internal" href="#start-3-1"><span>Package basics</span></a></li>
<li><a class="reference internal" href="#start-3-2"><span>Including/excluding packages</span></a></li>
<li><a class="reference internal" href="#start-3-3"><span>Packages that require extra libraries</span></a></li>
<li><a class="reference internal" href="#start-3-4"><span>Packages that require Makefile.machine settings</span></a></li>
</ul>
<p>Note that the following <a class="reference internal" href="#start-4"><span>Section 2.4</span></a> describes the Make.py
tool which can be used to install/un-install packages and build the
auxiliary libraries which some of them use. It can also auto-edit a
Makefile.machine to add settings needed by some packages.</p>
<hr class="docutils" />
<p id="start-3-1"><strong>*Package basics:*</strong></p>
<p>The source code for LAMMPS is structured as a set of core files which
are always included, plus optional packages. Packages are groups of
files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages.</p>
<p>You can see the list of all packages by typing “make package” from
within the src directory of the LAMMPS distribution. This also lists
various make commands that can be used to manipulate packages.</p>
<p>If you use a command in a LAMMPS input script that is specific to a
particular package, you must have built LAMMPS with that package, else
you will get an error that the style is invalid or the command is
unknown. Every command’s doc page specfies if it is part of a
package. You can also type</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">lmp_machine</span> <span class="o">-</span><span class="n">h</span>
</pre></div>
</div>
-<p>to run your executable with the optional <a class="reference internal" href="#start-7"><span>-h command-line switch</span></a> for “help”, which will list the styles and commands
-known to your executable.</p>
+<p>to run your executable with the optional <a class="reference internal" href="#start-7"><span>-h command-line switch</span></a> for “help”, which will simply list the styles and
+commands known to your executable, and immediately exit.</p>
<p>There are two kinds of packages in LAMMPS, standard and user packages.
More information about the contents of standard and user packages is
given in <a class="reference internal" href="Section_packages.html"><em>Section_packages</em></a> of the manual. The
difference between standard and user packages is as follows:</p>
-<p>Standard packages are supported by the LAMMPS developers and are
-written in a syntax and style consistent with the rest of LAMMPS.
-This means we will answer questions about them, debug and fix them if
-necessary, and keep them compatible with future changes to LAMMPS.</p>
-<p>User packages have been contributed by users, and always begin with
-the user prefix. If they are a single command (single file), they are
-typically in the user-misc package. Otherwise, they are a a set of
-files grouped together which add a specific functionality to the code.</p>
+<p>Standard packages, such as molecule or kspace, are supported by the
+LAMMPS developers and are written in a syntax and style consistent
+with the rest of LAMMPS. This means we will answer questions about
+them, debug and fix them if necessary, and keep them compatible with
+future changes to LAMMPS.</p>
+<p>User packages, such as user-atc or user-omp, have been contributed by
+users, and always begin with the user prefix. If they are a single
+command (single file), they are typically in the user-misc package.
+Otherwise, they are a a set of files grouped together which add a
+specific functionality to the code.</p>
<p>User packages don’t necessarily meet the requirements of the standard
packages. If you have problems using a feature provided in a user
-package, you will likely need to contact the contributor directly to
-get help. Information on how to submit additions you make to LAMMPS
-as a user-contributed package is given in <a class="reference internal" href="Section_modify.html#mod-15"><span>this section</span></a> of the documentation.</p>
-<p>Some packages (both standard and user) require additional libraries.
-See more details below.</p>
+package, you may need to contact the contributor directly to get help.
+Information on how to submit additions you make to LAMMPS as single
+files or either a standard or user-contributed package are given in
+<a class="reference internal" href="Section_modify.html#mod-15"><span>this section</span></a> of the documentation.</p>
+<p>Some packages (both standard and user) require additional auxiliary
+libraries when building LAMMPS. See more details below.</p>
<hr class="docutils" />
<p id="start-3-2"><strong>*Including/excluding packages:*</strong></p>
-<p>To use or not use a package you must include or exclude it before
-building LAMMPS. From the src directory, this is typically as simple
-as:</p>
+<p>To use (or not use) a package you must include it (or exclude it)
+before building LAMMPS. From the src directory, this is typically as
+simple as:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-colloid
make g++
</pre></div>
</div>
<p>or</p>
<div class="highlight-python"><div class="highlight"><pre>make no-manybody
make g++
</pre></div>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">You should NOT include/exclude packages and build
-LAMMPS in a single make command by using multiple targets, e.g. make
+LAMMPS in a single make command using multiple targets, e.g. make
yes-colloid g++. This is because the make procedure creates a list of
source files that will be out-of-date for the build if the package
-configuration changes during the same command.</p>
+configuration changes within the same command.</p>
</div>
<p>Some packages have individual files that depend on other packages
being included. LAMMPS checks for this and does the right thing.
I.e. individual files are only included if their dependencies are
already included. Likewise, if a package is excluded, other files
dependent on that package are also excluded.</p>
<p>If you will never run simulations that use the features in a
particular packages, there is no reason to include it in your build.
For some packages, this will keep you from having to build auxiliary
libraries (see below), and will also produce a smaller executable
which may run a bit faster.</p>
<p>When you download a LAMMPS tarball, these packages are pre-installed
in the src directory: KSPACE, MANYBODY,MOLECULE. When you download
LAMMPS source files from the SVN or Git repositories, no packages are
pre-installed.</p>
<p>Packages are included or excluded by typing “make yes-name” or “make
no-name”, where “name” is the name of the package in lower-case, e.g.
name = kspace for the KSPACE package or name = user-atc for the
USER-ATC package. You can also type “make yes-standard”, “make
no-standard”, “make yes-std”, “make no-std”, “make yes-user”, “make
no-user”, “make yes-all” or “make no-all” to include/exclude various
sets of packages. Type “make package” to see the all of the
package-related make options.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Inclusion/exclusion of a package works by simply
moving files back and forth between the main src directory and
sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
so that the files are seen or not seen when LAMMPS is built. After
you have included or excluded a package, you must re-build LAMMPS.</p>
</div>
<p>Additional package-related make options exist to help manage LAMMPS
files that exist in both the src directory and in package
sub-directories. You do not normally need to use these commands
unless you are editing LAMMPS files or have downloaded a patch from
the LAMMPS WWW site.</p>
<p>Typing “make package-update” or “make pu” will overwrite src files
with files from the package sub-directories if the package has been
included. It should be used after a patch is installed, since patches
only update the files in the package sub-directory, but not the src
files. Typing “make package-overwrite” will overwrite files in the
package sub-directories with src files.</p>
<p>Typing “make package-status” or “make ps” will show which packages are
currently included. Of those that are included, it will list files
that are different in the src directory and package sub-directory.
Typing “make package-diff” lists all differences between these files.
Again, type “make package” to see all of the package-related make
options.</p>
<hr class="docutils" />
<p id="start-3-3"><strong>*Packages that require extra libraries:*</strong></p>
<p>A few of the standard and user packages require additional auxiliary
-libraries. Most of them are provided with LAMMPS, in which case they
-must be compiled first, before LAMMPS is built if you wish to include
+libraries. Many of them are provided with LAMMPS, in which case they
+must be compiled first, before LAMMPS is built, if you wish to include
that package. If you get a LAMMPS build error about a missing
library, this is likely the reason. See the
<a class="reference internal" href="Section_packages.html"><em>Section_packages</em></a> doc page for a list of
packages that have these kinds of auxiliary libraries.</p>
<p>The lib directory in the distribution has sub-directories with package
-names that correspond to the needed auxiliary libs, e.g. lib/reax.
+names that correspond to the needed auxiliary libs, e.g. lib/gpu.
Each sub-directory has a README file that gives more details. Code
for most of the auxiliary libraries is included in that directory.
Examples are the USER-ATC and MEAM packages.</p>
<p>A few of the lib sub-directories do not include code, but do include
-instructions and sometimes scripts that automate the process of
+instructions (and sometimes scripts) that automate the process of
downloading the auxiliary library and installing it so LAMMPS can link
-to it. Examples are the KIM and VORONOI and USER-MOLFILE and USER-SMD
+to it. Examples are the KIM, VORONOI, USER-MOLFILE, and USER-SMD
packages.</p>
<p>The lib/python directory (for the PYTHON package) contains only a
choice of Makefile.lammps.* files. This is because no auxiliary code
or libraries are needed, only the Python library and other system libs
-that already available on your system. However, the Makefile.lammps
-file is needed to tell the LAMMPS build which libs to use and where to
-find them.</p>
+that should already available on your system. However, the
+Makefile.lammps file is needed to tell LAMMPS which libs to use and
+where to find them.</p>
<p>For libraries with provided code, the sub-directory README file
-(e.g. lib/reax/README) has instructions on how to build that library.
+(e.g. lib/atc/README) has instructions on how to build that library.
Typically this is done by typing something like:</p>
<div class="highlight-python"><div class="highlight"><pre>make -f Makefile.g++
</pre></div>
</div>
<p>If one of the provided Makefiles is not appropriate for your system
you will need to edit or add one. Note that all the Makefiles have a
setting for EXTRAMAKE at the top that specifies a Makefile.lammps.*
file.</p>
<p>If the library build is successful, it will produce 2 files in the lib
directory:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">libpackage</span><span class="o">.</span><span class="n">a</span>
<span class="n">Makefile</span><span class="o">.</span><span class="n">lammps</span>
</pre></div>
</div>
<p>The Makefile.lammps file will be a copy of the EXTRAMAKE file setting
specified in the library Makefile.* you used.</p>
<p>Note that you must insure that the settings in Makefile.lammps are
appropriate for your system. If they are not, the LAMMPS build will
fail.</p>
<p>As explained in the lib/package/README files, the settings in
Makefile.lammps are used to specify additional system libraries and
their locations so that LAMMPS can build with the auxiliary library.
-For example, if the MEAM or REAX packages are used, the auxiliary
-libraries consist of F90 code, built with a Fortran complier. To link
-that library with LAMMPS (a C++ code) via whatever C++ compiler LAMMPS
-is built with, typically requires additional Fortran-to-C libraries be
+For example, if the MEAM package is used, the auxiliary library
+consists of F90 code, built with a Fortran complier. To link that
+library with LAMMPS (a C++ code) via whatever C++ compiler LAMMPS is
+built with, typically requires additional Fortran-to-C libraries be
included in the link. Another example are the BLAS and LAPACK
libraries needed to use the USER-ATC or USER-AWPMD packages.</p>
<p>For libraries without provided code, the sub-directory README file has
information on where to download the library and how to build it,
e.g. lib/voronoi/README and lib/smd/README. The README files also
describe how you must either (a) create soft links, via the “ln”
command, in those directories to point to where you built or installed
the packages, or (b) check or edit the Makefile.lammps file in the
same directory to provide that information.</p>
<p>Some of the sub-directories, e.g. lib/voronoi, also have an install.py
script which can be used to automate the process of
downloading/building/installing the auxiliary library, and setting the
needed soft links. Type “python install.py” for further instructions.</p>
<p>As with the sub-directories containing library code, if the soft links
or settings in the lib/package/Makefile.lammps files are not correct,
the LAMMPS build will typically fail.</p>
<hr class="docutils" />
<p id="start-3-4"><strong>*Packages that require Makefile.machine settings*</strong></p>
<p>A few packages require specific settings in Makefile.machine, to
either build or use the package effectively. These are the
USER-INTEL, KOKKOS, USER-OMP, and OPT packages. The details of what
flags to add or what variables to define are given on the doc pages
that describe each of these accelerator packages in detail:</p>
<ul class="simple">
<li><a class="reference internal" href="accelerate_intel.html"><em>USER-INTEL package</em></a></li>
<li><a class="reference internal" href="accelerate_kokkos.html"><em>KOKKOS package</em></a></li>
<li><a class="reference internal" href="accelerate_omp.html"><em>USER-OMP package</em></a></li>
<li><a class="reference internal" href="accelerate_opt.html"><em>OPT package</em></a></li>
</ul>
<p>Here is a brief summary of what Makefile.machine changes are needed.
Note that the Make.py tool, described in the next <a class="reference internal" href="#start-4"><span>Section 2.4</span></a> can automatically add the needed info to an existing
machine Makefile, using simple command-line arguments.</p>
<p>In src/MAKE/OPTIONS see the following Makefiles for examples of the
changes described below:</p>
<ul class="simple">
<li>Makefile.intel_cpu</li>
<li>Makefile.intel_phi</li>
<li>Makefile.kokkos_omp</li>
<li>Makefile.kokkos_cuda</li>
<li>Makefile.kokkos_phi</li>
<li>Makefile.omp</li>
</ul>
<p>For the USER-INTEL package, you have 2 choices when building. You can
build with CPU or Phi support. The latter uses Xeon Phi chips in
“offload” mode. Each of these modes requires additional settings in
your Makefile.machine for CCFLAGS and LINKFLAGS.</p>
<p>For CPU mode (if using an Intel compiler):</p>
<ul class="simple">
<li>CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits</li>
<li>LINKFLAGS: add -fopenmp</li>
</ul>
<p>For Phi mode add the following in addition to the CPU mode flags:</p>
<ul class="simple">
<li>CCFLAGS: add -DLMP_INTEL_OFFLOAD and</li>
<li>LINKFLAGS: add -offload</li>
</ul>
<p>And also add this to CCFLAGS:</p>
<pre class="literal-block">
-offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs="gather_scatter_loop_unroll=4""
</pre>
<p>For the KOKKOS package, you have 3 choices when building. You can
build with OMP or Cuda or Phi support. Phi support uses Xeon Phi
chips in “native” mode. This can be done by setting the following
variables in your Makefile.machine:</p>
<ul class="simple">
<li>for OMP support, set OMP = yes</li>
<li>for Cuda support, set OMP = yes and CUDA = yes</li>
<li>for Phi support, set OMP = yes and MIC = yes</li>
</ul>
<p>These can also be set as additional arguments to the make command, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>make g++ OMP=yes MIC=yes
</pre></div>
</div>
<p>Building the KOKKOS package with CUDA support requires a Makefile
machine that uses the NVIDIA “nvcc” compiler, as well as an
appropriate “arch” setting appropriate to the GPU hardware and NVIDIA
software you have on your machine. See
src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine
Makefile.</p>
<p>For the USER-OMP package, your Makefile.machine needs additional
settings for CCFLAGS and LINKFLAGS.</p>
<ul class="simple">
<li>CCFLAGS: add -fopenmp and -restrict</li>
<li>LINKFLAGS: add -fopenmp</li>
</ul>
<p>For the OPT package, your Makefile.machine needs an additional
settings for CCFLAGS.</p>
<ul class="simple">
<li>CCFLAGS: add -restrict</li>
</ul>
<hr class="docutils" />
</div>
-<div class="section" id="building-lammps-via-the-make-py-script">
-<span id="start-4"></span><h2>2.4. Building LAMMPS via the Make.py script<a class="headerlink" href="#building-lammps-via-the-make-py-script" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="building-lammps-via-the-make-py-tool">
+<span id="start-4"></span><h2>2.4. Building LAMMPS via the Make.py tool<a class="headerlink" href="#building-lammps-via-the-make-py-tool" title="Permalink to this headline">¶</a></h2>
<p>The src directory includes a Make.py script, written in Python, which
can be used to automate various steps of the build process. It is
particularly useful for working with the accelerator packages, as well
as other packages which require auxiliary libraries to be built.</p>
<p>The goal of the Make.py tool is to allow any complex multi-step LAMMPS
build to be performed as a single Make.py command. And you can
archive the commands, so they can be re-invoked later via the -r
(redo) switch. If you find some LAMMPS build procedure that can’t be
done in a single Make.py command, let the developers know, and we’ll
see if we can augment the tool.</p>
<p>You can run Make.py from the src directory by typing either:</p>
<div class="highlight-python"><div class="highlight"><pre>Make.py -h
python Make.py -h
</pre></div>
</div>
<p>which will give you help info about the tool. For the former to work,
you may need to edit the first line of Make.py to point to your local
Python. And you may need to insure the script is executable:</p>
<div class="highlight-python"><div class="highlight"><pre>chmod +x Make.py
</pre></div>
</div>
<p>Here are examples of build tasks you can perform with Make.py:</p>
<table border="1" class="docutils">
<colgroup>
<col width="58%" />
<col width="42%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>Install/uninstall packages</td>
<td>Make.py -p no-lib kokkos omp intel</td>
</tr>
<tr class="row-even"><td>Build specific auxiliary libs</td>
<td>Make.py -a lib-atc lib-meam</td>
</tr>
<tr class="row-odd"><td>Build libs for all installed packages</td>
<td>Make.py -p cuda gpu -gpu mode=double arch=31 -a lib-all</td>
</tr>
<tr class="row-even"><td>Create a Makefile from scratch with compiler and MPI settings</td>
<td>Make.py -m none -cc g++ -mpi mpich -a file</td>
</tr>
<tr class="row-odd"><td>Augment Makefile.serial with settings for installed packages</td>
<td>Make.py -p intel -intel cpu -m serial -a file</td>
</tr>
<tr class="row-even"><td>Add JPG and FFTW support to Makefile.mpi</td>
<td>Make.py -m mpi -jpg -fft fftw -a file</td>
</tr>
<tr class="row-odd"><td>Build LAMMPS with a parallel make using Makefile.mpi</td>
<td>Make.py -j 16 -m mpi -a exe</td>
</tr>
<tr class="row-even"><td>Build LAMMPS and libs it needs using Makefile.serial with accelerator settings</td>
<td>Make.py -p gpu intel -intel cpu -a lib-all file serial</td>
</tr>
</tbody>
</table>
<p>The bench and examples directories give Make.py commands that can be
used to build LAMMPS with the various packages and options needed to
run all the benchmark and example input scripts. See these files for
more details:</p>
<ul class="simple">
<li>bench/README</li>
<li>bench/FERMI/README</li>
<li>bench/KEPLER/README</li>
<li>bench/PHI/README</li>
<li>examples/README</li>
<li>examples/accelerate/README</li>
<li>examples/accelerate/make.list</li>
</ul>
<p>All of the Make.py options and syntax help can be accessed by using
the “-h” switch.</p>
<p>E.g. typing “Make.py -h” gives</p>
<div class="highlight-python"><div class="highlight"><pre>Syntax: Make.py switch args ...
switches can be listed in any order
help switch:
-h prints help and syntax for all other specified switches
switch for actions:
-a lib-all, lib-dir, clean, file, exe or machine
list one or more actions, in any order
machine is a Makefile.machine suffix, must be last if used
one-letter switches:
-d (dir), -j (jmake), -m (makefile), -o (output),
-p (packages), -r (redo), -s (settings), -v (verbose)
switches for libs:
-atc, -awpmd, -colvars, -cuda
-gpu, -meam, -poems, -qmmm, -reax
switches for build and makefile options:
-intel, -kokkos, -cc, -mpi, -fft, -jpg, -png
</pre></div>
</div>
<p>Using the “-h” switch with other switches and actions gives additional
info on all the other specified switches or actions. The “-h” can be
anywhere in the command-line and the other switches do not need their
arguments. E.g. type “Make.py -h -d -atc -intel” will print:</p>
<div class="highlight-python"><div class="highlight"><pre>-d dir
dir = LAMMPS home dir
if -d not specified, working dir must be lammps/src
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>-atc make=suffix lammps=suffix2
all args are optional and can be in any order
make = use Makefile.suffix (def = g++)
lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>-intel mode
mode = cpu or phi (def = cpu)
build Intel package for CPU or Xeon Phi
</pre></div>
</div>
<p>Note that Make.py never overwrites an existing Makefile.machine.
Instead, it creates src/MAKE/MINE/Makefile.auto, which you can save or
rename if desired. Likewise it creates an executable named
src/lmp_auto, which you can rename using the -o switch if desired.</p>
<p>The most recently executed Make.py commmand is saved in
src/Make.py.last. You can use the “-r” switch (for redo) to re-invoke
the last command, or you can save a sequence of one or more Make.py
commands to a file and invoke the file of commands using “-r”. You
can also label the commands in the file and invoke one or more of them
by name.</p>
<p>A typical use of Make.py is to start with a valid Makefile.machine for
your system, that works for a vanilla LAMMPS build, i.e. when optional
packages are not installed. You can then use Make.py to add various
settings (FFT, JPG, PNG) to the Makefile.machine as well as change its
compiler and MPI options. You can also add additional packages to the
build, as well as build the needed supporting libraries.</p>
<p>You can also use Make.py to create a new Makefile.machine from
scratch, using the “-m none” switch, if you also specify what compiler
and MPI options to use, via the “-cc” and “-mpi” switches.</p>
<hr class="docutils" />
</div>
<div class="section" id="building-lammps-as-a-library">
<span id="start-5"></span><h2>2.5. Building LAMMPS as a library<a class="headerlink" href="#building-lammps-as-a-library" title="Permalink to this headline">¶</a></h2>
<p>LAMMPS can be built as either a static or shared library, which can
then be called from another application or a scripting language. See
<a class="reference internal" href="Section_howto.html#howto-10"><span>this section</span></a> for more info on coupling
LAMMPS to other codes. See <a class="reference internal" href="Section_python.html"><em>this section</em></a> for
more info on wrapping and running LAMMPS from Python.</p>
<div class="section" id="static-library">
<h3>2.5.1. <strong>Static library:</strong><a class="headerlink" href="#static-library" title="Permalink to this headline">¶</a></h3>
<p>To build LAMMPS as a static library (<a href="#id7"><span class="problematic" id="id8">*</span></a>.a file on Linux), type</p>
<div class="highlight-python"><div class="highlight"><pre>make foo mode=lib
</pre></div>
</div>
<p>where foo is the machine name. This kind of library is typically used
to statically link a driver application to LAMMPS, so that you can
insure all dependencies are satisfied at compile time. This will use
the ARCHIVE and ARFLAGS settings in src/MAKE/Makefile.foo. The build
will create the file liblammps_foo.a which another application can
link to. It will also create a soft link liblammps.a, which will
point to the most recently built static library.</p>
</div>
<div class="section" id="shared-library">
<h3>2.5.2. <strong>Shared library:</strong><a class="headerlink" href="#shared-library" title="Permalink to this headline">¶</a></h3>
<p>To build LAMMPS as a shared library (<a href="#id9"><span class="problematic" id="id10">*</span></a>.so file on Linux), which can be
dynamically loaded, e.g. from Python, type</p>
<div class="highlight-python"><div class="highlight"><pre>make foo mode=shlib
</pre></div>
</div>
<p>where foo is the machine name. This kind of library is required when
wrapping LAMMPS with Python; see <a class="reference internal" href="Section_python.html"><em>Section_python</em></a>
for details. This will use the SHFLAGS and SHLIBFLAGS settings in
src/MAKE/Makefile.foo and perform the build in the directory
Obj_shared_foo. This is so that each file can be compiled with the
-fPIC flag which is required for inclusion in a shared library. The
build will create the file liblammps_foo.so which another application
can link to dyamically. It will also create a soft link liblammps.so,
which will point to the most recently built shared library. This is
the file the Python wrapper loads by default.</p>
<p>Note that for a shared library to be usable by a calling program, all
the auxiliary libraries it depends on must also exist as shared
libraries. This will be the case for libraries included with LAMMPS,
such as the dummy MPI library in src/STUBS or any package libraries in
lib/packages, since they are always built as shared libraries using
the -fPIC switch. However, if a library like MPI or FFTW does not
exist as a shared library, the shared library build will generate an
error. This means you will need to install a shared library version
of the auxiliary library. The build instructions for the library
should tell you how to do this.</p>
<p>Here is an example of such errors when the system FFTW or provided
lib/colvars library have not been built as shared libraries:</p>
<div class="highlight-python"><div class="highlight"><pre>/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
R_X86_64_32 against `.rodata' can not be used when making a shared
object; recompile with -fPIC
/usr/local/lib/libfftw3.a: could not read symbols: Bad value
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>/usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
relocation R_X86_64_32 against `__pthread_key_create' can not be used
when making a shared object; recompile with -fPIC
../../lib/colvars/libcolvars.a: error adding symbols: Bad value
</pre></div>
</div>
<p>As an example, here is how to build and install the <a class="reference external" href="http://www-unix.mcs.anl.gov/mpi">MPICH library</a>, a popular open-source version of MPI, distributed by
Argonne National Labs, as a shared library in the default
/usr/local/lib location:</p>
<div class="highlight-python"><div class="highlight"><pre>./configure --enable-shared
make
make install
</pre></div>
</div>
<p>You may need to use “sudo make install” in place of the last line if
you do not have write privileges for /usr/local/lib. The end result
should be the file /usr/local/lib/libmpich.so.</p>
</div>
<div class="section" id="additional-requirement-for-using-a-shared-library">
<h3>2.5.3. <strong>Additional requirement for using a shared library:</strong><a class="headerlink" href="#additional-requirement-for-using-a-shared-library" title="Permalink to this headline">¶</a></h3>
<p>The operating system finds shared libraries to load at run-time using
the environment variable LD_LIBRARY_PATH. So you may wish to copy the
file src/liblammps.so or src/liblammps_g++.so (for example) to a place
the system can find it by default, such as /usr/local/lib, or you may
wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the
current version of the shared library is always available to programs
that use it.</p>
<p>For the csh or tcsh shells, you would add something like this to your
~/.cshrc file:</p>
<div class="highlight-python"><div class="highlight"><pre>setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
</pre></div>
</div>
</div>
<div class="section" id="calling-the-lammps-library">
<h3>2.5.4. <strong>Calling the LAMMPS library:</strong><a class="headerlink" href="#calling-the-lammps-library" title="Permalink to this headline">¶</a></h3>
<p>Either flavor of library (static or shared) allows one or more LAMMPS
objects to be instantiated from the calling program.</p>
<p>When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS
namespace; you can safely use any of its classes and methods from
within the calling code, as needed.</p>
<p>When used from a C or Fortran program or a scripting language like
Python, the library has a simple function-style interface, provided in
src/library.cpp and src/library.h.</p>
<p>See the sample codes in examples/COUPLE/simple for examples of C++ and
C and Fortran codes that invoke LAMMPS thru its library interface.
There are other examples as well in the COUPLE directory which are
discussed in <a class="reference internal" href="Section_howto.html#howto-10"><span>Section_howto 10</span></a> of the
manual. See <a class="reference internal" href="Section_python.html"><em>Section_python</em></a> of the manual for a
description of the Python wrapper provided with LAMMPS that operates
through the LAMMPS library interface.</p>
<p>The files src/library.cpp and library.h define the C-style API for
using LAMMPS as a library. See <a class="reference internal" href="Section_howto.html#howto-19"><span>Section_howto 19</span></a> of the manual for a description of the
interface and how to extend it for your needs.</p>
<hr class="docutils" />
</div>
</div>
<div class="section" id="running-lammps">
<span id="start-6"></span><h2>2.6. Running LAMMPS<a class="headerlink" href="#running-lammps" title="Permalink to this headline">¶</a></h2>
<p>By default, LAMMPS runs by reading commands from standard input. Thus
if you run the LAMMPS executable by itself, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">lmp_linux</span>
</pre></div>
</div>
<p>it will simply wait, expecting commands from the keyboard. Typically
you should put commands in an input script and use I/O redirection,
e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>lmp_linux < in.file
</pre></div>
</div>
<p>For parallel environments this should also work. If it does not, use
the ‘-in’ command-line switch, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>lmp_linux -in in.file
</pre></div>
</div>
<p><a class="reference internal" href="Section_commands.html"><em>This section</em></a> describes how input scripts are
structured and what commands they contain.</p>
<p>You can test LAMMPS on any of the sample inputs provided in the
examples or bench directory. Input scripts are named in.* and sample
outputs are named log.*.name.P where name is a machine and P is the
number of processors it was run on.</p>
<p>Here is how you might run a standard Lennard-Jones benchmark on a
Linux box, using mpirun to launch a parallel job:</p>
<div class="highlight-python"><div class="highlight"><pre>cd src
make linux
cp lmp_linux ../bench
cd ../bench
mpirun -np 4 lmp_linux -in in.lj
</pre></div>
</div>
<p>See <a class="reference external" href="http://lammps.sandia.gov/bench.html">this page</a> for timings for this and the other benchmarks on
various platforms. Note that some of the example scripts require
LAMMPS to be built with one or more of its optional packages.</p>
<hr class="docutils" />
<p>On a Windows box, you can skip making LAMMPS and simply download an
executable, as described above, though the pre-packaged executables
include only certain packages.</p>
<p>To run a LAMMPS executable on a Windows machine, first decide whether
you want to download the non-MPI (serial) or the MPI (parallel)
version of the executable. Download and save the version you have
chosen.</p>
<p>For the non-MPI version, follow these steps:</p>
<ul class="simple">
<li>Get a command prompt by going to Start->Run... ,
then typing “cmd”.</li>
<li>Move to the directory where you have saved lmp_win_no-mpi.exe
(e.g. by typing: cd “Documents”).</li>
<li>At the command prompt, type “lmp_win_no-mpi -in in.lj”, replacing in.lj
with the name of your LAMMPS input script.</li>
</ul>
<p>For the MPI version, which allows you to run LAMMPS under Windows on
multiple processors, follow these steps:</p>
<ul class="simple">
<li>Download and install
<a class="reference external" href="http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads">MPICH2</a>
for Windows.</li>
<li>You’ll need to use the mpiexec.exe and smpd.exe files from the MPICH2
package. Put them in same directory (or path) as the LAMMPS Windows
executable.</li>
<li>Get a command prompt by going to Start->Run... ,
then typing “cmd”.</li>
<li>Move to the directory where you have saved lmp_win_mpi.exe
(e.g. by typing: cd “Documents”).</li>
<li>Then type something like this: “mpiexec -localonly 4 lmp_win_mpi -in
in.lj”, replacing in.lj with the name of your LAMMPS input script.</li>
<li>Note that you may need to provide smpd with a passphrase (it doesn’t
matter what you type).</li>
<li>In this mode, output may not immediately show up on the screen, so if
your input script takes a long time to execute, you may need to be
patient before the output shows up. :l Alternatively, you can still
use this executable to run on a single processor by typing something
like: “lmp_win_mpi -in in.lj”.</li>
</ul>
<hr class="docutils" />
<p>The screen output from LAMMPS is described in the next section. As it
runs, LAMMPS also writes a log.lammps file with the same information.</p>
<p>Note that this sequence of commands copies the LAMMPS executable
(lmp_linux) to the directory with the input files. This may not be
necessary, but some versions of MPI reset the working directory to
where the executable is, rather than leave it as the directory where
you launch mpirun from (if you launch lmp_linux on its own and not
under mpirun). If that happens, LAMMPS will look for additional input
files and write its output files to the executable directory, rather
than your working directory, which is probably not what you want.</p>
<p>If LAMMPS encounters errors in the input script or while running a
simulation it will print an ERROR message and stop or a WARNING
message and continue. See <a class="reference internal" href="Section_errors.html"><em>Section_errors</em></a> for a
discussion of the various kinds of errors LAMMPS can or can’t detect,
a list of all ERROR and WARNING messages, and what to do about them.</p>
<p>LAMMPS can run a problem on any number of processors, including a
single processor. In theory you should get identical answers on any
number of processors and on any machine. In practice, numerical
round-off can cause slight differences and eventual divergence of
molecular dynamics phase space trajectories.</p>
<p>LAMMPS can run as large a problem as will fit in the physical memory
of one or more processors. If you run out of memory, you must run on
more processors or setup a smaller problem.</p>
<hr class="docutils" />
</div>
<div class="section" id="command-line-options">
<span id="start-7"></span><h2>2.7. Command-line options<a class="headerlink" href="#command-line-options" title="Permalink to this headline">¶</a></h2>
<p>At run time, LAMMPS recognizes several optional command-line switches
which may be used in any order. Either the full word or a one-or-two
letter abbreviation can be used:</p>
<ul class="simple">
<li>-c or -cuda</li>
<li>-e or -echo</li>
<li>-h or -help</li>
<li>-i or -in</li>
<li>-k or -kokkos</li>
<li>-l or -log</li>
<li>-nc or -nocite</li>
<li>-pk or -package</li>
<li>-p or -partition</li>
<li>-pl or -plog</li>
<li>-ps or -pscreen</li>
<li>-r or -restart</li>
<li>-ro or -reorder</li>
<li>-sc or -screen</li>
<li>-sf or -suffix</li>
<li>-v or -var</li>
</ul>
<p>For example, lmp_ibm might be launched as follows:</p>
<div class="highlight-python"><div class="highlight"><pre>mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy
mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloy
</pre></div>
</div>
<p>Here are the details on the options:</p>
<div class="highlight-python"><div class="highlight"><pre>-cuda on/off
</pre></div>
</div>
<p>Explicitly enable or disable CUDA support, as provided by the
USER-CUDA package. Even if LAMMPS is built with this package, as
described above in <a class="reference internal" href="#start-3"><span>Section 2.3</span></a>, this switch must be set to
enable running with the CUDA-enabled styles the package provides. If
the switch is not set (the default), LAMMPS will operate as if the
USER-CUDA package were not installed; i.e. you can run standard LAMMPS
or with the GPU package, for testing or benchmarking purposes.</p>
<div class="highlight-python"><div class="highlight"><pre>-echo style
</pre></div>
</div>
<p>Set the style of command echoing. The style can be <em>none</em> or <em>screen</em>
or <em>log</em> or <em>both</em>. Depending on the style, each command read from
the input script will be echoed to the screen and/or logfile. This
can be useful to figure out which line of your script is causing an
input error. The default value is <em>log</em>. The echo style can also be
set by using the <a class="reference internal" href="echo.html"><em>echo</em></a> command in the input script itself.</p>
<div class="highlight-python"><div class="highlight"><pre><span class="o">-</span><span class="n">help</span>
</pre></div>
</div>
<p>Print a brief help summary and a list of options compiled into this
executable for each LAMMPS style (atom_style, fix, compute,
pair_style, bond_style, etc). This can tell you if the command you
want to use was included via the appropriate package at compile time.
LAMMPS will print the info and immediately exit if this switch is
used.</p>
<div class="highlight-python"><div class="highlight"><pre>-in file
</pre></div>
</div>
<p>Specify a file to use as an input script. This is an optional switch
when running LAMMPS in one-partition mode. If it is not specified,
LAMMPS reads its script from standard input, typically from a script
via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should
also work in parallel, but if it does not (in the unlikely case that
an MPI implementation does not support it), then use the -in flag.
Note that this is a required switch when running LAMMPS in
multi-partition mode, since multiple processors cannot all read from
stdin.</p>
<div class="highlight-python"><div class="highlight"><pre>-kokkos on/off keyword/value ...
</pre></div>
</div>
<p>Explicitly enable or disable KOKKOS support, as provided by the KOKKOS
package. Even if LAMMPS is built with this package, as described
above in <a class="reference internal" href="#start-3"><span>Section 2.3</span></a>, this switch must be set to enable
running with the KOKKOS-enabled styles the package provides. If the
switch is not set (the default), LAMMPS will operate as if the KOKKOS
package were not installed; i.e. you can run standard LAMMPS or with
the GPU or USER-CUDA or USER-OMP packages, for testing or benchmarking
purposes.</p>
<p>Additional optional keyword/value pairs can be specified which
determine how Kokkos will use the underlying hardware on your
platform. These settings apply to each MPI task you launch via the
“mpirun” or “mpiexec” command. You may choose to run one or more MPI
tasks per physical node. Note that if you are running on a desktop
machine, you typically have one physical node. On a cluster or
supercomputer there may be dozens or 1000s of physical nodes.</p>
<p>Either the full word or an abbreviation can be used for the keywords.
Note that the keywords do not use a leading minus sign. I.e. the
keyword is “t”, not “-t”. Also note that each of the keywords has a
default setting. Example of when to use these options and what
settings to use on different platforms is given in <span class="xref std std-ref">Section 5.8</span>.</p>
<ul class="simple">
<li>d or device</li>
<li>g or gpus</li>
<li>t or threads</li>
<li>n or numa</li>
</ul>
<div class="highlight-python"><div class="highlight"><pre>device Nd
</pre></div>
</div>
<p>This option is only relevant if you built LAMMPS with CUDA=yes, you
have more than one GPU per node, and if you are running with only one
MPI task per node. The Nd setting is the ID of the GPU on the node to
run on. By default Nd = 0. If you have multiple GPUs per node, they
have consecutive IDs numbered as 0,1,2,etc. This setting allows you
to launch multiple independent jobs on the node, each with a single
MPI task per node, and assign each job to run on a different GPU.</p>
<div class="highlight-python"><div class="highlight"><pre>gpus Ng Ns
</pre></div>
</div>
<p>This option is only relevant if you built LAMMPS with CUDA=yes, you
have more than one GPU per node, and you are running with multiple MPI
tasks per node (up to one per GPU). The Ng setting is how many GPUs
you will use. The Ns setting is optional. If set, it is the ID of a
GPU to skip when assigning MPI tasks to GPUs. This may be useful if
your desktop system reserves one GPU to drive the screen and the rest
are intended for computational work like running LAMMPS. By default
Ng = 1 and Ns is not set.</p>
<p>Depending on which flavor of MPI you are running, LAMMPS will look for
one of these 3 environment variables</p>
<div class="highlight-python"><div class="highlight"><pre>SLURM_LOCALID (various MPI variants compiled with SLURM support)
MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI)
</pre></div>
</div>
<p>which are initialized by the “srun”, “mpirun” or “mpiexec” commands.
The environment variable setting for each MPI rank is used to assign a
unique GPU ID to the MPI task.</p>
<div class="highlight-python"><div class="highlight"><pre>threads Nt
</pre></div>
</div>
<p>This option assigns Nt number of threads to each MPI task for
performing work when Kokkos is executing in OpenMP or pthreads mode.
The default is Nt = 1, which essentially runs in MPI-only mode. If
there are Np MPI tasks per physical node, you generally want Np*Nt =
the number of physical cores per node, to use your available hardware
optimally. This also sets the number of threads used by the host when
LAMMPS is compiled with CUDA=yes.</p>
<div class="highlight-python"><div class="highlight"><pre>numa Nm
</pre></div>
</div>
<p>This option is only relevant when using pthreads with hwloc support.
In this case Nm defines the number of NUMA regions (typicaly sockets)
on a node which will be utilizied by a single MPI rank. By default Nm
= 1. If this option is used the total number of worker-threads per
MPI rank is threads*numa. Currently it is always almost better to
assign at least one MPI rank per NUMA region, and leave numa set to
its default value of 1. This is because letting a single process span
multiple NUMA regions induces a significant amount of cross NUMA data
traffic which is slow.</p>
<div class="highlight-python"><div class="highlight"><pre>-log file
</pre></div>
</div>
<p>Specify a log file for LAMMPS to write status information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the
file log.lammps. If this switch is used, LAMMPS writes to the
specified file. In multi-partition mode, if the switch is not used, a
log.lammps file is created with hi-level status information. Each
partition also writes to a log.lammps.N file where N is the partition
ID. If the switch is specified in multi-partition mode, the hi-level
logfile is named “file” and each partition also logs information to a
file.N. For both one-partition and multi-partition mode, if the
specified file is “none”, then no log files are created. Using a
<a class="reference internal" href="log.html"><em>log</em></a> command in the input script will override this setting.
Option -plog will override the name of the partition log files file.N.</p>
<div class="highlight-python"><div class="highlight"><pre><span class="o">-</span><span class="n">nocite</span>
</pre></div>
</div>
<p>Disable writing the log.cite file which is normally written to list
references for specific cite-able features used during a LAMMPS run.
See the <a class="reference external" href="http://lammps.sandia.gov/cite.html">citation page</a> for more
details.</p>
<div class="highlight-python"><div class="highlight"><pre>-package style args ....
</pre></div>
</div>
<p>Invoke the <a class="reference internal" href="package.html"><em>package</em></a> command with style and args. The
syntax is the same as if the command appeared at the top of the input
script. For example “-package gpu 2” or “-pk gpu 2” is the same as
<a class="reference internal" href="package.html"><em>package gpu 2</em></a> in the input script. The possible styles
and args are documented on the <a class="reference internal" href="package.html"><em>package</em></a> doc page. This
switch can be used multiple times, e.g. to set options for the
USER-INTEL and USER-OMP packages which can be used together.</p>
<p>Along with the “-suffix” command-line switch, this is a convenient
mechanism for invoking accelerator packages and their options without
having to edit an input script.</p>
<div class="highlight-python"><div class="highlight"><pre>-partition 8x2 4 5 ...
</pre></div>
</div>
<p>Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P
processors and this switch is not used, LAMMPS runs in one partition,
i.e. all P processors run a single simulation. If this switch is
used, the P processors are split into separate partitions and each
partition runs its own simulation. The arguments to the switch
specify the number of processors in each partition. Arguments of the
form MxN mean M partitions, each with N processors. Arguments of the
form N mean a single partition with N processors. The sum of
processors in all partitions must equal P. Thus the command
“-partition 8x2 4 5” has 10 partitions and runs on a total of 25
processors.</p>
<p>Running with multiple partitions can e useful for running
<a class="reference internal" href="Section_howto.html#howto-5"><span>multi-replica simulations</span></a>, where each
replica runs on on one or a few processors. Note that with MPI
installed on a machine (e.g. your desktop), you can run on more
(virtual) processors than you have physical processors.</p>
<p>To run multiple independent simulatoins from one input script, using
multiple partitions, see <a class="reference internal" href="Section_howto.html#howto-4"><span>Section_howto 4</span></a>
of the manual. World- and universe-style <a class="reference internal" href="variable.html"><em>variables</em></a>
are useful in this context.</p>
<div class="highlight-python"><div class="highlight"><pre>-plog file
</pre></div>
</div>
<p>Specify the base name for the partition log files, so partition N
writes log information to file.N. If file is none, then no partition
log files are created. This overrides the filename specified in the
-log command-line option. This option is useful when working with
large numbers of partitions, allowing the partition log files to be
suppressed (-plog none) or placed in a sub-directory (-plog
replica_files/log.lammps) If this option is not used the log file for
partition N is log.lammps.N or whatever is specified by the -log
command-line option.</p>
<div class="highlight-python"><div class="highlight"><pre>-pscreen file
</pre></div>
</div>
<p>Specify the base name for the partition screen file, so partition N
writes screen information to file.N. If file is none, then no
partition screen files are created. This overrides the filename
specified in the -screen command-line option. This option is useful
when working with large numbers of partitions, allowing the partition
screen files to be suppressed (-pscreen none) or placed in a
sub-directory (-pscreen replica_files/screen). If this option is not
used the screen file for partition N is screen.N or whatever is
specified by the -screen command-line option.</p>
<pre class="literal-block">
-restart restartfile <em>remap</em> datafile keyword value ...
</pre>
<p>Convert the restart file into a data file and immediately exit. This
is the same operation as if the following 2-line input script were
run:</p>
<pre class="literal-block">
read_restart restartfile <em>remap</em>
write_data datafile keyword value ...
</pre>
<p>Note that the specified restartfile and datafile can have wild-card
characters (“*”,%”) as described by the
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> and <a class="reference internal" href="write_data.html"><em>write_data</em></a>
commands. But a filename such as file.* will need to be enclosed in
quotes to avoid shell expansion of the “*” character.</p>
<p>Note that following restartfile, the optional flag <em>remap</em> can be
used. This has the same effect as adding it to the
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command, as explained on its doc
page. This is only useful if the reading of the restart file triggers
an error that atoms have been lost. In that case, use of the remap
flag should allow the data file to still be produced.</p>
<p>Also note that following datafile, the same optional keyword/value
pairs can be listed as used by the <a class="reference internal" href="write_data.html"><em>write_data</em></a>
command.</p>
<div class="highlight-python"><div class="highlight"><pre>-reorder nth N
-reorder custom filename
</pre></div>
</div>
<p>Reorder the processors in the MPI communicator used to instantiate
LAMMPS, in one of several ways. The original MPI communicator ranks
all P processors from 0 to P-1. The mapping of these ranks to
physical processors is done by MPI before LAMMPS begins. It may be
useful in some cases to alter the rank order. E.g. to insure that
cores within each node are ranked in a desired order. Or when using
the <a class="reference internal" href="run_style.html"><em>run_style verlet/split</em></a> command with 2 partitions
to insure that a specific Kspace processor (in the 2nd partition) is
matched up with a specific set of processors in the 1st partition.
See the <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> doc pages for
more details.</p>
<p>If the keyword <em>nth</em> is used with a setting <em>N</em>, then it means every
Nth processor will be moved to the end of the ranking. This is useful
when using the <a class="reference internal" href="run_style.html"><em>run_style verlet/split</em></a> command with 2
partitions via the -partition command-line switch. The first set of
processors will be in the first partition, the 2nd set in the 2nd
partition. The -reorder command-line switch can alter this so that
the 1st N procs in the 1st partition and one proc in the 2nd partition
will be ordered consecutively, e.g. as the cores on one physical node.
This can boost performance. For example, if you use “-reorder nth 4”
and “-partition 9 3” and you are running on 12 processors, the
processors will be reordered from</p>
<div class="highlight-python"><div class="highlight"><pre>0 1 2 3 4 5 6 7 8 9 10 11
</pre></div>
</div>
<p>to</p>
<div class="highlight-python"><div class="highlight"><pre>0 1 2 4 5 6 8 9 10 3 7 11
</pre></div>
</div>
<p>so that the processors in each partition will be</p>
<div class="highlight-python"><div class="highlight"><pre>0 1 2 4 5 6 8 9 10
3 7 11
</pre></div>
</div>
<p>See the “processors” command for how to insure processors from each
partition could then be grouped optimally for quad-core nodes.</p>
<p>If the keyword is <em>custom</em>, then a file that specifies a permutation
of the processor ranks is also specified. The format of the reorder
file is as follows. Any number of initial blank or comment lines
(starting with a “#” character) can be present. These should be
followed by P lines of the form:</p>
<div class="highlight-python"><div class="highlight"><pre>I J
</pre></div>
</div>
<p>where P is the number of processors LAMMPS was launched with. Note
that if running in multi-partition mode (see the -partition switch
above) P is the total number of processors in all partitions. The I
and J values describe a permutation of the P processors. Every I and
J should be values from 0 to P-1 inclusive. In the set of P I values,
every proc ID should appear exactly once. Ditto for the set of P J
values. A single I,J pairing means that the physical processor with
rank I in the original MPI communicator will have rank J in the
reordered communicator.</p>
<p>Note that rank ordering can also be specified by many MPI
implementations, either by environment variables that specify how to
order physical processors, or by config files that specify what
physical processors to assign to each MPI rank. The -reorder switch
simply gives you a portable way to do this without relying on MPI
itself. See the <a class="reference external" href="processors">processors out</a> command for how to output
info on the final assignment of physical processors to the LAMMPS
simulation domain.</p>
<div class="highlight-python"><div class="highlight"><pre>-screen file
</pre></div>
</div>
<p>Specify a file for LAMMPS to write its screen information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the
screen. If this switch is used, LAMMPS writes to the specified file
instead and you will see no screen output. In multi-partition mode,
if the switch is not used, hi-level status information is written to
the screen. Each partition also writes to a screen.N file where N is
the partition ID. If the switch is specified in multi-partition mode,
the hi-level screen dump is named “file” and each partition also
writes screen information to a file.N. For both one-partition and
multi-partition mode, if the specified file is “none”, then no screen
output is performed. Option -pscreen will override the name of the
partition screen files file.N.</p>
<div class="highlight-python"><div class="highlight"><pre>-suffix style args
</pre></div>
</div>
<p>Use variants of various styles if they exist. The specified style can
be <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, <em>opt</em>, or <em>hybrid</em>. These refer
to optional packages that LAMMPS can be built with, as described above in
<a class="reference internal" href="#start-3"><span>Section 2.3</span></a>. The “cuda” style corresponds to the USER-CUDA
package, the “gpu” style to the GPU package, the “intel” style to the
USER-INTEL package, the “kk” style to the KOKKOS package, the “opt”
style to the OPT package, and the “omp” style to the USER-OMP package. The
hybrid style is the only style that accepts arguments. It allows for two
packages to be specified. The first package specified is the default and
will be used if it is available. If no style is available for the first
package, the style for the second package will be used if available. For
example, “-suffix hybrid intel omp” will use styles from the USER-INTEL
package if they are installed and available, but styles for the USER-OMP
package otherwise.</p>
<p>Along with the “-package” command-line switch, this is a convenient
mechanism for invoking accelerator packages and their options without
having to edit an input script.</p>
<p>As an example, all of the packages provide a <a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut</em></a> variant, with style names lj/cut/cuda,
lj/cut/gpu, lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A
variant style can be specified explicitly in your input script,
e.g. pair_style lj/cut/gpu. If the -suffix switch is used the
specified suffix (cuda,gpu,intel,kk,omp,opt) is automatically appended
whenever your input script command creates a new
<a class="reference internal" href="atom_style.html"><em>atom</em></a>, <a class="reference internal" href="pair_style.html"><em>pair</em></a>, <a class="reference internal" href="fix.html"><em>fix</em></a>,
<a class="reference internal" href="compute.html"><em>compute</em></a>, or <a class="reference internal" href="run_style.html"><em>run</em></a> style. If the variant
version does not exist, the standard version is created.</p>
<p>For the GPU package, using this command-line switch also invokes the
default GPU settings, as if the command “package gpu 1” were used at
the top of your input script. These settings can be changed by using
the “-package gpu” command-line switch or the <a class="reference internal" href="package.html"><em>package gpu</em></a> command in your script.</p>
<p>For the USER-INTEL package, using this command-line switch also
invokes the default USER-INTEL settings, as if the command “package
intel 1” were used at the top of your input script. These settings
can be changed by using the “-package intel” command-line switch or
the <a class="reference internal" href="package.html"><em>package intel</em></a> command in your script. If the
USER-OMP package is also installed, the hybrid style with “intel omp”
arguments can be used to make the omp suffix a second choice, if a
requested style is not available in the USER-INTEL package. It will
also invoke the default USER-OMP settings, as if the command “package
omp 0” were used at the top of your input script. These settings can
be changed by using the “-package omp” command-line switch or the
<a class="reference internal" href="package.html"><em>package omp</em></a> command in your script.</p>
<p>For the KOKKOS package, using this command-line switch also invokes
the default KOKKOS settings, as if the command “package kokkos” were
used at the top of your input script. These settings can be changed
by using the “-package kokkos” command-line switch or the <a class="reference internal" href="package.html"><em>package kokkos</em></a> command in your script.</p>
<p>For the OMP package, using this command-line switch also invokes the
default OMP settings, as if the command “package omp 0” were used at
the top of your input script. These settings can be changed by using
the “-package omp” command-line switch or the <a class="reference internal" href="package.html"><em>package omp</em></a> command in your script.</p>
<p>The <a class="reference internal" href="suffix.html"><em>suffix</em></a> command can also be used within an input
script to set a suffix, or to turn off or back on any suffix setting
made via the command line.</p>
<div class="highlight-python"><div class="highlight"><pre>-var name value1 value2 ...
</pre></div>
</div>
<p>Specify a variable that will be defined for substitution purposes when
the input script is read. This switch can be used multiple times to
define multiple variables. “Name” is the variable name which can be a
single character (referenced as $x in the input script) or a full
string (referenced as ${abc}). An <a class="reference internal" href="variable.html"><em>index-style variable</em></a> will be created and populated with the
subsequent values, e.g. a set of filenames. Using this command-line
option is equivalent to putting the line “variable name index value1
value2 ...” at the beginning of the input script. Defining an index
variable as a command-line argument overrides any setting for the same
index variable in the input script, since index variables cannot be
re-defined. See the <a class="reference internal" href="variable.html"><em>variable</em></a> command for more info on
defining index and other kinds of variables and <a class="reference internal" href="Section_commands.html#cmd-2"><span>this section</span></a> for more info on using variables
in input scripts.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Currently, the command-line parser looks for arguments that
start with “-” to indicate new switches. Thus you cannot specify
multiple variable values if any of they start with a “-”, e.g. a
negative numeric value. It is OK if the first value1 starts with a
“-”, since it is automatically skipped.</p>
</div>
<hr class="docutils" />
</div>
<div class="section" id="lammps-screen-output">
<span id="start-8"></span><h2>2.8. LAMMPS screen output<a class="headerlink" href="#lammps-screen-output" title="Permalink to this headline">¶</a></h2>
<p>As LAMMPS reads an input script, it prints information to both the
screen and a log file about significant actions it takes to setup a
simulation. When the simulation is ready to begin, LAMMPS performs
various initializations and prints the amount of memory (in MBytes per
processor) that the simulation requires. It also prints details of
the initial thermodynamic state of the system. During the run itself,
thermodynamic information is printed periodically, every few
timesteps. When the run concludes, LAMMPS prints the final
thermodynamic state and a total run time for the simulation. It then
appends statistics about the CPU time and storage requirements for the
simulation. An example set of statistics is shown here:</p>
<p>Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms</p>
<div class="highlight-python"><div class="highlight"><pre>Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s
97.0% CPU use with 4 MPI tasks x no OpenMP threads
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9808 | 2.0134 | 2.0318 | 1.4 | 71.60
Bond | 0.0021894 | 0.0060319 | 0.010058 | 4.7 | 0.21
Kspace | 0.3207 | 0.3366 | 0.36616 | 3.1 | 11.97
Neigh | 0.28411 | 0.28464 | 0.28516 | 0.1 | 10.12
Comm | 0.075732 | 0.077018 | 0.07883 | 0.4 | 2.74
Output | 0.00030518 | 0.00042665 | 0.00078821 | 1.0 | 0.02
Modify | 0.086606 | 0.086631 | 0.086668 | 0.0 | 3.08
Other | | 0.007178 | | | 0.26
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Nlocal: 501 ave 508 max 490 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 6586.25 ave 6628 max 6548 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 177007 ave 180562 max 170212 min
Histogram: 1 0 0 0 0 0 0 1 1 1
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Total # of neighbors = 708028
Ave neighs/atom = 353.307
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0
</pre></div>
</div>
<p>The first section provides a global loop timing summary. The loop time
is the total wall time for the section. The <em>Performance</em> line is
provided for convenience to help predicting the number of loop
continuations required and for comparing performance with other
similar MD codes. The CPU use line provides the CPU utilzation per
MPI task; it should be close to 100% times the number of OpenMP
threads (or 1). Lower numbers correspond to delays due to file I/O or
insufficient thread utilization.</p>
<p>The MPI task section gives the breakdown of the CPU run time (in
seconds) into major categories:</p>
<ul class="simple">
<li><em>Pair</em> stands for all non-bonded force computation</li>
<li><em>Bond</em> stands for bonded interactions: bonds, angles, dihedrals, impropers</li>
<li><em>Kspace</em> stands for reciprocal space interactions: Ewald, PPPM, MSM</li>
<li><em>Neigh</em> stands for neighbor list construction</li>
<li><em>Comm</em> stands for communicating atoms and their properties</li>
<li><em>Output</em> stands for writing dumps and thermo output</li>
<li><em>Modify</em> stands for fixes and computes called by them</li>
<li><em>Other</em> is the remaining time</li>
</ul>
<p>For each category, there is a breakdown of the least, average and most
amount of wall time a processor spent on this section. Also you have the
variation from the average time. Together these numbers allow to gauge
the amount of load imbalance in this segment of the calculation. Ideally
the difference between minimum, maximum and average is small and thus
the variation from the average close to zero. The final column shows
the percentage of the total loop time is spent in this section.</p>
<p>When using the <a class="reference internal" href="timer.html"><em>timer full</em></a> setting, an additional column
is present that also prints the CPU utilization in percent. In
addition, when using <em>timer full</em> and the <a class="reference internal" href="package.html"><em>package omp</em></a>
command are active, a similar timing summary of time spent in threaded
regions to monitor thread utilization and load balance is provided. A
new entry is the <em>Reduce</em> section, which lists the time spend in
reducing the per-thread data elements to the storage for non-threaded
computation. These thread timings are taking from the first MPI rank
only and and thus, as the breakdown for MPI tasks can change from MPI
rank to MPI rank, this breakdown can be very different for individual
ranks. Here is an example output for this section:</p>
<p>Thread timings breakdown (MPI rank 0):
Total threaded time 0.6846 / 90.6%
Section | min time | avg time | max time <a href="#id17"><span class="problematic" id="id18">|%varavg|</span></a> %total
—————————————————————
Pair | 0.5127 | 0.5147 | 0.5167 | 0.3 | 75.18
Bond | 0.0043139 | 0.0046779 | 0.0050418 | 0.5 | 0.68
Kspace | 0.070572 | 0.074541 | 0.07851 | 1.5 | 10.89
Neigh | 0.084778 | 0.086969 | 0.089161 | 0.7 | 12.70
Reduce | 0.0036485 | 0.003737 | 0.0038254 | 0.1 | 0.55</p>
<p>The third section lists the number of owned atoms (Nlocal), ghost atoms
(Nghost), and pair-wise neighbors stored per processor. The max and min
values give the spread of these values across processors with a 10-bin
histogram showing the distribution. The total number of histogram counts
is equal to the number of processors.</p>
<p>The last section gives aggregate statistics for pair-wise neighbors
and special neighbors that LAMMPS keeps track of (see the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command). The number of times
neighbor lists were rebuilt during the run is given as well as the
number of potentially “dangerous” rebuilds. If atom movement
triggered neighbor list rebuilding (see the
<a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a> command), then dangerous
reneighborings are those that were triggered on the first timestep
atom movement was checked for. If this count is non-zero you may wish
to reduce the delay factor to insure no force interactions are missed
by atoms moving beyond the neighbor skin distance before a rebuild
takes place.</p>
<p>If an energy minimization was performed via the
<a class="reference internal" href="minimize.html"><em>minimize</em></a> command, additional information is printed,
e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-6372.3765206 -8328.46998942 -8328.46998942
Force two-norm initial, final = 1059.36 5.36874
Force max component initial, final = 58.6026 1.46872
Final line search alpha, max atom move = 2.7842e-10 4.0892e-10
Iterations, force evaluations = 701 1516
</pre></div>
</div>
<p>The first line prints the criterion that determined the minimization
to be completed. The third line lists the initial and final energy,
as well as the energy on the next-to-last iteration. The next 2 lines
give a measure of the gradient of the energy (force on all atoms).
The 2-norm is the “length” of this force vector; the inf-norm is the
largest component. Then some information about the line search and
statistics on how many iterations and force-evaluations the minimizer
required. Multiple force evaluations are typically done at each
iteration to perform a 1d line minimization in the search direction.</p>
<p>If a <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> long-range Coulombics solve was
performed during the run (PPPM, Ewald), then additional information is
printed, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>FFT time (% of Kspce) = 0.200313 (8.34477)
FFT Gflps 3d 1d-only = 2.31074 9.19989
</pre></div>
</div>
<p>The first line gives the time spent doing 3d FFTs (4 per timestep) and
the fraction it represents of the total KSpace time (listed above).
Each 3d FFT requires computation (3 sets of 1d FFTs) and communication
(transposes). The total flops performed is 5Nlog_2(N), where N is the
number of points in the 3d grid. The FFTs are timed with and without
the communication and a Gflop rate is computed. The 3d rate is with
communication; the 1d rate is without (just the 1d FFTs). Thus you
can estimate what fraction of your FFT time was spent in
communication, roughly 75% in the example above.</p>
<hr class="docutils" />
</div>
<div class="section" id="tips-for-users-of-previous-lammps-versions">
<span id="start-9"></span><h2>2.9. Tips for users of previous LAMMPS versions<a class="headerlink" href="#tips-for-users-of-previous-lammps-versions" title="Permalink to this headline">¶</a></h2>
<p>The current C++ began with a complete rewrite of LAMMPS 2001, which
was written in F90. Features of earlier versions of LAMMPS are listed
in <a class="reference internal" href="Section_history.html"><em>Section_history</em></a>. The F90 and F77 versions
(2001 and 99) are also freely distributed as open-source codes; check
the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> for distribution information if you prefer
those versions. The 99 and 2001 versions are no longer under active
development; they do not have all the features of C++ LAMMPS.</p>
<p>If you are a previous user of LAMMPS 2001, these are the most
significant changes you will notice in C++ LAMMPS:</p>
<p>(1) The names and arguments of many input script commands have
changed. All commands are now a single word (e.g. read_data instead
of read data).</p>
<p>(2) All the functionality of LAMMPS 2001 is included in C++ LAMMPS,
but you may need to specify the relevant commands in different ways.</p>
<p>(3) The format of the data file can be streamlined for some problems.
See the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for details. The data file
section “Nonbond Coeff” has been renamed to “Pair Coeff” in C++ LAMMPS.</p>
<p>(4) Binary restart files written by LAMMPS 2001 cannot be read by C++
LAMMPS with a <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command. This is
because they were output by F90 which writes in a different binary
format than C or C++ writes or reads. Use the <em>restart2data</em> tool
provided with LAMMPS 2001 to convert the 2001 restart file to a text
data file. Then edit the data file as necessary before using the C++
LAMMPS <a class="reference internal" href="read_data.html"><em>read_data</em></a> command to read it in.</p>
<p>(5) There are numerous small numerical changes in C++ LAMMPS that mean
you will not get identical answers when comparing to a 2001 run.
However, your initial thermodynamic energy and MD trajectory should be
close if you have setup the problem for both codes the same.</p>
</div>
</div>
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diff --git a/doc/Section_start.txt b/doc/Section_start.txt
index 755906538..744229991 100644
--- a/doc/Section_start.txt
+++ b/doc/Section_start.txt
@@ -1,1932 +1,1930 @@
"Previous Section"_Section_intro.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_commands.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
2. Getting Started :h3
This section describes how to build and run LAMMPS, for both new and
experienced users.
2.1 "What's in the LAMMPS distribution"_#start_1
2.2 "Making LAMMPS"_#start_2
2.3 "Making LAMMPS with optional packages"_#start_3
2.4 "Building LAMMPS via the Make.py script"_#start_4
2.5 "Building LAMMPS as a library"_#start_5
2.6 "Running LAMMPS"_#start_6
2.7 "Command-line options"_#start_7
2.8 "Screen output"_#start_8
2.9 "Tips for users of previous versions"_#start_9 :all(b)
:line
:line
2.1 What's in the LAMMPS distribution :h4,link(start_1)
When you download a LAMMPS tarball you will need to unzip and untar
the downloaded file with the following commands, after placing the
tarball in an appropriate directory.
gunzip lammps*.tar.gz
tar xvf lammps*.tar :pre
This will create a LAMMPS directory containing two files and several
sub-directories:
README: text file
LICENSE: the GNU General Public License (GPL)
bench: benchmark problems
doc: documentation
examples: simple test problems
potentials: embedded atom method (EAM) potential files
src: source files
tools: pre- and post-processing tools :tb(s=:)
Note that the "download page"_download also has links to download
Windows exectubles and installers, as well as pre-built executables
for a few specific Linux distributions. It also has instructions for
how to download/install LAMMPS for Macs (via Homebrew), and to
download and update LAMMPS from SVN and Git repositories, which gives
you the same files that are in the download tarball.
The Windows and Linux executables for serial or parallel only include
certain packages and bug-fixes/upgrades listed on "this
page"_http://lammps.sandia.gov/bug.html up to a certain date, as
stated on the download page. If you want an executable with
non-included packages or that is more current, then you'll need to
build LAMMPS yourself, as discussed in the next section.
Skip to the "Running LAMMPS"_#start_6 sections for info on how to
launch a LAMMPS Windows executable on a Windows box.
:line
2.2 Making LAMMPS :h4,link(start_2)
This section has the following sub-sections:
"Read this first"_#start_2_1
"Steps to build a LAMMPS executable"_#start_2_2
"Common errors that can occur when making LAMMPS"_#start_2_3
"Additional build tips"_#start_2_4
"Building for a Mac"_#start_2_5
"Building for Windows"_#start_2_6 :ul
:line
[{Read this first:}] :link(start_2_1)
If you want to avoid building LAMMPS yourself, read the preceeding
section about options available for downloading and installing
executables. Details are discussed on the "download"_download page.
Building LAMMPS can be simple or not-so-simple. If all you need are
the default packages installed in LAMMPS, and MPI is already installed
on your machine, or you just want to run LAMMPS in serial, then you
can typically use the Makefile.mpi or Makefile.serial files in
src/MAKE by typing one of these lines (from the src dir):
make mpi
make serial :pre
Note that on a facility supercomputer, there are often "modules"
loaded in your environment that provide the compilers and MPI you
should use. In this case, the "mpicxx" compile/link command in
Makefile.mpi should just work by accessing those modules.
It may be the case that one of the other Makefile.machine files in the
src/MAKE sub-directories is a better match to your system (type "make"
to see a list), you can use it as-is by typing (for example):
make stampede :pre
If any of these builds (with an existing Makefile.machine) works on
your system, then you're done!
If you want to do one of the following:
use optional LAMMPS features that require additional libraries
use optional packages that require additional libraries
use optional accelerator packages that require special compiler/linker settings
run on a specialized platform that has its own compilers, settings, or other libs to use :ul
then building LAMMPS is more complicated. You may need to find where
auxiliary libraries exist on your machine or install them if they
don't. You may need to build additional libraries that are part of
the LAMMPS package, before building LAMMPS. You may need to edit a
Makefile.machine file to make it compatible with your system.
Note that there is a Make.py tool in the src directory that automates
several of these steps, but you still have to know what you are doing.
"Section 2.4"_#start_4 below describes the tool. It is a convenient
way to work with installing/un-installing various packages, the
Makefile.machine changes required by some packages, and the auxiliary
libraries some of them use.
Please read the following sections carefully. If you are not
comfortable with makefiles, or building codes on a Unix platform, or
running an MPI job on your machine, please find a local expert to help
you. Many compilation, linking, and run problems that users have are
often not really LAMMPS issues - they are peculiar to the user's
system, compilers, libraries, etc. Such questions are better answered
by a local expert.
If you have a build problem that you are convinced is a LAMMPS issue
(e.g. the compiler complains about a line of LAMMPS source code), then
please post the issue to the "LAMMPS mail
list"_http://lammps.sandia.gov/mail.html.
If you succeed in building LAMMPS on a new kind of machine, for which
there isn't a similar machine Makefile included in the
src/MAKE/MACHINES directory, then send it to the developers and we can
include it in the LAMMPS distribution.
:line
[{Steps to build a LAMMPS executable:}] :link(start_2_2)
[Step 0]
The src directory contains the C++ source and header files for LAMMPS.
It also contains a top-level Makefile and a MAKE sub-directory with
low-level Makefile.* files for many systems and machines. See the
src/MAKE/README file for a quick overview of what files are available
and what sub-directories they are in.
The src/MAKE dir has a few files that should work as-is on many
platforms. The src/MAKE/OPTIONS dir has more that invoke additional
compiler, MPI, and other setting options commonly used by LAMMPS, to
illustrate their syntax. The src/MAKE/MACHINES dir has many more that
have been tweaked or optimized for specific machines. These files are
all good starting points if you find you need to change them for your
machine. Put any file you edit into the src/MAKE/MINE directory and
it will be never be touched by any LAMMPS updates.
>From within the src directory, type "make" or "gmake". You should see
a list of available choices from src/MAKE and all of its
sub-directories. If one of those has the options you want or is the
machine you want, you can type a command like:
make mpi
or
make serial_icc
or
gmake mac :pre
Note that the corresponding Makefile.machine can exist in src/MAKE or
any of its sub-directories. If a file with the same name appears in
multiple places (not a good idea), the order they are used is as
follows: src/MAKE/MINE, src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES.
This gives preference to a file you have created/edited and put in
src/MAKE/MINE.
Note that on a multi-processor or multi-core platform you can launch a
parallel make, by using the "-j" switch with the make command, which
will build LAMMPS more quickly.
If you get no errors and an executable like lmp_mpi or lmp_g++_serial
or lmp_mac is produced, then you're done; it's your lucky day.
Note that by default only a few of LAMMPS optional packages are
installed. To build LAMMPS with optional packages, see "this
section"_#start_3 below.
[Step 1]
If Step 0 did not work, you will need to create a low-level Makefile
for your machine, like Makefile.foo. You should make a copy of an
existing Makefile.* in src/MAKE or one of its sub-directories as a
starting point. The only portions of the file you need to edit are
the first line, the "compiler/linker settings" section, and the
"LAMMPS-specific settings" section. When it works, put the edited
file in src/MAKE/MINE and it will not be altered by any future LAMMPS
updates.
[Step 2]
Change the first line of Makefile.foo to list the word "foo" after the
"#", and whatever other options it will set. This is the line you
will see if you just type "make".
[Step 3]
The "compiler/linker settings" section lists compiler and linker
settings for your C++ compiler, including optimization flags. You can
use g++, the open-source GNU compiler, which is available on all Unix
systems. You can also use mpicxx which will typically be available if
MPI is installed on your system, though you should check which actual
compiler it wraps. Vendor compilers often produce faster code. On
boxes with Intel CPUs, we suggest using the Intel icc compiler, which
can be downloaded from "Intel's compiler site"_intel.
:link(intel,http://www.intel.com/software/products/noncom)
If building a C++ code on your machine requires additional libraries,
then you should list them as part of the LIB variable. You should
not need to do this if you use mpicxx.
The DEPFLAGS setting is what triggers the C++ compiler to create a
dependency list for a source file. This speeds re-compilation when
source (*.cpp) or header (*.h) files are edited. Some compilers do
not support dependency file creation, or may use a different switch
than -D. GNU g++ and Intel icc works with -D. If your compiler can't
create dependency files, then you'll need to create a Makefile.foo
patterned after Makefile.storm, which uses different rules that do not
involve dependency files. Note that when you build LAMMPS for the
first time on a new platform, a long list of *.d files will be printed
out rapidly. This is not an error; it is the Makefile doing its
normal creation of dependencies.
[Step 4]
The "system-specific settings" section has several parts. Note that
if you change any -D setting in this section, you should do a full
re-compile, after typing "make clean" (which will describe different
clean options).
The LMP_INC variable is used to include options that turn on ifdefs
within the LAMMPS code. The options that are currently recogized are:
-DLAMMPS_GZIP
-DLAMMPS_JPEG
-DLAMMPS_PNG
-DLAMMPS_FFMPEG
-DLAMMPS_MEMALIGN
-DLAMMPS_XDR
-DLAMMPS_SMALLBIG
-DLAMMPS_BIGBIG
-DLAMMPS_SMALLSMALL
-DLAMMPS_LONGLONG_TO_LONG
-DPACK_ARRAY
-DPACK_POINTER
-DPACK_MEMCPY :ul
The read_data and dump commands will read/write gzipped files if you
compile with -DLAMMPS_GZIP. It requires that your machine supports
the "popen()" function in the standard runtime library and that a gzip
executable can be found by LAMMPS during a run.
IMPORTANT NOTE: on some clusters with high-speed networks, using the
fork() library calls (required by popen()) can interfere with the fast
communication library and lead to simulations using compressed output
or input to hang or crash. For selected operations, compressed file
I/O is also available using a compression library instead, which are
provided in the COMPRESS package. From more details about compiling
LAMMPS with packages, please see below.
If you use -DLAMMPS_JPEG, the "dump image"_dump_image.html command
will be able to write out JPEG image files. For JPEG files, you must
also link LAMMPS with a JPEG library, as described below. If you use
-DLAMMPS_PNG, the "dump image"_dump.html command will be able to write
out PNG image files. For PNG files, you must also link LAMMPS with a
PNG library, as described below. If neither of those two defines are
used, LAMMPS will only be able to write out uncompressed PPM image
files.
If you use -DLAMMPS_FFMPEG, the "dump movie"_dump_image.html command
will be available to support on-the-fly generation of rendered movies
the need to store intermediate image files. It requires that your
machines supports the "popen" function in the standard runtime library
and that an FFmpeg executable can be found by LAMMPS during the run.
IMPORTANT NOTE: Similar to the note above, this option can conflict
with high-speed networks, because it uses popen().
Using -DLAMMPS_MEMALIGN=<bytes> enables the use of the
posix_memalign() call instead of malloc() when large chunks or memory
are allocated by LAMMPS. This can help to make more efficient use of
vector instructions of modern CPUS, since dynamically allocated memory
has to be aligned on larger than default byte boundaries (e.g. 16
bytes instead of 8 bytes on x86 type platforms) for optimal
performance.
If you use -DLAMMPS_XDR, the build will include XDR compatibility
files for doing particle dumps in XTC format. This is only necessary
if your platform does have its own XDR files available. See the
Restrictions section of the "dump"_dump.html command for details.
Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, -D-
DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These
settings refer to use of 4-byte (small) vs 8-byte (big) integers
within LAMMPS, as specified in src/lmptype.h. The only reason to use
the BIGBIG setting is to enable simulation of huge molecular systems
(which store bond topology info) with more than 2 billion atoms, or to
track the image flags of moving atoms that wrap around a periodic box
more than 512 times. Normally, the only reason to use SMALLSMALL is
if your machine does not support 64-bit integers, though you can use
SMALLSMALL setting if you are running in serial or on a desktop
machine or small cluster where you will never run large systems or for
long time (more than 2 billion atoms, more than 2 billion timesteps).
See the "Additional build tips"_#start_2_4 section below for more
details on these settings.
Note that two packages, USER-ATC and USER-CUDA are not currently
compatible with -DLAMMPS_BIGBIG. Also the GPU package requires the
lib/gpu library to be compiled with the same setting, or the link will
fail.
The -DLAMMPS_LONGLONG_TO_LONG setting may be needed if your system or
MPI version does not recognize "long long" data types. In this case a
"long" data type is likely already 64-bits, in which case this setting
will convert to that data type.
Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY
options can make for faster parallel FFTs (in the PPPM solver) on some
platforms. The -DPACK_ARRAY setting is the default. See the
"kspace_style"_kspace_style.html command for info about PPPM. See
Step 6 below for info about building LAMMPS with an FFT library.
[Step 5]
The 3 MPI variables are used to specify an MPI library to build LAMMPS
with. Note that you do not need to set these if you use the MPI
compiler mpicxx for your CC and LINK setting in the section above.
The MPI wrapper knows where to find the needed files.
If you want LAMMPS to run in parallel, you must have an MPI library
installed on your platform. If MPI is installed on your system in the
usual place (under /usr/local), you also may not need to specify these
3 variables, assuming /usr/local is in your path. On some large
parallel machines which use "modules" for their compile/link
environements, you may simply need to include the correct module in
your build environment, before building LAMMPS. Or the parallel
machine may have a vendor-provided MPI which the compiler has no
trouble finding.
Failing this, these 3 variables can be used to specify where the mpi.h
file (MPI_INC) and the MPI library file (MPI_PATH) are found and the
name of the library file (MPI_LIB).
If you are installing MPI yourself, we recommend Argonne's MPICH2
or OpenMPI. MPICH can be downloaded from the "Argonne MPI
site"_http://www.mcs.anl.gov/research/projects/mpich2/. OpenMPI can
be downloaded from the "OpenMPI site"_http://www.open-mpi.org.
Other MPI packages should also work. If you are running on a big
parallel platform, your system people or the vendor should have
already installed a version of MPI, which is likely to be faster
than a self-installed MPICH or OpenMPI, so find out how to build
and link with it. If you use MPICH or OpenMPI, you will have to
configure and build it for your platform. The MPI configure script
should have compiler options to enable you to use the same compiler
you are using for the LAMMPS build, which can avoid problems that can
arise when linking LAMMPS to the MPI library.
If you just want to run LAMMPS on a single processor, you can use the
dummy MPI library provided in src/STUBS, since you don't need a true
MPI library installed on your system. See src/MAKE/Makefile.serial
for how to specify the 3 MPI variables in this case. You will also
need to build the STUBS library for your platform before making LAMMPS
itself. Note that if you are building with src/MAKE/Makefile.serial,
e.g. by typing "make serial", then the STUBS library is built for you.
To build the STUBS library from the src directory, type "make
mpi-stubs", or from the src/STUBS dir, type "make". This should
create a libmpi_stubs.a file suitable for linking to LAMMPS. If the
build fails, you will need to edit the STUBS/Makefile for your
platform.
The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime()
that calls gettimeofday() . If your system doesn't support
gettimeofday() , you'll need to insert code to call another timer.
Note that the ANSI-standard function clock() rolls over after an hour
or so, and is therefore insufficient for timing long LAMMPS
simulations.
[Step 6]
The 3 FFT variables allow you to specify an FFT library which LAMMPS
uses (for performing 1d FFTs) when running the particle-particle
particle-mesh (PPPM) option for long-range Coulombics via the
"kspace_style"_kspace_style.html command.
LAMMPS supports various open-source or vendor-supplied FFT libraries
for this purpose. If you leave these 3 variables blank, LAMMPS will
use the open-source "KISS FFT library"_http://kissfft.sf.net, which is
included in the LAMMPS distribution. This library is portable to all
platforms and for typical LAMMPS simulations is almost as fast as FFTW
or vendor optimized libraries. If you are not including the KSPACE
package in your build, you can also leave the 3 variables blank.
Otherwise, select which kinds of FFTs to use as part of the FFT_INC
setting by a switch of the form -DFFT_XXX. Recommended values for XXX
are: MKL, SCSL, FFTW2, and FFTW3. Legacy options are: INTEL, SGI,
ACML, and T3E. For backward compatability, using -DFFT_FFTW will use
the FFTW2 library. Using -DFFT_NONE will use the KISS library
described above.
You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
so the compiler and linker can find the needed FFT header and library
files. Note that on some large parallel machines which use "modules"
for their compile/link environements, you may simply need to include
the correct module in your build environment. Or the parallel machine
may have a vendor-provided FFT library which the compiler has no
trouble finding.
FFTW is a fast, portable library that should also work on any
platform. You can download it from
"www.fftw.org"_http://www.fftw.org. Both the legacy version 2.1.X and
the newer 3.X versions are supported as -DFFT_FFTW2 or -DFFT_FFTW3.
Building FFTW for your box should be as simple as ./configure; make.
Note that on some platforms FFTW2 has been pre-installed, and uses
renamed files indicating the precision it was compiled with,
e.g. sfftw.h, or dfftw.h instead of fftw.h. In this case, you can
specify an additional define variable for FFT_INC called -DFFTW_SIZE,
which will select the correct include file. In this case, for FFT_LIB
you must also manually specify the correct library, namely -lsfftw or
-ldfftw.
The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
use single-precision FFTs with PPPM, which can speed-up long-range
calulations, particularly in parallel or on GPUs. Fourier transform
and related PPPM operations are somewhat insensitive to floating point
truncation errors and thus do not always need to be performed in
double precision. Using the -DFFT_SINGLE setting trades off a little
accuracy for reduced memory use and parallel communication costs for
transposing 3d FFT data. Note that single precision FFTs have only
been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
[Step 7]
The 3 JPG variables allow you to specify a JPEG and/or PNG library
which LAMMPS uses when writing out JPEG or PNG files via the "dump
image"_dump_image.html command. These can be left blank if you do not
use the -DLAMMPS_JPEG or -DLAMMPS_PNG switches discussed above in Step
4, since in that case JPEG/PNG output will be disabled.
A standard JPEG library usually goes by the name libjpeg.a or
libjpeg.so and has an associated header file jpeglib.h. Whichever
JPEG library you have on your platform, you'll need to set the
appropriate JPG_INC, JPG_PATH, and JPG_LIB variables, so that the
compiler and linker can find it.
A standard PNG library usually goes by the name libpng.a or libpng.so
and has an associated header file png.h. Whichever PNG library you
have on your platform, you'll need to set the appropriate JPG_INC,
JPG_PATH, and JPG_LIB variables, so that the compiler and linker can
find it.
As before, if these header and library files are in the usual place on
your machine, you may not need to set these variables.
[Step 8]
Note that by default only a few of LAMMPS optional packages are
installed. To build LAMMPS with optional packages, see "this
section"_#start_3 below, before proceeding to Step 9.
[Step 9]
That's it. Once you have a correct Makefile.foo, and you have
pre-built any other needed libraries (e.g. MPI, FFT, etc) all you need
to do from the src directory is type something like this:
make foo
or
gmake foo :pre
You should get the executable lmp_foo when the build is complete.
:line
[{Errors that can occur when making LAMMPS:}] :link(start_2_3)
IMPORTANT NOTE: If an error occurs when building LAMMPS, the compiler
or linker will state very explicitly what the problem is. The error
message should give you a hint as to which of the steps above has
failed, and what you need to do in order to fix it. Building a code
with a Makefile is a very logical process. The compiler and linker
need to find the appropriate files and those files need to be
compatible with LAMMPS source files. When a make fails, there is
usually a very simple reason, which you or a local expert will need to
fix.
Here are two non-obvious errors that can occur:
(1) If the make command breaks immediately with errors that indicate
it can't find files with a "*" in their names, this can be because
your machine's native make doesn't support wildcard expansion in a
makefile. Try gmake instead of make. If that doesn't work, try using
a -f switch with your make command to use a pre-generated
Makefile.list which explicitly lists all the needed files, e.g.
make makelist
make -f Makefile.list linux
gmake -f Makefile.list mac :pre
The first "make" command will create a current Makefile.list with all
the file names in your src dir. The 2nd "make" command (make or
gmake) will use it to build LAMMPS. Note that you should
include/exclude any desired optional packages before using the "make
makelist" command.
(2) If you get an error that says something like 'identifier "atoll"
is undefined', then your machine does not support "long long"
integers. Try using the -DLAMMPS_LONGLONG_TO_LONG setting described
above in Step 4.
:line
[{Additional build tips:}] :link(start_2_4)
(1) Building LAMMPS for multiple platforms.
You can make LAMMPS for multiple platforms from the same src
directory. Each target creates its own object sub-directory called
Obj_target where it stores the system-specific *.o files.
(2) Cleaning up.
Typing "make clean-all" or "make clean-machine" will delete *.o object
files created when LAMMPS is built, for either all builds or for a
particular machine.
(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
As explained above, any of these 3 settings can be specified on the
LMP_INC line in your low-level src/MAKE/Makefile.foo.
The default is -DLAMMPS_SMALLBIG which allows for systems with up to
2^63 atoms and 2^63 timesteps (about 9e18). The atom limit is for
atomic systems which do not store bond topology info and thus do not
require atom IDs. If you use atom IDs for atomic systems (which is
the default) or if you use a molecular model, which stores bond
topology info and thus requires atom IDs, the limit is 2^31 atoms
(about 2 billion). This is because the IDs are stored in 32-bit
integers.
Likewise, with this setting, the 3 image flags for each atom (see the
"dump"_dump.html doc page for a discussion) are stored in a 32-bit
integer, which means the atoms can only wrap around a periodic box (in
each dimension) at most 512 times. If atoms move through the periodic
box more than this many times, the image flags will "roll over",
e.g. from 511 to -512, which can cause diagnostics like the
mean-squared displacement, as calculated by the "compute
msd"_compute_msd.html command, to be faulty.
To allow for larger atomic systems with atom IDs or larger molecular
systems or larger image flags, compile with -DLAMMPS_BIGBIG. This
stores atom IDs and image flags in 64-bit integers. This enables
atomic or molecular systems with atom IDS of up to 2^63 atoms (about
9e18). And image flags will not "roll over" until they reach 2^20 =
1048576.
If your system does not support 8-byte integers, you will need to
compile with the -DLAMMPS_SMALLSMALL setting. This will restrict the
total number of atoms (for atomic or molecular systems) and timesteps
to 2^31 (about 2 billion). Image flags will roll over at 2^9 = 512.
Note that in src/lmptype.h there are definitions of all these data
types as well as the MPI data types associated with them. The MPI
types need to be consistent with the associated C data types, or else
LAMMPS will generate a run-time error. As far as we know, the
settings defined in src/lmptype.h are portable and work on every
current system.
In all cases, the size of problem that can be run on a per-processor
basis is limited by 4-byte integer storage to 2^31 atoms per processor
(about 2 billion). This should not normally be a limitation since such
a problem would have a huge per-processor memory footprint due to
neighbor lists and would run very slowly in terms of CPU secs/timestep.
:line
[{Building for a Mac:}] :link(start_2_5)
OS X is BSD Unix, so it should just work. See the
src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.
:line
[{Building for Windows:}] :link(start_2_6)
The LAMMPS download page has an option to download both a serial and
parallel pre-built Windows executable. See the "Running
LAMMPS"_#start_6 section for instructions on running these executables
on a Windows box.
The pre-built executables hosted on the "LAMMPS download
page"_http://lammps.sandia.gov/download.html are built with a subset
of the available packages; see the download page for the list. These
are single executable files. No examples or documentation in
included. You will need to download the full source code package to
obtain those.
As an alternative, you can download "daily builds" (and some older
versions) of the installer packages from
"rpm.lammps.org/windows.html"_http://rpm.lammps.org/windows.html.
These executables are built with most optional packages and the
download includes documentation, some tools and most examples.
If you want a Windows version with specific packages included and
excluded, you can build it yourself.
One way to do this is install and use cygwin to build LAMMPS with a
standard unix style make program, just as you would on a Linux box;
see src/MAKE/MACHINES/Makefile.cygwin.
-The other way to do this is using Visual Studio and project files.
-See the src/WINDOWS directory and its README.txt file for instructions
-on both a basic build and a customized build with pacakges you select.
-
:line
2.3 Making LAMMPS with optional packages :h4,link(start_3)
This section has the following sub-sections:
"Package basics"_#start_3_1
"Including/excluding packages"_#start_3_2
"Packages that require extra libraries"_#start_3_3
"Packages that require Makefile.machine settings"_#start_3_4 :ul
Note that the following "Section 2.4"_#start_4 describes the Make.py
tool which can be used to install/un-install packages and build the
auxiliary libraries which some of them use. It can also auto-edit a
Makefile.machine to add settings needed by some packages.
:line
[{Package basics:}] :link(start_3_1)
The source code for LAMMPS is structured as a set of core files which
are always included, plus optional packages. Packages are groups of
files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages.
You can see the list of all packages by typing "make package" from
within the src directory of the LAMMPS distribution. This also lists
various make commands that can be used to manipulate packages.
If you use a command in a LAMMPS input script that is specific to a
particular package, you must have built LAMMPS with that package, else
you will get an error that the style is invalid or the command is
unknown. Every command's doc page specfies if it is part of a
package. You can also type
lmp_machine -h :pre
to run your executable with the optional "-h command-line
-switch"_#start_7 for "help", which will list the styles and commands
-known to your executable.
+switch"_#start_7 for "help", which will simply list the styles and
+commands known to your executable, and immediately exit.
There are two kinds of packages in LAMMPS, standard and user packages.
More information about the contents of standard and user packages is
given in "Section_packages"_Section_packages.html of the manual. The
difference between standard and user packages is as follows:
-Standard packages are supported by the LAMMPS developers and are
-written in a syntax and style consistent with the rest of LAMMPS.
-This means we will answer questions about them, debug and fix them if
-necessary, and keep them compatible with future changes to LAMMPS.
+Standard packages, such as molecule or kspace, are supported by the
+LAMMPS developers and are written in a syntax and style consistent
+with the rest of LAMMPS. This means we will answer questions about
+them, debug and fix them if necessary, and keep them compatible with
+future changes to LAMMPS.
-User packages have been contributed by users, and always begin with
-the user prefix. If they are a single command (single file), they are
-typically in the user-misc package. Otherwise, they are a a set of
-files grouped together which add a specific functionality to the code.
+User packages, such as user-atc or user-omp, have been contributed by
+users, and always begin with the user prefix. If they are a single
+command (single file), they are typically in the user-misc package.
+Otherwise, they are a a set of files grouped together which add a
+specific functionality to the code.
User packages don't necessarily meet the requirements of the standard
packages. If you have problems using a feature provided in a user
-package, you will likely need to contact the contributor directly to
-get help. Information on how to submit additions you make to LAMMPS
-as a user-contributed package is given in "this
-section"_Section_modify.html#mod_15 of the documentation.
+package, you may need to contact the contributor directly to get help.
+Information on how to submit additions you make to LAMMPS as single
+files or either a standard or user-contributed package are given in
+"this section"_Section_modify.html#mod_15 of the documentation.
-Some packages (both standard and user) require additional libraries.
-See more details below.
+Some packages (both standard and user) require additional auxiliary
+libraries when building LAMMPS. See more details below.
:line
[{Including/excluding packages:}] :link(start_3_2)
-To use or not use a package you must include or exclude it before
-building LAMMPS. From the src directory, this is typically as simple
-as:
+To use (or not use) a package you must include it (or exclude it)
+before building LAMMPS. From the src directory, this is typically as
+simple as:
make yes-colloid
make g++ :pre
or
make no-manybody
make g++ :pre
IMPORTANT NOTE: You should NOT include/exclude packages and build
-LAMMPS in a single make command by using multiple targets, e.g. make
+LAMMPS in a single make command using multiple targets, e.g. make
yes-colloid g++. This is because the make procedure creates a list of
source files that will be out-of-date for the build if the package
-configuration changes during the same command.
+configuration changes within the same command.
Some packages have individual files that depend on other packages
being included. LAMMPS checks for this and does the right thing.
I.e. individual files are only included if their dependencies are
already included. Likewise, if a package is excluded, other files
dependent on that package are also excluded.
If you will never run simulations that use the features in a
particular packages, there is no reason to include it in your build.
For some packages, this will keep you from having to build auxiliary
libraries (see below), and will also produce a smaller executable
which may run a bit faster.
When you download a LAMMPS tarball, these packages are pre-installed
in the src directory: KSPACE, MANYBODY,MOLECULE. When you download
LAMMPS source files from the SVN or Git repositories, no packages are
pre-installed.
Packages are included or excluded by typing "make yes-name" or "make
no-name", where "name" is the name of the package in lower-case, e.g.
name = kspace for the KSPACE package or name = user-atc for the
USER-ATC package. You can also type "make yes-standard", "make
no-standard", "make yes-std", "make no-std", "make yes-user", "make
no-user", "make yes-all" or "make no-all" to include/exclude various
sets of packages. Type "make package" to see the all of the
package-related make options.
IMPORTANT NOTE: Inclusion/exclusion of a package works by simply
moving files back and forth between the main src directory and
sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
so that the files are seen or not seen when LAMMPS is built. After
you have included or excluded a package, you must re-build LAMMPS.
Additional package-related make options exist to help manage LAMMPS
files that exist in both the src directory and in package
sub-directories. You do not normally need to use these commands
unless you are editing LAMMPS files or have downloaded a patch from
the LAMMPS WWW site.
Typing "make package-update" or "make pu" will overwrite src files
with files from the package sub-directories if the package has been
included. It should be used after a patch is installed, since patches
only update the files in the package sub-directory, but not the src
files. Typing "make package-overwrite" will overwrite files in the
package sub-directories with src files.
Typing "make package-status" or "make ps" will show which packages are
currently included. Of those that are included, it will list files
that are different in the src directory and package sub-directory.
Typing "make package-diff" lists all differences between these files.
Again, type "make package" to see all of the package-related make
options.
:line
[{Packages that require extra libraries:}] :link(start_3_3)
A few of the standard and user packages require additional auxiliary
-libraries. Most of them are provided with LAMMPS, in which case they
-must be compiled first, before LAMMPS is built if you wish to include
+libraries. Many of them are provided with LAMMPS, in which case they
+must be compiled first, before LAMMPS is built, if you wish to include
that package. If you get a LAMMPS build error about a missing
library, this is likely the reason. See the
"Section_packages"_Section_packages.html doc page for a list of
packages that have these kinds of auxiliary libraries.
The lib directory in the distribution has sub-directories with package
-names that correspond to the needed auxiliary libs, e.g. lib/reax.
+names that correspond to the needed auxiliary libs, e.g. lib/gpu.
Each sub-directory has a README file that gives more details. Code
for most of the auxiliary libraries is included in that directory.
Examples are the USER-ATC and MEAM packages.
A few of the lib sub-directories do not include code, but do include
-instructions and sometimes scripts that automate the process of
+instructions (and sometimes scripts) that automate the process of
downloading the auxiliary library and installing it so LAMMPS can link
-to it. Examples are the KIM and VORONOI and USER-MOLFILE and USER-SMD
+to it. Examples are the KIM, VORONOI, USER-MOLFILE, and USER-SMD
packages.
The lib/python directory (for the PYTHON package) contains only a
choice of Makefile.lammps.* files. This is because no auxiliary code
or libraries are needed, only the Python library and other system libs
-that already available on your system. However, the Makefile.lammps
-file is needed to tell the LAMMPS build which libs to use and where to
-find them.
+that should already available on your system. However, the
+Makefile.lammps file is needed to tell LAMMPS which libs to use and
+where to find them.
For libraries with provided code, the sub-directory README file
-(e.g. lib/reax/README) has instructions on how to build that library.
+(e.g. lib/atc/README) has instructions on how to build that library.
Typically this is done by typing something like:
make -f Makefile.g++ :pre
If one of the provided Makefiles is not appropriate for your system
you will need to edit or add one. Note that all the Makefiles have a
setting for EXTRAMAKE at the top that specifies a Makefile.lammps.*
file.
If the library build is successful, it will produce 2 files in the lib
directory:
libpackage.a
Makefile.lammps :pre
The Makefile.lammps file will be a copy of the EXTRAMAKE file setting
specified in the library Makefile.* you used.
Note that you must insure that the settings in Makefile.lammps are
appropriate for your system. If they are not, the LAMMPS build will
fail.
As explained in the lib/package/README files, the settings in
Makefile.lammps are used to specify additional system libraries and
their locations so that LAMMPS can build with the auxiliary library.
-For example, if the MEAM package is used, the auxiliary libraries
-consist of F90 code, built with a Fortran complier. To link
-that library with LAMMPS (a C++ code) via whatever C++ compiler LAMMPS
-is built with, typically requires additional Fortran-to-C libraries be
+For example, if the MEAM package is used, the auxiliary library
+consists of F90 code, built with a Fortran complier. To link that
+library with LAMMPS (a C++ code) via whatever C++ compiler LAMMPS is
+built with, typically requires additional Fortran-to-C libraries be
included in the link. Another example are the BLAS and LAPACK
libraries needed to use the USER-ATC or USER-AWPMD packages.
For libraries without provided code, the sub-directory README file has
information on where to download the library and how to build it,
e.g. lib/voronoi/README and lib/smd/README. The README files also
describe how you must either (a) create soft links, via the "ln"
command, in those directories to point to where you built or installed
the packages, or (b) check or edit the Makefile.lammps file in the
same directory to provide that information.
Some of the sub-directories, e.g. lib/voronoi, also have an install.py
script which can be used to automate the process of
downloading/building/installing the auxiliary library, and setting the
needed soft links. Type "python install.py" for further instructions.
As with the sub-directories containing library code, if the soft links
or settings in the lib/package/Makefile.lammps files are not correct,
the LAMMPS build will typically fail.
:line
[{Packages that require Makefile.machine settings}] :link(start_3_4)
A few packages require specific settings in Makefile.machine, to
either build or use the package effectively. These are the
USER-INTEL, KOKKOS, USER-OMP, and OPT packages. The details of what
flags to add or what variables to define are given on the doc pages
that describe each of these accelerator packages in detail:
"USER-INTEL package"_accelerate_intel.html
"KOKKOS package"_accelerate_kokkos.html
"USER-OMP package"_accelerate_omp.html
"OPT package"_accelerate_opt.html :ul
Here is a brief summary of what Makefile.machine changes are needed.
Note that the Make.py tool, described in the next "Section
2.4"_#start_4 can automatically add the needed info to an existing
machine Makefile, using simple command-line arguments.
In src/MAKE/OPTIONS see the following Makefiles for examples of the
changes described below:
Makefile.intel_cpu
Makefile.intel_phi
Makefile.kokkos_omp
Makefile.kokkos_cuda
Makefile.kokkos_phi
Makefile.omp :ul
For the USER-INTEL package, you have 2 choices when building. You can
build with CPU or Phi support. The latter uses Xeon Phi chips in
"offload" mode. Each of these modes requires additional settings in
your Makefile.machine for CCFLAGS and LINKFLAGS.
For CPU mode (if using an Intel compiler):
CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
LINKFLAGS: add -fopenmp :ul
For Phi mode add the following in addition to the CPU mode flags:
CCFLAGS: add -DLMP_INTEL_OFFLOAD and
LINKFLAGS: add -offload :ul
And also add this to CCFLAGS:
-offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\"" :pre
For the KOKKOS package, you have 3 choices when building. You can
build with OMP or Cuda or Phi support. Phi support uses Xeon Phi
chips in "native" mode. This can be done by setting the following
variables in your Makefile.machine:
for OMP support, set OMP = yes
for Cuda support, set OMP = yes and CUDA = yes
for Phi support, set OMP = yes and MIC = yes :ul
These can also be set as additional arguments to the make command, e.g.
make g++ OMP=yes MIC=yes :pre
Building the KOKKOS package with CUDA support requires a Makefile
machine that uses the NVIDIA "nvcc" compiler, as well as an
appropriate "arch" setting appropriate to the GPU hardware and NVIDIA
software you have on your machine. See
src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine
Makefile.
For the USER-OMP package, your Makefile.machine needs additional
settings for CCFLAGS and LINKFLAGS.
CCFLAGS: add -fopenmp and -restrict
LINKFLAGS: add -fopenmp :ul
For the OPT package, your Makefile.machine needs an additional
settings for CCFLAGS.
CCFLAGS: add -restrict :ul
:line
-2.4 Building LAMMPS via the Make.py script :h4,link(start_4)
+2.4 Building LAMMPS via the Make.py tool :h4,link(start_4)
The src directory includes a Make.py script, written in Python, which
can be used to automate various steps of the build process. It is
particularly useful for working with the accelerator packages, as well
as other packages which require auxiliary libraries to be built.
The goal of the Make.py tool is to allow any complex multi-step LAMMPS
build to be performed as a single Make.py command. And you can
archive the commands, so they can be re-invoked later via the -r
(redo) switch. If you find some LAMMPS build procedure that can't be
done in a single Make.py command, let the developers know, and we'll
see if we can augment the tool.
You can run Make.py from the src directory by typing either:
Make.py -h
python Make.py -h :pre
which will give you help info about the tool. For the former to work,
you may need to edit the first line of Make.py to point to your local
Python. And you may need to insure the script is executable:
chmod +x Make.py :pre
Here are examples of build tasks you can perform with Make.py:
Install/uninstall packages: Make.py -p no-lib kokkos omp intel
Build specific auxiliary libs: Make.py -a lib-atc lib-meam
Build libs for all installed packages: Make.py -p cuda gpu -gpu mode=double arch=31 -a lib-all
Create a Makefile from scratch with compiler and MPI settings: Make.py -m none -cc g++ -mpi mpich -a file
Augment Makefile.serial with settings for installed packages: Make.py -p intel -intel cpu -m serial -a file
Add JPG and FFTW support to Makefile.mpi: Make.py -m mpi -jpg -fft fftw -a file
Build LAMMPS with a parallel make using Makefile.mpi: Make.py -j 16 -m mpi -a exe
Build LAMMPS and libs it needs using Makefile.serial with accelerator settings: Make.py -p gpu intel -intel cpu -a lib-all file serial :tb(s=:)
The bench and examples directories give Make.py commands that can be
used to build LAMMPS with the various packages and options needed to
run all the benchmark and example input scripts. See these files for
more details:
bench/README
bench/FERMI/README
bench/KEPLER/README
bench/PHI/README
examples/README
examples/accelerate/README
examples/accelerate/make.list :ul
All of the Make.py options and syntax help can be accessed by using
the "-h" switch.
E.g. typing "Make.py -h" gives
Syntax: Make.py switch args ...
switches can be listed in any order
help switch:
-h prints help and syntax for all other specified switches
switch for actions:
-a lib-all, lib-dir, clean, file, exe or machine
list one or more actions, in any order
machine is a Makefile.machine suffix, must be last if used
one-letter switches:
-d (dir), -j (jmake), -m (makefile), -o (output),
-p (packages), -r (redo), -s (settings), -v (verbose)
switches for libs:
-atc, -awpmd, -colvars, -cuda
-gpu, -meam, -poems, -qmmm, -reax
switches for build and makefile options:
-intel, -kokkos, -cc, -mpi, -fft, -jpg, -png :pre
Using the "-h" switch with other switches and actions gives additional
info on all the other specified switches or actions. The "-h" can be
anywhere in the command-line and the other switches do not need their
arguments. E.g. type "Make.py -h -d -atc -intel" will print:
-d dir
dir = LAMMPS home dir
if -d not specified, working dir must be lammps/src :pre
-atc make=suffix lammps=suffix2
all args are optional and can be in any order
make = use Makefile.suffix (def = g++)
lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile) :pre
-intel mode
mode = cpu or phi (def = cpu)
build Intel package for CPU or Xeon Phi :pre
Note that Make.py never overwrites an existing Makefile.machine.
Instead, it creates src/MAKE/MINE/Makefile.auto, which you can save or
rename if desired. Likewise it creates an executable named
src/lmp_auto, which you can rename using the -o switch if desired.
The most recently executed Make.py commmand is saved in
src/Make.py.last. You can use the "-r" switch (for redo) to re-invoke
the last command, or you can save a sequence of one or more Make.py
commands to a file and invoke the file of commands using "-r". You
can also label the commands in the file and invoke one or more of them
by name.
A typical use of Make.py is to start with a valid Makefile.machine for
your system, that works for a vanilla LAMMPS build, i.e. when optional
packages are not installed. You can then use Make.py to add various
settings (FFT, JPG, PNG) to the Makefile.machine as well as change its
compiler and MPI options. You can also add additional packages to the
build, as well as build the needed supporting libraries.
You can also use Make.py to create a new Makefile.machine from
scratch, using the "-m none" switch, if you also specify what compiler
and MPI options to use, via the "-cc" and "-mpi" switches.
:line
2.5 Building LAMMPS as a library :h4,link(start_5)
LAMMPS can be built as either a static or shared library, which can
then be called from another application or a scripting language. See
"this section"_Section_howto.html#howto_10 for more info on coupling
LAMMPS to other codes. See "this section"_Section_python.html for
more info on wrapping and running LAMMPS from Python.
[Static library:] :h5
To build LAMMPS as a static library (*.a file on Linux), type
make foo mode=lib :pre
where foo is the machine name. This kind of library is typically used
to statically link a driver application to LAMMPS, so that you can
insure all dependencies are satisfied at compile time. This will use
the ARCHIVE and ARFLAGS settings in src/MAKE/Makefile.foo. The build
will create the file liblammps_foo.a which another application can
link to. It will also create a soft link liblammps.a, which will
point to the most recently built static library.
[Shared library:] :h5
To build LAMMPS as a shared library (*.so file on Linux), which can be
dynamically loaded, e.g. from Python, type
make foo mode=shlib :pre
where foo is the machine name. This kind of library is required when
wrapping LAMMPS with Python; see "Section_python"_Section_python.html
for details. This will use the SHFLAGS and SHLIBFLAGS settings in
src/MAKE/Makefile.foo and perform the build in the directory
Obj_shared_foo. This is so that each file can be compiled with the
-fPIC flag which is required for inclusion in a shared library. The
build will create the file liblammps_foo.so which another application
can link to dyamically. It will also create a soft link liblammps.so,
which will point to the most recently built shared library. This is
the file the Python wrapper loads by default.
Note that for a shared library to be usable by a calling program, all
the auxiliary libraries it depends on must also exist as shared
libraries. This will be the case for libraries included with LAMMPS,
such as the dummy MPI library in src/STUBS or any package libraries in
lib/packages, since they are always built as shared libraries using
the -fPIC switch. However, if a library like MPI or FFTW does not
exist as a shared library, the shared library build will generate an
error. This means you will need to install a shared library version
of the auxiliary library. The build instructions for the library
should tell you how to do this.
Here is an example of such errors when the system FFTW or provided
lib/colvars library have not been built as shared libraries:
/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
R_X86_64_32 against `.rodata' can not be used when making a shared
object; recompile with -fPIC
/usr/local/lib/libfftw3.a: could not read symbols: Bad value :pre
/usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
relocation R_X86_64_32 against `__pthread_key_create' can not be used
when making a shared object; recompile with -fPIC
../../lib/colvars/libcolvars.a: error adding symbols: Bad value :pre
As an example, here is how to build and install the "MPICH
library"_mpich, a popular open-source version of MPI, distributed by
Argonne National Labs, as a shared library in the default
/usr/local/lib location:
:link(mpich,http://www-unix.mcs.anl.gov/mpi)
./configure --enable-shared
make
make install :pre
You may need to use "sudo make install" in place of the last line if
you do not have write privileges for /usr/local/lib. The end result
should be the file /usr/local/lib/libmpich.so.
[Additional requirement for using a shared library:] :h5
The operating system finds shared libraries to load at run-time using
the environment variable LD_LIBRARY_PATH. So you may wish to copy the
file src/liblammps.so or src/liblammps_g++.so (for example) to a place
the system can find it by default, such as /usr/local/lib, or you may
wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the
current version of the shared library is always available to programs
that use it.
For the csh or tcsh shells, you would add something like this to your
~/.cshrc file:
setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
[Calling the LAMMPS library:] :h5
Either flavor of library (static or shared) allows one or more LAMMPS
objects to be instantiated from the calling program.
When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS
namespace; you can safely use any of its classes and methods from
within the calling code, as needed.
When used from a C or Fortran program or a scripting language like
Python, the library has a simple function-style interface, provided in
src/library.cpp and src/library.h.
See the sample codes in examples/COUPLE/simple for examples of C++ and
C and Fortran codes that invoke LAMMPS thru its library interface.
There are other examples as well in the COUPLE directory which are
discussed in "Section_howto 10"_Section_howto.html#howto_10 of the
manual. See "Section_python"_Section_python.html of the manual for a
description of the Python wrapper provided with LAMMPS that operates
through the LAMMPS library interface.
The files src/library.cpp and library.h define the C-style API for
using LAMMPS as a library. See "Section_howto
19"_Section_howto.html#howto_19 of the manual for a description of the
interface and how to extend it for your needs.
:line
2.6 Running LAMMPS :h4,link(start_6)
By default, LAMMPS runs by reading commands from standard input. Thus
if you run the LAMMPS executable by itself, e.g.
lmp_linux :pre
it will simply wait, expecting commands from the keyboard. Typically
you should put commands in an input script and use I/O redirection,
e.g.
lmp_linux < in.file :pre
For parallel environments this should also work. If it does not, use
the '-in' command-line switch, e.g.
lmp_linux -in in.file :pre
"This section"_Section_commands.html describes how input scripts are
structured and what commands they contain.
You can test LAMMPS on any of the sample inputs provided in the
examples or bench directory. Input scripts are named in.* and sample
outputs are named log.*.name.P where name is a machine and P is the
number of processors it was run on.
Here is how you might run a standard Lennard-Jones benchmark on a
Linux box, using mpirun to launch a parallel job:
cd src
make linux
cp lmp_linux ../bench
cd ../bench
mpirun -np 4 lmp_linux -in in.lj :pre
See "this page"_bench for timings for this and the other benchmarks on
various platforms. Note that some of the example scripts require
LAMMPS to be built with one or more of its optional packages.
:link(bench,http://lammps.sandia.gov/bench.html)
:line
On a Windows box, you can skip making LAMMPS and simply download an
executable, as described above, though the pre-packaged executables
include only certain packages.
To run a LAMMPS executable on a Windows machine, first decide whether
you want to download the non-MPI (serial) or the MPI (parallel)
version of the executable. Download and save the version you have
chosen.
For the non-MPI version, follow these steps:
Get a command prompt by going to Start->Run... ,
then typing "cmd". :ulb,l
Move to the directory where you have saved lmp_win_no-mpi.exe
(e.g. by typing: cd "Documents"). :l
At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj
with the name of your LAMMPS input script. :l,ule
For the MPI version, which allows you to run LAMMPS under Windows on
multiple processors, follow these steps:
Download and install
"MPICH2"_http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads
for Windows. :ulb,l
You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2
package. Put them in same directory (or path) as the LAMMPS Windows
executable. :l
Get a command prompt by going to Start->Run... ,
then typing "cmd". :l
Move to the directory where you have saved lmp_win_mpi.exe
(e.g. by typing: cd "Documents"). :l
Then type something like this: "mpiexec -localonly 4 lmp_win_mpi -in
in.lj", replacing in.lj with the name of your LAMMPS input script. :l
Note that you may need to provide smpd with a passphrase (it doesn't
matter what you type). :l
In this mode, output may not immediately show up on the screen, so if
your input script takes a long time to execute, you may need to be
patient before the output shows up. :l Alternatively, you can still
use this executable to run on a single processor by typing something
like: "lmp_win_mpi -in in.lj". :l,ule
:line
The screen output from LAMMPS is described in the next section. As it
runs, LAMMPS also writes a log.lammps file with the same information.
Note that this sequence of commands copies the LAMMPS executable
(lmp_linux) to the directory with the input files. This may not be
necessary, but some versions of MPI reset the working directory to
where the executable is, rather than leave it as the directory where
you launch mpirun from (if you launch lmp_linux on its own and not
under mpirun). If that happens, LAMMPS will look for additional input
files and write its output files to the executable directory, rather
than your working directory, which is probably not what you want.
If LAMMPS encounters errors in the input script or while running a
simulation it will print an ERROR message and stop or a WARNING
message and continue. See "Section_errors"_Section_errors.html for a
discussion of the various kinds of errors LAMMPS can or can't detect,
a list of all ERROR and WARNING messages, and what to do about them.
LAMMPS can run a problem on any number of processors, including a
single processor. In theory you should get identical answers on any
number of processors and on any machine. In practice, numerical
round-off can cause slight differences and eventual divergence of
molecular dynamics phase space trajectories.
LAMMPS can run as large a problem as will fit in the physical memory
of one or more processors. If you run out of memory, you must run on
more processors or setup a smaller problem.
:line
2.7 Command-line options :h4,link(start_7)
At run time, LAMMPS recognizes several optional command-line switches
which may be used in any order. Either the full word or a one-or-two
letter abbreviation can be used:
-c or -cuda
-e or -echo
-h or -help
-i or -in
-k or -kokkos
-l or -log
-nc or -nocite
-pk or -package
-p or -partition
-pl or -plog
-ps or -pscreen
-r or -restart
-ro or -reorder
-sc or -screen
-sf or -suffix
-v or -var :ul
For example, lmp_ibm might be launched as follows:
mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy
mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloy :pre
Here are the details on the options:
-cuda on/off :pre
Explicitly enable or disable CUDA support, as provided by the
USER-CUDA package. Even if LAMMPS is built with this package, as
described above in "Section 2.3"_#start_3, this switch must be set to
enable running with the CUDA-enabled styles the package provides. If
the switch is not set (the default), LAMMPS will operate as if the
USER-CUDA package were not installed; i.e. you can run standard LAMMPS
or with the GPU package, for testing or benchmarking purposes.
-echo style :pre
Set the style of command echoing. The style can be {none} or {screen}
or {log} or {both}. Depending on the style, each command read from
the input script will be echoed to the screen and/or logfile. This
can be useful to figure out which line of your script is causing an
input error. The default value is {log}. The echo style can also be
set by using the "echo"_echo.html command in the input script itself.
-help :pre
Print a brief help summary and a list of options compiled into this
executable for each LAMMPS style (atom_style, fix, compute,
pair_style, bond_style, etc). This can tell you if the command you
want to use was included via the appropriate package at compile time.
LAMMPS will print the info and immediately exit if this switch is
used.
-in file :pre
Specify a file to use as an input script. This is an optional switch
when running LAMMPS in one-partition mode. If it is not specified,
LAMMPS reads its script from standard input, typically from a script
via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should
also work in parallel, but if it does not (in the unlikely case that
an MPI implementation does not support it), then use the -in flag.
Note that this is a required switch when running LAMMPS in
multi-partition mode, since multiple processors cannot all read from
stdin.
-kokkos on/off keyword/value ... :pre
Explicitly enable or disable KOKKOS support, as provided by the KOKKOS
package. Even if LAMMPS is built with this package, as described
above in "Section 2.3"_#start_3, this switch must be set to enable
running with the KOKKOS-enabled styles the package provides. If the
switch is not set (the default), LAMMPS will operate as if the KOKKOS
package were not installed; i.e. you can run standard LAMMPS or with
the GPU or USER-CUDA or USER-OMP packages, for testing or benchmarking
purposes.
Additional optional keyword/value pairs can be specified which
determine how Kokkos will use the underlying hardware on your
platform. These settings apply to each MPI task you launch via the
"mpirun" or "mpiexec" command. You may choose to run one or more MPI
tasks per physical node. Note that if you are running on a desktop
machine, you typically have one physical node. On a cluster or
supercomputer there may be dozens or 1000s of physical nodes.
Either the full word or an abbreviation can be used for the keywords.
Note that the keywords do not use a leading minus sign. I.e. the
keyword is "t", not "-t". Also note that each of the keywords has a
default setting. Example of when to use these options and what
settings to use on different platforms is given in "Section
5.8"_Section_accelerate.html#acc_8.
d or device
g or gpus
t or threads
n or numa :ul
device Nd :pre
This option is only relevant if you built LAMMPS with CUDA=yes, you
have more than one GPU per node, and if you are running with only one
MPI task per node. The Nd setting is the ID of the GPU on the node to
run on. By default Nd = 0. If you have multiple GPUs per node, they
have consecutive IDs numbered as 0,1,2,etc. This setting allows you
to launch multiple independent jobs on the node, each with a single
MPI task per node, and assign each job to run on a different GPU.
gpus Ng Ns :pre
This option is only relevant if you built LAMMPS with CUDA=yes, you
have more than one GPU per node, and you are running with multiple MPI
tasks per node (up to one per GPU). The Ng setting is how many GPUs
you will use. The Ns setting is optional. If set, it is the ID of a
GPU to skip when assigning MPI tasks to GPUs. This may be useful if
your desktop system reserves one GPU to drive the screen and the rest
are intended for computational work like running LAMMPS. By default
Ng = 1 and Ns is not set.
Depending on which flavor of MPI you are running, LAMMPS will look for
one of these 3 environment variables
SLURM_LOCALID (various MPI variants compiled with SLURM support)
MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI) :pre
which are initialized by the "srun", "mpirun" or "mpiexec" commands.
The environment variable setting for each MPI rank is used to assign a
unique GPU ID to the MPI task.
threads Nt :pre
This option assigns Nt number of threads to each MPI task for
performing work when Kokkos is executing in OpenMP or pthreads mode.
The default is Nt = 1, which essentially runs in MPI-only mode. If
there are Np MPI tasks per physical node, you generally want Np*Nt =
the number of physical cores per node, to use your available hardware
optimally. This also sets the number of threads used by the host when
LAMMPS is compiled with CUDA=yes.
numa Nm :pre
This option is only relevant when using pthreads with hwloc support.
In this case Nm defines the number of NUMA regions (typicaly sockets)
on a node which will be utilizied by a single MPI rank. By default Nm
= 1. If this option is used the total number of worker-threads per
MPI rank is threads*numa. Currently it is always almost better to
assign at least one MPI rank per NUMA region, and leave numa set to
its default value of 1. This is because letting a single process span
multiple NUMA regions induces a significant amount of cross NUMA data
traffic which is slow.
-log file :pre
Specify a log file for LAMMPS to write status information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the
file log.lammps. If this switch is used, LAMMPS writes to the
specified file. In multi-partition mode, if the switch is not used, a
log.lammps file is created with hi-level status information. Each
partition also writes to a log.lammps.N file where N is the partition
ID. If the switch is specified in multi-partition mode, the hi-level
logfile is named "file" and each partition also logs information to a
file.N. For both one-partition and multi-partition mode, if the
specified file is "none", then no log files are created. Using a
"log"_log.html command in the input script will override this setting.
Option -plog will override the name of the partition log files file.N.
-nocite :pre
Disable writing the log.cite file which is normally written to list
references for specific cite-able features used during a LAMMPS run.
See the "citation page"_http://lammps.sandia.gov/cite.html for more
details.
-package style args .... :pre
Invoke the "package"_package.html command with style and args. The
syntax is the same as if the command appeared at the top of the input
script. For example "-package gpu 2" or "-pk gpu 2" is the same as
"package gpu 2"_package.html in the input script. The possible styles
and args are documented on the "package"_package.html doc page. This
switch can be used multiple times, e.g. to set options for the
USER-INTEL and USER-OMP packages which can be used together.
Along with the "-suffix" command-line switch, this is a convenient
mechanism for invoking accelerator packages and their options without
having to edit an input script.
-partition 8x2 4 5 ... :pre
Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P
processors and this switch is not used, LAMMPS runs in one partition,
i.e. all P processors run a single simulation. If this switch is
used, the P processors are split into separate partitions and each
partition runs its own simulation. The arguments to the switch
specify the number of processors in each partition. Arguments of the
form MxN mean M partitions, each with N processors. Arguments of the
form N mean a single partition with N processors. The sum of
processors in all partitions must equal P. Thus the command
"-partition 8x2 4 5" has 10 partitions and runs on a total of 25
processors.
Running with multiple partitions can e useful for running
"multi-replica simulations"_Section_howto.html#howto_5, where each
replica runs on on one or a few processors. Note that with MPI
installed on a machine (e.g. your desktop), you can run on more
(virtual) processors than you have physical processors.
To run multiple independent simulatoins from one input script, using
multiple partitions, see "Section_howto 4"_Section_howto.html#howto_4
of the manual. World- and universe-style "variables"_variable.html
are useful in this context.
-plog file :pre
Specify the base name for the partition log files, so partition N
writes log information to file.N. If file is none, then no partition
log files are created. This overrides the filename specified in the
-log command-line option. This option is useful when working with
large numbers of partitions, allowing the partition log files to be
suppressed (-plog none) or placed in a sub-directory (-plog
replica_files/log.lammps) If this option is not used the log file for
partition N is log.lammps.N or whatever is specified by the -log
command-line option.
-pscreen file :pre
Specify the base name for the partition screen file, so partition N
writes screen information to file.N. If file is none, then no
partition screen files are created. This overrides the filename
specified in the -screen command-line option. This option is useful
when working with large numbers of partitions, allowing the partition
screen files to be suppressed (-pscreen none) or placed in a
sub-directory (-pscreen replica_files/screen). If this option is not
used the screen file for partition N is screen.N or whatever is
specified by the -screen command-line option.
-restart restartfile {remap} datafile keyword value ... :pre
Convert the restart file into a data file and immediately exit. This
is the same operation as if the following 2-line input script were
run:
read_restart restartfile {remap}
write_data datafile keyword value ... :pre
Note that the specified restartfile and datafile can have wild-card
characters ("*",%") as described by the
"read_restart"_read_restart.html and "write_data"_write_data.html
commands. But a filename such as file.* will need to be enclosed in
quotes to avoid shell expansion of the "*" character.
Note that following restartfile, the optional flag {remap} can be
used. This has the same effect as adding it to the
"read_restart"_read_restart.html command, as explained on its doc
page. This is only useful if the reading of the restart file triggers
an error that atoms have been lost. In that case, use of the remap
flag should allow the data file to still be produced.
Also note that following datafile, the same optional keyword/value
pairs can be listed as used by the "write_data"_write_data.html
command.
-reorder nth N
-reorder custom filename :pre
Reorder the processors in the MPI communicator used to instantiate
LAMMPS, in one of several ways. The original MPI communicator ranks
all P processors from 0 to P-1. The mapping of these ranks to
physical processors is done by MPI before LAMMPS begins. It may be
useful in some cases to alter the rank order. E.g. to insure that
cores within each node are ranked in a desired order. Or when using
the "run_style verlet/split"_run_style.html command with 2 partitions
to insure that a specific Kspace processor (in the 2nd partition) is
matched up with a specific set of processors in the 1st partition.
See the "Section_accelerate"_Section_accelerate.html doc pages for
more details.
If the keyword {nth} is used with a setting {N}, then it means every
Nth processor will be moved to the end of the ranking. This is useful
when using the "run_style verlet/split"_run_style.html command with 2
partitions via the -partition command-line switch. The first set of
processors will be in the first partition, the 2nd set in the 2nd
partition. The -reorder command-line switch can alter this so that
the 1st N procs in the 1st partition and one proc in the 2nd partition
will be ordered consecutively, e.g. as the cores on one physical node.
This can boost performance. For example, if you use "-reorder nth 4"
and "-partition 9 3" and you are running on 12 processors, the
processors will be reordered from
0 1 2 3 4 5 6 7 8 9 10 11 :pre
to
0 1 2 4 5 6 8 9 10 3 7 11 :pre
so that the processors in each partition will be
0 1 2 4 5 6 8 9 10
3 7 11 :pre
See the "processors" command for how to insure processors from each
partition could then be grouped optimally for quad-core nodes.
If the keyword is {custom}, then a file that specifies a permutation
of the processor ranks is also specified. The format of the reorder
file is as follows. Any number of initial blank or comment lines
(starting with a "#" character) can be present. These should be
followed by P lines of the form:
I J :pre
where P is the number of processors LAMMPS was launched with. Note
that if running in multi-partition mode (see the -partition switch
above) P is the total number of processors in all partitions. The I
and J values describe a permutation of the P processors. Every I and
J should be values from 0 to P-1 inclusive. In the set of P I values,
every proc ID should appear exactly once. Ditto for the set of P J
values. A single I,J pairing means that the physical processor with
rank I in the original MPI communicator will have rank J in the
reordered communicator.
Note that rank ordering can also be specified by many MPI
implementations, either by environment variables that specify how to
order physical processors, or by config files that specify what
physical processors to assign to each MPI rank. The -reorder switch
simply gives you a portable way to do this without relying on MPI
itself. See the "processors out"_processors command for how to output
info on the final assignment of physical processors to the LAMMPS
simulation domain.
-screen file :pre
Specify a file for LAMMPS to write its screen information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the
screen. If this switch is used, LAMMPS writes to the specified file
instead and you will see no screen output. In multi-partition mode,
if the switch is not used, hi-level status information is written to
the screen. Each partition also writes to a screen.N file where N is
the partition ID. If the switch is specified in multi-partition mode,
the hi-level screen dump is named "file" and each partition also
writes screen information to a file.N. For both one-partition and
multi-partition mode, if the specified file is "none", then no screen
output is performed. Option -pscreen will override the name of the
partition screen files file.N.
-suffix style args :pre
Use variants of various styles if they exist. The specified style can
be {cuda}, {gpu}, {intel}, {kk}, {omp}, {opt}, or {hybrid}. These refer
to optional packages that LAMMPS can be built with, as described above in
"Section 2.3"_#start_3. The "cuda" style corresponds to the USER-CUDA
package, the "gpu" style to the GPU package, the "intel" style to the
USER-INTEL package, the "kk" style to the KOKKOS package, the "opt"
style to the OPT package, and the "omp" style to the USER-OMP package. The
hybrid style is the only style that accepts arguments. It allows for two
packages to be specified. The first package specified is the default and
will be used if it is available. If no style is available for the first
package, the style for the second package will be used if available. For
example, "-suffix hybrid intel omp" will use styles from the USER-INTEL
package if they are installed and available, but styles for the USER-OMP
package otherwise.
Along with the "-package" command-line switch, this is a convenient
mechanism for invoking accelerator packages and their options without
having to edit an input script.
As an example, all of the packages provide a "pair_style
lj/cut"_pair_lj.html variant, with style names lj/cut/cuda,
lj/cut/gpu, lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A
variant style can be specified explicitly in your input script,
e.g. pair_style lj/cut/gpu. If the -suffix switch is used the
specified suffix (cuda,gpu,intel,kk,omp,opt) is automatically appended
whenever your input script command creates a new
"atom"_atom_style.html, "pair"_pair_style.html, "fix"_fix.html,
"compute"_compute.html, or "run"_run_style.html style. If the variant
version does not exist, the standard version is created.
For the GPU package, using this command-line switch also invokes the
default GPU settings, as if the command "package gpu 1" were used at
the top of your input script. These settings can be changed by using
the "-package gpu" command-line switch or the "package
gpu"_package.html command in your script.
For the USER-INTEL package, using this command-line switch also
invokes the default USER-INTEL settings, as if the command "package
intel 1" were used at the top of your input script. These settings
can be changed by using the "-package intel" command-line switch or
the "package intel"_package.html command in your script. If the
USER-OMP package is also installed, the hybrid style with "intel omp"
arguments can be used to make the omp suffix a second choice, if a
requested style is not available in the USER-INTEL package. It will
also invoke the default USER-OMP settings, as if the command "package
omp 0" were used at the top of your input script. These settings can
be changed by using the "-package omp" command-line switch or the
"package omp"_package.html command in your script.
For the KOKKOS package, using this command-line switch also invokes
the default KOKKOS settings, as if the command "package kokkos" were
used at the top of your input script. These settings can be changed
by using the "-package kokkos" command-line switch or the "package
kokkos"_package.html command in your script.
For the OMP package, using this command-line switch also invokes the
default OMP settings, as if the command "package omp 0" were used at
the top of your input script. These settings can be changed by using
the "-package omp" command-line switch or the "package
omp"_package.html command in your script.
The "suffix"_suffix.html command can also be used within an input
script to set a suffix, or to turn off or back on any suffix setting
made via the command line.
-var name value1 value2 ... :pre
Specify a variable that will be defined for substitution purposes when
the input script is read. This switch can be used multiple times to
define multiple variables. "Name" is the variable name which can be a
single character (referenced as $x in the input script) or a full
string (referenced as $\{abc\}). An "index-style
variable"_variable.html will be created and populated with the
subsequent values, e.g. a set of filenames. Using this command-line
option is equivalent to putting the line "variable name index value1
value2 ..." at the beginning of the input script. Defining an index
variable as a command-line argument overrides any setting for the same
index variable in the input script, since index variables cannot be
re-defined. See the "variable"_variable.html command for more info on
defining index and other kinds of variables and "this
section"_Section_commands.html#cmd_2 for more info on using variables
in input scripts.
NOTE: Currently, the command-line parser looks for arguments that
start with "-" to indicate new switches. Thus you cannot specify
multiple variable values if any of they start with a "-", e.g. a
negative numeric value. It is OK if the first value1 starts with a
"-", since it is automatically skipped.
:line
2.8 LAMMPS screen output :h4,link(start_8)
As LAMMPS reads an input script, it prints information to both the
screen and a log file about significant actions it takes to setup a
simulation. When the simulation is ready to begin, LAMMPS performs
various initializations and prints the amount of memory (in MBytes per
processor) that the simulation requires. It also prints details of
the initial thermodynamic state of the system. During the run itself,
thermodynamic information is printed periodically, every few
timesteps. When the run concludes, LAMMPS prints the final
thermodynamic state and a total run time for the simulation. It then
appends statistics about the CPU time and storage requirements for the
simulation. An example set of statistics is shown here:
Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s
97.0% CPU use with 4 MPI tasks x no OpenMP threads :pre
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9808 | 2.0134 | 2.0318 | 1.4 | 71.60
Bond | 0.0021894 | 0.0060319 | 0.010058 | 4.7 | 0.21
Kspace | 0.3207 | 0.3366 | 0.36616 | 3.1 | 11.97
Neigh | 0.28411 | 0.28464 | 0.28516 | 0.1 | 10.12
Comm | 0.075732 | 0.077018 | 0.07883 | 0.4 | 2.74
Output | 0.00030518 | 0.00042665 | 0.00078821 | 1.0 | 0.02
Modify | 0.086606 | 0.086631 | 0.086668 | 0.0 | 3.08
Other | | 0.007178 | | | 0.26 :pre
Nlocal: 501 ave 508 max 490 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 6586.25 ave 6628 max 6548 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 177007 ave 180562 max 170212 min
Histogram: 1 0 0 0 0 0 0 1 1 1 :pre
Total # of neighbors = 708028
Ave neighs/atom = 353.307
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0 :pre
The first section provides a global loop timing summary. The loop time
is the total wall time for the section. The {Performance} line is
provided for convenience to help predicting the number of loop
continuations required and for comparing performance with other
similar MD codes. The CPU use line provides the CPU utilzation per
MPI task; it should be close to 100% times the number of OpenMP
threads (or 1). Lower numbers correspond to delays due to file I/O or
insufficient thread utilization.
The MPI task section gives the breakdown of the CPU run time (in
seconds) into major categories:
{Pair} stands for all non-bonded force computation
{Bond} stands for bonded interactions: bonds, angles, dihedrals, impropers
{Kspace} stands for reciprocal space interactions: Ewald, PPPM, MSM
{Neigh} stands for neighbor list construction
{Comm} stands for communicating atoms and their properties
{Output} stands for writing dumps and thermo output
{Modify} stands for fixes and computes called by them
{Other} is the remaining time :ul
For each category, there is a breakdown of the least, average and most
amount of wall time a processor spent on this section. Also you have the
variation from the average time. Together these numbers allow to gauge
the amount of load imbalance in this segment of the calculation. Ideally
the difference between minimum, maximum and average is small and thus
the variation from the average close to zero. The final column shows
the percentage of the total loop time is spent in this section.
When using the "timer full"_timer.html setting, an additional column
is present that also prints the CPU utilization in percent. In
addition, when using {timer full} and the "package omp"_package.html
command are active, a similar timing summary of time spent in threaded
regions to monitor thread utilization and load balance is provided. A
new entry is the {Reduce} section, which lists the time spend in
reducing the per-thread data elements to the storage for non-threaded
computation. These thread timings are taking from the first MPI rank
only and and thus, as the breakdown for MPI tasks can change from MPI
rank to MPI rank, this breakdown can be very different for individual
ranks. Here is an example output for this section:
Thread timings breakdown (MPI rank 0):
Total threaded time 0.6846 / 90.6%
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.5127 | 0.5147 | 0.5167 | 0.3 | 75.18
Bond | 0.0043139 | 0.0046779 | 0.0050418 | 0.5 | 0.68
Kspace | 0.070572 | 0.074541 | 0.07851 | 1.5 | 10.89
Neigh | 0.084778 | 0.086969 | 0.089161 | 0.7 | 12.70
Reduce | 0.0036485 | 0.003737 | 0.0038254 | 0.1 | 0.55
The third section lists the number of owned atoms (Nlocal), ghost atoms
(Nghost), and pair-wise neighbors stored per processor. The max and min
values give the spread of these values across processors with a 10-bin
histogram showing the distribution. The total number of histogram counts
is equal to the number of processors.
The last section gives aggregate statistics for pair-wise neighbors
and special neighbors that LAMMPS keeps track of (see the
"special_bonds"_special_bonds.html command). The number of times
neighbor lists were rebuilt during the run is given as well as the
number of potentially "dangerous" rebuilds. If atom movement
triggered neighbor list rebuilding (see the
"neigh_modify"_neigh_modify.html command), then dangerous
reneighborings are those that were triggered on the first timestep
atom movement was checked for. If this count is non-zero you may wish
to reduce the delay factor to insure no force interactions are missed
by atoms moving beyond the neighbor skin distance before a rebuild
takes place.
If an energy minimization was performed via the
"minimize"_minimize.html command, additional information is printed,
e.g.
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-6372.3765206 -8328.46998942 -8328.46998942
Force two-norm initial, final = 1059.36 5.36874
Force max component initial, final = 58.6026 1.46872
Final line search alpha, max atom move = 2.7842e-10 4.0892e-10
Iterations, force evaluations = 701 1516 :pre
The first line prints the criterion that determined the minimization
to be completed. The third line lists the initial and final energy,
as well as the energy on the next-to-last iteration. The next 2 lines
give a measure of the gradient of the energy (force on all atoms).
The 2-norm is the "length" of this force vector; the inf-norm is the
largest component. Then some information about the line search and
statistics on how many iterations and force-evaluations the minimizer
required. Multiple force evaluations are typically done at each
iteration to perform a 1d line minimization in the search direction.
If a "kspace_style"_kspace_style.html long-range Coulombics solve was
performed during the run (PPPM, Ewald), then additional information is
printed, e.g.
FFT time (% of Kspce) = 0.200313 (8.34477)
FFT Gflps 3d 1d-only = 2.31074 9.19989 :pre
The first line gives the time spent doing 3d FFTs (4 per timestep) and
the fraction it represents of the total KSpace time (listed above).
Each 3d FFT requires computation (3 sets of 1d FFTs) and communication
(transposes). The total flops performed is 5Nlog_2(N), where N is the
number of points in the 3d grid. The FFTs are timed with and without
the communication and a Gflop rate is computed. The 3d rate is with
communication; the 1d rate is without (just the 1d FFTs). Thus you
can estimate what fraction of your FFT time was spent in
communication, roughly 75% in the example above.
:line
2.9 Tips for users of previous LAMMPS versions :h4,link(start_9)
The current C++ began with a complete rewrite of LAMMPS 2001, which
was written in F90. Features of earlier versions of LAMMPS are listed
in "Section_history"_Section_history.html. The F90 and F77 versions
(2001 and 99) are also freely distributed as open-source codes; check
the "LAMMPS WWW Site"_lws for distribution information if you prefer
those versions. The 99 and 2001 versions are no longer under active
development; they do not have all the features of C++ LAMMPS.
If you are a previous user of LAMMPS 2001, these are the most
significant changes you will notice in C++ LAMMPS:
(1) The names and arguments of many input script commands have
changed. All commands are now a single word (e.g. read_data instead
of read data).
(2) All the functionality of LAMMPS 2001 is included in C++ LAMMPS,
but you may need to specify the relevant commands in different ways.
(3) The format of the data file can be streamlined for some problems.
See the "read_data"_read_data.html command for details. The data file
section "Nonbond Coeff" has been renamed to "Pair Coeff" in C++ LAMMPS.
(4) Binary restart files written by LAMMPS 2001 cannot be read by C++
LAMMPS with a "read_restart"_read_restart.html command. This is
because they were output by F90 which writes in a different binary
format than C or C++ writes or reads. Use the {restart2data} tool
provided with LAMMPS 2001 to convert the 2001 restart file to a text
data file. Then edit the data file as necessary before using the C++
LAMMPS "read_data"_read_data.html command to read it in.
(5) There are numerous small numerical changes in C++ LAMMPS that mean
you will not get identical answers when comparing to a 2001 run.
However, your initial thermodynamic energy and MD trajectory should be
close if you have setup the problem for both codes the same.
diff --git a/doc/accelerate_intel.html b/doc/accelerate_intel.html
index 16722b968..1977931d9 100644
--- a/doc/accelerate_intel.html
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@@ -1,481 +1,461 @@
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<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>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<p><a class="reference internal" href="Section_accelerate.html"><em>Return to Section accelerate overview</em></a></p>
<div class="section" id="user-intel-package">
<h1>5.USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline">¶</a></h1>
<p>The USER-INTEL package was developed by Mike Brown at Intel
-Corporation. It provides a capability to accelerate simulations by
-offloading neighbor list and non-bonded force calculations to Intel(R)
-Xeon Phi(TM) coprocessors (not native mode like the KOKKOS package).
-Additionally, it supports running simulations in single, mixed, or
-double precision with vectorization, even if a coprocessor is not
-present, i.e. on an Intel(R) CPU. The same C++ code is used for both
-cases. When offloading to a coprocessor, the routine is run twice,
-once with an offload flag.</p>
-<p>The USER-INTEL package can be used in tandem with the USER-OMP
-package. This is useful when offloading pair style computations to
-coprocessors, so that other styles not supported by the USER-INTEL
-package, e.g. bond, angle, dihedral, improper, and long-range
-electrostatics, can run simultaneously in threaded mode on the CPU
-cores. Since less MPI tasks than CPU cores will typically be invoked
-when running with coprocessors, this enables the extra CPU cores to be
-used for useful computation.</p>
-<p>If LAMMPS is built with both the USER-INTEL and USER-OMP packages
-installed, this mode of operation is made easier to use, with the
-“-suffix hybrid intel omp” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>
-or the <a class="reference internal" href="suffix.html"><em>suffix hybrid intel omp</em></a> command will both set a
-second-choice suffix to “omp” so that styles from the USER-OMP package will be
-used if available, after first testing if a style from the USER-INTEL
-package is available.</p>
-<p>When using the USER-INTEL package, you must choose at build time whether the
-binary will support offload to Xeon Phi coprocessors. Binaries supporting
-offload can still be run in CPU-only (host-only) mode.</p>
-<p>Here is a quick overview of how to use the USER-INTEL package
-for CPU-only acceleration:</p>
-<ul class="simple">
-<li>specify these CCFLAGS in your src/MAKE/Makefile.machine: -openmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost</li>
-<li>specify -openmp with LINKFLAGS in your Makefile.machine</li>
-<li>include the USER-INTEL package and (optionally) USER-OMP package and build LAMMPS</li>
-<li>specify how many OpenMP threads per MPI task to use</li>
-<li>use USER-INTEL and (optionally) USER-OMP styles in your input script</li>
-</ul>
-<p>Note that many of these settings can only be used with the Intel
-compiler, as discussed below.</p>
-<p>Using the USER-INTEL package to offload work to the Intel(R)
-Xeon Phi(TM) coprocessor is the same except for these additional
-steps:</p>
-<ul class="simple">
-<li>add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in your Makefile.machine</li>
-<li>add the flag -offload to LINKFLAGS in your Makefile.machine</li>
-</ul>
-<p>The latter two steps in the first case and the last step in the
-coprocessor case can be done using the “-pk intel” and “-sf intel”
-<a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> respectively. Or
-the effect of the “-pk” or “-sf” switches can be duplicated by adding
-the <a class="reference internal" href="package.html"><em>package intel</em></a> or <a class="reference internal" href="suffix.html"><em>suffix intel</em></a>
-commands respectively to your input script.</p>
+Corporation. It provides two methods for accelerating simulations,
+depending on the hardware you have. The first is acceleration on
+Intel(R) CPUs by running in single, mixed, or double precision with
+vectorization. The second is acceleration on Intel(R) Xeon Phi(TM)
+coprocessors via offloading neighbor list and non-bonded force
+calculations to the Phi. The same C++ code is used in both cases.
+When offloading to a coprocessor from a CPU, the same routine is run
+twice, once on the CPU and once with an offload flag.</p>
+<p>Note that the USER-INTEL package supports use of the Phi in “offload”
+mode, not “native” mode like the <a class="reference internal" href="accelerate_kokkos.html"><em>KOKKOS package</em></a>.</p>
+<p>Also note that the USER-INTEL package can be used in tandem with the
+<a class="reference internal" href="accelerate_omp.html"><em>USER-OMP package</em></a>. This is useful when
+offloading pair style computations to the Phi, so that other styles
+not supported by the USER-INTEL package, e.g. bond, angle, dihedral,
+improper, and long-range electrostatics, can run simultaneously in
+threaded mode on the CPU cores. Since less MPI tasks than CPU cores
+will typically be invoked when running with coprocessors, this enables
+the extra CPU cores to be used for useful computation.</p>
+<p>As illustrated below, if LAMMPS is built with both the USER-INTEL and
+USER-OMP packages, this dual mode of operation is made easier to use,
+via the “-suffix hybrid intel omp” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> or the <a class="reference internal" href="suffix.html"><em>suffix hybrid intel omp</em></a> command. Both set a second-choice suffix to “omp” so
+that styles from the USER-INTEL package will be used if available,
+with styles from the USER-OMP package as a second choice.</p>
+<p>Here is a quick overview of how to use the USER-INTEL package for CPU
+acceleration, assuming one or more 16-core nodes. More details
+follow.</p>
+<div class="highlight-python"><div class="highlight"><pre>use an Intel compiler
+use these CCFLAGS settings in Makefile.machine: -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
+use these LINKFLAGS settings in Makefile.machine: -fopenmp, -xHost
+make yes-user-intel yes-user-omp # including user-omp is optional
+make mpi # build with the USER-INTEL package, if settings (including compiler) added to Makefile.mpi
+make intel_cpu # or Makefile.intel_cpu already has settings, uses Intel MPI wrapper
+Make.py -v -p intel omp -intel cpu -a file mpich_icc # or one-line build via Make.py for MPICH
+Make.py -v -p intel omp -intel cpu -a file ompi_icc # or for OpenMPI
+Make.py -v -p intel omp -intel cpu -a file intel_cpu # or for Intel MPI wrapper
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>lmp_machine -sf intel -pk intel 0 omp 16 -in in.script # 1 node, 1 MPI task/node, 16 threads/task, no USER-OMP
+mpirun -np 32 lmp_machine -sf intel -in in.script # 2 nodess, 16 MPI tasks/node, no threads, no USER-OMP
+lmp_machine -sf hybrid intel omp -pk intel 0 omp 16 -pk omp 16 -in in.script # 1 node, 1 MPI task/node, 16 threads/task, with USER-OMP
+mpirun -np 32 -ppn 4 lmp_machine -sf hybrid intel omp -pk omp 4 -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task, with USER-OMP
+</pre></div>
+</div>
+<p>Here is a quick overview of how to use the USER-INTEL package for the
+same CPUs as above (16 cores/node), with an additional Xeon Phi(TM)
+coprocessor per node. More details follow.</p>
+<div class="highlight-python"><div class="highlight"><pre>Same as above for building, with these additions/changes:
+add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in Makefile.machine
+add the flag -offload to LINKFLAGS in Makefile.machine
+for Make.py change "-intel cpu" to "-intel phi", and "file intel_cpu" to "file intel_phi"
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>mpirun -np 32 lmp_machine -sf intel -pk intel 1 -in in.script # 2 nodes, 16 MPI tasks/node, 240 total threads on coprocessor, no USER-OMP
+mpirun -np 16 -ppn 8 lmp_machine -sf intel -pk intel 1 omp 2 -in in.script # 2 nodes, 8 MPI tasks/node, 2 threads/task, 240 total threads on coprocessor, no USER-OMP
+mpirun -np 32 -ppn 8 lmp_machine -sf hybrid intel omp -pk intel 1 omp 2 -pk omp 2 -in in.script # 4 nodes, 8 MPI tasks/node, 2 threads/task, 240 total threads on coprocessor, with USER-OMP
+</pre></div>
+</div>
<p><strong>Required hardware/software:</strong></p>
-<p>To use the offload option, you must have one or more Intel(R) Xeon
-Phi(TM) coprocessors and use an Intel(R) C++ compiler.</p>
-<p>Optimizations for vectorization have only been tested with the
+<p>Your compiler must support the OpenMP interface. Use of an Intel(R)
+C++ compiler is recommended, but not required. However, g++ will not
+recognize some of the settings listed above, so they cannot be used.
+Optimizations for vectorization have only been tested with the
Intel(R) compiler. Use of other compilers may not result in
-vectorization or give poor performance.</p>
-<p>Use of an Intel C++ compiler is recommended, but not required (though
-g++ will not recognize some of the settings, so they cannot be used).
-The compiler must support the OpenMP interface.</p>
+vectorization, or give poor performance.</p>
<p>The recommended version of the Intel(R) compiler is 14.0.1.106.
-Versions 15.0.1.133 and later are also supported. If using Intel(R)
+Versions 15.0.1.133 and later are also supported. If using Intel(R)
MPI, versions 15.0.2.044 and later are recommended.</p>
+<p>To use the offload option, you must have one or more Intel(R) Xeon
+Phi(TM) coprocessors and use an Intel(R) C++ compiler.</p>
<p><strong>Building LAMMPS with the USER-INTEL package:</strong></p>
-<p>You can choose to build with or without support for offload to a
-Intel(R) Xeon Phi(TM) coprocessor. If you build with support for a
-coprocessor, the same binary can be used on nodes with and without
-coprocessors installed. However, if you do not have coprocessors
-on your system, building without offload support will produce a
-smaller binary.</p>
-<p>You can do either in one line, using the src/Make.py script, described
-in <a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a> of the manual. Type
-“Make.py -h” for help. If run from the src directory, these commands
-will create src/lmp_intel_cpu and lmp_intel_phi using
-src/MAKE/Makefile.mpi as the starting Makefile.machine:</p>
-<div class="highlight-python"><div class="highlight"><pre>Make.py -p intel omp -intel cpu -o intel_cpu -cc icc -a file mpi
-Make.py -p intel omp -intel phi -o intel_phi -cc icc -a file mpi
-</pre></div>
-</div>
-<p>Note that this assumes that your MPI and its mpicxx wrapper
-is using the Intel compiler. If it is not, you should
-leave off the “-cc icc” switch.</p>
-<p>Or you can follow these steps:</p>
-<div class="highlight-python"><div class="highlight"><pre>cd lammps/src
-make yes-user-intel
-make yes-user-omp (if desired)
-make machine
-</pre></div>
-</div>
-<p>Note that if the USER-OMP package is also installed, you can use
-styles from both packages, as described below.</p>
-<p>The Makefile.machine needs a “-fopenmp” flag for OpenMP support in
-both the CCFLAGS and LINKFLAGS variables. You also need to add
--DLAMMPS_MEMALIGN=64 and -restrict to CCFLAGS.</p>
+<p>The lines above illustrate how to include/build with the USER-INTEL
+package, for either CPU or Phi support, in two steps, using the “make”
+command. Or how to do it with one command via the src/Make.py script,
+described in <a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a> of the manual.
+Type “Make.py -h” for help. Because the mechanism for specifing what
+compiler to use (Intel in this case) is different for different MPI
+wrappers, 3 versions of the Make.py command are shown.</p>
+<p>Note that if you build with support for a Phi coprocessor, the same
+binary can be used on nodes with or without coprocessors installed.
+However, if you do not have coprocessors on your system, building
+without offload support will produce a smaller binary.</p>
+<p>If you also build with the USER-OMP package, you can use styles from
+both packages, as described below.</p>
+<p>Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
+include “-fopenmp”. Likewise, if you use an Intel compiler, the
+CCFLAGS setting must include “-restrict”. For Phi support, the
+“-DLMP_INTEL_OFFLOAD” (CCFLAGS) and “-offload” (LINKFLAGS) settings
+are required. The other settings listed above are optional, but will
+typically improve performance. The Make.py command will add all of
+these automatically.</p>
<p>If you are compiling on the same architecture that will be used for
-the runs, adding the flag <em>-xHost</em> to CCFLAGS will enable
-vectorization with the Intel(R) compiler. Otherwise, you must
-provide the correct compute node architecture to the -x option
-(e.g. -xAVX).</p>
-<p>In order to build with support for an Intel(R) Xeon Phi(TM)
-coprocessor, the flag <em>-offload</em> should be added to the LINKFLAGS line
-and the flag -DLMP_INTEL_OFFLOAD should be added to the CCFLAGS line.</p>
-<p>Example makefiles Makefile.intel_cpu and Makefile.intel_phi are
-included in the src/MAKE/OPTIONS directory with settings that perform
-well with the Intel(R) compiler. The latter file has support for
-offload to coprocessors; the former does not.</p>
-<p><strong>Notes on CPU and core affinity:</strong></p>
-<p>Setting core affinity is often used to pin MPI tasks and OpenMP
-threads to a core or group of cores so that memory access can be
-uniform. Unless disabled at build time, affinity for MPI tasks and
-OpenMP threads on the host will be set by default on the host
-when using offload to a coprocessor. In this case, it is unnecessary
-to use other methods to control affinity (e.g. taskset, numactl,
-I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input script
-with the <em>no_affinity</em> option to the <a class="reference internal" href="package.html"><em>package intel</em></a>
-command or by disabling the option at build time (by adding
--DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your Makefile).
-Disabling this option is not recommended, especially when running
-on a machine with hyperthreading disabled.</p>
-<p><strong>Running with the USER-INTEL package from the command line:</strong></p>
+the runs, adding the flag <em>-xHost</em> to CCFLAGS enables vectorization
+with the Intel(R) compiler. Otherwise, you must provide the correct
+compute node architecture to the -x option (e.g. -xAVX).</p>
+<p>Example machines makefiles Makefile.intel_cpu and Makefile.intel_phi
+are included in the src/MAKE/OPTIONS directory with settings that
+perform well with the Intel(R) compiler. The latter has support for
+offload to Phi coprocessors; the former does not.</p>
+<p><strong>Run with the USER-INTEL package from the command line:</strong></p>
<p>The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.</p>
-<p>If you plan to compute (any portion of) pairwise interactions using
-USER-INTEL pair styles on the CPU, or use USER-OMP styles on the CPU,
-you need to choose how many OpenMP threads per MPI task to use. Note
-that the product of MPI tasks * OpenMP threads/task should not exceed
-the physical number of cores (on a node), otherwise performance will
-suffer.</p>
-<p>If LAMMPS was built with coprocessor support for the USER-INTEL
-package, you also need to specify the number of coprocessor/node and
-optionally the number of coprocessor threads per MPI task to use. Note that
-coprocessor threads (which run on the coprocessor) are totally
-independent from OpenMP threads (which run on the CPU). The default
-values for the settings that affect coprocessor threads are typically
-fine, as discussed below.</p>
-<p>Use the “-sf intel” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>,
-which will automatically append “intel” to styles that support it.
-OpenMP threads per MPI task can be set via the “-pk intel Nphi omp Nt” or
-“-pk omp Nt” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a>, which
-set Nt = # of OpenMP threads per MPI task to use. The “-pk omp” form
-is only allowed if LAMMPS was also built with the USER-OMP package.</p>
-<p>Use the “-pk intel Nphi” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> to set Nphi = # of Xeon Phi(TM)
-coprocessors/node, if LAMMPS was built with coprocessor support. All
-the available coprocessor threads on each Phi will be divided among
-MPI tasks, unless the <em>tptask</em> option of the “-pk intel” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> is used to limit the coprocessor
-threads per MPI task. See the <a class="reference internal" href="package.html"><em>package intel</em></a> command
-for details.</p>
-<div class="highlight-python"><div class="highlight"><pre>CPU-only without USER-OMP (but using Intel vectorization on CPU):
-mpirun -np 32 lmp_machine -sf intel -in in.script # 32 MPI tasks on as many nodes as needed (e.g. 2 16-core nodes)
-lmp_machine -sf intel -pk intel 0 omp 16 -in in.script # 1 MPI task and 16 threads
-</pre></div>
-</div>
-<div class="highlight-python"><div class="highlight"><pre>CPU-only with USER-OMP (and Intel vectorization on CPU):
-lmp_machine -sf hybrid intel omp -pk intel 0 omp 16 -in in.script # 1 MPI task on a 16-core node with 16 threads
-mpirun -np 4 lmp_machine -sf hybrid intel omp -pk omp 4 -in in.script # 4 MPI tasks each with 4 threads on a single 16-core node
-</pre></div>
-</div>
-<div class="highlight-python"><div class="highlight"><pre>CPUs + Xeon Phi(TM) coprocessors with or without USER-OMP:
-mpirun -np 32 -ppn 16 lmp_machine -sf intel -pk intel 1 -in in.script # 2 nodes with 16 MPI tasks on each, 240 total threads on coprocessor
-mpirun -np 16 -ppn 8 lmp_machine -sf intel -pk intel 1 omp 2 -in in.script # 2 nodes, 8 MPI tasks on each node, 2 threads for each task, 240 total threads on coprocessor
-mpirun -np 16 -ppn 8 lmp_machine -sf hybrid intel omp -pk intel 1 omp 2 -in in.script # 2 nodes, 8 MPI tasks on each node, 2 threads for each task, 240 total threads on coprocessor, USER-OMP package for some styles
-</pre></div>
-</div>
-<p>Note that if the “-sf intel” switch is used, it also invokes a
-default command: <a class="reference internal" href="package.html"><em>package intel 1</em></a>. If the “-sf hybrid intel omp”
-switch is used, the default USER-OMP command <a class="reference internal" href="package.html"><em>package omp 0</em></a> is
-also invoked. Both set the number of OpenMP threads per MPI task via the
-OMP_NUM_THREADS environment variable. The first command sets the number of
-Xeon Phi(TM) coprocessors/node to 1 (and the precision mode to “mixed”, as one
-of its option defaults). The latter command is not invoked if LAMMPS was not
-built with the USER-OMP package. The Nphi = 1 value for the first command is
-ignored if LAMMPS was not built with coprocessor support.</p>
-<p>Using the “-pk intel” or “-pk omp” switches explicitly allows for
-direct setting of the number of OpenMP threads per MPI task, and
-additional options for either of the USER-INTEL or USER-OMP packages.
-In particular, the “-pk intel” switch sets the number of
-coprocessors/node and can limit the number of coprocessor threads per
-MPI task. The syntax for these two switches is the same as the
-<a class="reference internal" href="package.html"><em>package omp</em></a> and <a class="reference internal" href="package.html"><em>package intel</em></a> commands.
-See the <a class="reference internal" href="package.html"><em>package</em></a> command doc page for details, including
-the default values used for all its options if these switches are not
+<p>If you compute (any portion of) pairwise interactions using USER-INTEL
+pair styles on the CPU, or use USER-OMP styles on the CPU, you need to
+choose how many OpenMP threads per MPI task to use. If both packages
+are used, it must be done for both packages, and the same thread count
+value should be used for both. Note that the product of MPI tasks *
+threads/task should not exceed the physical number of cores (on a
+node), otherwise performance will suffer.</p>
+<p>When using the USER-INTEL package for the Phi, you also need to
+specify the number of coprocessor/node and optionally the number of
+coprocessor threads per MPI task to use. Note that coprocessor
+threads (which run on the coprocessor) are totally independent from
+OpenMP threads (which run on the CPU). The default values for the
+settings that affect coprocessor threads are typically fine, as
+discussed below.</p>
+<p>As in the lines above, use the “-sf intel” or “-sf hybrid intel omp”
+<a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>, which will
+automatically append “intel” to styles that support it. In the second
+case, “omp” will be appended if an “intel” style does not exist.</p>
+<p>Note that if either switch is used, it also invokes a default command:
+<a class="reference internal" href="package.html"><em>package intel 1</em></a>. If the “-sf hybrid intel omp” switch
+is used, the default USER-OMP command <a class="reference internal" href="package.html"><em>package omp 0</em></a> is
+also invoked (if LAMMPS was built with USER-OMP). Both set the number
+of OpenMP threads per MPI task via the OMP_NUM_THREADS environment
+variable. The first command sets the number of Xeon Phi(TM)
+coprocessors/node to 1 (ignored if USER-INTEL is built for CPU-only),
+and the precision mode to “mixed” (default value).</p>
+<p>You can also use the “-pk intel Nphi” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> to explicitly set Nphi = # of Xeon
+Phi(TM) coprocessors/node, as well as additional options. Nphi should
+be >= 1 if LAMMPS was built with coprocessor support, otherswise Nphi
+= 0 for a CPU-only build. All the available coprocessor threads on
+each Phi will be divided among MPI tasks, unless the <em>tptask</em> option
+of the “-pk intel” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> is
+used to limit the coprocessor threads per MPI task. See the <a class="reference internal" href="package.html"><em>package intel</em></a> command for details, including the default values
+used for all its options if not specified, and how to set the number
+of OpenMP threads via the OMP_NUM_THREADS environment variable if
+desired.</p>
+<p>If LAMMPS was built with the USER-OMP package, you can also use the
+“-pk omp Nt” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> to
+explicitly set Nt = # of OpenMP threads per MPI task to use, as well
+as additional options. Nt should be the same threads per MPI task as
+set for the USER-INTEL package, e.g. via the “-pk intel Nphi omp Nt”
+command. Again, see the <a class="reference internal" href="package.html"><em>package omp</em></a> command for
+details, including the default values used for all its options if not
specified, and how to set the number of OpenMP threads via the
OMP_NUM_THREADS environment variable if desired.</p>
<p><strong>Or run with the USER-INTEL package by editing an input script:</strong></p>
<p>The discussion above for the mpirun/mpiexec command, MPI tasks/node,
OpenMP threads per MPI task, and coprocessor threads per MPI task is
the same.</p>
-<p>Use the <a class="reference internal" href="suffix.html"><em>suffix intel</em></a> command, or you can explicitly add an
-“intel” suffix to individual styles in your input script, e.g.</p>
+<p>Use the <a class="reference internal" href="suffix.html"><em>suffix intel</em></a> or <a class="reference internal" href="suffix.html"><em>suffix hybrid intel omp</em></a> commands, or you can explicitly add an “intel” or
+“omp” suffix to individual styles in your input script, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/intel 2.5
</pre></div>
</div>
<p>You must also use the <a class="reference internal" href="package.html"><em>package intel</em></a> command, unless the
“-sf intel” or “-pk intel” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> were used. It specifies how many
coprocessors/node to use, as well as other OpenMP threading and
-coprocessor options. Its doc page explains how to set the number of
-OpenMP threads via an environment variable if desired.</p>
+coprocessor options. The <a class="reference internal" href="package.html"><em>package</em></a> doc page explains how
+to set the number of OpenMP threads via an environment variable if
+desired.</p>
<p>If LAMMPS was also built with the USER-OMP package, you must also use
the <a class="reference internal" href="package.html"><em>package omp</em></a> command to enable that package, unless
the “-sf hybrid intel omp” or “-pk omp” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> were used. It specifies how many
-OpenMP threads per MPI task to use, as well as other options. Its doc
-page explains how to set the number of OpenMP threads via an
-environment variable if desired.</p>
+OpenMP threads per MPI task to use (should be same as the setting for
+the USER-INTEL package), as well as other options. Its doc page
+explains how to set the number of OpenMP threads via an environment
+variable if desired.</p>
<p><strong>Speed-ups to expect:</strong></p>
-<p>If LAMMPS was not built with coprocessor support when including the
-USER-INTEL package, then acclerated styles will run on the CPU using
-vectorization optimizations and the specified precision. This may
-give a substantial speed-up for a pair style, particularly if mixed or
-single precision is used.</p>
+<p>If LAMMPS was not built with coprocessor support (CPU only) when
+including the USER-INTEL package, then acclerated styles will run on
+the CPU using vectorization optimizations and the specified precision.
+This may give a substantial speed-up for a pair style, particularly if
+mixed or single precision is used.</p>
<p>If LAMMPS was built with coproccesor support, the pair styles will run
on one or more Intel(R) Xeon Phi(TM) coprocessors (per node). The
performance of a Xeon Phi versus a multi-core CPU is a function of
your hardware, which pair style is used, the number of
atoms/coprocessor, and the precision used on the coprocessor (double,
single, mixed).</p>
<p>See the <a class="reference external" href="http://lammps.sandia.gov/bench.html">Benchmark page</a> of the
LAMMPS web site for performance of the USER-INTEL package on different
hardware.</p>
+<div class="admonition warning">
+<p class="first admonition-title">Warning</p>
+<p class="last">Setting core affinity is often used to pin MPI tasks
+and OpenMP threads to a core or group of cores so that memory access
+can be uniform. Unless disabled at build time, affinity for MPI tasks
+and OpenMP threads on the host (CPU) will be set by default on the
+host when using offload to a coprocessor. In this case, it is
+unnecessary to use other methods to control affinity (e.g. taskset,
+numactl, I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input
+script with the <em>no_affinity</em> option to the <a class="reference internal" href="package.html"><em>package intel</em></a> command or by disabling the option at build time
+(by adding -DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your
+Makefile). Disabling this option is not recommended, especially when
+running on a machine with hyperthreading disabled.</p>
+</div>
<p><strong>Guidelines for best performance on an Intel(R) Xeon Phi(TM)
coprocessor:</strong></p>
<ul class="simple">
<li>The default for the <a class="reference internal" href="package.html"><em>package intel</em></a> command is to have
all the MPI tasks on a given compute node use a single Xeon Phi(TM)
coprocessor. In general, running with a large number of MPI tasks on
each node will perform best with offload. Each MPI task will
automatically get affinity to a subset of the hardware threads
available on the coprocessor. For example, if your card has 61 cores,
with 60 cores available for offload and 4 hardware threads per core
(240 total threads), running with 24 MPI tasks per node will cause
each MPI task to use a subset of 10 threads on the coprocessor. Fine
tuning of the number of threads to use per MPI task or the number of
threads to use per core can be accomplished with keyword settings of
the <a class="reference internal" href="package.html"><em>package intel</em></a> command.</li>
<li>If desired, only a fraction of the pair style computation can be
offloaded to the coprocessors. This is accomplished by using the
<em>balance</em> keyword in the <a class="reference internal" href="package.html"><em>package intel</em></a> command. A
balance of 0 runs all calculations on the CPU. A balance of 1 runs
all calculations on the coprocessor. A balance of 0.5 runs half of
the calculations on the coprocessor. Setting the balance to -1 (the
default) will enable dynamic load balancing that continously adjusts
the fraction of offloaded work throughout the simulation. This option
typically produces results within 5 to 10 percent of the optimal fixed
balance.</li>
<li>When using offload with CPU hyperthreading disabled, it may help
performance to use fewer MPI tasks and OpenMP threads than available
cores. This is due to the fact that additional threads are generated
internally to handle the asynchronous offload tasks.</li>
<li>If running short benchmark runs with dynamic load balancing, adding a
short warm-up run (10-20 steps) will allow the load-balancer to find a
near-optimal setting that will carry over to additional runs.</li>
<li>If pair computations are being offloaded to an Intel(R) Xeon Phi(TM)
coprocessor, a diagnostic line is printed to the screen (not to the
log file), during the setup phase of a run, indicating that offload
mode is being used and indicating the number of coprocessor threads
per MPI task. Additionally, an offload timing summary is printed at
the end of each run. When offloading, the frequency for <a class="reference internal" href="atom_modify.html"><em>atom sorting</em></a> is changed to 1 so that the per-atom data is
effectively sorted at every rebuild of the neighbor lists.</li>
<li>For simulations with long-range electrostatics or bond, angle,
dihedral, improper calculations, computation and data transfer to the
coprocessor will run concurrently with computations and MPI
communications for these calculations on the host CPU. The USER-INTEL
package has two modes for deciding which atoms will be handled by the
coprocessor. This choice is controlled with the <em>ghost</em> keyword of
the <a class="reference internal" href="package.html"><em>package intel</em></a> command. When set to 0, ghost atoms
(atoms at the borders between MPI tasks) are not offloaded to the
card. This allows for overlap of MPI communication of forces with
computation on the coprocessor when the <a class="reference internal" href="newton.html"><em>newton</em></a> setting
is “on”. The default is dependent on the style being used, however,
better performance may be achieved by setting this option
explictly.</li>
</ul>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>When offloading to a coprocessor, <a class="reference internal" href="pair_hybrid.html"><em>hybrid</em></a> styles
that require skip lists for neighbor builds cannot be offloaded.
Using <a class="reference internal" href="pair_hybrid.html"><em>hybrid/overlay</em></a> is allowed. Only one intel
accelerated style may be used with hybrid styles.
<a class="reference internal" href="special_bonds.html"><em>Special_bonds</em></a> exclusion lists are not currently
supported with offload, however, the same effect can often be
accomplished by setting cutoffs for excluded atom types to 0. None of
the pair styles in the USER-INTEL package currently support the
“inner”, “middle”, “outer” options for rRESPA integration via the
<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command; only the “pair” option is
supported.</p>
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diff --git a/doc/accelerate_intel.txt b/doc/accelerate_intel.txt
index b78dbd629..bebcbcfb5 100644
--- a/doc/accelerate_intel.txt
+++ b/doc/accelerate_intel.txt
@@ -1,343 +1,321 @@
"Previous Section"_Section_packages.html - "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
"Return to Section accelerate overview"_Section_accelerate.html
5.3.3 USER-INTEL package :h4
The USER-INTEL package was developed by Mike Brown at Intel
-Corporation. It provides a capability to accelerate simulations by
-offloading neighbor list and non-bonded force calculations to Intel(R)
-Xeon Phi(TM) coprocessors (not native mode like the KOKKOS package).
-Additionally, it supports running simulations in single, mixed, or
-double precision with vectorization, even if a coprocessor is not
-present, i.e. on an Intel(R) CPU. The same C++ code is used for both
-cases. When offloading to a coprocessor, the routine is run twice,
-once with an offload flag.
-
-The USER-INTEL package can be used in tandem with the USER-OMP
-package. This is useful when offloading pair style computations to
-coprocessors, so that other styles not supported by the USER-INTEL
-package, e.g. bond, angle, dihedral, improper, and long-range
-electrostatics, can run simultaneously in threaded mode on the CPU
-cores. Since less MPI tasks than CPU cores will typically be invoked
-when running with coprocessors, this enables the extra CPU cores to be
-used for useful computation.
-
-If LAMMPS is built with both the USER-INTEL and USER-OMP packages
-installed, this mode of operation is made easier to use, with the
-"-suffix hybrid intel omp" "command-line switch"_Section_start.html#start_7
-or the "suffix hybrid intel omp"_suffix.html command will both set a
-second-choice suffix to "omp" so that styles from the USER-OMP package will be
-used if available, after first testing if a style from the USER-INTEL
-package is available.
-
-When using the USER-INTEL package, you must choose at build time whether the
-binary will support offload to Xeon Phi coprocessors. Binaries supporting
-offload can still be run in CPU-only (host-only) mode.
-
-Here is a quick overview of how to use the USER-INTEL package
-for CPU-only acceleration:
-
-specify these CCFLAGS in your src/MAKE/Makefile.machine: -openmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost
-specify -openmp with LINKFLAGS in your Makefile.machine
-include the USER-INTEL package and (optionally) USER-OMP package and build LAMMPS
-specify how many OpenMP threads per MPI task to use
-use USER-INTEL and (optionally) USER-OMP styles in your input script :ul
-
-Note that many of these settings can only be used with the Intel
-compiler, as discussed below.
-
-Using the USER-INTEL package to offload work to the Intel(R)
-Xeon Phi(TM) coprocessor is the same except for these additional
-steps:
-
-add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in your Makefile.machine
-add the flag -offload to LINKFLAGS in your Makefile.machine :ul
-
-The latter two steps in the first case and the last step in the
-coprocessor case can be done using the "-pk intel" and "-sf intel"
-"command-line switches"_Section_start.html#start_7 respectively. Or
-the effect of the "-pk" or "-sf" switches can be duplicated by adding
-the "package intel"_package.html or "suffix intel"_suffix.html
-commands respectively to your input script.
+Corporation. It provides two methods for accelerating simulations,
+depending on the hardware you have. The first is acceleration on
+Intel(R) CPUs by running in single, mixed, or double precision with
+vectorization. The second is acceleration on Intel(R) Xeon Phi(TM)
+coprocessors via offloading neighbor list and non-bonded force
+calculations to the Phi. The same C++ code is used in both cases.
+When offloading to a coprocessor from a CPU, the same routine is run
+twice, once on the CPU and once with an offload flag.
+
+Note that the USER-INTEL package supports use of the Phi in "offload"
+mode, not "native" mode like the "KOKKOS
+package"_accelerate_kokkos.html.
+
+Also note that the USER-INTEL package can be used in tandem with the
+"USER-OMP package"_accelerate_omp.html. This is useful when
+offloading pair style computations to the Phi, so that other styles
+not supported by the USER-INTEL package, e.g. bond, angle, dihedral,
+improper, and long-range electrostatics, can run simultaneously in
+threaded mode on the CPU cores. Since less MPI tasks than CPU cores
+will typically be invoked when running with coprocessors, this enables
+the extra CPU cores to be used for useful computation.
+
+As illustrated below, if LAMMPS is built with both the USER-INTEL and
+USER-OMP packages, this dual mode of operation is made easier to use,
+via the "-suffix hybrid intel omp" "command-line
+switch"_Section_start.html#start_7 or the "suffix hybrid intel
+omp"_suffix.html command. Both set a second-choice suffix to "omp" so
+that styles from the USER-INTEL package will be used if available,
+with styles from the USER-OMP package as a second choice.
+
+Here is a quick overview of how to use the USER-INTEL package for CPU
+acceleration, assuming one or more 16-core nodes. More details
+follow.
+
+use an Intel compiler
+use these CCFLAGS settings in Makefile.machine: -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
+use these LINKFLAGS settings in Makefile.machine: -fopenmp, -xHost
+make yes-user-intel yes-user-omp # including user-omp is optional
+make mpi # build with the USER-INTEL package, if settings (including compiler) added to Makefile.mpi
+make intel_cpu # or Makefile.intel_cpu already has settings, uses Intel MPI wrapper
+Make.py -v -p intel omp -intel cpu -a file mpich_icc # or one-line build via Make.py for MPICH
+Make.py -v -p intel omp -intel cpu -a file ompi_icc # or for OpenMPI
+Make.py -v -p intel omp -intel cpu -a file intel_cpu # or for Intel MPI wrapper :pre
+
+lmp_machine -sf intel -pk intel 0 omp 16 -in in.script # 1 node, 1 MPI task/node, 16 threads/task, no USER-OMP
+mpirun -np 32 lmp_machine -sf intel -in in.script # 2 nodess, 16 MPI tasks/node, no threads, no USER-OMP
+lmp_machine -sf hybrid intel omp -pk intel 0 omp 16 -pk omp 16 -in in.script # 1 node, 1 MPI task/node, 16 threads/task, with USER-OMP
+mpirun -np 32 -ppn 4 lmp_machine -sf hybrid intel omp -pk omp 4 -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task, with USER-OMP :pre
+
+Here is a quick overview of how to use the USER-INTEL package for the
+same CPUs as above (16 cores/node), with an additional Xeon Phi(TM)
+coprocessor per node. More details follow.
+
+Same as above for building, with these additions/changes:
+add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in Makefile.machine
+add the flag -offload to LINKFLAGS in Makefile.machine
+for Make.py change "-intel cpu" to "-intel phi", and "file intel_cpu" to "file intel_phi" :pre
+
+mpirun -np 32 lmp_machine -sf intel -pk intel 1 -in in.script # 2 nodes, 16 MPI tasks/node, 240 total threads on coprocessor, no USER-OMP
+mpirun -np 16 -ppn 8 lmp_machine -sf intel -pk intel 1 omp 2 -in in.script # 2 nodes, 8 MPI tasks/node, 2 threads/task, 240 total threads on coprocessor, no USER-OMP
+mpirun -np 32 -ppn 8 lmp_machine -sf hybrid intel omp -pk intel 1 omp 2 -pk omp 2 -in in.script # 4 nodes, 8 MPI tasks/node, 2 threads/task, 240 total threads on coprocessor, with USER-OMP :pre
[Required hardware/software:]
-To use the offload option, you must have one or more Intel(R) Xeon
-Phi(TM) coprocessors and use an Intel(R) C++ compiler.
-
+Your compiler must support the OpenMP interface. Use of an Intel(R)
+C++ compiler is recommended, but not required. However, g++ will not
+recognize some of the settings listed above, so they cannot be used.
Optimizations for vectorization have only been tested with the
Intel(R) compiler. Use of other compilers may not result in
-vectorization or give poor performance.
-
-Use of an Intel C++ compiler is recommended, but not required (though
-g++ will not recognize some of the settings, so they cannot be used).
-The compiler must support the OpenMP interface.
+vectorization, or give poor performance.
The recommended version of the Intel(R) compiler is 14.0.1.106.
-Versions 15.0.1.133 and later are also supported. If using Intel(R)
+Versions 15.0.1.133 and later are also supported. If using Intel(R)
MPI, versions 15.0.2.044 and later are recommended.
-[Building LAMMPS with the USER-INTEL package:]
-
-You can choose to build with or without support for offload to a
-Intel(R) Xeon Phi(TM) coprocessor. If you build with support for a
-coprocessor, the same binary can be used on nodes with and without
-coprocessors installed. However, if you do not have coprocessors
-on your system, building without offload support will produce a
-smaller binary.
-
-You can do either in one line, using the src/Make.py script, described
-in "Section 2.4"_Section_start.html#start_4 of the manual. Type
-"Make.py -h" for help. If run from the src directory, these commands
-will create src/lmp_intel_cpu and lmp_intel_phi using
-src/MAKE/Makefile.mpi as the starting Makefile.machine:
-
-Make.py -p intel omp -intel cpu -o intel_cpu -cc icc -a file mpi
-Make.py -p intel omp -intel phi -o intel_phi -cc icc -a file mpi :pre
-
-Note that this assumes that your MPI and its mpicxx wrapper
-is using the Intel compiler. If it is not, you should
-leave off the "-cc icc" switch.
+To use the offload option, you must have one or more Intel(R) Xeon
+Phi(TM) coprocessors and use an Intel(R) C++ compiler.
-Or you can follow these steps:
+[Building LAMMPS with the USER-INTEL package:]
-cd lammps/src
-make yes-user-intel
-make yes-user-omp (if desired)
-make machine :pre
+The lines above illustrate how to include/build with the USER-INTEL
+package, for either CPU or Phi support, in two steps, using the "make"
+command. Or how to do it with one command via the src/Make.py script,
+described in "Section 2.4"_Section_start.html#start_4 of the manual.
+Type "Make.py -h" for help. Because the mechanism for specifing what
+compiler to use (Intel in this case) is different for different MPI
+wrappers, 3 versions of the Make.py command are shown.
+
+Note that if you build with support for a Phi coprocessor, the same
+binary can be used on nodes with or without coprocessors installed.
+However, if you do not have coprocessors on your system, building
+without offload support will produce a smaller binary.
+
+If you also build with the USER-OMP package, you can use styles from
+both packages, as described below.
+
+Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
+include "-fopenmp". Likewise, if you use an Intel compiler, the
+CCFLAGS setting must include "-restrict". For Phi support, the
+"-DLMP_INTEL_OFFLOAD" (CCFLAGS) and "-offload" (LINKFLAGS) settings
+are required. The other settings listed above are optional, but will
+typically improve performance. The Make.py command will add all of
+these automatically.
-Note that if the USER-OMP package is also installed, you can use
-styles from both packages, as described below.
+If you are compiling on the same architecture that will be used for
+the runs, adding the flag {-xHost} to CCFLAGS enables vectorization
+with the Intel(R) compiler. Otherwise, you must provide the correct
+compute node architecture to the -x option (e.g. -xAVX).
-The Makefile.machine needs a "-fopenmp" flag for OpenMP support in
-both the CCFLAGS and LINKFLAGS variables. You also need to add
--DLAMMPS_MEMALIGN=64 and -restrict to CCFLAGS.
+Example machines makefiles Makefile.intel_cpu and Makefile.intel_phi
+are included in the src/MAKE/OPTIONS directory with settings that
+perform well with the Intel(R) compiler. The latter has support for
+offload to Phi coprocessors; the former does not.
-If you are compiling on the same architecture that will be used for
-the runs, adding the flag {-xHost} to CCFLAGS will enable
-vectorization with the Intel(R) compiler. Otherwise, you must
-provide the correct compute node architecture to the -x option
-(e.g. -xAVX).
-
-In order to build with support for an Intel(R) Xeon Phi(TM)
-coprocessor, the flag {-offload} should be added to the LINKFLAGS line
-and the flag -DLMP_INTEL_OFFLOAD should be added to the CCFLAGS line.
-
-Example makefiles Makefile.intel_cpu and Makefile.intel_phi are
-included in the src/MAKE/OPTIONS directory with settings that perform
-well with the Intel(R) compiler. The latter file has support for
-offload to coprocessors; the former does not.
-
-[Notes on CPU and core affinity:]
-
-Setting core affinity is often used to pin MPI tasks and OpenMP
-threads to a core or group of cores so that memory access can be
-uniform. Unless disabled at build time, affinity for MPI tasks and
-OpenMP threads on the host will be set by default on the host
-when using offload to a coprocessor. In this case, it is unnecessary
-to use other methods to control affinity (e.g. taskset, numactl,
-I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input script
-with the {no_affinity} option to the "package intel"_package.html
-command or by disabling the option at build time (by adding
--DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your Makefile).
-Disabling this option is not recommended, especially when running
-on a machine with hyperthreading disabled.
-
-[Running with the USER-INTEL package from the command line:]
+[Run with the USER-INTEL package from the command line:]
The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
-If you plan to compute (any portion of) pairwise interactions using
-USER-INTEL pair styles on the CPU, or use USER-OMP styles on the CPU,
-you need to choose how many OpenMP threads per MPI task to use. Note
-that the product of MPI tasks * OpenMP threads/task should not exceed
-the physical number of cores (on a node), otherwise performance will
-suffer.
-
-If LAMMPS was built with coprocessor support for the USER-INTEL
-package, you also need to specify the number of coprocessor/node and
-optionally the number of coprocessor threads per MPI task to use. Note that
-coprocessor threads (which run on the coprocessor) are totally
-independent from OpenMP threads (which run on the CPU). The default
-values for the settings that affect coprocessor threads are typically
-fine, as discussed below.
-
-Use the "-sf intel" "command-line switch"_Section_start.html#start_7,
-which will automatically append "intel" to styles that support it.
-OpenMP threads per MPI task can be set via the "-pk intel Nphi omp Nt" or
-"-pk omp Nt" "command-line switches"_Section_start.html#start_7, which
-set Nt = # of OpenMP threads per MPI task to use. The "-pk omp" form
-is only allowed if LAMMPS was also built with the USER-OMP package.
-
-Use the "-pk intel Nphi" "command-line
-switch"_Section_start.html#start_7 to set Nphi = # of Xeon Phi(TM)
-coprocessors/node, if LAMMPS was built with coprocessor support. All
-the available coprocessor threads on each Phi will be divided among
-MPI tasks, unless the {tptask} option of the "-pk intel" "command-line
-switch"_Section_start.html#start_7 is used to limit the coprocessor
-threads per MPI task. See the "package intel"_package.html command
-for details.
-
-CPU-only without USER-OMP (but using Intel vectorization on CPU):
-mpirun -np 32 lmp_machine -sf intel -in in.script # 32 MPI tasks on as many nodes as needed (e.g. 2 16-core nodes)
-lmp_machine -sf intel -pk intel 0 omp 16 -in in.script # 1 MPI task and 16 threads :pre
-
-CPU-only with USER-OMP (and Intel vectorization on CPU):
-lmp_machine -sf hybrid intel omp -pk intel 0 omp 16 -in in.script # 1 MPI task on a 16-core node with 16 threads
-mpirun -np 4 lmp_machine -sf hybrid intel omp -pk omp 4 -in in.script # 4 MPI tasks each with 4 threads on a single 16-core node :pre
-
-CPUs + Xeon Phi(TM) coprocessors with or without USER-OMP:
-mpirun -np 32 -ppn 16 lmp_machine -sf intel -pk intel 1 -in in.script # 2 nodes with 16 MPI tasks on each, 240 total threads on coprocessor
-mpirun -np 16 -ppn 8 lmp_machine -sf intel -pk intel 1 omp 2 -in in.script # 2 nodes, 8 MPI tasks on each node, 2 threads for each task, 240 total threads on coprocessor
-mpirun -np 16 -ppn 8 lmp_machine -sf hybrid intel omp -pk intel 1 omp 2 -in in.script # 2 nodes, 8 MPI tasks on each node, 2 threads for each task, 240 total threads on coprocessor, USER-OMP package for some styles :pre
-
-Note that if the "-sf intel" switch is used, it also invokes a
-default command: "package intel 1"_package.html. If the "-sf hybrid intel omp"
-switch is used, the default USER-OMP command "package omp 0"_package.html is
-also invoked. Both set the number of OpenMP threads per MPI task via the
-OMP_NUM_THREADS environment variable. The first command sets the number of
-Xeon Phi(TM) coprocessors/node to 1 (and the precision mode to "mixed", as one
-of its option defaults). The latter command is not invoked if LAMMPS was not
-built with the USER-OMP package. The Nphi = 1 value for the first command is
-ignored if LAMMPS was not built with coprocessor support.
-
-Using the "-pk intel" or "-pk omp" switches explicitly allows for
-direct setting of the number of OpenMP threads per MPI task, and
-additional options for either of the USER-INTEL or USER-OMP packages.
-In particular, the "-pk intel" switch sets the number of
-coprocessors/node and can limit the number of coprocessor threads per
-MPI task. The syntax for these two switches is the same as the
-"package omp"_package.html and "package intel"_package.html commands.
-See the "package"_package.html command doc page for details, including
-the default values used for all its options if these switches are not
+If you compute (any portion of) pairwise interactions using USER-INTEL
+pair styles on the CPU, or use USER-OMP styles on the CPU, you need to
+choose how many OpenMP threads per MPI task to use. If both packages
+are used, it must be done for both packages, and the same thread count
+value should be used for both. Note that the product of MPI tasks *
+threads/task should not exceed the physical number of cores (on a
+node), otherwise performance will suffer.
+
+When using the USER-INTEL package for the Phi, you also need to
+specify the number of coprocessor/node and optionally the number of
+coprocessor threads per MPI task to use. Note that coprocessor
+threads (which run on the coprocessor) are totally independent from
+OpenMP threads (which run on the CPU). The default values for the
+settings that affect coprocessor threads are typically fine, as
+discussed below.
+
+As in the lines above, use the "-sf intel" or "-sf hybrid intel omp"
+"command-line switch"_Section_start.html#start_7, which will
+automatically append "intel" to styles that support it. In the second
+case, "omp" will be appended if an "intel" style does not exist.
+
+Note that if either switch is used, it also invokes a default command:
+"package intel 1"_package.html. If the "-sf hybrid intel omp" switch
+is used, the default USER-OMP command "package omp 0"_package.html is
+also invoked (if LAMMPS was built with USER-OMP). Both set the number
+of OpenMP threads per MPI task via the OMP_NUM_THREADS environment
+variable. The first command sets the number of Xeon Phi(TM)
+coprocessors/node to 1 (ignored if USER-INTEL is built for CPU-only),
+and the precision mode to "mixed" (default value).
+
+You can also use the "-pk intel Nphi" "command-line
+switch"_Section_start.html#start_7 to explicitly set Nphi = # of Xeon
+Phi(TM) coprocessors/node, as well as additional options. Nphi should
+be >= 1 if LAMMPS was built with coprocessor support, otherswise Nphi
+= 0 for a CPU-only build. All the available coprocessor threads on
+each Phi will be divided among MPI tasks, unless the {tptask} option
+of the "-pk intel" "command-line switch"_Section_start.html#start_7 is
+used to limit the coprocessor threads per MPI task. See the "package
+intel"_package.html command for details, including the default values
+used for all its options if not specified, and how to set the number
+of OpenMP threads via the OMP_NUM_THREADS environment variable if
+desired.
+
+If LAMMPS was built with the USER-OMP package, you can also use the
+"-pk omp Nt" "command-line switch"_Section_start.html#start_7 to
+explicitly set Nt = # of OpenMP threads per MPI task to use, as well
+as additional options. Nt should be the same threads per MPI task as
+set for the USER-INTEL package, e.g. via the "-pk intel Nphi omp Nt"
+command. Again, see the "package omp"_package.html command for
+details, including the default values used for all its options if not
specified, and how to set the number of OpenMP threads via the
OMP_NUM_THREADS environment variable if desired.
[Or run with the USER-INTEL package by editing an input script:]
The discussion above for the mpirun/mpiexec command, MPI tasks/node,
OpenMP threads per MPI task, and coprocessor threads per MPI task is
the same.
-Use the "suffix intel"_suffix.html command, or you can explicitly add an
-"intel" suffix to individual styles in your input script, e.g.
+Use the "suffix intel"_suffix.html or "suffix hybrid intel
+omp"_suffix.html commands, or you can explicitly add an "intel" or
+"omp" suffix to individual styles in your input script, e.g.
pair_style lj/cut/intel 2.5 :pre
You must also use the "package intel"_package.html command, unless the
"-sf intel" or "-pk intel" "command-line
switches"_Section_start.html#start_7 were used. It specifies how many
coprocessors/node to use, as well as other OpenMP threading and
-coprocessor options. Its doc page explains how to set the number of
-OpenMP threads via an environment variable if desired.
+coprocessor options. The "package"_package.html doc page explains how
+to set the number of OpenMP threads via an environment variable if
+desired.
If LAMMPS was also built with the USER-OMP package, you must also use
the "package omp"_package.html command to enable that package, unless
the "-sf hybrid intel omp" or "-pk omp" "command-line
switches"_Section_start.html#start_7 were used. It specifies how many
-OpenMP threads per MPI task to use, as well as other options. Its doc
-page explains how to set the number of OpenMP threads via an
-environment variable if desired.
+OpenMP threads per MPI task to use (should be same as the setting for
+the USER-INTEL package), as well as other options. Its doc page
+explains how to set the number of OpenMP threads via an environment
+variable if desired.
[Speed-ups to expect:]
-If LAMMPS was not built with coprocessor support when including the
-USER-INTEL package, then acclerated styles will run on the CPU using
-vectorization optimizations and the specified precision. This may
-give a substantial speed-up for a pair style, particularly if mixed or
-single precision is used.
+If LAMMPS was not built with coprocessor support (CPU only) when
+including the USER-INTEL package, then acclerated styles will run on
+the CPU using vectorization optimizations and the specified precision.
+This may give a substantial speed-up for a pair style, particularly if
+mixed or single precision is used.
If LAMMPS was built with coproccesor support, the pair styles will run
on one or more Intel(R) Xeon Phi(TM) coprocessors (per node). The
performance of a Xeon Phi versus a multi-core CPU is a function of
your hardware, which pair style is used, the number of
atoms/coprocessor, and the precision used on the coprocessor (double,
single, mixed).
See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the
LAMMPS web site for performance of the USER-INTEL package on different
hardware.
+IMPORTANT NOTE: Setting core affinity is often used to pin MPI tasks
+and OpenMP threads to a core or group of cores so that memory access
+can be uniform. Unless disabled at build time, affinity for MPI tasks
+and OpenMP threads on the host (CPU) will be set by default on the
+host when using offload to a coprocessor. In this case, it is
+unnecessary to use other methods to control affinity (e.g. taskset,
+numactl, I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input
+script with the {no_affinity} option to the "package
+intel"_package.html command or by disabling the option at build time
+(by adding -DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your
+Makefile). Disabling this option is not recommended, especially when
+running on a machine with hyperthreading disabled.
+
[Guidelines for best performance on an Intel(R) Xeon Phi(TM)
coprocessor:]
The default for the "package intel"_package.html command is to have
all the MPI tasks on a given compute node use a single Xeon Phi(TM)
coprocessor. In general, running with a large number of MPI tasks on
each node will perform best with offload. Each MPI task will
automatically get affinity to a subset of the hardware threads
available on the coprocessor. For example, if your card has 61 cores,
with 60 cores available for offload and 4 hardware threads per core
(240 total threads), running with 24 MPI tasks per node will cause
each MPI task to use a subset of 10 threads on the coprocessor. Fine
tuning of the number of threads to use per MPI task or the number of
threads to use per core can be accomplished with keyword settings of
the "package intel"_package.html command. :ulb,l
If desired, only a fraction of the pair style computation can be
offloaded to the coprocessors. This is accomplished by using the
{balance} keyword in the "package intel"_package.html command. A
balance of 0 runs all calculations on the CPU. A balance of 1 runs
all calculations on the coprocessor. A balance of 0.5 runs half of
the calculations on the coprocessor. Setting the balance to -1 (the
default) will enable dynamic load balancing that continously adjusts
the fraction of offloaded work throughout the simulation. This option
typically produces results within 5 to 10 percent of the optimal fixed
balance. :l
When using offload with CPU hyperthreading disabled, it may help
performance to use fewer MPI tasks and OpenMP threads than available
cores. This is due to the fact that additional threads are generated
internally to handle the asynchronous offload tasks. :l
If running short benchmark runs with dynamic load balancing, adding a
short warm-up run (10-20 steps) will allow the load-balancer to find a
near-optimal setting that will carry over to additional runs. :l
If pair computations are being offloaded to an Intel(R) Xeon Phi(TM)
coprocessor, a diagnostic line is printed to the screen (not to the
log file), during the setup phase of a run, indicating that offload
mode is being used and indicating the number of coprocessor threads
per MPI task. Additionally, an offload timing summary is printed at
the end of each run. When offloading, the frequency for "atom
sorting"_atom_modify.html is changed to 1 so that the per-atom data is
effectively sorted at every rebuild of the neighbor lists. :l
For simulations with long-range electrostatics or bond, angle,
dihedral, improper calculations, computation and data transfer to the
coprocessor will run concurrently with computations and MPI
communications for these calculations on the host CPU. The USER-INTEL
package has two modes for deciding which atoms will be handled by the
coprocessor. This choice is controlled with the {ghost} keyword of
the "package intel"_package.html command. When set to 0, ghost atoms
(atoms at the borders between MPI tasks) are not offloaded to the
card. This allows for overlap of MPI communication of forces with
computation on the coprocessor when the "newton"_newton.html setting
is "on". The default is dependent on the style being used, however,
better performance may be achieved by setting this option
explictly. :l,ule
[Restrictions:]
When offloading to a coprocessor, "hybrid"_pair_hybrid.html styles
that require skip lists for neighbor builds cannot be offloaded.
Using "hybrid/overlay"_pair_hybrid.html is allowed. Only one intel
accelerated style may be used with hybrid styles.
"Special_bonds"_special_bonds.html exclusion lists are not currently
supported with offload, however, the same effect can often be
accomplished by setting cutoffs for excluded atom types to 0. None of
the pair styles in the USER-INTEL package currently support the
"inner", "middle", "outer" options for rRESPA integration via the
"run_style respa"_run_style.html command; only the "pair" option is
supported.
diff --git a/doc/accelerate_kokkos.html b/doc/accelerate_kokkos.html
index 31088c43d..23fccc5ca 100644
--- a/doc/accelerate_kokkos.html
+++ b/doc/accelerate_kokkos.html
@@ -1,620 +1,622 @@
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<p><a class="reference internal" href="Section_accelerate.html"><em>Return to Section accelerate overview</em></a></p>
<div class="section" id="kokkos-package">
<h1>5.KOKKOS package<a class="headerlink" href="#kokkos-package" title="Permalink to this headline">¶</a></h1>
-<p>The KOKKOS package was developed primaritly by Christian Trott
-(Sandia) with contributions of various styles by others, including
-Sikandar Mashayak (UIUC), Stan Moore (Sandia), and Ray Shan (Sandia).
-The underlying Kokkos library was written
-primarily by Carter Edwards, Christian Trott, and Dan Sunderland (all
-Sandia).</p>
+<p>The KOKKOS package was developed primarily by Christian Trott (Sandia)
+with contributions of various styles by others, including Sikandar
+Mashayak (UIUC), Stan Moore (Sandia), and Ray Shan (Sandia). The
+underlying Kokkos library was written primarily by Carter Edwards,
+Christian Trott, and Dan Sunderland (all Sandia).</p>
<p>The KOKKOS package contains versions of pair, fix, and atom styles
that use data structures and macros provided by the Kokkos library,
which is included with LAMMPS in lib/kokkos.</p>
<p>The Kokkos library is part of
-<a class="reference external" href="http://trilinos.sandia.gov/packages/kokkos">Trilinos</a> and can also
-be downloaded from <a class="reference external" href="https://github.com/kokkos/kokkos">Github</a>. Kokkos is a
+<a class="reference external" href="http://trilinos.sandia.gov/packages/kokkos">Trilinos</a> and can also be
+downloaded from <a class="reference external" href="https://github.com/kokkos/kokkos">Github</a>. Kokkos is a
templated C++ library that provides two key abstractions for an
application like LAMMPS. First, it allows a single implementation of
an application kernel (e.g. a pair style) to run efficiently on
different kinds of hardware, such as a GPU, Intel Phi, or many-core
-chip.</p>
+CPU.</p>
<p>The Kokkos library also provides data abstractions to adjust (at
compile time) the memory layout of basic data structures like 2d and
3d arrays and allow the transparent utilization of special hardware
load and store operations. Such data structures are used in LAMMPS to
store atom coordinates or forces or neighbor lists. The layout is
chosen to optimize performance on different platforms. Again this
functionality is hidden from the developer, and does not affect how
the kernel is coded.</p>
<p>These abstractions are set at build time, when LAMMPS is compiled with
-the KOKKOS package installed. This is done by selecting a “host” and
-“device” to build for, compatible with the compute nodes in your
-machine (one on a desktop machine or 1000s on a supercomputer).</p>
-<p>All Kokkos operations occur within the context of an individual MPI
-task running on a single node of the machine. The total number of MPI
-tasks used by LAMMPS (one or multiple per compute node) is set in the
-usual manner via the mpirun or mpiexec commands, and is independent of
-Kokkos.</p>
-<p>Kokkos provides support for two different modes of execution per MPI
-task. This means that computational tasks (pairwise interactions,
-neighbor list builds, time integration, etc) can be parallelized for
-one or the other of the two modes. The first mode is called the
-“host” and is one or more threads running on one or more physical CPUs
-(within the node). Currently, both multi-core CPUs and an Intel Phi
-processor (running in native mode, not offload mode like the
-USER-INTEL package) are supported. The second mode is called the
-“device” and is an accelerator chip of some kind. Currently only an
-NVIDIA GPU is supported via Cuda. If your compute node does not have
-a GPU, then there is only one mode of execution, i.e. the host and
-device are the same.</p>
-<p>When using the KOKKOS package, you must choose at build time whether
-you are building for OpenMP, GPU, or for using the Xeon Phi in native
-mode.</p>
-<p>Here is a quick overview of how to use the KOKKOS package:</p>
+the KOKKOS package installed. All Kokkos operations occur within the
+context of an individual MPI task running on a single node of the
+machine. The total number of MPI tasks used by LAMMPS (one or
+multiple per compute node) is set in the usual manner via the mpirun
+or mpiexec commands, and is independent of Kokkos.</p>
+<p>Kokkos currently provides support for 3 modes of execution (per MPI
+task). These are OpenMP (for many-core CPUs), Cuda (for NVIDIA GPUs),
+and OpenMP (for Intel Phi). Note that the KOKKOS package supports
+running on the Phi in native mode, not offload mode like the
+USER-INTEL package supports. You choose the mode at build time to
+produce an executable compatible with specific hardware.</p>
+<p>Here is a quick overview of how to use the KOKKOS package
+for CPU acceleration, assuming one or more 16-core nodes.
+More details follow.</p>
+<p>use a C++11 compatible compiler
+make yes-kokkos
+make mpi KOKKOS_DEVICES=OpenMP # build with the KOKKOS package
+make kokkos_omp # or Makefile.kokkos_omp already has variable set
+Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi # or one-line build via Make.py</p>
+<div class="highlight-python"><div class="highlight"><pre>mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no threads
+mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task
+mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task
+mpirun -np 32 -ppn 4 lmp_mpi -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task
+</pre></div>
+</div>
<ul class="simple">
<li>specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support</li>
<li>include the KOKKOS package and build LAMMPS</li>
<li>enable the KOKKOS package and its hardware options via the “-k on” command-line switch use KOKKOS styles in your input script</li>
</ul>
-<p>The latter two steps can be done using the “-k on”, “-pk kokkos” and
-“-sf kk” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a>
-respectively. Or the effect of the “-pk” or “-sf” switches can be
-duplicated by adding the <a class="reference internal" href="package.html"><em>package kokkos</em></a> or <a class="reference internal" href="suffix.html"><em>suffix kk</em></a> commands respectively to your input script.</p>
+<p>Here is a quick overview of how to use the KOKKOS package for GPUs,
+assuming one or more nodes, each with 16 cores and a GPU. More
+details follow.</p>
+<p>discuss use of NVCC, which Makefiles to examine</p>
+<p>use a C++11 compatible compiler
+KOKKOS_DEVICES = Cuda, OpenMP
+KOKKOS_ARCH = Kepler35
+make yes-kokkos
+make machine
+Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda</p>
+<div class="highlight-python"><div class="highlight"><pre>mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj # one MPI task, 6 threads on CPU
+mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj # ditto on 4 nodes
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # two MPI tasks, 8 threads per CPU
+mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # ditto on 16 nodes
+</pre></div>
+</div>
+<p>Here is a quick overview of how to use the KOKKOS package
+for the Intel Phi:</p>
+<div class="highlight-python"><div class="highlight"><pre>use a C++11 compatible compiler
+KOKKOS_DEVICES = OpenMP
+KOKKOS_ARCH = KNC
+make yes-kokkos
+make machine
+Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi
+</pre></div>
+</div>
+<p>host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
+mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240
+mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj # 30 MPI tasks on 1 Phi, 30*8 = 240
+mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj # 12 MPI tasks on 1 Phi, 12*20 = 240
+mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis</p>
<p><strong>Required hardware/software:</strong></p>
-<p>The KOKKOS package can be used to build and run LAMMPS on the
-following kinds of hardware:</p>
-<ul class="simple">
-<li>CPU-only: one MPI task per CPU core (MPI-only, but using KOKKOS styles)</li>
-<li>CPU-only: one or a few MPI tasks per node with additional threading via OpenMP</li>
-<li>Phi: on one or more Intel Phi coprocessors (per node)</li>
-<li>GPU: on the GPUs of a node with additional OpenMP threading on the CPUs</li>
-</ul>
<p>Kokkos support within LAMMPS must be built with a C++11 compatible
compiler. If using gcc, version 4.8.1 or later is required.</p>
-<p>Note that Intel Xeon Phi coprocessors are supported in “native” mode,
-not “offload” mode like the USER-INTEL package supports.</p>
-<p>Only NVIDIA GPUs are currently supported.</p>
+<p>To build with Kokkos support for CPUs, your compiler must support the
+OpenMP interface. You should have one or more multi-core CPUs so that
+multiple threads can be launched by each MPI task running on a CPU.</p>
+<p>To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
+version 6.5 or later must be installed on your system. See the
+discussion for the <a class="reference internal" href="accelerate_cuda.html"><em>USER-CUDA</em></a> and
+<a class="reference internal" href="accelerate_gpu.html"><em>GPU</em></a> packages for details of how to check and do
+this.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">For good performance of the KOKKOS package on GPUs,
you must have Kepler generation GPUs (or later). The Kokkos library
exploits texture cache options not supported by Telsa generation GPUs
(or older).</p>
</div>
-<p>To build the KOKKOS package for GPUs, NVIDIA Cuda software version 6.5 or later must be
-installed on your system. See the discussion above for the USER-CUDA
-and GPU packages for details of how to check and do this.</p>
+<p>To build with Kokkos support for Intel Xeon Phi coprocessors, your
+sysmte must be configured to use them in “native” mode, not “offload”
+mode like the USER-INTEL package supports.</p>
<p><strong>Building LAMMPS with the KOKKOS package:</strong></p>
-<p>You must choose at build time whether to build for OpenMP, Cuda, or
-Phi.</p>
+<p>You must choose at build time whether to build for CPUs (OpenMP),
+GPUs, or Phi.</p>
<p>You can do any of these in one line, using the src/Make.py script,
described in <a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a> of the manual.
Type “Make.py -h” for help. If run from the src directory, these
commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and
lmp_kokkos_phi. Note that the OMP and PHI options use
src/MAKE/Makefile.mpi as the starting Makefile.machine. The CUDA
option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda.</p>
-<div class="highlight-python"><div class="highlight"><pre>Make.py -p kokkos -kokkos omp -o kokkos_omp -a file mpi
-Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda
-Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi
-</pre></div>
-</div>
+<p>The latter two steps can be done using the “-k on”, “-pk kokkos” and
+“-sf kk” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a>
+respectively. Or the effect of the “-pk” or “-sf” switches can be
+duplicated by adding the <a class="reference internal" href="package.html"><em>package kokkos</em></a> or <a class="reference internal" href="suffix.html"><em>suffix kk</em></a> commands respectively to your input script.</p>
<p>Or you can follow these steps:</p>
<p>CPU-only (run all-MPI or with OpenMP threading):</p>
<div class="highlight-python"><div class="highlight"><pre>cd lammps/src
make yes-kokkos
make g++ KOKKOS_DEVICES=OpenMP
</pre></div>
</div>
<p>Intel Xeon Phi:</p>
<div class="highlight-python"><div class="highlight"><pre>cd lammps/src
make yes-kokkos
make g++ KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=KNC
</pre></div>
</div>
<p>CPUs and GPUs:</p>
<div class="highlight-python"><div class="highlight"><pre>cd lammps/src
make yes-kokkos
make cuda KOKKOS_DEVICES=Cuda
</pre></div>
</div>
<p>These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
make command line which requires a GNU-compatible make command. Try
“gmake” if your system’s standard make complains.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If you build using make line variables and re-build
LAMMPS twice with different KOKKOS options and the <em>same</em> target,
e.g. g++ in the first two examples above, then you <em>must</em> perform a
“make clean-all” or “make clean-machine” before each build. This is
to force all the KOKKOS-dependent files to be re-compiled with the new
options.</p>
</div>
<p>You can also hardwire these make variables in the specified machine
makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
with a line like:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">KOKKOS_ARCH</span> <span class="o">=</span> <span class="n">KNC</span>
</pre></div>
</div>
<p>Note that if you build LAMMPS multiple times in this manner, using
different KOKKOS options (defined in different machine makefiles), you
do not have to worry about doing a “clean” in between. This is
because the targets will be different.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The 3rd example above for a GPU, uses a different
machine makefile, in this case src/MAKE/Makefile.cuda, which is
included in the LAMMPS distribution. To build the KOKKOS package for
a GPU, this makefile must use the NVIDA “nvcc” compiler. And it must
have a KOKKOS_ARCH setting that is appropriate for your NVIDIA
hardware and installed software. Typical values for KOKKOS_ARCH are given
below, as well
as other settings that must be included in the machine makefile, if
you create your own.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Currently, there are no precision options with the
KOKKOS package. All compilation and computation is performed in
double precision.</p>
</div>
<p>There are other allowed options when building with the KOKKOS package.
As above, they can be set either as variables on the make command line
or in Makefile.machine. This is the full list of options, including
those discussed above, Each takes a value shown below. The
default value is listed, which is set in the
lib/kokkos/Makefile.kokkos file.</p>
<p>#Default settings specific options
#Options: force_uvm,use_ldg,rdc</p>
<ul class="simple">
<li>KOKKOS_DEVICES, values = <em>OpenMP</em>, <em>Serial</em>, <em>Pthreads</em>, <em>Cuda</em>, default = <em>OpenMP</em></li>
<li>KOKKOS_ARCH, values = <em>KNC</em>, <em>SNB</em>, <em>HSW</em>, <em>Kepler</em>, <em>Kepler30</em>, <em>Kepler32</em>, <em>Kepler35</em>, <em>Kepler37</em>, <em>Maxwell</em>, <em>Maxwell50</em>, <em>Maxwell52</em>, <em>Maxwell53</em>, <em>ARMv8</em>, <em>BGQ</em>, <em>Power7</em>, <em>Power8</em>, default = <em>none</em></li>
<li>KOKKOS_DEBUG, values = <em>yes</em>, <em>no</em>, default = <em>no</em></li>
<li>KOKKOS_USE_TPLS, values = <em>hwloc</em>, <em>librt</em>, default = <em>none</em></li>
<li>KOKKOS_CUDA_OPTIONS, values = <em>force_uvm</em>, <em>use_ldg</em>, <em>rdc</em></li>
</ul>
<p>KOKKOS_DEVICE sets the parallelization method used for Kokkos code
(within LAMMPS). KOKKOS_DEVICES=OpenMP means that OpenMP will be
used. KOKKOS_DEVICES=Pthreads means that pthreads will be used.
KOKKOS_DEVICES=Cuda means an NVIDIA GPU running CUDA will be used.</p>
<p>If KOKKOS_DEVICES=Cuda, then the lo-level Makefile in the src/MAKE
directory must use “nvcc” as its compiler, via its CC setting. For
best performance its CCFLAGS setting should use -O3 and have a
KOKKOS_ARCH setting that matches the compute capability of your NVIDIA
hardware and software installation, e.g. KOKKOS_ARCH=Kepler30. Note
the minimal required compute capability is 2.0, but this will give
signicantly reduced performance compared to Kepler generation GPUs
with compute capability 3.x. For the LINK setting, “nvcc” should not
be used; instead use g++ or another compiler suitable for linking C++
applications. Often you will want to use your MPI compiler wrapper
for this setting (i.e. mpicxx). Finally, the lo-level Makefile must
also have a “Compilation rule” for creating <a href="#id1"><span class="problematic" id="id2">*</span></a>.o files from <a href="#id3"><span class="problematic" id="id4">*</span></a>.cu files.
See src/Makefile.cuda for an example of a lo-level Makefile with all
of these settings.</p>
<p>KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be
used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
provides alternative methods via environment variables for binding
threads to hardware cores. More info on binding threads to cores is
given in <span class="xref std std-ref">this section</span>.</p>
<p>KOKKOS_ARCH=KNC enables compiler switches needed when compling for an
Intel Phi processor.</p>
<p>KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
on most Unix platforms. This library is not available on all
platforms.</p>
<p>KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style
within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time
debugging information that can be useful. It also enables runtime
bounds checking on Kokkos data structures.</p>
<p>KOKKOS_CUDA_OPTIONS are additional options for CUDA.</p>
<p>For more information on Kokkos see the Kokkos programmers’ guide here:
/lib/kokkos/doc/Kokkos_PG.pdf.</p>
<p><strong>Run with the KOKKOS package from the command line:</strong></p>
<p>The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.</p>
<p>When using KOKKOS built with host=OMP, you need to choose how many
OpenMP threads per MPI task will be used (via the “-k” command-line
switch discussed below). Note that the product of MPI tasks * OpenMP
threads/task should not exceed the physical number of cores (on a
node), otherwise performance will suffer.</p>
<p>When using the KOKKOS package built with device=CUDA, you must use
exactly one MPI task per physical GPU.</p>
<p>When using the KOKKOS package built with host=MIC for Intel Xeon Phi
coprocessor support you need to insure there are one or more MPI tasks
per coprocessor, and choose the number of coprocessor threads to use
per MPI task (via the “-k” command-line switch discussed below). The
product of MPI tasks * coprocessor threads/task should not exceed the
maximum number of threads the coproprocessor is designed to run,
otherwise performance will suffer. This value is 240 for current
generation Xeon Phi(TM) chips, which is 60 physical cores * 4
threads/core. Note that with the KOKKOS package you do not need to
specify how many Phi coprocessors there are per node; each
coprocessors is simply treated as running some number of MPI tasks.</p>
<p>You must use the “-k on” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> to enable the KOKKOS package. It
takes additional arguments for hardware settings appropriate to your
system. Those arguments are <a class="reference internal" href="Section_start.html#start-7"><span>documented here</span></a>. The two most commonly used
options are:</p>
<div class="highlight-python"><div class="highlight"><pre>-k on t Nt g Ng
</pre></div>
</div>
<p>The “t Nt” option applies to host=OMP (even if device=CUDA) and
host=MIC. For host=OMP, it specifies how many OpenMP threads per MPI
task to use with a node. For host=MIC, it specifies how many Xeon Phi
threads per MPI task to use within a node. The default is Nt = 1.
Note that for host=OMP this is effectively MPI-only mode which may be
fine. But for host=MIC you will typically end up using far less than
all the 240 available threads, which could give very poor performance.</p>
<p>The “g Ng” option applies to device=CUDA. It specifies how many GPUs
per compute node to use. The default is 1, so this only needs to be
specified is you have 2 or more GPUs per compute node.</p>
<p>The “-k on” switch also issues a “package kokkos” command (with no
additional arguments) which sets various KOKKOS options to default
values, as discussed on the <a class="reference internal" href="package.html"><em>package</em></a> command doc page.</p>
<p>Use the “-sf kk” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>,
which will automatically append “kk” to styles that support it. Use
the “-pk kokkos” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> if
you wish to change any of the default <a class="reference internal" href="package.html"><em>package kokkos</em></a>
optionns set by the “-k on” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>.</p>
-<div class="highlight-python"><div class="highlight"><pre>host=OMP, dual hex-core nodes (12 threads/node):
-mpirun -np 12 lmp_g++ -in in.lj # MPI-only mode with no Kokkos
-mpirun -np 12 lmp_g++ -k on -sf kk -in in.lj # MPI-only mode with Kokkos
-mpirun -np 1 lmp_g++ -k on t 12 -sf kk -in in.lj # one MPI task, 12 threads
-mpirun -np 2 lmp_g++ -k on t 6 -sf kk -in in.lj # two MPI tasks, 6 threads/task
-mpirun -np 32 -ppn 2 lmp_g++ -k on t 6 -sf kk -in in.lj # ditto on 16 nodes
-</pre></div>
-</div>
-<p>host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
-mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240
-mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj # 30 MPI tasks on 1 Phi, 30*8 = 240
-mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj # 12 MPI tasks on 1 Phi, 12*20 = 240
-mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis</p>
-<div class="highlight-python"><div class="highlight"><pre>host=OMP, device=CUDA, node = dual hex-core CPUs and a single GPU:
-mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj # one MPI task, 6 threads on CPU
-mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj # ditto on 4 nodes
-</pre></div>
-</div>
-<div class="highlight-python"><div class="highlight"><pre>host=OMP, device=CUDA, node = dual 8-core CPUs and 2 GPUs:
-mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # two MPI tasks, 8 threads per CPU
-mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # ditto on 16 nodes
-</pre></div>
-</div>
<p>Note that the default for the <a class="reference internal" href="package.html"><em>package kokkos</em></a> command is
to use “full” neighbor lists and set the Newton flag to “off” for both
pairwise and bonded interactions. This typically gives fastest
performance. If the <a class="reference internal" href="newton.html"><em>newton</em></a> command is used in the input
script, it can override the Newton flag defaults.</p>
<p>However, when running in MPI-only mode with 1 thread per MPI task, it
will typically be faster to use “half” neighbor lists and set the
Newton flag to “on”, just as is the case for non-accelerated pair
styles. You can do this with the “-pk” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>.</p>
<p><strong>Or run with the KOKKOS package by editing an input script:</strong></p>
<p>The discussion above for the mpirun/mpiexec command and setting
appropriate thread and GPU values for host=OMP or host=MIC or
device=CUDA are the same.</p>
<p>You must still use the “-k on” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> to enable the KOKKOS package, and
specify its additional arguments for hardware options appopriate to
your system, as documented above.</p>
<p>Use the <a class="reference internal" href="suffix.html"><em>suffix kk</em></a> command, or you can explicitly add a
“kk” suffix to individual styles in your input script, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/kk 2.5
</pre></div>
</div>
<p>You only need to use the <a class="reference internal" href="package.html"><em>package kokkos</em></a> command if you
wish to change any of its option defaults, as set by the “-k on”
<a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>.</p>
<p><strong>Speed-ups to expect:</strong></p>
<p>The performance of KOKKOS running in different modes is a function of
your hardware, which KOKKOS-enable styles are used, and the problem
size.</p>
<p>Generally speaking, the following rules of thumb apply:</p>
<ul class="simple">
<li>When running on CPUs only, with a single thread per MPI task,
performance of a KOKKOS style is somewhere between the standard
(un-accelerated) styles (MPI-only mode), and those provided by the
USER-OMP package. However the difference between all 3 is small (less
than 20%).</li>
<li>When running on CPUs only, with multiple threads per MPI task,
performance of a KOKKOS style is a bit slower than the USER-OMP
package.</li>
<li>When running on GPUs, KOKKOS is typically faster than the USER-CUDA
and GPU packages.</li>
<li>When running on Intel Xeon Phi, KOKKOS is not as fast as
the USER-INTEL package, which is optimized for that hardware.</li>
</ul>
<p>See the <a class="reference external" href="http://lammps.sandia.gov/bench.html">Benchmark page</a> of the
LAMMPS web site for performance of the KOKKOS package on different
hardware.</p>
<p><strong>Guidelines for best performance:</strong></p>
<p>Here are guidline for using the KOKKOS package on the different
hardware configurations listed above.</p>
<p>Many of the guidelines use the <a class="reference internal" href="package.html"><em>package kokkos</em></a> command
See its doc page for details and default settings. Experimenting with
its options can provide a speed-up for specific calculations.</p>
<p><strong>Running on a multi-core CPU:</strong></p>
<p>If N is the number of physical cores/node, then the number of MPI
tasks/node * number of threads/task should not exceed N, and should
typically equal N. Note that the default threads/task is 1, as set by
the “t” keyword of the “-k” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>. If you do not change this, no
additional parallelism (beyond MPI) will be invoked on the host
CPU(s).</p>
<p>You can compare the performance running in different modes:</p>
<ul class="simple">
<li>run with 1 MPI task/node and N threads/task</li>
<li>run with N MPI tasks/node and 1 thread/task</li>
<li>run with settings in between these extremes</li>
</ul>
<p>Examples of mpirun commands in these modes are shown above.</p>
<p>When using KOKKOS to perform multi-threading, it is important for
performance to bind both MPI tasks to physical cores, and threads to
physical cores, so they do not migrate during a simulation.</p>
<p>If you are not certain MPI tasks are being bound (check the defaults
for your MPI installation), binding can be forced with these flags:</p>
<div class="highlight-python"><div class="highlight"><pre>OpenMPI 1.8: mpirun -np 2 -bind-to socket -map-by socket ./lmp_openmpi ...
Mvapich2 2.0: mpiexec -np 2 -bind-to socket -map-by socket ./lmp_mvapich ...
</pre></div>
</div>
<p>For binding threads with the KOKKOS OMP option, use thread affinity
environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
later, intel 12 or later) setting the environment variable
OMP_PROC_BIND=true should be sufficient. For binding threads with the
KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option, as
discussed in <a class="reference internal" href="Section_start.html#start-3-4"><span>Section 2.3.4</span></a> of the
manual.</p>
<p><strong>Running on GPUs:</strong></p>
<p>Insure the -arch setting in the machine makefile you are using,
e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software
(see <a class="reference internal" href="Section_start.html#start-3-4"><span>this section</span></a> of the manual for
details).</p>
<p>The -np setting of the mpirun command should set the number of MPI
tasks/node to be equal to the # of physical GPUs on the node.</p>
<p>Use the “-k” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> to
specify the number of GPUs per node, and the number of threads per MPI
task. As above for multi-core CPUs (and no GPU), if N is the number
of physical cores/node, then the number of MPI tasks/node * number of
threads/task should not exceed N. With one GPU (and one MPI task) it
may be faster to use less than all the available cores, by setting
threads/task to a smaller value. This is because using all the cores
on a dual-socket node will incur extra cost to copy memory from the
2nd socket to the GPU.</p>
<p>Examples of mpirun commands that follow these rules are shown above.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">When using a GPU, you will achieve the best
performance if your input script does not use any fix or compute
styles which are not yet Kokkos-enabled. This allows data to stay on
the GPU for multiple timesteps, without being copied back to the host
CPU. Invoking a non-Kokkos fix or compute, or performing I/O for
<a class="reference internal" href="thermo_style.html"><em>thermo</em></a> or <a class="reference internal" href="dump.html"><em>dump</em></a> output will cause data
to be copied back to the CPU.</p>
</div>
<p>You cannot yet assign multiple MPI tasks to the same GPU with the
KOKKOS package. We plan to support this in the future, similar to the
GPU package in LAMMPS.</p>
<p>You cannot yet use both the host (multi-threaded) and device (GPU)
together to compute pairwise interactions with the KOKKOS package. We
hope to support this in the future, similar to the GPU package in
LAMMPS.</p>
<p><strong>Running on an Intel Phi:</strong></p>
<p>Kokkos only uses Intel Phi processors in their “native” mode, i.e.
not hosted by a CPU.</p>
<p>As illustrated above, build LAMMPS with OMP=yes (the default) and
MIC=yes. The latter insures code is correctly compiled for the Intel
Phi. The OMP setting means OpenMP will be used for parallelization on
the Phi, which is currently the best option within Kokkos. In the
future, other options may be added.</p>
<p>Current-generation Intel Phi chips have either 61 or 57 cores. One
core should be excluded for running the OS, leaving 60 or 56 cores.
Each core is hyperthreaded, so there are effectively N = 240 (4*60) or
N = 224 (4*56) cores to run on.</p>
<p>The -np setting of the mpirun command sets the number of MPI
tasks/node. The “-k on t Nt” command-line switch sets the number of
threads/task as Nt. The product of these 2 values should be N, i.e.
240 or 224. Also, the number of threads/task should be a multiple of
4 so that logical threads from more than one MPI task do not run on
the same physical core.</p>
<p>Examples of mpirun commands that follow these rules are shown above.</p>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>As noted above, if using GPUs, the number of MPI tasks per compute
node should equal to the number of GPUs per compute node. In the
future Kokkos will support assigning multiple MPI tasks to a single
GPU.</p>
<p>Currently Kokkos does not support AMD GPUs due to limits in the
available backend programming models. Specifically, Kokkos requires
extensive C++ support from the Kernel language. This is expected to
change in the future.</p>
</div>
</div>
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\ No newline at end of file
diff --git a/doc/accelerate_kokkos.txt b/doc/accelerate_kokkos.txt
index dd9143bc6..4ca026f31 100644
--- a/doc/accelerate_kokkos.txt
+++ b/doc/accelerate_kokkos.txt
@@ -1,504 +1,516 @@
"Previous Section"_Section_packages.html - "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
"Return to Section accelerate overview"_Section_accelerate.html
5.3.4 KOKKOS package :h4
-The KOKKOS package was developed primaritly by Christian Trott
-(Sandia) with contributions of various styles by others, including
-Sikandar Mashayak (UIUC), Stan Moore (Sandia), and Ray Shan (Sandia).
-The underlying Kokkos library was written
-primarily by Carter Edwards, Christian Trott, and Dan Sunderland (all
-Sandia).
+The KOKKOS package was developed primarily by Christian Trott (Sandia)
+with contributions of various styles by others, including Sikandar
+Mashayak (UIUC), Stan Moore (Sandia), and Ray Shan (Sandia). The
+underlying Kokkos library was written primarily by Carter Edwards,
+Christian Trott, and Dan Sunderland (all Sandia).
The KOKKOS package contains versions of pair, fix, and atom styles
that use data structures and macros provided by the Kokkos library,
which is included with LAMMPS in lib/kokkos.
The Kokkos library is part of
-"Trilinos"_http://trilinos.sandia.gov/packages/kokkos and can also
-be downloaded from "Github"_https://github.com/kokkos/kokkos. Kokkos is a
+"Trilinos"_http://trilinos.sandia.gov/packages/kokkos and can also be
+downloaded from "Github"_https://github.com/kokkos/kokkos. Kokkos is a
templated C++ library that provides two key abstractions for an
application like LAMMPS. First, it allows a single implementation of
an application kernel (e.g. a pair style) to run efficiently on
different kinds of hardware, such as a GPU, Intel Phi, or many-core
-chip.
+CPU.
The Kokkos library also provides data abstractions to adjust (at
compile time) the memory layout of basic data structures like 2d and
3d arrays and allow the transparent utilization of special hardware
load and store operations. Such data structures are used in LAMMPS to
store atom coordinates or forces or neighbor lists. The layout is
chosen to optimize performance on different platforms. Again this
functionality is hidden from the developer, and does not affect how
the kernel is coded.
These abstractions are set at build time, when LAMMPS is compiled with
-the KOKKOS package installed. This is done by selecting a "host" and
-"device" to build for, compatible with the compute nodes in your
-machine (one on a desktop machine or 1000s on a supercomputer).
-
-All Kokkos operations occur within the context of an individual MPI
-task running on a single node of the machine. The total number of MPI
-tasks used by LAMMPS (one or multiple per compute node) is set in the
-usual manner via the mpirun or mpiexec commands, and is independent of
-Kokkos.
-
-Kokkos provides support for two different modes of execution per MPI
-task. This means that computational tasks (pairwise interactions,
-neighbor list builds, time integration, etc) can be parallelized for
-one or the other of the two modes. The first mode is called the
-"host" and is one or more threads running on one or more physical CPUs
-(within the node). Currently, both multi-core CPUs and an Intel Phi
-processor (running in native mode, not offload mode like the
-USER-INTEL package) are supported. The second mode is called the
-"device" and is an accelerator chip of some kind. Currently only an
-NVIDIA GPU is supported via Cuda. If your compute node does not have
-a GPU, then there is only one mode of execution, i.e. the host and
-device are the same.
-
-When using the KOKKOS package, you must choose at build time whether
-you are building for OpenMP, GPU, or for using the Xeon Phi in native
-mode.
-
-Here is a quick overview of how to use the KOKKOS package:
+the KOKKOS package installed. All Kokkos operations occur within the
+context of an individual MPI task running on a single node of the
+machine. The total number of MPI tasks used by LAMMPS (one or
+multiple per compute node) is set in the usual manner via the mpirun
+or mpiexec commands, and is independent of Kokkos.
+
+Kokkos currently provides support for 3 modes of execution (per MPI
+task). These are OpenMP (for many-core CPUs), Cuda (for NVIDIA GPUs),
+and OpenMP (for Intel Phi). Note that the KOKKOS package supports
+running on the Phi in native mode, not offload mode like the
+USER-INTEL package supports. You choose the mode at build time to
+produce an executable compatible with specific hardware.
+
+Here is a quick overview of how to use the KOKKOS package
+for CPU acceleration, assuming one or more 16-core nodes.
+More details follow.
+
+use a C++11 compatible compiler
+make yes-kokkos
+make mpi KOKKOS_DEVICES=OpenMP # build with the KOKKOS package
+make kokkos_omp # or Makefile.kokkos_omp already has variable set
+Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi # or one-line build via Make.py
+
+mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no threads
+mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task
+mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task
+mpirun -np 32 -ppn 4 lmp_mpi -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
+
+
+
specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support
include the KOKKOS package and build LAMMPS
enable the KOKKOS package and its hardware options via the "-k on" command-line switch use KOKKOS styles in your input script :ul
-The latter two steps can be done using the "-k on", "-pk kokkos" and
-"-sf kk" "command-line switches"_Section_start.html#start_7
-respectively. Or the effect of the "-pk" or "-sf" switches can be
-duplicated by adding the "package kokkos"_package.html or "suffix
-kk"_suffix.html commands respectively to your input script.
+Here is a quick overview of how to use the KOKKOS package for GPUs,
+assuming one or more nodes, each with 16 cores and a GPU. More
+details follow.
-[Required hardware/software:]
+discuss use of NVCC, which Makefiles to examine
+
+use a C++11 compatible compiler
+KOKKOS_DEVICES = Cuda, OpenMP
+KOKKOS_ARCH = Kepler35
+make yes-kokkos
+make machine
+Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda
+
+mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj # one MPI task, 6 threads on CPU
+mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj # ditto on 4 nodes :pre
+
+mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # two MPI tasks, 8 threads per CPU
+mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # ditto on 16 nodes :pre
+
+Here is a quick overview of how to use the KOKKOS package
+for the Intel Phi:
+
+use a C++11 compatible compiler
+KOKKOS_DEVICES = OpenMP
+KOKKOS_ARCH = KNC
+make yes-kokkos
+make machine
+Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi :pre
+
+host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
+mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240
+mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj # 30 MPI tasks on 1 Phi, 30*8 = 240
+mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj # 12 MPI tasks on 1 Phi, 12*20 = 240
+mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis
-The KOKKOS package can be used to build and run LAMMPS on the
-following kinds of hardware:
-CPU-only: one MPI task per CPU core (MPI-only, but using KOKKOS styles)
-CPU-only: one or a few MPI tasks per node with additional threading via OpenMP
-Phi: on one or more Intel Phi coprocessors (per node)
-GPU: on the GPUs of a node with additional OpenMP threading on the CPUs :ul
+[Required hardware/software:]
Kokkos support within LAMMPS must be built with a C++11 compatible
compiler. If using gcc, version 4.8.1 or later is required.
-Note that Intel Xeon Phi coprocessors are supported in "native" mode,
-not "offload" mode like the USER-INTEL package supports.
+To build with Kokkos support for CPUs, your compiler must support the
+OpenMP interface. You should have one or more multi-core CPUs so that
+multiple threads can be launched by each MPI task running on a CPU.
-Only NVIDIA GPUs are currently supported.
+To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
+version 6.5 or later must be installed on your system. See the
+discussion for the "USER-CUDA"_accelerate_cuda.html and
+"GPU"_accelerate_gpu.html packages for details of how to check and do
+this.
IMPORTANT NOTE: For good performance of the KOKKOS package on GPUs,
you must have Kepler generation GPUs (or later). The Kokkos library
exploits texture cache options not supported by Telsa generation GPUs
(or older).
-To build the KOKKOS package for GPUs, NVIDIA Cuda software version 6.5 or later must be
-installed on your system. See the discussion above for the USER-CUDA
-and GPU packages for details of how to check and do this.
+To build with Kokkos support for Intel Xeon Phi coprocessors, your
+sysmte must be configured to use them in "native" mode, not "offload"
+mode like the USER-INTEL package supports.
[Building LAMMPS with the KOKKOS package:]
-You must choose at build time whether to build for OpenMP, Cuda, or
-Phi.
+You must choose at build time whether to build for CPUs (OpenMP),
+GPUs, or Phi.
You can do any of these in one line, using the src/Make.py script,
described in "Section 2.4"_Section_start.html#start_4 of the manual.
Type "Make.py -h" for help. If run from the src directory, these
commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and
lmp_kokkos_phi. Note that the OMP and PHI options use
src/MAKE/Makefile.mpi as the starting Makefile.machine. The CUDA
option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda.
-Make.py -p kokkos -kokkos omp -o kokkos_omp -a file mpi
-Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda
-Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi :pre
+The latter two steps can be done using the "-k on", "-pk kokkos" and
+"-sf kk" "command-line switches"_Section_start.html#start_7
+respectively. Or the effect of the "-pk" or "-sf" switches can be
+duplicated by adding the "package kokkos"_package.html or "suffix
+kk"_suffix.html commands respectively to your input script.
+
Or you can follow these steps:
CPU-only (run all-MPI or with OpenMP threading):
cd lammps/src
make yes-kokkos
make g++ KOKKOS_DEVICES=OpenMP :pre
Intel Xeon Phi:
cd lammps/src
make yes-kokkos
make g++ KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=KNC :pre
CPUs and GPUs:
cd lammps/src
make yes-kokkos
make cuda KOKKOS_DEVICES=Cuda :pre
These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
make command line which requires a GNU-compatible make command. Try
"gmake" if your system's standard make complains.
IMPORTANT NOTE: If you build using make line variables and re-build
LAMMPS twice with different KOKKOS options and the *same* target,
e.g. g++ in the first two examples above, then you *must* perform a
"make clean-all" or "make clean-machine" before each build. This is
to force all the KOKKOS-dependent files to be re-compiled with the new
options.
You can also hardwire these make variables in the specified machine
makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
with a line like:
KOKKOS_ARCH = KNC :pre
Note that if you build LAMMPS multiple times in this manner, using
different KOKKOS options (defined in different machine makefiles), you
do not have to worry about doing a "clean" in between. This is
because the targets will be different.
IMPORTANT NOTE: The 3rd example above for a GPU, uses a different
machine makefile, in this case src/MAKE/Makefile.cuda, which is
included in the LAMMPS distribution. To build the KOKKOS package for
a GPU, this makefile must use the NVIDA "nvcc" compiler. And it must
have a KOKKOS_ARCH setting that is appropriate for your NVIDIA
hardware and installed software. Typical values for KOKKOS_ARCH are given
below, as well
as other settings that must be included in the machine makefile, if
you create your own.
IMPORTANT NOTE: Currently, there are no precision options with the
KOKKOS package. All compilation and computation is performed in
double precision.
There are other allowed options when building with the KOKKOS package.
As above, they can be set either as variables on the make command line
or in Makefile.machine. This is the full list of options, including
those discussed above, Each takes a value shown below. The
default value is listed, which is set in the
lib/kokkos/Makefile.kokkos file.
#Default settings specific options
#Options: force_uvm,use_ldg,rdc
KOKKOS_DEVICES, values = {OpenMP}, {Serial}, {Pthreads}, {Cuda}, default = {OpenMP}
KOKKOS_ARCH, values = {KNC}, {SNB}, {HSW}, {Kepler}, {Kepler30}, {Kepler32}, {Kepler35}, {Kepler37}, {Maxwell}, {Maxwell50}, {Maxwell52}, {Maxwell53}, {ARMv8}, {BGQ}, {Power7}, {Power8}, default = {none}
KOKKOS_DEBUG, values = {yes}, {no}, default = {no}
KOKKOS_USE_TPLS, values = {hwloc}, {librt}, default = {none}
KOKKOS_CUDA_OPTIONS, values = {force_uvm}, {use_ldg}, {rdc} :ul
KOKKOS_DEVICE sets the parallelization method used for Kokkos code
(within LAMMPS). KOKKOS_DEVICES=OpenMP means that OpenMP will be
used. KOKKOS_DEVICES=Pthreads means that pthreads will be used.
KOKKOS_DEVICES=Cuda means an NVIDIA GPU running CUDA will be used.
If KOKKOS_DEVICES=Cuda, then the lo-level Makefile in the src/MAKE
directory must use "nvcc" as its compiler, via its CC setting. For
best performance its CCFLAGS setting should use -O3 and have a
KOKKOS_ARCH setting that matches the compute capability of your NVIDIA
hardware and software installation, e.g. KOKKOS_ARCH=Kepler30. Note
the minimal required compute capability is 2.0, but this will give
signicantly reduced performance compared to Kepler generation GPUs
with compute capability 3.x. For the LINK setting, "nvcc" should not
be used; instead use g++ or another compiler suitable for linking C++
applications. Often you will want to use your MPI compiler wrapper
for this setting (i.e. mpicxx). Finally, the lo-level Makefile must
also have a "Compilation rule" for creating *.o files from *.cu files.
See src/Makefile.cuda for an example of a lo-level Makefile with all
of these settings.
KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be
used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
provides alternative methods via environment variables for binding
threads to hardware cores. More info on binding threads to cores is
given in "this section"_Section_accelerate.html#acc_8.
KOKKOS_ARCH=KNC enables compiler switches needed when compling for an
Intel Phi processor.
KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
on most Unix platforms. This library is not available on all
platforms.
KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style
within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time
debugging information that can be useful. It also enables runtime
bounds checking on Kokkos data structures.
KOKKOS_CUDA_OPTIONS are additional options for CUDA.
For more information on Kokkos see the Kokkos programmers' guide here:
/lib/kokkos/doc/Kokkos_PG.pdf.
[Run with the KOKKOS package from the command line:]
The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
When using KOKKOS built with host=OMP, you need to choose how many
OpenMP threads per MPI task will be used (via the "-k" command-line
switch discussed below). Note that the product of MPI tasks * OpenMP
threads/task should not exceed the physical number of cores (on a
node), otherwise performance will suffer.
When using the KOKKOS package built with device=CUDA, you must use
exactly one MPI task per physical GPU.
When using the KOKKOS package built with host=MIC for Intel Xeon Phi
coprocessor support you need to insure there are one or more MPI tasks
per coprocessor, and choose the number of coprocessor threads to use
per MPI task (via the "-k" command-line switch discussed below). The
product of MPI tasks * coprocessor threads/task should not exceed the
maximum number of threads the coproprocessor is designed to run,
otherwise performance will suffer. This value is 240 for current
generation Xeon Phi(TM) chips, which is 60 physical cores * 4
threads/core. Note that with the KOKKOS package you do not need to
specify how many Phi coprocessors there are per node; each
coprocessors is simply treated as running some number of MPI tasks.
You must use the "-k on" "command-line
switch"_Section_start.html#start_7 to enable the KOKKOS package. It
takes additional arguments for hardware settings appropriate to your
system. Those arguments are "documented
here"_Section_start.html#start_7. The two most commonly used
options are:
-k on t Nt g Ng :pre
The "t Nt" option applies to host=OMP (even if device=CUDA) and
host=MIC. For host=OMP, it specifies how many OpenMP threads per MPI
task to use with a node. For host=MIC, it specifies how many Xeon Phi
threads per MPI task to use within a node. The default is Nt = 1.
Note that for host=OMP this is effectively MPI-only mode which may be
fine. But for host=MIC you will typically end up using far less than
all the 240 available threads, which could give very poor performance.
The "g Ng" option applies to device=CUDA. It specifies how many GPUs
per compute node to use. The default is 1, so this only needs to be
specified is you have 2 or more GPUs per compute node.
The "-k on" switch also issues a "package kokkos" command (with no
additional arguments) which sets various KOKKOS options to default
values, as discussed on the "package"_package.html command doc page.
Use the "-sf kk" "command-line switch"_Section_start.html#start_7,
which will automatically append "kk" to styles that support it. Use
the "-pk kokkos" "command-line switch"_Section_start.html#start_7 if
you wish to change any of the default "package kokkos"_package.html
optionns set by the "-k on" "command-line
switch"_Section_start.html#start_7.
-host=OMP, dual hex-core nodes (12 threads/node):
-mpirun -np 12 lmp_g++ -in in.lj # MPI-only mode with no Kokkos
-mpirun -np 12 lmp_g++ -k on -sf kk -in in.lj # MPI-only mode with Kokkos
-mpirun -np 1 lmp_g++ -k on t 12 -sf kk -in in.lj # one MPI task, 12 threads
-mpirun -np 2 lmp_g++ -k on t 6 -sf kk -in in.lj # two MPI tasks, 6 threads/task
-mpirun -np 32 -ppn 2 lmp_g++ -k on t 6 -sf kk -in in.lj # ditto on 16 nodes :pre
-
-host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
-mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240
-mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj # 30 MPI tasks on 1 Phi, 30*8 = 240
-mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj # 12 MPI tasks on 1 Phi, 12*20 = 240
-mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis
-
-host=OMP, device=CUDA, node = dual hex-core CPUs and a single GPU:
-mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj # one MPI task, 6 threads on CPU
-mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj # ditto on 4 nodes :pre
-host=OMP, device=CUDA, node = dual 8-core CPUs and 2 GPUs:
-mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # two MPI tasks, 8 threads per CPU
-mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # ditto on 16 nodes :pre
Note that the default for the "package kokkos"_package.html command is
to use "full" neighbor lists and set the Newton flag to "off" for both
pairwise and bonded interactions. This typically gives fastest
performance. If the "newton"_newton.html command is used in the input
script, it can override the Newton flag defaults.
However, when running in MPI-only mode with 1 thread per MPI task, it
will typically be faster to use "half" neighbor lists and set the
Newton flag to "on", just as is the case for non-accelerated pair
styles. You can do this with the "-pk" "command-line
switch"_Section_start.html#start_7.
[Or run with the KOKKOS package by editing an input script:]
The discussion above for the mpirun/mpiexec command and setting
appropriate thread and GPU values for host=OMP or host=MIC or
device=CUDA are the same.
You must still use the "-k on" "command-line
switch"_Section_start.html#start_7 to enable the KOKKOS package, and
specify its additional arguments for hardware options appopriate to
your system, as documented above.
Use the "suffix kk"_suffix.html command, or you can explicitly add a
"kk" suffix to individual styles in your input script, e.g.
pair_style lj/cut/kk 2.5 :pre
You only need to use the "package kokkos"_package.html command if you
wish to change any of its option defaults, as set by the "-k on"
"command-line switch"_Section_start.html#start_7.
[Speed-ups to expect:]
The performance of KOKKOS running in different modes is a function of
your hardware, which KOKKOS-enable styles are used, and the problem
size.
Generally speaking, the following rules of thumb apply:
When running on CPUs only, with a single thread per MPI task,
performance of a KOKKOS style is somewhere between the standard
(un-accelerated) styles (MPI-only mode), and those provided by the
USER-OMP package. However the difference between all 3 is small (less
than 20%). :ulb,l
When running on CPUs only, with multiple threads per MPI task,
performance of a KOKKOS style is a bit slower than the USER-OMP
package. :l
When running on GPUs, KOKKOS is typically faster than the USER-CUDA
and GPU packages. :l
When running on Intel Xeon Phi, KOKKOS is not as fast as
the USER-INTEL package, which is optimized for that hardware. :l,ule
See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the
LAMMPS web site for performance of the KOKKOS package on different
hardware.
[Guidelines for best performance:]
Here are guidline for using the KOKKOS package on the different
hardware configurations listed above.
Many of the guidelines use the "package kokkos"_package.html command
See its doc page for details and default settings. Experimenting with
its options can provide a speed-up for specific calculations.
[Running on a multi-core CPU:]
If N is the number of physical cores/node, then the number of MPI
tasks/node * number of threads/task should not exceed N, and should
typically equal N. Note that the default threads/task is 1, as set by
the "t" keyword of the "-k" "command-line
switch"_Section_start.html#start_7. If you do not change this, no
additional parallelism (beyond MPI) will be invoked on the host
CPU(s).
You can compare the performance running in different modes:
run with 1 MPI task/node and N threads/task
run with N MPI tasks/node and 1 thread/task
run with settings in between these extremes :ul
Examples of mpirun commands in these modes are shown above.
When using KOKKOS to perform multi-threading, it is important for
performance to bind both MPI tasks to physical cores, and threads to
physical cores, so they do not migrate during a simulation.
If you are not certain MPI tasks are being bound (check the defaults
for your MPI installation), binding can be forced with these flags:
OpenMPI 1.8: mpirun -np 2 -bind-to socket -map-by socket ./lmp_openmpi ...
Mvapich2 2.0: mpiexec -np 2 -bind-to socket -map-by socket ./lmp_mvapich ... :pre
For binding threads with the KOKKOS OMP option, use thread affinity
environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
later, intel 12 or later) setting the environment variable
OMP_PROC_BIND=true should be sufficient. For binding threads with the
KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option, as
discussed in "Section 2.3.4"_Sections_start.html#start_3_4 of the
manual.
[Running on GPUs:]
Insure the -arch setting in the machine makefile you are using,
e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software
(see "this section"_Section_start.html#start_3_4 of the manual for
details).
The -np setting of the mpirun command should set the number of MPI
tasks/node to be equal to the # of physical GPUs on the node.
Use the "-k" "command-line switch"_Section_commands.html#start_7 to
specify the number of GPUs per node, and the number of threads per MPI
task. As above for multi-core CPUs (and no GPU), if N is the number
of physical cores/node, then the number of MPI tasks/node * number of
threads/task should not exceed N. With one GPU (and one MPI task) it
may be faster to use less than all the available cores, by setting
threads/task to a smaller value. This is because using all the cores
on a dual-socket node will incur extra cost to copy memory from the
2nd socket to the GPU.
Examples of mpirun commands that follow these rules are shown above.
IMPORTANT NOTE: When using a GPU, you will achieve the best
performance if your input script does not use any fix or compute
styles which are not yet Kokkos-enabled. This allows data to stay on
the GPU for multiple timesteps, without being copied back to the host
CPU. Invoking a non-Kokkos fix or compute, or performing I/O for
"thermo"_thermo_style.html or "dump"_dump.html output will cause data
to be copied back to the CPU.
You cannot yet assign multiple MPI tasks to the same GPU with the
KOKKOS package. We plan to support this in the future, similar to the
GPU package in LAMMPS.
You cannot yet use both the host (multi-threaded) and device (GPU)
together to compute pairwise interactions with the KOKKOS package. We
hope to support this in the future, similar to the GPU package in
LAMMPS.
[Running on an Intel Phi:]
Kokkos only uses Intel Phi processors in their "native" mode, i.e.
not hosted by a CPU.
As illustrated above, build LAMMPS with OMP=yes (the default) and
MIC=yes. The latter insures code is correctly compiled for the Intel
Phi. The OMP setting means OpenMP will be used for parallelization on
the Phi, which is currently the best option within Kokkos. In the
future, other options may be added.
Current-generation Intel Phi chips have either 61 or 57 cores. One
core should be excluded for running the OS, leaving 60 or 56 cores.
Each core is hyperthreaded, so there are effectively N = 240 (4*60) or
N = 224 (4*56) cores to run on.
The -np setting of the mpirun command sets the number of MPI
tasks/node. The "-k on t Nt" command-line switch sets the number of
threads/task as Nt. The product of these 2 values should be N, i.e.
240 or 224. Also, the number of threads/task should be a multiple of
4 so that logical threads from more than one MPI task do not run on
the same physical core.
Examples of mpirun commands that follow these rules are shown above.
[Restrictions:]
As noted above, if using GPUs, the number of MPI tasks per compute
node should equal to the number of GPUs per compute node. In the
future Kokkos will support assigning multiple MPI tasks to a single
GPU.
Currently Kokkos does not support AMD GPUs due to limits in the
available backend programming models. Specifically, Kokkos requires
extensive C++ support from the Kernel language. This is expected to
change in the future.
diff --git a/doc/accelerate_omp.html b/doc/accelerate_omp.html
index 2a78e2f1f..605d44402 100644
--- a/doc/accelerate_omp.html
+++ b/doc/accelerate_omp.html
@@ -1,355 +1,338 @@
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<p><a class="reference internal" href="Section_accelerate.html"><em>Return to Section accelerate overview</em></a></p>
<div class="section" id="user-omp-package">
<h1>5.USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline">¶</a></h1>
<p>The USER-OMP package was developed by Axel Kohlmeyer at Temple
University. It provides multi-threaded versions of most pair styles,
nearly all bonded styles (bond, angle, dihedral, improper), several
-Kspace styles, and a few fix styles. The package currently
-uses the OpenMP interface for multi-threading.</p>
-<p>Here is a quick overview of how to use the USER-OMP package:</p>
-<ul class="simple">
-<li>use the -fopenmp flag for compiling and linking in your Makefile.machine</li>
-<li>include the USER-OMP package and build LAMMPS</li>
-<li>use the mpirun command to set the number of MPI tasks/node</li>
-<li>specify how many threads per MPI task to use</li>
-<li>use USER-OMP styles in your input script</li>
-</ul>
-<p>The latter two steps can be done using the “-pk omp” and “-sf omp”
-<a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> respectively. Or
-the effect of the “-pk” or “-sf” switches can be duplicated by adding
-the <a class="reference internal" href="package.html"><em>package omp</em></a> or <a class="reference internal" href="suffix.html"><em>suffix omp</em></a> commands
-respectively to your input script.</p>
-<p><strong>Required hardware/software:</strong></p>
-<p>Your compiler must support the OpenMP interface. You should have one
-or more multi-core CPUs so that multiple threads can be launched by an
-MPI task running on a CPU.</p>
-<p><strong>Building LAMMPS with the USER-OMP package:</strong></p>
-<p>To do this in one line, use the src/Make.py script, described in
-<a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a> of the manual. Type “Make.py
--h” for help. If run from the src directory, this command will create
-src/lmp_omp using src/MAKE/Makefile.mpi as the starting
-Makefile.machine:</p>
-<div class="highlight-python"><div class="highlight"><pre>Make.py -p omp -o omp -a file mpi
+Kspace styles, and a few fix styles. The package currently uses the
+OpenMP interface for multi-threading.</p>
+<p>Here is a quick overview of how to use the USER-OMP package, assuming
+one or more 16-core nodes. More details follow.</p>
+<div class="highlight-python"><div class="highlight"><pre>use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine
+make yes-user-omp
+make mpi # build with USER-OMP package, if settings added to Makefile.mpi
+make omp # or Makefile.omp already has settings
+Make.py -v -p omp -o mpi -a file mpi # or one-line build via Make.py
</pre></div>
</div>
-<p>Or you can follow these steps:</p>
-<div class="highlight-python"><div class="highlight"><pre>cd lammps/src
-make yes-user-omp
-make machine
+<div class="highlight-python"><div class="highlight"><pre>lmp_mpi -sf omp -pk omp 16 < in.script # 1 MPI task, 16 threads
+mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task
+mpirun -np 32 -ppn 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task
</pre></div>
</div>
-<p>The CCFLAGS setting in Makefile.machine needs “-fopenmp” to add OpenMP
-support. This works for both the GNU and Intel compilers. Without
-this flag the USER-OMP styles will still be compiled and work, but
-will not support multi-threading. For the Intel compilers the CCFLAGS
-setting also needs to include “-restrict”.</p>
+<p><strong>Required hardware/software:</strong></p>
+<p>Your compiler must support the OpenMP interface. You should have one
+or more multi-core CPUs so that multiple threads can be launched by
+each MPI task running on a CPU.</p>
+<p><strong>Building LAMMPS with the USER-OMP package:</strong></p>
+<p>The lines above illustrate how to include/build with the USER-OMP
+package in two steps, using the “make” command. Or how to do it with
+one command via the src/Make.py script, described in <a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a> of the manual. Type “Make.py -h” for
+help.</p>
+<p>Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
+include “-fopenmp”. Likewise, if you use an Intel compiler, the
+CCFLAGS setting must include “-restrict”. The Make.py command will
+add these automatically.</p>
<p><strong>Run with the USER-OMP package from the command line:</strong></p>
<p>The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.</p>
-<p>You need to choose how many threads per MPI task will be used by the
-USER-OMP package. Note that the product of MPI tasks * threads/task
-should not exceed the physical number of cores (on a node), otherwise
-performance will suffer.</p>
-<p>Use the “-sf omp” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>,
-which will automatically append “omp” to styles that support it. Use
-the “-pk omp Nt” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>, to
-set Nt = # of OpenMP threads per MPI task to use.</p>
-<div class="highlight-python"><div class="highlight"><pre>lmp_machine -sf omp -pk omp 16 -in in.script # 1 MPI task on a 16-core node
-mpirun -np 4 lmp_machine -sf omp -pk omp 4 -in in.script # 4 MPI tasks each with 4 threads on a single 16-core node
-mpirun -np 32 -ppn 4 lmp_machine -sf omp -pk omp 4 -in in.script # ditto on 8 16-core nodes
-</pre></div>
-</div>
-<p>Note that if the “-sf omp” switch is used, it also issues a default
-<a class="reference internal" href="package.html"><em>package omp 0</em></a> command, which sets the number of threads
-per MPI task via the OMP_NUM_THREADS environment variable.</p>
-<p>Using the “-pk” switch explicitly allows for direct setting of the
-number of threads and additional options. Its syntax is the same as
-the “package omp” command. See the <a class="reference internal" href="package.html"><em>package</em></a> command doc
-page for details, including the default values used for all its
-options if it is not specified, and how to set the number of threads
-via the OMP_NUM_THREADS environment variable if desired.</p>
+<p>You need to choose how many OpenMP threads per MPI task will be used
+by the USER-OMP package. Note that the product of MPI tasks *
+threads/task should not exceed the physical number of cores (on a
+node), otherwise performance will suffer.</p>
+<p>As in the lines above, use the “-sf omp” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>, which will automatically append
+“omp” to styles that support it. The “-sf omp” switch also issues a
+default <a class="reference internal" href="package.html"><em>package omp 0</em></a> command, which will set the
+number of threads per MPI task via the OMP_NUM_THREADS environment
+variable.</p>
+<p>You can also use the “-pk omp Nt” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>, to explicitly set Nt = # of OpenMP
+threads per MPI task to use, as well as additional options. Its
+syntax is the same as the <a class="reference internal" href="package.html"><em>package omp</em></a> command whose doc
+page gives details, including the default values used if it is not
+specified. It also gives more details on how to set the number of
+threads via the OMP_NUM_THREADS environment variable.</p>
<p><strong>Or run with the USER-OMP package by editing an input script:</strong></p>
<p>The discussion above for the mpirun/mpiexec command, MPI tasks/node,
and threads/MPI task is the same.</p>
<p>Use the <a class="reference internal" href="suffix.html"><em>suffix omp</em></a> command, or you can explicitly add an
“omp” suffix to individual styles in your input script, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/omp 2.5
</pre></div>
</div>
<p>You must also use the <a class="reference internal" href="package.html"><em>package omp</em></a> command to enable the
-USER-OMP package, unless the “-sf omp” or “-pk omp” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switches</span></a> were used. It specifies how many
-threads per MPI task to use, as well as other options. Its doc page
-explains how to set the number of threads via an environment variable
-if desired.</p>
+USER-OMP package. When you do this you also specify how many threads
+per MPI task to use. The command doc page explains other options and
+how to set the number of threads via the OMP_NUM_THREADS environment
+variable.</p>
<p><strong>Speed-ups to expect:</strong></p>
<p>Depending on which styles are accelerated, you should look for a
reduction in the “Pair time”, “Bond time”, “KSpace time”, and “Loop
time” values printed at the end of a run.</p>
<p>You may see a small performance advantage (5 to 20%) when running a
USER-OMP style (in serial or parallel) with a single thread per MPI
-task, versus running standard LAMMPS with its standard
-(un-accelerated) styles (in serial or all-MPI parallelization with 1
-task/core). This is because many of the USER-OMP styles contain
-similar optimizations to those used in the OPT package, as described
-above.</p>
-<p>With multiple threads/task, the optimal choice of MPI tasks/node and
-OpenMP threads/task can vary a lot and should always be tested via
-benchmark runs for a specific simulation running on a specific
-machine, paying attention to guidelines discussed in the next
+task, versus running standard LAMMPS with its standard un-accelerated
+styles (in serial or all-MPI parallelization with 1 task/core). This
+is because many of the USER-OMP styles contain similar optimizations
+to those used in the OPT package, described in <a class="reference internal" href="accelerate_opt.html"><em>Section accelerate 5.3.6</em></a>.</p>
+<p>With multiple threads/task, the optimal choice of number of MPI
+tasks/node and OpenMP threads/task can vary a lot and should always be
+tested via benchmark runs for a specific simulation running on a
+specific machine, paying attention to guidelines discussed in the next
sub-section.</p>
<p>A description of the multi-threading strategy used in the USER-OMP
package and some performance examples are <a class="reference external" href="http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1">presented here</a></p>
<p><strong>Guidelines for best performance:</strong></p>
<p>For many problems on current generation CPUs, running the USER-OMP
package with a single thread/task is faster than running with multiple
threads/task. This is because the MPI parallelization in LAMMPS is
often more efficient than multi-threading as implemented in the
USER-OMP package. The parallel efficiency (in a threaded sense) also
varies for different USER-OMP styles.</p>
<p>Using multiple threads/task can be more effective under the following
circumstances:</p>
<ul class="simple">
<li>Individual compute nodes have a significant number of CPU cores but
the CPU itself has limited memory bandwidth, e.g. for Intel Xeon 53xx
-(Clovertown) and 54xx (Harpertown) quad core processors. Running one
+(Clovertown) and 54xx (Harpertown) quad-core processors. Running one
MPI task per CPU core will result in significant performance
degradation, so that running with 4 or even only 2 MPI tasks per node
is faster. Running in hybrid MPI+OpenMP mode will reduce the
inter-node communication bandwidth contention in the same way, but
offers an additional speedup by utilizing the otherwise idle CPU
cores.</li>
<li>The interconnect used for MPI communication does not provide
sufficient bandwidth for a large number of MPI tasks per node. For
example, this applies to running over gigabit ethernet or on Cray XT4
or XT5 series supercomputers. As in the aforementioned case, this
effect worsens when using an increasing number of nodes.</li>
<li>The system has a spatially inhomogeneous particle density which does
not map well to the <a class="reference internal" href="processors.html"><em>domain decomposition scheme</em></a> or
<a class="reference internal" href="balance.html"><em>load-balancing</em></a> options that LAMMPS provides. This is
because multi-threading achives parallelism over the number of
particles, not via their distribution in space.</li>
<li>A machine is being used in “capability mode”, i.e. near the point
where MPI parallelism is maxed out. For example, this can happen when
using the <a class="reference internal" href="kspace_style.html"><em>PPPM solver</em></a> for long-range
electrostatics on large numbers of nodes. The scaling of the KSpace
calculation (see the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command) becomes
the performance-limiting factor. Using multi-threading allows less
MPI tasks to be invoked and can speed-up the long-range solver, while
increasing overall performance by parallelizing the pairwise and
bonded calculations via OpenMP. Likewise additional speedup can be
sometimes be achived by increasing the length of the Coulombic cutoff
and thus reducing the work done by the long-range solver. Using the
<a class="reference internal" href="run_style.html"><em>run_style verlet/split</em></a> command, which is compatible
with the USER-OMP package, is an alternative way to reduce the number
of MPI tasks assigned to the KSpace calculation.</li>
</ul>
<p>Additional performance tips are as follows:</p>
<ul class="simple">
<li>The best parallel efficiency from <em>omp</em> styles is typically achieved
-when there is at least one MPI task per physical processor,
-i.e. socket or die.</li>
+when there is at least one MPI task per physical CPU chip, i.e. socket
+or die.</li>
<li>It is usually most efficient to restrict threading to a single
socket, i.e. use one or more MPI task per socket.</li>
-<li>Several current MPI implementation by default use a processor affinity
-setting that restricts each MPI task to a single CPU core. Using
-multi-threading in this mode will force the threads to share that core
-and thus is likely to be counterproductive. Instead, binding MPI
-tasks to a (multi-core) socket, should solve this issue.</li>
+<li>IMPORTANT NOTE: By default, several current MPI implementations use a
+processor affinity setting that restricts each MPI task to a single
+CPU core. Using multi-threading in this mode will force all threads
+to share the one core and thus is likely to be counterproductive.
+Instead, binding MPI tasks to a (multi-core) socket, should solve this
+issue.</li>
</ul>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>None.</p>
</div>
</div>
</div>
</div>
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diff --git a/doc/accelerate_omp.txt b/doc/accelerate_omp.txt
index 9d461f519..7a5bef9d9 100644
--- a/doc/accelerate_omp.txt
+++ b/doc/accelerate_omp.txt
@@ -1,201 +1,186 @@
"Previous Section"_Section_packages.html - "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
"Return to Section accelerate overview"_Section_accelerate.html
5.3.5 USER-OMP package :h4
The USER-OMP package was developed by Axel Kohlmeyer at Temple
University. It provides multi-threaded versions of most pair styles,
nearly all bonded styles (bond, angle, dihedral, improper), several
-Kspace styles, and a few fix styles. The package currently
-uses the OpenMP interface for multi-threading.
+Kspace styles, and a few fix styles. The package currently uses the
+OpenMP interface for multi-threading.
-Here is a quick overview of how to use the USER-OMP package:
+Here is a quick overview of how to use the USER-OMP package, assuming
+one or more 16-core nodes. More details follow.
-use the -fopenmp flag for compiling and linking in your Makefile.machine
-include the USER-OMP package and build LAMMPS
-use the mpirun command to set the number of MPI tasks/node
-specify how many threads per MPI task to use
-use USER-OMP styles in your input script :ul
+use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine
+make yes-user-omp
+make mpi # build with USER-OMP package, if settings added to Makefile.mpi
+make omp # or Makefile.omp already has settings
+Make.py -v -p omp -o mpi -a file mpi # or one-line build via Make.py :pre
-The latter two steps can be done using the "-pk omp" and "-sf omp"
-"command-line switches"_Section_start.html#start_7 respectively. Or
-the effect of the "-pk" or "-sf" switches can be duplicated by adding
-the "package omp"_package.html or "suffix omp"_suffix.html commands
-respectively to your input script.
+lmp_mpi -sf omp -pk omp 16 < in.script # 1 MPI task, 16 threads
+mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task
+mpirun -np 32 -ppn 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
[Required hardware/software:]
Your compiler must support the OpenMP interface. You should have one
-or more multi-core CPUs so that multiple threads can be launched by an
-MPI task running on a CPU.
+or more multi-core CPUs so that multiple threads can be launched by
+each MPI task running on a CPU.
[Building LAMMPS with the USER-OMP package:]
-To do this in one line, use the src/Make.py script, described in
-"Section 2.4"_Section_start.html#start_4 of the manual. Type "Make.py
--h" for help. If run from the src directory, this command will create
-src/lmp_omp using src/MAKE/Makefile.mpi as the starting
-Makefile.machine:
-
-Make.py -p omp -o omp -a file mpi :pre
-
-Or you can follow these steps:
-
-cd lammps/src
-make yes-user-omp
-make machine :pre
+The lines above illustrate how to include/build with the USER-OMP
+package in two steps, using the "make" command. Or how to do it with
+one command via the src/Make.py script, described in "Section
+2.4"_Section_start.html#start_4 of the manual. Type "Make.py -h" for
+help.
-The CCFLAGS setting in Makefile.machine needs "-fopenmp" to add OpenMP
-support. This works for both the GNU and Intel compilers. Without
-this flag the USER-OMP styles will still be compiled and work, but
-will not support multi-threading. For the Intel compilers the CCFLAGS
-setting also needs to include "-restrict".
+Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
+include "-fopenmp". Likewise, if you use an Intel compiler, the
+CCFLAGS setting must include "-restrict". The Make.py command will
+add these automatically.
[Run with the USER-OMP package from the command line:]
The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
-You need to choose how many threads per MPI task will be used by the
-USER-OMP package. Note that the product of MPI tasks * threads/task
-should not exceed the physical number of cores (on a node), otherwise
-performance will suffer.
-
-Use the "-sf omp" "command-line switch"_Section_start.html#start_7,
-which will automatically append "omp" to styles that support it. Use
-the "-pk omp Nt" "command-line switch"_Section_start.html#start_7, to
-set Nt = # of OpenMP threads per MPI task to use.
-
-lmp_machine -sf omp -pk omp 16 -in in.script # 1 MPI task on a 16-core node
-mpirun -np 4 lmp_machine -sf omp -pk omp 4 -in in.script # 4 MPI tasks each with 4 threads on a single 16-core node
-mpirun -np 32 -ppn 4 lmp_machine -sf omp -pk omp 4 -in in.script # ditto on 8 16-core nodes :pre
-
-Note that if the "-sf omp" switch is used, it also issues a default
-"package omp 0"_package.html command, which sets the number of threads
-per MPI task via the OMP_NUM_THREADS environment variable.
-
-Using the "-pk" switch explicitly allows for direct setting of the
-number of threads and additional options. Its syntax is the same as
-the "package omp" command. See the "package"_package.html command doc
-page for details, including the default values used for all its
-options if it is not specified, and how to set the number of threads
-via the OMP_NUM_THREADS environment variable if desired.
+You need to choose how many OpenMP threads per MPI task will be used
+by the USER-OMP package. Note that the product of MPI tasks *
+threads/task should not exceed the physical number of cores (on a
+node), otherwise performance will suffer.
+
+As in the lines above, use the "-sf omp" "command-line
+switch"_Section_start.html#start_7, which will automatically append
+"omp" to styles that support it. The "-sf omp" switch also issues a
+default "package omp 0"_package.html command, which will set the
+number of threads per MPI task via the OMP_NUM_THREADS environment
+variable.
+
+You can also use the "-pk omp Nt" "command-line
+switch"_Section_start.html#start_7, to explicitly set Nt = # of OpenMP
+threads per MPI task to use, as well as additional options. Its
+syntax is the same as the "package omp"_package.html command whose doc
+page gives details, including the default values used if it is not
+specified. It also gives more details on how to set the number of
+threads via the OMP_NUM_THREADS environment variable.
[Or run with the USER-OMP package by editing an input script:]
The discussion above for the mpirun/mpiexec command, MPI tasks/node,
and threads/MPI task is the same.
Use the "suffix omp"_suffix.html command, or you can explicitly add an
"omp" suffix to individual styles in your input script, e.g.
pair_style lj/cut/omp 2.5 :pre
You must also use the "package omp"_package.html command to enable the
-USER-OMP package, unless the "-sf omp" or "-pk omp" "command-line
-switches"_Section_start.html#start_7 were used. It specifies how many
-threads per MPI task to use, as well as other options. Its doc page
-explains how to set the number of threads via an environment variable
-if desired.
+USER-OMP package. When you do this you also specify how many threads
+per MPI task to use. The command doc page explains other options and
+how to set the number of threads via the OMP_NUM_THREADS environment
+variable.
[Speed-ups to expect:]
Depending on which styles are accelerated, you should look for a
reduction in the "Pair time", "Bond time", "KSpace time", and "Loop
time" values printed at the end of a run.
You may see a small performance advantage (5 to 20%) when running a
USER-OMP style (in serial or parallel) with a single thread per MPI
-task, versus running standard LAMMPS with its standard
-(un-accelerated) styles (in serial or all-MPI parallelization with 1
-task/core). This is because many of the USER-OMP styles contain
-similar optimizations to those used in the OPT package, as described
-above.
-
-With multiple threads/task, the optimal choice of MPI tasks/node and
-OpenMP threads/task can vary a lot and should always be tested via
-benchmark runs for a specific simulation running on a specific
-machine, paying attention to guidelines discussed in the next
+task, versus running standard LAMMPS with its standard un-accelerated
+styles (in serial or all-MPI parallelization with 1 task/core). This
+is because many of the USER-OMP styles contain similar optimizations
+to those used in the OPT package, described in "Section accelerate
+5.3.6"_accelerate_opt.html.
+
+With multiple threads/task, the optimal choice of number of MPI
+tasks/node and OpenMP threads/task can vary a lot and should always be
+tested via benchmark runs for a specific simulation running on a
+specific machine, paying attention to guidelines discussed in the next
sub-section.
A description of the multi-threading strategy used in the USER-OMP
package and some performance examples are "presented
here"_http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1
[Guidelines for best performance:]
For many problems on current generation CPUs, running the USER-OMP
package with a single thread/task is faster than running with multiple
threads/task. This is because the MPI parallelization in LAMMPS is
often more efficient than multi-threading as implemented in the
USER-OMP package. The parallel efficiency (in a threaded sense) also
varies for different USER-OMP styles.
Using multiple threads/task can be more effective under the following
circumstances:
Individual compute nodes have a significant number of CPU cores but
the CPU itself has limited memory bandwidth, e.g. for Intel Xeon 53xx
-(Clovertown) and 54xx (Harpertown) quad core processors. Running one
+(Clovertown) and 54xx (Harpertown) quad-core processors. Running one
MPI task per CPU core will result in significant performance
degradation, so that running with 4 or even only 2 MPI tasks per node
is faster. Running in hybrid MPI+OpenMP mode will reduce the
inter-node communication bandwidth contention in the same way, but
offers an additional speedup by utilizing the otherwise idle CPU
cores. :ulb,l
The interconnect used for MPI communication does not provide
sufficient bandwidth for a large number of MPI tasks per node. For
example, this applies to running over gigabit ethernet or on Cray XT4
or XT5 series supercomputers. As in the aforementioned case, this
effect worsens when using an increasing number of nodes. :l
The system has a spatially inhomogeneous particle density which does
not map well to the "domain decomposition scheme"_processors.html or
"load-balancing"_balance.html options that LAMMPS provides. This is
because multi-threading achives parallelism over the number of
particles, not via their distribution in space. :l
A machine is being used in "capability mode", i.e. near the point
where MPI parallelism is maxed out. For example, this can happen when
using the "PPPM solver"_kspace_style.html for long-range
electrostatics on large numbers of nodes. The scaling of the KSpace
calculation (see the "kspace_style"_kspace_style.html command) becomes
the performance-limiting factor. Using multi-threading allows less
MPI tasks to be invoked and can speed-up the long-range solver, while
increasing overall performance by parallelizing the pairwise and
bonded calculations via OpenMP. Likewise additional speedup can be
sometimes be achived by increasing the length of the Coulombic cutoff
and thus reducing the work done by the long-range solver. Using the
"run_style verlet/split"_run_style.html command, which is compatible
with the USER-OMP package, is an alternative way to reduce the number
of MPI tasks assigned to the KSpace calculation. :l,ule
Additional performance tips are as follows:
The best parallel efficiency from {omp} styles is typically achieved
-when there is at least one MPI task per physical processor,
-i.e. socket or die. :ulb,l
+when there is at least one MPI task per physical CPU chip, i.e. socket
+or die. :ulb,l
It is usually most efficient to restrict threading to a single
socket, i.e. use one or more MPI task per socket. :l
-Several current MPI implementation by default use a processor affinity
-setting that restricts each MPI task to a single CPU core. Using
-multi-threading in this mode will force the threads to share that core
-and thus is likely to be counterproductive. Instead, binding MPI
-tasks to a (multi-core) socket, should solve this issue. :l,ule
+IMPORTANT NOTE: By default, several current MPI implementations use a
+processor affinity setting that restricts each MPI task to a single
+CPU core. Using multi-threading in this mode will force all threads
+to share the one core and thus is likely to be counterproductive.
+Instead, binding MPI tasks to a (multi-core) socket, should solve this
+issue. :l,ule
[Restrictions:]
None.
diff --git a/doc/accelerate_opt.html b/doc/accelerate_opt.html
index fc5c77952..09c0da0ff 100644
--- a/doc/accelerate_opt.html
+++ b/doc/accelerate_opt.html
@@ -1,250 +1,239 @@
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<p><a class="reference internal" href="Section_accelerate.html"><em>Return to Section accelerate overview</em></a></p>
<div class="section" id="opt-package">
<h1>5.OPT package<a class="headerlink" href="#opt-package" title="Permalink to this headline">¶</a></h1>
<p>The OPT package was developed by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technologies). It contains a handful of pair styles whose compute()
methods were rewritten in C++ templated form to reduce the overhead
due to if tests and other conditional code.</p>
-<p>Here is a quick overview of how to use the OPT package:</p>
-<ul class="simple">
-<li>include the OPT package and build LAMMPS</li>
-<li>use OPT pair styles in your input script</li>
-</ul>
-<p>The last step can be done using the “-sf opt” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>. Or the effect of the “-sf” switch
-can be duplicated by adding a <a class="reference internal" href="suffix.html"><em>suffix opt</em></a> command to your
-input script.</p>
-<p><strong>Required hardware/software:</strong></p>
-<p>None.</p>
-<p><strong>Building LAMMPS with the OPT package:</strong></p>
-<p>Include the package and build LAMMPS:</p>
-<p>To do this in one line, use the src/Make.py script, described in
-<a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a> of the manual. Type “Make.py
--h” for help. If run from the src directory, this command will create
-src/lmp_opt using src/MAKE/Makefile.mpi as the starting
-Makefile.machine:</p>
-<div class="highlight-python"><div class="highlight"><pre>Make.py -p opt -o opt -a file mpi
+<p>Here is a quick overview of how to use the OPT package. More details
+follow.</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-opt
+make mpi # build with the OPT pacakge
+Make.py -v -p opt -o mpi -a file mpi # or one-line build via Make.py
</pre></div>
</div>
-<p>Or you can follow these steps:</p>
-<div class="highlight-python"><div class="highlight"><pre>cd lammps/src
-make yes-opt
-make machine
+<div class="highlight-python"><div class="highlight"><pre>lmp_mpi -sf opt -in in.script # run in serial
+mpirun -np 4 lmp_mpi -sf opt -in in.script # run in parallel
</pre></div>
</div>
-<p>If you are using Intel compilers, then the CCFLAGS setting in
-Makefile.machine needs to include “-restrict”.</p>
+<p><strong>Required hardware/software:</strong></p>
+<p>None.</p>
+<p><strong>Building LAMMPS with the OPT package:</strong></p>
+<p>The lines above illustrate how to build LAMMPS with the OPT package in
+two steps, using the “make” command. Or how to do it with one command
+via the src/Make.py script, described in <a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a> of the manual. Type “Make.py -h” for
+help.</p>
+<p>Note that if you use an Intel compiler to build with the OPT package,
+the CCFLAGS setting in your Makefile.machine must include “-restrict”.
+The Make.py command will add this automatically.</p>
<p><strong>Run with the OPT package from the command line:</strong></p>
-<p>Use the “-sf opt” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>,
-which will automatically append “opt” to styles that support it.</p>
-<div class="highlight-python"><div class="highlight"><pre>lmp_machine -sf opt -in in.script
-mpirun -np 4 lmp_machine -sf opt -in in.script
-</pre></div>
-</div>
+<p>As in the lines above, use the “-sf opt” <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a>, which will automatically append
+“opt” to styles that support it.</p>
<p><strong>Or run with the OPT package by editing an input script:</strong></p>
<p>Use the <a class="reference internal" href="suffix.html"><em>suffix opt</em></a> command, or you can explicitly add an
“opt” suffix to individual styles in your input script, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/opt 2.5
</pre></div>
</div>
<p><strong>Speed-ups to expect:</strong></p>
<p>You should see a reduction in the “Pair time” value printed at the end
of a run. On most machines for reasonable problem sizes, it will be a
5 to 20% savings.</p>
<p><strong>Guidelines for best performance:</strong></p>
-<p>None. Just try out an OPT pair style to see how it performs.</p>
+<p>Just try out an OPT pair style to see how it performs.</p>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>None.</p>
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diff --git a/doc/accelerate_opt.txt b/doc/accelerate_opt.txt
index 23e853aec..c2ff97879 100644
--- a/doc/accelerate_opt.txt
+++ b/doc/accelerate_opt.txt
@@ -1,82 +1,71 @@
"Previous Section"_Section_packages.html - "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
"Return to Section accelerate overview"_Section_accelerate.html
5.3.6 OPT package :h4
The OPT package was developed by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technologies). It contains a handful of pair styles whose compute()
methods were rewritten in C++ templated form to reduce the overhead
due to if tests and other conditional code.
-Here is a quick overview of how to use the OPT package:
+Here is a quick overview of how to use the OPT package. More details
+follow.
-include the OPT package and build LAMMPS
-use OPT pair styles in your input script :ul
+make yes-opt
+make mpi # build with the OPT pacakge
+Make.py -v -p opt -o mpi -a file mpi # or one-line build via Make.py :pre
-The last step can be done using the "-sf opt" "command-line
-switch"_Section_start.html#start_7. Or the effect of the "-sf" switch
-can be duplicated by adding a "suffix opt"_suffix.html command to your
-input script.
+lmp_mpi -sf opt -in in.script # run in serial
+mpirun -np 4 lmp_mpi -sf opt -in in.script # run in parallel :pre
[Required hardware/software:]
None.
[Building LAMMPS with the OPT package:]
-Include the package and build LAMMPS:
-
-To do this in one line, use the src/Make.py script, described in
-"Section 2.4"_Section_start.html#start_4 of the manual. Type "Make.py
--h" for help. If run from the src directory, this command will create
-src/lmp_opt using src/MAKE/Makefile.mpi as the starting
-Makefile.machine:
+The lines above illustrate how to build LAMMPS with the OPT package in
+two steps, using the "make" command. Or how to do it with one command
+via the src/Make.py script, described in "Section
+2.4"_Section_start.html#start_4 of the manual. Type "Make.py -h" for
+help.
-Make.py -p opt -o opt -a file mpi :pre
-
-Or you can follow these steps:
-
-cd lammps/src
-make yes-opt
-make machine :pre
-
-If you are using Intel compilers, then the CCFLAGS setting in
-Makefile.machine needs to include "-restrict".
+Note that if you use an Intel compiler to build with the OPT package,
+the CCFLAGS setting in your Makefile.machine must include "-restrict".
+The Make.py command will add this automatically.
[Run with the OPT package from the command line:]
-Use the "-sf opt" "command-line switch"_Section_start.html#start_7,
-which will automatically append "opt" to styles that support it.
-
-lmp_machine -sf opt -in in.script
-mpirun -np 4 lmp_machine -sf opt -in in.script :pre
+As in the lines above, use the "-sf opt" "command-line
+switch"_Section_start.html#start_7, which will automatically append
+"opt" to styles that support it.
[Or run with the OPT package by editing an input script:]
Use the "suffix opt"_suffix.html command, or you can explicitly add an
"opt" suffix to individual styles in your input script, e.g.
pair_style lj/cut/opt 2.5 :pre
[Speed-ups to expect:]
You should see a reduction in the "Pair time" value printed at the end
of a run. On most machines for reasonable problem sizes, it will be a
5 to 20% savings.
[Guidelines for best performance:]
-None. Just try out an OPT pair style to see how it performs.
+Just try out an OPT pair style to see how it performs.
[Restrictions:]
None.
diff --git a/doc/compute_temp_cs.html b/doc/compute_temp_cs.html
index be1397a6e..22f0ab741 100644
--- a/doc/compute_temp_cs.html
+++ b/doc/compute_temp_cs.html
@@ -1,288 +1,288 @@
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<div class="section" id="compute-temp-cs-command">
<span id="index-0"></span><h1>compute temp/cs command<a class="headerlink" href="#compute-temp-cs-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 temp/cs group1 group2
</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>temp/cs = style name of this compute command</li>
<li>group1 = group-ID of either cores or shells</li>
<li>group2 = group-ID of either shells or cores</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 oxygen_c-s all temp/cs O_core O_shell
compute core_shells all temp/cs cores shells
</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 temperature of a system based
on the center-of-mass velocity of atom pairs that are bonded to each
other. This compute is designed to be used with the adiabatic
core/shell model of <a class="reference internal" href="#mitchellfinchham"><span>(Mitchell and Finchham)</span></a>. See
<a class="reference internal" href="Section_howto.html#howto-25"><span>Section_howto 25</span></a> of the manual for an
overview of the model as implemented in LAMMPS. Specifically, this
compute enables correct temperature calculation and thermostatting of
core/shell pairs where it is desirable for the internal degrees of
freedom of the core/shell pairs to not be influenced by a thermostat.
A compute of this style can be used by any command that computes a
temperature via <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> e.g. <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a>, etc.</p>
<p>Note that this compute does not require all ions to be polarized,
hence defined as core/shell pairs. One can mix core/shell pairs and
ions without a satellite particle if desired. The compute will
consider the non-polarized ions according to the physical system.</p>
<p>For this compute, core and shell particles are specified by two
respective group IDs, which can be defined using the
<a class="reference internal" href="group.html"><em>group</em></a> command. The number of atoms in the two groups
must be the same and there should be one bond defined between a pair
of atoms in the two groups. Non-polarized ions which might also be
included in the treated system should not be included into either of
these groups, they are taken into account by the <em>group-ID</em> (2nd
argument) of the compute.</p>
<p>The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in the group, k = Boltzmann constant, and T = temperature. Note that
the velocity of each core or shell atom used in the KE calculation is
the velocity of the center-of-mass (COM) of the core/shell pair the
atom is part of.</p>
<p>A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that v^2 is replaced by vx*vy for the xy
component, etc. The 6 components of the vector are ordered xx, yy,
-zz, xy, xz, yz. Again, the velocity of each core or shell atom is its
-COM velocity.</p>
+zz, xy, xz, yz. In contrast to the temperature, the velocity of
+each core or shell atom is taken individually.</p>
<p>The change this fix makes to core/shell atom velocities is essentially
computing the temperature after a “bias” has been removed from the
velocity of the atoms. This “bias” is the velocity of the atom
relative to the COM velocity of the core/shell pair. If this compute
is used with a fix command that performs thermostatting then this bias
will be subtracted from each atom, thermostatting of the remaining COM
velocity will be performed, and the bias will be added back in. This
means the thermostating will effectively be performed on the
core/shell pairs, instead of on the individual core and shell atoms.
Thermostatting fixes that work in this way include <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a>, <a class="reference internal" href="fix_temp_berendsen.html"><em>fix temp/berendsen</em></a>, and <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a>.</p>
<p>The internal energy of core/shell pairs can be calculated by the
<a class="reference internal" href="compute_temp_chunk.html"><em>compute temp/chunk</em></a> command, if chunks are
defined as core/shell pairs. See <a class="reference internal" href="Section_howto.html#howto-25"><span>Section_howto 25</span></a> for more discussion on how to do this.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input.</p>
<p>The scalar value calculated by this compute is “intensive”. The
vector values are “extensive”.</p>
<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><em>units</em></a>. The
vector values will be in energy <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>The number of core/shell pairs contributing to the temperature is
assumed to be constant for the duration of the run. No fixes should
be used which generate new molecules or atoms during a simulation.</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_temp.html"><em>compute temp</em></a>, <a class="reference internal" href="compute_temp_chunk.html"><em>compute temp/chunk</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="mitchellfinchham"><strong>(Mitchell and Finchham)</strong> Mitchell, Finchham, J Phys Condensed Matter,
5, 1031-1038 (1993).</p>
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diff --git a/doc/compute_temp_cs.txt b/doc/compute_temp_cs.txt
index f43c7214e..9cdb3a9ba 100644
--- a/doc/compute_temp_cs.txt
+++ b/doc/compute_temp_cs.txt
@@ -1,119 +1,119 @@
"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 temp/cs command :h3
[Syntax:]
compute ID group-ID temp/cs group1 group2 :pre
ID, group-ID are documented in "compute"_compute.html command
temp/cs = style name of this compute command
group1 = group-ID of either cores or shells
group2 = group-ID of either shells or cores :ul
[Examples:]
compute oxygen_c-s all temp/cs O_core O_shell
compute core_shells all temp/cs cores shells :pre
[Description:]
Define a computation that calculates the temperature of a system based
on the center-of-mass velocity of atom pairs that are bonded to each
other. This compute is designed to be used with the adiabatic
core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham. See
"Section_howto 25"_Section_howto.html#howto_25 of the manual for an
overview of the model as implemented in LAMMPS. Specifically, this
compute enables correct temperature calculation and thermostatting of
core/shell pairs where it is desirable for the internal degrees of
freedom of the core/shell pairs to not be influenced by a thermostat.
A compute of this style can be used by any command that computes a
temperature via "fix_modify"_fix_modify.html e.g. "fix
temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc.
Note that this compute does not require all ions to be polarized,
hence defined as core/shell pairs. One can mix core/shell pairs and
ions without a satellite particle if desired. The compute will
consider the non-polarized ions according to the physical system.
For this compute, core and shell particles are specified by two
respective group IDs, which can be defined using the
"group"_group.html command. The number of atoms in the two groups
must be the same and there should be one bond defined between a pair
of atoms in the two groups. Non-polarized ions which might also be
included in the treated system should not be included into either of
these groups, they are taken into account by the {group-ID} (2nd
argument) of the compute.
The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in the group, k = Boltzmann constant, and T = temperature. Note that
the velocity of each core or shell atom used in the KE calculation is
the velocity of the center-of-mass (COM) of the core/shell pair the
atom is part of.
A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that v^2 is replaced by vx*vy for the xy
component, etc. The 6 components of the vector are ordered xx, yy,
-zz, xy, xz, yz. Again, the velocity of each core or shell atom is its
-COM velocity.
+zz, xy, xz, yz. In contrast to the temperature, the velocity of
+each core or shell atom is taken individually.
The change this fix makes to core/shell atom velocities is essentially
computing the temperature after a "bias" has been removed from the
velocity of the atoms. This "bias" is the velocity of the atom
relative to the COM velocity of the core/shell pair. If this compute
is used with a fix command that performs thermostatting then this bias
will be subtracted from each atom, thermostatting of the remaining COM
velocity will be performed, and the bias will be added back in. This
means the thermostating will effectively be performed on the
core/shell pairs, instead of on the individual core and shell atoms.
Thermostatting fixes that work in this way include "fix
nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix
temp/berendsen"_fix_temp_berendsen.html, and "fix
langevin"_fix_langevin.html.
The internal energy of core/shell pairs can be calculated by the
"compute temp/chunk"_compute_temp_chunk.html command, if chunks are
defined as core/shell pairs. See "Section_howto
25"_Section_howto.html#howto_25 for more discussion on how to do this.
[Output info:]
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature "units"_units.html. The
vector values will be in energy "units"_units.html.
[Restrictions:]
The number of core/shell pairs contributing to the temperature is
assumed to be constant for the duration of the run. No fixes should
be used which generate new molecules or atoms during a simulation.
[Related commands:]
"compute temp"_compute_temp.html, "compute
temp/chunk"_compute_temp_chunk.html
[Default:] none
:line
:link(MitchellFinchham)
[(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
5, 1031-1038 (1993).
diff --git a/doc/doc2/Manual.html.html b/doc/doc2/Manual.html.html
index 25313b599..f76689504 100644
--- a/doc/doc2/Manual.html.html
+++ b/doc/doc2/Manual.html.html
@@ -1,318 +1,318 @@
<HTML>
<HTML>
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="25 Sep 2015 version">
+<META NAME="docnumber" CONTENT="22 Oct 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>
<BODY>
<!-- END_HTML_ONLY -->
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H1></H1>
<P><CENTER><H3>LAMMPS Documentation
</H3></CENTER>
-<CENTER><H4>25 Sep 2015 version
+<CENTER><H4>22 Oct 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 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>
<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.
</P>
<P><LI>If you browse the HTML doc pages included in your tarball, they
describe the version you have.
</P>
<P><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.
</P>
<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.
</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 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 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 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>
<!-- END_HTML_ONLY -->
</BODY>
</HTML>
</HTML>
diff --git a/doc/doc2/Section_accelerate.html b/doc/doc2/Section_accelerate.html
index 7a5b054aa..28aaca1ea 100644
--- a/doc/doc2/Section_accelerate.html
+++ b/doc/doc2/Section_accelerate.html
@@ -1,401 +1,420 @@
<HTML>
<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_howto.html">Next
Section</A>
</CENTER>
<HR>
<H3>5. Accelerating LAMMPS performance
</H3>
<P>This section describes various methods for improving LAMMPS
performance for different classes of problems running on different
kinds of machines.
</P>
<P>There are two thrusts to the discussion that follows. The
first is using code options that implement alternate algorithms
that can speed-up a simulation. The second is to use one
of the several accelerator packages provided with LAMMPS that
contain code optimized for certain kinds of hardware, including
multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors.
</P>
<UL><LI>5.1 <A HREF = "#acc_1">Measuring performance</A>
<LI>5.2 <A HREF = "#acc_2">Algorithms and code options to boost performace</A>
<LI>5.3 <A HREF = "#acc_3">Accelerator packages with optimized styles</A>
<UL><LI> 5.3.1 <A HREF = "accelerate_cuda.html">USER-CUDA package</A>
<LI> 5.3.2 <A HREF = "accelerate_gpu.html">GPU package</A>
<LI> 5.3.3 <A HREF = "accelerate_intel.html">USER-INTEL package</A>
<LI> 5.3.4 <A HREF = "accelerate_kokkos.html">KOKKOS package</A>
<LI> 5.3.5 <A HREF = "accelerate_omp.html">USER-OMP package</A>
<LI> 5.3.6 <A HREF = "accelerate_opt.html">OPT package</A>
</UL>
<LI>5.4 <A HREF = "#acc_4">Comparison of various accelerator packages</A>
</UL>
<P>The <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark page</A> of the LAMMPS
web site gives performance results for the various accelerator
packages discussed in Section 5.2, for several of the standard LAMMPS
benchmark problems, as a function of problem size and number of
compute nodes, on different hardware platforms.
</P>
<HR>
<HR>
<H4><A NAME = "acc_1"></A>5.1 Measuring performance
</H4>
<P>Before trying to make your simulation run faster, you should
understand how it currently performs and where the bottlenecks are.
</P>
<P>The best way to do this is run the your system (actual number of
atoms) for a modest number of timesteps (say 100 steps) on several
different processor counts, including a single processor if possible.
Do this for an equilibrium version of your system, so that the
100-step timings are representative of a much longer run. There is
typically no need to run for 1000s of timesteps to get accurate
timings; you can simply extrapolate from short runs.
</P>
<P>For the set of runs, look at the timing data printed to the screen and
log file at the end of each LAMMPS run. <A HREF = "Section_start.html#start_8">This
section</A> of the manual has an overview.
</P>
<P>Running on one (or a few processors) should give a good estimate of
the serial performance and what portions of the timestep are taking
the most time. Running the same problem on a few different processor
counts should give an estimate of parallel scalability. I.e. if the
simulation runs 16x faster on 16 processors, its 100% parallel
efficient; if it runs 8x faster on 16 processors, it's 50% efficient.
</P>
<P>The most important data to look at in the timing info is the timing
breakdown and relative percentages. For example, trying different
options for speeding up the long-range solvers will have little impact
if they only consume 10% of the run time. If the pairwise time is
dominating, you may want to look at GPU or OMP versions of the pair
style, as discussed below. Comparing how the percentages change as
you increase the processor count gives you a sense of how different
operations within the timestep are scaling. Note that if you are
running with a Kspace solver, there is additional output on the
breakdown of the Kspace time. For PPPM, this includes the fraction
spent on FFTs, which can be communication intensive.
</P>
<P>Another important detail in the timing info are the histograms of
atoms counts and neighbor counts. If these vary widely across
processors, you have a load-imbalance issue. This often results in
inaccurate relative timing data, because processors have to wait when
communication occurs for other processors to catch up. Thus the
reported times for "Communication" or "Other" may be higher than they
really are, due to load-imbalance. If this is an issue, you can
uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
LAMMPS, to obtain synchronized timings.
</P>
<HR>
<H4><A NAME = "acc_2"></A>5.2 General strategies
</H4>
<P>NOTE: this section 5.2 is still a work in progress
</P>
<P>Here is a list of general ideas for improving simulation performance.
Most of them are only applicable to certain models and certain
bottlenecks in the current performance, so let the timing data you
generate be your guide. It is hard, if not impossible, to predict how
much difference these options will make, since it is a function of
problem size, number of processors used, and your machine. There is
no substitute for identifying performance bottlenecks, and trying out
various options.
</P>
<UL><LI>rRESPA
<LI>2-FFT PPPM
<LI>Staggered PPPM
<LI>single vs double PPPM
<LI>partial charge PPPM
<LI>verlet/split run style
<LI>processor command for proc layout and numa layout
<LI>load-balancing: balance and fix balance
</UL>
<P>2-FFT PPPM, also called <I>analytic differentiation</I> or <I>ad</I> PPPM, uses
2 FFTs instead of the 4 FFTs used by the default <I>ik differentiation</I>
PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
cost is the performance bottleneck (typically large problems running
on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.
</P>
<P>Staggered PPPM performs calculations using two different meshes, one
shifted slightly with respect to the other. This can reduce force
aliasing errors and increase the accuracy of the method, but also
doubles the amount of work required. For high relative accuracy, using
staggered PPPM allows one to half the mesh size in each dimension as
compared to regular PPPM, which can give around a 4x speedup in the
kspace time. However, for low relative accuracy, using staggered PPPM
gives little benefit and can be up to 2x slower in the kspace
time. For example, the rhodopsin benchmark was run on a single
processor, and results for kspace time vs. relative accuracy for the
different methods are shown in the figure below. For this system,
staggered PPPM (using ik differentiation) becomes useful when using a
relative accuracy of slightly greater than 1e-5 and above.
</P>
<CENTER><IMG SRC = "JPG/rhodo_staggered.jpg">
</CENTER>
<P>IMPORTANT NOTE: Using staggered PPPM may not give the same increase in
accuracy of energy and pressure as it does in forces, so some caution
must be used if energy and/or pressure are quantities of interest,
such as when using a barostat.
</P>
<HR>
<H4><A NAME = "acc_3"></A>5.3 Packages with optimized styles
</H4>
<P>Accelerated versions of various <A HREF = "pair_style.html">pair_style</A>,
<A HREF = "fix.html">fixes</A>, <A HREF = "compute.html">computes</A>, and other commands have
been added to LAMMPS, which will typically run faster than the
standard non-accelerated versions. Some require appropriate hardware
to be present on your system, e.g. GPUs or Intel Xeon Phi
coprocessors.
</P>
<P>All of these commands are in packages provided with LAMMPS. An
overview of packages is give in <A HREF = "Section_packages.html">Section
-packages</A>. These are the accelerator packages
+packages</A>.
+</P>
+<P>These are the accelerator packages
currently in LAMMPS, either as standard or user packages:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD ><A HREF = "accelerate_cuda.html">USER-CUDA</A> </TD><TD > for NVIDIA GPUs</TD></TR>
<TR><TD ><A HREF = "accelerate_gpu.html">GPU</A> </TD><TD > for NVIDIA GPUs as well as OpenCL support</TD></TR>
<TR><TD ><A HREF = "accelerate_intel.html">USER-INTEL</A> </TD><TD > for Intel CPUs and Intel Xeon Phi</TD></TR>
<TR><TD ><A HREF = "accelerate_kokkos.html">KOKKOS</A> </TD><TD > for GPUs, Intel Xeon Phi, and OpenMP threading</TD></TR>
<TR><TD ><A HREF = "accelerate_omp.html">USER-OMP</A> </TD><TD > for OpenMP threading</TD></TR>
<TR><TD ><A HREF = "accelerate_opt.html">OPT</A> </TD><TD > generic CPU optimizations
</TD></TR></TABLE></DIV>
+<P>Inverting this list, LAMMPS currently has acceleration support for
+three kinds of hardware, via the listed packages:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR><TD >Many-core CPUs </TD><TD > <A HREF = "accelerate_intel.html">USER-INTEL</A>, <A HREF = "accelerate_kokkos.html">KOKKOS</A>, <A HREF = "accelerate_omp.html">USER-OMP</A>, <A HREF = "accelerate_opt.html">OPT</A> packages</TD></TR>
+<TR><TD >NVIDIA GPUs </TD><TD > <A HREF = "accelerate_cuda.html">USER-CUDA</A>, <A HREF = "accelerate_gpu.html">GPU</A>, <A HREF = "accelerate_kokkos.html">KOKKOS</A> packages</TD></TR>
+<TR><TD >Intel Phi </TD><TD > <A HREF = "accelerate_intel.html">USER-INTEL</A>, <A HREF = "accelerate_kokkos.html">KOKKOS</A> packages
+</TD></TR></TABLE></DIV>
+
+<P>Which package is fastest for your hardware may depend on the size
+problem you are running and what commands (accelerated and
+non-accelerated) are invoked by your input script. While these doc
+pages include performance guidelines, there is no substitute for
+trying out the different packages appropriate to your hardware.
+</P>
<P>Any accelerated style has the same name as the corresponding standard
style, except that a suffix is appended. Otherwise, the syntax for
the command that uses the style is identical, their functionality is
the same, and the numerical results it produces should also be the
same, except for precision and round-off effects.
</P>
<P>For example, all of these styles are accelerated variants of the
Lennard-Jones <A HREF = "pair_lj.html">pair_style lj/cut</A>:
</P>
<UL><LI><A HREF = "pair_lj.html">pair_style lj/cut/cuda</A>
<LI><A HREF = "pair_lj.html">pair_style lj/cut/gpu</A>
<LI><A HREF = "pair_lj.html">pair_style lj/cut/intel</A>
<LI><A HREF = "pair_lj.html">pair_style lj/cut/kk</A>
<LI><A HREF = "pair_lj.html">pair_style lj/cut/omp</A>
<LI><A HREF = "pair_lj.html">pair_style lj/cut/opt</A>
</UL>
<P>To see what accelerate styles are currently available, see
<A HREF = "Section_commands.html#cmd_5">Section_commands 5</A> of the manual. The
doc pages for individual commands (e.g. <A HREF = "pair_lj.html">pair lj/cut</A> or
<A HREF = "fix_nve.html">fix nve</A>) also list any accelerated variants available
for that style.
</P>
<P>To use an accelerator package in LAMMPS, and one or more of the styles
it provides, follow these general steps. Details vary from package to
package and are explained in the individual accelerator doc pages,
listed above:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >build the accelerator library </TD><TD > only for USER-CUDA and GPU packages </TD></TR>
<TR><TD >install the accelerator package </TD><TD > make yes-opt, make yes-user-intel, etc </TD></TR>
-<TR><TD >add compile/link flags to Makefile.machine </TD><TD > in src/MAKE, <br> only for USER-INTEL, KOKKOS, USER-OMP packages </TD></TR>
+<TR><TD >add compile/link flags to Makefile.machine </TD><TD > in src/MAKE, <br> only for USER-INTEL, KOKKOS, USER-OMP, OPT packages </TD></TR>
<TR><TD >re-build LAMMPS </TD><TD > make machine </TD></TR>
-<TR><TD >run a LAMMPS simulation </TD><TD > lmp_machine < in.script </TD></TR>
+<TR><TD >run a LAMMPS simulation </TD><TD > lmp_machine < in.script <br> mpirun -np 32 lmp_machine -in in.script </TD></TR>
<TR><TD >enable the accelerator package </TD><TD > via "-c on" and "-k on" <A HREF = "Section_start.html#start_7">command-line switches</A>, <br> only for USER-CUDA and KOKKOS packages </TD></TR>
<TR><TD >set any needed options for the package </TD><TD > via "-pk" <A HREF = "Section_start.html#start_7">command-line switch</A> or <A HREF = "package.html">package</A> command, <br> only if defaults need to be changed </TD></TR>
<TR><TD >use accelerated styles in your input script </TD><TD > via "-sf" <A HREF = "Section_start.html#start_7">command-line switch</A> or <A HREF = "suffix.html">suffix</A> command
</TD></TR></TABLE></DIV>
-<P>The first 4 steps can be done as a single command, using the
-src/Make.py tool. The Make.py tool is discussed in <A HREF = "Section_start.html#start_4">Section
+<P>Note that the first 4 steps can be done as a single command, using the
+src/Make.py tool. This tool is discussed in <A HREF = "Section_start.html#start_4">Section
2.4</A> of the manual, and its use is
illustrated in the individual accelerator sections. Typically these
steps only need to be done once, to create an executable that uses one
or more accelerator packages.
</P>
<P>The last 4 steps can all be done from the command-line when LAMMPS is
launched, without changing your input script, as illustrated in the
individual accelerator sections. Or you can add
<A HREF = "package.html">package</A> and <A HREF = "suffix.html">suffix</A> commands to your input
script.
</P>
<P>IMPORTANT NOTE: With a few exceptions, you can build a single LAMMPS
-executable with all its accelerator packages installed. Note that the
-USER-INTEL and KOKKOS packages require you to choose one of their
-options when building. I.e. CPU or Phi for USER-INTEL. OpenMP, Cuda,
-or Phi for KOKKOS. Here are the exceptions; you cannot build a single
-executable with:
+executable with all its accelerator packages installed. Note however
+that the USER-INTEL and KOKKOS packages require you to choose one of
+their hardware options when building for a specific platform.
+I.e. CPU or Phi option for the USER-INTEL package. Or the OpenMP,
+Cuda, or Phi option for the KOKKOS package.
+</P>
+<P>These are the exceptions. You cannot build a single executable with:
</P>
<UL><LI>both the USER-INTEL Phi and KOKKOS Phi options
<LI>the USER-INTEL Phi or Kokkos Phi option, and either the USER-CUDA or GPU packages
</UL>
<P>See the examples/accelerate/README and make.list files for sample
Make.py commands that build LAMMPS with any or all of the accelerator
packages. As an example, here is a command that builds with all the
GPU related packages installed (USER-CUDA, GPU, KOKKOS with Cuda),
including settings to build the needed auxiliary USER-CUDA and GPU
libraries for Kepler GPUs:
</P>
<PRE>Make.py -j 16 -p omp gpu cuda kokkos -cc nvcc wrap=mpi -cuda mode=double arch=35 -gpu mode=double arch=35 \ -kokkos cuda arch=35 lib-all file mpi
</PRE>
<P>The examples/accelerate directory also has input scripts that can be
used with all of the accelerator packages. See its README file for
details.
</P>
<P>Likewise, the bench directory has FERMI and KEPLER and PHI
sub-directories with Make.py commands and input scripts for using all
the accelerator packages on various machines. See the README files in
those dirs.
</P>
<P>As mentioned above, the <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark
page</A> of the LAMMPS web site gives
performance results for the various accelerator packages for several
of the standard LAMMPS benchmark problems, as a function of problem
size and number of compute nodes, on different hardware platforms.
</P>
<P>Here is a brief summary of what the various packages provide. Details
are in the individual accelerator sections.
</P>
<UL><LI>Styles with a "cuda" or "gpu" suffix are part of the USER-CUDA or GPU
packages, and can be run on NVIDIA GPUs. The speed-up on a GPU
depends on a variety of factors, discussed in the accelerator
sections.
<LI>Styles with an "intel" suffix are part of the USER-INTEL
package. These styles support vectorized single and mixed precision
calculations, in addition to full double precision. In extreme cases,
this can provide speedups over 3.5x on CPUs. The package also
supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
coprocessors. This can result in additional speedup over 2x depending
on the hardware configuration.
<LI>Styles with a "kk" suffix are part of the KOKKOS package, and can be
run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
Xeon Phi in "native" mode. The speed-up depends on a variety of
factors, as discussed on the KOKKOS accelerator page.
<LI>Styles with an "omp" suffix are part of the USER-OMP package and allow
a pair-style to be run in multi-threaded mode using OpenMP. This can
be useful on nodes with high-core counts when using less MPI processes
than cores is advantageous, e.g. when running with PPPM so that FFTs
are run on fewer MPI processors or when the many MPI tasks would
overload the available bandwidth for communication.
<LI>Styles with an "opt" suffix are part of the OPT package and typically
speed-up the pairwise calculations of your simulation by 5-25% on a
CPU.
</UL>
<P>The individual accelerator package doc pages explain:
</P>
<UL><LI>what hardware and software the accelerated package requires
<LI>how to build LAMMPS with the accelerated package
<LI>how to run with the accelerated package either via command-line switches or modifying the input script
<LI>speed-ups to expect
<LI>guidelines for best performance
<LI>restrictions
</UL>
<HR>
<H4><A NAME = "acc_4"></A>5.4 Comparison of various accelerator packages
</H4>
<P>NOTE: this section still needs to be re-worked with additional KOKKOS
and USER-INTEL information.
</P>
<P>The next section compares and contrasts the various accelerator
options, since there are multiple ways to perform OpenMP threading,
run on GPUs, and run on Intel Xeon Phi coprocessors.
</P>
<P>All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
hardware, but they do it in different ways.
</P>
<P>As a consequence, for a particular simulation on specific hardware,
one package may be faster than the other. We give guidelines below,
but the best way to determine which package is faster for your input
script is to try both of them on your machine. See the benchmarking
section below for examples where this has been done.
</P>
<P><B>Guidelines for using each package optimally:</B>
</P>
<UL><LI>The GPU package allows you to assign multiple CPUs (cores) to a single
GPU (a common configuration for "hybrid" nodes that contain multicore
CPU(s) and GPU(s)) and works effectively in this mode. The USER-CUDA
package does not allow this; you can only use one CPU per GPU.
<LI>The GPU package moves per-atom data (coordinates, forces)
back-and-forth between the CPU and GPU every timestep. The USER-CUDA
package only does this on timesteps when a CPU calculation is required
(e.g. to invoke a fix or compute that is non-GPU-ized). Hence, if you
can formulate your input script to only use GPU-ized fixes and
computes, and avoid doing I/O too often (thermo output, dump file
snapshots, restart files), then the data transfer cost of the
USER-CUDA package can be very low, causing it to run faster than the
GPU package.
<LI>The GPU package is often faster than the USER-CUDA package, if the
-number of atoms per GPU is "small". The crossover point, in terms of
+number of atoms per GPU is smaller. The crossover point, in terms of
atoms/GPU at which the USER-CUDA package becomes faster depends
strongly on the pair style. For example, for a simple Lennard Jones
system the crossover (in single precision) is often about 50K-100K
atoms per GPU. When performing double precision calculations the
crossover point can be significantly smaller.
<LI>Both packages compute bonded interactions (bonds, angles, etc) on the
CPU. This means a model with bonds will force the USER-CUDA package
to transfer per-atom data back-and-forth between the CPU and GPU every
timestep. If the GPU package is running with several MPI processes
assigned to one GPU, the cost of computing the bonded interactions is
spread across more CPUs and hence the GPU package can run faster.
<LI>When using the GPU package with multiple CPUs assigned to one GPU, its
performance depends to some extent on high bandwidth between the CPUs
and the GPU. Hence its performance is affected if full 16 PCIe lanes
are not available for each GPU. In HPC environments this can be the
case if S2050/70 servers are used, where two devices generally share
one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide
full 16 lanes to each of the PCIe 2.0 16x slots.
</UL>
<P><B>Differences between the two packages:</B>
</P>
<UL><LI>The GPU package accelerates only pair force, neighbor list, and PPPM
calculations. The USER-CUDA package currently supports a wider range
of pair styles and can also accelerate many fix styles and some
compute styles, as well as neighbor list and PPPM calculations.
<LI>The USER-CUDA package does not support acceleration for minimization.
<LI>The USER-CUDA package does not support hybrid pair styles.
<LI>The USER-CUDA package can order atoms in the neighbor list differently
from run to run resulting in a different order for force accumulation.
<LI>The USER-CUDA package has a limit on the number of atom types that can be
used in a simulation.
<LI>The GPU package requires neighbor lists to be built on the CPU when using
exclusion lists or a triclinic simulation box.
<LI>The GPU package uses more GPU memory than the USER-CUDA package. This
is generally not a problem since typical runs are computation-limited
rather than memory-limited.
</UL>
<P><B>Examples:</B>
</P>
<P>The LAMMPS distribution has two directories with sample input scripts
for the GPU and USER-CUDA packages.
</P>
<UL><LI>lammps/examples/gpu = GPU package files
<LI>lammps/examples/USER/cuda = USER-CUDA package files
</UL>
<P>These contain input scripts for identical systems, so they can be used
to benchmark the performance of both packages on your system.
</P>
</HTML>
diff --git a/doc/doc2/Section_commands.html b/doc/doc2/Section_commands.html
index 82f06d539..411376f9d 100644
--- a/doc/doc2/Section_commands.html
+++ b/doc/doc2/Section_commands.html
@@ -1,668 +1,668 @@
<HTML>
<CENTER><A HREF = "Section_start.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_packages.html">Next Section</A>
</CENTER>
<HR>
<H3>3. Commands
</H3>
<P>This section describes how a LAMMPS input script is formatted and the
input script commands used to define a LAMMPS simulation.
</P>
3.1 <A HREF = "#cmd_1">LAMMPS input script</A><BR>
3.2 <A HREF = "#cmd_2">Parsing rules</A><BR>
3.3 <A HREF = "#cmd_3">Input script structure</A><BR>
3.4 <A HREF = "#cmd_4">Commands listed by category</A><BR>
3.5 <A HREF = "#cmd_5">Commands listed alphabetically</A> <BR>
<HR>
<HR>
<A NAME = "cmd_1"></A><H4>3.1 LAMMPS input script
</H4>
<P>LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
command causes LAMMPS to take some action. It may set an internal
variable, read in a file, or run a simulation. Most commands have
default settings, which means you only need to use the command if you
wish to change the default.
</P>
<P>In many cases, the ordering of commands in an input script is not
important. However the following rules apply:
</P>
<P>(1) LAMMPS does not read your entire input script and then perform a
simulation with all the settings. Rather, the input script is read
one line at a time and each command takes effect when it is read.
Thus this sequence of commands:
</P>
<PRE>timestep 0.5
run 100
run 100
</PRE>
<P>does something different than this sequence:
</P>
<PRE>run 100
timestep 0.5
run 100
</PRE>
<P>In the first case, the specified timestep (0.5 fmsec) is used for two
simulations of 100 timesteps each. In the 2nd case, the default
timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
fmsec timestep is used for the 2nd one.
</P>
<P>(2) Some commands are only valid when they follow other commands. For
example you cannot set the temperature of a group of atoms until atoms
have been defined and a group command is used to define which atoms
belong to the group.
</P>
<P>(3) Sometimes command B will use values that can be set by command A.
This means command A must precede command B in the input script if it
is to have the desired effect. For example, the
<A HREF = "read_data.html">read_data</A> command initializes the system by setting
up the simulation box and assigning atoms to processors. If default
values are not desired, the <A HREF = "processors.html">processors</A> and
<A HREF = "boundary.html">boundary</A> commands need to be used before read_data to
tell LAMMPS how to map processors to the simulation box.
</P>
<P>Many input script errors are detected by LAMMPS and an ERROR or
WARNING message is printed. <A HREF = "Section_errors.html">This section</A> gives
more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used.
</P>
<HR>
<A NAME = "cmd_2"></A><H4>3.2 Parsing rules
</H4>
<P>Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
are specified command arguments. Upper case letters may be used in
file names or user-chosen ID strings.
</P>
<P>Here is how each line in the input script is parsed by LAMMPS:
</P>
<P>(1) If the last printable character on the line is a "&" character,
the command is assumed to continue on the next line. The next line is
concatenated to the previous line by removing the "&" character and
line break. This allows long commands to be continued across two or
more lines. See the discussion of triple quotes in (6) for how to
continue a command across multiple line without using "&" characters.
</P>
<P>(2) All characters from the first "#" character onward are treated as
comment and discarded. See an exception in (6). Note that a
comment after a trailing "&" character will prevent the command from
continuing on the next line. Also note that for multi-line commands a
single leading "#" will comment out the entire command.
</P>
<P>(3) The line is searched repeatedly for $ characters, which indicate
variables that are replaced with a text string. See an exception in
(6).
</P>
<P>If the $ is followed by curly brackets, then the variable name is the
text inside the curly brackets. If no curly brackets follow the $,
then the variable name is the single character immediately following
the $. Thus ${myTemp} and $x refer to variable names "myTemp" and
"x".
</P>
<P>How the variable is converted to a text string depends on what style
of variable it is; see the <A HREF = "variable">variable</A> doc page for details.
It can be a variable that stores multiple text strings, and return one
of them. The returned text string can be multiple "words" (space
separated) which will then be interpreted as multiple arguments in the
input command. The variable can also store a numeric formula which
will be evaluated and its numeric result returned as a string.
</P>
<P>As a special case, if the $ is followed by parenthesis, then the text
inside the parenthesis is treated as an "immediate" variable and
evaluated as an <A HREF = "variable.html">equal-style variable</A>. This is a way
to use numeric formulas in an input script without having to assign
them to variable names. For example, these 3 input script lines:
</P>
<PRE>variable X equal (xlo+xhi)/2+sqrt(v_area)
region 1 block $X 2 INF INF EDGE EDGE
variable X delete
</PRE>
<P>can be replaced by
</P>
<PRE>region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
</PRE>
<P>so that you do not have to define (or discard) a temporary variable X.
</P>
<P>Note that neither the curly-bracket or immediate form of variables can
contain nested $ characters for other variables to substitute for.
Thus you cannot do this:
</P>
<PRE>variable a equal 2
variable b2 equal 4
print "B2 = ${b$a}"
</PRE>
<P>Nor can you specify this $($x-1.0) for an immediate variable, but
you could use $(v_x-1.0), since the latter is valid syntax for an
<A HREF = "variable.html">equal-style variable</A>.
</P>
<P>See the <A HREF = "variable.html">variable</A> command for more details of how
strings are assigned to variables and evaluated, and how they can be
used in input script commands.
</P>
<P>(4) The line is broken into "words" separated by whitespace (tabs,
spaces). Note that words can thus contain letters, digits,
underscores, or punctuation characters.
</P>
<P>(5) The first word is the command name. All successive words in the
line are arguments.
</P>
<P>(6) If you want text with spaces to be treated as a single argument,
it can be enclosed in either single or double or triple quotes. A
long single argument enclosed in single or double quotes can span
multiple lines if the "&" character is used, as described above. When
the lines are concatenated together (and the "&" characters and line
breaks removed), the text will become a single line. If you want
multiple lines of an argument to retain their line breaks, the text
can be enclosed in triple quotes, in which case "&" characters are not
needed. For example:
</P>
<PRE>print "Volume = $v"
print 'Volume = $v'
if "${steps} > 1000" then quit
variable a string "red green blue &
purple orange cyan"
print """
System volume = $v
System temperature = $t
"""
</PRE>
<P>In each case, the single, double, or triple quotes are removed when
the single argument they enclose is stored internally.
</P>
<P>See the <A HREF = "dump_modify.html">dump modify format</A>, <A HREF = "print.html">print</A>,
<A HREF = "if.html">if</A>, and <A HREF = "python.html">python</A> commands for examples.
</P>
<P>A "#" or "$" character that is between quotes will not be treated as a
comment indicator in (2) or substituted for as a variable in (3).
</P>
<P>IMPORTANT NOTE: If the argument is itself a command that requires a
quoted argument (e.g. using a <A HREF = "print.html">print</A> command as part of an
<A HREF = "if.html">if</A> or <A HREF = "run.html">run every</A> command), then single, double, or
triple quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.
</P>
<HR>
<H4><A NAME = "cmd_3"></A>3.3 Input script structure
</H4>
<P>This section describes the structure of a typical LAMMPS input script.
The "examples" directory in the LAMMPS distribution contains many
sample input scripts; the corresponding problems are discussed in
<A HREF = "Section_example.html">Section_example</A>, and animated on the <A HREF = "http://lammps.sandia.gov">LAMMPS
WWW Site</A>.
</P>
<P>A LAMMPS input script typically has 4 parts:
</P>
<OL><LI>Initialization
<LI>Atom definition
<LI>Settings
<LI>Run a simulation
</OL>
<P>The last 2 parts can be repeated as many times as desired. I.e. run a
simulation, change some settings, run some more, etc. Each of the 4
parts is now described in more detail. Remember that almost all the
commands need only be used if a non-default value is desired.
</P>
<P>(1) Initialization
</P>
<P>Set parameters that need to be defined before atoms are created or
read-in from a file.
</P>
<P>The relevant commands are <A HREF = "units.html">units</A>,
<A HREF = "dimension.html">dimension</A>, <A HREF = "newton.html">newton</A>,
<A HREF = "processors.html">processors</A>, <A HREF = "boundary.html">boundary</A>,
<A HREF = "atom_style.html">atom_style</A>, <A HREF = "atom_modify.html">atom_modify</A>.
</P>
<P>If force-field parameters appear in the files that will be read, these
commands tell LAMMPS what kinds of force fields are being used:
<A HREF = "pair_style.html">pair_style</A>, <A HREF = "bond_style.html">bond_style</A>,
<A HREF = "angle_style.html">angle_style</A>, <A HREF = "dihedral_style.html">dihedral_style</A>,
<A HREF = "improper_style.html">improper_style</A>.
</P>
<P>(2) Atom definition
</P>
<P>There are 3 ways to define atoms in LAMMPS. Read them in from a data
or restart file via the <A HREF = "read_data.html">read_data</A> or
<A HREF = "read_restart.html">read_restart</A> commands. These files can contain
molecular topology information. Or create atoms on a lattice (with no
molecular topology), using these commands: <A HREF = "lattice.html">lattice</A>,
<A HREF = "region.html">region</A>, <A HREF = "create_box.html">create_box</A>,
<A HREF = "create_atoms.html">create_atoms</A>. The entire set of atoms can be
duplicated to make a larger simulation using the
<A HREF = "replicate.html">replicate</A> command.
</P>
<P>(3) Settings
</P>
<P>Once atoms and molecular topology are defined, a variety of settings
can be specified: force field coefficients, simulation parameters,
output options, etc.
</P>
<P>Force field coefficients are set by these commands (they can also be
set in the read-in files): <A HREF = "pair_coeff.html">pair_coeff</A>,
<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "angle_coeff.html">angle_coeff</A>,
<A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
<A HREF = "improper_coeff.html">improper_coeff</A>,
<A HREF = "kspace_style.html">kspace_style</A>, <A HREF = "dielectric.html">dielectric</A>,
<A HREF = "special_bonds.html">special_bonds</A>.
</P>
<P>Various simulation parameters are set by these commands:
<A HREF = "neighbor.html">neighbor</A>, <A HREF = "neigh_modify.html">neigh_modify</A>,
<A HREF = "group.html">group</A>, <A HREF = "timestep.html">timestep</A>,
<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
<A HREF = "min_style.html">min_style</A>, <A HREF = "min_modify.html">min_modify</A>.
</P>
<P>Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The <A HREF = "fix.html">fix</A> command comes in many flavors.
</P>
<P>Various computations can be specified for execution during a
simulation using the <A HREF = "compute.html">compute</A>,
<A HREF = "compute_modify.html">compute_modify</A>, and <A HREF = "variable.html">variable</A>
commands.
</P>
<P>Output options are set by the <A HREF = "thermo.html">thermo</A>, <A HREF = "dump.html">dump</A>,
and <A HREF = "restart.html">restart</A> commands.
</P>
<P>(4) Run a simulation
</P>
<P>A molecular dynamics simulation is run using the <A HREF = "run.html">run</A>
command. Energy minimization (molecular statics) is performed using
the <A HREF = "minimize.html">minimize</A> command. A parallel tempering
(replica-exchange) simulation can be run using the
<A HREF = "temper.html">temper</A> command.
</P>
<HR>
<A NAME = "cmd_4"></A><H4>3.4 Commands listed by category
</H4>
<P>This section lists all LAMMPS commands, grouped by category. The
<A HREF = "#cmd_5">next section</A> lists the same commands alphabetically. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
</P>
<P>Initialization:
</P>
<P><A HREF = "atom_modify.html">atom_modify</A>, <A HREF = "atom_style.html">atom_style</A>,
<A HREF = "boundary.html">boundary</A>, <A HREF = "dimension.html">dimension</A>,
<A HREF = "newton.html">newton</A>, <A HREF = "processors.html">processors</A>, <A HREF = "units.html">units</A>
</P>
<P>Atom definition:
</P>
<P><A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "create_box.html">create_box</A>,
<A HREF = "lattice.html">lattice</A>, <A HREF = "read_data.html">read_data</A>,
<A HREF = "read_dump.html">read_dump</A>, <A HREF = "read_restart.html">read_restart</A>,
<A HREF = "region.html">region</A>, <A HREF = "replicate.html">replicate</A>
</P>
<P>Force fields:
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_style.html">angle_style</A>,
<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "bond_style.html">bond_style</A>,
<A HREF = "dielectric.html">dielectric</A>, <A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
<A HREF = "dihedral_style.html">dihedral_style</A>,
<A HREF = "improper_coeff.html">improper_coeff</A>,
<A HREF = "improper_style.html">improper_style</A>,
<A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "kspace_style.html">kspace_style</A>,
<A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_modify.html">pair_modify</A>,
<A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_write.html">pair_write</A>,
<A HREF = "special_bonds.html">special_bonds</A>
</P>
<P>Settings:
</P>
<P><A HREF = "comm_style.html">comm_style</A>, <A HREF = "group.html">group</A>, <A HREF = "mass.html">mass</A>,
<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
<A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "neighbor.html">neighbor</A>,
<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
<A HREF = "set.html">set</A>, <A HREF = "timestep.html">timestep</A>, <A HREF = "velocity.html">velocity</A>
</P>
<P>Fixes:
</P>
<P><A HREF = "fix.html">fix</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "unfix.html">unfix</A>
</P>
<P>Computes:
</P>
<P><A HREF = "compute.html">compute</A>, <A HREF = "compute_modify.html">compute_modify</A>,
<A HREF = "uncompute.html">uncompute</A>
</P>
<P>Output:
</P>
<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_image.html">dump image</A>,
<A HREF = "dump_modify.html">dump_modify</A>, <A HREF = "dump_image.html">dump movie</A>,
<A HREF = "restart.html">restart</A>, <A HREF = "thermo.html">thermo</A>,
<A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "thermo_style.html">thermo_style</A>,
<A HREF = "undump.html">undump</A>, <A HREF = "write_data.html">write_data</A>,
<A HREF = "write_dump.html">write_dump</A>, <A HREF = "write_restart.html">write_restart</A>
</P>
<P>Actions:
</P>
<P><A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
<A HREF = "displace_atoms.html">displace_atoms</A>, <A HREF = "change_box.html">change_box</A>,
<A HREF = "minimize.html">minimize</A>, <A HREF = "neb.html">neb</A> <A HREF = "prd.html">prd</A>,
<A HREF = "rerun.html">rerun</A>, <A HREF = "run.html">run</A>, <A HREF = "temper.html">temper</A>
</P>
<P>Miscellaneous:
</P>
<P><A HREF = "clear.html">clear</A>, <A HREF = "echo.html">echo</A>, <A HREF = "if.html">if</A>,
<A HREF = "include.html">include</A>, <A HREF = "jump.html">jump</A>, <A HREF = "label.html">label</A>,
<A HREF = "log.html">log</A>, <A HREF = "next.html">next</A>, <A HREF = "print.html">print</A>,
<A HREF = "shell.html">shell</A>, <A HREF = "variable.html">variable</A>
</P>
<HR>
<H4><A NAME = "cmd_5"></A><A NAME = "comm"></A>3.5 Individual commands
</H4>
<P>This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The <A HREF = "#cmd_4">previous
section</A> lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "angle_coeff.html">angle_coeff</A></TD><TD ><A HREF = "angle_style.html">angle_style</A></TD><TD ><A HREF = "atom_modify.html">atom_modify</A></TD><TD ><A HREF = "atom_style.html">atom_style</A></TD><TD ><A HREF = "balance.html">balance</A></TD><TD ><A HREF = "bond_coeff.html">bond_coeff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "bond_style.html">bond_style</A></TD><TD ><A HREF = "boundary.html">boundary</A></TD><TD ><A HREF = "box.html">box</A></TD><TD ><A HREF = "change_box.html">change_box</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "comm_modify.html">comm_modify</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "comm_style.html">comm_style</A></TD><TD ><A HREF = "compute.html">compute</A></TD><TD ><A HREF = "compute_modify.html">compute_modify</A></TD><TD ><A HREF = "create_atoms.html">create_atoms</A></TD><TD ><A HREF = "create_bonds.html">create_bonds</A></TD><TD ><A HREF = "create_box.html">create_box</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "delete_atoms.html">delete_atoms</A></TD><TD ><A HREF = "delete_bonds.html">delete_bonds</A></TD><TD ><A HREF = "dielectric.html">dielectric</A></TD><TD ><A HREF = "dihedral_coeff.html">dihedral_coeff</A></TD><TD ><A HREF = "dihedral_style.html">dihedral_style</A></TD><TD ><A HREF = "dimension.html">dimension</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD><TD ><A HREF = "dump.html">dump</A></TD><TD ><A HREF = "dump_image.html">dump image</A></TD><TD ><A HREF = "dump_modify.html">dump_modify</A></TD><TD ><A HREF = "dump_image.html">dump movie</A></TD><TD ><A HREF = "echo.html">echo</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix.html">fix</A></TD><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD><TD ><A HREF = "if.html">if</A></TD><TD ><A HREF = "info.html">info</A></TD><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "improper_style.html">improper_style</A></TD><TD ><A HREF = "include.html">include</A></TD><TD ><A HREF = "jump.html">jump</A></TD><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD><TD ><A HREF = "label.html">label</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "lattice.html">lattice</A></TD><TD ><A HREF = "log.html">log</A></TD><TD ><A HREF = "mass.html">mass</A></TD><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD><TD ><A HREF = "min_style.html">min_style</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "molecule.html">molecule</A></TD><TD ><A HREF = "neb.html">neb</A></TD><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD><TD ><A HREF = "next.html">next</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "package.html">package</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "partition.html">partition</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "prd.html">prd</A></TD><TD ><A HREF = "print.html">print</A></TD><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "python.html">python</A></TD><TD ><A HREF = "quit.html">quit</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "read_dump.html">read_dump</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "rerun.html">rerun</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "suffix.html">suffix</A></TD><TD ><A HREF = "tad.html">tad</A></TD><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "timer.html">timer</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_data.html">write_data</A></TD><TD ><A HREF = "write_dump.html">write_dump</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
</TD></TR></TABLE></DIV>
<P>These are additional commands in USER packages, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "group2ndx.html">group2ndx</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Fix styles
</H4>
<P>See the <A HREF = "fix.html">fix</A> command for one-line descriptions of each style
or click on the style itself for a full description. Some of the
styles have accelerated versions, which can be used if LAMMPS is built
with the <A HREF = "Section_accelerate.html">appropriate accelerated package</A>.
This is indicated by additional letters in parenthesis: c = USER-CUDA,
g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_adapt.html">adapt</A></TD><TD ><A HREF = "fix_addforce.html">addforce (c)</A></TD><TD ><A HREF = "fix_append_atoms.html">append/atoms</A></TD><TD ><A HREF = "fix_atom_swap.html">atom/swap</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce (c)</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_chunk.html">ave/chunk</A></TD><TD ><A HREF = "fix_ave_correlate.html">ave/correlate</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_ave_histo.html">ave/histo</A></TD><TD ><A HREF = "fix_ave_histo.html">ave/histo/weight</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_balance.html">balance</A></TD><TD ><A HREF = "fix_bond_break.html">bond/break</A></TD><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_deform.html">deform (k)</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d (c)</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_external.html">external</A></TD><TD ><A HREF = "fix_freeze.html">freeze (c)</A></TD><TD ><A HREF = "fix_gcmc.html">gcmc</A></TD><TD ><A HREF = "fix_gld.html">gld</A></TD><TD ><A HREF = "fix_gravity.html">gravity (co)</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin (k)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_move.html">move</A></TD><TD ><A HREF = "fix_msst.html">msst</A></TD><TD ><A HREF = "fix_neb.html">neb</A></TD><TD ><A HREF = "fix_nh.html">nph (ko)</A></TD><TD ><A HREF = "fix_nphug.html">nphug (o)</A></TD><TD ><A HREF = "fix_nph_asphere.html">nph/asphere (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nph_sphere.html">nph/sphere (o)</A></TD><TD ><A HREF = "fix_nh.html">npt (cko)</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere (o)</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere (o)</A></TD><TD ><A HREF = "fix_nve.html">nve (cko)</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_asphere_noforce.html">nve/asphere/noforce</A></TD><TD ><A HREF = "fix_nve_body.html">nve/body</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_line.html">nve/line</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere (o)</A></TD><TD ><A HREF = "fix_nve_tri.html">nve/tri</A></TD><TD ><A HREF = "fix_nh.html">nvt (cko)</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere (o)</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere (o)</A></TD><TD ><A HREF = "fix_oneway.html">oneway</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_property_atom.html">property/atom</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb (o)</A></TD><TD ><A HREF = "fix_qeq.html">qeq/dynamic</A></TD><TD ><A HREF = "fix_qeq.html">qeq/point</A></TD><TD ><A HREF = "fix_qeq.html">qeq/shielded</A></TD><TD ><A HREF = "fix_qeq.html">qeq/slater</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_restrain.html">restrain</A></TD><TD ><A HREF = "fix_rigid.html">rigid (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nph (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/npt (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small (o)</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nph</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid/small/npt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nvt</A></TD><TD ><A HREF = "fix_setforce.html">setforce (c)</A></TD><TD ><A HREF = "fix_shake.html">shake (c)</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen (c)</A></TD><TD ><A HREF = "fix_temp_csvr.html">temp/csld</A></TD><TD ><A HREF = "fix_temp_csvr.html">temp/csvr</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale (c)</A></TD><TD ><A HREF = "fix_tfmc.html">tfmc</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_tune_kspace.html">tune/kspace</A></TD><TD ><A HREF = "fix_vector.html">vector</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous (c)</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj1043</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_piston.html">wall/piston</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect (k)</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
</TD></TR></TABLE></DIV>
<P>These are additional fix styles in USER packages, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "fix_adapt_fep.html">adapt/fep</A></TD><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_ave_spatial_sphere.html">ave/spatial/sphere</A></TD><TD ><A HREF = "fix_drude.html">drude</A></TD><TD ><A HREF = "fix_drude_transform.html">drude/transform/direct</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_drude_transform.html">drude/transform/reverse</A></TD><TD ><A HREF = "fix_colvars.html">colvars</A></TD><TD ><A HREF = "fix_gle.html">gle</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_ipi.html">ipi</A></TD><TD ><A HREF = "fix_langevin_drude.html">langevin/drude</A></TD></TR>
-<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_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>
+<TR ALIGN="center"><TD ><A HREF = "fix_adapt_fep.html">adapt/fep</A></TD><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_ave_correlate_long.html">ave/correlate/long</A></TD><TD ><A HREF = "fix_ave_spatial_sphere.html">ave/spatial/sphere</A></TD><TD ><A HREF = "fix_drude.html">drude</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_drude_transform.html">drude/transform/direct</A></TD><TD ><A HREF = "fix_drude_transform.html">drude/transform/reverse</A></TD><TD ><A HREF = "fix_colvars.html">colvars</A></TD><TD ><A HREF = "fix_gle.html">gle</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_ipi.html">ipi</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_langevin_drude.html">langevin/drude</A></TD><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></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_lb_viscous.html">lb/viscous</A></TD><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></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><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></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD><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></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_smd_adjust_dt.html">smd/adjust/dt</A></TD><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></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_smd_wall_surface.html">smd/wall/surface</A></TD><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>
<H4>Compute styles
</H4>
<P>See the <A HREF = "compute.html">compute</A> command for one-line descriptions of
each style or click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_angmom_chunk.html">angmom/chunk</A></TD><TD ><A HREF = "compute_body_local.html">body/local</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_chunk_atom.html">chunk/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_cluster_atom.html">cluster/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_com_chunk.html">com/chunk</A></TD><TD ><A HREF = "compute_contact_atom.html">contact/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_dilatation_atom.html">dilatation/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_rigid.html">erotate/rigid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_erotate_sphere_atom.html">erotate/sphere/atom</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_chunk.html">gyration/chunk</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_inertia_chunk.html">inertia/chunk</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_ke_rigid.html">ke/rigid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_chunk.html">msd/chunk</A></TD><TD ><A HREF = "compute_msd_nongauss.html">msd/nongauss</A></TD><TD ><A HREF = "compute_omega_chunk.html">omega/chunk</A></TD><TD ><A HREF = "compute_pair.html">pair</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_pe.html">pe (c)</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_plasticity_atom.html">plasticity/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure (c)</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_property_chunk.html">property/chunk</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD><TD ><A HREF = "compute_sna_atom.html">sna/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_sna_atom.html">snad/atom</A></TD><TD ><A HREF = "compute_sna_atom.html">snav/atom</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp (ck)</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_chunk.html">temp/chunk</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial (c)</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A></TD><TD ><A HREF = "compute_torque_chunk.html">torque/chunk</A></TD><TD ><A HREF = "compute_vacf.html">vacf</A></TD><TD ><A HREF = "compute_vcm_chunk.html">vcm/chunk</A></TD><TD ><A HREF = "compute_voronoi_atom.html">voronoi/atom</A>
</TD></TR></TABLE></DIV>
<P>These are additional compute styles in USER packages, which can be
used if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
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_tally.html">force/tally</A></TD><TD ><A HREF = "compute_tally.html">heat/flux/tally</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD></TR>
<TR ALIGN="center"><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><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_tally.html">pe/tally</A></TD><TD ><A HREF = "compute_saed.html">saed</A></TD></TR>
<TR ALIGN="center"><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><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></TR>
<TR ALIGN="center"><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><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></TR>
<TR ALIGN="center"><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><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></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_smd_ulsph_stress.html">smd/ulsph/stress</A></TD><TD ><A HREF = "compute_smd_vol.html">smd/vol</A></TD><TD ><A HREF = "compute_tally.html">stress/tally</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>
</TD></TR></TABLE></DIV>
<HR>
<H4>Pair_style potentials
</H4>
<P>See the <A HREF = "pair_style.html">pair_style</A> command for an overview of pair
potentials. Click on the style itself for a full description. Many
of the styles have accelerated versions, which can be used if LAMMPS
is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid/overlay</A></TD><TD ><A HREF = "pair_adp.html">adp (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">airebo (o)</A></TD><TD ><A HREF = "pair_beck.html">beck (go)</A></TD><TD ><A HREF = "pair_body.html">body</A></TD><TD ><A HREF = "pair_bop.html">bop</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born (go)</A></TD><TD ><A HREF = "pair_born.html">born/coul/long (cgo)</A></TD><TD ><A HREF = "pair_born.html">born/coul/long/cs</A></TD><TD ><A HREF = "pair_born.html">born/coul/msm (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born/coul/wolf (go)</A></TD><TD ><A HREF = "pair_brownian.html">brownian (o)</A></TD><TD ><A HREF = "pair_brownian.html">brownian/poly (o)</A></TD><TD ><A HREF = "pair_buck.html">buck (cgko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/cut (cgko)</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long (cgko)</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long/cs</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/msm (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck_long.html">buck/long/coul/long (o)</A></TD><TD ><A HREF = "pair_colloid.html">colloid (go)</A></TD><TD ><A HREF = "pair_comb.html">comb (o)</A></TD><TD ><A HREF = "pair_comb.html">comb3</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/cut (gko)</A></TD><TD ><A HREF = "pair_coul.html">coul/debye (gko)</A></TD><TD ><A HREF = "pair_coul.html">coul/dsf (gko)</A></TD><TD ><A HREF = "pair_coul.html">coul/long (gko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/long/cs</A></TD><TD ><A HREF = "pair_coul.html">coul/msm</A></TD><TD ><A HREF = "pair_coul.html">coul/streitz</A></TD><TD ><A HREF = "pair_coul.html">coul/wolf (ko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd (o)</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat (o)</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam (cgkot)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy (cgkot)</A></TD><TD ><A HREF = "pair_eam.html">eam/fs (cgkot)</A></TD><TD ><A HREF = "pair_eim.html">eim (o)</A></TD><TD ><A HREF = "pair_gauss.html">gauss (go)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne (gio)</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history (o)</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke (co)</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj (o)</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse (o)</A></TD><TD ><A HREF = "pair_kim.html">kim</A></TD><TD ><A HREF = "pair_lcbop.html">lcbop</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_line_lj.html">line/lj (o)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm (cko)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit (cko)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long (cgiko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/msm</A></TD><TD ><A HREF = "pair_class2.html">lj/class2 (cgko)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut (cko)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long (cgko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_cubic.html">lj/cubic (go)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut (cgko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye (cgko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf (gko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/cs</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm (go)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut (go)</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut (o)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long (ot)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand (cgko)</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs (cgko)</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs (cko)</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/long/dipole/long</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/tip4p/long</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth (co)</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj96.html">lj96/cut (cgo)</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate (o)</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly (o)</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD><TD ><A HREF = "pair_meam.html">meam (o)</A></TD><TD ><A HREF = "pair_mie.html">mie/cut (o)</A></TD><TD ><A HREF = "pair_morse.html">morse (cgot)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/long (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/eps</A></TD><TD ><A HREF = "pair_peri.html">peri/lps (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/ves</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_polymorphic.html">polymorphic</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo (o)</A></TD><TD ><A HREF = "pair_resquared.html">resquared (go)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_snap.html">snap</A></TD><TD ><A HREF = "pair_soft.html">soft (go)</A></TD><TD ><A HREF = "pair_sw.html">sw (cgkio)</A></TD><TD ><A HREF = "pair_table.html">table (gko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff (cgko)</A></TD><TD ><A HREF = "pair_tersoff_mod.html">tersoff/mod (ko)</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl (ko)</A></TD><TD ><A HREF = "pair_coul.html">tip4p/cut (o)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">tip4p/long (o)</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj (o)</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa (go)</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid (go)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_zbl.html">zbl (go)</A>
+<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">tip4p/long (o)</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj (o)</A></TD><TD ><A HREF = "pair_vashishta.html">vashishta (o)</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa (go)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid (go)</A></TD><TD ><A HREF = "pair_zbl.html">zbl (go)</A>
</TD></TR></TABLE></DIV>
<P>These are additional pair styles in USER packages, which can be used
if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_awpmd.html">awpmd/cut</A></TD><TD ><A HREF = "pair_lj_soft.html">coul/cut/soft (o)</A></TD><TD ><A HREF = "pair_coul_diel.html">coul/diel (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">coul/long/soft (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/cd (o)</A></TD><TD ><A HREF = "pair_edip.html">edip (o)</A></TD><TD ><A HREF = "pair_eff.html">eff/cut</A></TD><TD ><A HREF = "pair_gauss.html">gauss/cut</A></TD></TR>
<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_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>
</TD></TR></TABLE></DIV>
<HR>
<H4>Bond_style potentials
</H4>
<P>See the <A HREF = "bond_style.html">bond_style</A> command for an overview of bond
potentials. Click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "bond_none.html">none</A></TD><TD ><A HREF = "bond_hybrid.html">hybrid</A></TD><TD ><A HREF = "bond_class2.html">class2 (o)</A></TD><TD ><A HREF = "bond_fene.html">fene (ko)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "bond_fene_expand.html">fene/expand (o)</A></TD><TD ><A HREF = "bond_harmonic.html">harmonic (ko)</A></TD><TD ><A HREF = "bond_morse.html">morse (o)</A></TD><TD ><A HREF = "bond_nonlinear.html">nonlinear (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "bond_quartic.html">quartic (o)</A></TD><TD ><A HREF = "bond_table.html">table (o)</A>
</TD></TR></TABLE></DIV>
<P>These are additional bond styles in USER packages, which can be used
if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "bond_harmonic_shift.html">harmonic/shift (o)</A></TD><TD ><A HREF = "bond_harmonic_shift_cut.html">harmonic/shift/cut (o)</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Angle_style potentials
</H4>
<P>See the <A HREF = "angle_style.html">angle_style</A> command for an overview of
angle potentials. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "angle_none.html">none</A></TD><TD ><A HREF = "angle_hybrid.html">hybrid</A></TD><TD ><A HREF = "angle_charmm.html">charmm (ko)</A></TD><TD ><A HREF = "angle_class2.html">class2 (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "angle_cosine.html">cosine (o)</A></TD><TD ><A HREF = "angle_cosine_delta.html">cosine/delta (o)</A></TD><TD ><A HREF = "angle_cosine_periodic.html">cosine/periodic (o)</A></TD><TD ><A HREF = "angle_cosine_squared.html">cosine/squared (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "angle_harmonic.html">harmonic (ko)</A></TD><TD ><A HREF = "angle_table.html">table (o)</A>
</TD></TR></TABLE></DIV>
<P>These are additional angle styles in USER packages, which can be used
if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "angle_cosine_shift.html">cosine/shift (o)</A></TD><TD ><A HREF = "angle_cosine_shift_exp.html">cosine/shift/exp (o)</A></TD><TD ><A HREF = "angle_dipole.html">dipole (o)</A></TD><TD ><A HREF = "angle_fourier.html">fourier (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "angle_fourier_simple.html">fourier/simple (o)</A></TD><TD ><A HREF = "angle_quartic.html">quartic (o)</A></TD><TD ><A HREF = "angle_sdk.html">sdk</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Dihedral_style potentials
</H4>
<P>See the <A HREF = "dihedral_style.html">dihedral_style</A> command for an overview
of dihedral potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
be used if LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "dihedral_none.html">none</A></TD><TD ><A HREF = "dihedral_hybrid.html">hybrid</A></TD><TD ><A HREF = "dihedral_charmm.html">charmm (ko)</A></TD><TD ><A HREF = "dihedral_class2.html">class2 (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "dihedral_harmonic.html">harmonic (o)</A></TD><TD ><A HREF = "dihedral_helix.html">helix (o)</A></TD><TD ><A HREF = "dihedral_multi_harmonic.html">multi/harmonic (o)</A></TD><TD ><A HREF = "dihedral_opls.html">opls (ko)</A>
</TD></TR></TABLE></DIV>
<P>These are additional dihedral styles in USER packages, which can be
used if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "dihedral_cosine_shift_exp.html">cosine/shift/exp (o)</A></TD><TD ><A HREF = "dihedral_fourier.html">fourier (o)</A></TD><TD ><A HREF = "dihedral_nharmonic.html">nharmonic (o)</A></TD><TD ><A HREF = "dihedral_quadratic.html">quadratic (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "dihedral_table.html">table (o)</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Improper_style potentials
</H4>
<P>See the <A HREF = "improper_style.html">improper_style</A> command for an overview
of improper potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
be used if LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "improper_none.html">none</A></TD><TD ><A HREF = "improper_hybrid.html">hybrid</A></TD><TD ><A HREF = "improper_class2.html">class2 (o)</A></TD><TD ><A HREF = "improper_cvff.html">cvff (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "improper_harmonic.html">harmonic (ko)</A></TD><TD ><A HREF = "improper_umbrella.html">umbrella (o)</A>
</TD></TR></TABLE></DIV>
<P>These are additional improper styles in USER packages, which can be
used if <A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "improper_cossq.html">cossq (o)</A></TD><TD ><A HREF = "improper_fourier.html">fourier (o)</A></TD><TD ><A HREF = "improper_ring.html">ring (o)</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Kspace solvers
</H4>
<P>See the <A HREF = "kspace_style.html">kspace_style</A> command for an overview of
Kspace solvers. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
LAMMPS is built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>. This is indicated by additional
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">ewald (o)</A></TD><TD ><A HREF = "kspace_style.html">ewald/disp</A></TD><TD ><A HREF = "kspace_style.html">msm (o)</A></TD><TD ><A HREF = "kspace_style.html">msm/cg (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">pppm (cgo)</A></TD><TD ><A HREF = "kspace_style.html">pppm/cg (o)</A></TD><TD ><A HREF = "kspace_style.html">pppm/disp</A></TD><TD ><A HREF = "kspace_style.html">pppm/disp/tip4p</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">pppm/tip4p (o)</A>
</TD></TR></TABLE></DIV>
</HTML>
diff --git a/doc/doc2/Section_example.html b/doc/doc2/Section_example.html
index 438e23780..e8b392a12 100644
--- a/doc/doc2/Section_example.html
+++ b/doc/doc2/Section_example.html
@@ -1,126 +1,132 @@
<HTML>
<CENTER><A HREF = "Section_howto.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_perf.html">Next Section</A>
</CENTER>
<HR>
<H3>7. Example problems
</H3>
<P>The LAMMPS distribution includes an examples sub-directory with
several sample problems. Each problem is in a sub-directory of its
own. Most are 2d models so that they run quickly, requiring at most a
couple of minutes to run on a desktop machine. Each problem has an
input script (in.*) and produces a log file (log.*) and dump file
(dump.*) when it runs. Some use a data file (data.*) of initial
coordinates as additional input. A few sample log file outputs on
different machines and different numbers of processors are included in
the directories to compare your answers to. E.g. a log file like
log.crack.foo.P means it ran on P processors of machine "foo".
</P>
<P>For examples that use input data files, many of them were produced by
<A HREF = "http://pizza.sandia.gov">Pizza.py</A> or setup tools described in the
<A HREF = "Section_tools.html">Additional Tools</A> section of the LAMMPS
documentation and provided with the LAMMPS distribution.
</P>
<P>If you uncomment the <A HREF = "dump.html">dump</A> command in the input script, a
text dump file will be produced, which can be animated by various
<A HREF = "http://lammps.sandia.gov/viz.html">visualization programs</A>. It can
also be animated using the xmovie tool described in the <A HREF = "Section_tools.html">Additional
Tools</A> section of the LAMMPS documentation.
</P>
<P>If you uncomment the <A HREF = "dump.html">dump image</A> command in the input
script, and assuming you have built LAMMPS with a JPG library, JPG
snapshot images will be produced when the simulation runs. They can
be quickly post-processed into a movie using commands described on the
<A HREF = "dump_image.html">dump image</A> doc page.
</P>
<P>Animations of many of these examples can be viewed on the Movies
section of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
</P>
<P>These are the sample problems in the examples sub-directories:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >balance</TD><TD > dynamic load balancing, 2d system</TD></TR>
<TR><TD >body</TD><TD > body particles, 2d system</TD></TR>
<TR><TD >colloid</TD><TD > big colloid particles in a small particle solvent, 2d system</TD></TR>
<TR><TD >comb</TD><TD > models using the COMB potential</TD></TR>
<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
<TR><TD >cuda</TD><TD > use of the USER-CUDA package for GPU acceleration</TD></TR>
<TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR>
<TR><TD >dreiding</TD><TD > methanol via Dreiding FF</TD></TR>
<TR><TD >eim</TD><TD > NaCl using the EIM potential</TD></TR>
<TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR>
<TR><TD >flow</TD><TD > Couette and Poiseuille flow in a 2d channel</TD></TR>
<TR><TD >friction</TD><TD > frictional contact of spherical asperities between 2d surfaces</TD></TR>
<TR><TD >gpu</TD><TD > use of the GPU package for GPU acceleration</TD></TR>
<TR><TD >hugoniostat</TD><TD > Hugoniostat shock dynamics</TD></TR>
<TR><TD >indent</TD><TD > spherical indenter into a 2d solid</TD></TR>
<TR><TD >intel</TD><TD > use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor</TD></TR>
<TR><TD >kim</TD><TD > use of potentials in Knowledge Base for Interatomic Models (KIM)</TD></TR>
<TR><TD >line</TD><TD > line segment particles in 2d rigid bodies</TD></TR>
<TR><TD >meam</TD><TD > MEAM test for SiC and shear (same as shear examples)</TD></TR>
<TR><TD >melt</TD><TD > rapid melt of 3d LJ system</TD></TR>
<TR><TD >micelle</TD><TD > self-assembly of small lipid-like molecules into 2d bilayers</TD></TR>
<TR><TD >min</TD><TD > energy minimization of 2d LJ melt</TD></TR>
<TR><TD >msst</TD><TD > MSST shock dynamics</TD></TR>
<TR><TD >nb3b</TD><TD > use of nonbonded 3-body harmonic pair style</TD></TR>
<TR><TD >neb</TD><TD > nudged elastic band (NEB) calculation for barrier finding</TD></TR>
<TR><TD >nemd</TD><TD > non-equilibrium MD of 2d sheared system</TD></TR>
<TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
<TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR>
<TR><TD >peri</TD><TD > Peridynamic model of cylinder impacted by indenter</TD></TR>
<TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR>
<TR><TD >prd</TD><TD > parallel replica dynamics of vacancy diffusion in bulk Si</TD></TR>
<TR><TD >qeq</TD><TD > use of the QEQ pacakge for charge equilibration</TD></TR>
<TR><TD >reax</TD><TD > RDX and TATB models using the ReaxFF</TD></TR>
<TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR>
<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void</TD></TR>
<TR><TD >snap</TD><TD > NVE dynamics for BCC tantalum crystal using SNAP potential</TD></TR>
<TR><TD >srd</TD><TD > stochastic rotation dynamics (SRD) particles as solvent</TD></TR>
<TR><TD >tad</TD><TD > temperature-accelerated dynamics of vacancy diffusion in bulk Si</TD></TR>
<TR><TD >tri</TD><TD > triangular particles in rigid bodies
</TD></TR></TABLE></DIV>
+<P>vashishta: models using the Vashishta potential
+</P>
<P>Here is how you might run and visualize one of the sample problems:
</P>
<PRE>cd indent
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
lmp_linux -in in.indent # run the problem
</PRE>
<P>Running the simulation produces the files <I>dump.indent</I> and
<I>log.lammps</I>. You can visualize the dump file as follows:
</P>
<PRE>../../tools/xmovie/xmovie -scale dump.indent
</PRE>
<P>If you uncomment the <A HREF = "dump_image.html">dump image</A> line(s) in the input
script a series of JPG images will be produced by the run. These can
be viewed individually or turned into a movie or animated by tools
like ImageMagick or QuickTime or various Windows-based tools. See the
<A HREF = "dump_image.html">dump image</A> doc page for more details. E.g. this
Imagemagick command would create a GIF file suitable for viewing in a
browser.
</P>
<PRE>% convert -loop 1 *.jpg foo.gif
</PRE>
<HR>
<P>There is also a COUPLE directory with examples of how to use LAMMPS as
a library, either by itself or in tandem with another code or library.
See the COUPLE/README file to get started.
</P>
<P>There is also an ELASTIC directory with an example script for
-computing elastic constants, using a zero temperature Si example. See
-the in.elastic file for more info.
+computing elastic constants at zero temperature, using an Si example. See
+the ELASTIC/in.elastic file for more info.
+</P>
+<P>There is also an ELASTIC_T directory with an example script for
+computing elastic constants at finite temperature, using an Si example. See
+the ELASTIC_T/in.elastic file for more info.
</P>
<P>There is also a USER directory which contains subdirectories of
user-provided examples for user packages. See the README files in
those directories for more info. See the
<A HREF = "Section_start.html">Section_start.html</A> file for more info about user
packages.
</P>
</HTML>
diff --git a/doc/doc2/Section_howto.html b/doc/doc2/Section_howto.html
index 4991250bc..4aa8cabb6 100644
--- a/doc/doc2/Section_howto.html
+++ b/doc/doc2/Section_howto.html
@@ -1,2821 +1,2840 @@
<HTML>
<CENTER><A HREF = "Section_accelerate.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_example.html">Next Section</A>
</CENTER>
<HR>
<H3>6. How-to discussions
</H3>
<P>This section describes how to perform common tasks using LAMMPS.
</P>
6.1 <A HREF = "#howto_1">Restarting a simulation</A><BR>
6.2 <A HREF = "#howto_2">2d simulations</A><BR>
6.3 <A HREF = "#howto_3">CHARMM, AMBER, and DREIDING force fields</A><BR>
6.4 <A HREF = "#howto_4">Running multiple simulations from one input script</A><BR>
6.5 <A HREF = "#howto_5">Multi-replica simulations</A><BR>
6.6 <A HREF = "#howto_6">Granular models</A><BR>
6.7 <A HREF = "#howto_7">TIP3P water model</A><BR>
6.8 <A HREF = "#howto_8">TIP4P water model</A><BR>
6.9 <A HREF = "#howto_9">SPC water model</A><BR>
6.10 <A HREF = "#howto_10">Coupling LAMMPS to other codes</A><BR>
6.11 <A HREF = "#howto_11">Visualizing LAMMPS snapshots</A><BR>
6.12 <A HREF = "#howto_12">Triclinic (non-orthogonal) simulation boxes</A><BR>
6.13 <A HREF = "#howto_13">NEMD simulations</A><BR>
6.14 <A HREF = "#howto_14">Finite-size spherical and aspherical particles</A><BR>
6.15 <A HREF = "#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A><BR>
6.16 <A HREF = "#howto_16">Thermostatting, barostatting and computing temperature</A><BR>
6.17 <A HREF = "#howto_17">Walls</A><BR>
6.18 <A HREF = "#howto_18">Elastic constants</A><BR>
6.19 <A HREF = "#howto_19">Library interface to LAMMPS</A><BR>
6.20 <A HREF = "#howto_20">Calculating thermal conductivity</A><BR>
6.21 <A HREF = "#howto_21">Calculating viscosity</A><BR>
6.22 <A HREF = "#howto_22">Calculating a diffusion coefficient</A><BR>
6.23 <A HREF = "#howto_23">Using chunks to calculate system properties</A><BR>
6.24 <A HREF = "#howto_24">Setting parameters for the kspace_style pppm/disp command</A><BR>
6.25 <A HREF = "#howto_25">Polarizable models</A><BR>
6.26 <A HREF = "#howto_26">Adiabatic core/shell model</A><BR>
6.27 <A HREF = "#howto_27">Drude induced dipoles</A> <BR>
<P>The example input scripts included in the LAMMPS distribution and
highlighted in <A HREF = "Section_example.html">Section_example</A> also show how to
setup and run various kinds of simulations.
</P>
<HR>
<HR>
<A NAME = "howto_1"></A><H4>6.1 Restarting a simulation
</H4>
<P>There are 3 ways to continue a long LAMMPS simulation. Multiple
<A HREF = "run.html">run</A> commands can be used in the same input script. Each
run will continue from where the previous run left off. Or binary
restart files can be saved to disk using the <A HREF = "restart.html">restart</A>
command. At a later time, these binary files can be read via a
<A HREF = "read_restart.html">read_restart</A> command in a new script. Or they can
be converted to text data files using the <A HREF = "Section_start.html#start_7">-r command-line
switch</A> and read by a
<A HREF = "read_data.html">read_data</A> command in a new script.
</P>
<P>Here we give examples of 2 scripts that read either a binary restart
file or a converted data file and then issue a new run command to
continue where the previous run left off. They illustrate what
settings must be made in the new script. Details are discussed in the
documentation for the <A HREF = "read_restart.html">read_restart</A> and
<A HREF = "read_data.html">read_data</A> commands.
</P>
<P>Look at the <I>in.chain</I> input script provided in the <I>bench</I> directory
of the LAMMPS distribution to see the original script that these 2
scripts are based on. If that script had the line
</P>
<PRE>restart 50 tmp.restart
</PRE>
<P>added to it, it would produce 2 binary restart files (tmp.restart.50
and tmp.restart.100) as it ran.
</P>
<P>This script could be used to read the 1st restart file and re-run the
last 50 timesteps:
</P>
<PRE>read_restart tmp.restart.50
</PRE>
<PRE>neighbor 0.4 bin
neigh_modify every 1 delay 1
</PRE>
<PRE>fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
</PRE>
<PRE>timestep 0.012
</PRE>
<PRE>run 50
</PRE>
<P>Note that the following commands do not need to be repeated because
their settings are included in the restart file: <I>units, atom_style,
special_bonds, pair_style, bond_style</I>. However these commands do
need to be used, since their settings are not in the restart file:
<I>neighbor, fix, timestep</I>.
</P>
<P>If you actually use this script to perform a restarted run, you will
notice that the thermodynamic data match at step 50 (if you also put a
"thermo 50" command in the original script), but do not match at step
100. This is because the <A HREF = "fix_langevin.html">fix langevin</A> command
uses random numbers in a way that does not allow for perfect restarts.
</P>
<P>As an alternate approach, the restart file could be converted to a data
file as follows:
</P>
<PRE>lmp_g++ -r tmp.restart.50 tmp.restart.data
</PRE>
<P>Then, this script could be used to re-run the last 50 steps:
</P>
<PRE>units lj
atom_style bond
pair_style lj/cut 1.12
pair_modify shift yes
bond_style fene
special_bonds 0.0 1.0 1.0
</PRE>
<PRE>read_data tmp.restart.data
</PRE>
<PRE>neighbor 0.4 bin
neigh_modify every 1 delay 1
</PRE>
<PRE>fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
</PRE>
<PRE>timestep 0.012
</PRE>
<PRE>reset_timestep 50
run 50
</PRE>
<P>Note that nearly all the settings specified in the original <I>in.chain</I>
script must be repeated, except the <I>pair_coeff</I> and <I>bond_coeff</I>
commands since the new data file lists the force field coefficients.
Also, the <A HREF = "reset_timestep.html">reset_timestep</A> command is used to tell
LAMMPS the current timestep. This value is stored in restart files,
but not in data files.
</P>
<HR>
<A NAME = "howto_2"></A><H4>6.2 2d simulations
</H4>
<P>Use the <A HREF = "dimension.html">dimension</A> command to specify a 2d simulation.
</P>
<P>Make the simulation box periodic in z via the <A HREF = "boundary.html">boundary</A>
command. This is the default.
</P>
<P>If using the <A HREF = "create_box.html">create box</A> command to define a
simulation box, set the z dimensions narrow, but finite, so that the
create_atoms command will tile the 3d simulation box with a single z
plane of atoms - e.g.
</P>
<PRE><A HREF = "create_box.html">create box</A> 1 -10 10 -10 10 -0.25 0.25
</PRE>
<P>If using the <A HREF = "read_data.html">read data</A> command to read in a file of
atom coordinates, set the "zlo zhi" values to be finite but narrow,
similar to the create_box command settings just described. For each
atom in the file, assign a z coordinate so it falls inside the
z-boundaries of the box - e.g. 0.0.
</P>
<P>Use the <A HREF = "fix_enforce2d.html">fix enforce2d</A> command as the last
defined fix to insure that the z-components of velocities and forces
are zeroed out every timestep. The reason to make it the last fix is
so that any forces induced by other fixes will be zeroed out.
</P>
<P>Many of the example input scripts included in the LAMMPS distribution
are for 2d models.
</P>
<P>IMPORTANT NOTE: Some models in LAMMPS treat particles as finite-size
spheres, as opposed to point particles. In 2d, the particles will
still be spheres, not disks, meaning their moment of inertia will be
the same as in 3d.
</P>
<HR>
<A NAME = "howto_3"></A><H4>6.3 CHARMM, AMBER, and DREIDING force fields
</H4>
<P>A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
formulas implemented in LAMMPS that correspond to formulas commonly
used in the CHARMM, AMBER, and DREIDING force fields. Setting
coefficients is done in the input data file via the
<A HREF = "read_data.html">read_data</A> command or in the input script with
commands like <A HREF = "pair_coeff.html">pair_coeff</A> or
<A HREF = "bond_coeff.html">bond_coeff</A>. See <A HREF = "Section_tools.html">Section_tools</A>
for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input.
</P>
<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
field. See <A HREF = "#Cornell">(Cornell)</A> for a description of the AMBER force
field.
</P>
<P>These style choices compute force field formulas that are consistent
with common options in CHARMM or AMBER. See each command's
documentation for the formula it computes.
</P>
<UL><LI><A HREF = "bond_harmonic.html">bond_style</A> harmonic
<LI><A HREF = "angle_charmm.html">angle_style</A> charmm
<LI><A HREF = "dihedral_charmm.html">dihedral_style</A> charmm
<LI><A HREF = "pair_charmm.html">pair_style</A> lj/charmm/coul/charmm
<LI><A HREF = "pair_charmm.html">pair_style</A> lj/charmm/coul/charmm/implicit
<LI><A HREF = "pair_charmm.html">pair_style</A> lj/charmm/coul/long
</UL>
<UL><LI><A HREF = "special_bonds.html">special_bonds</A> charmm
<LI><A HREF = "special_bonds.html">special_bonds</A> amber
</UL>
<P>DREIDING is a generic force field developed by the <A HREF = "http://www.wag.caltech.edu">Goddard
group</A> at Caltech and is useful for
predicting structures and dynamics of organic, biological and
main-group inorganic molecules. The philosophy in DREIDING is to use
general force constants and geometry parameters based on simple
hybridization considerations, rather than individual force constants
and geometric parameters that depend on the particular combinations of
atoms involved in the bond, angle, or torsion terms. DREIDING has an
<A HREF = "pair_hbond_dreiding.html">explicit hydrogen bond term</A> to describe
interactions involving a hydrogen atom on very electronegative atoms
(N, O, F).
</P>
<P>See <A HREF = "#Mayo">(Mayo)</A> for a description of the DREIDING force field
</P>
<P>These style choices compute force field formulas that are consistent
with the DREIDING force field. See each command's
documentation for the formula it computes.
</P>
<UL><LI><A HREF = "bond_harmonic.html">bond_style</A> harmonic
<LI><A HREF = "bond_morse.html">bond_style</A> morse
</UL>
<UL><LI><A HREF = "angle_harmonic.html">angle_style</A> harmonic
<LI><A HREF = "angle_cosine.html">angle_style</A> cosine
<LI><A HREF = "angle_cosine_periodic.html">angle_style</A> cosine/periodic
</UL>
<UL><LI><A HREF = "dihedral_charmm.html">dihedral_style</A> charmm
<LI><A HREF = "improper_umbrella.html">improper_style</A> umbrella
</UL>
<UL><LI><A HREF = "pair_buck.html">pair_style</A> buck
<LI><A HREF = "pair_buck.html">pair_style</A> buck/coul/cut
<LI><A HREF = "pair_buck.html">pair_style</A> buck/coul/long
<LI><A HREF = "pair_lj.html">pair_style</A> lj/cut
<LI><A HREF = "pair_lj.html">pair_style</A> lj/cut/coul/cut
<LI><A HREF = "pair_lj.html">pair_style</A> lj/cut/coul/long
</UL>
<UL><LI><A HREF = "pair_hbond_dreiding.html">pair_style</A> hbond/dreiding/lj
<LI><A HREF = "pair_hbond_dreiding.html">pair_style</A> hbond/dreiding/morse
</UL>
<UL><LI><A HREF = "special_bonds.html">special_bonds</A> dreiding
</UL>
<HR>
<A NAME = "howto_4"></A><H4>6.4 Running multiple simulations from one input script
</H4>
<P>This can be done in several ways. See the documentation for
individual commands for more details on how these examples work.
</P>
<P>If "multiple simulations" means continue a previous simulation for
more timesteps, then you simply use the <A HREF = "run.html">run</A> command
multiple times. For example, this script
</P>
<PRE>units lj
atom_style atomic
read_data data.lj
run 10000
run 10000
run 10000
run 10000
run 10000
</PRE>
<P>would run 5 successive simulations of the same system for a total of
50,000 timesteps.
</P>
<P>If you wish to run totally different simulations, one after the other,
the <A HREF = "clear.html">clear</A> command can be used in between them to
re-initialize LAMMPS. For example, this script
</P>
<PRE>units lj
atom_style atomic
read_data data.lj
run 10000
clear
units lj
atom_style atomic
read_data data.lj.new
run 10000
</PRE>
<P>would run 2 independent simulations, one after the other.
</P>
<P>For large numbers of independent simulations, you can use
<A HREF = "variable.html">variables</A> and the <A HREF = "next.html">next</A> and
<A HREF = "jump.html">jump</A> commands to loop over the same input script
multiple times with different settings. For example, this
script, named in.polymer
</P>
<PRE>variable d index run1 run2 run3 run4 run5 run6 run7 run8
shell cd $d
read_data data.polymer
run 10000
shell cd ..
clear
next d
jump in.polymer
</PRE>
<P>would run 8 simulations in different directories, using a data.polymer
file in each directory. The same concept could be used to run the
same system at 8 different temperatures, using a temperature variable
and storing the output in different log and dump files, for example
</P>
<PRE>variable a loop 8
variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
log log.$a
read data.polymer
velocity all create $t 352839
fix 1 all nvt $t $t 100.0
dump 1 all atom 1000 dump.$a
run 100000
clear
next t
next a
jump in.polymer
</PRE>
<P>All of the above examples work whether you are running on 1 or
multiple processors, but assumed you are running LAMMPS on a single
partition of processors. LAMMPS can be run on multiple partitions via
the "-partition" command-line switch as described in <A HREF = "Section_start.html#start_7">this
section</A> of the manual.
</P>
<P>In the last 2 examples, if LAMMPS were run on 3 partitions, the same
scripts could be used if the "index" and "loop" variables were
replaced with <I>universe</I>-style variables, as described in the
<A HREF = "variable.html">variable</A> command. Also, the "next t" and "next a"
commands would need to be replaced with a single "next a t" command.
With these modifications, the 8 simulations of each script would run
on the 3 partitions one after the other until all were finished.
Initially, 3 simulations would be started simultaneously, one on each
partition. When one finished, that partition would then start
the 4th simulation, and so forth, until all 8 were completed.
</P>
<HR>
<A NAME = "howto_5"></A><H4>6.5 Multi-replica simulations
</H4>
<P>Several commands in LAMMPS run mutli-replica simulations, meaning
that multiple instances (replicas) of your simulation are run
simultaneously, with small amounts of data exchanged between replicas
periodically.
</P>
<P>These are the relevant commands:
</P>
<UL><LI><A HREF = "neb.html">neb</A> for nudged elastic band calculations
<LI><A HREF = "prd.html">prd</A> for parallel replica dynamics
<LI><A HREF = "tad.html">tad</A> for temperature accelerated dynamics
<LI><A HREF = "temper.html">temper</A> for parallel tempering
<LI><A HREF = "fix_pimd.html">fix pimd</A> for path-integral molecular dynamics (PIMD)
</UL>
<P>NEB is a method for finding transition states and barrier energies.
PRD and TAD are methods for performing accelerated dynamics to find
and perform infrequent events. Parallel tempering or replica exchange
runs different replicas at a series of temperature to facilitate
rare-event sampling.
</P>
<P>These commands can only be used if LAMMPS was built with the REPLICA
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P>PIMD runs different replicas whose individual particles are coupled
together by springs to model a system or ring-polymers.
</P>
<P>This commands can only be used if LAMMPS was built with the USER-MISC
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P>In all these cases, you must run with one or more processors per
replica. The processors assigned to each replica are determined at
run-time by using the <A HREF = "Section_start.html#start_7">-partition command-line
switch</A> to launch LAMMPS on multiple
partitions, which in this context are the same as replicas. E.g.
these commands:
</P>
<PRE>mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
mpirun -np 8 lmp_linux -partition 8x1 -in in.neb
</PRE>
<P>would each run 8 replicas, on either 16 or 8 processors. Note the use
of the <A HREF = "Section_start.html#start_7">-in command-line switch</A> to specify
the input script which is required when running in multi-replica mode.
</P>
<P>Also note that with MPI installed on a machine (e.g. your desktop),
you can run on more (virtual) processors than you have physical
processors. Thus the above commands could be run on a
single-processor (or few-processor) desktop so that you can run
a multi-replica simulation on more replicas than you have
physical processors.
</P>
<HR>
<A NAME = "howto_6"></A><H4>6.6 Granular models
</H4>
<P>Granular system are composed of spherical particles with a diameter,
as opposed to point particles. This means they have an angular
velocity and torque can be imparted to them to cause them to rotate.
</P>
<P>To run a simulation of a granular model, you will want to use
the following commands:
</P>
<UL><LI><A HREF = "atom_style.html">atom_style sphere</A>
<LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
<LI><A HREF = "fix_gravity.html">fix gravity</A>
</UL>
<P>This compute
</P>
<UL><LI><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
</UL>
<P>calculates rotational kinetic energy which can be <A HREF = "Section_howto.html#howto_15">output with
thermodynamic info</A>.
</P>
<P>Use one of these 3 pair potentials, which compute forces and torques
between interacting pairs of particles:
</P>
<UL><LI><A HREF = "pair_style.html">pair_style</A> gran/history
<LI><A HREF = "pair_style.html">pair_style</A> gran/no_history
<LI><A HREF = "pair_style.html">pair_style</A> gran/hertzian
</UL>
<P>These commands implement fix options specific to granular systems:
</P>
<UL><LI><A HREF = "fix_freeze.html">fix freeze</A>
<LI><A HREF = "fix_pour.html">fix pour</A>
<LI><A HREF = "fix_viscous.html">fix viscous</A>
<LI><A HREF = "fix_wall_gran.html">fix wall/gran</A>
</UL>
<P>The fix style <I>freeze</I> zeroes both the force and torque of frozen
atoms, and should be used for granular system instead of the fix style
<I>setforce</I>.
</P>
<P>For computational efficiency, you can eliminate needless pairwise
computations between frozen atoms by using this command:
</P>
<UL><LI><A HREF = "neigh_modify.html">neigh_modify</A> exclude
</UL>
<HR>
<A NAME = "howto_7"></A><H4>6.7 TIP3P water model
</H4>
<P>The TIP3P water model as implemented in CHARMM
<A HREF = "#MacKerell">(MacKerell)</A> specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the <A HREF = "fix_shake.html">fix shake</A> command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
<I>harmonic</I> and an angle style of <I>harmonic</I> or <I>charmm</I> should also be
used.
</P>
<P>These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
cutoff. The K values can be used if a flexible TIP3P model (without
fix shake) is desired. If the LJ epsilon and sigma for HH and OH are
set to 0.0, it corresponds to the original 1983 TIP3P model
<A HREF = "#Jorgensen">(Jorgensen)</A>.
</P>
<P>O mass = 15.9994<BR>
H mass = 1.008<BR>
O charge = -0.834<BR>
H charge = 0.417<BR>
LJ epsilon of OO = 0.1521<BR>
LJ sigma of OO = 3.1507<BR>
LJ epsilon of HH = 0.0460<BR>
LJ sigma of HH = 0.4000<BR>
LJ epsilon of OH = 0.0836<BR>
LJ sigma of OH = 1.7753<BR>
K of OH bond = 450<BR>
r0 of OH bond = 0.9572<BR>
K of HOH angle = 55<BR>
theta of HOH angle = 104.52 <BR>
</P>
<P>These are the parameters to use for TIP3P with a long-range Coulombic
solver (e.g. Ewald or PPPM in LAMMPS), see <A HREF = "#Price">(Price)</A> for
details:
</P>
<P>O mass = 15.9994<BR>
H mass = 1.008<BR>
O charge = -0.830<BR>
H charge = 0.415<BR>
LJ epsilon of OO = 0.102<BR>
LJ sigma of OO = 3.188<BR>
LJ epsilon, sigma of OH, HH = 0.0<BR>
K of OH bond = 450<BR>
r0 of OH bond = 0.9572<BR>
K of HOH angle = 55<BR>
theta of HOH angle = 104.52 <BR>
</P>
<P>Wikipedia also has a nice article on <A HREF = "http://en.wikipedia.org/wiki/Water_model">water
models</A>.
</P>
<HR>
<A NAME = "howto_8"></A><H4>6.8 TIP4P water model
</H4>
<P>The four-point TIP4P rigid water model extends the traditional
three-point TIP3P model by adding an additional site, usually
massless, where the charge associated with the oxygen atom is placed.
This site M is located at a fixed distance away from the oxygen along
the bisector of the HOH bond angle. A bond style of <I>harmonic</I> and an
angle style of <I>harmonic</I> or <I>charmm</I> should also be used.
</P>
<P>A TIP4P model is run with LAMMPS using either this command
for a cutoff model:
</P>
<P><A HREF = "pair_lj.html">pair_style lj/cut/tip4p/cut</A>
</P>
<P>or these two commands for a long-range model:
</P>
<UL><LI><A HREF = "pair_lj.html">pair_style lj/cut/tip4p/long</A>
<LI><A HREF = "kspace_style.html">kspace_style pppm/tip4p</A>
</UL>
<P>For both models, the bond lengths and bond angles should be held fixed
using the <A HREF = "fix_shake.html">fix shake</A> command.
</P>
<P>These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP4P model with a cutoff
<A HREF = "#Jorgensen">(Jorgensen)</A>. Note that the OM distance is specified in
the <A HREF = "pair_style.html">pair_style</A> command, not as part of the pair
coefficients.
</P>
<P>O mass = 15.9994<BR>
H mass = 1.008<BR>
O charge = -1.040<BR>
H charge = 0.520<BR>
r0 of OH bond = 0.9572<BR>
theta of HOH angle = 104.52 <BR>
OM distance = 0.15<BR>
LJ epsilon of O-O = 0.1550<BR>
LJ sigma of O-O = 3.1536<BR>
LJ epsilon, sigma of OH, HH = 0.0<BR>
Coulombic cutoff = 8.5 <BR>
</P>
<P>For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
http://dx.doi.org/10.1063/1.1931662) these values can be used:
</P>
<P>O mass = 15.9994<BR>
H mass = 1.008<BR>
O charge = -1.1794<BR>
H charge = 0.5897<BR>
r0 of OH bond = 0.9572<BR>
theta of HOH angle = 104.52<BR>
OM distance = 0.1577<BR>
LJ epsilon of O-O = 0.21084<BR>
LJ sigma of O-O = 3.1668<BR>
LJ epsilon, sigma of OH, HH = 0.0<BR>
Coulombic cutoff = 8.5 <BR>
</P>
<P>For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
http://dx.doi.org/10.1063/1.2121687), these values can be used:
</P>
<P>O mass = 15.9994<BR>
H mass = 1.008<BR>
O charge = -1.1128<BR>
H charge = 0.5564<BR>
r0 of OH bond = 0.9572<BR>
theta of HOH angle = 104.52<BR>
OM distance = 0.1546<BR>
LJ epsilon of O-O = 0.1852<BR>
LJ sigma of O-O = 3.1589<BR>
LJ epsilon, sigma of OH, HH = 0.0<BR>
Coulombic cutoff = 8.5 <BR>
</P>
<P>These are the parameters to use for TIP4P with a long-range Coulombic
solver (e.g. Ewald or PPPM in LAMMPS):
</P>
<P>O mass = 15.9994<BR>
H mass = 1.008<BR>
O charge = -1.0484<BR>
H charge = 0.5242<BR>
r0 of OH bond = 0.9572<BR>
theta of HOH angle = 104.52<BR>
OM distance = 0.1250<BR>
LJ epsilon of O-O = 0.16275<BR>
LJ sigma of O-O = 3.16435<BR>
LJ epsilon, sigma of OH, HH = 0.0 <BR>
</P>
<P>Note that the when using the TIP4P pair style, the neighobr list
cutoff for Coulomb interactions is effectively extended by a distance
2 * (OM distance), to account for the offset distance of the
fictitious charges on O atoms in water molecules. Thus it is
typically best in an efficiency sense to use a LJ cutoff >= Coulomb
cutoff + 2*(OM distance), to shrink the size of the neighbor list.
This leads to slightly larger cost for the long-range calculation, so
you can test the trade-off for your model. The OM distance and the LJ
and Coulombic cutoffs are set in the <A HREF = "pair_lj.html">pair_style
lj/cut/tip4p/long</A> command.
</P>
<P>Wikipedia also has a nice article on <A HREF = "http://en.wikipedia.org/wiki/Water_model">water
models</A>.
</P>
<HR>
<A NAME = "howto_9"></A><H4>6.9 SPC water model
</H4>
<P>The SPC water model specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the <A HREF = "fix_shake.html">fix shake</A> command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
<I>harmonic</I> and an angle style of <I>harmonic</I> or <I>charmm</I> should also be
used.
</P>
<P>These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid SPC model.
</P>
<P>O mass = 15.9994<BR>
H mass = 1.008<BR>
O charge = -0.820<BR>
H charge = 0.410<BR>
LJ epsilon of OO = 0.1553<BR>
LJ sigma of OO = 3.166<BR>
LJ epsilon, sigma of OH, HH = 0.0<BR>
r0 of OH bond = 1.0<BR>
theta of HOH angle = 109.47 <BR>
</P>
<P>Note that as originally proposed, the SPC model was run with a 9
Angstrom cutoff for both LJ and Coulommbic terms. It can also be used
with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
any of the parameters above, though it becomes a different model in
that mode of usage.
</P>
<P>The SPC/E (extended) water model is the same, except
the partial charge assignemnts change:
</P>
<P>O charge = -0.8476<BR>
H charge = 0.4238 <BR>
</P>
<P>See the <A HREF = "#Berendsen">(Berendsen)</A> reference for more details on both
the SPC and SPC/E models.
</P>
<P>Wikipedia also has a nice article on <A HREF = "http://en.wikipedia.org/wiki/Water_model">water
models</A>.
</P>
<HR>
<A NAME = "howto_10"></A><H4>6.10 Coupling LAMMPS to other codes
</H4>
<P>LAMMPS is designed to allow it to be coupled to other codes. For
example, a quantum mechanics code might compute forces on a subset of
atoms and pass those forces to LAMMPS. Or a continuum finite element
(FE) simulation might use atom positions as boundary conditions on FE
nodal points, compute a FE solution, and return interpolated forces on
MD atoms.
</P>
<P>LAMMPS can be coupled to other codes in at least 3 ways. Each has
advantages and disadvantages, which you'll have to think about in the
context of your application.
</P>
<P>(1) Define a new <A HREF = "fix.html">fix</A> command that calls the other code. In
this scenario, LAMMPS is the driver code. During its timestepping,
the fix is invoked, and can make library calls to the other code,
which has been linked to LAMMPS as a library. This is the way the
<A HREF = "http://www.rpi.edu/~anderk5/lab">POEMS</A> package that performs constrained rigid-body motion on
groups of atoms is hooked to LAMMPS. See the
<A HREF = "fix_poems.html">fix_poems</A> command for more details. See <A HREF = "Section_modify.html">this
section</A> of the documentation for info on how to add
a new fix to LAMMPS.
</P>
<P>(2) Define a new LAMMPS command that calls the other code. This is
conceptually similar to method (1), but in this case LAMMPS and the
other code are on a more equal footing. Note that now the other code
is not called during the timestepping of a LAMMPS run, but between
runs. The LAMMPS input script can be used to alternate LAMMPS runs
with calls to the other code, invoked via the new command. The
<A HREF = "run.html">run</A> command facilitates this with its <I>every</I> option, which
makes it easy to run a few steps, invoke the command, run a few steps,
invoke the command, etc.
</P>
<P>In this scenario, the other code can be called as a library, as in
(1), or it could be a stand-alone code, invoked by a system() call
made by the command (assuming your parallel machine allows one or more
processors to start up another program). In the latter case the
stand-alone code could communicate with LAMMPS thru files that the
command writes and reads.
</P>
<P>See <A HREF = "Section_modify.html">Section_modify</A> of the documentation for how
to add a new command to LAMMPS.
</P>
<P>(3) Use LAMMPS as a library called by another code. In this case the
other code is the driver and calls LAMMPS as needed. Or a wrapper
code could link and call both LAMMPS and another code as libraries.
Again, the <A HREF = "run.html">run</A> command has options that allow it to be
invoked with minimal overhead (no setup or clean-up) if you wish to do
multiple short runs, driven by another program.
</P>
<P>Examples of driver codes that call LAMMPS as a library are included in
the examples/COUPLE directory of the LAMMPS distribution; see
examples/COUPLE/README for more details:
</P>
<UL><LI>simple: simple driver programs in C++ and C which invoke LAMMPS as a
library
<LI>lammps_quest: coupling of LAMMPS and <A HREF = "http://dft.sandia.gov/Quest">Quest</A>, to run classical
MD with quantum forces calculated by a density functional code
<LI>lammps_spparks: coupling of LAMMPS and <A HREF = "http://www.sandia.gov/~sjplimp/spparks.html">SPPARKS</A>, to couple
a kinetic Monte Carlo model for grain growth using MD to calculate
strain induced across grain boundaries
</UL>
<P><A HREF = "Section_start.html#start_5">This section</A> of the documentation
describes how to build LAMMPS as a library. Once this is done, you
can interface with LAMMPS either via C++, C, Fortran, or Python (or
any other language that supports a vanilla C-like interface). For
example, from C++ you could create one (or more) "instances" of
LAMMPS, pass it an input script to process, or execute individual
commands, all by invoking the correct class methods in LAMMPS. From C
or Fortran you can make function calls to do the same things. See
<A HREF = "Section_python.html">Section_python</A> of the manual for a description
of the Python wrapper provided with LAMMPS that operates through the
LAMMPS library interface.
</P>
<P>The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See <A HREF = "Section_howto.html#howto_19">Section_howto 19</A> of the
manual for a description of the interface and how to extend it for
your needs.
</P>
<P>Note that the lammps_open() function that creates an instance of
LAMMPS takes an MPI communicator as an argument. This means that
instance of LAMMPS will run on the set of processors in the
communicator. Thus the calling code can run LAMMPS on all or a subset
of processors. For example, a wrapper script might decide to
alternate between LAMMPS and another code, allowing them both to run
on all the processors. Or it might allocate half the processors to
LAMMPS and half to the other code and run both codes simultaneously
before syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.
</P>
<HR>
<A NAME = "howto_11"></A><H4>6.11 Visualizing LAMMPS snapshots
</H4>
<P>LAMMPS itself does not do visualization, but snapshots from LAMMPS
simulations can be visualized (and analyzed) in a variety of ways.
</P>
<P>LAMMPS snapshots are created by the <A HREF = "dump.html">dump</A> command which can
create files in several formats. The native LAMMPS dump format is a
text file (see "dump atom" or "dump custom") which can be visualized
by the <A HREF = "Section_tools.html#xmovie">xmovie</A> program, included with the
LAMMPS package. This produces simple, fast 2d projections of 3d
systems, and can be useful for rapid debugging of simulation geometry
and atom trajectories.
</P>
<P>Several programs included with LAMMPS as auxiliary tools can convert
native LAMMPS dump files to other formats. See the
<A HREF = "Section_tools.html">Section_tools</A> doc page for details. The first is
the <A HREF = "Section_tools.html#charmm">ch2lmp tool</A>, which contains a
lammps2pdb Perl script which converts LAMMPS dump files into PDB
files. The second is the <A HREF = "Section_tools.html#arc">lmp2arc tool</A> which
converts LAMMPS dump files into Accelrys' Insight MD program files.
The third is the <A HREF = "Section_tools.html#cfg">lmp2cfg tool</A> which converts
LAMMPS dump files into CFG files which can be read into the
<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualizer.
</P>
<P>A Python-based toolkit distributed by our group can read native LAMMPS
dump files, including custom dump files with additional columns of
user-specified atom information, and convert them to various formats
or pipe them into visualization software directly. See the <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py
WWW site</A> for details. Specifically, Pizza.py can convert
LAMMPS dump files into PDB, XYZ, <A HREF = "http://www.ensight.com">Ensight</A>, and VTK formats.
Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
RasMol visualization programs. Pizza.py has tools that do interactive
3d OpenGL visualization and one that creates SVG images of dump file
snapshots.
</P>
<P>LAMMPS can create XYZ files directly (via "dump xyz") which is a
simple text-based file format used by many visualization programs
including <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>.
</P>
<P>LAMMPS can create DCD files directly (via "dump dcd") which can be
read by <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> in conjunction with a CHARMM PSF file. Using this
form of output avoids the need to convert LAMMPS snapshots to PDB
files. See the <A HREF = "dump.html">dump</A> command for more information on DCD
files.
</P>
<P>LAMMPS can create XTC files directly (via "dump xtc") which is GROMACS
file format which can also be read by <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> for visualization.
See the <A HREF = "dump.html">dump</A> command for more information on XTC files.
</P>
<HR>
<A NAME = "howto_12"></A><H4>6.12 Triclinic (non-orthogonal) simulation boxes
</H4>
<P>By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The <A HREF = "boundary.html">boundary</A> command sets the boundary
conditions of the box (periodic, non-periodic, etc). The orthogonal
box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
starting from the origin given by <B>a</B> = (xhi-xlo,0,0); <B>b</B> =
(0,yhi-ylo,0); <B>c</B> = (0,0,zhi-zlo). The 6 parameters
(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box
is created, e.g. by the <A HREF = "create_box.html">create_box</A> or
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands. Additionally, LAMMPS defines box size parameters lx,ly,lz
where lx = xhi-xlo, and similarly in the y and z dimensions. The 6
parameters, as well as lx,ly,lz, can be output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command.
</P>
<P>LAMMPS also allows simulations to be performed in triclinic
(non-orthogonal) simulation boxes shaped as a parallelepiped with
triclinic symmetry. The parallelepiped has its "origin" at
(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the
origin given by <B>a</B> = (xhi-xlo,0,0); <B>b</B> = (xy,yhi-ylo,0); <B>c</B> =
(xz,yz,zhi-zlo). <I>xy,xz,yz</I> can be 0.0 or positive or negative values
and are called "tilt factors" because they are the amount of
displacement applied to faces of an originally orthogonal box to
transform it into the parallelepiped. In LAMMPS the triclinic
simulation box edge vectors <B>a</B>, <B>b</B>, and <B>c</B> cannot be arbitrary
vectors. As indicated, <B>a</B> must lie on the positive x axis. <B>b</B> must
lie in the xy plane, with strictly positive y component. <B>c</B> may have
any orientation with strictly positive z component. The requirement
that <B>a</B>, <B>b</B>, and <B>c</B> have strictly positive x, y, and z components,
respectively, ensures that <B>a</B>, <B>b</B>, and <B>c</B> form a complete
right-handed basis. These restrictions impose no loss of generality,
since it is possible to rotate/invert any set of 3 crystal basis
vectors so that they conform to the restrictions.
</P>
<P>For example, assume that the 3 vectors <B>A</B>,<B>B</B>,<B>C</B> are the edge
vectors of a general parallelepiped, where there is no restriction on
<B>A</B>,<B>B</B>,<B>C</B> other than they form a complete right-handed basis i.e.
<B>A</B> x <B>B</B> . <B>C</B> > 0. The equivalent LAMMPS <B>a</B>,<B>b</B>,<B>c</B> are a linear
rotation of <B>A</B>, <B>B</B>, and <B>C</B> and can be computed as follows:
</P>
<CENTER><IMG SRC = "Eqs/transform.jpg">
</CENTER>
<P>where A = |<B>A</B>| indicates the scalar length of <B>A</B>. The ^ hat symbol
indicates the corresponding unit vector. <I>beta</I> and <I>gamma</I> are angles
between the vectors described below. Note that by construction,
<B>a</B>, <B>b</B>, and <B>c</B> have strictly positive x, y, and z components, respectively.
If it should happen that
<B>A</B>, <B>B</B>, and <B>C</B> form a left-handed basis, then the above equations
are not valid for <B>c</B>. In this case, it is necessary
to first apply an inversion. This can be achieved
by interchanging two basis vectors or by changing the sign of one of them.
</P>
<P>For consistency, the same rotation/inversion applied to the basis vectors
must also be applied to atom positions, velocities,
and any other vector quantities.
This can be conveniently achieved by first converting to
fractional coordinates in the
old basis and then converting to distance coordinates in the new basis.
The transformation is given by the following equation:
</P>
<CENTER><IMG SRC = "Eqs/rotate.jpg">
</CENTER>
<P>where <I>V</I> is the volume of the box, <B>X</B> is the original vector quantity and
<B>x</B> is the vector in the LAMMPS basis.
</P>
<P>There is no requirement that a triclinic box be periodic in any
dimension, though it typically should be in at least the 2nd dimension
of the tilt (y in xy) if you want to enforce a shift in periodic
boundary conditions across that boundary. Some commands that work
with triclinic boxes, e.g. the <A HREF = "fix_deform.html">fix deform</A> and <A HREF = "fix_nh.html">fix
npt</A> commands, require periodicity or non-shrink-wrap
boundary conditions in specific dimensions. See the command doc pages
for details.
</P>
<P>The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
time the simluation box is created. This happens in one of 3 ways.
If the <A HREF = "create_box.html">create_box</A> command is used with a region of
style <I>prism</I>, then a triclinic box is setup. See the
<A HREF = "region.html">region</A> command for details. If the
<A HREF = "read_data.html">read_data</A> command is used to define the simulation
box, and the header of the data file contains a line with the "xy xz
yz" keyword, then a triclinic box is setup. See the
<A HREF = "read_data.html">read_data</A> command for details. Finally, if the
<A HREF = "read_restart.html">read_restart</A> command reads a restart file which
was written from a simulation using a triclinic box, then a triclinic
box will be setup for the restarted simulation.
</P>
<P>Note that you can define a triclinic box with all 3 tilt factors =
0.0, so that it is initially orthogonal. This is necessary if the box
will become non-orthogonal, e.g. due to the <A HREF = "fix_nh.html">fix npt</A> or
<A HREF = "fix_deform.html">fix deform</A> commands. Alternatively, you can use the
<A HREF = "change_box.html">change_box</A> command to convert a simulation box from
orthogonal to triclinic and vice versa.
</P>
<P>As with orthogonal boxes, LAMMPS defines triclinic box size parameters
lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions.
The 9 parameters, as well as lx,ly,lz, can be output via the
<A HREF = "thermo_style.html">thermo_style custom</A> command.
</P>
<P>To avoid extremely tilted boxes (which would be computationally
inefficient), LAMMPS normally requires that no tilt factor can skew
the box more than half the distance of the parallel box length, which
is the 1st dimension in the tilt factor (x for xz). This is required
both when the simulation box is created, e.g. via the
<A HREF = "create_box.html">create_box</A> or <A HREF = "read_data.html">read_data</A> commands,
as well as when the box shape changes dynamically during a simulation,
e.g. via the <A HREF = "fix_deform.html">fix deform</A> or <A HREF = "fix_nh.html">fix npt</A>
commands.
</P>
<P>For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
the xy tilt factor must be between -5 and 5. Similarly, both xz and
yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is
not a limitation, since if the maximum tilt factor is 5 (as in this
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
... are geometrically all equivalent. If the box tilt exceeds this
limit during a dynamics run (e.g. via the <A HREF = "fix_deform.html">fix deform</A>
command), then the box is "flipped" to an equivalent shape with a tilt
factor within the bounds, so the run can continue. See the <A HREF = "fix_deform.html">fix
deform</A> doc page for further details.
</P>
<P>One exception to this rule is if the 1st dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this
mode, if you tilt the system to extreme angles, the simulation will
simply become inefficient, due to the highly skewed simulation box.
</P>
<P>The limitation on not creating a simulation box with a tilt factor
skewing the box more than half the distance of the parallel box length
can be overridden via the <A HREF = "box.html">box</A> command. Setting the <I>tilt</I>
keyword to <I>large</I> allows any tilt factors to be specified.
</P>
<P>Box flips that may occur using the <A HREF = "fix_deform.html">fix deform</A> or
<A HREF = "fix_nh.html">fix npt</A> commands can be turned off using the <I>flip no</I>
option with either of the commands.
</P>
<P>Note that if a simulation box has a large tilt factor, LAMMPS will run
less efficiently, due to the large volume of communication needed to
acquire ghost atoms around a processor's irregular-shaped sub-domain.
For extreme values of tilt, LAMMPS may also lose atoms and generate an
error.
</P>
<P>Triclinic crystal structures are often defined using three lattice
constants <I>a</I>, <I>b</I>, and <I>c</I>, and three angles <I>alpha</I>, <I>beta</I> and
<I>gamma</I>. Note that in this nomenclature, the a, b, and c lattice
constants are the scalar lengths of the edge vectors <B>a</B>, <B>b</B>, and <B>c</B>
defined above. The relationship between these 6 quantities
(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) =
(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
</P>
<CENTER><IMG SRC = "Eqs/box.jpg">
</CENTER>
<P>The inverse relationship can be written as follows:
</P>
<CENTER><IMG SRC = "Eqs/box_inverse.jpg">
</CENTER>
<P>The values of <I>a</I>, <I>b</I>, <I>c</I> , <I>alpha</I>, <I>beta</I> , and <I>gamma</I> can be printed
out or accessed by computes using the
<A HREF = "thermo_style.html">thermo_style custom</A> keywords
<I>cella</I>, <I>cellb</I>, <I>cellc</I>, <I>cellalpha</I>, <I>cellbeta</I>, <I>cellgamma</I>,
respectively.
</P>
<P>As discussed on the <A HREF = "dump.html">dump</A> command doc page, when the BOX
BOUNDS for a snapshot is written to a dump file for a triclinic box,
an orthogonal bounding box which encloses the triclinic simulation box
is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
box, formatted as follows:
</P>
<PRE>ITEM: BOX BOUNDS xy xz yz
xlo_bound xhi_bound xy
ylo_bound yhi_bound xz
zlo_bound zhi_bound yz
</PRE>
<P>This bounding box is convenient for many visualization programs and is
calculated from the 9 triclinic box parameters
(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:
</P>
<PRE>xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
ylo_bound = ylo + MIN(0.0,yz)
yhi_bound = yhi + MAX(0.0,yz)
zlo_bound = zlo
zhi_bound = zhi
</PRE>
<P>These formulas can be inverted if you need to convert the bounding box
back into the triclinic box parameters, e.g. xlo = xlo_bound -
MIN(0.0,xy,xz,xy+xz).
</P>
<P>One use of triclinic simulation boxes is to model solid-state crystals
with triclinic symmetry. The <A HREF = "lattice.html">lattice</A> command can be
used with non-orthogonal basis vectors to define a lattice that will
tile a triclinic simulation box via the
<A HREF = "create_atoms.html">create_atoms</A> command.
</P>
<P>A second use is to run Parinello-Rahman dyanamics via the <A HREF = "fix_nh.html">fix
npt</A> command, which will adjust the xy, xz, yz tilt
factors to compensate for off-diagonal components of the pressure
tensor. The analalog for an <A HREF = "minimize.html">energy minimization</A> is
the <A HREF = "fix_box_relax.html">fix box/relax</A> command.
</P>
<P>A third use is to shear a bulk solid to study the response of the
material. The <A HREF = "fix_deform.html">fix deform</A> command can be used for
this purpose. It allows dynamic control of the xy, xz, yz tilt
factors as a simulation runs. This is discussed in the next section
on non-equilibrium MD (NEMD) simulations.
</P>
<HR>
<A NAME = "howto_13"></A><H4>6.13 NEMD simulations
</H4>
<P>Non-equilibrium molecular dynamics or NEMD simulations are typically
used to measure a fluid's rheological properties such as viscosity.
In LAMMPS, such simulations can be performed by first setting up a
non-orthogonal simulation box (see the preceding Howto section).
</P>
<P>A shear strain can be applied to the simulation box at a desired
strain rate by using the <A HREF = "fix_deform.html">fix deform</A> command. The
<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> command can be used to thermostat
the sheared fluid and integrate the SLLOD equations of motion for the
system. Fix nvt/sllod uses <A HREF = "compute_temp_deform.html">compute
temp/deform</A> to compute a thermal temperature
by subtracting out the streaming velocity of the shearing atoms. The
velocity profile or other properties of the fluid can be monitored via
the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command.
</P>
<P>As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by
LAMMPS for computational efficiency to be 1/2 of the parallel box
length. However, <A HREF = "fix_deform.html">fix deform</A> can continuously strain
a box by an arbitrary amount. As discussed in the <A HREF = "fix_deform.html">fix
deform</A> command, when the tilt value reaches a limit,
the box is flipped to the opposite limit which is an equivalent tiling
of periodic space. The strain rate can then continue to change as
before. In a long NEMD simulation these box re-shaping events may
occur many times.
</P>
<P>In a NEMD simulation, the "remap" option of <A HREF = "fix_deform.html">fix
deform</A> should be set to "remap v", since that is what
<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> assumes to generate a velocity
profile consistent with the applied shear strain rate.
</P>
<P>An alternative method for calculating viscosities is provided via the
<A HREF = "fix_viscosity.html">fix viscosity</A> command.
</P>
<HR>
<A NAME = "howto_14"></A><H4>6.14 Finite-size spherical and aspherical particles
</H4>
<P>Typical MD models treat atoms or particles as point masses. Sometimes
it is desirable to have a model with finite-size particles such as
spheroids or ellipsoids or generalized aspherical bodies. The
difference is that such particles have a moment of inertia, rotational
energy, and angular momentum. Rotation is induced by torque coming
from interactions with other particles.
</P>
<P>LAMMPS has several options for running simulations with these kinds of
particles. The following aspects are discussed in turn:
</P>
<UL><LI>atom styles
<LI>pair potentials
<LI>time integration
<LI>computes, thermodynamics, and dump output
<LI>rigid bodies composed of finite-size particles
</UL>
<P>Example input scripts for these kinds of models are in the body,
colloid, dipole, ellipse, line, peri, pour, and tri directories of the
<A HREF = "Section_example.html">examples directory</A> in the LAMMPS distribution.
</P>
<H5>Atom styles
</H5>
<P>There are several <A HREF = "atom_style.html">atom styles</A> that allow for
definition of finite-size particles: sphere, dipole, ellipsoid, line,
tri, peri, and body.
</P>
<P>The sphere style defines particles that are spheriods and each
particle can have a unique diameter and mass (or density). These
particles store an angular velocity (omega) and can be acted upon by
torque. The "set" command can be used to modify the diameter and mass
of individual particles, after then are created.
</P>
<P>The dipole style does not actually define finite-size particles, but
is often used in conjunction with spherical particles, via a command
like
</P>
<PRE>atom_style hybrid sphere dipole
</PRE>
<P>This is because when dipoles interact with each other, they induce
torques, and a particle must be finite-size (i.e. have a moment of
inertia) in order to respond and rotate. See the <A HREF = "atom_style.html">atom_style
dipole</A> command for details. The "set" command can be
used to modify the orientation and length of the dipole moment of
individual particles, after then are created.
</P>
<P>The ellipsoid style defines particles that are ellipsoids and thus can
be aspherical. Each particle has a shape, specified by 3 diameters,
and mass (or density). These particles store an angular momentum and
their orientation (quaternion), and can be acted upon by torque. They
do not store an angular velocity (omega), which can be in a different
direction than angular momentum, rather they compute it as needed.
The "set" command can be used to modify the diameter, orientation, and
mass of individual particles, after then are created. It also has a
brief explanation of what quaternions are.
</P>
<P>The line style defines line segment particles with two end points and
a mass (or density). They can be used in 2d simulations, and they can
be joined together to form rigid bodies which represent arbitrary
polygons.
</P>
<P>The tri style defines triangular particles with three corner points
and a mass (or density). They can be used in 3d simulations, and they
can be joined together to form rigid bodies which represent arbitrary
particles with a triangulated surface.
</P>
<P>The peri style is used with <A HREF = "pair_peri.html">Peridynamic models</A> and
defines particles as having a volume, that is used internally in the
<A HREF = "pair_peri.html">pair_style peri</A> potentials.
</P>
<P>The body style allows for definition of particles which can represent
complex entities, such as surface meshes of discrete points,
collections of sub-particles, deformable objects, etc. The body style
is discussed in more detail on the <A HREF = "body.html">body</A> doc page.
</P>
<P>Note that if one of these atom styles is used (or multiple styles via
the <A HREF = "atom_style.html">atom_style hybrid</A> command), not all particles in
the system are required to be finite-size or aspherical.
</P>
<P>For example, in the ellipsoid style, if the 3 shape parameters are set
to the same value, the particle will be a sphere rather than an
ellipsoid. If the 3 shape parameters are all set to 0.0 or if the
diameter is set to 0.0, it will be a point particle. In the line or
tri style, if the lineflag or triflag is specified as 0, then it
will be a point particle.
</P>
<P>Some of the pair styles used to compute pairwise interactions between
finite-size particles also compute the correct interaction with point
particles as well, e.g. the interaction between a point particle and a
finite-size particle or between two point particles. If necessary,
<A HREF = "pair_hybrid.html">pair_style hybrid</A> can be used to insure the correct
interactions are computed for the appropriate style of interactions.
Likewise, using groups to partition particles (ellipsoids versus
spheres versus point particles) will allow you to use the appropriate
time integrators and temperature computations for each class of
particles. See the doc pages for various commands for details.
</P>
<P>Also note that for <A HREF = "dimension.html">2d simulations</A>, atom styles sphere
and ellipsoid still use 3d particles, rather than as circular disks or
ellipses. This means they have the same moment of inertia as the 3d
object. When temperature is computed, the correct degrees of freedom
are used for rotation in a 2d versus 3d system.
</P>
<H5>Pair potentials
</H5>
<P>When a system with finite-size particles is defined, the particles
will only rotate and experience torque if the force field computes
such interactions. These are the various <A HREF = "pair_style.html">pair
styles</A> that generate torque:
</P>
<UL><LI><A HREF = "pair_gran.html">pair_style gran/history</A>
<LI><A HREF = "pair_gran.html">pair_style gran/hertzian</A>
<LI><A HREF = "pair_gran.html">pair_style gran/no_history</A>
<LI><A HREF = "pair_dipole.html">pair_style dipole/cut</A>
<LI><A HREF = "pair_gayberne.html">pair_style gayberne</A>
<LI><A HREF = "pair_resquared.html">pair_style resquared</A>
<LI><A HREF = "pair_brownian.html">pair_style brownian</A>
<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A>
<LI><A HREF = "pair_line_lj.html">pair_style line/lj</A>
<LI><A HREF = "pair_tri_lj.html">pair_style tri/lj</A>
<LI><A HREF = "pair_body.html">pair_style body</A>
</UL>
<P>The granular pair styles are used with spherical particles. The
dipole pair style is used with the dipole atom style, which could be
applied to spherical or ellipsoidal particles. The GayBerne and
REsquared potentials require ellipsoidal particles, though they will
also work if the 3 shape parameters are the same (a sphere). The
Brownian and lubrication potentials are used with spherical particles.
The line, tri, and body potentials are used with line segment,
triangular, and body particles respectively.
</P>
<H5>Time integration
</H5>
<P>There are several fixes that perform time integration on finite-size
spherical particles, meaning the integrators update the rotational
orientation and angular velocity or angular momentum of the particles:
</P>
<UL><LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
<LI><A HREF = "fix_nvt_sphere.html">fix nvt/sphere</A>
<LI><A HREF = "fix_npt_sphere.html">fix npt/sphere</A>
</UL>
<P>Likewise, there are 3 fixes that perform time integration on
ellipsoidal particles:
</P>
<UL><LI><A HREF = "fix_nve_asphere.html">fix nve/asphere</A>
<LI><A HREF = "fix_nvt_asphere.html">fix nvt/asphere</A>
<LI><A HREF = "fix_npt_asphere.html">fix npt/asphere</A>
</UL>
<P>The advantage of these fixes is that those which thermostat the
particles include the rotational degrees of freedom in the temperature
calculation and thermostatting. The <A HREF = "fix_langevin">fix langevin</A>
command can also be used with its <I>omgea</I> or <I>angmom</I> options to
thermostat the rotational degrees of freedom for spherical or
ellipsoidal particles. Other thermostatting fixes only operate on the
translational kinetic energy of finite-size particles.
</P>
<P>These fixes perform constant NVE time integration on line segment,
triangular, and body particles:
</P>
<UL><LI><A HREF = "fix_nve_line.html">fix nve/line</A>
<LI><A HREF = "fix_nve_tri.html">fix nve/tri</A>
<LI><A HREF = "fix_nve_body.html">fix nve/body</A>
</UL>
<P>Note that for mixtures of point and finite-size particles, these
integration fixes can only be used with <A HREF = "group.html">groups</A> which
contain finite-size particles.
</P>
<H5>Computes, thermodynamics, and dump output
</H5>
<P>There are several computes that calculate the temperature or
rotational energy of spherical or ellipsoidal particles:
</P>
<UL><LI><A HREF = "compute_temp_sphere.html">compute temp/sphere</A>
<LI><A HREF = "compute_temp_asphere.html">compute temp/asphere</A>
<LI><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
<LI><A HREF = "compute_erotate_asphere.html">compute erotate/asphere</A>
</UL>
<P>These include rotational degrees of freedom in their computation. If
you wish the thermodynamic output of temperature or pressure to use
one of these computes (e.g. for a system entirely composed of
finite-size particles), then the compute can be defined and the
<A HREF = "thermo_modify.html">thermo_modify</A> command used. Note that by default
thermodynamic quantities will be calculated with a temperature that
only includes translational degrees of freedom. See the
<A HREF = "thermo_style.html">thermo_style</A> command for details.
</P>
<P>These commands can be used to output various attributes of finite-size
particles:
</P>
<UL><LI><A HREF = "dump.html">dump custom</A>
<LI><A HREF = "compute_property_atom.html">compute property/atom</A>
<LI><A HREF = "dump.html">dump local</A>
<LI><A HREF = "compute_body_local.html">compute body/local</A>
</UL>
<P>Attributes include the dipole moment, the angular velocity, the
angular momentum, the quaternion, the torque, the end-point and
corner-point coordinates (for line and tri particles), and
sub-particle attributes of body particles.
</P>
<H5>Rigid bodies composed of finite-size particles
</H5>
<P>The <A HREF = "fix_rigid.html">fix rigid</A> command treats a collection of
particles as a rigid body, computes its inertia tensor, sums the total
force and torque on the rigid body each timestep due to forces on its
constituent particles, and integrates the motion of the rigid body.
</P>
<P>If any of the constituent particles of a rigid body are finite-size
particles (spheres or ellipsoids or line segments or triangles), then
their contribution to the inertia tensor of the body is different than
if they were point particles. This means the rotational dynamics of
the rigid body will be different. Thus a model of a dimer is
different if the dimer consists of two point masses versus two
spheroids, even if the two particles have the same mass. Finite-size
particles that experience torque due to their interaction with other
particles will also impart that torque to a rigid body they are part
of.
</P>
<P>See the "fix rigid" command for example of complex rigid-body models
it is possible to define in LAMMPS.
</P>
<P>Note that the <A HREF = "fix_shake.html">fix shake</A> command can also be used to
treat 2, 3, or 4 particles as a rigid body, but it always assumes the
particles are point masses.
</P>
<P>Also note that body particles cannot be modeled with the <A HREF = "fix_rigid.html">fix
rigid</A> command. Body particles are treated by LAMMPS
as single particles, though they can store internal state, such as a
list of sub-particles. Individual body partices are typically treated
as rigid bodies, and their motion integrated with a command like <A HREF = "fix_nve_body.html">fix
nve/body</A>. Interactions between pairs of body
particles are computed via a command like <A HREF = "pair_body.html">pair_style
body</A>.
</P>
<HR>
<A NAME = "howto_15"></A><H4>6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)
</H4>
<P>There are four basic kinds of LAMMPS output:
</P>
<UL><LI><A HREF = "thermo_style.html">Thermodynamic output</A>, which is a list
of quantities printed every few timesteps to the screen and logfile.
<LI><A HREF = "dump.html">Dump files</A>, which contain snapshots of atoms and various
per-atom values and are written at a specified frequency.
<LI>Certain fixes can output user-specified quantities to files: <A HREF = "fix_ave_time.html">fix
ave/time</A> for time averaging, <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> for spatial averaging, and <A HREF = "fix_print.html">fix
print</A> for single-line output of
<A HREF = "variable.html">variables</A>. Fix print can also output to the
screen.
<LI><A HREF = "restart.html">Restart files</A>.
</UL>
<P>A simulation prints one set of thermodynamic output and (optionally)
restart files. It can generate any number of dump files and fix
output files, depending on what <A HREF = "dump.html">dump</A> and <A HREF = "fix.html">fix</A>
commands you specify.
</P>
<P>As discussed below, LAMMPS gives you a variety of ways to determine
what quantities are computed and printed when the thermodynamics,
dump, or fix commands listed above perform output. Throughout this
discussion, note that users can also <A HREF = "Section_modify.html">add their own computes and fixes
to LAMMPS</A> which can then generate values that can
then be output with these commands.
</P>
<P>The following sub-sections discuss different LAMMPS command related
to output and the kind of data they operate on and produce:
</P>
<UL><LI><A HREF = "#global">Global/per-atom/local data</A>
<LI><A HREF = "#scalar">Scalar/vector/array data</A>
<LI><A HREF = "#thermo">Thermodynamic output</A>
<LI><A HREF = "#dump">Dump file output</A>
<LI><A HREF = "#fixoutput">Fixes that write output files</A>
<LI><A HREF = "#computeoutput">Computes that process output quantities</A>
<LI><A HREF = "#fixoutput">Fixes that process output quantities</A>
<LI><A HREF = "#compute">Computes that generate values to output</A>
<LI><A HREF = "#fix">Fixes that generate values to output</A>
<LI><A HREF = "#variable">Variables that generate values to output</A>
<LI><A HREF = "#table">Summary table of output options and data flow between commands</A>
</UL>
<H5><A NAME = "global"></A>Global/per-atom/local data
</H5>
<P>Various output-related commands work with three different styles of
data: global, per-atom, or local. A global datum is one or more
system-wide values, e.g. the temperature of the system. A per-atom
datum is one or more values per atom, e.g. the kinetic energy of each
atom. Local datums are calculated by each processor based on the
atoms it owns, but there may be zero or more per atom, e.g. a list of
bond distances.
</P>
<H5><A NAME = "scalar"></A>Scalar/vector/array data
</H5>
<P>Global, per-atom, and local datums can each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The
doc page for a "compute" or "fix" or "variable" that generates data
will specify both the style and kind of data it produces, e.g. a
per-atom vector.
</P>
<P>When a quantity is accessed, as in many of the output commands
discussed below, it can be referenced via the following bracket
notation, where ID in this case is the ID of a compute. The leading
"c_" would be replaced by "f_" for a fix, or "v_" for a variable:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >c_ID </TD><TD > entire scalar, vector, or array</TD></TR>
<TR><TD >c_ID[I] </TD><TD > one element of vector, one column of array</TD></TR>
<TR><TD >c_ID[I][J] </TD><TD > one element of array
</TD></TR></TABLE></DIV>
<P>In other words, using one bracket reduces the dimension of the data
once (vector -> scalar, array -> vector). Using two brackets reduces
the dimension twice (array -> scalar). Thus a command that uses
scalar values as input can typically also process elements of a vector
or array.
</P>
<H5><A NAME = "thermo"></A>Thermodynamic output
</H5>
<P>The frequency and format of thermodynamic output is set by the
<A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_style.html">thermo_style</A>, and
<A HREF = "thermo_modify.html">thermo_modify</A> commands. The
<A HREF = "thermo_style.html">thermo_style</A> command also specifies what values
are calculated and written out. Pre-defined keywords can be specified
(e.g. press, etotal, etc). Three additional kinds of keywords can
also be specified (c_ID, f_ID, v_name), where a <A HREF = "compute.html">compute</A>
or <A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A> provides the value to be
output. In each case, the compute, fix, or variable must generate
global values for input to the <A HREF = "dump.html">thermo_style custom</A>
command.
</P>
<P>Note that thermodynamic output values can be "extensive" or
"intensive". The former scale with the number of atoms in the system
(e.g. total energy), the latter do not (e.g. temperature). The
setting for <A HREF = "thermo_modify.html">thermo_modify norm</A> determines whether
extensive quantities are normalized or not. Computes and fixes
produce either extensive or intensive values; see their individual doc
pages for details. <A HREF = "variable.html">Equal-style variables</A> produce only
intensive values; you can include a division by "natoms" in the
formula if desired, to make an extensive calculation produce an
intensive result.
</P>
<H5><A NAME = "dump"></A>Dump file output
</H5>
<P>Dump file output is specified by the <A HREF = "dump.html">dump</A> and
<A HREF = "dump_modify.html">dump_modify</A> commands. There are several
pre-defined formats (dump atom, dump xtc, etc).
</P>
<P>There is also a <A HREF = "dump.html">dump custom</A> format where the user
specifies what values are output with each atom. Pre-defined atom
attributes can be specified (id, x, fx, etc). Three additional kinds
of keywords can also be specified (c_ID, f_ID, v_name), where a
<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A>
provides the values to be output. In each case, the compute, fix, or
variable must generate per-atom values for input to the <A HREF = "dump.html">dump
custom</A> command.
</P>
<P>There is also a <A HREF = "dump.html">dump local</A> format where the user specifies
what local values to output. A pre-defined index keyword can be
specified to enumuerate the local values. Two additional kinds of
keywords can also be specified (c_ID, f_ID), where a
<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A>
provides the values to be output. In each case, the compute or fix
must generate local values for input to the <A HREF = "dump.html">dump local</A>
command.
</P>
<H5><A NAME = "fixoutput"></A>Fixes that write output files
</H5>
<P>Several fixes take various quantities as input and can write output
files: <A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>,
<A HREF = "fix_ave_correlate.html">fix ave/correlate</A>, and <A HREF = "fix_print.html">fix
print</A>.
</P>
<P>The <A HREF = "fix_ave_time.html">fix ave/time</A> command enables direct output to
a file and/or time-averaging of global scalars or vectors. The user
specifies one or more quantities as input. These can be global
<A HREF = "compute.html">compute</A> values, global <A HREF = "fix.html">fix</A> values, or
<A HREF = "variable.html">variables</A> of any style except the atom style which
produces per-atom values. Since a variable can refer to keywords used
by the <A HREF = "thermo_style.html">thermo_style custom</A> command (like temp or
press) and individual per-atom values, a wide variety of quantities
can be time averaged and/or output in this way. If the inputs are one
or more scalar values, then the fix generate a global scalar or vector
of output. If the inputs are one or more vector values, then the fix
generates a global vector or array of output. The time-averaged
output of this fix can also be used as input to other output commands.
</P>
<P>The <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command enables direct
output to a file of spatial-averaged per-atom quantities like those
output in dump files, within 1d layers of the simulation box. The
per-atom quantities can be atom density (mass or number) or atom
attributes such as position, velocity, force. They can also be
per-atom quantities calculated by a <A HREF = "compute.html">compute</A>, by a
<A HREF = "fix.html">fix</A>, or by an atom-style <A HREF = "variable.html">variable</A>. The
spatial-averaged output of this fix can also be used as input to other
output commands.
</P>
<P>The <A HREF = "fix_ave_histo.html">fix ave/histo</A> command enables direct output
to a file of histogrammed quantities, which can be global or per-atom
or local quantities. The histogram output of this fix can also be
used as input to other output commands.
</P>
<P>The <A HREF = "fix_ave_correlate.html">fix ave/correlate</A> command enables direct
output to a file of time-correlated quantities, which can be global
scalars. The correlation matrix output of this fix can also be used
as input to other output commands.
</P>
<P>The <A HREF = "fix_print.html">fix print</A> command can generate a line of output
written to the screen and log file or to a separate file, periodically
during a running simulation. The line can contain one or more
<A HREF = "variable.html">variable</A> values for any style variable except the atom
style). As explained above, variables themselves can contain
references to global values generated by <A HREF = "thermo_style.html">thermodynamic
keywords</A>, <A HREF = "compute.html">computes</A>,
<A HREF = "fix.html">fixes</A>, or other <A HREF = "variable.html">variables</A>, or to per-atom
values for a specific atom. Thus the <A HREF = "fix_print.html">fix print</A>
command is a means to output a wide variety of quantities separate
from normal thermodynamic or dump file output.
</P>
<H5><A NAME = "computeoutput"></A>Computes that process output quantities
</H5>
<P>The <A HREF = "compute_reduce.html">compute reduce</A> and <A HREF = "compute_reduce.html">compute
reduce/region</A> commands take one or more per-atom
or local vector quantities as inputs and "reduce" them (sum, min, max,
ave) to scalar quantities. These are produced as output values which
can be used as input to other output commands.
</P>
<P>The <A HREF = "compute_slice.html">compute slice</A> command take one or more global
vector or array quantities as inputs and extracts a subset of their
values to create a new vector or array. These are produced as output
values which can be used as input to other output commands.
</P>
<P>The <A HREF = "compute_property_atom.html">compute property/atom</A> command takes a
list of one or more pre-defined atom attributes (id, x, fx, etc) and
stores the values in a per-atom vector or array. These are produced
as output values which can be used as input to other output commands.
The list of atom attributes is the same as for the <A HREF = "dump.html">dump
custom</A> command.
</P>
<P>The <A HREF = "compute_property_local.html">compute property/local</A> command takes
a list of one or more pre-defined local attributes (bond info, angle
info, etc) and stores the values in a local vector or array. These
are produced as output values which can be used as input to other
output commands.
</P>
<H5><A NAME = "fixoutput"></A>Fixes that process output quantities
</H5>
<P>The <A HREF = "fix_vector.html">fix vector</A> command can create global vectors as
output from global scalars as input, accumulating them one element at
a time.
</P>
<P>The <A HREF = "fix_ave_atom.html">fix ave/atom</A> command performs time-averaging
of per-atom vectors. The per-atom quantities can be atom attributes
such as position, velocity, force. They can also be per-atom
quantities calculated by a <A HREF = "compute.html">compute</A>, by a
<A HREF = "fix.html">fix</A>, or by an atom-style <A HREF = "variable.html">variable</A>. The
time-averaged per-atom output of this fix can be used as input to
other output commands.
</P>
<P>The <A HREF = "fix_store_state.html">fix store/state</A> command can archive one or
more per-atom attributes at a particular time, so that the old values
can be used in a future calculation or output. The list of atom
attributes is the same as for the <A HREF = "dump.html">dump custom</A> command,
including per-atom quantities calculated by a <A HREF = "compute.html">compute</A>,
by a <A HREF = "fix.html">fix</A>, or by an atom-style <A HREF = "variable.html">variable</A>.
The output of this fix can be used as input to other output commands.
</P>
<H5><A NAME = "compute"></A>Computes that generate values to output
</H5>
<P>Every <A HREF = "compute.html">compute</A> in LAMMPS produces either global or
per-atom or local values. The values can be scalars or vectors or
arrays of data. These values can be output using the other commands
described in this section. The doc page for each compute command
describes what it produces. Computes that produce per-atom or local
values have the word "atom" or "local" in their style name. Computes
without the word "atom" or "local" produce global values.
</P>
<H5><A NAME = "fix"></A>Fixes that generate values to output
</H5>
<P>Some <A HREF = "fix.html">fixes</A> in LAMMPS produces either global or per-atom or
local values which can be accessed by other commands. The values can
be scalars or vectors or arrays of data. These values can be output
using the other commands described in this section. The doc page for
each fix command tells whether it produces any output quantities and
describes them.
</P>
<H5><A NAME = "variable"></A>Variables that generate values to output
</H5>
<P>Every <A HREF = "variable.html">variables</A> defined in an input script generates
either a global scalar value or a per-atom vector (only atom-style
variables) when it is accessed. The formulas used to define equal-
and atom-style variables can contain references to the thermodynamic
keywords and to global and per-atom data generated by computes, fixes,
and other variables. The values generated by variables can be output
using the other commands described in this section.
</P>
<H5><A NAME = "table"></A>Summary table of output options and data flow between commands
</H5>
<P>This table summarizes the various commands that can be used for
generating output from LAMMPS. Each command produces output data of
some kind and/or writes data to a file. Most of the commands can take
data from other commands as input. Thus you can link many of these
commands together in pipeline form, where data produced by one command
is used as input to another command and eventually written to the
screen or to a file. Note that to hook two commands together the
output and input data types must match, e.g. global/per-atom/local
data and scalar/vector/array data.
</P>
<P>Also note that, as described above, when a command takes a scalar as
input, that could be an element of a vector or array. Likewise a
vector input could be a column of an array.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >Command</TD><TD > Input</TD><TD > Output</TD><TD ></TD></TR>
<TR><TD ><A HREF = "thermo_style.html">thermo_style custom</A></TD><TD > global scalars</TD><TD > screen, log file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "dump.html">dump custom</A></TD><TD > per-atom vectors</TD><TD > dump file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "dump.html">dump local</A></TD><TD > local vectors</TD><TD > dump file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_print.html">fix print</A></TD><TD > global scalar from variable</TD><TD > screen, file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "print.html">print</A></TD><TD > global scalar from variable</TD><TD > screen</TD><TD ></TD></TR>
<TR><TD ><A HREF = "compute.html">computes</A></TD><TD > N/A</TD><TD > global/per-atom/local scalar/vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix.html">fixes</A></TD><TD > N/A</TD><TD > global/per-atom/local scalar/vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "variable.html">variables</A></TD><TD > global scalars, per-atom vectors</TD><TD > global scalar, per-atom vector</TD><TD ></TD></TR>
<TR><TD ><A HREF = "compute_reduce.html">compute reduce</A></TD><TD > per-atom/local vectors</TD><TD > global scalar/vector</TD><TD ></TD></TR>
<TR><TD ><A HREF = "compute_slice.html">compute slice</A></TD><TD > global vectors/arrays</TD><TD > global vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "compute_property_atom.html">compute property/atom</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "compute_property_local.html">compute property/local</A></TD><TD > local vectors</TD><TD > local vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_vector.html">fix vector</A></TD><TD > global scalars</TD><TD > global vector</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_ave_atom.html">fix ave/atom</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_ave_time.html">fix ave/time</A></TD><TD > global scalars/vectors</TD><TD > global scalar/vector/array, file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_ave_spatial.html">fix ave/spatial</A></TD><TD > per-atom vectors</TD><TD > global array, file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_ave_histo.html">fix ave/histo</A></TD><TD > global/per-atom/local scalars and vectors</TD><TD > global array, file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_ave_correlate.html">fix ave/correlate</A></TD><TD > global scalars</TD><TD > global array, file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_store_state.html">fix store/state</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
<TR><TD >
</TD></TR></TABLE></DIV>
<HR>
<A NAME = "howto_16"></A><H4>6.16 Thermostatting, barostatting, and computing temperature
</H4>
<P>Thermostatting means controlling the temperature of particles in an MD
simulation. Barostatting means controlling the pressure. Since the
pressure includes a kinetic component due to particle velocities, both
these operations require calculation of the temperature. Typically a
target temperature (T) and/or pressure (P) is specified by the user,
and the thermostat or barostat attempts to equilibrate the system to
the requested T and/or P.
</P>
<P>Temperature is computed as kinetic energy divided by some number of
degrees of freedom (and the Boltzmann constant). Since kinetic energy
is a function of particle velocity, there is often a need to
distinguish between a particle's advection velocity (due to some
aggregate motiion of particles) and its thermal velocity. The sum of
the two is the particle's total velocity, but the latter is often what
is wanted to compute a temperature.
</P>
<P>LAMMPS has several options for computing temperatures, any of which
can be used in thermostatting and barostatting. These <A HREF = "compute.html">compute
commands</A> calculate temperature, and the <A HREF = "compute_pressure.html">compute
pressure</A> command calculates pressure.
</P>
<UL><LI><A HREF = "compute_temp.html">compute temp</A>
<LI><A HREF = "compute_temp_sphere.html">compute temp/sphere</A>
<LI><A HREF = "compute_temp_asphere.html">compute temp/asphere</A>
<LI><A HREF = "compute_temp_com.html">compute temp/com</A>
<LI><A HREF = "compute_temp_deform.html">compute temp/deform</A>
<LI><A HREF = "compute_temp_partial.html">compute temp/partial</A>
<LI><A HREF = "compute_temp_profile.html">compute temp/profile</A>
<LI><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>
<LI><A HREF = "compute_temp_region.html">compute temp/region</A>
</UL>
<P>All but the first 3 calculate velocity biases directly (e.g. advection
velocities) that are removed when computing the thermal temperature.
<A HREF = "compute_temp_sphere.html">Compute temp/sphere</A> and <A HREF = "compute_temp_asphere.html">compute
temp/asphere</A> compute kinetic energy for
finite-size particles that includes rotational degrees of freedom.
They both allow for velocity biases indirectly, via an optional extra
argument, another temperature compute that subtracts a velocity bias.
This allows the translational velocity of spherical or aspherical
particles to be adjusted in prescribed ways.
</P>
<P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>, or in one
case by a pair style. Several thermostatting fixes are available:
Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling
(temp/rescale). Dissipative particle dynamics (DPD) thermostatting
can be invoked via the <I>dpd/tstat</I> pair style:
</P>
<UL><LI><A HREF = "fix_nh.html">fix nvt</A>
<LI><A HREF = "fix_nvt_sphere.html">fix nvt/sphere</A>
<LI><A HREF = "fix_nvt_asphere.html">fix nvt/asphere</A>
<LI><A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
<LI><A HREF = "fix_temp_berendsen.html">fix temp/berendsen</A>
<LI><A HREF = "fix_temp_csvr.html">fix temp/csvr</A>
<LI><A HREF = "fix_langevin.html">fix langevin</A>
<LI><A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
<LI><A HREF = "pair_dpd.html">pair_style dpd/tstat</A>
</UL>
<P><A HREF = "fix_nh.html">Fix nvt</A> only thermostats the translational velocity of
particles. <A HREF = "fix_nvt_sllod.html">Fix nvt/sllod</A> also does this, except
that it subtracts out a velocity bias due to a deforming box and
integrates the SLLOD equations of motion. See the <A HREF = "#howto_13">NEMD
simulations</A> section of this page for further details. <A HREF = "fix_nvt_sphere.html">Fix
nvt/sphere</A> and <A HREF = "fix_nvt_asphere.html">fix
nvt/asphere</A> thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
particles.
</P>
<P>DPD thermostatting alters pairwise interactions in a manner analagous
to the per-particle thermostatting of <A HREF = "fix_langevin.html">fix
langevin</A>.
</P>
<P>Any of the thermostatting fixes can use temperature computes that
remove bias which has two effects. First, the current calculated
temperature, which is compared to the requested target temperature, is
caluclated with the velocity bias removed. Second, the thermostat
adjusts only the thermal temperature component of the particle's
velocities, which are the velocities with the bias removed. The
removed bias is then added back to the adjusted velocities. See the
doc pages for the individual fixes and for the
<A HREF = "fix_modify.html">fix_modify</A> command for instructions on how to assign
a temperature compute to a thermostatting fix. For example, you can
apply a thermostat to only the x and z components of velocity by using
it in conjunction with <A HREF = "compute_temp_partial.html">compute
temp/partial</A>. Of you could thermostat only
the thermal temperature of a streaming flow of particles without
affecting the streaming velocity, by using <A HREF = "compute_temp_profile.html">compute
temp/profile</A>.
</P>
<P>IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
they update the velocities and positions of particles due to forces
and velocities respectively. The other thermostat fixes only adjust
velocities; they do NOT perform time integration updates. Thus they
should be used in conjunction with a constant NVE integration fix such
as these:
</P>
<UL><LI><A HREF = "fix_nve.html">fix nve</A>
<LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
<LI><A HREF = "fix_nve_asphere.html">fix nve/asphere</A>
</UL>
<P>Barostatting in LAMMPS is also performed by <A HREF = "fix.html">fixes</A>. Two
barosttating methods are currently available: Nose-Hoover (npt and
nph) and Berendsen:
</P>
<UL><LI><A HREF = "fix_nh.html">fix npt</A>
<LI><A HREF = "fix_npt_sphere.html">fix npt/sphere</A>
<LI><A HREF = "fix_npt_asphere.html">fix npt/asphere</A>
<LI><A HREF = "fix_nh.html">fix nph</A>
<LI><A HREF = "fix_press_berendsen.html">fix press/berendsen</A>
</UL>
<P>The <A HREF = "fix_nh.html">fix npt</A> commands include a Nose-Hoover thermostat
and barostat. <A HREF = "fix_nh.html">Fix nph</A> is just a Nose/Hoover barostat;
it does no thermostatting. Both <A HREF = "fix_nh.html">fix nph</A> and <A HREF = "fix_press_berendsen.html">fix
press/bernendsen</A> can be used in conjunction
with any of the thermostatting fixes.
</P>
<P>As with the thermostats, <A HREF = "fix_nh.html">fix npt</A> and <A HREF = "fix_nh.html">fix
nph</A> only use translational motion of the particles in
computing T and P and performing thermo/barostatting. <A HREF = "fix_npt_sphere.html">Fix
npt/sphere</A> and <A HREF = "fix_npt_asphere.html">fix
npt/asphere</A> thermo/barostat using not only
translation velocities but also rotational velocities for spherical
and aspherical particles.
</P>
<P>All of the barostatting fixes use the <A HREF = "compute_pressure.html">compute
pressure</A> compute to calculate a current
pressure. By default, this compute is created with a simple <A HREF = "compute_temp.html">compute
temp</A> (see the last argument of the <A HREF = "compute_pressure.html">compute
pressure</A> command), which is used to calculated
the kinetic componenet of the pressure. The barostatting fixes can
also use temperature computes that remove bias for the purpose of
computing the kinetic componenet which contributes to the current
pressure. See the doc pages for the individual fixes and for the
<A HREF = "fix_modify.html">fix_modify</A> command for instructions on how to assign
a temperature or pressure compute to a barostatting fix.
</P>
<P>IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods (<A HREF = "fix_nh.html">fix
npt</A> and <A HREF = "fix_nh.html">fix nph</A>) perform time
integration. <A HREF = "fix_press_berendsen.html">Fix press/berendsen</A> does NOT,
so it should be used with one of the constant NVE fixes or with one of
the NVT fixes.
</P>
<P>Finally, thermodynamic output, which can be setup via the
<A HREF = "thermo_style.html">thermo_style</A> command, often includes temperature
and pressure values. As explained on the doc page for the
<A HREF = "thermo_style.html">thermo_style</A> command, the default T and P are
setup by the thermo command itself. They are NOT the ones associated
with any thermostatting or barostatting fix you have defined or with
any compute that calculates a temperature or pressure. Thus if you
want to view these values of T and P, you need to specify them
explicitly via a <A HREF = "thermo_style.html">thermo_style custom</A> command. Or
you can use the <A HREF = "thermo_modify.html">thermo_modify</A> command to
re-define what temperature or pressure compute is used for default
thermodynamic output.
</P>
<HR>
<A NAME = "howto_17"></A><H4>6.17 Walls
</H4>
<P>Walls in an MD simulation are typically used to bound particle motion,
i.e. to serve as a boundary condition.
</P>
<P>Walls in LAMMPS can be of rough (made of particles) or idealized
surfaces. Ideal walls can be smooth, generating forces only in the
normal direction, or frictional, generating forces also in the
tangential direction.
</P>
<P>Rough walls, built of particles, can be created in various ways. The
particles themselves can be generated like any other particle, via the
<A HREF = "lattice.html">lattice</A> and <A HREF = "create_atoms.html">create_atoms</A> commands,
or read in via the <A HREF = "read_data.html">read_data</A> command.
</P>
<P>Their motion can be constrained by many different commands, so that
they do not move at all, move together as a group at constant velocity
or in response to a net force acting on them, move in a prescribed
fashion (e.g. rotate around a point), etc. Note that if a time
integration fix like <A HREF = "fix_nve.html">fix nve</A> or <A HREF = "fix_nh.html">fix nvt</A>
is not used with the group that contains wall particles, their
positions and velocities will not be updated.
</P>
<UL><LI><A HREF = "fix_aveforce.html">fix aveforce</A> - set force on particles to average value, so they move together
<LI><A HREF = "fix_setforce.html">fix setforce</A> - set force on particles to a value, e.g. 0.0
<LI><A HREF = "fix_freeze.html">fix freeze</A> - freeze particles for use as granular walls
<LI><A HREF = "fix_nve_noforce.html">fix nve/noforce</A> - advect particles by their velocity, but without force
<LI><A HREF = "fix_move.html">fix move</A> - prescribe motion of particles by a linear velocity, oscillation, rotation, variable
</UL>
<P>The <A HREF = "fix_move.html">fix move</A> command offers the most generality, since
the motion of individual particles can be specified with
<A HREF = "variable.html">variable</A> formula which depends on time and/or the
particle position.
</P>
<P>For rough walls, it may be useful to turn off pairwise interactions
between wall particles via the <A HREF = "neigh_modify.html">neigh_modify
exclude</A> command.
</P>
<P>Rough walls can also be created by specifying frozen particles that do
not move and do not interact with mobile particles, and then tethering
other particles to the fixed particles, via a <A HREF = "bond_style.html">bond</A>.
The bonded particles do interact with other mobile particles.
</P>
<P>Idealized walls can be specified via several fix commands. <A HREF = "fix_wall_gran.html">Fix
wall/gran</A> creates frictional walls for use with
granular particles; all the other commands create smooth walls.
</P>
<UL><LI><A HREF = "fix_wall_reflect.html">fix wall/reflect</A> - reflective flat walls
<LI><A HREF = "fix_wall.html">fix wall/lj93</A> - flat walls, with Lennard-Jones 9/3 potential
<LI><A HREF = "fix_wall.html">fix wall/lj126</A> - flat walls, with Lennard-Jones 12/6 potential
<LI><A HREF = "fix_wall.html">fix wall/colloid</A> - flat walls, with <A HREF = "pair_colloid.html">pair_style colloid</A> potential
<LI><A HREF = "fix_wall.html">fix wall/harmonic</A> - flat walls, with repulsive harmonic spring potential
<LI><A HREF = "fix_wall_region.html">fix wall/region</A> - use region surface as wall
<LI><A HREF = "fix_wall_gran.html">fix wall/gran</A> - flat or curved walls with <A HREF = "pair_gran.html">pair_style granular</A> potential
</UL>
<P>The <I>lj93</I>, <I>lj126</I>, <I>colloid</I>, and <I>harmonic</I> styles all allow the
flat walls to move with a constant velocity, or oscillate in time.
The <A HREF = "fix_wall_region.html">fix wall/region</A> command offers the most
generality, since the region surface is treated as a wall, and the
geometry of the region can be a simple primitive volume (e.g. a
sphere, or cube, or plane), or a complex volume made from the union
and intersection of primitive volumes. <A HREF = "region.html">Regions</A> can also
specify a volume "interior" or "exterior" to the specified primitive
shape or <I>union</I> or <I>intersection</I>. <A HREF = "region.html">Regions</A> can also be
"dynamic" meaning they move with constant velocity, oscillate, or
rotate.
</P>
<P>The only frictional idealized walls currently in LAMMPS are flat or
curved surfaces specified by the <A HREF = "fix_wall_gran.html">fix wall/gran</A>
command. At some point we plan to allow regoin surfaces to be used as
frictional walls, as well as triangulated surfaces.
</P>
<HR>
<A NAME = "howto_18"></A><H4>6.18 Elastic constants
</H4>
<P>Elastic constants characterize the stiffness of a material. The formal
definition is provided by the linear relation that holds between the
stress and strain tensors in the limit of infinitesimal deformation.
In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where
the repeated indices imply summation. s_ij are the elements of the
symmetric stress tensor. e_kl are the elements of the symmetric strain
tensor. C_ijkl are the elements of the fourth rank tensor of elastic
constants. In three dimensions, this tensor has 3^4=81 elements. Using
Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij
is now the derivative of s_i w.r.t. e_j. Because s_i is itself a
derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
most 7*6/2 = 21 distinct elements.
</P>
<P>At zero temperature, it is easy to estimate these derivatives by
deforming the simulation box in one of the six directions using the
<A HREF = "change_box.html">change_box</A> command and measuring the change in the
stress tensor. A general-purpose script that does this is given in the
examples/elastic directory described in <A HREF = "Section_example.html">this
section</A>.
</P>
<P>Calculating elastic constants at finite temperature is more
challenging, because it is necessary to run a simulation that perfoms
time averages of differential properties. One way to do this is to
measure the change in average stress tensor in an NVT simulations when
the cell volume undergoes a finite deformation. In order to balance
the systematic and statistical errors in this method, the magnitude of
the deformation must be chosen judiciously, and care must be taken to
fully equilibrate the deformed cell before sampling the stress
tensor. Another approach is to sample the triclinic cell fluctuations
that occur in an NPT simulation. This method can also be slow to
converge and requires careful post-processing <A HREF = "#Shinoda">(Shinoda)</A>
</P>
<HR>
<A NAME = "howto_19"></A><H4>6.19 Library interface to LAMMPS
</H4>
<P>As described in <A HREF = "Section_start.html#start_5">Section_start 5</A>, LAMMPS
can be built as a library, so that it can be called by another code,
used in a <A HREF = "Section_howto.html#howto_10">coupled manner</A> with other
codes, or driven through a <A HREF = "Section_python.html">Python interface</A>.
</P>
<P>All of these methodologies use a C-style interface to LAMMPS that is
provided in the files src/library.cpp and src/library.h. The
functions therein have a C-style argument list, but contain C++ code
you could write yourself in a C++ application that was invoking LAMMPS
directly. The C++ code in the functions illustrates how to invoke
internal LAMMPS operations. Note that LAMMPS classes are defined
within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
application.
</P>
<P>Library.cpp contains these 5 basic functions:
</P>
<PRE>void lammps_open(int, char **, MPI_Comm, void **)
void lammps_close(void *)
int lammps_version(void *)
void lammps_file(void *, char *)
char *lammps_command(void *, char *)
</PRE>
<P>The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were <A HREF = "Section_start.html#start_7">command-line
arguments</A> when LAMMPS is run in
stand-alone mode from the command line, and a MPI communicator for
LAMMPS to run under. It returns a ptr to the LAMMPS object that is
created, and which is used in subsequent library calls. The
lammps_open() function can be called multiple times, to create
multiple instances of LAMMPS.
</P>
<P>LAMMPS will run on the set of processors in the communicator. This
means the calling code can run LAMMPS on all or a subset of
processors. For example, a wrapper script might decide to alternate
between LAMMPS and another code, allowing them both to run on all the
processors. Or it might allocate half the processors to LAMMPS and
half to the other code and run both codes simultaneously before
syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.
</P>
<P>The lammps_close() function is used to shut down an instance of LAMMPS
and free all its memory.
</P>
<P>The lammps_version() function can be used to determined the specific
version of the underlying LAMMPS code. This is particularly useful
when loading LAMMPS as a shared library via dlopen(). The code using
the library interface can than use this information to adapt to
changes to the LAMMPS command syntax between versions. The returned
LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
20150902) that grows with every new LAMMPS version.
</P>
<P>The lammps_file() and lammps_command() functions are used to pass a
file or string to LAMMPS as if it were an input script or single
command in an input script. Thus the calling code can read or
generate a series of LAMMPS commands one line at a time and pass it
thru the library interface to setup a problem and then run it,
interleaving the lammps_command() calls with other calls to extract
information from LAMMPS, perform its own operations, or call another
code's library.
</P>
<P>Other useful functions are also included in library.cpp. For example:
</P>
<PRE>void *lammps_extract_global(void *, char *)
void *lammps_extract_atom(void *, char *)
void *lammps_extract_compute(void *, char *, int, int)
void *lammps_extract_fix(void *, char *, int, int, int, int)
void *lammps_extract_variable(void *, char *, char *)
int lammps_set_variable(void *, char *, char *)
int lammps_get_natoms(void *)
void lammps_get_coords(void *, double *)
void lammps_put_coords(void *, double *)
</PRE>
<P>These can extract various global or per-atom quantities from LAMMPS as
well as values calculated by a compute, fix, or variable. The
"set_variable" function can set an existing string-style variable to a
new value, so that subsequent LAMMPS commands can access the variable.
The "get" and "put" operations can retrieve and reset atom
coordinates. See the library.cpp file and its associated header file
library.h for details.
</P>
<P>The key idea of the library interface is that you can write any
functions you wish to define how your code talks to LAMMPS and add
them to src/library.cpp and src/library.h, as well as to the <A HREF = "Section_python.html">Python
interface</A>. The routines you add can access or
change any LAMMPS data you wish. The examples/COUPLE and python
directories have example C++ and C and Python codes which show how a
driver code can link to LAMMPS as a library, run LAMMPS on a subset of
processors, grab data from LAMMPS, change it, and put it back into
LAMMPS.
</P>
<HR>
<A NAME = "howto_20"></A><H4>6.20 Calculating thermal conductivity
</H4>
<P>The thermal conductivity kappa of a material can be measured in at
least 4 ways using various options in LAMMPS. See the examples/KAPPA
directory for scripts that implement the 4 methods discussed here for
a simple Lennard-Jones fluid model. Also, see <A HREF = "Section_howto.html#howto_21">this
section</A> of the manual for an analogous
discussion for viscosity.
</P>
<P>The thermal conducitivity tensor kappa is a measure of the propensity
of a material to transmit heat energy in a diffusive manner as given
by Fourier's law
</P>
<P>J = -kappa grad(T)
</P>
<P>where J is the heat flux in units of energy per area per time and
grad(T) is the spatial gradient of temperature. The thermal
conductivity thus has units of energy per distance per time per degree
K and is often approximated as an isotropic quantity, i.e. as a
scalar.
</P>
<P>The first method is to setup two thermostatted regions at opposite
ends of a simulation box, or one in the middle and one at the end of a
periodic box. By holding the two regions at different temperatures
with a <A HREF = "Section_howto.html#howto_13">thermostatting fix</A>, the energy
added to the hot region should equal the energy subtracted from the
cold region and be proportional to the heat flux moving between the
regions. See the paper by <A HREF = "#Ikeshoji">Ikeshoji and Hafskjold</A> for
details of this idea. Note that thermostatting fixes such as <A HREF = "fix_nh.html">fix
nvt</A>, <A HREF = "fix_langevin.html">fix langevin</A>, and <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A> store the cumulative energy they
add/subtract.
</P>
<P>Alternatively, as a second method, the <A HREF = "fix_heat.html">fix heat</A>
command can used in place of thermostats on each of two regions to
add/subtract specified amounts of energy to both regions. In both
cases, the resulting temperatures of the two regions can be monitored
with the "compute temp/region" command and the temperature profile of
the intermediate region can be monitored with the <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> and <A HREF = "compute_ke_atom.html">compute
ke/atom</A> commands.
</P>
<P>The third method is to perform a reverse non-equilibrium MD simulation
using the <A HREF = "fix_thermal_conductivity.html">fix thermal/conductivity</A>
command which implements the rNEMD algorithm of Muller-Plathe.
Kinetic energy is swapped between atoms in two different layers of the
simulation box. This induces a temperature gradient between the two
layers which can be monitored with the <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> and <A HREF = "compute_ke_atom.html">compute
ke/atom</A> commands. The fix tallies the
cumulative energy transfer that it performs. See the <A HREF = "fix_thermal_conductivity.html">fix
thermal/conductivity</A> command for
details.
</P>
<P>The fourth method is based on the Green-Kubo (GK) formula which
relates the ensemble average of the auto-correlation of the heat flux
to kappa. The heat flux can be calculated from the fluctuations of
per-atom potential and kinetic energies and per-atom stress tensor in
a steady-state equilibrated simulation. This is in contrast to the
two preceding non-equilibrium methods, where energy flows continuously
between hot and cold regions of the simulation box.
</P>
<P>The <A HREF = "compute_heat_flux.html">compute heat/flux</A> command can calculate
the needed heat flux and describes how to implement the Green_Kubo
formalism using additional LAMMPS commands, such as the <A HREF = "fix_ave_correlate.html">fix
ave/correlate</A> command to calculate the needed
auto-correlation. See the doc page for the <A HREF = "compute_heat_flux.html">compute
heat/flux</A> command for an example input script
that calculates the thermal conductivity of solid Ar via the GK
formalism.
</P>
<HR>
<A NAME = "howto_21"></A><H4>6.21 Calculating viscosity
</H4>
<P>The shear viscosity eta of a fluid can be measured in at least 4 ways
using various options in LAMMPS. See the examples/VISCOSITY directory
for scripts that implement the 4 methods discussed here for a simple
Lennard-Jones fluid model. Also, see <A HREF = "Section_howto.html#howto_20">this
section</A> of the manual for an analogous
discussion for thermal conductivity.
</P>
<P>Eta is a measure of the propensity of a fluid to transmit momentum in
a direction perpendicular to the direction of velocity or momentum
flow. Alternatively it is the resistance the fluid has to being
sheared. It is given by
</P>
<P>J = -eta grad(Vstream)
</P>
<P>where J is the momentum flux in units of momentum per area per time.
and grad(Vstream) is the spatial gradient of the velocity of the fluid
moving in another direction, normal to the area through which the
momentum flows. Viscosity thus has units of pressure-time.
</P>
<P>The first method is to perform a non-equlibrium MD (NEMD) simulation
by shearing the simulation box via the <A HREF = "fix_deform.html">fix deform</A>
command, and using the <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> command to
thermostat the fluid via the SLLOD equations of motion.
Alternatively, as a second method, one or more moving walls can be
used to shear the fluid in between them, again with some kind of
thermostat that modifies only the thermal (non-shearing) components of
velocity to prevent the fluid from heating up.
</P>
<P>In both cases, the velocity profile setup in the fluid by this
procedure can be monitored by the <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> command, which determines
grad(Vstream) in the equation above. E.g. the derivative in the
y-direction of the Vx component of fluid motion or grad(Vstream) =
dVx/dy. The Pxy off-diagonal component of the pressure or stress
tensor, as calculated by the <A HREF = "compute_pressure.html">compute pressure</A>
command, can also be monitored, which is the J term in the equation
above. See <A HREF = "Section_howto.html#howto_13">this section</A> of the manual
for details on NEMD simulations.
</P>
<P>The third method is to perform a reverse non-equilibrium MD simulation
using the <A HREF = "fix_viscosity.html">fix viscosity</A> command which implements
the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is
swapped between atoms in two different layers of the simulation box in
a different dimension. This induces a velocity gradient which can be
monitored with the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command.
The fix tallies the cummulative momentum transfer that it performs.
See the <A HREF = "fix_viscosity.html">fix viscosity</A> command for details.
</P>
<P>The fourth method is based on the Green-Kubo (GK) formula which
relates the ensemble average of the auto-correlation of the
stress/pressure tensor to eta. This can be done in a steady-state
equilibrated simulation which is in contrast to the two preceding
non-equilibrium methods, where momentum flows continuously through the
simulation box.
</P>
<P>Here is an example input script that calculates the viscosity of
liquid Ar via the GK formalism:
</P>
<PRE># Sample LAMMPS input script for viscosity of liquid Ar
</PRE>
<PRE>units real
variable T equal 86.4956
variable V equal vol
variable dt equal 4.0
variable p equal 400 # correlation length
variable s equal 5 # sample interval
variable d equal $p*$s # dump interval
</PRE>
<PRE># convert from LAMMPS real units to SI
</PRE>
<PRE>variable kB equal 1.3806504e-23 # [J/K/</B> Boltzmann
variable atm2Pa equal 101325.0
variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15
variable convert equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m}
</PRE>
<PRE># setup problem
</PRE>
<PRE>dimension 3
boundary p p p
lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region box block 0 4 0 4 0 4
create_box 1 box
create_atoms 1 box
mass 1 39.948
pair_style lj/cut 13.0
pair_coeff * * 0.2381 3.405
timestep ${dt}
thermo $d
</PRE>
<PRE># equilibration and thermalization
</PRE>
<PRE>velocity all create $T 102486 mom yes rot yes dist gaussian
fix NVT all nvt temp $T $T 10 drag 0.2
run 8000
</PRE>
<PRE># viscosity calculation, switch to NVE if desired
</PRE>
<PRE>#unfix NVT
#fix NVE all nve
</PRE>
<PRE>reset_timestep 0
variable pxy equal pxy
variable pxz equal pxz
variable pyz equal pyz
fix SS all ave/correlate $s $p $d &
v_pxy v_pxz v_pyz type auto file S0St.dat ave running
variable scale equal ${convert}/(${kB}*$T)*$V*$s*${dt}
variable v11 equal trap(f_SS[3])*${scale}
variable v22 equal trap(f_SS[4])*${scale}
variable v33 equal trap(f_SS[5])*${scale}
thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
run 100000
variable v equal (v_v11+v_v22+v_v33)/3.0
variable ndens equal count(all)/vol
print "average viscosity: $v [Pa.s/</B> @ $T K, ${ndens} /A^3"
</PRE>
<HR>
<A NAME = "howto_22"></A><H4>6.22 Calculating a diffusion coefficient
</H4>
<P>The diffusion coefficient D of a material can be measured in at least
2 ways using various options in LAMMPS. See the examples/DIFFUSE
directory for scripts that implement the 2 methods discussed here for
a simple Lennard-Jones fluid model.
</P>
<P>The first method is to measure the mean-squared displacement (MSD) of
the system, via the <A HREF = "compute_msd.html">compute msd</A> command. The slope
of the MSD versus time is proportional to the diffusion coefficient.
The instantaneous MSD values can be accumulated in a vector via the
<A HREF = "fix_vector.html">fix vector</A> command, and a line fit to the vector to
compute its slope via the <A HREF = "variable.html">variable slope</A> function, and
thus extract D.
</P>
<P>The second method is to measure the velocity auto-correlation function
(VACF) of the system, via the <A HREF = "compute_vacf.html">compute vacf</A>
command. The time-integral of the VACF is proportional to the
diffusion coefficient. The instantaneous VACF values can be
accumulated in a vector via the <A HREF = "fix_vector.html">fix vector</A> command,
and time integrated via the <A HREF = "variable.html">variable trap</A> function,
and thus extract D.
</P>
<HR>
<A NAME = "howto_23"></A><H4>6.23 Using chunks to calculate system properties
</H4>
<P>In LAMMS, "chunks" are collections of atoms, as defined by the
<A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command, which assigns
each atom to a chunk ID (or to no chunk at all). The number of chunks
and the assignment of chunk IDs to atoms can be static or change over
time. Examples of "chunks" are molecules or spatial bins or atoms
with similar values (e.g. coordination number or potential energy).
</P>
<P>The per-atom chunk IDs can be used as input to two other kinds of
commands, to calculate various properties of a system:
</P>
<UL><LI><A HREF = "fix_ave_chunk.html">fix ave/chunk</A>
<LI>any of the <A HREF = "compute.html">compute */chunk</A> commands
</UL>
<P>Here, each of the 3 kinds of chunk-related commands is briefly
overviewed. Then some examples are given of how to compute different
properties with chunk commands.
</P>
<H5>Compute chunk/atom command:
</H5>
<P>This compute can assign atoms to chunks of various styles. Only atoms
in the specified group and optional specified region are assigned to a
chunk. Here are some possible chunk definitions:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >atoms in same molecule </TD><TD > chunk ID = molecule ID </TD></TR>
<TR><TD >atoms of same atom type </TD><TD > chunk ID = atom type </TD></TR>
<TR><TD >all atoms with same atom property (charge, radius, etc) </TD><TD > chunk ID = output of compute property/atom </TD></TR>
<TR><TD >atoms in same cluster </TD><TD > chunk ID = output of <A HREF = "compute_cluster_atom.html">compute cluster/atom</A> command </TD></TR>
<TR><TD >atoms in same spatial bin </TD><TD > chunk ID = bin ID </TD></TR>
<TR><TD >atoms in same rigid body </TD><TD > chunk ID = molecule ID used to define rigid bodies </TD></TR>
<TR><TD >atoms with similar potential energy </TD><TD > chunk ID = output of <A HREF = "compute_pe_atom.html">compute pe/atom</A> </TD></TR>
<TR><TD >atoms with same local defect structure </TD><TD > chunk ID = output of <A HREF = "compute_centro_atom.html">compute centro/atom</A> or <A HREF = "compute_coord_atom.html">compute coord/atom</A> command
</TD></TR></TABLE></DIV>
<P>Note that chunk IDs are integer values, so for atom properties or
computes that produce a floating point value, they will be truncated
to an integer. You could also use the compute in a variable that
scales the floating point value to spread it across multiple intergers.
</P>
<P>Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
pencils, 3d bins = boxes, spherical bins, cylindrical bins.
</P>
<P>This compute also calculates the number of chunks <I>Nchunk</I>, which is
used by other commands to tally per-chunk data. <I>Nchunk</I> can be a
static value or change over time (e.g. the number of clusters). The
chunk ID for an individual atom can also be static (e.g. a molecule
ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
</P>
<P>Note that this compute allows the per-atom output of other
<A HREF = "compute.html">computes</A>, <A HREF = "fix.html">fixes</A>, and
<A HREF = "variable.html">variables</A> to be used to define chunk IDs for each
atom. This means you can write your own compute or fix to output a
per-atom quantity to use as chunk ID. See
<A HREF = "Section_modify.html">Section_modify</A> of the documentation for how to
do this. You can also define a <A HREF = "variable.html">per-atom variable</A> in
the input script that uses a formula to generate a chunk ID for each
atom.
</P>
<H5>Fix ave/chunk command:
</H5>
<P>This fix takes the ID of a <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> command as input. For each chunk,
it then sums one or more specified per-atom values over the atoms in
each chunk. The per-atom values can be any atom property, such as
velocity, force, charge, potential energy, kinetic energy, stress,
etc. Additional keywords are defined for per-chunk properties like
density and temperature. More generally any per-atom value generated
by other <A HREF = "compute.html">computes</A>, <A HREF = "fix.html">fixes</A>, and <A HREF = "variable.html">per-atom
variables</A>, can be summed over atoms in each chunk.
</P>
<P>Similar to other averaging fixes, this fix allows the summed per-chunk
values to be time-averaged in various ways, and output to a file. The
fix produces a global array as output with one row of values per
chunk.
</P>
<H5>Compute */chunk commands:
</H5>
<P>Currently the following computes operate on chunks of atoms to produce
per-chunk values.
</P>
<UL><LI><A HREF = "compute_com_chunk.html">compute com/chunk</A>
<LI><A HREF = "compute_gyration_chunk.html">compute gyration/chunk</A>
<LI><A HREF = "compute_inertia_chunk.html">compute inertia/chunk</A>
<LI><A HREF = "compute_msd_chunk.html">compute msd/chunk</A>
<LI><A HREF = "compute_property_chunk.html">compute property/chunk</A>
<LI><A HREF = "compute_temp_chunk.html">compute temp/chunk</A>
<LI><A HREF = "compute_vcm_chunk.html">compute torque/chunk</A>
<LI><A HREF = "compute_vcm_chunk.html">compute vcm/chunk</A>
</UL>
<P>They each take the ID of a <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> command as input. As their names
indicate, they calculate the center-of-mass, radius of gyration,
moments of inertia, mean-squared displacement, temperature, torque,
and velocity of center-of-mass for each chunk of atoms. The <A HREF = "compute_property_chunk.html">compute
property/chunk</A> command can tally the
count of atoms in each chunk and extract other per-chunk properties.
</P>
<P>The reason these various calculations are not part of the <A HREF = "fix_ave_chunk.html">fix
ave/chunk command</A>, is that each requires a more
complicated operation than simply summing and averaging over per-atom
values in each chunk. For example, many of them require calculation
of a center of mass, which requires summing mass*position over the
atoms and then dividing by summed mass.
</P>
<P>All of these computes produce a global vector or global array as
output, wih one or more values per chunk. They can be used
in various ways:
</P>
<UL><LI>As input to the <A HREF = "fix_ave_time.html">fix ave/time</A> command, which can
write the values to a file and optionally time average them.
<LI>As input to the <A HREF = "fix_ave_histo.html">fix ave/histo</A> command to
histogram values across chunks. E.g. a histogram of cluster sizes or
molecule diffusion rates.
<LI>As input to special functions of <A HREF = "variable.html">equal-style
variables</A>, like sum() and max(). E.g. to find the
largest cluster or fastest diffusing molecule.
</UL>
<H5>Example calculations with chunks
</H5>
<P>Here are eaxmples using chunk commands to calculate various
properties:
</P>
<P>(1) Average velocity in each of 1000 2d spatial bins:
</P>
<PRE>compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out
</PRE>
<P>(2) Temperature in each spatial bin, after subtracting a flow
velocity:
</P>
<PRE>compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
compute vbias all temp/profile 1 0 0 y 10
fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out
</PRE>
<P>(3) Center of mass of each molecule:
</P>
<PRE>compute cc1 all chunk/atom molecule
compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</PRE>
<P>(4) Total force on each molecule and ave/max across all molecules:
</P>
<PRE>compute cc1 all chunk/atom molecule
fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
variable xave equal ave(f_1<B>2</B>)
variable xmax equal max(f_1<B>2</B>)
thermo 1000
thermo_style custom step temp v_xave v_xmax
</PRE>
<P>(5) Histogram of cluster sizes:
</P>
<PRE>compute cluster all cluster/atom 1.0
compute cc1 all chunk/atom c_cluster compress yes
compute size all property/chunk cc1 count
fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
</PRE>
<HR>
<A NAME = "howto_24"></A><H4>6.24 Setting parameters for the <A HREF = "kspace_style.html">kspace_style pppm/disp</A> command
</H4>
<P>The PPPM method computes interactions by splitting the pair potential
into two parts, one of which is computed in a normal pairwise fashion,
the so-called real-space part, and one of which is computed using the
Fourier transform, the so called reciprocal-space or kspace part. For
both parts, the potential is not computed exactly but is approximated.
Thus, there is an error in both parts of the computation, the
real-space and the kspace error. The just mentioned facts are true
both for the PPPM for Coulomb as well as dispersion interactions. The
deciding difference - and also the reason why the parameters for
pppm/disp have to be selected with more care - is the impact of the
errors on the results: The kspace error of the PPPM for Coulomb and
dispersion interaction and the real-space error of the PPPM for
Coulomb interaction have the character of noise. In contrast, the
real-space error of the PPPM for dispersion has a clear physical
interpretation: the underprediction of cohesion. As a consequence, the
real-space error has a much stronger effect than the kspace error on
simulation results for pppm/disp. Parameters must thus be chosen in a
way that this error is much smaller than the kspace error.
</P>
<P>When using pppm/disp and not making any specifications on the PPPM
parameters via the kspace modify command, parameters will be tuned
such that the real-space error and the kspace error are equal. This
will result in simulations that are either inaccurate or slow, both of
which is not desirable. For selecting parameters for the pppm/disp
that provide fast and accurate simulations, there are two approaches,
which both have their up- and downsides.
</P>
<P>The first approach is to set desired real-space an kspace accuracies
via the <I>kspace_modify force/disp/real</I> and <I>kspace_modify
force/disp/kspace</I> commands. Note that the accuracies have to be
specified in force units and are thus dependend on the chosen unit
settings. For real units, 0.0001 and 0.002 seem to provide reasonable
accurate and efficient computations for the real-space and kspace
accuracies. 0.002 and 0.05 work well for most systems using lj
units. PPPM parameters will be generated based on the desired
accuracies. The upside of this approach is that it usually provides a
good set of parameters and will work for both the <I>kspace_modify diff
ad</I> and <I>kspace_modify diff ik</I> options. The downside of the method
is that setting the PPPM parameters will take some time during the
initialization of the simulation.
</P>
<P>The second approach is to set the parameters for the pppm/disp
explicitly using the <I>kspace_modify mesh/disp</I>, <I>kspace_modify
order/disp</I>, and <I>kspace_modify gewald/disp</I> commands. This approach
requires a more experienced user who understands well the impact of
the choice of parameters on the simulation accuracy and
performance. This approach provides a fast initialization of the
simulation. However, it is sensitive to errors: A combination of
parameters that will perform well for one system might result in
far-from-optimal conditions for other simulations. For example,
parametes that provide accurate and fast computations for
all-atomistic force fields can provide insufficient accuracy or
united-atomistic force fields (which is related to that the latter
typically have larger dispersion coefficients).
</P>
<P>To avoid inaccurate or inefficient simulations, the pppm/disp stops
simulations with an error message if no action is taken to control the
PPPM parameters. If the automatic parameter generation is desired and
real-space and kspace accuracies are desired to be equal, this error
message can be suppressed using the <I>kspace_modify disp/auto yes</I>
command.
</P>
<P>A reasonable approach that combines the upsides of both methods is to
make the first run using the <I>kspace_modify force/disp/real</I> and
<I>kspace_modify force/disp/kspace</I> commands, write down the PPPM
parameters from the outut, and specify these parameters using the
second approach in subsequent runs (which have the same composition,
force field, and approximately the same volume).
</P>
<P>Concerning the performance of the pppm/disp there are two more things
to consider. The first is that when using the pppm/disp, the cutoff
parameter does no longer affect the accuracy of the simulation
(subject to that gewald/disp is adjusted when changing the cutoff).
The performance can thus be increased by examining different values
for the cutoff parameter. A lower bound for the cutoff is only set by
the truncation error of the repulsive term of pair potentials.
</P>
<P>The second is that the mixing rule of the pair style has an impact on
the computation time when using the pppm/disp. Fastest computations
are achieved when using the geometric mixing rule. Using the
arithmetic mixing rule substantially increases the computational cost.
The computational overhead can be reduced using the <I>kspace_modify
mix/disp geom</I> and <I>kspace_modify splittol</I> commands. The first
command simply enforces geometric mixing of the dispersion
coeffiecients in kspace computations. This introduces some error in
the computations but will also significantly speed-up the
simulations. The second keyword sets the accuracy with which the
dispersion coefficients are approximated using a matrix factorization
approach. This may result in better accuracy then using the first
command, but will usually also not provide an equally good increase of
efficiency.
</P>
<P>Finally, pppm/disp can also be used when no mixing rules apply.
This can be achieved using the <I>kspace_modify mix/disp none</I> command.
Note that the code does not check automatically whether any mixing
rule is fulfilled. If mixing rules do not apply, the user will have
to specify this command explicitly.
</P>
<HR>
<A NAME = "howto_25"></A><H4>6.25 Polarizable models
</H4>
<P>In polarizable force fields the charge distributions in molecules and
materials respond to their electrostatic environements. Polarizable
systems can be simulated in LAMMPS using three methods:
</P>
<UL><LI>the fluctuating charge method, implemented in the <A HREF = "fix_qeq.html">QEQ</A>
package,
<LI>the adiabatic core-shell method, implemented in the
<A HREF = "#howto_26">CORESHELL</A> package,
<LI>the thermalized Drude dipole method, implemented in the
<A HREF = "#howto_27">USER-DRUDE</A> package.
</UL>
<P>The fluctuating charge method calculates instantaneous charges on
interacting atoms based on the electronegativity equalization
principle. It is implemented in the <A HREF = "fix_qeq.html">fix qeq</A> which is
available in several variants. It is a relatively efficient technique
since no additional particles are introduced. This method allows for
charge transfer between molecules or atom groups. However, because the
charges are located at the interaction sites, off-plane components of
polarization cannot be represented in planar molecules or atom groups.
</P>
<P>The two other methods share the same basic idea: polarizable atoms are
split into one core atom and one satellite particle (called shell or
Drude particle) attached to it by a harmonic spring. Both atoms bear
a charge and they represent collectively an induced electric dipole.
These techniques are computationally more expensive than the QEq
method because of additional particles and bonds. These two
charge-on-spring methods differ in certain features, with the
core-shell model being normally used for ionic/crystalline materials,
whereas the so-called Drude model is normally used for molecular
systems and fluid states.
</P>
<P>The core-shell model is applicable to crystalline materials where the
high symmetry around each site leads to stable trajectories of the
core-shell pairs. However, bonded atoms in molecules can be so close
that a core would interact too strongly or even capture the Drude
particle of a neighbor. The Drude dipole model is relatively more
complex in order to remediate this and other issues. Specifically, the
Drude model includes specific thermostating of the core-Drude pairs
and short-range damping of the induced dipoles.
</P>
<P>The three polarization methods can be implemented through a
self-consistent calculation of charges or induced dipoles at each
timestep. In the fluctuating charge scheme this is done by the matrix
inversion method in <A HREF = "fix_qeq.html">fix qeq/point</A>, but for core-shell
or Drude-dipoles the relaxed-dipoles technique would require an slow
iterative procedure. These self-consistent solutions yield accurate
trajectories since the additional degrees of freedom representing
polarization are massless. An alternative is to attribute a mass to
the additional degrees of freedom and perform time integration using
an extended Lagrangian technique. For the fluctuating charge scheme
this is done by <A HREF = "fix_qeq.html">fix qeq/dynamic</A>, and for the
charge-on-spring models by the methods outlined in the next two
sections. The assignment of masses to the additional degrees of
freedom can lead to unphysical trajectories if care is not exerted in
choosing the parameters of the poarizable models and the simulation
conditions.
</P>
<P>In the core-shell model the vibration of the shells is kept faster
than the ionic vibrations to mimic the fast response of the
polarizable electrons. But in molecular systems thermalizing the
core-Drude pairs at temperatures comparable to the rest of the
simulation leads to several problems (kinetic energy transfer, too
short a timestep, etc.) In order to avoid these problems the relative
motion of the Drude particles with respect to their cores is kept
"cold" so the vibration of the core-Drude pairs is very slow,
approaching the self-consistent regime. In both models the
temperature is regulated using the velocities of the center of mass of
core+shell (or Drude) pairs, but in the Drude model the actual
relative core-Drude particle motion is thermostated separately as
well.
</P>
<HR>
<A NAME = "howto_26"></A><H4>6.26 Adiabatic core/shell model
</H4>
<P>The adiabatic core-shell model by <A HREF = "#MitchellFinchham">Mitchell and
Finchham</A> is a simple method for adding
polarizability to a system. In order to mimic the electron shell of
an ion, a satellite particle is attached to it. This way the ions are
split into a core and a shell where the latter is meant to react to
the electrostatic environment inducing polarizability.
</P>
<P>Technically, shells are attached to the cores by a spring force f =
k*r where k is a parametrized spring constant and r is the distance
between the core and the shell. The charges of the core and the shell
-add up to the ion charge, thus q(ion) = q(core) + q(shell). In a
+add up to the ion charge, thus q(ion) = q(core) + q(shell). This
+setup introduces the ion polarizability (alpha) given by
+alpha = q(shell)^2 / k. In a
similar fashion the mass of the ion is distributed on the core and the
shell with the core having the larger mass.
</P>
<P>To run this model in LAMMPS, <A HREF = "atom_style.html">atom_style</A> <I>full</I> can
be used since atom charge and bonds are needed. Each kind of
core/shell pair requires two atom types and a bond type. The core and
shell of a core/shell pair should be bonded to each other with a
harmonic bond that provides the spring force. For example, a data file
for NaCl, as found in examples/coreshell, has this format:
</P>
<PRE>432 atoms # core and shell atoms
216 bonds # number of core/shell springs
</PRE>
<PRE>4 atom types # 2 cores and 2 shells for Na and Cl
2 bond types
</PRE>
<PRE>0.0 24.09597 xlo xhi
0.0 24.09597 ylo yhi
0.0 24.09597 zlo zhi
</PRE>
<PRE>Masses # core/shell mass ratio = 0.1
</PRE>
<PRE>1 20.690784 # Na core
2 31.90500 # Cl core
3 2.298976 # Na shell
4 3.54500 # Cl shell
</PRE>
<PRE>Atoms
</PRE>
<PRE>1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1
2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1
3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2
4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2
(...)
</PRE>
<PRE>Bonds # Bond topology for spring forces
</PRE>
<PRE>1 2 1 2 # spring for core/shell pair 1
2 2 3 4 # spring for core/shell pair 2
(...)
</PRE>
<P>Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
defined between the shells. Coulombic interactions are defined
between all cores and shells. If desired, additional bonds can be
-specified between cores.
+specified between cores.
</P>
<P>The <A HREF = "special_bonds.html">special_bonds</A> command should be used to
turn-off the Coulombic interaction within core/shell pairs, since that
interaction is set by the bond spring. This is done using the
<A HREF = "special_bonds.html">special_bonds</A> command with a 1-2 weight = 0.0,
which is the default value. It needs to be considered whether one has
to adjust the <A HREF = "special_bonds.html">special_bonds</A> weighting according
to the molecular topology since the interactions of the shells are
bypassed over an extra bond.
</P>
<P>Note that this core/shell implementation does not require all ions to
be polarized. One can mix core/shell pairs and ions without a
satellite particle if desired.
</P>
<P>Since the core/shell model permits distances of r = 0.0 between the
core and shell, a pair style with a "cs" suffix needs to be used to
-implement a valid long-rangeCoulombic correction. Several such pair
+implement a valid long-range Coulombic correction. Several such pair
styles are provided in the CORESHELL package. See <A HREF = "pair_cs.html">this doc
page</A> for details. All of the core/shell enabled pair
styles require the use of a long-range Coulombic solver, as specified
by the <A HREF = "kspace_style.html">kspace_style</A> command. Either the PPPM or
Ewald solvers can be used.
</P>
<P>For the NaCL example problem, these pair style and bond style settings
are used:
</P>
<PRE>pair_style born/coul/long/cs 20.0 20.0
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
</PRE>
<PRE>bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0
</PRE>
<P>When running dynamics with the adiabatic core/shell model, the
following issues should be considered. Since the relative motion of
the core and shell particles corresponds to the polarization, typical
-thermostats can alter the polarization behaviour, meaining the shell
-will not react freely to its electrostatic environment. Therefore
+thermostats can alter the polarization behaviour, meaning the shell
+will not react freely to its electrostatic environment. This is
+critical during the equilibration of the system. Therefore
it's typically desirable to decouple the relative motion of the
core/shell pair, which is an imaginary degree of freedom, from the
real physical system. To do that, the <A HREF = "compute_temp_cs.html">compute
temp/cs</A> command can be used, in conjunction with
any of the thermostat fixes, such as <A HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_langevin">fix
langevin</A>. This compute uses the center-of-mass velocity
of the core/shell pairs to calculate a temperature, and insures that
velocity is what is rescaled for thermostatting purposes. This
compute also works for a system with both core/shell pairs and
non-polarized ions (ions without an attached satellite particle). The
<A HREF = "compute_temp_cs.html">compute temp/cs</A> command requires input of two
groups, one for the core atoms, another for the shell atoms.
Non-polarized ions which might also be included in the treated system
should not be included into either of these groups, they are taken
into account by the <I>group-ID</I> (2nd argument) of the compute. The
groups can be defined using the <A HREF = "group.html">group <I>type</I></A> command.
Note that to perform thermostatting using this definition of
temperature, the <A HREF = "fix_modify.html">fix modify temp</A> command should be
-used to assign the comptue to the thermostat fix. Likewise the
+used to assign the compute to the thermostat fix. Likewise the
<A HREF = "thermo_modify.html">thermo_modify temp</A> command can be used to make
-this temperature be output for the overall system.
+this temperature be output for the overall system.
</P>
<P>For the NaCl example, this can be done as follows:
</P>
<PRE>group cores type 1 2
group shells type 3 4
compute CSequ all temp/cs cores shells
fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system
fix thermostatequ all nve # integrator as needed for the berendsen thermostat
fix_modify thermoberendsen temp CSequ
thermo_modify temp CSequ # output of center-of-mass derived temperature
</PRE>
+<P>If <A HREF = "compute_temp_cs.html">compute temp/cs</A> is used, the decoupled
+relative motion of the core and the shell should in theory be
+stable. However numerical fluctuation can introduce a small
+momentum to the system, which is noticable over long trajectories.
+Therefore it is recomendable to use the <A HREF = "fix_momentum.html">fix
+momentum</A> command in combination with <A HREF = "compute_temp_cs.html">compute
+temp/cs</A> when equilibrating the system to
+prevent any drift.
+</P>
<P>When intializing the velocities of a system with core/shell pairs, it
is also desirable to not introduce energy into the relative motion of
the core/shell particles, but only assign a center-of-mass velocity to
the pairs. This can be done by using the <I>bias</I> keyword of the
<A HREF = "velocity.html">velocity create</A> command and assigning the <A HREF = "compute_temp_cs.html">compute
temp/cs</A> command to the <I>temp</I> keyword of the
<A HREF = "velocity.html">velocity</A> commmand, e.g.
</P>
<PRE>velocity all create 1427 134 bias yes temp CSequ
velocity all scale 1427 temp CSequ
</PRE>
<P>It is important to note that the polarizability of the core/shell
pairs is based on their relative motion. Therefore the choice of
spring force and mass ratio need to ensure much faster relative motion
of the 2 atoms within the core/shell pair than their center-of-mass
velocity. This allow the shells to effectively react instantaneously
to the electrostatic environment. This fast movement also limits the
timestep size that can be used.
</P>
-<P>Additionally, the mass mismatch of the core and shell particles means
-that only a small amount of energy is transfered to the decoupled
-imaginary degrees of freedom. However, this transfer will typically
-lead to a a small drift in total energy over time. This internal
-energy can be monitored using the <A HREF = "compute_chunk_atom.html">compute
-chunk/atom</A> and <A HREF = "compute_temp_chunk.html">compute
+<P>The primary literature of the adiabatic core/shell model suggests that
+the fast relative motion of the core/shell pairs only allows negligible
+energy transfer to the environment. Therefore it is not intended to
+decouple the core/shell degree of freedom from the physical system
+during production runs. In other words, the <A HREF = "compute_temp_cs.html">compute
+temp/cs</A> command should not be used during
+production runs and is only required during equilibration. This way one
+is consistent with literature (based on the code packages DL_POLY or
+GULP for instance).
+</P>
+<P>The mentioned energy transfer will typically lead to a a small drift
+in total energy over time. This internal energy can be monitored
+using the <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> and <A HREF = "compute_temp_chunk.html">compute
temp/chunk</A> commands. The internal kinetic
energies of each core/shell pair can then be summed using the sum()
special function of the <A HREF = "variable.html">variable</A> command. Or they can
be time/averaged and output using the <A HREF = "fix_ave_time.html">fix ave/time</A>
command. To use these commands, each core/shell pair must be defined
as a "chunk". If each core/shell pair is defined as its own molecule,
the molecule ID can be used to define the chunks. If cores are bonded
to each other to form larger molecules, the chunks can be identified
by the <A HREF = "fix_property_atom.html">fix property/atom</A> via assigning a
core/shell ID to each atom using a special field in the data file read
by the <A HREF = "read_data.html">read_data</A> command. This field can then be
accessed by the <A HREF = "compute_property_atom.html">compute property/atom</A>
command, to use as input to the <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> command to define the core/shell
pairs as chunks.
</P>
<P>For example,
</P>
<PRE>fix csinfo all property/atom i_CSID # property/atom command
read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file
compute prop all property/atom i_CSID
compute cs_chunk all chunk/atom c_prop
compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
</PRE>
<P>The additional section in the date file would be formatted like this:
</P>
<PRE>CS-Info # header of additional section
</PRE>
<PRE>1 1 # column 1 = atom ID, column 2 = core/shell ID
2 1
3 2
4 2
5 3
6 3
7 4
8 4
(...)
</PRE>
<HR>
<A NAME = "howto_27"></A><H4>6.27 Drude induced dipoles
</H4>
<P>The thermalized Drude model, similarly to the <A HREF = "#howto_26">core-shell</A>
model, representes induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems
(<A HREF = "#Lamoureux">Lamoureux and Roux</A>):
</P>
<UL><LI>Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced
coordinates of the Drude particles with respect to their cores. This
makes the trajectory close to that of relaxed induced dipoles.
<LI>Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle
pair represents a single (polarizable) atom, so the special screening
factors in a covalent structure should be the same for the core and
the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4
special neighbor relations from their respective cores.
<LI>Stabilization of the interactions between induced dipoles. Drude
dipoles on covalently bonded atoms interact too strongly due to the
short distances, so an atom may capture the Drude particle of a
neighbor, or the induced dipoles within the same molecule may align
too much. To avoid this, damping at short range can be done by Thole
functions (for which there are physical grounds). This Thole damping
is applied to the point charges composing the induced dipole (the
charge of the Drude particle and the opposite charge on the core, not
to the total charge of the core atom).
</UL>
<P>A detailed tutorial covering the usage of Drude induced dipoles in
LAMMPS is <A HREF = "tutorial_drude.html">available here</A>.
</P>
<P>As with the core-shell model, the cores and Drude particles should
appear in the data file as standard atoms. The same holds for the
springs between them, which are described by standard harmonic bonds.
The nature of the atoms (core, Drude particle or non-polarizable) is
specified via the <A HREF = "fix_drude.html">fix drude</A> command. The special
list of neighbors is automatically refactored to account for the
equivalence of core and Drude particles as regards special 1-2 to 1-4
screening. It may be necessary to use the <I>extra</I> keyword of the
<A HREF = "special_bonds.html">special_bonds</A> command. If using <A HREF = "fix_shake.html">fix
shake</A>, make sure no Drude particle is in this fix
group.
</P>
<P>There are two ways to thermostat the Drude particles at a low
temperature: use either <A HREF = "fix_langevin_drude.html">fix langevin/drude</A>
for a Langevin thermostat, or <A HREF = "fix_drude_transform.html">fix
drude/transform/*</A> for a Nose-Hoover
thermostat. The former requires use of the command <A HREF = "comm_modify.html">comm_modify vel
yes</A>. The latter requires two separate integration
fixes like <I>nvt</I> or <I>npt</I>. The correct temperatures of the reduced
degrees of freedom can be calculated using the <A HREF = "compute_temp_drude.html">compute
temp/drude</A>. This requires also to use the
command <I>comm_modify vel yes</I>.
</P>
<P>Short-range damping of the induced dipole interactions can be achieved
using Thole functions through the the <A HREF = "pair_thole.html">pair style
thole</A> in <A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A>
with a Coulomb pair style. It may be useful to use <I>coul/long/cs</I> or
similar from the CORESHELL package if the core and Drude particle come
too close, which can cause numerical issues.
</P>
<HR>
<HR>
<A NAME = "Berendsen"></A>
<P><B>(Berendsen)</B> Berendsen, Grigera, Straatsma, J Phys Chem, 91,
6269-6271 (1987).
</P>
<A NAME = "Cornell"></A>
<P><B>(Cornell)</B> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
</P>
<A NAME = "Horn"></A>
<P><B>(Horn)</B> Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon,
J Chem Phys, 120, 9665 (2004).
</P>
<A NAME = "Ikeshoji"></A>
<P><B>(Ikeshoji)</B> Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
(1994).
</P>
<A NAME = "MacKerell"></A>
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
</P>
<A NAME = "Mayo"></A>
<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
</P>
<A NAME = "Jorgensen"></A>
<P><B>(Jorgensen)</B> Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
</P>
<A NAME = "Price"></A>
<P><B>(Price)</B> Price and Brooks, J Chem Phys, 121, 10096 (2004).
</P>
<A NAME = "Shinoda"></A>
<P><B>(Shinoda)</B> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
</P>
<A NAME = "MitchellFinchham"></A>
<P><B>(Mitchell and Finchham)</B> Mitchell, Finchham, J Phys Condensed Matter,
5, 1031-1038 (1993).
</P>
<A NAME = "Lamoureux"></A>
<P><B>(Lamoureux and Roux)</B> G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
</P>
</HTML>
diff --git a/doc/doc2/Section_packages.html b/doc/doc2/Section_packages.html
index 9452fd107..16186a05d 100644
--- a/doc/doc2/Section_packages.html
+++ b/doc/doc2/Section_packages.html
@@ -1,721 +1,821 @@
<HTML>
<CENTER><A HREF = "Section_commands.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_accelerate.html">Next
Section</A>
</CENTER>
<HR>
<H3>4. Packages
</H3>
<P>This section gives a quick overview of the add-on packages that extend
LAMMPS functionality.
</P>
4.1 <A HREF = "#pkg_1">Standard packages</A><BR>
4.2 <A HREF = "#pkg_2">User packages</A> <BR>
<P>LAMMPS includes many optional packages, which are groups of files that
enable a specific set of features. For example, force fields for
molecular systems or granular systems are in packages. You can see
the list of all packages by typing "make package" from within the src
directory of the LAMMPS distribution.
</P>
<P>See <A HREF = "Section_start.html#start_3">Section_start 3</A> of the manual for
details on how to include/exclude specific packages as part of the
LAMMPS build process, and for more details about the differences
-between standard packages and user packages in LAMMPS.
-</P>
-<P>Below, the packages currently availabe in LAMMPS are listed. For
-standard packages, just a one-line description is given. For user
-packages, more details are provided.
+between standard packages and user packages.
+</P>
+<P>Unless otherwise noted below, every package is independent of all the
+others. I.e. any package can be included or excluded in a LAMMPS
+build, independent of all other packages. However, note that some
+packages include commands derived from commands in other packages. If
+the other package is not installed, the derived command from the new
+package will also not be installed when you include the new one.
+E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package
+will not be installed as part of the USER-OMP package if the KSPACE
+package is not also installed, since it contains the pair
+lj/cut/coul/long command. If you later install the KSPACE pacakge and
+the USER-OMP package is already installed, both the pair
+lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.
+</P>
+<P>The two tables below list currently available packages in LAMMPS, with
+a one-line descriptions of each. The sections below give a few more
+details, including instructions for building LAMMPS with the package,
+either via the make command or the Make.py tool described in <A HREF = "Section_start.html#start_4">Section
+2.4</A>.
</P>
<HR>
<HR>
<H4><A NAME = "pkg_1"></A>4.1 Standard packages
</H4>
-<P>The current list of standard packages is as follows:
+<P>The current list of standard packages is as follows.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Library</TD></TR>
<TR ALIGN="center"><TD >ASPHERE</TD><TD > aspherical particles</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_14">Section_howto 6.14</A></TD><TD > ellipse</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >BODY</TD><TD > body-style particles</TD><TD > -</TD><TD > <A HREF = "body.html">body</A></TD><TD > body</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >CLASS2</TD><TD > class 2 force fields</TD><TD > -</TD><TD > <A HREF = "pair_class2.html">pair_style lj/class2</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >COLLOID</TD><TD > colloidal particles</TD><TD > -</TD><TD > <A HREF = "atom_style.html">atom_style colloid</A></TD><TD > colloid</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >COMPRESS</TD><TD > I/O compression</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "dump.html">dump */gz</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >CORESHELL</TD><TD > adiabatic core/shell model</TD><TD > Hendrik Heenen (Technical U of Munich)</TD><TD > <A HREF = "Section_howto.html#howto_25">Section_howto 6.25</A></TD><TD > coreshell</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >DIPOLE</TD><TD > point dipole particles</TD><TD > -</TD><TD > <A HREF = "pair_dipole.html">pair_style dipole/cut</A></TD><TD > dipole</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >FLD</TD><TD > Fast Lubrication Dynamics</TD><TD > Kumar & Bybee & Higdon (1)</TD><TD > <A HREF = "pair_lubricateU.html">pair_style lubricateU</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >GPU</TD><TD > GPU-enabled styles</TD><TD > Mike Brown (ORNL)</TD><TD > <A HREF = "accelerate_gpu.html">Section accelerate</A></TD><TD > gpu</TD><TD > lib/gpu</TD></TR>
<TR ALIGN="center"><TD >GRANULAR</TD><TD > granular systems</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_6">Section_howto 6.6</A></TD><TD > pour</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >KIM</TD><TD > openKIM potentials</TD><TD > Smirichinski & Elliot & Tadmor (3)</TD><TD > <A HREF = "pair_kim.html">pair_style kim</A></TD><TD > kim</TD><TD > KIM</TD></TR>
<TR ALIGN="center"><TD >KOKKOS</TD><TD > Kokkos-enabled styles</TD><TD > Trott & Edwards (4)</TD><TD > <A HREF = "accelerate_kokkos.html">Section_accelerate</A></TD><TD > kokkos</TD><TD > lib/kokkos</TD></TR>
<TR ALIGN="center"><TD >KSPACE</TD><TD > long-range Coulombic solvers</TD><TD > -</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > peptide</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MANYBODY</TD><TD > many-body potentials</TD><TD > -</TD><TD > <A HREF = "pair_tersoff.html">pair_style tersoff</A></TD><TD > shear</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MEAM</TD><TD > modified EAM potential</TD><TD > Greg Wagner (Sandia)</TD><TD > <A HREF = "pair_meam.html">pair_style meam</A></TD><TD > meam</TD><TD > lib/meam</TD></TR>
<TR ALIGN="center"><TD >MC</TD><TD > Monte Carlo options</TD><TD > -</TD><TD > <A HREF = "fix_gcmc.html">fix gcmc</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MOLECULE</TD><TD > molecular system force fields</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_3">Section_howto 6.3</A></TD><TD > peptide</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >OPT</TD><TD > optimized pair styles</TD><TD > Fischer & Richie & Natoli (2)</TD><TD > <A HREF = "accelerate_opt.html">Section accelerate</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >PERI</TD><TD > Peridynamics models</TD><TD > Mike Parks (Sandia)</TD><TD > <A HREF = "pair_peri.html">pair_style peri</A></TD><TD > peri</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >POEMS</TD><TD > coupled rigid body motion</TD><TD > Rudra Mukherjee (JPL)</TD><TD > <A HREF = "fix_poems.html">fix poems</A></TD><TD > rigid</TD><TD > lib/poems</TD></TR>
<TR ALIGN="center"><TD >PYTHON</TD><TD > embed Python code in an input script</TD><TD > -</TD><TD > <A HREF = "python.html">python</A></TD><TD > python</TD><TD > lib/python</TD></TR>
<TR ALIGN="center"><TD >REAX</TD><TD > ReaxFF potential</TD><TD > Aidan Thompson (Sandia)</TD><TD > <A HREF = "pair_reax.html">pair_style reax</A></TD><TD > reax</TD><TD > lib/reax</TD></TR>
<TR ALIGN="center"><TD >REPLICA</TD><TD > multi-replica methods</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_5">Section_howto 6.5</A></TD><TD > tad</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >RIGID</TD><TD > rigid bodies</TD><TD > -</TD><TD > <A HREF = "fix_rigid.html">fix rigid</A></TD><TD > rigid</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >SHOCK</TD><TD > shock loading methods</TD><TD > -</TD><TD > <A HREF = "fix_msst.html">fix msst</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >SNAP</TD><TD > quantum-fit potential</TD><TD > Aidan Thompson (Sandia)</TD><TD > <A HREF = "pair_snap.html">pair snap</A></TD><TD > snap</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >SRD</TD><TD > stochastic rotation dynamics</TD><TD > -</TD><TD > <A HREF = "fix_srd.html">fix srd</A></TD><TD > srd</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >VORONOI</TD><TD > Voronoi tesselations</TD><TD > Daniel Schwen (LANL)</TD><TD > <A HREF = "compute_voronoi_atom.html">compute voronoi/atom</A></TD><TD > -</TD><TD > Voro++</TD></TR>
<TR ALIGN="center"><TD >XTC</TD><TD > dumps in XTC format</TD><TD > -</TD><TD > <A HREF = "dump.html">dump</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >
</TD></TR></TABLE></DIV>
<P>The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
+More details on
+multiple authors are give below.
</P>
<P>(1) The FLD package was created by Amit Kumar and Michael Bybee from
Jonathan Higdon's group at UIUC.
</P>
<P>(2) The OPT package was created by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technolgy).
</P>
<P>(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
and Ellad Tadmor (U Minn).
</P>
<P>(4) The KOKKOS package was created primarily by Christian Trott
(Sandia). It uses the Kokkos library which was developed by Carter
Edwards, Christian, and collaborators at Sandia.
</P>
<P>The "Doc page" column links to either a portion of the
<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
command implemented as part of the package.
</P>
<P>The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory.
</P>
<P>The "Library" column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See the src/package/README or src/package/Makefile.lammps file for
info on where to download the library. <A HREF = "Section_start.html#start_3_3">Section
start</A> of the manual also gives details
on how to build LAMMPS with both kinds of auxiliary libraries.
</P>
+<P>Except where explained below, all of these packages can be installed,
+and LAMMPS re-built, by issuing these commands from the src dir.
+</P>
+<PRE>make yes-package
+make machine
+or
+Make.py -p package -a machine
+</PRE>
+<P>To un-install the package and re-build LAMMPS without it:
+</P>
+<PRE>make no-package
+make machine
+or
+Make.py -p ^package -a machine
+</PRE>
+<P>"Package" is the name of the package in lower-case letters,
+e.g. asphere or rigid, and "machine" is the build target, e.g. mpi or
+serial.
+</P>
+<HR>
+
+<HR>
+
+<H4>Build instructions for COMPRESS package
+</H4>
+<HR>
+
+<H4>Build instructions for GPU package
+</H4>
+<HR>
+
+<H4>Build instructions for KIM package
+</H4>
+<HR>
+
+<H4>Build instructions for KOKKOS package
+</H4>
+<HR>
+
+<H4>Build instructions for KSPACE package
+</H4>
+<HR>
+
+<H4>Build instructions for MEAM package
+</H4>
+<HR>
+
+<H4>Build instructions for POEMS package
+</H4>
+<HR>
+
+<H4>Build instructions for PYTHON package
+</H4>
+<HR>
+
+<H4>Build instructions for REAX package
+</H4>
+<HR>
+
+<H4>Build instructions for VORONOI package
+</H4>
+<HR>
+
+<H4>Build instructions for XTC package
+</H4>
<HR>
<HR>
<H4><A NAME = "pkg_2"></A>4.2 User packages
</H4>
<P>The current list of user-contributed packages is as follows:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Pic/movie</TD><TD > Library</TD></TR>
<TR ALIGN="center"><TD >USER-ATC</TD><TD > atom-to-continuum coupling</TD><TD > Jones & Templeton & Zimmerman (1)</TD><TD > <A HREF = "fix_atc.html">fix atc</A></TD><TD > USER/atc</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#atc">atc</A></TD><TD > lib/atc</TD></TR>
<TR ALIGN="center"><TD >USER-AWPMD</TD><TD > wave-packet MD</TD><TD > Ilya Valuev (JIHT)</TD><TD > <A HREF = "pair_awpmd.html">pair_style awpmd/cut</A></TD><TD > USER/awpmd</TD><TD > -</TD><TD > lib/awpmd</TD></TR>
<TR ALIGN="center"><TD >USER-CG-CMM</TD><TD > coarse-graining model</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "pair_sdk.html">pair_style lj/sdk</A></TD><TD > USER/cg-cmm</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#cg">cg</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-COLVARS</TD><TD > collective variables</TD><TD > Fiorin & Henin & Kohlmeyer (2)</TD><TD > <A HREF = "fix_colvars.html">fix colvars</A></TD><TD > USER/colvars</TD><TD > <A HREF = "colvars">colvars</A></TD><TD > lib/colvars</TD></TR>
<TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "accelerate_cuda.html">Section accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
<TR ALIGN="center"><TD >USER-DIFFRACTION</TD><TD > virutal x-ray and electron diffraction</TD><TD > Shawn Coleman (ARL)</TD><TD ><A HREF = "compute_xrd.html">compute xrd</A></TD><TD > USER/diffraction</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-DRUDE</TD><TD > Drude oscillators</TD><TD > Dequidt & Devemy & Padua (3)</TD><TD > <A HREF = "tutorial_drude.html">tutorial</A></TD><TD > USER/drude</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-FEP</TD><TD > free energy perturbation</TD><TD > Agilio Padua (U Blaise Pascal Clermont-Ferrand)</TD><TD > <A HREF = "compute_fep.html">compute fep</A></TD><TD > USER/fep</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-H5MD</TD><TD > dump output via HDF5</TD><TD > Pierre de Buyl (KU Leuven)</TD><TD > <A HREF = "dump_h5md.html">dump h5md</A></TD><TD > -</TD><TD > -</TD><TD > lib/h5md</TD></TR>
<TR ALIGN="center"><TD >USER-INTEL</TD><TD > Vectorized CPU and Intel(R) coprocessor styles</TD><TD > W. Michael Brown (Intel)</TD><TD > <A HREF = "accelerate_intel.html">Section accelerate</A></TD><TD > examples/intel</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-LB</TD><TD > Lattice Boltzmann fluid</TD><TD > Colin Denniston (U Western Ontario)</TD><TD > <A HREF = "fix_lb_fluid.html">fix lb/fluid</A></TD><TD > USER/lb</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-MOLFILE</TD><TD > <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> molfile plug-ins</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "dump_molfile.html">dump molfile</A></TD><TD > -</TD><TD > -</TD><TD > VMD-MOLFILE</TD></TR>
<TR ALIGN="center"><TD >USER-OMP</TD><TD > OpenMP threaded styles</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "accelerate_omp.html">Section accelerate</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-PHONON</TD><TD > phonon dynamical matrix</TD><TD > Ling-Ti Kong (Shanghai Jiao Tong U)</TD><TD > <A HREF = "fix_phonon.html">fix phonon</A></TD><TD > USER/phonon</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-QMMM</TD><TD > QM/MM coupling</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "fix_qmmm.html">fix qmmm</A></TD><TD > USER/qmmm</TD><TD > -</TD><TD > lib/qmmm</TD></TR>
<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 = "PDF/SMD_LAMMPS_userguide.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 = "PDF/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 >USER-TALLY</TD><TD > Pairwise tallied computes</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "compute_tally.html">compute <...>/tally</A></TD><TD > USER/tally</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >
</TD></TR></TABLE></DIV>
<P>The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
</P>
-<P>If the Library is not listed as lib/package, then it is a third-party
-library not included in the LAMMPS distribution. See the
-src/package/Makefile.lammps file for info on where to download the
-library from.
-</P>
-<P>(2) The ATC package was created by Reese Jones, Jeremy Templeton, and
+<P>(1) The ATC package was created by Reese Jones, Jeremy Templeton, and
Jon Zimmerman (Sandia).
</P>
<P>(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
the colvars module library written by Giacomo Fiorin (Temple U) and
Jerome Henin (LISM, Marseille, France).
</P>
<P>(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal
Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
(U Blaise Pascal).
</P>
+<P>If the Library is not listed as lib/package, then it is a third-party
+library not included in the LAMMPS distribution. See the
+src/package/Makefile.lammps file for info on where to download the
+library from.
+</P>
<P>The "Doc page" column links to either a portion of the
<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
command implemented as part of the package, or to additional
-documentation provided witht he package.
+documentation provided within the package.
</P>
<P>The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory. USER/cuda
refers to the examples/USER/cuda directory.
</P>
<P>The "Library" column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See the src/package/Makefile.lammps file for info on where to download
the library. <A HREF = "Section_start.html#start_3_3">Section start</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-*/README file is given
-below.
+<P>Except where explained below, all of these packages can be installed,
+and LAMMPS re-built, by issuing these commands from the src dir.
+</P>
+<PRE>make yes-user-package
+make machine
+or
+Make.py -p package -a machine
+</PRE>
+<P>To un-install the package and re-build LAMMPS without it:
+</P>
+<PRE>make no-user-package
+make machine
+or
+Make.py -p ^package -a machine
+</PRE>
+<P>"Package" is the name of the package (in this case without the user
+prefix) in lower-case letters, e.g. drude or phonon, and "machine" is
+the build target, e.g. mpi or serial.
</P>
<HR>
+<HR>
+
<H4>USER-ATC package
</H4>
<P>This package implements a "fix atc" command which can be used in a
LAMMPS input script. This fix can be employed to either do concurrent
coupling of MD with FE-based physics surrogates or on-the-fly
post-processing of atomic information to continuum fields.
</P>
<P>See the doc page for the fix atc command to get started. At the
bottom of the doc page are many links to additional documentation
contained in the doc/USER/atc directory.
</P>
<P>There are example scripts for using this package in examples/USER/atc.
</P>
<P>This package uses an external library in lib/atc which must be
compiled before making LAMMPS. See the lib/atc/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
</P>
<P>The primary people who created this package are Reese Jones (rjones at
sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
you have questions.
</P>
<HR>
<H4>USER-AWPMD package
</H4>
<P>This package contains a LAMMPS implementation of the Antisymmetrized
Wave Packet Molecular Dynamics (AWPMD) method.
</P>
<P>See the doc page for the pair_style awpmd/cut command to get started.
</P>
<P>There are example scripts for using this package in examples/USER/awpmd.
</P>
<P>This package uses an external library in lib/awpmd which must be
compiled before making LAMMPS. See the lib/awpmd/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
</P>
<P>The person who created this package is Ilya Valuev at the JIHT in
Russia (valuev at physik.hu-berlin.de). Contact him directly if you
have questions.
</P>
<HR>
<H4>USER-CG-CMM package
</H4>
<P>This package implements 3 commands which can be used in a LAMMPS input
script:
</P>
<UL><LI>pair_style lj/sdk
<LI>pair_style lj/sdk/coul/long
<LI>angle_style sdk
</UL>
<P>These styles allow coarse grained MD simulations with the
parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
(SDK), with extensions to simulate ionic liquids, electrolytes, lipids
and charged amino acids.
</P>
<P>See the doc pages for these commands for details.
</P>
<P>There are example scripts for using this package in
examples/USER/cg-cmm.
</P>
<P>This is the second generation implementation reducing the the clutter
of the previous version. For many systems with electrostatics, it will
be faster to use pair_style hybrid/overlay with lj/sdk and coul/long
instead of the combined lj/sdk/coul/long style. since the number of
charged atom types is usually small. For any other coulomb
interactions this is now required. To exploit this property, the use
of the kspace_style pppm/cg is recommended over regular pppm. For all
new styles, input file backward compatibility is provided. The old
implementation is still available through appending the /old
suffix. These will be discontinued and removed after the new
implementation has been fully validated.
</P>
<P>The current version of this package should be considered beta
quality. The CG potentials work correctly for "normal" situations, but
have not been testing with all kinds of potential parameters and
simulation systems.
</P>
<P>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-COLVARS package
</H4>
<P>This package implements the "fix colvars" command which can be
used in a LAMMPS input script.
</P>
<P>This fix allows to use "collective variables" to implement
Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
Sampling and Restraints. This code consists of two parts:
</P>
<UL><LI>A portable collective variable module library written and maintained
<LI>by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
<LI>Jerome Henin (LISM, CNRS, Marseille, France). This code is located in
<LI>the directory lib/colvars and needs to be compiled first. The colvars
<LI>fix and an interface layer, exchanges information between LAMMPS and
<LI>the collective variable module.
</UL>
<P>See the doc page of <A HREF = "fix_colvars.html">fix colvars</A> for more details.
</P>
<P>There are example scripts for using this package in
examples/USER/colvars
</P>
<P>This is a very new interface that does not yet support all
features in the module and will see future optimizations
and improvements. The colvars module library is also available
in NAMD has been thoroughly used and tested there. Bugs and
problems are likely due to the interface layers code.
Thus the current version of this package should be considered
beta quality.
</P>
<P>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-CUDA package
</H4>
<P>This package provides acceleration of various LAMMPS pair styles, fix
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
GPUs.
</P>
<P>See this section of the manual to get started:
</P>
<P><A HREF = "Section_accelerate.html#acc_7">Section_accelerate</A>
</P>
<P>There are example scripts for using this package in
examples/USER/cuda.
</P>
<P>This package uses an external library in lib/cuda which must be
compiled before making LAMMPS. See the lib/cuda/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
</P>
<P>The person who created this package is Christian Trott at the
University of Technology Ilmenau, Germany (christian.trott at
tu-ilmenau.de). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-DIFFRACTION package
</H4>
<P>This package contains the commands neeed to calculate x-ray and
electron diffraction intensities based on kinematic diffraction
theory.
</P>
<P>See these doc pages and their related commands to get started:
</P>
<UL><LI><A HREF = "compute_xrd.html">compute xrd</A>
<LI><A HREF = "compute_saed.html">compute saed</A>
<LI><A HREF = "fix_saed_vtk.html">fix saed/vtk</A>
</UL>
<P>The person who created this package is Shawn P. Coleman
(shawn.p.coleman8.ctr at mail.mil) while at the University of
Arkansas. Contact him directly if you have questions.
</P>
<HR>
<H4>USER-DRUDE package
</H4>
<P>This package implements methods for simulating polarizable systems
in LAMMPS using thermalized Drude oscillators.
</P>
<P>See these doc pages and their related commands to get started:
</P>
<UL><LI><A HREF = "tutorial_drude.html">Drude tutorial</A>
<LI><A HREF = "fix_drude.html">fix drude</A>
<LI><A HREF = "compute_temp_drude.html">compute temp/drude</A>
<LI><A HREF = "fix_langevin_drude.html">fix langevin/drude</A>
<LI><A HREF = "fix_drude_transform.html">fix drude/transform/...</A>
<LI><A HREF = "pair_thole.html">pair thole</A>
</UL>
<P>There are auxiliary tools for using this package in tools/drude.
</P>
<P>The person who created this package is Alain Dequidt at Universite
Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
Contact him directly if you have questions. Co-authors: Julien Devemy,
Agilio Padua.
</P>
<HR>
<H4>USER-EFF package
</H4>
<P>This package contains a LAMMPS implementation of the electron Force
Field (eFF) currently under development at Caltech, as described in
A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
2010. The eFF potential was first introduced by Su and Goddard, in
2007.
</P>
<P>eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
structure methods to describe atomic structure, bonding, and chemistry
in materials, and of plasma methods to describe nonequilibrium
dynamics of large systems with a large number of highly excited
electrons. We classify it as a mixed QM-classical approach rather than
a conventional force field method, which introduces QM-based terms (a
spin-dependent repulsion term to account for the Pauli exclusion
principle and the electron wavefunction kinetic energy associated with
the Heisenberg principle) that reduce, along with classical
electrostatic terms between nuclei and electrons, to the sum of a set
of effective pairwise potentials. This makes eFF uniquely suited to
simulate materials over a wide range of temperatures and pressures
where electronically excited and ionized states of matter can occur
and coexist.
</P>
<P>The necessary customizations to the LAMMPS core are in place to
enable the correct handling of explicit electron properties during
minimization and dynamics.
</P>
<P>See the doc page for the pair_style eff/cut command to get started.
</P>
<P>There are example scripts for using this package in
examples/USER/eff.
</P>
<P>There are auxiliary tools for using this package in tools/eff.
</P>
<P>The person who created this package is Andres Jaramillo-Botero at
CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
have questions.
</P>
<HR>
<H4>USER-FEP package
</H4>
<P>This package provides methods for performing free energy perturbation
simulations with soft-core pair potentials in LAMMPS.
</P>
<P>See these doc pages and their related commands to get started:
</P>
<UL><LI><A HREF = "fix_adapt_fep.html">fix adapt/fep</A>
<LI><A HREF = "compute_fep.html">compute fep</A>
<LI><A HREF = "pair_lj_soft.html">soft pair styles</A>
</UL>
<P>The person who created this package is Agilio Padua at Universite
Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
Contact him directly if you have questions.
</P>
<HR>
<H4>USER-H5MD package
</H4>
<P>This package contains a <A HREF = "dump_h5md.html">dump h5md</A> command for
performing a dump of atom properties in HDF5 format. <A HREF = "http://www.hdfgroup.org/HDF5/">HDF5
files</A> are binary, portable and self-describing and can be
examined and used by a variety of auxiliary tools. The output HDF5
files are structured in a format called H5MD, which was designed to
store molecular data, and can be used and produced by various MD and
MD-related codes. The <A HREF = "doc/dump_h5md.html">dump h5md</A> command gives a
citation to a paper describing the format.
</P>
<P>The person who created this package and the underlying H5MD format is
Pierre de Buyl at KU Leuven (see http://pdebuyl.be). Contact him
directly if you have questions.
</P>
<HR>
<H4>USER-INTEL package
</H4>
<P>This package provides options for performing neighbor list and
non-bonded force calculations in single, mixed, or double precision
and also a capability for accelerating calculations with an
Intel(R) Xeon Phi(TM) coprocessor.
</P>
<P>See this section of the manual to get started:
</P>
<P><A HREF = "Section_accelerate.html#acc_9">Section_accelerate</A>
</P>
<P>The person who created this package is W. Michael Brown at Intel
(michael.w.brown at intel.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-LB package
</H4>
<P>This package contains a LAMMPS implementation of a background
Lattice-Boltzmann fluid, which can be used to model MD particles
influenced by hydrodynamic forces.
</P>
<P>See this doc page and its related commands to get started:
</P>
<P><A HREF = "fix_lb_fluid.html">fix lb/fluid</A>
</P>
<P>The people who created this package are Frances Mackay (fmackay at
uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
Western Ontario. Contact them directly if you have questions.
</P>
<HR>
<H4>USER-MISC package
</H4>
<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 (*.cpp and *.h).
</P>
<P>More information about each feature can be found by reading its doc
page in the LAMMPS doc directory. The doc page which lists all LAMMPS
input script commands is as follows:
</P>
<P><A HREF = "Section_commands.html#cmd_5">Section_commands</A>
</P>
<P>User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections.
</P>
<P>The list of features and author of each is given in the
src/USER-MISC/README file.
</P>
<P>You should contact the author directly if you have specific questions
about the feature or its coding.
</P>
<HR>
<H4>USER-MOLFILE package
</H4>
<P>This package contains a dump molfile command which uses molfile
plugins that are bundled with the
<A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> molecular visualization and
analysis program, to enable LAMMPS to dump its information in formats
compatible with various molecular simulation tools.
</P>
<P>The package only provides the interface code, not the plugins. These
can be obtained from a VMD installation which has to match the
platform that you are using to compile LAMMPS for. By adding plugins
to VMD, support for new file formats can be added to LAMMPS (or VMD or
other programs that use them) without having to recompile the
application itself.
</P>
<P>See this doc page to get started:
</P>
<P><A HREF = "dump_molfile.html#acc_5">dump molfile</A>
</P>
<P>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-OMP package
</H4>
<P>This package provides OpenMP multi-threading support and
other optimizations of various LAMMPS pair styles, dihedral
styles, and fix styles.
</P>
<P>See this section of the manual to get started:
</P>
<P><A HREF = "Section_accelerate.html#acc_5">Section_accelerate</A>
</P>
<P>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-PHONON package
</H4>
<P>This package contains a fix phonon command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
relations, directly from molecular dynamics simulations.
</P>
<P>See this doc page to get started:
</P>
<P><A HREF = "fix_phonon.html">fix phonon</A>
</P>
<P>The person who created this package is Ling-Ti Kong (konglt at
sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly
if you have questions.
</P>
<HR>
<H4>USER-QMMM package
</H4>
<P>This package provides a fix qmmm command which allows LAMMPS to be
used in a QM/MM simulation, currently only in combination with pw.x
code from the <A HREF = "http://www.quantum-espresso.org">Quantum ESPRESSO</A> package.
</P>
<P>The current implementation only supports an ONIOM style mechanical
coupling to the Quantum ESPRESSO plane wave DFT package.
Electrostatic coupling is in preparation and the interface has been
written in a manner that coupling to other QM codes should be possible
without changes to LAMMPS itself.
</P>
<P>See this doc page to get started:
</P>
<P><A HREF = "fix_qmmm.html">fix qmmm</A>
</P>
<P>as well as the lib/qmmm/README file.
</P>
<P>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-QTB package
</H4>
<P>This package provides a self-consistent quantum treatment of the
vibrational modes in a classical molecular dynamics simulation. By
coupling the MD simulation to a colored thermostat, it introduces zero
point energy into the system, alter the energy power spectrum and the
heat capacity towards their quantum nature. This package could be of
interest if one wants to model systems at temperatures lower than
their classical limits or when temperatures ramp up across the
classical limits in the simulation.
</P>
<P>See these two doc pages to get started:
</P>
<P><A HREF = "fix_qtb.html">fix qtb</A> provides quantum nulcear correction through a
colored thermostat and can be used with other time integration schemes
like <A HREF = "fix_nve.html">fix nve</A> or <A HREF = "fix_nh.html">fix nph</A>.
</P>
<P><A HREF = "fix_qbmsst.html">fix qbmsst</A> enables quantum nuclear correction of a
multi-scale shock technique simulation by coupling the quantum thermal
bath with the shocked system.
</P>
<P>The person who created this package is Yuan Shen (sy0302 at
stanford.edu) at Stanford University. Contact him directly if you
have questions.
</P>
<HR>
<H4>USER-REAXC package
</H4>
<P>This package contains a implementation for LAMMPS of the ReaxFF force
field. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. It was originally developed by Adri van Duin and the Goddard
group at CalTech.
</P>
<P>The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
C, should give identical or very similar results to pair_style reax,
which is a ReaxFF implementation on top of a Fortran library, a
version of which library was originally authored by Adri van Duin.
</P>
<P>The reax/c version should be somewhat faster and more scalable,
particularly with respect to the charge equilibration calculation. It
should also be easier to build and use since there are no complicating
issues with Fortran memory allocation or linking to a Fortran library.
</P>
<P>For technical details about this implemention of ReaxFF, see
this paper:
</P>
<P>Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011).
</P>
<P>See the doc page for the pair_style reax/c command for details
of how to use it in LAMMPS.
</P>
<P>The person who created this package is Hasan Metin Aktulga (hmaktulga
at lbl.gov), while at Purdue University. Contact him directly, or
Aidan Thompson at Sandia (athomps at sandia.gov), if you have
questions.
</P>
<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>* Does liquids via traditional Smooth Particle Hydrodynamics (SPH)
</P>
<P>* Also solves solids mechanics problems via a state of the art
stabilized meshless method with hourglass control.
</P>
<P>* Can specify hydrostatic interactions independently from material
strength models, i.e. pressure and deviatoric stresses are separated.
</P>
<P>* Many material models available (Johnson-Cook, plasticity with
hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
material models.
</P>
<P>* Rigid boundary conditions (walls) can be loaded as surface geometries
from *.STL files.
</P>
<P>See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.
</P>
<P>There are example scripts for using this package in examples/USER/smd.
</P>
<P>The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.
</P>
<H4>USER-SPH package
</H4>
<P>This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:
</P>
<P>* Tait, ideal gas, Lennard-Jones equation of states, full support for
complete (i.e. internal-energy dependent) equations of state
</P>
<P>* Plain or Monaghans XSPH integration of the equations of motion
</P>
<P>* Density continuity or density summation to propagate the density field
</P>
<P>* Commands to set internal energy and density of particles from the
input script
</P>
<P>* Output commands to access internal energy and density for dumping and
thermo output
</P>
<P>See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.
</P>
<P>There are example scripts for using this package in examples/USER/sph.
</P>
<P>The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.
</P>
</HTML>
diff --git a/doc/doc2/Section_start.html b/doc/doc2/Section_start.html
index 021793821..33d64e0f6 100644
--- a/doc/doc2/Section_start.html
+++ b/doc/doc2/Section_start.html
@@ -1,1942 +1,1940 @@
<HTML>
<CENTER><A HREF = "Section_intro.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_commands.html">Next Section</A>
</CENTER>
<HR>
<H3>2. Getting Started
</H3>
<P>This section describes how to build and run LAMMPS, for both new and
experienced users.
</P>
2.1 <A HREF = "#start_1">What's in the LAMMPS distribution</A><BR>
2.2 <A HREF = "#start_2">Making LAMMPS</A><BR>
2.3 <A HREF = "#start_3">Making LAMMPS with optional packages</A><BR>
2.4 <A HREF = "#start_4">Building LAMMPS via the Make.py script</A><BR>
2.5 <A HREF = "#start_5">Building LAMMPS as a library</A><BR>
2.6 <A HREF = "#start_6">Running LAMMPS</A><BR>
2.7 <A HREF = "#start_7">Command-line options</A><BR>
2.8 <A HREF = "#start_8">Screen output</A><BR>
2.9 <A HREF = "#start_9">Tips for users of previous versions</A> <BR>
<HR>
<HR>
<H4><A NAME = "start_1"></A>2.1 What's in the LAMMPS distribution
</H4>
<P>When you download a LAMMPS tarball you will need to unzip and untar
the downloaded file with the following commands, after placing the
tarball in an appropriate directory.
</P>
<PRE>gunzip lammps*.tar.gz
tar xvf lammps*.tar
</PRE>
<P>This will create a LAMMPS directory containing two files and several
sub-directories:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >README</TD><TD > text file</TD></TR>
<TR><TD >LICENSE</TD><TD > the GNU General Public License (GPL)</TD></TR>
<TR><TD >bench</TD><TD > benchmark problems</TD></TR>
<TR><TD >doc</TD><TD > documentation</TD></TR>
<TR><TD >examples</TD><TD > simple test problems</TD></TR>
<TR><TD >potentials</TD><TD > embedded atom method (EAM) potential files</TD></TR>
<TR><TD >src</TD><TD > source files</TD></TR>
<TR><TD >tools</TD><TD > pre- and post-processing tools
</TD></TR></TABLE></DIV>
<P>Note that the <A HREF = "download">download page</A> also has links to download
Windows exectubles and installers, as well as pre-built executables
for a few specific Linux distributions. It also has instructions for
how to download/install LAMMPS for Macs (via Homebrew), and to
download and update LAMMPS from SVN and Git repositories, which gives
you the same files that are in the download tarball.
</P>
<P>The Windows and Linux executables for serial or parallel only include
certain packages and bug-fixes/upgrades listed on <A HREF = "http://lammps.sandia.gov/bug.html">this
page</A> up to a certain date, as
stated on the download page. If you want an executable with
non-included packages or that is more current, then you'll need to
build LAMMPS yourself, as discussed in the next section.
</P>
<P>Skip to the <A HREF = "#start_6">Running LAMMPS</A> sections for info on how to
launch a LAMMPS Windows executable on a Windows box.
</P>
<HR>
<H4><A NAME = "start_2"></A>2.2 Making LAMMPS
</H4>
<P>This section has the following sub-sections:
</P>
<UL><LI><A HREF = "#start_2_1">Read this first</A>
<LI><A HREF = "#start_2_2">Steps to build a LAMMPS executable</A>
<LI><A HREF = "#start_2_3">Common errors that can occur when making LAMMPS</A>
<LI><A HREF = "#start_2_4">Additional build tips</A>
<LI><A HREF = "#start_2_5">Building for a Mac</A>
<LI><A HREF = "#start_2_6">Building for Windows</A>
</UL>
<HR>
<A NAME = "start_2_1"></A><B><I>Read this first:</I></B>
<P>If you want to avoid building LAMMPS yourself, read the preceeding
section about options available for downloading and installing
executables. Details are discussed on the <A HREF = "download">download</A> page.
</P>
<P>Building LAMMPS can be simple or not-so-simple. If all you need are
the default packages installed in LAMMPS, and MPI is already installed
on your machine, or you just want to run LAMMPS in serial, then you
can typically use the Makefile.mpi or Makefile.serial files in
src/MAKE by typing one of these lines (from the src dir):
</P>
<PRE>make mpi
make serial
</PRE>
<P>Note that on a facility supercomputer, there are often "modules"
loaded in your environment that provide the compilers and MPI you
should use. In this case, the "mpicxx" compile/link command in
Makefile.mpi should just work by accessing those modules.
</P>
<P>It may be the case that one of the other Makefile.machine files in the
src/MAKE sub-directories is a better match to your system (type "make"
to see a list), you can use it as-is by typing (for example):
</P>
<PRE>make stampede
</PRE>
<P>If any of these builds (with an existing Makefile.machine) works on
your system, then you're done!
</P>
<P>If you want to do one of the following:
</P>
<UL><LI>use optional LAMMPS features that require additional libraries
<LI>use optional packages that require additional libraries
<LI>use optional accelerator packages that require special compiler/linker settings
<LI>run on a specialized platform that has its own compilers, settings, or other libs to use
</UL>
<P>then building LAMMPS is more complicated. You may need to find where
auxiliary libraries exist on your machine or install them if they
don't. You may need to build additional libraries that are part of
the LAMMPS package, before building LAMMPS. You may need to edit a
Makefile.machine file to make it compatible with your system.
</P>
<P>Note that there is a Make.py tool in the src directory that automates
several of these steps, but you still have to know what you are doing.
<A HREF = "#start_4">Section 2.4</A> below describes the tool. It is a convenient
way to work with installing/un-installing various packages, the
Makefile.machine changes required by some packages, and the auxiliary
libraries some of them use.
</P>
<P>Please read the following sections carefully. If you are not
comfortable with makefiles, or building codes on a Unix platform, or
running an MPI job on your machine, please find a local expert to help
you. Many compilation, linking, and run problems that users have are
often not really LAMMPS issues - they are peculiar to the user's
system, compilers, libraries, etc. Such questions are better answered
by a local expert.
</P>
<P>If you have a build problem that you are convinced is a LAMMPS issue
(e.g. the compiler complains about a line of LAMMPS source code), then
please post the issue to the <A HREF = "http://lammps.sandia.gov/mail.html">LAMMPS mail
list</A>.
</P>
<P>If you succeed in building LAMMPS on a new kind of machine, for which
there isn't a similar machine Makefile included in the
src/MAKE/MACHINES directory, then send it to the developers and we can
include it in the LAMMPS distribution.
</P>
<HR>
<A NAME = "start_2_2"></A><B><I>Steps to build a LAMMPS executable:</I></B>
<P><B>Step 0</B>
</P>
<P>The src directory contains the C++ source and header files for LAMMPS.
It also contains a top-level Makefile and a MAKE sub-directory with
low-level Makefile.* files for many systems and machines. See the
src/MAKE/README file for a quick overview of what files are available
and what sub-directories they are in.
</P>
<P>The src/MAKE dir has a few files that should work as-is on many
platforms. The src/MAKE/OPTIONS dir has more that invoke additional
compiler, MPI, and other setting options commonly used by LAMMPS, to
illustrate their syntax. The src/MAKE/MACHINES dir has many more that
have been tweaked or optimized for specific machines. These files are
all good starting points if you find you need to change them for your
machine. Put any file you edit into the src/MAKE/MINE directory and
it will be never be touched by any LAMMPS updates.
</P>
<P>>From within the src directory, type "make" or "gmake". You should see
a list of available choices from src/MAKE and all of its
sub-directories. If one of those has the options you want or is the
machine you want, you can type a command like:
</P>
<PRE>make mpi
or
make serial_icc
or
gmake mac
</PRE>
<P>Note that the corresponding Makefile.machine can exist in src/MAKE or
any of its sub-directories. If a file with the same name appears in
multiple places (not a good idea), the order they are used is as
follows: src/MAKE/MINE, src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES.
This gives preference to a file you have created/edited and put in
src/MAKE/MINE.
</P>
<P>Note that on a multi-processor or multi-core platform you can launch a
parallel make, by using the "-j" switch with the make command, which
will build LAMMPS more quickly.
</P>
<P>If you get no errors and an executable like lmp_mpi or lmp_g++_serial
or lmp_mac is produced, then you're done; it's your lucky day.
</P>
<P>Note that by default only a few of LAMMPS optional packages are
installed. To build LAMMPS with optional packages, see <A HREF = "#start_3">this
section</A> below.
</P>
<P><B>Step 1</B>
</P>
<P>If Step 0 did not work, you will need to create a low-level Makefile
for your machine, like Makefile.foo. You should make a copy of an
existing Makefile.* in src/MAKE or one of its sub-directories as a
starting point. The only portions of the file you need to edit are
the first line, the "compiler/linker settings" section, and the
"LAMMPS-specific settings" section. When it works, put the edited
file in src/MAKE/MINE and it will not be altered by any future LAMMPS
updates.
</P>
<P><B>Step 2</B>
</P>
<P>Change the first line of Makefile.foo to list the word "foo" after the
"#", and whatever other options it will set. This is the line you
will see if you just type "make".
</P>
<P><B>Step 3</B>
</P>
<P>The "compiler/linker settings" section lists compiler and linker
settings for your C++ compiler, including optimization flags. You can
use g++, the open-source GNU compiler, which is available on all Unix
systems. You can also use mpicxx which will typically be available if
MPI is installed on your system, though you should check which actual
compiler it wraps. Vendor compilers often produce faster code. On
boxes with Intel CPUs, we suggest using the Intel icc compiler, which
can be downloaded from <A HREF = "http://www.intel.com/software/products/noncom">Intel's compiler site</A>.
</P>
<P>If building a C++ code on your machine requires additional libraries,
then you should list them as part of the LIB variable. You should
not need to do this if you use mpicxx.
</P>
<P>The DEPFLAGS setting is what triggers the C++ compiler to create a
dependency list for a source file. This speeds re-compilation when
source (*.cpp) or header (*.h) files are edited. Some compilers do
not support dependency file creation, or may use a different switch
than -D. GNU g++ and Intel icc works with -D. If your compiler can't
create dependency files, then you'll need to create a Makefile.foo
patterned after Makefile.storm, which uses different rules that do not
involve dependency files. Note that when you build LAMMPS for the
first time on a new platform, a long list of *.d files will be printed
out rapidly. This is not an error; it is the Makefile doing its
normal creation of dependencies.
</P>
<P><B>Step 4</B>
</P>
<P>The "system-specific settings" section has several parts. Note that
if you change any -D setting in this section, you should do a full
re-compile, after typing "make clean" (which will describe different
clean options).
</P>
<P>The LMP_INC variable is used to include options that turn on ifdefs
within the LAMMPS code. The options that are currently recogized are:
</P>
<UL><LI>-DLAMMPS_GZIP
<LI>-DLAMMPS_JPEG
<LI>-DLAMMPS_PNG
<LI>-DLAMMPS_FFMPEG
<LI>-DLAMMPS_MEMALIGN
<LI>-DLAMMPS_XDR
<LI>-DLAMMPS_SMALLBIG
<LI>-DLAMMPS_BIGBIG
<LI>-DLAMMPS_SMALLSMALL
<LI>-DLAMMPS_LONGLONG_TO_LONG
<LI>-DPACK_ARRAY
<LI>-DPACK_POINTER
<LI>-DPACK_MEMCPY
</UL>
<P>The read_data and dump commands will read/write gzipped files if you
compile with -DLAMMPS_GZIP. It requires that your machine supports
the "popen()" function in the standard runtime library and that a gzip
executable can be found by LAMMPS during a run.
</P>
<P>IMPORTANT NOTE: on some clusters with high-speed networks, using the
fork() library calls (required by popen()) can interfere with the fast
communication library and lead to simulations using compressed output
or input to hang or crash. For selected operations, compressed file
I/O is also available using a compression library instead, which are
provided in the COMPRESS package. From more details about compiling
LAMMPS with packages, please see below.
</P>
<P>If you use -DLAMMPS_JPEG, the <A HREF = "dump_image.html">dump image</A> command
will be able to write out JPEG image files. For JPEG files, you must
also link LAMMPS with a JPEG library, as described below. If you use
-DLAMMPS_PNG, the <A HREF = "dump.html">dump image</A> command will be able to write
out PNG image files. For PNG files, you must also link LAMMPS with a
PNG library, as described below. If neither of those two defines are
used, LAMMPS will only be able to write out uncompressed PPM image
files.
</P>
<P>If you use -DLAMMPS_FFMPEG, the <A HREF = "dump_image.html">dump movie</A> command
will be available to support on-the-fly generation of rendered movies
the need to store intermediate image files. It requires that your
machines supports the "popen" function in the standard runtime library
and that an FFmpeg executable can be found by LAMMPS during the run.
</P>
<P>IMPORTANT NOTE: Similar to the note above, this option can conflict
with high-speed networks, because it uses popen().
</P>
<P>Using -DLAMMPS_MEMALIGN=<bytes> enables the use of the
posix_memalign() call instead of malloc() when large chunks or memory
are allocated by LAMMPS. This can help to make more efficient use of
vector instructions of modern CPUS, since dynamically allocated memory
has to be aligned on larger than default byte boundaries (e.g. 16
bytes instead of 8 bytes on x86 type platforms) for optimal
performance.
</P>
<P>If you use -DLAMMPS_XDR, the build will include XDR compatibility
files for doing particle dumps in XTC format. This is only necessary
if your platform does have its own XDR files available. See the
Restrictions section of the <A HREF = "dump.html">dump</A> command for details.
</P>
<P>Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, -D-
DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These
settings refer to use of 4-byte (small) vs 8-byte (big) integers
within LAMMPS, as specified in src/lmptype.h. The only reason to use
the BIGBIG setting is to enable simulation of huge molecular systems
(which store bond topology info) with more than 2 billion atoms, or to
track the image flags of moving atoms that wrap around a periodic box
more than 512 times. Normally, the only reason to use SMALLSMALL is
if your machine does not support 64-bit integers, though you can use
SMALLSMALL setting if you are running in serial or on a desktop
machine or small cluster where you will never run large systems or for
long time (more than 2 billion atoms, more than 2 billion timesteps).
See the <A HREF = "#start_2_4">Additional build tips</A> section below for more
details on these settings.
</P>
<P>Note that two packages, USER-ATC and USER-CUDA are not currently
compatible with -DLAMMPS_BIGBIG. Also the GPU package requires the
lib/gpu library to be compiled with the same setting, or the link will
fail.
</P>
<P>The -DLAMMPS_LONGLONG_TO_LONG setting may be needed if your system or
MPI version does not recognize "long long" data types. In this case a
"long" data type is likely already 64-bits, in which case this setting
will convert to that data type.
</P>
<P>Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY
options can make for faster parallel FFTs (in the PPPM solver) on some
platforms. The -DPACK_ARRAY setting is the default. See the
<A HREF = "kspace_style.html">kspace_style</A> command for info about PPPM. See
Step 6 below for info about building LAMMPS with an FFT library.
</P>
<P><B>Step 5</B>
</P>
<P>The 3 MPI variables are used to specify an MPI library to build LAMMPS
with. Note that you do not need to set these if you use the MPI
compiler mpicxx for your CC and LINK setting in the section above.
The MPI wrapper knows where to find the needed files.
</P>
<P>If you want LAMMPS to run in parallel, you must have an MPI library
installed on your platform. If MPI is installed on your system in the
usual place (under /usr/local), you also may not need to specify these
3 variables, assuming /usr/local is in your path. On some large
parallel machines which use "modules" for their compile/link
environements, you may simply need to include the correct module in
your build environment, before building LAMMPS. Or the parallel
machine may have a vendor-provided MPI which the compiler has no
trouble finding.
</P>
<P>Failing this, these 3 variables can be used to specify where the mpi.h
file (MPI_INC) and the MPI library file (MPI_PATH) are found and the
name of the library file (MPI_LIB).
</P>
<P>If you are installing MPI yourself, we recommend Argonne's MPICH2
or OpenMPI. MPICH can be downloaded from the <A HREF = "http://www.mcs.anl.gov/research/projects/mpich2/">Argonne MPI
site</A>. OpenMPI can
be downloaded from the <A HREF = "http://www.open-mpi.org">OpenMPI site</A>.
Other MPI packages should also work. If you are running on a big
parallel platform, your system people or the vendor should have
already installed a version of MPI, which is likely to be faster
than a self-installed MPICH or OpenMPI, so find out how to build
and link with it. If you use MPICH or OpenMPI, you will have to
configure and build it for your platform. The MPI configure script
should have compiler options to enable you to use the same compiler
you are using for the LAMMPS build, which can avoid problems that can
arise when linking LAMMPS to the MPI library.
</P>
<P>If you just want to run LAMMPS on a single processor, you can use the
dummy MPI library provided in src/STUBS, since you don't need a true
MPI library installed on your system. See src/MAKE/Makefile.serial
for how to specify the 3 MPI variables in this case. You will also
need to build the STUBS library for your platform before making LAMMPS
itself. Note that if you are building with src/MAKE/Makefile.serial,
e.g. by typing "make serial", then the STUBS library is built for you.
</P>
<P>To build the STUBS library from the src directory, type "make
mpi-stubs", or from the src/STUBS dir, type "make". This should
create a libmpi_stubs.a file suitable for linking to LAMMPS. If the
build fails, you will need to edit the STUBS/Makefile for your
platform.
</P>
<P>The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime()
that calls gettimeofday() . If your system doesn't support
gettimeofday() , you'll need to insert code to call another timer.
Note that the ANSI-standard function clock() rolls over after an hour
or so, and is therefore insufficient for timing long LAMMPS
simulations.
</P>
<P><B>Step 6</B>
</P>
<P>The 3 FFT variables allow you to specify an FFT library which LAMMPS
uses (for performing 1d FFTs) when running the particle-particle
particle-mesh (PPPM) option for long-range Coulombics via the
<A HREF = "kspace_style.html">kspace_style</A> command.
</P>
<P>LAMMPS supports various open-source or vendor-supplied FFT libraries
for this purpose. If you leave these 3 variables blank, LAMMPS will
use the open-source <A HREF = "http://kissfft.sf.net">KISS FFT library</A>, which is
included in the LAMMPS distribution. This library is portable to all
platforms and for typical LAMMPS simulations is almost as fast as FFTW
or vendor optimized libraries. If you are not including the KSPACE
package in your build, you can also leave the 3 variables blank.
</P>
<P>Otherwise, select which kinds of FFTs to use as part of the FFT_INC
setting by a switch of the form -DFFT_XXX. Recommended values for XXX
are: MKL, SCSL, FFTW2, and FFTW3. Legacy options are: INTEL, SGI,
ACML, and T3E. For backward compatability, using -DFFT_FFTW will use
the FFTW2 library. Using -DFFT_NONE will use the KISS library
described above.
</P>
<P>You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
so the compiler and linker can find the needed FFT header and library
files. Note that on some large parallel machines which use "modules"
for their compile/link environements, you may simply need to include
the correct module in your build environment. Or the parallel machine
may have a vendor-provided FFT library which the compiler has no
trouble finding.
</P>
<P>FFTW is a fast, portable library that should also work on any
platform. You can download it from
<A HREF = "http://www.fftw.org">www.fftw.org</A>. Both the legacy version 2.1.X and
the newer 3.X versions are supported as -DFFT_FFTW2 or -DFFT_FFTW3.
Building FFTW for your box should be as simple as ./configure; make.
Note that on some platforms FFTW2 has been pre-installed, and uses
renamed files indicating the precision it was compiled with,
e.g. sfftw.h, or dfftw.h instead of fftw.h. In this case, you can
specify an additional define variable for FFT_INC called -DFFTW_SIZE,
which will select the correct include file. In this case, for FFT_LIB
you must also manually specify the correct library, namely -lsfftw or
-ldfftw.
</P>
<P>The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
use single-precision FFTs with PPPM, which can speed-up long-range
calulations, particularly in parallel or on GPUs. Fourier transform
and related PPPM operations are somewhat insensitive to floating point
truncation errors and thus do not always need to be performed in
double precision. Using the -DFFT_SINGLE setting trades off a little
accuracy for reduced memory use and parallel communication costs for
transposing 3d FFT data. Note that single precision FFTs have only
been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
</P>
<P><B>Step 7</B>
</P>
<P>The 3 JPG variables allow you to specify a JPEG and/or PNG library
which LAMMPS uses when writing out JPEG or PNG files via the <A HREF = "dump_image.html">dump
image</A> command. These can be left blank if you do not
use the -DLAMMPS_JPEG or -DLAMMPS_PNG switches discussed above in Step
4, since in that case JPEG/PNG output will be disabled.
</P>
<P>A standard JPEG library usually goes by the name libjpeg.a or
libjpeg.so and has an associated header file jpeglib.h. Whichever
JPEG library you have on your platform, you'll need to set the
appropriate JPG_INC, JPG_PATH, and JPG_LIB variables, so that the
compiler and linker can find it.
</P>
<P>A standard PNG library usually goes by the name libpng.a or libpng.so
and has an associated header file png.h. Whichever PNG library you
have on your platform, you'll need to set the appropriate JPG_INC,
JPG_PATH, and JPG_LIB variables, so that the compiler and linker can
find it.
</P>
<P>As before, if these header and library files are in the usual place on
your machine, you may not need to set these variables.
</P>
<P><B>Step 8</B>
</P>
<P>Note that by default only a few of LAMMPS optional packages are
installed. To build LAMMPS with optional packages, see <A HREF = "#start_3">this
section</A> below, before proceeding to Step 9.
</P>
<P><B>Step 9</B>
</P>
<P>That's it. Once you have a correct Makefile.foo, and you have
pre-built any other needed libraries (e.g. MPI, FFT, etc) all you need
to do from the src directory is type something like this:
</P>
<PRE>make foo
or
gmake foo
</PRE>
<P>You should get the executable lmp_foo when the build is complete.
</P>
<HR>
<A NAME = "start_2_3"></A><B><I>Errors that can occur when making LAMMPS:</I></B>
<P>IMPORTANT NOTE: If an error occurs when building LAMMPS, the compiler
or linker will state very explicitly what the problem is. The error
message should give you a hint as to which of the steps above has
failed, and what you need to do in order to fix it. Building a code
with a Makefile is a very logical process. The compiler and linker
need to find the appropriate files and those files need to be
compatible with LAMMPS source files. When a make fails, there is
usually a very simple reason, which you or a local expert will need to
fix.
</P>
<P>Here are two non-obvious errors that can occur:
</P>
<P>(1) If the make command breaks immediately with errors that indicate
it can't find files with a "*" in their names, this can be because
your machine's native make doesn't support wildcard expansion in a
makefile. Try gmake instead of make. If that doesn't work, try using
a -f switch with your make command to use a pre-generated
Makefile.list which explicitly lists all the needed files, e.g.
</P>
<PRE>make makelist
make -f Makefile.list linux
gmake -f Makefile.list mac
</PRE>
<P>The first "make" command will create a current Makefile.list with all
the file names in your src dir. The 2nd "make" command (make or
gmake) will use it to build LAMMPS. Note that you should
include/exclude any desired optional packages before using the "make
makelist" command.
</P>
<P>(2) If you get an error that says something like 'identifier "atoll"
is undefined', then your machine does not support "long long"
integers. Try using the -DLAMMPS_LONGLONG_TO_LONG setting described
above in Step 4.
</P>
<HR>
<A NAME = "start_2_4"></A><B><I>Additional build tips:</I></B>
<P>(1) Building LAMMPS for multiple platforms.
</P>
<P>You can make LAMMPS for multiple platforms from the same src
directory. Each target creates its own object sub-directory called
Obj_target where it stores the system-specific *.o files.
</P>
<P>(2) Cleaning up.
</P>
<P>Typing "make clean-all" or "make clean-machine" will delete *.o object
files created when LAMMPS is built, for either all builds or for a
particular machine.
</P>
<P>(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
</P>
<P>As explained above, any of these 3 settings can be specified on the
LMP_INC line in your low-level src/MAKE/Makefile.foo.
</P>
<P>The default is -DLAMMPS_SMALLBIG which allows for systems with up to
2^63 atoms and 2^63 timesteps (about 9e18). The atom limit is for
atomic systems which do not store bond topology info and thus do not
require atom IDs. If you use atom IDs for atomic systems (which is
the default) or if you use a molecular model, which stores bond
topology info and thus requires atom IDs, the limit is 2^31 atoms
(about 2 billion). This is because the IDs are stored in 32-bit
integers.
</P>
<P>Likewise, with this setting, the 3 image flags for each atom (see the
<A HREF = "dump.html">dump</A> doc page for a discussion) are stored in a 32-bit
integer, which means the atoms can only wrap around a periodic box (in
each dimension) at most 512 times. If atoms move through the periodic
box more than this many times, the image flags will "roll over",
e.g. from 511 to -512, which can cause diagnostics like the
mean-squared displacement, as calculated by the <A HREF = "compute_msd.html">compute
msd</A> command, to be faulty.
</P>
<P>To allow for larger atomic systems with atom IDs or larger molecular
systems or larger image flags, compile with -DLAMMPS_BIGBIG. This
stores atom IDs and image flags in 64-bit integers. This enables
atomic or molecular systems with atom IDS of up to 2^63 atoms (about
9e18). And image flags will not "roll over" until they reach 2^20 =
1048576.
</P>
<P>If your system does not support 8-byte integers, you will need to
compile with the -DLAMMPS_SMALLSMALL setting. This will restrict the
total number of atoms (for atomic or molecular systems) and timesteps
to 2^31 (about 2 billion). Image flags will roll over at 2^9 = 512.
</P>
<P>Note that in src/lmptype.h there are definitions of all these data
types as well as the MPI data types associated with them. The MPI
types need to be consistent with the associated C data types, or else
LAMMPS will generate a run-time error. As far as we know, the
settings defined in src/lmptype.h are portable and work on every
current system.
</P>
<P>In all cases, the size of problem that can be run on a per-processor
basis is limited by 4-byte integer storage to 2^31 atoms per processor
(about 2 billion). This should not normally be a limitation since such
a problem would have a huge per-processor memory footprint due to
neighbor lists and would run very slowly in terms of CPU secs/timestep.
</P>
<HR>
<A NAME = "start_2_5"></A><B><I>Building for a Mac:</I></B>
<P>OS X is BSD Unix, so it should just work. See the
src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.
</P>
<HR>
<A NAME = "start_2_6"></A><B><I>Building for Windows:</I></B>
<P>The LAMMPS download page has an option to download both a serial and
parallel pre-built Windows executable. See the <A HREF = "#start_6">Running
LAMMPS</A> section for instructions on running these executables
on a Windows box.
</P>
<P>The pre-built executables hosted on the <A HREF = "http://lammps.sandia.gov/download.html">LAMMPS download
page</A> are built with a subset
of the available packages; see the download page for the list. These
are single executable files. No examples or documentation in
included. You will need to download the full source code package to
obtain those.
</P>
<P>As an alternative, you can download "daily builds" (and some older
versions) of the installer packages from
<A HREF = "http://rpm.lammps.org/windows.html">rpm.lammps.org/windows.html</A>.
These executables are built with most optional packages and the
download includes documentation, some tools and most examples.
</P>
<P>If you want a Windows version with specific packages included and
excluded, you can build it yourself.
</P>
<P>One way to do this is install and use cygwin to build LAMMPS with a
standard unix style make program, just as you would on a Linux box;
see src/MAKE/MACHINES/Makefile.cygwin.
</P>
-<P>The other way to do this is using Visual Studio and project files.
-See the src/WINDOWS directory and its README.txt file for instructions
-on both a basic build and a customized build with pacakges you select.
-</P>
<HR>
<H4><A NAME = "start_3"></A>2.3 Making LAMMPS with optional packages
</H4>
<P>This section has the following sub-sections:
</P>
<UL><LI><A HREF = "#start_3_1">Package basics</A>
<LI><A HREF = "#start_3_2">Including/excluding packages</A>
<LI><A HREF = "#start_3_3">Packages that require extra libraries</A>
<LI><A HREF = "#start_3_4">Packages that require Makefile.machine settings</A>
</UL>
<P>Note that the following <A HREF = "#start_4">Section 2.4</A> describes the Make.py
tool which can be used to install/un-install packages and build the
auxiliary libraries which some of them use. It can also auto-edit a
Makefile.machine to add settings needed by some packages.
</P>
<HR>
<A NAME = "start_3_1"></A><B><I>Package basics:</I></B>
<P>The source code for LAMMPS is structured as a set of core files which
are always included, plus optional packages. Packages are groups of
files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages.
</P>
<P>You can see the list of all packages by typing "make package" from
within the src directory of the LAMMPS distribution. This also lists
various make commands that can be used to manipulate packages.
</P>
<P>If you use a command in a LAMMPS input script that is specific to a
particular package, you must have built LAMMPS with that package, else
you will get an error that the style is invalid or the command is
unknown. Every command's doc page specfies if it is part of a
package. You can also type
</P>
<PRE>lmp_machine -h
</PRE>
<P>to run your executable with the optional <A HREF = "#start_7">-h command-line
-switch</A> for "help", which will list the styles and commands
-known to your executable.
+switch</A> for "help", which will simply list the styles and
+commands known to your executable, and immediately exit.
</P>
<P>There are two kinds of packages in LAMMPS, standard and user packages.
More information about the contents of standard and user packages is
given in <A HREF = "Section_packages.html">Section_packages</A> of the manual. The
difference between standard and user packages is as follows:
</P>
-<P>Standard packages are supported by the LAMMPS developers and are
-written in a syntax and style consistent with the rest of LAMMPS.
-This means we will answer questions about them, debug and fix them if
-necessary, and keep them compatible with future changes to LAMMPS.
+<P>Standard packages, such as molecule or kspace, are supported by the
+LAMMPS developers and are written in a syntax and style consistent
+with the rest of LAMMPS. This means we will answer questions about
+them, debug and fix them if necessary, and keep them compatible with
+future changes to LAMMPS.
</P>
-<P>User packages have been contributed by users, and always begin with
-the user prefix. If they are a single command (single file), they are
-typically in the user-misc package. Otherwise, they are a a set of
-files grouped together which add a specific functionality to the code.
+<P>User packages, such as user-atc or user-omp, have been contributed by
+users, and always begin with the user prefix. If they are a single
+command (single file), they are typically in the user-misc package.
+Otherwise, they are a a set of files grouped together which add a
+specific functionality to the code.
</P>
<P>User packages don't necessarily meet the requirements of the standard
packages. If you have problems using a feature provided in a user
-package, you will likely need to contact the contributor directly to
-get help. Information on how to submit additions you make to LAMMPS
-as a user-contributed package is given in <A HREF = "Section_modify.html#mod_15">this
-section</A> of the documentation.
+package, you may need to contact the contributor directly to get help.
+Information on how to submit additions you make to LAMMPS as single
+files or either a standard or user-contributed package are given in
+<A HREF = "Section_modify.html#mod_15">this section</A> of the documentation.
</P>
-<P>Some packages (both standard and user) require additional libraries.
-See more details below.
+<P>Some packages (both standard and user) require additional auxiliary
+libraries when building LAMMPS. See more details below.
</P>
<HR>
<A NAME = "start_3_2"></A><B><I>Including/excluding packages:</I></B>
-<P>To use or not use a package you must include or exclude it before
-building LAMMPS. From the src directory, this is typically as simple
-as:
+<P>To use (or not use) a package you must include it (or exclude it)
+before building LAMMPS. From the src directory, this is typically as
+simple as:
</P>
<PRE>make yes-colloid
make g++
</PRE>
<P>or
</P>
<PRE>make no-manybody
make g++
</PRE>
<P>IMPORTANT NOTE: You should NOT include/exclude packages and build
-LAMMPS in a single make command by using multiple targets, e.g. make
+LAMMPS in a single make command using multiple targets, e.g. make
yes-colloid g++. This is because the make procedure creates a list of
source files that will be out-of-date for the build if the package
-configuration changes during the same command.
+configuration changes within the same command.
</P>
<P>Some packages have individual files that depend on other packages
being included. LAMMPS checks for this and does the right thing.
I.e. individual files are only included if their dependencies are
already included. Likewise, if a package is excluded, other files
dependent on that package are also excluded.
</P>
<P>If you will never run simulations that use the features in a
particular packages, there is no reason to include it in your build.
For some packages, this will keep you from having to build auxiliary
libraries (see below), and will also produce a smaller executable
which may run a bit faster.
</P>
<P>When you download a LAMMPS tarball, these packages are pre-installed
in the src directory: KSPACE, MANYBODY,MOLECULE. When you download
LAMMPS source files from the SVN or Git repositories, no packages are
pre-installed.
</P>
<P>Packages are included or excluded by typing "make yes-name" or "make
no-name", where "name" is the name of the package in lower-case, e.g.
name = kspace for the KSPACE package or name = user-atc for the
USER-ATC package. You can also type "make yes-standard", "make
no-standard", "make yes-std", "make no-std", "make yes-user", "make
no-user", "make yes-all" or "make no-all" to include/exclude various
sets of packages. Type "make package" to see the all of the
package-related make options.
</P>
<P>IMPORTANT NOTE: Inclusion/exclusion of a package works by simply
moving files back and forth between the main src directory and
sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
so that the files are seen or not seen when LAMMPS is built. After
you have included or excluded a package, you must re-build LAMMPS.
</P>
<P>Additional package-related make options exist to help manage LAMMPS
files that exist in both the src directory and in package
sub-directories. You do not normally need to use these commands
unless you are editing LAMMPS files or have downloaded a patch from
the LAMMPS WWW site.
</P>
<P>Typing "make package-update" or "make pu" will overwrite src files
with files from the package sub-directories if the package has been
included. It should be used after a patch is installed, since patches
only update the files in the package sub-directory, but not the src
files. Typing "make package-overwrite" will overwrite files in the
package sub-directories with src files.
</P>
<P>Typing "make package-status" or "make ps" will show which packages are
currently included. Of those that are included, it will list files
that are different in the src directory and package sub-directory.
Typing "make package-diff" lists all differences between these files.
Again, type "make package" to see all of the package-related make
options.
</P>
<HR>
<A NAME = "start_3_3"></A><B><I>Packages that require extra libraries:</I></B>
<P>A few of the standard and user packages require additional auxiliary
-libraries. Most of them are provided with LAMMPS, in which case they
-must be compiled first, before LAMMPS is built if you wish to include
+libraries. Many of them are provided with LAMMPS, in which case they
+must be compiled first, before LAMMPS is built, if you wish to include
that package. If you get a LAMMPS build error about a missing
library, this is likely the reason. See the
<A HREF = "Section_packages.html">Section_packages</A> doc page for a list of
packages that have these kinds of auxiliary libraries.
</P>
<P>The lib directory in the distribution has sub-directories with package
-names that correspond to the needed auxiliary libs, e.g. lib/reax.
+names that correspond to the needed auxiliary libs, e.g. lib/gpu.
Each sub-directory has a README file that gives more details. Code
for most of the auxiliary libraries is included in that directory.
Examples are the USER-ATC and MEAM packages.
</P>
<P>A few of the lib sub-directories do not include code, but do include
-instructions and sometimes scripts that automate the process of
+instructions (and sometimes scripts) that automate the process of
downloading the auxiliary library and installing it so LAMMPS can link
-to it. Examples are the KIM and VORONOI and USER-MOLFILE and USER-SMD
+to it. Examples are the KIM, VORONOI, USER-MOLFILE, and USER-SMD
packages.
</P>
<P>The lib/python directory (for the PYTHON package) contains only a
choice of Makefile.lammps.* files. This is because no auxiliary code
or libraries are needed, only the Python library and other system libs
-that already available on your system. However, the Makefile.lammps
-file is needed to tell the LAMMPS build which libs to use and where to
-find them.
+that should already available on your system. However, the
+Makefile.lammps file is needed to tell LAMMPS which libs to use and
+where to find them.
</P>
<P>For libraries with provided code, the sub-directory README file
-(e.g. lib/reax/README) has instructions on how to build that library.
+(e.g. lib/atc/README) has instructions on how to build that library.
Typically this is done by typing something like:
</P>
<PRE>make -f Makefile.g++
</PRE>
<P>If one of the provided Makefiles is not appropriate for your system
you will need to edit or add one. Note that all the Makefiles have a
setting for EXTRAMAKE at the top that specifies a Makefile.lammps.*
file.
</P>
<P>If the library build is successful, it will produce 2 files in the lib
directory:
</P>
<PRE>libpackage.a
Makefile.lammps
</PRE>
<P>The Makefile.lammps file will be a copy of the EXTRAMAKE file setting
specified in the library Makefile.* you used.
</P>
<P>Note that you must insure that the settings in Makefile.lammps are
appropriate for your system. If they are not, the LAMMPS build will
fail.
</P>
<P>As explained in the lib/package/README files, the settings in
Makefile.lammps are used to specify additional system libraries and
their locations so that LAMMPS can build with the auxiliary library.
-For example, if the MEAM or REAX packages are used, the auxiliary
-libraries consist of F90 code, built with a Fortran complier. To link
-that library with LAMMPS (a C++ code) via whatever C++ compiler LAMMPS
-is built with, typically requires additional Fortran-to-C libraries be
+For example, if the MEAM package is used, the auxiliary library
+consists of F90 code, built with a Fortran complier. To link that
+library with LAMMPS (a C++ code) via whatever C++ compiler LAMMPS is
+built with, typically requires additional Fortran-to-C libraries be
included in the link. Another example are the BLAS and LAPACK
libraries needed to use the USER-ATC or USER-AWPMD packages.
</P>
<P>For libraries without provided code, the sub-directory README file has
information on where to download the library and how to build it,
e.g. lib/voronoi/README and lib/smd/README. The README files also
describe how you must either (a) create soft links, via the "ln"
command, in those directories to point to where you built or installed
the packages, or (b) check or edit the Makefile.lammps file in the
same directory to provide that information.
</P>
<P>Some of the sub-directories, e.g. lib/voronoi, also have an install.py
script which can be used to automate the process of
downloading/building/installing the auxiliary library, and setting the
needed soft links. Type "python install.py" for further instructions.
</P>
<P>As with the sub-directories containing library code, if the soft links
or settings in the lib/package/Makefile.lammps files are not correct,
the LAMMPS build will typically fail.
</P>
<HR>
<A NAME = "start_3_4"></A><B><I>Packages that require Makefile.machine settings</I></B>
<P>A few packages require specific settings in Makefile.machine, to
either build or use the package effectively. These are the
USER-INTEL, KOKKOS, USER-OMP, and OPT packages. The details of what
flags to add or what variables to define are given on the doc pages
that describe each of these accelerator packages in detail:
</P>
<UL><LI><A HREF = "accelerate_intel.html">USER-INTEL package</A>
<LI><A HREF = "accelerate_kokkos.html">KOKKOS package</A>
<LI><A HREF = "accelerate_omp.html">USER-OMP package</A>
<LI><A HREF = "accelerate_opt.html">OPT package</A>
</UL>
<P>Here is a brief summary of what Makefile.machine changes are needed.
Note that the Make.py tool, described in the next <A HREF = "#start_4">Section
2.4</A> can automatically add the needed info to an existing
machine Makefile, using simple command-line arguments.
</P>
<P>In src/MAKE/OPTIONS see the following Makefiles for examples of the
changes described below:
</P>
<UL><LI>Makefile.intel_cpu
<LI>Makefile.intel_phi
<LI>Makefile.kokkos_omp
<LI>Makefile.kokkos_cuda
<LI>Makefile.kokkos_phi
<LI>Makefile.omp
</UL>
<P>For the USER-INTEL package, you have 2 choices when building. You can
build with CPU or Phi support. The latter uses Xeon Phi chips in
"offload" mode. Each of these modes requires additional settings in
your Makefile.machine for CCFLAGS and LINKFLAGS.
</P>
<P>For CPU mode (if using an Intel compiler):
</P>
<UL><LI>CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
<LI>LINKFLAGS: add -fopenmp
</UL>
<P>For Phi mode add the following in addition to the CPU mode flags:
</P>
<UL><LI>CCFLAGS: add -DLMP_INTEL_OFFLOAD and
<LI>LINKFLAGS: add -offload
</UL>
<P>And also add this to CCFLAGS:
</P>
<PRE>-offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\""
</PRE>
<P>For the KOKKOS package, you have 3 choices when building. You can
build with OMP or Cuda or Phi support. Phi support uses Xeon Phi
chips in "native" mode. This can be done by setting the following
variables in your Makefile.machine:
</P>
<UL><LI>for OMP support, set OMP = yes
<LI>for Cuda support, set OMP = yes and CUDA = yes
<LI>for Phi support, set OMP = yes and MIC = yes
</UL>
<P>These can also be set as additional arguments to the make command, e.g.
</P>
<PRE>make g++ OMP=yes MIC=yes
</PRE>
<P>Building the KOKKOS package with CUDA support requires a Makefile
machine that uses the NVIDIA "nvcc" compiler, as well as an
appropriate "arch" setting appropriate to the GPU hardware and NVIDIA
software you have on your machine. See
src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine
Makefile.
</P>
<P>For the USER-OMP package, your Makefile.machine needs additional
settings for CCFLAGS and LINKFLAGS.
</P>
<UL><LI>CCFLAGS: add -fopenmp and -restrict
<LI>LINKFLAGS: add -fopenmp
</UL>
<P>For the OPT package, your Makefile.machine needs an additional
settings for CCFLAGS.
</P>
<UL><LI>CCFLAGS: add -restrict
</UL>
<HR>
-<H4><A NAME = "start_4"></A>2.4 Building LAMMPS via the Make.py script
+<H4><A NAME = "start_4"></A>2.4 Building LAMMPS via the Make.py tool
</H4>
<P>The src directory includes a Make.py script, written in Python, which
can be used to automate various steps of the build process. It is
particularly useful for working with the accelerator packages, as well
as other packages which require auxiliary libraries to be built.
</P>
<P>The goal of the Make.py tool is to allow any complex multi-step LAMMPS
build to be performed as a single Make.py command. And you can
archive the commands, so they can be re-invoked later via the -r
(redo) switch. If you find some LAMMPS build procedure that can't be
done in a single Make.py command, let the developers know, and we'll
see if we can augment the tool.
</P>
<P>You can run Make.py from the src directory by typing either:
</P>
<PRE>Make.py -h
python Make.py -h
</PRE>
<P>which will give you help info about the tool. For the former to work,
you may need to edit the first line of Make.py to point to your local
Python. And you may need to insure the script is executable:
</P>
<PRE>chmod +x Make.py
</PRE>
<P>Here are examples of build tasks you can perform with Make.py:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >Install/uninstall packages</TD><TD > Make.py -p no-lib kokkos omp intel</TD></TR>
<TR><TD >Build specific auxiliary libs</TD><TD > Make.py -a lib-atc lib-meam</TD></TR>
<TR><TD >Build libs for all installed packages</TD><TD > Make.py -p cuda gpu -gpu mode=double arch=31 -a lib-all</TD></TR>
<TR><TD >Create a Makefile from scratch with compiler and MPI settings</TD><TD > Make.py -m none -cc g++ -mpi mpich -a file</TD></TR>
<TR><TD >Augment Makefile.serial with settings for installed packages</TD><TD > Make.py -p intel -intel cpu -m serial -a file</TD></TR>
<TR><TD >Add JPG and FFTW support to Makefile.mpi</TD><TD > Make.py -m mpi -jpg -fft fftw -a file</TD></TR>
<TR><TD >Build LAMMPS with a parallel make using Makefile.mpi</TD><TD > Make.py -j 16 -m mpi -a exe</TD></TR>
<TR><TD >Build LAMMPS and libs it needs using Makefile.serial with accelerator settings</TD><TD > Make.py -p gpu intel -intel cpu -a lib-all file serial
</TD></TR></TABLE></DIV>
<P>The bench and examples directories give Make.py commands that can be
used to build LAMMPS with the various packages and options needed to
run all the benchmark and example input scripts. See these files for
more details:
</P>
<UL><LI>bench/README
<LI>bench/FERMI/README
<LI>bench/KEPLER/README
<LI>bench/PHI/README
<LI>examples/README
<LI>examples/accelerate/README
<LI>examples/accelerate/make.list
</UL>
<P>All of the Make.py options and syntax help can be accessed by using
the "-h" switch.
</P>
<P>E.g. typing "Make.py -h" gives
</P>
<PRE>Syntax: Make.py switch args ...
switches can be listed in any order
help switch:
-h prints help and syntax for all other specified switches
switch for actions:
-a lib-all, lib-dir, clean, file, exe or machine
list one or more actions, in any order
machine is a Makefile.machine suffix, must be last if used
one-letter switches:
-d (dir), -j (jmake), -m (makefile), -o (output),
-p (packages), -r (redo), -s (settings), -v (verbose)
switches for libs:
-atc, -awpmd, -colvars, -cuda
-gpu, -meam, -poems, -qmmm, -reax
switches for build and makefile options:
-intel, -kokkos, -cc, -mpi, -fft, -jpg, -png
</PRE>
<P>Using the "-h" switch with other switches and actions gives additional
info on all the other specified switches or actions. The "-h" can be
anywhere in the command-line and the other switches do not need their
arguments. E.g. type "Make.py -h -d -atc -intel" will print:
</P>
<PRE>-d dir
dir = LAMMPS home dir
if -d not specified, working dir must be lammps/src
</PRE>
<PRE>-atc make=suffix lammps=suffix2
all args are optional and can be in any order
make = use Makefile.suffix (def = g++)
lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
</PRE>
<PRE>-intel mode
mode = cpu or phi (def = cpu)
build Intel package for CPU or Xeon Phi
</PRE>
<P>Note that Make.py never overwrites an existing Makefile.machine.
Instead, it creates src/MAKE/MINE/Makefile.auto, which you can save or
rename if desired. Likewise it creates an executable named
src/lmp_auto, which you can rename using the -o switch if desired.
</P>
<P>The most recently executed Make.py commmand is saved in
src/Make.py.last. You can use the "-r" switch (for redo) to re-invoke
the last command, or you can save a sequence of one or more Make.py
commands to a file and invoke the file of commands using "-r". You
can also label the commands in the file and invoke one or more of them
by name.
</P>
<P>A typical use of Make.py is to start with a valid Makefile.machine for
your system, that works for a vanilla LAMMPS build, i.e. when optional
packages are not installed. You can then use Make.py to add various
settings (FFT, JPG, PNG) to the Makefile.machine as well as change its
compiler and MPI options. You can also add additional packages to the
build, as well as build the needed supporting libraries.
</P>
<P>You can also use Make.py to create a new Makefile.machine from
scratch, using the "-m none" switch, if you also specify what compiler
and MPI options to use, via the "-cc" and "-mpi" switches.
</P>
<HR>
<H4><A NAME = "start_5"></A>2.5 Building LAMMPS as a library
</H4>
<P>LAMMPS can be built as either a static or shared library, which can
then be called from another application or a scripting language. See
<A HREF = "Section_howto.html#howto_10">this section</A> for more info on coupling
LAMMPS to other codes. See <A HREF = "Section_python.html">this section</A> for
more info on wrapping and running LAMMPS from Python.
</P>
<H5><B>Static library:</B>
</H5>
<P>To build LAMMPS as a static library (*.a file on Linux), type
</P>
<PRE>make foo mode=lib
</PRE>
<P>where foo is the machine name. This kind of library is typically used
to statically link a driver application to LAMMPS, so that you can
insure all dependencies are satisfied at compile time. This will use
the ARCHIVE and ARFLAGS settings in src/MAKE/Makefile.foo. The build
will create the file liblammps_foo.a which another application can
link to. It will also create a soft link liblammps.a, which will
point to the most recently built static library.
</P>
<H5><B>Shared library:</B>
</H5>
<P>To build LAMMPS as a shared library (*.so file on Linux), which can be
dynamically loaded, e.g. from Python, type
</P>
<PRE>make foo mode=shlib
</PRE>
<P>where foo is the machine name. This kind of library is required when
wrapping LAMMPS with Python; see <A HREF = "Section_python.html">Section_python</A>
for details. This will use the SHFLAGS and SHLIBFLAGS settings in
src/MAKE/Makefile.foo and perform the build in the directory
Obj_shared_foo. This is so that each file can be compiled with the
-fPIC flag which is required for inclusion in a shared library. The
build will create the file liblammps_foo.so which another application
can link to dyamically. It will also create a soft link liblammps.so,
which will point to the most recently built shared library. This is
the file the Python wrapper loads by default.
</P>
<P>Note that for a shared library to be usable by a calling program, all
the auxiliary libraries it depends on must also exist as shared
libraries. This will be the case for libraries included with LAMMPS,
such as the dummy MPI library in src/STUBS or any package libraries in
lib/packages, since they are always built as shared libraries using
the -fPIC switch. However, if a library like MPI or FFTW does not
exist as a shared library, the shared library build will generate an
error. This means you will need to install a shared library version
of the auxiliary library. The build instructions for the library
should tell you how to do this.
</P>
<P>Here is an example of such errors when the system FFTW or provided
lib/colvars library have not been built as shared libraries:
</P>
<PRE>/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
R_X86_64_32 against `.rodata' can not be used when making a shared
object; recompile with -fPIC
/usr/local/lib/libfftw3.a: could not read symbols: Bad value
</PRE>
<PRE>/usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
relocation R_X86_64_32 against `__pthread_key_create' can not be used
when making a shared object; recompile with -fPIC
../../lib/colvars/libcolvars.a: error adding symbols: Bad value
</PRE>
<P>As an example, here is how to build and install the <A HREF = "http://www-unix.mcs.anl.gov/mpi">MPICH
library</A>, a popular open-source version of MPI, distributed by
Argonne National Labs, as a shared library in the default
/usr/local/lib location:
</P>
<PRE>./configure --enable-shared
make
make install
</PRE>
<P>You may need to use "sudo make install" in place of the last line if
you do not have write privileges for /usr/local/lib. The end result
should be the file /usr/local/lib/libmpich.so.
</P>
<H5><B>Additional requirement for using a shared library:</B>
</H5>
<P>The operating system finds shared libraries to load at run-time using
the environment variable LD_LIBRARY_PATH. So you may wish to copy the
file src/liblammps.so or src/liblammps_g++.so (for example) to a place
the system can find it by default, such as /usr/local/lib, or you may
wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the
current version of the shared library is always available to programs
that use it.
</P>
<P>For the csh or tcsh shells, you would add something like this to your
~/.cshrc file:
</P>
<PRE>setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
</PRE>
<H5><B>Calling the LAMMPS library:</B>
</H5>
<P>Either flavor of library (static or shared) allows one or more LAMMPS
objects to be instantiated from the calling program.
</P>
<P>When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS
namespace; you can safely use any of its classes and methods from
within the calling code, as needed.
</P>
<P>When used from a C or Fortran program or a scripting language like
Python, the library has a simple function-style interface, provided in
src/library.cpp and src/library.h.
</P>
<P>See the sample codes in examples/COUPLE/simple for examples of C++ and
C and Fortran codes that invoke LAMMPS thru its library interface.
There are other examples as well in the COUPLE directory which are
discussed in <A HREF = "Section_howto.html#howto_10">Section_howto 10</A> of the
manual. See <A HREF = "Section_python.html">Section_python</A> of the manual for a
description of the Python wrapper provided with LAMMPS that operates
through the LAMMPS library interface.
</P>
<P>The files src/library.cpp and library.h define the C-style API for
using LAMMPS as a library. See <A HREF = "Section_howto.html#howto_19">Section_howto
19</A> of the manual for a description of the
interface and how to extend it for your needs.
</P>
<HR>
<H4><A NAME = "start_6"></A>2.6 Running LAMMPS
</H4>
<P>By default, LAMMPS runs by reading commands from standard input. Thus
if you run the LAMMPS executable by itself, e.g.
</P>
<PRE>lmp_linux
</PRE>
<P>it will simply wait, expecting commands from the keyboard. Typically
you should put commands in an input script and use I/O redirection,
e.g.
</P>
<PRE>lmp_linux < in.file
</PRE>
<P>For parallel environments this should also work. If it does not, use
the '-in' command-line switch, e.g.
</P>
<PRE>lmp_linux -in in.file
</PRE>
<P><A HREF = "Section_commands.html">This section</A> describes how input scripts are
structured and what commands they contain.
</P>
<P>You can test LAMMPS on any of the sample inputs provided in the
examples or bench directory. Input scripts are named in.* and sample
outputs are named log.*.name.P where name is a machine and P is the
number of processors it was run on.
</P>
<P>Here is how you might run a standard Lennard-Jones benchmark on a
Linux box, using mpirun to launch a parallel job:
</P>
<PRE>cd src
make linux
cp lmp_linux ../bench
cd ../bench
mpirun -np 4 lmp_linux -in in.lj
</PRE>
<P>See <A HREF = "http://lammps.sandia.gov/bench.html">this page</A> for timings for this and the other benchmarks on
various platforms. Note that some of the example scripts require
LAMMPS to be built with one or more of its optional packages.
</P>
<HR>
<P>On a Windows box, you can skip making LAMMPS and simply download an
executable, as described above, though the pre-packaged executables
include only certain packages.
</P>
<P>To run a LAMMPS executable on a Windows machine, first decide whether
you want to download the non-MPI (serial) or the MPI (parallel)
version of the executable. Download and save the version you have
chosen.
</P>
<P>For the non-MPI version, follow these steps:
</P>
<UL><LI>Get a command prompt by going to Start->Run... ,
then typing "cmd".
<LI>Move to the directory where you have saved lmp_win_no-mpi.exe
(e.g. by typing: cd "Documents").
<LI>At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj
with the name of your LAMMPS input script.
</UL>
<P>For the MPI version, which allows you to run LAMMPS under Windows on
multiple processors, follow these steps:
</P>
<UL><LI>Download and install
<A HREF = "http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads">MPICH2</A>
for Windows.
<LI>You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2
package. Put them in same directory (or path) as the LAMMPS Windows
executable.
<LI>Get a command prompt by going to Start->Run... ,
then typing "cmd".
<LI>Move to the directory where you have saved lmp_win_mpi.exe
(e.g. by typing: cd "Documents").
<LI>Then type something like this: "mpiexec -localonly 4 lmp_win_mpi -in
in.lj", replacing in.lj with the name of your LAMMPS input script.
<LI>Note that you may need to provide smpd with a passphrase (it doesn't
matter what you type).
<LI>In this mode, output may not immediately show up on the screen, so if
your input script takes a long time to execute, you may need to be
patient before the output shows up. :l Alternatively, you can still
use this executable to run on a single processor by typing something
like: "lmp_win_mpi -in in.lj".
</UL>
<HR>
<P>The screen output from LAMMPS is described in the next section. As it
runs, LAMMPS also writes a log.lammps file with the same information.
</P>
<P>Note that this sequence of commands copies the LAMMPS executable
(lmp_linux) to the directory with the input files. This may not be
necessary, but some versions of MPI reset the working directory to
where the executable is, rather than leave it as the directory where
you launch mpirun from (if you launch lmp_linux on its own and not
under mpirun). If that happens, LAMMPS will look for additional input
files and write its output files to the executable directory, rather
than your working directory, which is probably not what you want.
</P>
<P>If LAMMPS encounters errors in the input script or while running a
simulation it will print an ERROR message and stop or a WARNING
message and continue. See <A HREF = "Section_errors.html">Section_errors</A> for a
discussion of the various kinds of errors LAMMPS can or can't detect,
a list of all ERROR and WARNING messages, and what to do about them.
</P>
<P>LAMMPS can run a problem on any number of processors, including a
single processor. In theory you should get identical answers on any
number of processors and on any machine. In practice, numerical
round-off can cause slight differences and eventual divergence of
molecular dynamics phase space trajectories.
</P>
<P>LAMMPS can run as large a problem as will fit in the physical memory
of one or more processors. If you run out of memory, you must run on
more processors or setup a smaller problem.
</P>
<HR>
<H4><A NAME = "start_7"></A>2.7 Command-line options
</H4>
<P>At run time, LAMMPS recognizes several optional command-line switches
which may be used in any order. Either the full word or a one-or-two
letter abbreviation can be used:
</P>
<UL><LI>-c or -cuda
<LI>-e or -echo
<LI>-h or -help
<LI>-i or -in
<LI>-k or -kokkos
<LI>-l or -log
<LI>-nc or -nocite
<LI>-pk or -package
<LI>-p or -partition
<LI>-pl or -plog
<LI>-ps or -pscreen
<LI>-r or -restart
<LI>-ro or -reorder
<LI>-sc or -screen
<LI>-sf or -suffix
<LI>-v or -var
</UL>
<P>For example, lmp_ibm might be launched as follows:
</P>
<PRE>mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy
mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloy
</PRE>
<P>Here are the details on the options:
</P>
<PRE>-cuda on/off
</PRE>
<P>Explicitly enable or disable CUDA support, as provided by the
USER-CUDA package. Even if LAMMPS is built with this package, as
described above in <A HREF = "#start_3">Section 2.3</A>, this switch must be set to
enable running with the CUDA-enabled styles the package provides. If
the switch is not set (the default), LAMMPS will operate as if the
USER-CUDA package were not installed; i.e. you can run standard LAMMPS
or with the GPU package, for testing or benchmarking purposes.
</P>
<PRE>-echo style
</PRE>
<P>Set the style of command echoing. The style can be <I>none</I> or <I>screen</I>
or <I>log</I> or <I>both</I>. Depending on the style, each command read from
the input script will be echoed to the screen and/or logfile. This
can be useful to figure out which line of your script is causing an
input error. The default value is <I>log</I>. The echo style can also be
set by using the <A HREF = "echo.html">echo</A> command in the input script itself.
</P>
<PRE>-help
</PRE>
<P>Print a brief help summary and a list of options compiled into this
executable for each LAMMPS style (atom_style, fix, compute,
pair_style, bond_style, etc). This can tell you if the command you
want to use was included via the appropriate package at compile time.
LAMMPS will print the info and immediately exit if this switch is
used.
</P>
<PRE>-in file
</PRE>
<P>Specify a file to use as an input script. This is an optional switch
when running LAMMPS in one-partition mode. If it is not specified,
LAMMPS reads its script from standard input, typically from a script
via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should
also work in parallel, but if it does not (in the unlikely case that
an MPI implementation does not support it), then use the -in flag.
Note that this is a required switch when running LAMMPS in
multi-partition mode, since multiple processors cannot all read from
stdin.
</P>
<PRE>-kokkos on/off keyword/value ...
</PRE>
<P>Explicitly enable or disable KOKKOS support, as provided by the KOKKOS
package. Even if LAMMPS is built with this package, as described
above in <A HREF = "#start_3">Section 2.3</A>, this switch must be set to enable
running with the KOKKOS-enabled styles the package provides. If the
switch is not set (the default), LAMMPS will operate as if the KOKKOS
package were not installed; i.e. you can run standard LAMMPS or with
the GPU or USER-CUDA or USER-OMP packages, for testing or benchmarking
purposes.
</P>
<P>Additional optional keyword/value pairs can be specified which
determine how Kokkos will use the underlying hardware on your
platform. These settings apply to each MPI task you launch via the
"mpirun" or "mpiexec" command. You may choose to run one or more MPI
tasks per physical node. Note that if you are running on a desktop
machine, you typically have one physical node. On a cluster or
supercomputer there may be dozens or 1000s of physical nodes.
</P>
<P>Either the full word or an abbreviation can be used for the keywords.
Note that the keywords do not use a leading minus sign. I.e. the
keyword is "t", not "-t". Also note that each of the keywords has a
default setting. Example of when to use these options and what
settings to use on different platforms is given in <A HREF = "Section_accelerate.html#acc_8">Section
5.8</A>.
</P>
<UL><LI>d or device
<LI>g or gpus
<LI>t or threads
<LI>n or numa
</UL>
<PRE>device Nd
</PRE>
<P>This option is only relevant if you built LAMMPS with CUDA=yes, you
have more than one GPU per node, and if you are running with only one
MPI task per node. The Nd setting is the ID of the GPU on the node to
run on. By default Nd = 0. If you have multiple GPUs per node, they
have consecutive IDs numbered as 0,1,2,etc. This setting allows you
to launch multiple independent jobs on the node, each with a single
MPI task per node, and assign each job to run on a different GPU.
</P>
<PRE>gpus Ng Ns
</PRE>
<P>This option is only relevant if you built LAMMPS with CUDA=yes, you
have more than one GPU per node, and you are running with multiple MPI
tasks per node (up to one per GPU). The Ng setting is how many GPUs
you will use. The Ns setting is optional. If set, it is the ID of a
GPU to skip when assigning MPI tasks to GPUs. This may be useful if
your desktop system reserves one GPU to drive the screen and the rest
are intended for computational work like running LAMMPS. By default
Ng = 1 and Ns is not set.
</P>
<P>Depending on which flavor of MPI you are running, LAMMPS will look for
one of these 3 environment variables
</P>
<PRE>SLURM_LOCALID (various MPI variants compiled with SLURM support)
MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI)
</PRE>
<P>which are initialized by the "srun", "mpirun" or "mpiexec" commands.
The environment variable setting for each MPI rank is used to assign a
unique GPU ID to the MPI task.
</P>
<PRE>threads Nt
</PRE>
<P>This option assigns Nt number of threads to each MPI task for
performing work when Kokkos is executing in OpenMP or pthreads mode.
The default is Nt = 1, which essentially runs in MPI-only mode. If
there are Np MPI tasks per physical node, you generally want Np*Nt =
the number of physical cores per node, to use your available hardware
optimally. This also sets the number of threads used by the host when
LAMMPS is compiled with CUDA=yes.
</P>
<PRE>numa Nm
</PRE>
<P>This option is only relevant when using pthreads with hwloc support.
In this case Nm defines the number of NUMA regions (typicaly sockets)
on a node which will be utilizied by a single MPI rank. By default Nm
= 1. If this option is used the total number of worker-threads per
MPI rank is threads*numa. Currently it is always almost better to
assign at least one MPI rank per NUMA region, and leave numa set to
its default value of 1. This is because letting a single process span
multiple NUMA regions induces a significant amount of cross NUMA data
traffic which is slow.
</P>
<PRE>-log file
</PRE>
<P>Specify a log file for LAMMPS to write status information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the
file log.lammps. If this switch is used, LAMMPS writes to the
specified file. In multi-partition mode, if the switch is not used, a
log.lammps file is created with hi-level status information. Each
partition also writes to a log.lammps.N file where N is the partition
ID. If the switch is specified in multi-partition mode, the hi-level
logfile is named "file" and each partition also logs information to a
file.N. For both one-partition and multi-partition mode, if the
specified file is "none", then no log files are created. Using a
<A HREF = "log.html">log</A> command in the input script will override this setting.
Option -plog will override the name of the partition log files file.N.
</P>
<PRE>-nocite
</PRE>
<P>Disable writing the log.cite file which is normally written to list
references for specific cite-able features used during a LAMMPS run.
See the <A HREF = "http://lammps.sandia.gov/cite.html">citation page</A> for more
details.
</P>
<PRE>-package style args ....
</PRE>
<P>Invoke the <A HREF = "package.html">package</A> command with style and args. The
syntax is the same as if the command appeared at the top of the input
script. For example "-package gpu 2" or "-pk gpu 2" is the same as
<A HREF = "package.html">package gpu 2</A> in the input script. The possible styles
and args are documented on the <A HREF = "package.html">package</A> doc page. This
switch can be used multiple times, e.g. to set options for the
USER-INTEL and USER-OMP packages which can be used together.
</P>
<P>Along with the "-suffix" command-line switch, this is a convenient
mechanism for invoking accelerator packages and their options without
having to edit an input script.
</P>
<PRE>-partition 8x2 4 5 ...
</PRE>
<P>Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P
processors and this switch is not used, LAMMPS runs in one partition,
i.e. all P processors run a single simulation. If this switch is
used, the P processors are split into separate partitions and each
partition runs its own simulation. The arguments to the switch
specify the number of processors in each partition. Arguments of the
form MxN mean M partitions, each with N processors. Arguments of the
form N mean a single partition with N processors. The sum of
processors in all partitions must equal P. Thus the command
"-partition 8x2 4 5" has 10 partitions and runs on a total of 25
processors.
</P>
<P>Running with multiple partitions can e useful for running
<A HREF = "Section_howto.html#howto_5">multi-replica simulations</A>, where each
replica runs on on one or a few processors. Note that with MPI
installed on a machine (e.g. your desktop), you can run on more
(virtual) processors than you have physical processors.
</P>
<P>To run multiple independent simulatoins from one input script, using
multiple partitions, see <A HREF = "Section_howto.html#howto_4">Section_howto 4</A>
of the manual. World- and universe-style <A HREF = "variable.html">variables</A>
are useful in this context.
</P>
<PRE>-plog file
</PRE>
<P>Specify the base name for the partition log files, so partition N
writes log information to file.N. If file is none, then no partition
log files are created. This overrides the filename specified in the
-log command-line option. This option is useful when working with
large numbers of partitions, allowing the partition log files to be
suppressed (-plog none) or placed in a sub-directory (-plog
replica_files/log.lammps) If this option is not used the log file for
partition N is log.lammps.N or whatever is specified by the -log
command-line option.
</P>
<PRE>-pscreen file
</PRE>
<P>Specify the base name for the partition screen file, so partition N
writes screen information to file.N. If file is none, then no
partition screen files are created. This overrides the filename
specified in the -screen command-line option. This option is useful
when working with large numbers of partitions, allowing the partition
screen files to be suppressed (-pscreen none) or placed in a
sub-directory (-pscreen replica_files/screen). If this option is not
used the screen file for partition N is screen.N or whatever is
specified by the -screen command-line option.
</P>
<PRE>-restart restartfile <I>remap</I> datafile keyword value ...
</PRE>
<P>Convert the restart file into a data file and immediately exit. This
is the same operation as if the following 2-line input script were
run:
</P>
<PRE>read_restart restartfile <I>remap</I>
write_data datafile keyword value ...
</PRE>
<P>Note that the specified restartfile and datafile can have wild-card
characters ("*",%") as described by the
<A HREF = "read_restart.html">read_restart</A> and <A HREF = "write_data.html">write_data</A>
commands. But a filename such as file.* will need to be enclosed in
quotes to avoid shell expansion of the "*" character.
</P>
<P>Note that following restartfile, the optional flag <I>remap</I> can be
used. This has the same effect as adding it to the
<A HREF = "read_restart.html">read_restart</A> command, as explained on its doc
page. This is only useful if the reading of the restart file triggers
an error that atoms have been lost. In that case, use of the remap
flag should allow the data file to still be produced.
</P>
<P>Also note that following datafile, the same optional keyword/value
pairs can be listed as used by the <A HREF = "write_data.html">write_data</A>
command.
</P>
<PRE>-reorder nth N
-reorder custom filename
</PRE>
<P>Reorder the processors in the MPI communicator used to instantiate
LAMMPS, in one of several ways. The original MPI communicator ranks
all P processors from 0 to P-1. The mapping of these ranks to
physical processors is done by MPI before LAMMPS begins. It may be
useful in some cases to alter the rank order. E.g. to insure that
cores within each node are ranked in a desired order. Or when using
the <A HREF = "run_style.html">run_style verlet/split</A> command with 2 partitions
to insure that a specific Kspace processor (in the 2nd partition) is
matched up with a specific set of processors in the 1st partition.
See the <A HREF = "Section_accelerate.html">Section_accelerate</A> doc pages for
more details.
</P>
<P>If the keyword <I>nth</I> is used with a setting <I>N</I>, then it means every
Nth processor will be moved to the end of the ranking. This is useful
when using the <A HREF = "run_style.html">run_style verlet/split</A> command with 2
partitions via the -partition command-line switch. The first set of
processors will be in the first partition, the 2nd set in the 2nd
partition. The -reorder command-line switch can alter this so that
the 1st N procs in the 1st partition and one proc in the 2nd partition
will be ordered consecutively, e.g. as the cores on one physical node.
This can boost performance. For example, if you use "-reorder nth 4"
and "-partition 9 3" and you are running on 12 processors, the
processors will be reordered from
</P>
<PRE>0 1 2 3 4 5 6 7 8 9 10 11
</PRE>
<P>to
</P>
<PRE>0 1 2 4 5 6 8 9 10 3 7 11
</PRE>
<P>so that the processors in each partition will be
</P>
<PRE>0 1 2 4 5 6 8 9 10
3 7 11
</PRE>
<P>See the "processors" command for how to insure processors from each
partition could then be grouped optimally for quad-core nodes.
</P>
<P>If the keyword is <I>custom</I>, then a file that specifies a permutation
of the processor ranks is also specified. The format of the reorder
file is as follows. Any number of initial blank or comment lines
(starting with a "#" character) can be present. These should be
followed by P lines of the form:
</P>
<PRE>I J
</PRE>
<P>where P is the number of processors LAMMPS was launched with. Note
that if running in multi-partition mode (see the -partition switch
above) P is the total number of processors in all partitions. The I
and J values describe a permutation of the P processors. Every I and
J should be values from 0 to P-1 inclusive. In the set of P I values,
every proc ID should appear exactly once. Ditto for the set of P J
values. A single I,J pairing means that the physical processor with
rank I in the original MPI communicator will have rank J in the
reordered communicator.
</P>
<P>Note that rank ordering can also be specified by many MPI
implementations, either by environment variables that specify how to
order physical processors, or by config files that specify what
physical processors to assign to each MPI rank. The -reorder switch
simply gives you a portable way to do this without relying on MPI
itself. See the <A HREF = "processors">processors out</A> command for how to output
info on the final assignment of physical processors to the LAMMPS
simulation domain.
</P>
<PRE>-screen file
</PRE>
<P>Specify a file for LAMMPS to write its screen information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the
screen. If this switch is used, LAMMPS writes to the specified file
instead and you will see no screen output. In multi-partition mode,
if the switch is not used, hi-level status information is written to
the screen. Each partition also writes to a screen.N file where N is
the partition ID. If the switch is specified in multi-partition mode,
the hi-level screen dump is named "file" and each partition also
writes screen information to a file.N. For both one-partition and
multi-partition mode, if the specified file is "none", then no screen
output is performed. Option -pscreen will override the name of the
partition screen files file.N.
</P>
<PRE>-suffix style args
</PRE>
<P>Use variants of various styles if they exist. The specified style can
be <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, <I>opt</I>, or <I>hybrid</I>. These refer
to optional packages that LAMMPS can be built with, as described above in
<A HREF = "#start_3">Section 2.3</A>. The "cuda" style corresponds to the USER-CUDA
package, the "gpu" style to the GPU package, the "intel" style to the
USER-INTEL package, the "kk" style to the KOKKOS package, the "opt"
style to the OPT package, and the "omp" style to the USER-OMP package. The
hybrid style is the only style that accepts arguments. It allows for two
packages to be specified. The first package specified is the default and
will be used if it is available. If no style is available for the first
package, the style for the second package will be used if available. For
example, "-suffix hybrid intel omp" will use styles from the USER-INTEL
package if they are installed and available, but styles for the USER-OMP
package otherwise.
</P>
<P>Along with the "-package" command-line switch, this is a convenient
mechanism for invoking accelerator packages and their options without
having to edit an input script.
</P>
<P>As an example, all of the packages provide a <A HREF = "pair_lj.html">pair_style
lj/cut</A> variant, with style names lj/cut/cuda,
lj/cut/gpu, lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A
variant style can be specified explicitly in your input script,
e.g. pair_style lj/cut/gpu. If the -suffix switch is used the
specified suffix (cuda,gpu,intel,kk,omp,opt) is automatically appended
whenever your input script command creates a new
<A HREF = "atom_style.html">atom</A>, <A HREF = "pair_style.html">pair</A>, <A HREF = "fix.html">fix</A>,
<A HREF = "compute.html">compute</A>, or <A HREF = "run_style.html">run</A> style. If the variant
version does not exist, the standard version is created.
</P>
<P>For the GPU package, using this command-line switch also invokes the
default GPU settings, as if the command "package gpu 1" were used at
the top of your input script. These settings can be changed by using
the "-package gpu" command-line switch or the <A HREF = "package.html">package
gpu</A> command in your script.
</P>
<P>For the USER-INTEL package, using this command-line switch also
invokes the default USER-INTEL settings, as if the command "package
intel 1" were used at the top of your input script. These settings
can be changed by using the "-package intel" command-line switch or
the <A HREF = "package.html">package intel</A> command in your script. If the
USER-OMP package is also installed, the hybrid style with "intel omp"
arguments can be used to make the omp suffix a second choice, if a
requested style is not available in the USER-INTEL package. It will
also invoke the default USER-OMP settings, as if the command "package
omp 0" were used at the top of your input script. These settings can
be changed by using the "-package omp" command-line switch or the
<A HREF = "package.html">package omp</A> command in your script.
</P>
<P>For the KOKKOS package, using this command-line switch also invokes
the default KOKKOS settings, as if the command "package kokkos" were
used at the top of your input script. These settings can be changed
by using the "-package kokkos" command-line switch or the <A HREF = "package.html">package
kokkos</A> command in your script.
</P>
<P>For the OMP package, using this command-line switch also invokes the
default OMP settings, as if the command "package omp 0" were used at
the top of your input script. These settings can be changed by using
the "-package omp" command-line switch or the <A HREF = "package.html">package
omp</A> command in your script.
</P>
<P>The <A HREF = "suffix.html">suffix</A> command can also be used within an input
script to set a suffix, or to turn off or back on any suffix setting
made via the command line.
</P>
<PRE>-var name value1 value2 ...
</PRE>
<P>Specify a variable that will be defined for substitution purposes when
the input script is read. This switch can be used multiple times to
define multiple variables. "Name" is the variable name which can be a
single character (referenced as $x in the input script) or a full
string (referenced as ${abc}). An <A HREF = "variable.html">index-style
variable</A> will be created and populated with the
subsequent values, e.g. a set of filenames. Using this command-line
option is equivalent to putting the line "variable name index value1
value2 ..." at the beginning of the input script. Defining an index
variable as a command-line argument overrides any setting for the same
index variable in the input script, since index variables cannot be
re-defined. See the <A HREF = "variable.html">variable</A> command for more info on
defining index and other kinds of variables and <A HREF = "Section_commands.html#cmd_2">this
section</A> for more info on using variables
in input scripts.
</P>
<P>NOTE: Currently, the command-line parser looks for arguments that
start with "-" to indicate new switches. Thus you cannot specify
multiple variable values if any of they start with a "-", e.g. a
negative numeric value. It is OK if the first value1 starts with a
"-", since it is automatically skipped.
</P>
<HR>
<H4><A NAME = "start_8"></A>2.8 LAMMPS screen output
</H4>
<P>As LAMMPS reads an input script, it prints information to both the
screen and a log file about significant actions it takes to setup a
simulation. When the simulation is ready to begin, LAMMPS performs
various initializations and prints the amount of memory (in MBytes per
processor) that the simulation requires. It also prints details of
the initial thermodynamic state of the system. During the run itself,
thermodynamic information is printed periodically, every few
timesteps. When the run concludes, LAMMPS prints the final
thermodynamic state and a total run time for the simulation. It then
appends statistics about the CPU time and storage requirements for the
simulation. An example set of statistics is shown here:
</P>
<P>Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
</P>
<PRE>Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s
97.0% CPU use with 4 MPI tasks x no OpenMP threads
</PRE>
<PRE>MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9808 | 2.0134 | 2.0318 | 1.4 | 71.60
Bond | 0.0021894 | 0.0060319 | 0.010058 | 4.7 | 0.21
Kspace | 0.3207 | 0.3366 | 0.36616 | 3.1 | 11.97
Neigh | 0.28411 | 0.28464 | 0.28516 | 0.1 | 10.12
Comm | 0.075732 | 0.077018 | 0.07883 | 0.4 | 2.74
Output | 0.00030518 | 0.00042665 | 0.00078821 | 1.0 | 0.02
Modify | 0.086606 | 0.086631 | 0.086668 | 0.0 | 3.08
Other | | 0.007178 | | | 0.26
</PRE>
<PRE>Nlocal: 501 ave 508 max 490 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 6586.25 ave 6628 max 6548 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 177007 ave 180562 max 170212 min
Histogram: 1 0 0 0 0 0 0 1 1 1
</PRE>
<PRE>Total # of neighbors = 708028
Ave neighs/atom = 353.307
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0
</PRE>
<P>The first section provides a global loop timing summary. The loop time
is the total wall time for the section. The <I>Performance</I> line is
provided for convenience to help predicting the number of loop
continuations required and for comparing performance with other
similar MD codes. The CPU use line provides the CPU utilzation per
MPI task; it should be close to 100% times the number of OpenMP
threads (or 1). Lower numbers correspond to delays due to file I/O or
insufficient thread utilization.
</P>
<P>The MPI task section gives the breakdown of the CPU run time (in
seconds) into major categories:
</P>
<UL><LI><I>Pair</I> stands for all non-bonded force computation
<LI><I>Bond</I> stands for bonded interactions: bonds, angles, dihedrals, impropers
<LI><I>Kspace</I> stands for reciprocal space interactions: Ewald, PPPM, MSM
<LI><I>Neigh</I> stands for neighbor list construction
<LI><I>Comm</I> stands for communicating atoms and their properties
<LI><I>Output</I> stands for writing dumps and thermo output
<LI><I>Modify</I> stands for fixes and computes called by them
<LI><I>Other</I> is the remaining time
</UL>
<P>For each category, there is a breakdown of the least, average and most
amount of wall time a processor spent on this section. Also you have the
variation from the average time. Together these numbers allow to gauge
the amount of load imbalance in this segment of the calculation. Ideally
the difference between minimum, maximum and average is small and thus
the variation from the average close to zero. The final column shows
the percentage of the total loop time is spent in this section.
</P>
<P>When using the <A HREF = "timer.html">timer full</A> setting, an additional column
is present that also prints the CPU utilization in percent. In
addition, when using <I>timer full</I> and the <A HREF = "package.html">package omp</A>
command are active, a similar timing summary of time spent in threaded
regions to monitor thread utilization and load balance is provided. A
new entry is the <I>Reduce</I> section, which lists the time spend in
reducing the per-thread data elements to the storage for non-threaded
computation. These thread timings are taking from the first MPI rank
only and and thus, as the breakdown for MPI tasks can change from MPI
rank to MPI rank, this breakdown can be very different for individual
ranks. Here is an example output for this section:
</P>
<P>Thread timings breakdown (MPI rank 0):
Total threaded time 0.6846 / 90.6%
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.5127 | 0.5147 | 0.5167 | 0.3 | 75.18
Bond | 0.0043139 | 0.0046779 | 0.0050418 | 0.5 | 0.68
Kspace | 0.070572 | 0.074541 | 0.07851 | 1.5 | 10.89
Neigh | 0.084778 | 0.086969 | 0.089161 | 0.7 | 12.70
Reduce | 0.0036485 | 0.003737 | 0.0038254 | 0.1 | 0.55
</P>
<P>The third section lists the number of owned atoms (Nlocal), ghost atoms
(Nghost), and pair-wise neighbors stored per processor. The max and min
values give the spread of these values across processors with a 10-bin
histogram showing the distribution. The total number of histogram counts
is equal to the number of processors.
</P>
<P>The last section gives aggregate statistics for pair-wise neighbors
and special neighbors that LAMMPS keeps track of (see the
<A HREF = "special_bonds.html">special_bonds</A> command). The number of times
neighbor lists were rebuilt during the run is given as well as the
number of potentially "dangerous" rebuilds. If atom movement
triggered neighbor list rebuilding (see the
<A HREF = "neigh_modify.html">neigh_modify</A> command), then dangerous
reneighborings are those that were triggered on the first timestep
atom movement was checked for. If this count is non-zero you may wish
to reduce the delay factor to insure no force interactions are missed
by atoms moving beyond the neighbor skin distance before a rebuild
takes place.
</P>
<P>If an energy minimization was performed via the
<A HREF = "minimize.html">minimize</A> command, additional information is printed,
e.g.
</P>
<PRE>Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-6372.3765206 -8328.46998942 -8328.46998942
Force two-norm initial, final = 1059.36 5.36874
Force max component initial, final = 58.6026 1.46872
Final line search alpha, max atom move = 2.7842e-10 4.0892e-10
Iterations, force evaluations = 701 1516
</PRE>
<P>The first line prints the criterion that determined the minimization
to be completed. The third line lists the initial and final energy,
as well as the energy on the next-to-last iteration. The next 2 lines
give a measure of the gradient of the energy (force on all atoms).
The 2-norm is the "length" of this force vector; the inf-norm is the
largest component. Then some information about the line search and
statistics on how many iterations and force-evaluations the minimizer
required. Multiple force evaluations are typically done at each
iteration to perform a 1d line minimization in the search direction.
</P>
<P>If a <A HREF = "kspace_style.html">kspace_style</A> long-range Coulombics solve was
performed during the run (PPPM, Ewald), then additional information is
printed, e.g.
</P>
<PRE>FFT time (% of Kspce) = 0.200313 (8.34477)
FFT Gflps 3d 1d-only = 2.31074 9.19989
</PRE>
<P>The first line gives the time spent doing 3d FFTs (4 per timestep) and
the fraction it represents of the total KSpace time (listed above).
Each 3d FFT requires computation (3 sets of 1d FFTs) and communication
(transposes). The total flops performed is 5Nlog_2(N), where N is the
number of points in the 3d grid. The FFTs are timed with and without
the communication and a Gflop rate is computed. The 3d rate is with
communication; the 1d rate is without (just the 1d FFTs). Thus you
can estimate what fraction of your FFT time was spent in
communication, roughly 75% in the example above.
</P>
<HR>
<H4><A NAME = "start_9"></A>2.9 Tips for users of previous LAMMPS versions
</H4>
<P>The current C++ began with a complete rewrite of LAMMPS 2001, which
was written in F90. Features of earlier versions of LAMMPS are listed
in <A HREF = "Section_history.html">Section_history</A>. The F90 and F77 versions
(2001 and 99) are also freely distributed as open-source codes; check
the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> for distribution information if you prefer
those versions. The 99 and 2001 versions are no longer under active
development; they do not have all the features of C++ LAMMPS.
</P>
<P>If you are a previous user of LAMMPS 2001, these are the most
significant changes you will notice in C++ LAMMPS:
</P>
<P>(1) The names and arguments of many input script commands have
changed. All commands are now a single word (e.g. read_data instead
of read data).
</P>
<P>(2) All the functionality of LAMMPS 2001 is included in C++ LAMMPS,
but you may need to specify the relevant commands in different ways.
</P>
<P>(3) The format of the data file can be streamlined for some problems.
See the <A HREF = "read_data.html">read_data</A> command for details. The data file
section "Nonbond Coeff" has been renamed to "Pair Coeff" in C++ LAMMPS.
</P>
<P>(4) Binary restart files written by LAMMPS 2001 cannot be read by C++
LAMMPS with a <A HREF = "read_restart.html">read_restart</A> command. This is
because they were output by F90 which writes in a different binary
format than C or C++ writes or reads. Use the <I>restart2data</I> tool
provided with LAMMPS 2001 to convert the 2001 restart file to a text
data file. Then edit the data file as necessary before using the C++
LAMMPS <A HREF = "read_data.html">read_data</A> command to read it in.
</P>
<P>(5) There are numerous small numerical changes in C++ LAMMPS that mean
you will not get identical answers when comparing to a 2001 run.
However, your initial thermodynamic energy and MD trajectory should be
close if you have setup the problem for both codes the same.
</P>
</HTML>
diff --git a/doc/doc2/accelerate_intel.html b/doc/doc2/accelerate_intel.html
index aa1a7f938..63c739f92 100644
--- a/doc/doc2/accelerate_intel.html
+++ b/doc/doc2/accelerate_intel.html
@@ -1,348 +1,326 @@
<HTML>
<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
</P>
<H4>5.3.3 USER-INTEL package
</H4>
<P>The USER-INTEL package was developed by Mike Brown at Intel
-Corporation. It provides a capability to accelerate simulations by
-offloading neighbor list and non-bonded force calculations to Intel(R)
-Xeon Phi(TM) coprocessors (not native mode like the KOKKOS package).
-Additionally, it supports running simulations in single, mixed, or
-double precision with vectorization, even if a coprocessor is not
-present, i.e. on an Intel(R) CPU. The same C++ code is used for both
-cases. When offloading to a coprocessor, the routine is run twice,
-once with an offload flag.
-</P>
-<P>The USER-INTEL package can be used in tandem with the USER-OMP
-package. This is useful when offloading pair style computations to
-coprocessors, so that other styles not supported by the USER-INTEL
-package, e.g. bond, angle, dihedral, improper, and long-range
-electrostatics, can run simultaneously in threaded mode on the CPU
-cores. Since less MPI tasks than CPU cores will typically be invoked
-when running with coprocessors, this enables the extra CPU cores to be
-used for useful computation.
-</P>
-<P>If LAMMPS is built with both the USER-INTEL and USER-OMP packages
-installed, this mode of operation is made easier to use, with the
-"-suffix hybrid intel omp" <A HREF = "Section_start.html#start_7">command-line switch</A>
-or the <A HREF = "suffix.html">suffix hybrid intel omp</A> command will both set a
-second-choice suffix to "omp" so that styles from the USER-OMP package will be
-used if available, after first testing if a style from the USER-INTEL
-package is available.
-</P>
-<P>When using the USER-INTEL package, you must choose at build time whether the
-binary will support offload to Xeon Phi coprocessors. Binaries supporting
-offload can still be run in CPU-only (host-only) mode.
-</P>
-<P>Here is a quick overview of how to use the USER-INTEL package
-for CPU-only acceleration:
-</P>
-<UL><LI>specify these CCFLAGS in your src/MAKE/Makefile.machine: -openmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost
-<LI>specify -openmp with LINKFLAGS in your Makefile.machine
-<LI>include the USER-INTEL package and (optionally) USER-OMP package and build LAMMPS
-<LI>specify how many OpenMP threads per MPI task to use
-<LI>use USER-INTEL and (optionally) USER-OMP styles in your input script
-</UL>
-<P>Note that many of these settings can only be used with the Intel
-compiler, as discussed below.
-</P>
-<P>Using the USER-INTEL package to offload work to the Intel(R)
-Xeon Phi(TM) coprocessor is the same except for these additional
-steps:
-</P>
-<UL><LI>add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in your Makefile.machine
-<LI>add the flag -offload to LINKFLAGS in your Makefile.machine
-</UL>
-<P>The latter two steps in the first case and the last step in the
-coprocessor case can be done using the "-pk intel" and "-sf intel"
-<A HREF = "Section_start.html#start_7">command-line switches</A> respectively. Or
-the effect of the "-pk" or "-sf" switches can be duplicated by adding
-the <A HREF = "package.html">package intel</A> or <A HREF = "suffix.html">suffix intel</A>
-commands respectively to your input script.
-</P>
+Corporation. It provides two methods for accelerating simulations,
+depending on the hardware you have. The first is acceleration on
+Intel(R) CPUs by running in single, mixed, or double precision with
+vectorization. The second is acceleration on Intel(R) Xeon Phi(TM)
+coprocessors via offloading neighbor list and non-bonded force
+calculations to the Phi. The same C++ code is used in both cases.
+When offloading to a coprocessor from a CPU, the same routine is run
+twice, once on the CPU and once with an offload flag.
+</P>
+<P>Note that the USER-INTEL package supports use of the Phi in "offload"
+mode, not "native" mode like the <A HREF = "accelerate_kokkos.html">KOKKOS
+package</A>.
+</P>
+<P>Also note that the USER-INTEL package can be used in tandem with the
+<A HREF = "accelerate_omp.html">USER-OMP package</A>. This is useful when
+offloading pair style computations to the Phi, so that other styles
+not supported by the USER-INTEL package, e.g. bond, angle, dihedral,
+improper, and long-range electrostatics, can run simultaneously in
+threaded mode on the CPU cores. Since less MPI tasks than CPU cores
+will typically be invoked when running with coprocessors, this enables
+the extra CPU cores to be used for useful computation.
+</P>
+<P>As illustrated below, if LAMMPS is built with both the USER-INTEL and
+USER-OMP packages, this dual mode of operation is made easier to use,
+via the "-suffix hybrid intel omp" <A HREF = "Section_start.html#start_7">command-line
+switch</A> or the <A HREF = "suffix.html">suffix hybrid intel
+omp</A> command. Both set a second-choice suffix to "omp" so
+that styles from the USER-INTEL package will be used if available,
+with styles from the USER-OMP package as a second choice.
+</P>
+<P>Here is a quick overview of how to use the USER-INTEL package for CPU
+acceleration, assuming one or more 16-core nodes. More details
+follow.
+</P>
+<PRE>use an Intel compiler
+use these CCFLAGS settings in Makefile.machine: -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
+use these LINKFLAGS settings in Makefile.machine: -fopenmp, -xHost
+make yes-user-intel yes-user-omp # including user-omp is optional
+make mpi # build with the USER-INTEL package, if settings (including compiler) added to Makefile.mpi
+make intel_cpu # or Makefile.intel_cpu already has settings, uses Intel MPI wrapper
+Make.py -v -p intel omp -intel cpu -a file mpich_icc # or one-line build via Make.py for MPICH
+Make.py -v -p intel omp -intel cpu -a file ompi_icc # or for OpenMPI
+Make.py -v -p intel omp -intel cpu -a file intel_cpu # or for Intel MPI wrapper
+</PRE>
+<PRE>lmp_machine -sf intel -pk intel 0 omp 16 -in in.script # 1 node, 1 MPI task/node, 16 threads/task, no USER-OMP
+mpirun -np 32 lmp_machine -sf intel -in in.script # 2 nodess, 16 MPI tasks/node, no threads, no USER-OMP
+lmp_machine -sf hybrid intel omp -pk intel 0 omp 16 -pk omp 16 -in in.script # 1 node, 1 MPI task/node, 16 threads/task, with USER-OMP
+mpirun -np 32 -ppn 4 lmp_machine -sf hybrid intel omp -pk omp 4 -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task, with USER-OMP
+</PRE>
+<P>Here is a quick overview of how to use the USER-INTEL package for the
+same CPUs as above (16 cores/node), with an additional Xeon Phi(TM)
+coprocessor per node. More details follow.
+</P>
+<PRE>Same as above for building, with these additions/changes:
+add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in Makefile.machine
+add the flag -offload to LINKFLAGS in Makefile.machine
+for Make.py change "-intel cpu" to "-intel phi", and "file intel_cpu" to "file intel_phi"
+</PRE>
+<PRE>mpirun -np 32 lmp_machine -sf intel -pk intel 1 -in in.script # 2 nodes, 16 MPI tasks/node, 240 total threads on coprocessor, no USER-OMP
+mpirun -np 16 -ppn 8 lmp_machine -sf intel -pk intel 1 omp 2 -in in.script # 2 nodes, 8 MPI tasks/node, 2 threads/task, 240 total threads on coprocessor, no USER-OMP
+mpirun -np 32 -ppn 8 lmp_machine -sf hybrid intel omp -pk intel 1 omp 2 -pk omp 2 -in in.script # 4 nodes, 8 MPI tasks/node, 2 threads/task, 240 total threads on coprocessor, with USER-OMP
+</PRE>
<P><B>Required hardware/software:</B>
</P>
-<P>To use the offload option, you must have one or more Intel(R) Xeon
-Phi(TM) coprocessors and use an Intel(R) C++ compiler.
-</P>
-<P>Optimizations for vectorization have only been tested with the
+<P>Your compiler must support the OpenMP interface. Use of an Intel(R)
+C++ compiler is recommended, but not required. However, g++ will not
+recognize some of the settings listed above, so they cannot be used.
+Optimizations for vectorization have only been tested with the
Intel(R) compiler. Use of other compilers may not result in
-vectorization or give poor performance.
-</P>
-<P>Use of an Intel C++ compiler is recommended, but not required (though
-g++ will not recognize some of the settings, so they cannot be used).
-The compiler must support the OpenMP interface.
+vectorization, or give poor performance.
</P>
<P>The recommended version of the Intel(R) compiler is 14.0.1.106.
-Versions 15.0.1.133 and later are also supported. If using Intel(R)
+Versions 15.0.1.133 and later are also supported. If using Intel(R)
MPI, versions 15.0.2.044 and later are recommended.
</P>
+<P>To use the offload option, you must have one or more Intel(R) Xeon
+Phi(TM) coprocessors and use an Intel(R) C++ compiler.
+</P>
<P><B>Building LAMMPS with the USER-INTEL package:</B>
</P>
-<P>You can choose to build with or without support for offload to a
-Intel(R) Xeon Phi(TM) coprocessor. If you build with support for a
-coprocessor, the same binary can be used on nodes with and without
-coprocessors installed. However, if you do not have coprocessors
-on your system, building without offload support will produce a
-smaller binary.
-</P>
-<P>You can do either in one line, using the src/Make.py script, described
-in <A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual. Type
-"Make.py -h" for help. If run from the src directory, these commands
-will create src/lmp_intel_cpu and lmp_intel_phi using
-src/MAKE/Makefile.mpi as the starting Makefile.machine:
-</P>
-<PRE>Make.py -p intel omp -intel cpu -o intel_cpu -cc icc -a file mpi
-Make.py -p intel omp -intel phi -o intel_phi -cc icc -a file mpi
-</PRE>
-<P>Note that this assumes that your MPI and its mpicxx wrapper
-is using the Intel compiler. If it is not, you should
-leave off the "-cc icc" switch.
+<P>The lines above illustrate how to include/build with the USER-INTEL
+package, for either CPU or Phi support, in two steps, using the "make"
+command. Or how to do it with one command via the src/Make.py script,
+described in <A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual.
+Type "Make.py -h" for help. Because the mechanism for specifing what
+compiler to use (Intel in this case) is different for different MPI
+wrappers, 3 versions of the Make.py command are shown.
+</P>
+<P>Note that if you build with support for a Phi coprocessor, the same
+binary can be used on nodes with or without coprocessors installed.
+However, if you do not have coprocessors on your system, building
+without offload support will produce a smaller binary.
+</P>
+<P>If you also build with the USER-OMP package, you can use styles from
+both packages, as described below.
+</P>
+<P>Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
+include "-fopenmp". Likewise, if you use an Intel compiler, the
+CCFLAGS setting must include "-restrict". For Phi support, the
+"-DLMP_INTEL_OFFLOAD" (CCFLAGS) and "-offload" (LINKFLAGS) settings
+are required. The other settings listed above are optional, but will
+typically improve performance. The Make.py command will add all of
+these automatically.
</P>
-<P>Or you can follow these steps:
+<P>If you are compiling on the same architecture that will be used for
+the runs, adding the flag <I>-xHost</I> to CCFLAGS enables vectorization
+with the Intel(R) compiler. Otherwise, you must provide the correct
+compute node architecture to the -x option (e.g. -xAVX).
</P>
-<PRE>cd lammps/src
-make yes-user-intel
-make yes-user-omp (if desired)
-make machine
-</PRE>
-<P>Note that if the USER-OMP package is also installed, you can use
-styles from both packages, as described below.
+<P>Example machines makefiles Makefile.intel_cpu and Makefile.intel_phi
+are included in the src/MAKE/OPTIONS directory with settings that
+perform well with the Intel(R) compiler. The latter has support for
+offload to Phi coprocessors; the former does not.
</P>
-<P>The Makefile.machine needs a "-fopenmp" flag for OpenMP support in
-both the CCFLAGS and LINKFLAGS variables. You also need to add
--DLAMMPS_MEMALIGN=64 and -restrict to CCFLAGS.
-</P>
-<P>If you are compiling on the same architecture that will be used for
-the runs, adding the flag <I>-xHost</I> to CCFLAGS will enable
-vectorization with the Intel(R) compiler. Otherwise, you must
-provide the correct compute node architecture to the -x option
-(e.g. -xAVX).
-</P>
-<P>In order to build with support for an Intel(R) Xeon Phi(TM)
-coprocessor, the flag <I>-offload</I> should be added to the LINKFLAGS line
-and the flag -DLMP_INTEL_OFFLOAD should be added to the CCFLAGS line.
-</P>
-<P>Example makefiles Makefile.intel_cpu and Makefile.intel_phi are
-included in the src/MAKE/OPTIONS directory with settings that perform
-well with the Intel(R) compiler. The latter file has support for
-offload to coprocessors; the former does not.
-</P>
-<P><B>Notes on CPU and core affinity:</B>
-</P>
-<P>Setting core affinity is often used to pin MPI tasks and OpenMP
-threads to a core or group of cores so that memory access can be
-uniform. Unless disabled at build time, affinity for MPI tasks and
-OpenMP threads on the host will be set by default on the host
-when using offload to a coprocessor. In this case, it is unnecessary
-to use other methods to control affinity (e.g. taskset, numactl,
-I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input script
-with the <I>no_affinity</I> option to the <A HREF = "package.html">package intel</A>
-command or by disabling the option at build time (by adding
--DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your Makefile).
-Disabling this option is not recommended, especially when running
-on a machine with hyperthreading disabled.
-</P>
-<P><B>Running with the USER-INTEL package from the command line:</B>
+<P><B>Run with the USER-INTEL package from the command line:</B>
</P>
<P>The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
</P>
-<P>If you plan to compute (any portion of) pairwise interactions using
-USER-INTEL pair styles on the CPU, or use USER-OMP styles on the CPU,
-you need to choose how many OpenMP threads per MPI task to use. Note
-that the product of MPI tasks * OpenMP threads/task should not exceed
-the physical number of cores (on a node), otherwise performance will
-suffer.
-</P>
-<P>If LAMMPS was built with coprocessor support for the USER-INTEL
-package, you also need to specify the number of coprocessor/node and
-optionally the number of coprocessor threads per MPI task to use. Note that
-coprocessor threads (which run on the coprocessor) are totally
-independent from OpenMP threads (which run on the CPU). The default
-values for the settings that affect coprocessor threads are typically
-fine, as discussed below.
-</P>
-<P>Use the "-sf intel" <A HREF = "Section_start.html#start_7">command-line switch</A>,
-which will automatically append "intel" to styles that support it.
-OpenMP threads per MPI task can be set via the "-pk intel Nphi omp Nt" or
-"-pk omp Nt" <A HREF = "Section_start.html#start_7">command-line switches</A>, which
-set Nt = # of OpenMP threads per MPI task to use. The "-pk omp" form
-is only allowed if LAMMPS was also built with the USER-OMP package.
-</P>
-<P>Use the "-pk intel Nphi" <A HREF = "Section_start.html#start_7">command-line
-switch</A> to set Nphi = # of Xeon Phi(TM)
-coprocessors/node, if LAMMPS was built with coprocessor support. All
-the available coprocessor threads on each Phi will be divided among
-MPI tasks, unless the <I>tptask</I> option of the "-pk intel" <A HREF = "Section_start.html#start_7">command-line
-switch</A> is used to limit the coprocessor
-threads per MPI task. See the <A HREF = "package.html">package intel</A> command
-for details.
-</P>
-<PRE>CPU-only without USER-OMP (but using Intel vectorization on CPU):
-mpirun -np 32 lmp_machine -sf intel -in in.script # 32 MPI tasks on as many nodes as needed (e.g. 2 16-core nodes)
-lmp_machine -sf intel -pk intel 0 omp 16 -in in.script # 1 MPI task and 16 threads
-</PRE>
-<PRE>CPU-only with USER-OMP (and Intel vectorization on CPU):
-lmp_machine -sf hybrid intel omp -pk intel 0 omp 16 -in in.script # 1 MPI task on a 16-core node with 16 threads
-mpirun -np 4 lmp_machine -sf hybrid intel omp -pk omp 4 -in in.script # 4 MPI tasks each with 4 threads on a single 16-core node
-</PRE>
-<PRE>CPUs + Xeon Phi(TM) coprocessors with or without USER-OMP:
-mpirun -np 32 -ppn 16 lmp_machine -sf intel -pk intel 1 -in in.script # 2 nodes with 16 MPI tasks on each, 240 total threads on coprocessor
-mpirun -np 16 -ppn 8 lmp_machine -sf intel -pk intel 1 omp 2 -in in.script # 2 nodes, 8 MPI tasks on each node, 2 threads for each task, 240 total threads on coprocessor
-mpirun -np 16 -ppn 8 lmp_machine -sf hybrid intel omp -pk intel 1 omp 2 -in in.script # 2 nodes, 8 MPI tasks on each node, 2 threads for each task, 240 total threads on coprocessor, USER-OMP package for some styles
-</PRE>
-<P>Note that if the "-sf intel" switch is used, it also invokes a
-default command: <A HREF = "package.html">package intel 1</A>. If the "-sf hybrid intel omp"
-switch is used, the default USER-OMP command <A HREF = "package.html">package omp 0</A> is
-also invoked. Both set the number of OpenMP threads per MPI task via the
-OMP_NUM_THREADS environment variable. The first command sets the number of
-Xeon Phi(TM) coprocessors/node to 1 (and the precision mode to "mixed", as one
-of its option defaults). The latter command is not invoked if LAMMPS was not
-built with the USER-OMP package. The Nphi = 1 value for the first command is
-ignored if LAMMPS was not built with coprocessor support.
-</P>
-<P>Using the "-pk intel" or "-pk omp" switches explicitly allows for
-direct setting of the number of OpenMP threads per MPI task, and
-additional options for either of the USER-INTEL or USER-OMP packages.
-In particular, the "-pk intel" switch sets the number of
-coprocessors/node and can limit the number of coprocessor threads per
-MPI task. The syntax for these two switches is the same as the
-<A HREF = "package.html">package omp</A> and <A HREF = "package.html">package intel</A> commands.
-See the <A HREF = "package.html">package</A> command doc page for details, including
-the default values used for all its options if these switches are not
+<P>If you compute (any portion of) pairwise interactions using USER-INTEL
+pair styles on the CPU, or use USER-OMP styles on the CPU, you need to
+choose how many OpenMP threads per MPI task to use. If both packages
+are used, it must be done for both packages, and the same thread count
+value should be used for both. Note that the product of MPI tasks *
+threads/task should not exceed the physical number of cores (on a
+node), otherwise performance will suffer.
+</P>
+<P>When using the USER-INTEL package for the Phi, you also need to
+specify the number of coprocessor/node and optionally the number of
+coprocessor threads per MPI task to use. Note that coprocessor
+threads (which run on the coprocessor) are totally independent from
+OpenMP threads (which run on the CPU). The default values for the
+settings that affect coprocessor threads are typically fine, as
+discussed below.
+</P>
+<P>As in the lines above, use the "-sf intel" or "-sf hybrid intel omp"
+<A HREF = "Section_start.html#start_7">command-line switch</A>, which will
+automatically append "intel" to styles that support it. In the second
+case, "omp" will be appended if an "intel" style does not exist.
+</P>
+<P>Note that if either switch is used, it also invokes a default command:
+<A HREF = "package.html">package intel 1</A>. If the "-sf hybrid intel omp" switch
+is used, the default USER-OMP command <A HREF = "package.html">package omp 0</A> is
+also invoked (if LAMMPS was built with USER-OMP). Both set the number
+of OpenMP threads per MPI task via the OMP_NUM_THREADS environment
+variable. The first command sets the number of Xeon Phi(TM)
+coprocessors/node to 1 (ignored if USER-INTEL is built for CPU-only),
+and the precision mode to "mixed" (default value).
+</P>
+<P>You can also use the "-pk intel Nphi" <A HREF = "Section_start.html#start_7">command-line
+switch</A> to explicitly set Nphi = # of Xeon
+Phi(TM) coprocessors/node, as well as additional options. Nphi should
+be >= 1 if LAMMPS was built with coprocessor support, otherswise Nphi
+= 0 for a CPU-only build. All the available coprocessor threads on
+each Phi will be divided among MPI tasks, unless the <I>tptask</I> option
+of the "-pk intel" <A HREF = "Section_start.html#start_7">command-line switch</A> is
+used to limit the coprocessor threads per MPI task. See the <A HREF = "package.html">package
+intel</A> command for details, including the default values
+used for all its options if not specified, and how to set the number
+of OpenMP threads via the OMP_NUM_THREADS environment variable if
+desired.
+</P>
+<P>If LAMMPS was built with the USER-OMP package, you can also use the
+"-pk omp Nt" <A HREF = "Section_start.html#start_7">command-line switch</A> to
+explicitly set Nt = # of OpenMP threads per MPI task to use, as well
+as additional options. Nt should be the same threads per MPI task as
+set for the USER-INTEL package, e.g. via the "-pk intel Nphi omp Nt"
+command. Again, see the <A HREF = "package.html">package omp</A> command for
+details, including the default values used for all its options if not
specified, and how to set the number of OpenMP threads via the
OMP_NUM_THREADS environment variable if desired.
</P>
<P><B>Or run with the USER-INTEL package by editing an input script:</B>
</P>
<P>The discussion above for the mpirun/mpiexec command, MPI tasks/node,
OpenMP threads per MPI task, and coprocessor threads per MPI task is
the same.
</P>
-<P>Use the <A HREF = "suffix.html">suffix intel</A> command, or you can explicitly add an
-"intel" suffix to individual styles in your input script, e.g.
+<P>Use the <A HREF = "suffix.html">suffix intel</A> or <A HREF = "suffix.html">suffix hybrid intel
+omp</A> commands, or you can explicitly add an "intel" or
+"omp" suffix to individual styles in your input script, e.g.
</P>
<PRE>pair_style lj/cut/intel 2.5
</PRE>
<P>You must also use the <A HREF = "package.html">package intel</A> command, unless the
"-sf intel" or "-pk intel" <A HREF = "Section_start.html#start_7">command-line
switches</A> were used. It specifies how many
coprocessors/node to use, as well as other OpenMP threading and
-coprocessor options. Its doc page explains how to set the number of
-OpenMP threads via an environment variable if desired.
+coprocessor options. The <A HREF = "package.html">package</A> doc page explains how
+to set the number of OpenMP threads via an environment variable if
+desired.
</P>
<P>If LAMMPS was also built with the USER-OMP package, you must also use
the <A HREF = "package.html">package omp</A> command to enable that package, unless
the "-sf hybrid intel omp" or "-pk omp" <A HREF = "Section_start.html#start_7">command-line
switches</A> were used. It specifies how many
-OpenMP threads per MPI task to use, as well as other options. Its doc
-page explains how to set the number of OpenMP threads via an
-environment variable if desired.
+OpenMP threads per MPI task to use (should be same as the setting for
+the USER-INTEL package), as well as other options. Its doc page
+explains how to set the number of OpenMP threads via an environment
+variable if desired.
</P>
<P><B>Speed-ups to expect:</B>
</P>
-<P>If LAMMPS was not built with coprocessor support when including the
-USER-INTEL package, then acclerated styles will run on the CPU using
-vectorization optimizations and the specified precision. This may
-give a substantial speed-up for a pair style, particularly if mixed or
-single precision is used.
+<P>If LAMMPS was not built with coprocessor support (CPU only) when
+including the USER-INTEL package, then acclerated styles will run on
+the CPU using vectorization optimizations and the specified precision.
+This may give a substantial speed-up for a pair style, particularly if
+mixed or single precision is used.
</P>
<P>If LAMMPS was built with coproccesor support, the pair styles will run
on one or more Intel(R) Xeon Phi(TM) coprocessors (per node). The
performance of a Xeon Phi versus a multi-core CPU is a function of
your hardware, which pair style is used, the number of
atoms/coprocessor, and the precision used on the coprocessor (double,
single, mixed).
</P>
<P>See the <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark page</A> of the
LAMMPS web site for performance of the USER-INTEL package on different
hardware.
</P>
+<P>IMPORTANT NOTE: Setting core affinity is often used to pin MPI tasks
+and OpenMP threads to a core or group of cores so that memory access
+can be uniform. Unless disabled at build time, affinity for MPI tasks
+and OpenMP threads on the host (CPU) will be set by default on the
+host when using offload to a coprocessor. In this case, it is
+unnecessary to use other methods to control affinity (e.g. taskset,
+numactl, I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input
+script with the <I>no_affinity</I> option to the <A HREF = "package.html">package
+intel</A> command or by disabling the option at build time
+(by adding -DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your
+Makefile). Disabling this option is not recommended, especially when
+running on a machine with hyperthreading disabled.
+</P>
<P><B>Guidelines for best performance on an Intel(R) Xeon Phi(TM)
coprocessor:</B>
</P>
<UL><LI>The default for the <A HREF = "package.html">package intel</A> command is to have
all the MPI tasks on a given compute node use a single Xeon Phi(TM)
coprocessor. In general, running with a large number of MPI tasks on
each node will perform best with offload. Each MPI task will
automatically get affinity to a subset of the hardware threads
available on the coprocessor. For example, if your card has 61 cores,
with 60 cores available for offload and 4 hardware threads per core
(240 total threads), running with 24 MPI tasks per node will cause
each MPI task to use a subset of 10 threads on the coprocessor. Fine
tuning of the number of threads to use per MPI task or the number of
threads to use per core can be accomplished with keyword settings of
the <A HREF = "package.html">package intel</A> command.
<LI>If desired, only a fraction of the pair style computation can be
offloaded to the coprocessors. This is accomplished by using the
<I>balance</I> keyword in the <A HREF = "package.html">package intel</A> command. A
balance of 0 runs all calculations on the CPU. A balance of 1 runs
all calculations on the coprocessor. A balance of 0.5 runs half of
the calculations on the coprocessor. Setting the balance to -1 (the
default) will enable dynamic load balancing that continously adjusts
the fraction of offloaded work throughout the simulation. This option
typically produces results within 5 to 10 percent of the optimal fixed
balance.
<LI>When using offload with CPU hyperthreading disabled, it may help
performance to use fewer MPI tasks and OpenMP threads than available
cores. This is due to the fact that additional threads are generated
internally to handle the asynchronous offload tasks.
<LI>If running short benchmark runs with dynamic load balancing, adding a
short warm-up run (10-20 steps) will allow the load-balancer to find a
near-optimal setting that will carry over to additional runs.
<LI>If pair computations are being offloaded to an Intel(R) Xeon Phi(TM)
coprocessor, a diagnostic line is printed to the screen (not to the
log file), during the setup phase of a run, indicating that offload
mode is being used and indicating the number of coprocessor threads
per MPI task. Additionally, an offload timing summary is printed at
the end of each run. When offloading, the frequency for <A HREF = "atom_modify.html">atom
sorting</A> is changed to 1 so that the per-atom data is
effectively sorted at every rebuild of the neighbor lists.
<LI>For simulations with long-range electrostatics or bond, angle,
dihedral, improper calculations, computation and data transfer to the
coprocessor will run concurrently with computations and MPI
communications for these calculations on the host CPU. The USER-INTEL
package has two modes for deciding which atoms will be handled by the
coprocessor. This choice is controlled with the <I>ghost</I> keyword of
the <A HREF = "package.html">package intel</A> command. When set to 0, ghost atoms
(atoms at the borders between MPI tasks) are not offloaded to the
card. This allows for overlap of MPI communication of forces with
computation on the coprocessor when the <A HREF = "newton.html">newton</A> setting
is "on". The default is dependent on the style being used, however,
better performance may be achieved by setting this option
explictly.
</UL>
<P><B>Restrictions:</B>
</P>
<P>When offloading to a coprocessor, <A HREF = "pair_hybrid.html">hybrid</A> styles
that require skip lists for neighbor builds cannot be offloaded.
Using <A HREF = "pair_hybrid.html">hybrid/overlay</A> is allowed. Only one intel
accelerated style may be used with hybrid styles.
<A HREF = "special_bonds.html">Special_bonds</A> exclusion lists are not currently
supported with offload, however, the same effect can often be
accomplished by setting cutoffs for excluded atom types to 0. None of
the pair styles in the USER-INTEL package currently support the
"inner", "middle", "outer" options for rRESPA integration via the
<A HREF = "run_style.html">run_style respa</A> command; only the "pair" option is
supported.
</P>
</HTML>
diff --git a/doc/doc2/accelerate_kokkos.html b/doc/doc2/accelerate_kokkos.html
index 2a425e842..79240c2bc 100644
--- a/doc/doc2/accelerate_kokkos.html
+++ b/doc/doc2/accelerate_kokkos.html
@@ -1,509 +1,514 @@
<HTML>
<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
</P>
<H4>5.3.4 KOKKOS package
</H4>
-<P>The KOKKOS package was developed primaritly by Christian Trott
-(Sandia) with contributions of various styles by others, including
-Sikandar Mashayak (UIUC), Stan Moore (Sandia), and Ray Shan (Sandia).
-The underlying Kokkos library was written
-primarily by Carter Edwards, Christian Trott, and Dan Sunderland (all
-Sandia).
+<P>The KOKKOS package was developed primarily by Christian Trott (Sandia)
+with contributions of various styles by others, including Sikandar
+Mashayak (UIUC), Stan Moore (Sandia), and Ray Shan (Sandia). The
+underlying Kokkos library was written primarily by Carter Edwards,
+Christian Trott, and Dan Sunderland (all Sandia).
</P>
<P>The KOKKOS package contains versions of pair, fix, and atom styles
that use data structures and macros provided by the Kokkos library,
which is included with LAMMPS in lib/kokkos.
</P>
<P>The Kokkos library is part of
-<A HREF = "http://trilinos.sandia.gov/packages/kokkos">Trilinos</A> and can also
-be downloaded from <A HREF = "https://github.com/kokkos/kokkos">Github</A>. Kokkos is a
+<A HREF = "http://trilinos.sandia.gov/packages/kokkos">Trilinos</A> and can also be
+downloaded from <A HREF = "https://github.com/kokkos/kokkos">Github</A>. Kokkos is a
templated C++ library that provides two key abstractions for an
application like LAMMPS. First, it allows a single implementation of
an application kernel (e.g. a pair style) to run efficiently on
different kinds of hardware, such as a GPU, Intel Phi, or many-core
-chip.
+CPU.
</P>
<P>The Kokkos library also provides data abstractions to adjust (at
compile time) the memory layout of basic data structures like 2d and
3d arrays and allow the transparent utilization of special hardware
load and store operations. Such data structures are used in LAMMPS to
store atom coordinates or forces or neighbor lists. The layout is
chosen to optimize performance on different platforms. Again this
functionality is hidden from the developer, and does not affect how
the kernel is coded.
</P>
<P>These abstractions are set at build time, when LAMMPS is compiled with
-the KOKKOS package installed. This is done by selecting a "host" and
-"device" to build for, compatible with the compute nodes in your
-machine (one on a desktop machine or 1000s on a supercomputer).
-</P>
-<P>All Kokkos operations occur within the context of an individual MPI
-task running on a single node of the machine. The total number of MPI
-tasks used by LAMMPS (one or multiple per compute node) is set in the
-usual manner via the mpirun or mpiexec commands, and is independent of
-Kokkos.
-</P>
-<P>Kokkos provides support for two different modes of execution per MPI
-task. This means that computational tasks (pairwise interactions,
-neighbor list builds, time integration, etc) can be parallelized for
-one or the other of the two modes. The first mode is called the
-"host" and is one or more threads running on one or more physical CPUs
-(within the node). Currently, both multi-core CPUs and an Intel Phi
-processor (running in native mode, not offload mode like the
-USER-INTEL package) are supported. The second mode is called the
-"device" and is an accelerator chip of some kind. Currently only an
-NVIDIA GPU is supported via Cuda. If your compute node does not have
-a GPU, then there is only one mode of execution, i.e. the host and
-device are the same.
-</P>
-<P>When using the KOKKOS package, you must choose at build time whether
-you are building for OpenMP, GPU, or for using the Xeon Phi in native
-mode.
-</P>
-<P>Here is a quick overview of how to use the KOKKOS package:
-</P>
+the KOKKOS package installed. All Kokkos operations occur within the
+context of an individual MPI task running on a single node of the
+machine. The total number of MPI tasks used by LAMMPS (one or
+multiple per compute node) is set in the usual manner via the mpirun
+or mpiexec commands, and is independent of Kokkos.
+</P>
+<P>Kokkos currently provides support for 3 modes of execution (per MPI
+task). These are OpenMP (for many-core CPUs), Cuda (for NVIDIA GPUs),
+and OpenMP (for Intel Phi). Note that the KOKKOS package supports
+running on the Phi in native mode, not offload mode like the
+USER-INTEL package supports. You choose the mode at build time to
+produce an executable compatible with specific hardware.
+</P>
+<P>Here is a quick overview of how to use the KOKKOS package
+for CPU acceleration, assuming one or more 16-core nodes.
+More details follow.
+</P>
+<P>use a C++11 compatible compiler
+make yes-kokkos
+make mpi KOKKOS_DEVICES=OpenMP # build with the KOKKOS package
+make kokkos_omp # or Makefile.kokkos_omp already has variable set
+Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi # or one-line build via Make.py
+</P>
+<PRE>mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no threads
+mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task
+mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task
+mpirun -np 32 -ppn 4 lmp_mpi -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task
+</PRE>
<UL><LI>specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support
<LI>include the KOKKOS package and build LAMMPS
<LI>enable the KOKKOS package and its hardware options via the "-k on" command-line switch use KOKKOS styles in your input script
</UL>
-<P>The latter two steps can be done using the "-k on", "-pk kokkos" and
-"-sf kk" <A HREF = "Section_start.html#start_7">command-line switches</A>
-respectively. Or the effect of the "-pk" or "-sf" switches can be
-duplicated by adding the <A HREF = "package.html">package kokkos</A> or <A HREF = "suffix.html">suffix
-kk</A> commands respectively to your input script.
+<P>Here is a quick overview of how to use the KOKKOS package for GPUs,
+assuming one or more nodes, each with 16 cores and a GPU. More
+details follow.
</P>
-<P><B>Required hardware/software:</B>
+<P>discuss use of NVCC, which Makefiles to examine
</P>
-<P>The KOKKOS package can be used to build and run LAMMPS on the
-following kinds of hardware:
+<P>use a C++11 compatible compiler
+KOKKOS_DEVICES = Cuda, OpenMP
+KOKKOS_ARCH = Kepler35
+make yes-kokkos
+make machine
+Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda
+</P>
+<PRE>mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj # one MPI task, 6 threads on CPU
+mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj # ditto on 4 nodes
+</PRE>
+<PRE>mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # two MPI tasks, 8 threads per CPU
+mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # ditto on 16 nodes
+</PRE>
+<P>Here is a quick overview of how to use the KOKKOS package
+for the Intel Phi:
+</P>
+<PRE>use a C++11 compatible compiler
+KOKKOS_DEVICES = OpenMP
+KOKKOS_ARCH = KNC
+make yes-kokkos
+make machine
+Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi
+</PRE>
+<P>host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
+mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240
+mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj # 30 MPI tasks on 1 Phi, 30*8 = 240
+mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj # 12 MPI tasks on 1 Phi, 12*20 = 240
+mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis
+</P>
+<P><B>Required hardware/software:</B>
</P>
-<UL><LI>CPU-only: one MPI task per CPU core (MPI-only, but using KOKKOS styles)
-<LI>CPU-only: one or a few MPI tasks per node with additional threading via OpenMP
-<LI>Phi: on one or more Intel Phi coprocessors (per node)
-<LI>GPU: on the GPUs of a node with additional OpenMP threading on the CPUs
-</UL>
<P>Kokkos support within LAMMPS must be built with a C++11 compatible
compiler. If using gcc, version 4.8.1 or later is required.
</P>
-<P>Note that Intel Xeon Phi coprocessors are supported in "native" mode,
-not "offload" mode like the USER-INTEL package supports.
+<P>To build with Kokkos support for CPUs, your compiler must support the
+OpenMP interface. You should have one or more multi-core CPUs so that
+multiple threads can be launched by each MPI task running on a CPU.
</P>
-<P>Only NVIDIA GPUs are currently supported.
+<P>To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
+version 6.5 or later must be installed on your system. See the
+discussion for the <A HREF = "accelerate_cuda.html">USER-CUDA</A> and
+<A HREF = "accelerate_gpu.html">GPU</A> packages for details of how to check and do
+this.
</P>
<P>IMPORTANT NOTE: For good performance of the KOKKOS package on GPUs,
you must have Kepler generation GPUs (or later). The Kokkos library
exploits texture cache options not supported by Telsa generation GPUs
(or older).
</P>
-<P>To build the KOKKOS package for GPUs, NVIDIA Cuda software version 6.5 or later must be
-installed on your system. See the discussion above for the USER-CUDA
-and GPU packages for details of how to check and do this.
+<P>To build with Kokkos support for Intel Xeon Phi coprocessors, your
+sysmte must be configured to use them in "native" mode, not "offload"
+mode like the USER-INTEL package supports.
</P>
<P><B>Building LAMMPS with the KOKKOS package:</B>
</P>
-<P>You must choose at build time whether to build for OpenMP, Cuda, or
-Phi.
+<P>You must choose at build time whether to build for CPUs (OpenMP),
+GPUs, or Phi.
</P>
<P>You can do any of these in one line, using the src/Make.py script,
described in <A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual.
Type "Make.py -h" for help. If run from the src directory, these
commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and
lmp_kokkos_phi. Note that the OMP and PHI options use
src/MAKE/Makefile.mpi as the starting Makefile.machine. The CUDA
option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda.
</P>
-<PRE>Make.py -p kokkos -kokkos omp -o kokkos_omp -a file mpi
-Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda
-Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi
-</PRE>
+<P>The latter two steps can be done using the "-k on", "-pk kokkos" and
+"-sf kk" <A HREF = "Section_start.html#start_7">command-line switches</A>
+respectively. Or the effect of the "-pk" or "-sf" switches can be
+duplicated by adding the <A HREF = "package.html">package kokkos</A> or <A HREF = "suffix.html">suffix
+kk</A> commands respectively to your input script.
+</P>
<P>Or you can follow these steps:
</P>
<P>CPU-only (run all-MPI or with OpenMP threading):
</P>
<PRE>cd lammps/src
make yes-kokkos
make g++ KOKKOS_DEVICES=OpenMP
</PRE>
<P>Intel Xeon Phi:
</P>
<PRE>cd lammps/src
make yes-kokkos
make g++ KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=KNC
</PRE>
<P>CPUs and GPUs:
</P>
<PRE>cd lammps/src
make yes-kokkos
make cuda KOKKOS_DEVICES=Cuda
</PRE>
<P>These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
make command line which requires a GNU-compatible make command. Try
"gmake" if your system's standard make complains.
</P>
<P>IMPORTANT NOTE: If you build using make line variables and re-build
LAMMPS twice with different KOKKOS options and the *same* target,
e.g. g++ in the first two examples above, then you *must* perform a
"make clean-all" or "make clean-machine" before each build. This is
to force all the KOKKOS-dependent files to be re-compiled with the new
options.
</P>
<P>You can also hardwire these make variables in the specified machine
makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
with a line like:
</P>
<PRE>KOKKOS_ARCH = KNC
</PRE>
<P>Note that if you build LAMMPS multiple times in this manner, using
different KOKKOS options (defined in different machine makefiles), you
do not have to worry about doing a "clean" in between. This is
because the targets will be different.
</P>
<P>IMPORTANT NOTE: The 3rd example above for a GPU, uses a different
machine makefile, in this case src/MAKE/Makefile.cuda, which is
included in the LAMMPS distribution. To build the KOKKOS package for
a GPU, this makefile must use the NVIDA "nvcc" compiler. And it must
have a KOKKOS_ARCH setting that is appropriate for your NVIDIA
hardware and installed software. Typical values for KOKKOS_ARCH are given
below, as well
as other settings that must be included in the machine makefile, if
you create your own.
</P>
<P>IMPORTANT NOTE: Currently, there are no precision options with the
KOKKOS package. All compilation and computation is performed in
double precision.
</P>
<P>There are other allowed options when building with the KOKKOS package.
As above, they can be set either as variables on the make command line
or in Makefile.machine. This is the full list of options, including
those discussed above, Each takes a value shown below. The
default value is listed, which is set in the
lib/kokkos/Makefile.kokkos file.
</P>
<P>#Default settings specific options
#Options: force_uvm,use_ldg,rdc
</P>
<UL><LI>KOKKOS_DEVICES, values = <I>OpenMP</I>, <I>Serial</I>, <I>Pthreads</I>, <I>Cuda</I>, default = <I>OpenMP</I>
<LI>KOKKOS_ARCH, values = <I>KNC</I>, <I>SNB</I>, <I>HSW</I>, <I>Kepler</I>, <I>Kepler30</I>, <I>Kepler32</I>, <I>Kepler35</I>, <I>Kepler37</I>, <I>Maxwell</I>, <I>Maxwell50</I>, <I>Maxwell52</I>, <I>Maxwell53</I>, <I>ARMv8</I>, <I>BGQ</I>, <I>Power7</I>, <I>Power8</I>, default = <I>none</I>
<LI>KOKKOS_DEBUG, values = <I>yes</I>, <I>no</I>, default = <I>no</I>
<LI>KOKKOS_USE_TPLS, values = <I>hwloc</I>, <I>librt</I>, default = <I>none</I>
<LI>KOKKOS_CUDA_OPTIONS, values = <I>force_uvm</I>, <I>use_ldg</I>, <I>rdc</I>
</UL>
<P>KOKKOS_DEVICE sets the parallelization method used for Kokkos code
(within LAMMPS). KOKKOS_DEVICES=OpenMP means that OpenMP will be
used. KOKKOS_DEVICES=Pthreads means that pthreads will be used.
KOKKOS_DEVICES=Cuda means an NVIDIA GPU running CUDA will be used.
</P>
<P>If KOKKOS_DEVICES=Cuda, then the lo-level Makefile in the src/MAKE
directory must use "nvcc" as its compiler, via its CC setting. For
best performance its CCFLAGS setting should use -O3 and have a
KOKKOS_ARCH setting that matches the compute capability of your NVIDIA
hardware and software installation, e.g. KOKKOS_ARCH=Kepler30. Note
the minimal required compute capability is 2.0, but this will give
signicantly reduced performance compared to Kepler generation GPUs
with compute capability 3.x. For the LINK setting, "nvcc" should not
be used; instead use g++ or another compiler suitable for linking C++
applications. Often you will want to use your MPI compiler wrapper
for this setting (i.e. mpicxx). Finally, the lo-level Makefile must
also have a "Compilation rule" for creating *.o files from *.cu files.
See src/Makefile.cuda for an example of a lo-level Makefile with all
of these settings.
</P>
<P>KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be
used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
provides alternative methods via environment variables for binding
threads to hardware cores. More info on binding threads to cores is
given in <A HREF = "Section_accelerate.html#acc_8">this section</A>.
</P>
<P>KOKKOS_ARCH=KNC enables compiler switches needed when compling for an
Intel Phi processor.
</P>
<P>KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
on most Unix platforms. This library is not available on all
platforms.
</P>
<P>KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style
within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time
debugging information that can be useful. It also enables runtime
bounds checking on Kokkos data structures.
</P>
<P>KOKKOS_CUDA_OPTIONS are additional options for CUDA.
</P>
<P>For more information on Kokkos see the Kokkos programmers' guide here:
/lib/kokkos/doc/Kokkos_PG.pdf.
</P>
<P><B>Run with the KOKKOS package from the command line:</B>
</P>
<P>The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
</P>
<P>When using KOKKOS built with host=OMP, you need to choose how many
OpenMP threads per MPI task will be used (via the "-k" command-line
switch discussed below). Note that the product of MPI tasks * OpenMP
threads/task should not exceed the physical number of cores (on a
node), otherwise performance will suffer.
</P>
<P>When using the KOKKOS package built with device=CUDA, you must use
exactly one MPI task per physical GPU.
</P>
<P>When using the KOKKOS package built with host=MIC for Intel Xeon Phi
coprocessor support you need to insure there are one or more MPI tasks
per coprocessor, and choose the number of coprocessor threads to use
per MPI task (via the "-k" command-line switch discussed below). The
product of MPI tasks * coprocessor threads/task should not exceed the
maximum number of threads the coproprocessor is designed to run,
otherwise performance will suffer. This value is 240 for current
generation Xeon Phi(TM) chips, which is 60 physical cores * 4
threads/core. Note that with the KOKKOS package you do not need to
specify how many Phi coprocessors there are per node; each
coprocessors is simply treated as running some number of MPI tasks.
</P>
<P>You must use the "-k on" <A HREF = "Section_start.html#start_7">command-line
switch</A> to enable the KOKKOS package. It
takes additional arguments for hardware settings appropriate to your
system. Those arguments are <A HREF = "Section_start.html#start_7">documented
here</A>. The two most commonly used
options are:
</P>
<PRE>-k on t Nt g Ng
</PRE>
<P>The "t Nt" option applies to host=OMP (even if device=CUDA) and
host=MIC. For host=OMP, it specifies how many OpenMP threads per MPI
task to use with a node. For host=MIC, it specifies how many Xeon Phi
threads per MPI task to use within a node. The default is Nt = 1.
Note that for host=OMP this is effectively MPI-only mode which may be
fine. But for host=MIC you will typically end up using far less than
all the 240 available threads, which could give very poor performance.
</P>
<P>The "g Ng" option applies to device=CUDA. It specifies how many GPUs
per compute node to use. The default is 1, so this only needs to be
specified is you have 2 or more GPUs per compute node.
</P>
<P>The "-k on" switch also issues a "package kokkos" command (with no
additional arguments) which sets various KOKKOS options to default
values, as discussed on the <A HREF = "package.html">package</A> command doc page.
</P>
<P>Use the "-sf kk" <A HREF = "Section_start.html#start_7">command-line switch</A>,
which will automatically append "kk" to styles that support it. Use
the "-pk kokkos" <A HREF = "Section_start.html#start_7">command-line switch</A> if
you wish to change any of the default <A HREF = "package.html">package kokkos</A>
optionns set by the "-k on" <A HREF = "Section_start.html#start_7">command-line
switch</A>.
</P>
-<PRE>host=OMP, dual hex-core nodes (12 threads/node):
-mpirun -np 12 lmp_g++ -in in.lj # MPI-only mode with no Kokkos
-mpirun -np 12 lmp_g++ -k on -sf kk -in in.lj # MPI-only mode with Kokkos
-mpirun -np 1 lmp_g++ -k on t 12 -sf kk -in in.lj # one MPI task, 12 threads
-mpirun -np 2 lmp_g++ -k on t 6 -sf kk -in in.lj # two MPI tasks, 6 threads/task
-mpirun -np 32 -ppn 2 lmp_g++ -k on t 6 -sf kk -in in.lj # ditto on 16 nodes
-</PRE>
-<P>host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
-mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240
-mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj # 30 MPI tasks on 1 Phi, 30*8 = 240
-mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj # 12 MPI tasks on 1 Phi, 12*20 = 240
-mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis
-</P>
-<PRE>host=OMP, device=CUDA, node = dual hex-core CPUs and a single GPU:
-mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj # one MPI task, 6 threads on CPU
-mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj # ditto on 4 nodes
-</PRE>
-<PRE>host=OMP, device=CUDA, node = dual 8-core CPUs and 2 GPUs:
-mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # two MPI tasks, 8 threads per CPU
-mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # ditto on 16 nodes
-</PRE>
<P>Note that the default for the <A HREF = "package.html">package kokkos</A> command is
to use "full" neighbor lists and set the Newton flag to "off" for both
pairwise and bonded interactions. This typically gives fastest
performance. If the <A HREF = "newton.html">newton</A> command is used in the input
script, it can override the Newton flag defaults.
</P>
<P>However, when running in MPI-only mode with 1 thread per MPI task, it
will typically be faster to use "half" neighbor lists and set the
Newton flag to "on", just as is the case for non-accelerated pair
styles. You can do this with the "-pk" <A HREF = "Section_start.html#start_7">command-line
switch</A>.
</P>
<P><B>Or run with the KOKKOS package by editing an input script:</B>
</P>
<P>The discussion above for the mpirun/mpiexec command and setting
appropriate thread and GPU values for host=OMP or host=MIC or
device=CUDA are the same.
</P>
<P>You must still use the "-k on" <A HREF = "Section_start.html#start_7">command-line
switch</A> to enable the KOKKOS package, and
specify its additional arguments for hardware options appopriate to
your system, as documented above.
</P>
<P>Use the <A HREF = "suffix.html">suffix kk</A> command, or you can explicitly add a
"kk" suffix to individual styles in your input script, e.g.
</P>
<PRE>pair_style lj/cut/kk 2.5
</PRE>
<P>You only need to use the <A HREF = "package.html">package kokkos</A> command if you
wish to change any of its option defaults, as set by the "-k on"
<A HREF = "Section_start.html#start_7">command-line switch</A>.
</P>
<P><B>Speed-ups to expect:</B>
</P>
<P>The performance of KOKKOS running in different modes is a function of
your hardware, which KOKKOS-enable styles are used, and the problem
size.
</P>
<P>Generally speaking, the following rules of thumb apply:
</P>
<UL><LI>When running on CPUs only, with a single thread per MPI task,
performance of a KOKKOS style is somewhere between the standard
(un-accelerated) styles (MPI-only mode), and those provided by the
USER-OMP package. However the difference between all 3 is small (less
than 20%).
<LI>When running on CPUs only, with multiple threads per MPI task,
performance of a KOKKOS style is a bit slower than the USER-OMP
package.
<LI>When running on GPUs, KOKKOS is typically faster than the USER-CUDA
and GPU packages.
<LI>When running on Intel Xeon Phi, KOKKOS is not as fast as
the USER-INTEL package, which is optimized for that hardware.
</UL>
<P>See the <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark page</A> of the
LAMMPS web site for performance of the KOKKOS package on different
hardware.
</P>
<P><B>Guidelines for best performance:</B>
</P>
<P>Here are guidline for using the KOKKOS package on the different
hardware configurations listed above.
</P>
<P>Many of the guidelines use the <A HREF = "package.html">package kokkos</A> command
See its doc page for details and default settings. Experimenting with
its options can provide a speed-up for specific calculations.
</P>
<P><B>Running on a multi-core CPU:</B>
</P>
<P>If N is the number of physical cores/node, then the number of MPI
tasks/node * number of threads/task should not exceed N, and should
typically equal N. Note that the default threads/task is 1, as set by
the "t" keyword of the "-k" <A HREF = "Section_start.html#start_7">command-line
switch</A>. If you do not change this, no
additional parallelism (beyond MPI) will be invoked on the host
CPU(s).
</P>
<P>You can compare the performance running in different modes:
</P>
<UL><LI>run with 1 MPI task/node and N threads/task
<LI>run with N MPI tasks/node and 1 thread/task
<LI>run with settings in between these extremes
</UL>
<P>Examples of mpirun commands in these modes are shown above.
</P>
<P>When using KOKKOS to perform multi-threading, it is important for
performance to bind both MPI tasks to physical cores, and threads to
physical cores, so they do not migrate during a simulation.
</P>
<P>If you are not certain MPI tasks are being bound (check the defaults
for your MPI installation), binding can be forced with these flags:
</P>
<PRE>OpenMPI 1.8: mpirun -np 2 -bind-to socket -map-by socket ./lmp_openmpi ...
Mvapich2 2.0: mpiexec -np 2 -bind-to socket -map-by socket ./lmp_mvapich ...
</PRE>
<P>For binding threads with the KOKKOS OMP option, use thread affinity
environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
later, intel 12 or later) setting the environment variable
OMP_PROC_BIND=true should be sufficient. For binding threads with the
KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option, as
discussed in <A HREF = "Sections_start.html#start_3_4">Section 2.3.4</A> of the
manual.
</P>
<P><B>Running on GPUs:</B>
</P>
<P>Insure the -arch setting in the machine makefile you are using,
e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software
(see <A HREF = "Section_start.html#start_3_4">this section</A> of the manual for
details).
</P>
<P>The -np setting of the mpirun command should set the number of MPI
tasks/node to be equal to the # of physical GPUs on the node.
</P>
<P>Use the "-k" <A HREF = "Section_commands.html#start_7">command-line switch</A> to
specify the number of GPUs per node, and the number of threads per MPI
task. As above for multi-core CPUs (and no GPU), if N is the number
of physical cores/node, then the number of MPI tasks/node * number of
threads/task should not exceed N. With one GPU (and one MPI task) it
may be faster to use less than all the available cores, by setting
threads/task to a smaller value. This is because using all the cores
on a dual-socket node will incur extra cost to copy memory from the
2nd socket to the GPU.
</P>
<P>Examples of mpirun commands that follow these rules are shown above.
</P>
<P>IMPORTANT NOTE: When using a GPU, you will achieve the best
performance if your input script does not use any fix or compute
styles which are not yet Kokkos-enabled. This allows data to stay on
the GPU for multiple timesteps, without being copied back to the host
CPU. Invoking a non-Kokkos fix or compute, or performing I/O for
<A HREF = "thermo_style.html">thermo</A> or <A HREF = "dump.html">dump</A> output will cause data
to be copied back to the CPU.
</P>
<P>You cannot yet assign multiple MPI tasks to the same GPU with the
KOKKOS package. We plan to support this in the future, similar to the
GPU package in LAMMPS.
</P>
<P>You cannot yet use both the host (multi-threaded) and device (GPU)
together to compute pairwise interactions with the KOKKOS package. We
hope to support this in the future, similar to the GPU package in
LAMMPS.
</P>
<P><B>Running on an Intel Phi:</B>
</P>
<P>Kokkos only uses Intel Phi processors in their "native" mode, i.e.
not hosted by a CPU.
</P>
<P>As illustrated above, build LAMMPS with OMP=yes (the default) and
MIC=yes. The latter insures code is correctly compiled for the Intel
Phi. The OMP setting means OpenMP will be used for parallelization on
the Phi, which is currently the best option within Kokkos. In the
future, other options may be added.
</P>
<P>Current-generation Intel Phi chips have either 61 or 57 cores. One
core should be excluded for running the OS, leaving 60 or 56 cores.
Each core is hyperthreaded, so there are effectively N = 240 (4*60) or
N = 224 (4*56) cores to run on.
</P>
<P>The -np setting of the mpirun command sets the number of MPI
tasks/node. The "-k on t Nt" command-line switch sets the number of
threads/task as Nt. The product of these 2 values should be N, i.e.
240 or 224. Also, the number of threads/task should be a multiple of
4 so that logical threads from more than one MPI task do not run on
the same physical core.
</P>
<P>Examples of mpirun commands that follow these rules are shown above.
</P>
<P><B>Restrictions:</B>
</P>
<P>As noted above, if using GPUs, the number of MPI tasks per compute
node should equal to the number of GPUs per compute node. In the
future Kokkos will support assigning multiple MPI tasks to a single
GPU.
</P>
<P>Currently Kokkos does not support AMD GPUs due to limits in the
available backend programming models. Specifically, Kokkos requires
extensive C++ support from the Kernel language. This is expected to
change in the future.
</P>
</HTML>
diff --git a/doc/doc2/accelerate_omp.html b/doc/doc2/accelerate_omp.html
index 9514c4ec5..c898c3d11 100644
--- a/doc/doc2/accelerate_omp.html
+++ b/doc/doc2/accelerate_omp.html
@@ -1,206 +1,191 @@
<HTML>
<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
</P>
<H4>5.3.5 USER-OMP package
</H4>
<P>The USER-OMP package was developed by Axel Kohlmeyer at Temple
University. It provides multi-threaded versions of most pair styles,
nearly all bonded styles (bond, angle, dihedral, improper), several
-Kspace styles, and a few fix styles. The package currently
-uses the OpenMP interface for multi-threading.
+Kspace styles, and a few fix styles. The package currently uses the
+OpenMP interface for multi-threading.
</P>
-<P>Here is a quick overview of how to use the USER-OMP package:
-</P>
-<UL><LI>use the -fopenmp flag for compiling and linking in your Makefile.machine
-<LI>include the USER-OMP package and build LAMMPS
-<LI>use the mpirun command to set the number of MPI tasks/node
-<LI>specify how many threads per MPI task to use
-<LI>use USER-OMP styles in your input script
-</UL>
-<P>The latter two steps can be done using the "-pk omp" and "-sf omp"
-<A HREF = "Section_start.html#start_7">command-line switches</A> respectively. Or
-the effect of the "-pk" or "-sf" switches can be duplicated by adding
-the <A HREF = "package.html">package omp</A> or <A HREF = "suffix.html">suffix omp</A> commands
-respectively to your input script.
+<P>Here is a quick overview of how to use the USER-OMP package, assuming
+one or more 16-core nodes. More details follow.
</P>
+<PRE>use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine
+make yes-user-omp
+make mpi # build with USER-OMP package, if settings added to Makefile.mpi
+make omp # or Makefile.omp already has settings
+Make.py -v -p omp -o mpi -a file mpi # or one-line build via Make.py
+</PRE>
+<PRE>lmp_mpi -sf omp -pk omp 16 < in.script # 1 MPI task, 16 threads
+mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task
+mpirun -np 32 -ppn 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task
+</PRE>
<P><B>Required hardware/software:</B>
</P>
<P>Your compiler must support the OpenMP interface. You should have one
-or more multi-core CPUs so that multiple threads can be launched by an
-MPI task running on a CPU.
+or more multi-core CPUs so that multiple threads can be launched by
+each MPI task running on a CPU.
</P>
<P><B>Building LAMMPS with the USER-OMP package:</B>
</P>
-<P>To do this in one line, use the src/Make.py script, described in
-<A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual. Type "Make.py
--h" for help. If run from the src directory, this command will create
-src/lmp_omp using src/MAKE/Makefile.mpi as the starting
-Makefile.machine:
+<P>The lines above illustrate how to include/build with the USER-OMP
+package in two steps, using the "make" command. Or how to do it with
+one command via the src/Make.py script, described in <A HREF = "Section_start.html#start_4">Section
+2.4</A> of the manual. Type "Make.py -h" for
+help.
</P>
-<PRE>Make.py -p omp -o omp -a file mpi
-</PRE>
-<P>Or you can follow these steps:
-</P>
-<PRE>cd lammps/src
-make yes-user-omp
-make machine
-</PRE>
-<P>The CCFLAGS setting in Makefile.machine needs "-fopenmp" to add OpenMP
-support. This works for both the GNU and Intel compilers. Without
-this flag the USER-OMP styles will still be compiled and work, but
-will not support multi-threading. For the Intel compilers the CCFLAGS
-setting also needs to include "-restrict".
+<P>Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
+include "-fopenmp". Likewise, if you use an Intel compiler, the
+CCFLAGS setting must include "-restrict". The Make.py command will
+add these automatically.
</P>
<P><B>Run with the USER-OMP package from the command line:</B>
</P>
<P>The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
</P>
-<P>You need to choose how many threads per MPI task will be used by the
-USER-OMP package. Note that the product of MPI tasks * threads/task
-should not exceed the physical number of cores (on a node), otherwise
-performance will suffer.
-</P>
-<P>Use the "-sf omp" <A HREF = "Section_start.html#start_7">command-line switch</A>,
-which will automatically append "omp" to styles that support it. Use
-the "-pk omp Nt" <A HREF = "Section_start.html#start_7">command-line switch</A>, to
-set Nt = # of OpenMP threads per MPI task to use.
-</P>
-<PRE>lmp_machine -sf omp -pk omp 16 -in in.script # 1 MPI task on a 16-core node
-mpirun -np 4 lmp_machine -sf omp -pk omp 4 -in in.script # 4 MPI tasks each with 4 threads on a single 16-core node
-mpirun -np 32 -ppn 4 lmp_machine -sf omp -pk omp 4 -in in.script # ditto on 8 16-core nodes
-</PRE>
-<P>Note that if the "-sf omp" switch is used, it also issues a default
-<A HREF = "package.html">package omp 0</A> command, which sets the number of threads
-per MPI task via the OMP_NUM_THREADS environment variable.
-</P>
-<P>Using the "-pk" switch explicitly allows for direct setting of the
-number of threads and additional options. Its syntax is the same as
-the "package omp" command. See the <A HREF = "package.html">package</A> command doc
-page for details, including the default values used for all its
-options if it is not specified, and how to set the number of threads
-via the OMP_NUM_THREADS environment variable if desired.
+<P>You need to choose how many OpenMP threads per MPI task will be used
+by the USER-OMP package. Note that the product of MPI tasks *
+threads/task should not exceed the physical number of cores (on a
+node), otherwise performance will suffer.
+</P>
+<P>As in the lines above, use the "-sf omp" <A HREF = "Section_start.html#start_7">command-line
+switch</A>, which will automatically append
+"omp" to styles that support it. The "-sf omp" switch also issues a
+default <A HREF = "package.html">package omp 0</A> command, which will set the
+number of threads per MPI task via the OMP_NUM_THREADS environment
+variable.
+</P>
+<P>You can also use the "-pk omp Nt" <A HREF = "Section_start.html#start_7">command-line
+switch</A>, to explicitly set Nt = # of OpenMP
+threads per MPI task to use, as well as additional options. Its
+syntax is the same as the <A HREF = "package.html">package omp</A> command whose doc
+page gives details, including the default values used if it is not
+specified. It also gives more details on how to set the number of
+threads via the OMP_NUM_THREADS environment variable.
</P>
<P><B>Or run with the USER-OMP package by editing an input script:</B>
</P>
<P>The discussion above for the mpirun/mpiexec command, MPI tasks/node,
and threads/MPI task is the same.
</P>
<P>Use the <A HREF = "suffix.html">suffix omp</A> command, or you can explicitly add an
"omp" suffix to individual styles in your input script, e.g.
</P>
<PRE>pair_style lj/cut/omp 2.5
</PRE>
<P>You must also use the <A HREF = "package.html">package omp</A> command to enable the
-USER-OMP package, unless the "-sf omp" or "-pk omp" <A HREF = "Section_start.html#start_7">command-line
-switches</A> were used. It specifies how many
-threads per MPI task to use, as well as other options. Its doc page
-explains how to set the number of threads via an environment variable
-if desired.
+USER-OMP package. When you do this you also specify how many threads
+per MPI task to use. The command doc page explains other options and
+how to set the number of threads via the OMP_NUM_THREADS environment
+variable.
</P>
<P><B>Speed-ups to expect:</B>
</P>
<P>Depending on which styles are accelerated, you should look for a
reduction in the "Pair time", "Bond time", "KSpace time", and "Loop
time" values printed at the end of a run.
</P>
<P>You may see a small performance advantage (5 to 20%) when running a
USER-OMP style (in serial or parallel) with a single thread per MPI
-task, versus running standard LAMMPS with its standard
-(un-accelerated) styles (in serial or all-MPI parallelization with 1
-task/core). This is because many of the USER-OMP styles contain
-similar optimizations to those used in the OPT package, as described
-above.
-</P>
-<P>With multiple threads/task, the optimal choice of MPI tasks/node and
-OpenMP threads/task can vary a lot and should always be tested via
-benchmark runs for a specific simulation running on a specific
-machine, paying attention to guidelines discussed in the next
+task, versus running standard LAMMPS with its standard un-accelerated
+styles (in serial or all-MPI parallelization with 1 task/core). This
+is because many of the USER-OMP styles contain similar optimizations
+to those used in the OPT package, described in <A HREF = "accelerate_opt.html">Section accelerate
+5.3.6</A>.
+</P>
+<P>With multiple threads/task, the optimal choice of number of MPI
+tasks/node and OpenMP threads/task can vary a lot and should always be
+tested via benchmark runs for a specific simulation running on a
+specific machine, paying attention to guidelines discussed in the next
sub-section.
</P>
<P>A description of the multi-threading strategy used in the USER-OMP
package and some performance examples are <A HREF = "http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1">presented
here</A>
</P>
<P><B>Guidelines for best performance:</B>
</P>
<P>For many problems on current generation CPUs, running the USER-OMP
package with a single thread/task is faster than running with multiple
threads/task. This is because the MPI parallelization in LAMMPS is
often more efficient than multi-threading as implemented in the
USER-OMP package. The parallel efficiency (in a threaded sense) also
varies for different USER-OMP styles.
</P>
<P>Using multiple threads/task can be more effective under the following
circumstances:
</P>
<UL><LI>Individual compute nodes have a significant number of CPU cores but
the CPU itself has limited memory bandwidth, e.g. for Intel Xeon 53xx
-(Clovertown) and 54xx (Harpertown) quad core processors. Running one
+(Clovertown) and 54xx (Harpertown) quad-core processors. Running one
MPI task per CPU core will result in significant performance
degradation, so that running with 4 or even only 2 MPI tasks per node
is faster. Running in hybrid MPI+OpenMP mode will reduce the
inter-node communication bandwidth contention in the same way, but
offers an additional speedup by utilizing the otherwise idle CPU
cores.
<LI>The interconnect used for MPI communication does not provide
sufficient bandwidth for a large number of MPI tasks per node. For
example, this applies to running over gigabit ethernet or on Cray XT4
or XT5 series supercomputers. As in the aforementioned case, this
effect worsens when using an increasing number of nodes.
<LI>The system has a spatially inhomogeneous particle density which does
not map well to the <A HREF = "processors.html">domain decomposition scheme</A> or
<A HREF = "balance.html">load-balancing</A> options that LAMMPS provides. This is
because multi-threading achives parallelism over the number of
particles, not via their distribution in space.
<LI>A machine is being used in "capability mode", i.e. near the point
where MPI parallelism is maxed out. For example, this can happen when
using the <A HREF = "kspace_style.html">PPPM solver</A> for long-range
electrostatics on large numbers of nodes. The scaling of the KSpace
calculation (see the <A HREF = "kspace_style.html">kspace_style</A> command) becomes
the performance-limiting factor. Using multi-threading allows less
MPI tasks to be invoked and can speed-up the long-range solver, while
increasing overall performance by parallelizing the pairwise and
bonded calculations via OpenMP. Likewise additional speedup can be
sometimes be achived by increasing the length of the Coulombic cutoff
and thus reducing the work done by the long-range solver. Using the
<A HREF = "run_style.html">run_style verlet/split</A> command, which is compatible
with the USER-OMP package, is an alternative way to reduce the number
of MPI tasks assigned to the KSpace calculation.
</UL>
<P>Additional performance tips are as follows:
</P>
<UL><LI>The best parallel efficiency from <I>omp</I> styles is typically achieved
-when there is at least one MPI task per physical processor,
-i.e. socket or die.
+when there is at least one MPI task per physical CPU chip, i.e. socket
+or die.
<LI>It is usually most efficient to restrict threading to a single
socket, i.e. use one or more MPI task per socket.
-<LI>Several current MPI implementation by default use a processor affinity
-setting that restricts each MPI task to a single CPU core. Using
-multi-threading in this mode will force the threads to share that core
-and thus is likely to be counterproductive. Instead, binding MPI
-tasks to a (multi-core) socket, should solve this issue.
+<LI>IMPORTANT NOTE: By default, several current MPI implementations use a
+processor affinity setting that restricts each MPI task to a single
+CPU core. Using multi-threading in this mode will force all threads
+to share the one core and thus is likely to be counterproductive.
+Instead, binding MPI tasks to a (multi-core) socket, should solve this
+issue.
</UL>
<P><B>Restrictions:</B>
</P>
<P>None.
</P>
</HTML>
diff --git a/doc/doc2/accelerate_opt.html b/doc/doc2/accelerate_opt.html
index 3d96b9b51..53613ba2b 100644
--- a/doc/doc2/accelerate_opt.html
+++ b/doc/doc2/accelerate_opt.html
@@ -1,87 +1,76 @@
<HTML>
<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<P><A HREF = "Section_accelerate.html">Return to Section accelerate overview</A>
</P>
<H4>5.3.6 OPT package
</H4>
<P>The OPT package was developed by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technologies). It contains a handful of pair styles whose compute()
methods were rewritten in C++ templated form to reduce the overhead
due to if tests and other conditional code.
</P>
-<P>Here is a quick overview of how to use the OPT package:
-</P>
-<UL><LI>include the OPT package and build LAMMPS
-<LI>use OPT pair styles in your input script
-</UL>
-<P>The last step can be done using the "-sf opt" <A HREF = "Section_start.html#start_7">command-line
-switch</A>. Or the effect of the "-sf" switch
-can be duplicated by adding a <A HREF = "suffix.html">suffix opt</A> command to your
-input script.
+<P>Here is a quick overview of how to use the OPT package. More details
+follow.
</P>
+<PRE>make yes-opt
+make mpi # build with the OPT pacakge
+Make.py -v -p opt -o mpi -a file mpi # or one-line build via Make.py
+</PRE>
+<PRE>lmp_mpi -sf opt -in in.script # run in serial
+mpirun -np 4 lmp_mpi -sf opt -in in.script # run in parallel
+</PRE>
<P><B>Required hardware/software:</B>
</P>
<P>None.
</P>
<P><B>Building LAMMPS with the OPT package:</B>
</P>
-<P>Include the package and build LAMMPS:
-</P>
-<P>To do this in one line, use the src/Make.py script, described in
-<A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual. Type "Make.py
--h" for help. If run from the src directory, this command will create
-src/lmp_opt using src/MAKE/Makefile.mpi as the starting
-Makefile.machine:
+<P>The lines above illustrate how to build LAMMPS with the OPT package in
+two steps, using the "make" command. Or how to do it with one command
+via the src/Make.py script, described in <A HREF = "Section_start.html#start_4">Section
+2.4</A> of the manual. Type "Make.py -h" for
+help.
</P>
-<PRE>Make.py -p opt -o opt -a file mpi
-</PRE>
-<P>Or you can follow these steps:
-</P>
-<PRE>cd lammps/src
-make yes-opt
-make machine
-</PRE>
-<P>If you are using Intel compilers, then the CCFLAGS setting in
-Makefile.machine needs to include "-restrict".
+<P>Note that if you use an Intel compiler to build with the OPT package,
+the CCFLAGS setting in your Makefile.machine must include "-restrict".
+The Make.py command will add this automatically.
</P>
<P><B>Run with the OPT package from the command line:</B>
</P>
-<P>Use the "-sf opt" <A HREF = "Section_start.html#start_7">command-line switch</A>,
-which will automatically append "opt" to styles that support it.
+<P>As in the lines above, use the "-sf opt" <A HREF = "Section_start.html#start_7">command-line
+switch</A>, which will automatically append
+"opt" to styles that support it.
</P>
-<PRE>lmp_machine -sf opt -in in.script
-mpirun -np 4 lmp_machine -sf opt -in in.script
-</PRE>
<P><B>Or run with the OPT package by editing an input script:</B>
</P>
<P>Use the <A HREF = "suffix.html">suffix opt</A> command, or you can explicitly add an
"opt" suffix to individual styles in your input script, e.g.
</P>
<PRE>pair_style lj/cut/opt 2.5
</PRE>
<P><B>Speed-ups to expect:</B>
</P>
<P>You should see a reduction in the "Pair time" value printed at the end
of a run. On most machines for reasonable problem sizes, it will be a
5 to 20% savings.
</P>
<P><B>Guidelines for best performance:</B>
</P>
-<P>None. Just try out an OPT pair style to see how it performs.
+<P>Just try out an OPT pair style to see how it performs.
</P>
<P><B>Restrictions:</B>
</P>
<P>None.
</P>
</HTML>
diff --git a/doc/doc2/compute_temp_cs.html b/doc/doc2/compute_temp_cs.html
index abb50d2dd..cf8fdbedc 100644
--- a/doc/doc2/compute_temp_cs.html
+++ b/doc/doc2/compute_temp_cs.html
@@ -1,125 +1,125 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute temp/cs command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID temp/cs group1 group2
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>temp/cs = style name of this compute command
<LI>group1 = group-ID of either cores or shells
<LI>group2 = group-ID of either shells or cores
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute oxygen_c-s all temp/cs O_core O_shell
compute core_shells all temp/cs cores shells
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a system based
on the center-of-mass velocity of atom pairs that are bonded to each
other. This compute is designed to be used with the adiabatic
core/shell model of <A HREF = "#MitchellFinchham">(Mitchell and Finchham)</A>. See
<A HREF = "Section_howto.html#howto_25">Section_howto 25</A> of the manual for an
overview of the model as implemented in LAMMPS. Specifically, this
compute enables correct temperature calculation and thermostatting of
core/shell pairs where it is desirable for the internal degrees of
freedom of the core/shell pairs to not be influenced by a thermostat.
A compute of this style can be used by any command that computes a
temperature via <A HREF = "fix_modify.html">fix_modify</A> e.g. <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
</P>
<P>Note that this compute does not require all ions to be polarized,
hence defined as core/shell pairs. One can mix core/shell pairs and
ions without a satellite particle if desired. The compute will
consider the non-polarized ions according to the physical system.
</P>
<P>For this compute, core and shell particles are specified by two
respective group IDs, which can be defined using the
<A HREF = "group.html">group</A> command. The number of atoms in the two groups
must be the same and there should be one bond defined between a pair
of atoms in the two groups. Non-polarized ions which might also be
included in the treated system should not be included into either of
these groups, they are taken into account by the <I>group-ID</I> (2nd
argument) of the compute.
</P>
<P>The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in the group, k = Boltzmann constant, and T = temperature. Note that
the velocity of each core or shell atom used in the KE calculation is
the velocity of the center-of-mass (COM) of the core/shell pair the
atom is part of.
</P>
<P>A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that v^2 is replaced by vx*vy for the xy
component, etc. The 6 components of the vector are ordered xx, yy,
-zz, xy, xz, yz. Again, the velocity of each core or shell atom is its
-COM velocity.
+zz, xy, xz, yz. In contrast to the temperature, the velocity of
+each core or shell atom is taken individually.
</P>
<P>The change this fix makes to core/shell atom velocities is essentially
computing the temperature after a "bias" has been removed from the
velocity of the atoms. This "bias" is the velocity of the atom
relative to the COM velocity of the core/shell pair. If this compute
is used with a fix command that performs thermostatting then this bias
will be subtracted from each atom, thermostatting of the remaining COM
velocity will be performed, and the bias will be added back in. This
means the thermostating will effectively be performed on the
core/shell pairs, instead of on the individual core and shell atoms.
Thermostatting fixes that work in this way include <A HREF = "fix_nh.html">fix
nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
langevin</A>.
</P>
<P>The internal energy of core/shell pairs can be calculated by the
<A HREF = "compute_temp_chunk.html">compute temp/chunk</A> command, if chunks are
defined as core/shell pairs. See <A HREF = "Section_howto.html#howto_25">Section_howto
25</A> for more discussion on how to do this.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input.
</P>
<P>The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
</P>
<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>The number of core/shell pairs contributing to the temperature is
assumed to be constant for the duration of the run. No fixes should
be used which generate new molecules or atoms during a simulation.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_chunk.html">compute
temp/chunk</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "MitchellFinchham"></A>
<P><B>(Mitchell and Finchham)</B> Mitchell, Finchham, J Phys Condensed Matter,
5, 1031-1038 (1993).
</P>
</HTML>
diff --git a/doc/doc2/fix_adapt.html b/doc/doc2/fix_adapt.html
index 51ad3ce48..27e0e3322 100644
--- a/doc/doc2/fix_adapt.html
+++ b/doc/doc2/fix_adapt.html
@@ -1,263 +1,267 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix adapt command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID adapt N attribute args ... keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>adapt = style name of this fix command
<LI>N = adapt simulation settings every this many timesteps
<LI>one or more attribute/arg pairs may be appended
<LI>attribute = <I>pair</I> or <I>kspace</I> or <I>atom</I>
<PRE> <I>pair</I> args = pstyle pparam I J v_name
pstyle = pair style name, e.g. lj/cut
pparam = parameter to adapt over time
I,J = type pair(s) to set parameter for
v_name = variable with name that calculates value of pparam
<I>kspace</I> arg = v_name
v_name = variable with name that calculates scale factor on K-space terms
<I>atom</I> args = aparam v_name
aparam = parameter to adapt over time
v_name = variable with name that calculates value of aparam
</PRE>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>scale</I> or <I>reset</I>
<PRE> <I>scale</I> value = <I>no</I> or <I>yes</I>
<I>no</I> = the variable value is the new setting
<I>yes</I> = the variable value multiplies the original setting
<I>reset</I> value = <I>no</I> or <I>yes</I>
<I>no</I> = values will remain altered at the end of a run
<I>yes</I> = reset altered values to their original values at the end of a run
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all adapt 1 pair soft a 1 1 v_prefactor
fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
fix 1 all adapt 10 atom diameter v_size
</PRE>
<P><B>Description:</B>
</P>
<P>Change or adapt one or more specific simulation attributes or settings
over time as a simulation runs. Pair potential and K-space and atom
attributes which can be varied by this fix are discussed below. Many
other fixes can also be used to time-vary simulation parameters,
e.g. the "fix deform" command will change the simulation box
size/shape and the "fix move" command will change atom positions and
velocities in a prescribed manner. Also note that many commands allow
variables as arguments for specific parameters, if described in that
manner on their doc pages. An equal-style variable can calculate a
time-dependent quantity, so this is another way to vary a simulation
parameter over time.
</P>
<P>If <I>N</I> is specified as 0, the specified attributes are only changed
once, before the simulation begins. This is all that is needed if the
associated variables are not time-dependent. If <I>N</I> > 0, then changes
are made every <I>N</I> steps during the simulation, presumably with a
variable that is time-dependent.
</P>
<P>Depending on the value of the <I>reset</I> keyword, attributes changed by
this fix will or will not be reset back to their original values at
the end of a simulation. Even if <I>reset</I> is specified as <I>yes</I>, a
restart file written during a simulation will contain the modified
settings.
</P>
<P>If the <I>scale</I> keyword is set to <I>no</I>, then the value the parameter is
set to will be whatever the variable generates. If the <I>scale</I>
keyword is set to <I>yes</I>, then the value of the altered parameter will
be the initial value of that parameter multiplied by whatever the
variable generates. I.e. the variable is now a "scale factor" applied
in (presumably) a time-varying fashion to the parameter.
</P>
<P>Note that whether scale is <I>no</I> or <I>yes</I>, internally, the parameters
themselves are actually altered by this fix. Make sure you use the
<I>reset yes</I> option if you want the parameters to be restored to their
initial values after the run.
</P>
<HR>
<P>The <I>pair</I> keyword enables various parameters of potentials defined by
the <A HREF = "pair_style.html">pair_style</A> command to be changed, if the pair
style supports it. Note that the <A HREF = "pair_style.html">pair_style</A> and
<A HREF = "pair_coeff.html">pair_coeff</A> commands must be used in the usual manner
to specify these parameters initially; the fix adapt command simply
overrides the parameters.
</P>
<P>The <I>pstyle</I> argument is the name of the pair style. If <A HREF = "pair_hybrid.html">pair_style
hybrid or hybrid/overlay</A> is used, <I>pstyle</I> should be
-a sub-style name. For example, <I>pstyle</I> could be specified as "soft"
-or "lubricate". The <I>pparam</I> argument is the name of the parameter to
-change. This is the current list of pair styles and parameters that
-can be varied by this fix. See the doc pages for individual pair
-styles and their energy formulas for the meaning of these parameters:
+a sub-style name. If there are multiple sub-styles using the same
+pair style, then <I>pstyle</I> should be specified as "style:N" where N is
+which instance of the pair style you wish to adapt, e.g. the first,
+second, etc. For example, <I>pstyle</I> could be specified as "soft" or
+"lubricate" or "lj/cut:1" or "lj/cut:2". The <I>pparam</I> argument is the
+name of the parameter to change. This is the current list of pair
+styles and parameters that can be varied by this fix. See the doc
+pages for individual pair styles and their energy formulas for the
+meaning of these parameters:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD ><A HREF = "pair_born.html">born</A></TD><TD > a,b,c</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_buck.html">buck</A></TD><TD > a,c</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_coul.html">coul/cut</A></TD><TD > scale</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_coul.html">coul/debye</A></TD><TD > scale</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_coul.html">coul/long</A></TD><TD > scale</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD > epsilon,sigma</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD > epsilon,sigma,delta</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD > mu</TD><TD > global</TD></TR>
<TR><TD ><A HREF = "pair_gauss.html">gauss</A></TD><TD > a</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_morse.html">morse</A></TD><TD > d0,r0,alpha</TD><TD > type pairs</TD></TR>
<TR><TD ><A HREF = "pair_soft.html">soft</A></TD><TD > a</TD><TD > type pairs
</TD></TR></TABLE></DIV>
<P>IMPORTANT NOTE: It is easy to add new potentials and their parameters
to this list. All it typically takes is adding an extract() method to
the pair_*.cpp file associated with the potential.
</P>
<P>Some parameters are global settings for the pair style, e.g. the
viscosity setting "mu" for <A HREF = "pair_lubricate.html">pair_style lubricate</A>.
Other parameters apply to atom type pairs within the pair style,
e.g. the prefactor "a" for <A HREF = "pair_soft.html">pair_style soft</A>.
</P>
<P>Note that for many of the potentials, the parameter that can be varied
is effectively a prefactor on the entire energy expression for the
potential, e.g. the lj/cut epsilon. The parameters listed as "scale"
are exactly that, since the energy expression for the
<A HREF = "pair_coul.html">coul/cut</A> potential (for example) has no labeled
prefactor in its formula. To apply an effective prefactor to some
potentials, multiple parameters need to be altered. For example, the
<A HREF = "pair_buck.html">Buckingham potential</A> needs both the A and C terms
altered together. To scale the Buckingham potential, you should thus
list the pair style twice, once for A and once for C.
</P>
<P>If a type pair parameter is specified, the <I>I</I> and <I>J</I> settings should
be specified to indicate which type pairs to apply it to. If a global
parameter is specified, the <I>I</I> and <I>J</I> settings still need to be
specified, but are ignored.
</P>
<P>Similar to the <A HREF = "pair_coeff.html">pair_coeff command</A>, I and J can be
specified in one of two ways. Explicit numeric values can be used for
each, as in the 1st example above. I <= J is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same values.
</P>
<P>A wild-card asterisk can be used in place of or in conjunction with
the I,J arguments to set the coefficients for multiple pairs of atom
types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
number of atom types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive). Note that only type pairs with I <= J are considered; if
asterisks imply type pairs where J < I, they are ignored.
</P>
<P>IMPROTANT NOTE: If <A HREF = "pair_hybrid.html">pair_style hybrid or
hybrid/overlay</A> is being used, then the <I>pstyle</I> will
be a sub-style name. You must specify I,J arguments that correspond
to type pair values defined (via the <A HREF = "pair_coeff.html">pair_coeff</A>
command) for that sub-style.
</P>
<P>The <I>v_name</I> argument for keyword <I>pair</I> is the name of an
<A HREF = "variable.html">equal-style variable</A> which will be evaluated each time
this fix is invoked to set the parameter to a new value. It should be
specified as v_name, where name is the variable name. Equal-style
variables can specify formulas with various mathematical functions,
and include <A HREF = "thermo_style.html">thermo_style</A> command keywords for the
simulation box parameters and timestep and elapsed time. Thus it is
easy to specify parameters that change as a function of time or span
consecutive runs in a continuous fashion. For the latter, see the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command and the
<I>elaplong</I> keyword of <A HREF = "thermo_style.html">thermo_style custom</A> for
details.
</P>
<P>For example, these commands would change the prefactor coefficient of
the <A HREF = "pair_soft.html">pair_style soft</A> potential from 10.0 to 30.0 in a
linear fashion over the course of a simulation:
</P>
<PRE>variable prefactor equal ramp(10,30)
fix 1 all adapt 1 pair soft a * * v_prefactor
</PRE>
<HR>
<P>The <I>kspace</I> keyword used the specified variable as a scale factor on
the energy, forces, virial calculated by whatever K-Space solver is
defined by the <A HREF = "kspace_style.html">kspace_style</A> command. If the
variable has a value of 1.0, then the solver is unaltered.
</P>
<P>The <I>kspace</I> keyword works this way whether the <I>scale</I> keyword
is set to <I>no</I> or <I>yes</I>.
</P>
<HR>
<P>The <I>atom</I> keyword enables various atom properties to be changed. The
<I>aparam</I> argument is the name of the parameter to change. This is the
current list of atom parameters that can be varied by this fix:
</P>
<UL><LI>charge = charge on particle
<LI>diameter = diameter of particle
</UL>
<P>The <I>v_name</I> argument of the <I>atom</I> keyword is the name of an
<A HREF = "variable.html">equal-style variable</A> which will be evaluated each time
this fix is invoked to set the parameter to a new value. It should be
specified as v_name, where name is the variable name. See the
discussion above describing the formulas associated with equal-style
variables. The new value is assigned to the corresponding attribute
for all atoms in the fix group.
</P>
<P>IMPORTANT NOTE: The <I>atom</I> keyword works this way whether the <I>scale</I>
keyword is set to <I>no</I> or <I>yes</I>. I.e. the use of scale yes is not yet
supported by the <I>atom</I> keyword.
</P>
<P>If the atom parameter is <I>diameter</I> and per-atom density and per-atom
mass are defined for particles (e.g. <A HREF = "atom_style.html">atom_style
granular</A>), then the mass of each particle is also
changed when the diameter changes (density is assumed to stay
constant).
</P>
<P>For example, these commands would shrink the diameter of all granular
particles in the "center" group from 1.0 to 0.1 in a linear fashion
over the course of a 1000-step simulation:
</P>
<PRE>variable size equal ramp(1.0,0.1)
fix 1 center adapt 10 atom diameter v_size
</PRE>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P>For <A HREF = "run_style.html">rRESPA time integration</A>, this fix changes
parameters on the outermost rRESPA level.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_ti.html">compute ti</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are scale = no, reset = no.
</P>
</HTML>
diff --git a/doc/doc2/fix_ave_correlate.html b/doc/doc2/fix_ave_correlate.html
index eda6a0785..860459bdb 100644
--- a/doc/doc2/fix_ave_correlate.html
+++ b/doc/doc2/fix_ave_correlate.html
@@ -1,349 +1,353 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix ave/correlate command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID ave/correlate Nevery Nrepeat Nfreq value1 value2 ... keyword args ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>ave/correlate = style name of this fix command
<LI>Nevery = use input values every this many timesteps
<LI>Nrepeat = # of correlation time windows to accumulate
-<LI>Nfreq = calculate tine window averages every this many timesteps
+<LI>Nfreq = calculate time window averages every this many timesteps
<LI>one or more input values can be listed
<LI>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
<PRE> c_ID = global scalar calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID
f_ID = global scalar calculated by a fix with ID
f_ID[I] = Ith component of global vector calculated by a fix with ID
v_name = global value calculated by an equal-style variable with name
</PRE>
<LI>zero or more keyword/arg pairs may be appended
<LI>keyword = <I>type</I> or <I>ave</I> or <I>start</I> or <I>prefactor</I> or <I>file</I> or <I>overwrite</I> or <I>title1</I> or <I>title2</I> or <I>title3</I>
<PRE> <I>type</I> arg = <I>auto</I> or <I>upper</I> or <I>lower</I> or <I>auto/upper</I> or <I>auto/lower</I> or <I>full</I>
auto = correlate each value with itself
upper = correlate each value with each succeeding value
lower = correlate each value with each preceding value
auto/upper = auto + upper
auto/lower = auto + lower
full = correlate each value with every other value, including itself = auto + upper + lower
<I>ave</I> args = <I>one</I> or <I>running</I>
one = zero the correlation accumulation every Nfreq steps
running = accumulate correlations continuously
<I>start</I> args = Nstart
Nstart = start accumulating correlations on this timestep
<I>prefactor</I> args = value
value = prefactor to scale all the correlation data by
<I>file</I> arg = filename
filename = name of file to output correlation data to
<I>overwrite</I> arg = none = overwrite output file with only latest output
<I>title1</I> arg = string
string = text to print as 1st line of output file
<I>title2</I> arg = string
string = text to print as 2nd line of output file
<I>title3</I> arg = string
string = text to print as 3rd line of output file
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
fix 1 all ave/correlate 1 50 10000 &
c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
type upper ave running title1 "My correlation data"
</PRE>
<P><B>Description:</B>
</P>
<P>Use one or more global scalar values as inputs every few timesteps,
calculate time correlations bewteen them at varying time intervals,
and average the correlation data over longer timescales. The
resulting correlation values can be time integrated by
<A HREF = "variable.html">variables</A> or used by other <A HREF = "Section_howto.html#howto_15">output
commands</A> such as <A HREF = "thermo_style.html">thermo_style
-custom</A>, and can also be written to a file.
+custom</A>, and can also be written to a file. See the
+<A HREF = "fix_ave_correlate_long.html">fix ave/correlate/long</A> command for an
+alternate method for computing correlation functions efficiently over
+very long time windows.
</P>
<P>The group specified with this command is ignored. However, note that
specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
</P>
<P>Each listed value can be the result of a <A HREF = "compute.html">compute</A> or
<A HREF = "fix.html">fix</A> or the evaluation of an equal-style
<A HREF = "variable.html">variable</A>. In each case, the compute, fix, or variable
must produce a global quantity, not a per-atom or local quantity. If
you wish to spatial- or time-average or histogram per-atom quantities
from a compute, fix, or variable, then see the <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>,
or <A HREF = "fix_ave_histo.html">fix ave/histo</A> commands. If you wish to sum a
per-atom quantity into a single global quantity, see the <A HREF = "compute_reduce.html">compute
reduce</A> command.
</P>
<P><A HREF = "compute.html">Computes</A> that produce global quantities are those which
do not have the word <I>atom</I> in their style name. Only a few
<A HREF = "fix.html">fixes</A> produce global quantities. See the doc pages for
individual fixes for info on which ones produce such values.
<A HREF = "variable.html">Variables</A> of style <I>equal</I> are the only ones that can
be used with this fix. Variables of style <I>atom</I> cannot be used,
since they produce per-atom values.
</P>
<P>The input values must either be all scalars. What kinds of
correlations between input values are calculated is determined by the
<I>type</I> keyword as discussed below.
</P>
<HR>
<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
timesteps the input values will be used to calculate correlation data.
The input values are sampled every <I>Nevery</I> timesteps. The
correlation data for the preceding samples is computed on timesteps
that are a multiple of <I>Nfreq</I>. Consider a set of samples from some
initial time up to an output timestep. The initial time could be the
beginning of the simulation or the last output time; see the <I>ave</I>
keyword for options. For the set of samples, the correlation value
Cij is calculated as:
</P>
<PRE>Cij(delta) = ave(Vi(t)*Vj(t+delta))
</PRE>
<P>which is the correlation value between input values Vi and Vj,
separated by time delta. Note that the second value Vj in the pair is
always the one sampled at the later time. The ave() represents an
average over every pair of samples in the set that are separated by
time delta. The maximum delta used is of size (<I>Nrepeat</I>-1)*<I>Nevery</I>.
Thus the correlation between a pair of input values yields <I>Nrepeat</I>
correlation datums:
</P>
<PRE>Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij((Nrepeat-1)*Nevery)
</PRE>
<P>For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on
timesteps 0,5,10,15,...,100 will be used to compute the final averages
on timestep 100. Six averages will be computed: Cij(0), Cij(5),
Cij(10), Cij(15), Cij(20), and Cij(25). Cij(10) on timestep 100 will
be the average of 19 samples, namely Vi(0)*Vj(10), Vi(5)*Vj(15),
Vi(10)*V j20), Vi(15)*Vj(25), ..., Vi(85)*Vj(95), Vi(90)*Vj(100).
</P>
<P><I>Nfreq</I> must be a multiple of <I>Nevery</I>; <I>Nevery</I> and <I>Nrepeat</I> must be
non-zero. Also, if the <I>ave</I> keyword is set to <I>one</I> which is the
default, then <I>Nfreq</I> >= (<I>Nrepeat</I>-1)*<I>Nevery</I> is required.
</P>
<HR>
<P>If a value begins with "c_", a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the compute is used. If a
bracketed term is appended, the Ith element of the global vector
calculated by the compute is used.
</P>
<P>Note that there is a <A HREF = "compute_reduce.html">compute reduce</A> command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix ave/correlate. Or it can be a compute
defined not in your input script, but by <A HREF = "thermo_style.html">thermodynamic
output</A> or other fixes such as <A HREF = "fix_nh.html">fix nvt</A>
or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and <A HREF = "Section_modify.html">add them to
LAMMPS</A>.
</P>
<P>If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the fix is used. If a
bracketed term is appended, the Ith element of the global vector
calculated by the fix is used.
</P>
<P>Note that some fixes only produce their values on certain timesteps,
which must be compatible with <I>Nevery</I>, else an error will result.
Users can also write code for their own fix styles and <A HREF = "Section_modify.html">add them to
LAMMPS</A>.
</P>
<P>If a value begins with "v_", a variable name must follow which has
been previously defined in the input script. Only equal-style
variables can be referenced. See the <A HREF = "variable.html">variable</A> command
for details. Note that variables of style <I>equal</I> define a formula
which can reference individual atom properties or thermodynamic
keywords, or they can invoke other computes, fixes, or variables when
they are evaluated, so this is a very general means of specifying
quantities to time correlate.
</P>
<HR>
<P>Additional optional keywords also affect the operation of this fix.
</P>
<P>The <I>type</I> keyword determines which pairs of input values are
correlated with each other. For N input values Vi, for i = 1 to N,
let the number of pairs = Npair. Note that the second value in the
pair Vi(t)*Vj(t+delta) is always the one sampled at the later time.
</P>
<UL><LI>If <I>type</I> is set to <I>auto</I> then each input value is correlated with
itself. I.e. Cii = Vi*Vi, for i = 1 to N, so Npair = N.
<LI>If <I>type</I> is set
to <I>upper</I> then each input value is correlated with every succeeding
value. I.e. Cij = Vi*Vj, for i < j, so Npair = N*(N-1)/2.
<LI>If <I>type</I> is set
to <I>lower</I> then each input value is correlated with every preceeding
value. I.e. Cij = Vi*Vj, for i > j, so Npair = N*(N-1)/2.
<LI>If <I>type</I> is set to <I>auto/upper</I> then each input value is correlated
with itself and every succeeding value. I.e. Cij = Vi*Vj, for i >= j,
so Npair = N*(N+1)/2.
<LI>If <I>type</I> is set to <I>auto/lower</I> then each input value is correlated
with itself and every preceding value. I.e. Cij = Vi*Vj, for i <= j,
so Npair = N*(N+1)/2.
<LI>If <I>type</I> is set to <I>full</I> then each input value is correlated with
itself and every other value. I.e. Cij = Vi*Vj, for i,j = 1,N so
Npair = N^2.
</UL>
<P>The <I>ave</I> keyword determines what happens to the accumulation of
correlation samples every <I>Nfreq</I> timesteps. If the <I>ave</I> setting is
<I>one</I>, then the accumulation is restarted or zeroed every <I>Nfreq</I>
timesteps. Thus the outputs on successive <I>Nfreq</I> timesteps are
essentially independent of each other. The exception is that the
Cij(0) = Vi(T)*Vj(T) value at a timestep T, where T is a multiple of
<I>Nfreq</I>, contributes to the correlation output both at time T and at
time T+Nfreq.
</P>
<P>If the <I>ave</I> setting is <I>running</I>, then the accumulation is never
zeroed. Thus the output of correlation data at any timestep is the
average over samples accumulated every <I>Nevery</I> steps since the fix
was defined. it can only be restarted by deleting the fix via the
<A HREF = "unfix.html">unfix</A> command, or by re-defining the fix by re-specifying
it.
</P>
<P>The <I>start</I> keyword specifies what timestep the accumulation of
correlation samples will begin on. The default is step 0. Setting it
to a larger value can avoid adding non-equilibrated data to the
correlation averages.
</P>
<P>The <I>prefactor</I> keyword specifies a constant which will be used as a
multiplier on the correlation data after it is averaged. It is
effectively a scale factor on Vi*Vj, which can be used to account for
the size of the time window or other unit conversions.
</P>
<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
steps, an array of correlation data is written to the file. The
number of rows is <I>Nrepeat</I>, as described above. The number of
columns is the Npair+2, also as described above. Thus the file ends
up to be a series of these array sections.
</P>
<P>The <I>overwrite</I> keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of
output. This option can only be used with the <I>ave running</I> setting.
</P>
<P>The <I>title1</I> and <I>title2</I> and <I>title3</I> keywords allow specification of
the strings that will be printed as the first 3 lines of the output
file, assuming the <I>file</I> keyword was used. LAMMPS uses default
values for each of these, so they do not need to be specified.
</P>
<P>By default, these header lines are as follows:
</P>
<PRE># Time-correlated data for fix ID
# TimeStep Number-of-time-windows
# Index TimeDelta Ncount valueI*valueJ valueI*valueJ ...
</PRE>
<P>In the first line, ID is replaced with the fix-ID. The second line
describes the two values that are printed at the first of each section
of output. In the third line the value pairs are replaced with the
appropriate fields from the fix ave/correlate command.
</P>
<HR>
<P>Let Sij = a set of time correlation data for input values I and J,
namely the <I>Nrepeat</I> values:
</P>
<PRE>Sij = Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij(*Nrepeat-1)*Nevery)
</PRE>
<P>As explained below, these datums are output as one column of a global
array, which is effectively the correlation matrix.
</P>
<P>The <I>trap</I> function defined for <A HREF = "variable.html">equal-style variables</A>
can be used to perform a time integration of this vector of datums,
using a trapezoidal rule. This is useful for calculating various
quantities which can be derived from time correlation data. If a
normalization factor is needed for the time integration, it can be
included in the variable formula or via the <I>prefactor</I> keyword.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>This fix computes a global array of values which can be accessed by
various <A HREF = "Section_howto.html#howto_15">output commands</A>. The values can
only be accessed on timesteps that are multiples of <I>Nfreq</I> since that
is when averaging is performed. The global array has # of rows =
<I>Nrepeat</I> and # of columns = Npair+2. The first column has the time
delta (in timesteps) between the pairs of input values used to
calculate the correlation, as described above. The 2nd column has the
number of samples contributing to the correlation average, as
described above. The remaining Npair columns are for I,J pairs of the
N input values, as determined by the <I>type</I> keyword, as described
above.
</P>
<UL><LI>For <I>type</I> = <I>auto</I>, the Npair = N columns are ordered: C11, C22, ...,
CNN.
<LI>For <I>type</I> = <I>upper</I>, the Npair = N*(N-1)/2 columns are ordered: C12,
C13, ..., C1N, C23, ..., C2N, C34, ..., CN-1N.
<LI>For <I>type</I> = <I>lower</I>, the Npair = N*(N-1)/2 columns are ordered: C21,
C31, C32, C41, C42, C43, ..., CN1, CN2, ..., CNN-1.
<LI>For <I>type</I> = <I>auto/upper</I>, the Npair = N*(N+1)/2 columns are ordered:
C11, C12, C13, ..., C1N, C22, C23, ..., C2N, C33, C34, ..., CN-1N,
CNN.
<LI>For <I>type</I> = <I>auto/lower</I>, the Npair = N*(N+1)/2 columns are ordered:
C11, C21, C22, C31, C32, C33, C41, ..., C44, CN1, CN2, ..., CNN-1,
CNN.
<LI>For <I>type</I> = <I>full</I>, the Npair = N^2 columns are ordered: C11, C12,
..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1,
CNN.
</UL>
<P>The array values calculated by this fix are treated as "intensive".
If you need to divide them by the number of atoms, you must do this in
a later processing step, e.g. when using them in a
<A HREF = "variable.html">variable</A>.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
-<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "fix_ave_atom.html">fix
+<P><A HREF = "fix_ave_correlate_long.html">fix ave/correlate/long</A>,
+<A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "fix_ave_atom.html">fix
ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>,
<A HREF = "fix_ave_histo.html">fix ave/histo</A>, <A HREF = "variable.html">variable</A>
</P>
<P><B>Default:</B> none
</P>
<P>The option defaults are ave = one, type = auto, start = 0, no file
output, title 1,2,3 = strings as described above, and prefactor = 1.0.
</P>
</HTML>
diff --git a/doc/doc2/fix_ave_correlate_long.html b/doc/doc2/fix_ave_correlate_long.html
new file mode 100644
index 000000000..05f452665
--- /dev/null
+++ b/doc/doc2/fix_ave_correlate_long.html
@@ -0,0 +1,159 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix ave/correlate/long command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID ave/correlate/long Nevery Nfreq value1 value2 ... keyword args ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>ave/correlate/long = style name of this fix command
+
+<LI>Nevery = use input values every this many timesteps
+
+<LI>Nfreq = save state of the time correlation functions every this many timesteps
+
+<LI>one or more input values can be listed
+
+<LI>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
+
+<PRE> c_ID = global scalar calculated by a compute with ID
+ c_ID[I] = Ith component of global vector calculated by a compute with ID
+ f_ID = global scalar calculated by a fix with ID
+ f_ID[I] = Ith component of global vector calculated by a fix with ID
+ v_name = global value calculated by an equal-style variable with name
+</PRE>
+<LI>zero or more keyword/arg pairs may be appended
+
+<LI>keyword = <I>type</I> or <I>start</I> or <I>file</I> or <I>overwrite</I> or <I>title1</I> or <I>title2</I> or <I>ncorr</I> or <I>p</I> or <I>m</I>
+
+<PRE> <I>type</I> arg = <I>auto</I> or <I>upper</I> or <I>lower</I> or <I>auto/upper</I> or <I>auto/lower</I> or <I>full</I>
+ auto = correlate each value with itself
+ upper = correlate each value with each succeeding value
+ lower = correlate each value with each preceding value
+ auto/upper = auto + upper
+ auto/lower = auto + lower
+ full = correlate each value with every other value, including itself = auto + upper + lower
+ <I>start</I> args = Nstart
+ Nstart = start accumulating correlations on this timestep
+ <I>file</I> arg = filename
+ filename = name of file to output correlation data to
+ <I>overwrite</I> arg = none = overwrite output file with only latest output
+ <I>title1</I> arg = string
+ string = text to print as 1st line of output file
+ <I>title2</I> arg = string
+ string = text to print as 2nd line of output file
+ <I>ncorr</I> arg = Ncorrelators
+ Ncorrelators = number of correlators to store
+ <I>nlen</I> args = Nlen
+ Nlen = length of each correlator
+ <I>ncount</I> args = Ncount
+ Ncount = number of values over which succesive correlators are averaged
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
+fix 1 all ave/correlate/long 1 10000 &
+ c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
+ type upper title1 "My correlation data" nlen 15 ncount 3
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>This fix is similar in spirit and syntax to the <A HREF = "fix_ave_correlate.html">fix
+ave/correlate</A>. However, this fix allows the
+efficient calculation of time correlation functions on the fly over
+extremely long time windows without too much CPU overhead, using a
+multiple-tau method <A HREF = "#Ramirez">(Ramirez)</A> that decreases the resolution
+of the stored correlation function with time.
+</P>
+<P>The group specified with this command is ignored. However, note that
+specified values may represent calculations performed by computes and
+fixes which store their own "group" definitions.
+</P>
+<P>Each listed value can be the result of a compute or fix or the
+evaluation of an equal-style variable. See the <A HREF = "fix_ave_correlate.html">fix
+ave/correlate</A> doc page for details.
+</P>
+<P>The <I>Nevery</I> and <I>Nfreq</I> arguments specify on what timesteps the input
+values will be used to calculate correlation data, and the frequency
+with which the time correlation functions will be output to a file.
+Note that there is no <I>Nrepeat</I> argument, unlike the <A HREF = "fix_ave_correlate.html">fix
+ave/correlate</A> command.
+</P>
+<P>The optional keywords <I>ncorr</I>, <I>nlen</I>, and <I>ncount</I> are unique to this
+command and determine the number of correlation points calculated and
+the memory and CPU overhead used by this calculation. <I>Nlen</I> and
+<I>ncount</I> determine the amount of averaging done at longer correlation
+times. The default values <I>nlen=16</I>, <I>ncount=2</I> ensure that the
+systematic error of the multiple-tau correlator is always below the
+level of the statistical error of a typical simulation (which depends
+on the ensemble size and the simulation length).
+</P>
+<P>The maximum correlation time (in time steps) that can be reached is
+given by the formula (nlen-1) * ncount^(ncorr-1). Longer correlation
+times are discarded and not calculated. With the default values of
+the parameters (ncorr=20, nlen=16 and ncount=2), this corresponds to
+7864320 time steps. If longer correlation times are needed, the value
+of ncorr should be increased. Using nlen=16 and ncount=2, with
+ncorr=30, the maximum number of steps that can be correlated is
+80530636808. If ncorr=40, correlation times in excess of 8e12 time
+steps can be calculated.
+</P>
+<P>The total memory needed for each correlation pair is roughly
+4*ncorr*nlen*8 bytes. With the default values of the parameters, this
+corresponds to about 10 KB.
+</P>
+<P>For the meaning of the additional optional keywords, see the <A HREF = "fix_ave_correlate.html">fix
+ave/correlate</A> doc page.
+</P>
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>Since this fix in intended for the calculation of time correlation
+functions over very long MD simulations, the information about this
+fix is written automatically to binary restart files, so that the time
+correlation calculation can continue in subsequent simulations. None
+of the fix_modify options are relevant to this fix.
+</P>
+<P>No parameter of this fix can be used with the start/stop keywords of
+the run command. This fix is not invoked during energy minimization.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_ave_correlate.html">fix ave/correlate</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<P>The option defaults for keywords that are also keywords for the <A HREF = "fix_ave_correlate.html">fix
+ave/correlate</A> command are as follows: type =
+auto, start = 0, no file output, title 1,2 = strings as described on
+the <A HREF = "fix_ave_correlate.html">fix ave/correlate</A> doc page.
+</P>
+<P>The option defaults for keywords unique to this command are as
+follows: ncorr=20, nlen=16, ncount=2.
+</P>
+<HR>
+
+<A NAME = "Ramirez"></A>
+
+<P><B>(Ramirez)</B> J. Ramirez, S.K. Sukumaran, B. Vorselaars and
+A.E. Likhtman, J. Chem. Phys. 133, 154103 (2010).
+</P>
+</HTML>
diff --git a/doc/doc2/fix_gcmc.html b/doc/doc2/fix_gcmc.html
index e01d62478..21864923c 100644
--- a/doc/doc2/fix_gcmc.html
+++ b/doc/doc2/fix_gcmc.html
@@ -1,348 +1,369 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix gcmc command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID gcmc N X M type seed T mu displace keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>gcmc = style name of this fix command
<LI>N = invoke this fix every N steps
<LI>X = average number of GCMC exchanges to attempt every N steps
<LI>M = average number of MC moves to attempt every N steps
-<LI>type = atom type to assign to inserted atoms (offset for molecule insertion)
+<LI>type = atom type for inserted atoms (must be 0 if mol keyword used)
<LI>seed = random # seed (positive integer)
<LI>T = temperature of the ideal gas reservoir (temperature units)
<LI>mu = chemical potential of the ideal gas reservoir (energy units)
<LI>translate = maximum Monte Carlo translation distance (length units)
<LI>zero or more keyword/value pairs may be appended to args
-<PRE>keyword = <I>mol</I>, <I>region</I>, <I>maxangle</I>, <I>pressure</I>, <I>fugacity_coeff</I>, <I>full_energy</I>, <I>charge</I>, <I>group</I>, <I>grouptype</I>, or <I>intra_energy</I>
+<PRE>keyword = <I>mol</I>, <I>region</I>, <I>maxangle</I>, <I>pressure</I>, <I>fugacity_coeff</I>, <I>full_energy</I>, <I>charge</I>, <I>group</I>, <I>grouptype</I>, <I>intra_energy</I>, or <I>tfac_insert</I>
<I>mol</I> value = template-ID
template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
<I>shake</I> value = fix-ID
fix-ID = ID of <A HREF = "fix_shake.html">fix shake</A> command
<I>region</I> value = region-ID
region-ID = ID of region where MC moves are allowed
<I>maxangle</I> value = maximum molecular rotation angle (degrees)
<I>pressure</I> value = pressure of the gas reservoir (pressure units)
<I>fugacity_coeff</I> value = fugacity coefficient of the gas reservoir (unitless)
<I>full_energy</I> = compute the entire system energy when performing MC moves
<I>charge</I> value = charge of inserted atoms (charge units)
<I>group</I> value = group-ID
group-ID = group-ID for inserted atoms (string)
<I>grouptype</I> values = type group-ID
type = atom type (int)
group-ID = group-ID for inserted atoms (string)
- <I>intra_energy</I> value = intramolecular energy (energy units)
+ <I>intra_energy</I> value = intramolecular energy (energy units)
+ <I>tfac_insert</I> value = scale up/down temperature of inserted atoms (unitless)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
</PRE>
<P><B>Description:</B>
</P>
<P>This fix performs grand canonical Monte Carlo (GCMC) exchanges of
atoms or molecules of the given type with an imaginary ideal gas reservoir at
the specified T and chemical potential (mu) as discussed in
<A HREF = "#Frenkel">(Frenkel)</A>. If used with the <A HREF = "fix_nh.html">fix nvt</A> command,
simulations in the grand canonical ensemble (muVT, constant chemical
potential, constant volume, and constant temperature) can be
performed. Specific uses include computing isotherms in microporous
materials, or computing vapor-liquid coexistence curves.
</P>
<P>Every N timesteps the fix attempts a number of GCMC exchanges (insertions
or deletions) of gas atoms or molecules of
the given type between the simulation cell and the imaginary
reservoir. It also attempts a number of Monte Carlo
moves (translations and molecule rotations) of gas of the given type
within the simulation cell or region. The average number of
attempted GCMC exchanges is X. The average number of attempted MC moves is M.
M should typically be chosen to be
approximately equal to the expected number of gas atoms or molecules
of the given type within the simulation cell or region,
which will result in roughly one
MC translation per atom or molecule per MC cycle.
</P>
<P>For MC moves of molecular gasses, rotations and translations are each
attempted with 50% probability. For MC moves of atomic gasses,
translations are attempted 100% of the time. For MC exchanges of
either molecular or atomic gasses, deletions and insertions are each
attempted with 50% probability.
</P>
<P>All inserted particles are always assigned to two groups: the default group
"all" and the group specified in the fix gcmc command (which can also
be "all"). In addition, particles are also added to any groups specified
by the <I>group</I> and <I>grouptype</I> keywords.
If inserted particles are individual atoms, they are
-assigned the specified atom type. If they are molecules, the type of
-each atom in the inserted molecule is specified in the file read by
-the <A HREF = "molecule.html">molecule</A> command, and those values are added to
-the specified atom type. E.g. if <I>type</I> = 2, and the file specifies
-atom types 1,2,3, then the inserted molecule will have atom types
-3,4,5.
+assigned the atom type given by the type argument. If they are molecules,
+the type argument has no effect and must be set to zero. Instead,
+the type of each atom in the inserted molecule is specified
+in the file read by the <A HREF = "molecule.html">molecule</A> command.
</P>
<P>This fix cannot be used to perform MC insertions of gas atoms or
molecules other than the exchanged type, but MC deletions,
translations, and rotations can be performed on any atom/molecule in
the fix group. All atoms in the simulation cell can be moved using
regular time integration translations, e.g. via
<A HREF = "fix_nvt.html">fix_nvt</A>, resulting in a hybrid GCMC+MD simulation. A
smaller-than-usual timestep size may be needed when running such a
hybrid simulation, especially if the inserted molecules are not well
equilibrated.
</P>
<P>This command may optionally use the <I>region</I> keyword to define an
exchange and move volume. The specified region must have been
previously defined with a <A HREF = "region.html">region</A> command. It must be
defined with side = <I>in</I>. Insertion attempts occur only within the
specified region. For non-rectangular regions, random trial
points are generated within the rectangular bounding box until a point is found
that lies inside the region. If no valid point is generated after 1000 trials,
no insertion is performed, but it is counted as an attempted insertion.
Move and deletion attempt candidates are selected
from gas atoms or molecules within the region. If there are no candidates,
no move or deletion is performed, but it is counted as an attempt move
or deletion. If an attempted move places the atom or molecule center-of-mass outside
the specified region, a new attempted move is generated. This process is repeated
until the atom or molecule center-of-mass is inside the specified region.
</P>
<P>If used with <A HREF = "fix_nvt.html">fix_nvt</A>, the temperature of the imaginary
reservoir, T, should be set to be equivalent to the target temperature
used in <A HREF = "fix_nvt.html">fix_nvt</A>. Otherwise, the imaginary reservoir
-will not be in thermal equilibrium with the simulation cell.
-</P>
+will not be in thermal equilibrium with the simulation cell. Also,
+it is important that the temperature used by fix nvt be dynamic,
+which can be achieved as follows:
+</P>
+<PRE>compute mdtemp mdatoms temp
+compute_modify mdtemp dynamic yes
+fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
+fix_modify mdnvt temp mdtemp
+</PRE>
<P>Note that neighbor lists are re-built every timestep that this fix is
invoked, so you should not set N to be too small. However, periodic
rebuilds are necessary in order to avoid dangerous rebuilds and missed
interactions. Specifically, avoid performing so many MC translations
per timestep that atoms can move beyond the neighbor list skin
distance. See the <A HREF = "neighbor.html">neighbor</A> command for details.
</P>
<P>When an atom or molecule is to be inserted, its
coordinates are chosen at a random position within the current
simulation cell or region, and new atom velocities are randomly chosen from
-the specified temperature distribution given by T. Relative
+the specified temperature distribution given by T. The effective
+temperature for new atom velocities can be increased or decreased
+using the optional keyword <I>tfac_insert</I> (see below). Relative
coordinates for atoms in a molecule are taken from the template
molecule provided by the user. The center of mass of the molecule
is placed at the insertion point. The orientation of the molecule
is chosen at random by rotating about this point.
</P>
<P>Individual atoms are inserted, unless the <I>mol</I> keyword is used. It
specifies a <I>template-ID</I> previously defined using the
<A HREF = "molecule.html">molecule</A> command, which reads a file that defines the
molecule. The coordinates, atom types, charges, etc, as well as any
bond/angle/etc and special neighbor information for the molecule can
be specified in the molecule file. See the <A HREF = "molecule.html">molecule</A>
command for details. The only settings required to be in this file
are the coordinates and types of atoms in the molecule.
</P>
<P>When not using the <I>mol</I> keyword, you should ensure you do not delete
atoms that are bonded to other atoms, or LAMMPS will
soon generate an error when it tries to find bonded neighbors. LAMMPS will
warn you if any of the atoms eligible for deletion have a non-zero
molecule ID, but does not check for this at the time of deletion.
</P>
<P>If you wish to insert molecules via the <I>mol</I> keyword, that will have
their bonds or angles constrained via SHAKE, use the <I>shake</I> keyword,
specifying as its value the ID of a separate <A HREF = "fix_shake.html">fix
shake</A> command which also appears in your input script.
</P>
<P>Optionally, users may specify the maximum rotation angle for
molecular rotations using the <I>maxangle</I> keyword and specifying
the angle in degrees. Rotations are performed by generating a random
point on the unit sphere and a random rotation angle on the
range [0,maxangle). The molecule is then rotated by that angle about an
axis passing through the molecule center of mass. The axis is parallel
to the unit vector defined by the point on the unit sphere.
The same procedure is used for randomly rotating molecules when they
are inserted, except that the maximum angle is 360 degrees.
</P>
<P>Note that fix GCMC does not use configurational bias
MC or any other kind of sampling of intramolecular degrees of freedom.
Inserted molecules can have different orientations, but they will all
have the same intramolecular configuration,
which was specified in the molecule command input.
</P>
<P>For atomic gasses, inserted atoms have the specified atom type, but
deleted atoms are any atoms that have been inserted or that belong
to the user-specified fix group. For molecular gasses, exchanged
molecules use the same atom types as in the template molecule
supplied by the user. In both cases, exchanged
atoms/molecules are assigned to two groups: the default group "all"
and the group specified in the fix gcmc command (which can also be
"all").
</P>
<P>The gas reservoir pressure can be specified using the <I>pressure</I>
keyword, in which case the user-specified chemical potential is
ignored. For non-ideal gas reservoirs, the user may also specify the
fugacity coefficient using the <I>fugacity_coeff</I> keyword.
</P>
<P>The <I>full_energy</I> option means that fix GCMC will compute the total
potential energy of the entire simulated system. The total system
energy before and after the proposed GCMC move is then used in the
Metropolis criterion to determine whether or not to accept the
proposed GCMC move. By default, this option is off, in which case
only partial energies are computed to determine the difference in
energy that would be caused by the proposed GCMC move.
</P>
<P>The <I>full_energy</I> option is needed for systems with complicated
potential energy calculations, including the following:
</P>
<UL><LI> long-range electrostatics (kspace)
<LI> many-body pair styles
<LI> hybrid pair styles
<LI> eam pair styles
<LI> triclinic systems
<LI> need to include potential energy contributions from other fixes
</UL>
<P>In these cases, LAMMPS will automatically apply the <I>full_energy</I>
keyword and issue a warning message.
</P>
<P>When the <I>mol</I> keyword is used, the <I>full_energy</I> option also includes
the intramolecular energy of inserted and deleted molecules. If this
is not desired, the <I>intra_energy</I> keyword can be used to define an
amount of energy that is subtracted from the final energy when a molecule
is inserted, and added to the initial energy when a molecule is
deleted. For molecules that have a non-zero intramolecular energy, this
will ensure roughly the same behavior whether or not the <I>full_energy</I>
option is used.
</P>
+<P>Inserted atoms and molecules are assigned random velocities based on the
+specified temperature T. Because the relative velocity of
+all atoms in the molecule is zero, this may result in inserted molecules
+that are systematically too cold. In addition, the intramolecular potential
+energy of the inserted molecule may cause the kinetic energy
+of the molecule to quickly increase or decrease after insertion.
+The <I>tfac_insert</I> keyword allows the user to counteract these effects
+by changing the temperature used to assign velocities to
+inserted atoms and molecules by a constant factor. For a
+particular application, some experimentation may be required
+to find a value of <I>tfac_insert</I> that results in inserted molecules that
+equilibrate quickly to the correct temperature.
+</P>
<P>Some fixes have an associated potential energy. Examples of such fixes
include: <A HREF = "fix_efield.html">efield</A>, <A HREF = "fix_gravity.html">gravity</A>,
<A HREF = "fix_addforce.html">addforce</A>, <A HREF = "fix_langevin.html">langevin</A>,
<A HREF = "fix_restrain.html">restrain</A>, <A HREF = "fix_temp_berendsen.html">temp/berendsen</A>,
<A HREF = "fix_temp_rescale.html">temp/rescale</A>, and <A HREF = "fix_wall.html">wall fixes</A>.
For that energy to be included in the total potential energy of the
system (the quantity used when performing GCMC moves),
you MUST enable the <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for
that fix. The doc pages for individual <A HREF = "fix.html">fix</A> commands
specify if this should be done.
</P>
<P>Use the <I>charge</I> option to insert atoms with a user-specified point
charge. Note that doing so will cause the system to become non-neutral.
LAMMPS issues a warning when using long-range electrostatics (kspace)
with non-neutral systems. See the
<A HREF = "compute_group_group.html">compute_group_group</A> documentation for more
details about simulating non-neutral systems with kspace on.
</P>
<P>Use of this fix typically will cause the number of atoms to fluctuate,
therefore, you will want to use the
<A HREF = "compute_modify.html">compute_modify</A> command to insure that the
current number of atoms is used as a normalizing factor each time
temperature is computed. Here is the necessary command:
</P>
<PRE>compute_modify thermo_temp dynamic yes
</PRE>
<P>If LJ units are used, note that a value of 0.18292026 is used by this
fix as the reduced value for Planck's constant. This value was
derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 *
epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
mass = 39.948 amu.
</P>
<P>The <I>group</I> keyword assigns all inserted atoms to the <A HREF = "group.html">group</A>
of the group-ID value. The <I>grouptype</I> keyword assigns all
inserted atoms of the specified type to the <A HREF = "group.html">group</A>
of the group-ID value.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the fix to <A HREF = "restart.html">binary restart
files</A>. This includes information about the random
number generator seed, the next timestep for MC exchanges, etc. See
the <A HREF = "read_restart.html">read_restart</A> command for info on how to
re-specify a fix in an input script that reads a restart file, so that
the operation of the fix continues in an uninterrupted fashion.
</P>
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
fix.
</P>
<P>This fix computes a global vector of length 8, which can be accessed
by various <A HREF = "Section_howto.html#howto_15">output commands</A>. The vector
values are the following global cumulative quantities:
</P>
<UL><LI>1 = translation attempts
<LI>2 = translation successes
<LI>3 = insertion attempts
<LI>4 = insertion successes
<LI>5 = deletion attempts
<LI>6 = deletion successes
<LI>7 = rotation attempts
<LI>8 = rotation successes
</UL>
<P>The vector values calculated by this fix are "extensive".
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>Do not set "neigh_modify once yes" or else this fix will never be
called. Reneighboring is required.
</P>
<P>Can be run in parallel, but aspects of the GCMC part will not scale
well in parallel. Only usable for 3D simulations.
</P>
<P>Note that very lengthy simulations involving insertions/deletions of
billions of gas molecules may run out of atom or molecule IDs and
trigger an error, so it is better to run multiple shorter-duration
simulations. Likewise, very large molecules have not been tested
and may turn out to be problematic.
</P>
<P>Use of multiple fix gcmc commands in the same input script can be
problematic if using a template molecule. The issue is that the
user-referenced template molecule in the second fix gcmc command
may no longer exist since it might have been deleted by the first
fix gcmc command. An existing template molecule will need to be
referenced by the user for each subsequent fix gcmc command.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_atom_swap.html">fix atom/swap</A>,
<A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "neighbor.html">neighbor</A>,
<A HREF = "fix_deposit.html">fix deposit</A>, <A HREF = "fix_evaporate.html">fix evaporate</A>,
<A HREF = "delete_atoms.html">delete_atoms</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are mol = no, maxangle = 10, full_energy = no,
except for the situations where full_energy is required, as
listed above.
</P>
<HR>
<A NAME = "Frenkel"></A>
<P><B>(Frenkel)</B> Frenkel and Smit, Understanding Molecular Simulation,
Academic Press, London, 2002.
</P>
</HTML>
diff --git a/doc/doc2/genindex.html b/doc/doc2/genindex.html
index 7ef4cf69a..36d13dad4 100644
--- a/doc/doc2/genindex.html
+++ b/doc/doc2/genindex.html
@@ -1,2220 +1,2228 @@
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<h1 id="index">Index</h1>
<div class="genindex-jumpbox">
<a href="#A"><strong>A</strong></a>
| <a href="#B"><strong>B</strong></a>
| <a href="#C"><strong>C</strong></a>
| <a href="#D"><strong>D</strong></a>
| <a href="#E"><strong>E</strong></a>
| <a href="#F"><strong>F</strong></a>
| <a href="#G"><strong>G</strong></a>
| <a href="#I"><strong>I</strong></a>
| <a href="#J"><strong>J</strong></a>
| <a href="#K"><strong>K</strong></a>
| <a href="#L"><strong>L</strong></a>
| <a href="#M"><strong>M</strong></a>
| <a href="#N"><strong>N</strong></a>
| <a href="#P"><strong>P</strong></a>
| <a href="#Q"><strong>Q</strong></a>
| <a href="#R"><strong>R</strong></a>
| <a href="#S"><strong>S</strong></a>
| <a href="#T"><strong>T</strong></a>
| <a href="#U"><strong>U</strong></a>
| <a href="#V"><strong>V</strong></a>
| <a href="#W"><strong>W</strong></a>
</div>
<h2 id="A">A</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="angle_coeff.html#index-0">angle_coeff</a>
</dt>
<dt><a href="angle_style.html#index-0">angle_style</a>
</dt>
<dt><a href="angle_charmm.html#index-0">angle_style charmm</a>
</dt>
<dt><a href="angle_class2.html#index-0">angle_style class2</a>
</dt>
<dt><a href="angle_cosine.html#index-0">angle_style cosine</a>
</dt>
<dt><a href="angle_cosine_delta.html#index-0">angle_style cosine/delta</a>
</dt>
<dt><a href="angle_cosine_periodic.html#index-0">angle_style cosine/periodic</a>
</dt>
<dt><a href="angle_cosine_shift.html#index-0">angle_style cosine/shift</a>
</dt>
<dt><a href="angle_cosine_shift_exp.html#index-0">angle_style cosine/shift/exp</a>
</dt>
<dt><a href="angle_cosine_squared.html#index-0">angle_style cosine/squared</a>
</dt>
<dt><a href="angle_dipole.html#index-0">angle_style dipole</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="angle_fourier.html#index-0">angle_style fourier</a>
</dt>
<dt><a href="angle_fourier_simple.html#index-0">angle_style fourier/simple</a>
</dt>
<dt><a href="angle_harmonic.html#index-0">angle_style harmonic</a>
</dt>
<dt><a href="angle_hybrid.html#index-0">angle_style hybrid</a>
</dt>
<dt><a href="angle_none.html#index-0">angle_style none</a>
</dt>
<dt><a href="angle_quartic.html#index-0">angle_style quartic</a>
</dt>
<dt><a href="angle_sdk.html#index-0">angle_style sdk</a>
</dt>
<dt><a href="angle_table.html#index-0">angle_style table</a>
</dt>
<dt><a href="atom_modify.html#index-0">atom_modify</a>
</dt>
<dt><a href="atom_style.html#index-0">atom_style</a>
</dt>
</dl></td>
</tr></table>
<h2 id="B">B</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="balance.html#index-0">balance</a>
</dt>
<dt><a href="bond_coeff.html#index-0">bond_coeff</a>
</dt>
<dt><a href="bond_style.html#index-0">bond_style</a>
</dt>
<dt><a href="bond_class2.html#index-0">bond_style class2</a>
</dt>
<dt><a href="bond_fene.html#index-0">bond_style fene</a>
</dt>
<dt><a href="bond_fene_expand.html#index-0">bond_style fene/expand</a>
</dt>
<dt><a href="bond_harmonic.html#index-0">bond_style harmonic</a>
</dt>
<dt><a href="bond_harmonic_shift.html#index-0">bond_style harmonic/shift</a>
</dt>
<dt><a href="bond_harmonic_shift_cut.html#index-0">bond_style harmonic/shift/cut</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="bond_hybrid.html#index-0">bond_style hybrid</a>
</dt>
<dt><a href="bond_morse.html#index-0">bond_style morse</a>
</dt>
<dt><a href="bond_none.html#index-0">bond_style none</a>
</dt>
<dt><a href="bond_nonlinear.html#index-0">bond_style nonlinear</a>
</dt>
<dt><a href="bond_quartic.html#index-0">bond_style quartic</a>
</dt>
<dt><a href="bond_table.html#index-0">bond_style table</a>
</dt>
<dt><a href="boundary.html#index-0">boundary</a>
</dt>
<dt><a href="box.html#index-0">box</a>
</dt>
</dl></td>
</tr></table>
<h2 id="C">C</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="change_box.html#index-0">change_box</a>
</dt>
<dt><a href="clear.html#index-0">clear</a>
</dt>
<dt><a href="comm_modify.html#index-0">comm_modify</a>
</dt>
<dt><a href="comm_style.html#index-0">comm_style</a>
</dt>
<dt><a href="compute.html#index-0">compute</a>
</dt>
<dt><a href="compute_ackland_atom.html#index-0">compute ackland/atom</a>
</dt>
<dt><a href="compute_angle_local.html#index-0">compute angle/local</a>
</dt>
<dt><a href="compute_angmom_chunk.html#index-0">compute angmom/chunk</a>
</dt>
<dt><a href="compute_basal_atom.html#index-0">compute basal/atom</a>
</dt>
<dt><a href="compute_body_local.html#index-0">compute body/local</a>
</dt>
<dt><a href="compute_bond_local.html#index-0">compute bond/local</a>
</dt>
<dt><a href="compute_centro_atom.html#index-0">compute centro/atom</a>
</dt>
<dt><a href="compute_chunk_atom.html#index-0">compute chunk/atom</a>
</dt>
<dt><a href="compute_cluster_atom.html#index-0">compute cluster/atom</a>
</dt>
<dt><a href="compute_cna_atom.html#index-0">compute cna/atom</a>
</dt>
<dt><a href="compute_com.html#index-0">compute com</a>
</dt>
<dt><a href="compute_com_chunk.html#index-0">compute com/chunk</a>
</dt>
<dt><a href="compute_contact_atom.html#index-0">compute contact/atom</a>
</dt>
<dt><a href="compute_coord_atom.html#index-0">compute coord/atom</a>
</dt>
<dt><a href="compute_damage_atom.html#index-0">compute damage/atom</a>
</dt>
<dt><a href="compute_dihedral_local.html#index-0">compute dihedral/local</a>
</dt>
<dt><a href="compute_dilatation_atom.html#index-0">compute dilatation/atom</a>
</dt>
<dt><a href="compute_displace_atom.html#index-0">compute displace/atom</a>
</dt>
<dt><a href="compute_erotate_asphere.html#index-0">compute erotate/asphere</a>
</dt>
<dt><a href="compute_erotate_rigid.html#index-0">compute erotate/rigid</a>
</dt>
<dt><a href="compute_erotate_sphere.html#index-0">compute erotate/sphere</a>
</dt>
<dt><a href="compute_erotate_sphere_atom.html#index-0">compute erotate/sphere/atom</a>
</dt>
<dt><a href="compute_event_displace.html#index-0">compute event/displace</a>
</dt>
<dt><a href="compute_fep.html#index-0">compute fep</a>
</dt>
<dt><a href="compute_tally.html#index-0">compute force/tally</a>
</dt>
<dt><a href="compute_group_group.html#index-0">compute group/group</a>
</dt>
<dt><a href="compute_gyration.html#index-0">compute gyration</a>
</dt>
<dt><a href="compute_gyration_chunk.html#index-0">compute gyration/chunk</a>
</dt>
<dt><a href="compute_heat_flux.html#index-0">compute heat/flux</a>
</dt>
<dt><a href="compute_improper_local.html#index-0">compute improper/local</a>
</dt>
<dt><a href="compute_inertia_chunk.html#index-0">compute inertia/chunk</a>
</dt>
<dt><a href="compute_ke.html#index-0">compute ke</a>
</dt>
<dt><a href="compute_ke_atom.html#index-0">compute ke/atom</a>
</dt>
<dt><a href="compute_ke_atom_eff.html#index-0">compute ke/atom/eff</a>
</dt>
<dt><a href="compute_ke_eff.html#index-0">compute ke/eff</a>
</dt>
<dt><a href="compute_ke_rigid.html#index-0">compute ke/rigid</a>
</dt>
<dt><a href="compute_meso_e_atom.html#index-0">compute meso_e/atom</a>
</dt>
<dt><a href="compute_meso_rho_atom.html#index-0">compute meso_rho/atom</a>
</dt>
<dt><a href="compute_meso_t_atom.html#index-0">compute meso_t/atom</a>
</dt>
<dt><a href="compute_msd.html#index-0">compute msd</a>
</dt>
<dt><a href="compute_msd_chunk.html#index-0">compute msd/chunk</a>
</dt>
<dt><a href="compute_msd_nongauss.html#index-0">compute msd/nongauss</a>
</dt>
<dt><a href="compute_omega_chunk.html#index-0">compute omega/chunk</a>
</dt>
<dt><a href="compute_pair.html#index-0">compute pair</a>
</dt>
<dt><a href="compute_pair_local.html#index-0">compute pair/local</a>
</dt>
<dt><a href="compute_pe.html#index-0">compute pe</a>
</dt>
<dt><a href="compute_pe_atom.html#index-0">compute pe/atom</a>
</dt>
<dt><a href="compute_plasticity_atom.html#index-0">compute plasticity/atom</a>
</dt>
<dt><a href="compute_pressure.html#index-0">compute pressure</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="compute_property_atom.html#index-0">compute property/atom</a>
</dt>
<dt><a href="compute_property_chunk.html#index-0">compute property/chunk</a>
</dt>
<dt><a href="compute_property_local.html#index-0">compute property/local</a>
</dt>
<dt><a href="compute_rdf.html#index-0">compute rdf</a>
</dt>
<dt><a href="compute_reduce.html#index-0">compute reduce</a>
</dt>
<dt><a href="compute_saed.html#index-0">compute saed</a>
</dt>
<dt><a href="compute_slice.html#index-0">compute slice</a>
</dt>
<dt><a href="compute_smd_contact_radius.html#index-0">compute smd/contact_radius</a>
</dt>
<dt><a href="compute_smd_damage.html#index-0">compute smd/damage</a>
</dt>
<dt><a href="compute_smd_hourglass_error.html#index-0">compute smd/hourglass_error</a>
</dt>
<dt><a href="compute_smd_internal_energy.html#index-0">compute smd/internal_energy</a>
</dt>
<dt><a href="compute_smd_plastic_strain.html#index-0">compute smd/plastic_strain</a>
</dt>
<dt><a href="compute_smd_plastic_strain_rate.html#index-0">compute smd/plastic_strain_rate</a>
</dt>
<dt><a href="compute_smd_rho.html#index-0">compute smd/rho</a>
</dt>
<dt><a href="compute_smd_tlsph_defgrad.html#index-0">compute smd/tlsph_defgrad</a>
</dt>
<dt><a href="compute_smd_tlsph_dt.html#index-0">compute smd/tlsph_dt</a>
</dt>
<dt><a href="compute_smd_tlsph_num_neighs.html#index-0">compute smd/tlsph_num_neighs</a>
</dt>
<dt><a href="compute_smd_tlsph_shape.html#index-0">compute smd/tlsph_shape</a>
</dt>
<dt><a href="compute_smd_tlsph_strain.html#index-0">compute smd/tlsph_strain</a>
</dt>
<dt><a href="compute_smd_tlsph_strain_rate.html#index-0">compute smd/tlsph_strain_rate</a>
</dt>
<dt><a href="compute_smd_tlsph_stress.html#index-0">compute smd/tlsph_stress</a>
</dt>
<dt><a href="compute_smd_ulsph_num_neighs.html#index-0">compute smd/ulsph_num_neighs</a>
</dt>
<dt><a href="compute_smd_ulsph_strain.html#index-0">compute smd/ulsph_strain</a>
</dt>
<dt><a href="compute_smd_ulsph_strain_rate.html#index-0">compute smd/ulsph_strain_rate</a>
</dt>
<dt><a href="compute_smd_ulsph_stress.html#index-0">compute smd/ulsph_stress</a>
</dt>
<dt><a href="compute_smd_vol.html#index-0">compute smd/vol</a>
</dt>
<dt><a href="compute_sna_atom.html#index-0">compute sna/atom</a>
</dt>
<dt><a href="compute_stress_atom.html#index-0">compute stress/atom</a>
</dt>
<dt><a href="compute_temp.html#index-0">compute temp</a>
</dt>
<dt><a href="compute_temp_asphere.html#index-0">compute temp/asphere</a>
</dt>
<dt><a href="compute_temp_chunk.html#index-0">compute temp/chunk</a>
</dt>
<dt><a href="compute_temp_com.html#index-0">compute temp/com</a>
</dt>
<dt><a href="compute_temp_cs.html#index-0">compute temp/cs</a>
</dt>
<dt><a href="compute_temp_deform.html#index-0">compute temp/deform</a>
</dt>
<dt><a href="compute_temp_deform_eff.html#index-0">compute temp/deform/eff</a>
</dt>
<dt><a href="compute_temp_drude.html#index-0">compute temp/drude</a>
</dt>
<dt><a href="compute_temp_eff.html#index-0">compute temp/eff</a>
</dt>
<dt><a href="compute_temp_partial.html#index-0">compute temp/partial</a>
</dt>
<dt><a href="compute_temp_profile.html#index-0">compute temp/profile</a>
</dt>
<dt><a href="compute_temp_ramp.html#index-0">compute temp/ramp</a>
</dt>
<dt><a href="compute_temp_region.html#index-0">compute temp/region</a>
</dt>
<dt><a href="compute_temp_region_eff.html#index-0">compute temp/region/eff</a>
</dt>
<dt><a href="compute_temp_rotate.html#index-0">compute temp/rotate</a>
</dt>
<dt><a href="compute_temp_sphere.html#index-0">compute temp/sphere</a>
</dt>
<dt><a href="compute_ti.html#index-0">compute ti</a>
</dt>
<dt><a href="compute_torque_chunk.html#index-0">compute torque/chunk</a>
</dt>
<dt><a href="compute_vacf.html#index-0">compute vacf</a>
</dt>
<dt><a href="compute_vcm_chunk.html#index-0">compute vcm/chunk</a>
</dt>
<dt><a href="compute_voronoi_atom.html#index-0">compute voronoi/atom</a>
</dt>
<dt><a href="compute_xrd.html#index-0">compute xrd</a>
</dt>
<dt><a href="compute_modify.html#index-0">compute_modify</a>
</dt>
<dt><a href="create_atoms.html#index-0">create_atoms</a>
</dt>
<dt><a href="create_bonds.html#index-0">create_bonds</a>
</dt>
<dt><a href="create_box.html#index-0">create_box</a>
</dt>
</dl></td>
</tr></table>
<h2 id="D">D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="delete_atoms.html#index-0">delete_atoms</a>
</dt>
<dt><a href="delete_bonds.html#index-0">delete_bonds</a>
</dt>
<dt><a href="dielectric.html#index-0">dielectric</a>
</dt>
<dt><a href="dihedral_coeff.html#index-0">dihedral_coeff</a>
</dt>
<dt><a href="dihedral_style.html#index-0">dihedral_style</a>
</dt>
<dt><a href="dihedral_charmm.html#index-0">dihedral_style charmm</a>
</dt>
<dt><a href="dihedral_class2.html#index-0">dihedral_style class2</a>
</dt>
<dt><a href="dihedral_cosine_shift_exp.html#index-0">dihedral_style cosine/shift/exp</a>
</dt>
<dt><a href="dihedral_fourier.html#index-0">dihedral_style fourier</a>
</dt>
<dt><a href="dihedral_harmonic.html#index-0">dihedral_style harmonic</a>
</dt>
<dt><a href="dihedral_helix.html#index-0">dihedral_style helix</a>
</dt>
<dt><a href="dihedral_hybrid.html#index-0">dihedral_style hybrid</a>
</dt>
<dt><a href="dihedral_multi_harmonic.html#index-0">dihedral_style multi/harmonic</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="dihedral_nharmonic.html#index-0">dihedral_style nharmonic</a>
</dt>
<dt><a href="dihedral_none.html#index-0">dihedral_style none</a>
</dt>
<dt><a href="dihedral_opls.html#index-0">dihedral_style opls</a>
</dt>
<dt><a href="dihedral_quadratic.html#index-0">dihedral_style quadratic</a>
</dt>
<dt><a href="dihedral_table.html#index-0">dihedral_style table</a>
</dt>
<dt><a href="dimension.html#index-0">dimension</a>
</dt>
<dt><a href="displace_atoms.html#index-0">displace_atoms</a>
</dt>
<dt><a href="dump.html#index-0">dump</a>
</dt>
<dt><a href="dump_h5md.html#index-0">dump h5md</a>
</dt>
<dt><a href="dump_image.html#index-0">dump image</a>
</dt>
<dt><a href="dump_molfile.html#index-0">dump molfile</a>
</dt>
<dt><a href="dump_modify.html#index-0">dump_modify</a>
</dt>
</dl></td>
</tr></table>
<h2 id="E">E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="echo.html#index-0">echo</a>
</dt>
</dl></td>
</tr></table>
<h2 id="F">F</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="fix.html#index-0">fix</a>
</dt>
<dt><a href="fix_adapt.html#index-0">fix adapt</a>
</dt>
<dt><a href="fix_adapt_fep.html#index-0">fix adapt/fep</a>
</dt>
<dt><a href="fix_addforce.html#index-0">fix addforce</a>
</dt>
<dt><a href="fix_addtorque.html#index-0">fix addtorque</a>
</dt>
<dt><a href="fix_append_atoms.html#index-0">fix append/atoms</a>
</dt>
<dt><a href="fix_atc.html#index-0">fix atc</a>
</dt>
<dt><a href="fix_atom_swap.html#index-0">fix atom/swap</a>
</dt>
<dt><a href="fix_ave_atom.html#index-0">fix ave/atom</a>
</dt>
<dt><a href="fix_ave_chunk.html#index-0">fix ave/chunk</a>
</dt>
<dt><a href="fix_ave_correlate.html#index-0">fix ave/correlate</a>
</dt>
+ <dt><a href="fix_ave_correlate_long.html#index-0">fix ave/correlate/long</a>
+ </dt>
+
+
<dt><a href="fix_ave_histo.html#index-0">fix ave/histo</a>
</dt>
<dt><a href="fix_ave_spatial.html#index-0">fix ave/spatial</a>
</dt>
<dt><a href="fix_ave_spatial_sphere.html#index-0">fix ave/spatial/sphere</a>
</dt>
<dt><a href="fix_ave_time.html#index-0">fix ave/time</a>
</dt>
<dt><a href="fix_aveforce.html#index-0">fix aveforce</a>
</dt>
<dt><a href="fix_balance.html#index-0">fix balance</a>
</dt>
<dt><a href="fix_bond_break.html#index-0">fix bond/break</a>
</dt>
<dt><a href="fix_bond_create.html#index-0">fix bond/create</a>
</dt>
<dt><a href="fix_bond_swap.html#index-0">fix bond/swap</a>
</dt>
<dt><a href="fix_box_relax.html#index-0">fix box/relax</a>
</dt>
<dt><a href="fix_colvars.html#index-0">fix colvars</a>
</dt>
<dt><a href="fix_deform.html#index-0">fix deform</a>
</dt>
<dt><a href="fix_deposit.html#index-0">fix deposit</a>
</dt>
<dt><a href="fix_drag.html#index-0">fix drag</a>
</dt>
<dt><a href="fix_drude.html#index-0">fix drude</a>
</dt>
<dt><a href="fix_drude_transform.html#index-0">fix drude/transform/direct</a>
</dt>
<dt><a href="fix_dt_reset.html#index-0">fix dt/reset</a>
</dt>
<dt><a href="fix_efield.html#index-0">fix efield</a>
</dt>
<dt><a href="fix_enforce2d.html#index-0">fix enforce2d</a>
</dt>
<dt><a href="fix_evaporate.html#index-0">fix evaporate</a>
</dt>
<dt><a href="fix_external.html#index-0">fix external</a>
</dt>
<dt><a href="fix_freeze.html#index-0">fix freeze</a>
</dt>
<dt><a href="fix_gcmc.html#index-0">fix gcmc</a>
</dt>
<dt><a href="fix_gld.html#index-0">fix gld</a>
</dt>
<dt><a href="fix_gle.html#index-0">fix gle</a>
</dt>
<dt><a href="fix_gravity.html#index-0">fix gravity</a>
</dt>
<dt><a href="fix_heat.html#index-0">fix heat</a>
</dt>
<dt><a href="fix_imd.html#index-0">fix imd</a>
</dt>
<dt><a href="fix_indent.html#index-0">fix indent</a>
</dt>
<dt><a href="fix_ipi.html#index-0">fix ipi</a>
</dt>
<dt><a href="fix_langevin.html#index-0">fix langevin</a>
</dt>
<dt><a href="fix_langevin_drude.html#index-0">fix langevin/drude</a>
</dt>
<dt><a href="fix_langevin_eff.html#index-0">fix langevin/eff</a>
</dt>
<dt><a href="fix_lb_fluid.html#index-0">fix lb/fluid</a>
</dt>
<dt><a href="fix_lb_momentum.html#index-0">fix lb/momentum</a>
</dt>
<dt><a href="fix_lb_pc.html#index-0">fix lb/pc</a>
</dt>
<dt><a href="fix_lb_rigid_pc_sphere.html#index-0">fix lb/rigid/pc/sphere</a>
</dt>
<dt><a href="fix_lb_viscous.html#index-0">fix lb/viscous</a>
</dt>
<dt><a href="fix_lineforce.html#index-0">fix lineforce</a>
</dt>
<dt><a href="fix_meso.html#index-0">fix meso</a>
</dt>
<dt><a href="fix_meso_stationary.html#index-0">fix meso/stationary</a>
</dt>
<dt><a href="fix_momentum.html#index-0">fix momentum</a>
</dt>
<dt><a href="fix_move.html#index-0">fix move</a>
</dt>
<dt><a href="fix_msst.html#index-0">fix msst</a>
</dt>
<dt><a href="fix_neb.html#index-0">fix neb</a>
</dt>
<dt><a href="fix_nph_asphere.html#index-0">fix nph/asphere</a>
</dt>
<dt><a href="fix_nph_sphere.html#index-0">fix nph/sphere</a>
</dt>
<dt><a href="fix_nphug.html#index-0">fix nphug</a>
</dt>
<dt><a href="fix_npt_asphere.html#index-0">fix npt/asphere</a>
</dt>
<dt><a href="fix_npt_sphere.html#index-0">fix npt/sphere</a>
</dt>
<dt><a href="fix_nve.html#index-0">fix nve</a>
</dt>
<dt><a href="fix_nve_asphere.html#index-0">fix nve/asphere</a>
</dt>
<dt><a href="fix_nve_asphere_noforce.html#index-0">fix nve/asphere/noforce</a>
</dt>
<dt><a href="fix_nve_body.html#index-0">fix nve/body</a>
</dt>
<dt><a href="fix_nve_eff.html#index-0">fix nve/eff</a>
</dt>
<dt><a href="fix_nve_limit.html#index-0">fix nve/limit</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="fix_nve_line.html#index-0">fix nve/line</a>
</dt>
<dt><a href="fix_nve_noforce.html#index-0">fix nve/noforce</a>
</dt>
<dt><a href="fix_nve_sphere.html#index-0">fix nve/sphere</a>
</dt>
<dt><a href="fix_nve_tri.html#index-0">fix nve/tri</a>
</dt>
<dt><a href="fix_nh.html#index-0">fix nvt</a>
</dt>
<dt><a href="fix_nvt_asphere.html#index-0">fix nvt/asphere</a>
</dt>
<dt><a href="fix_nh_eff.html#index-0">fix nvt/eff</a>
</dt>
<dt><a href="fix_nvt_sllod.html#index-0">fix nvt/sllod</a>
</dt>
<dt><a href="fix_nvt_sllod_eff.html#index-0">fix nvt/sllod/eff</a>
</dt>
<dt><a href="fix_nvt_sphere.html#index-0">fix nvt/sphere</a>
</dt>
<dt><a href="fix_oneway.html#index-0">fix oneway</a>
</dt>
<dt><a href="fix_orient_fcc.html#index-0">fix orient/fcc</a>
</dt>
<dt><a href="fix_phonon.html#index-0">fix phonon</a>
</dt>
<dt><a href="fix_pimd.html#index-0">fix pimd</a>
</dt>
<dt><a href="fix_planeforce.html#index-0">fix planeforce</a>
</dt>
<dt><a href="fix_pour.html#index-0">fix pour</a>
</dt>
<dt><a href="fix_press_berendsen.html#index-0">fix press/berendsen</a>
</dt>
<dt><a href="fix_print.html#index-0">fix print</a>
</dt>
<dt><a href="fix_property_atom.html#index-0">fix property/atom</a>
</dt>
<dt><a href="fix_qbmsst.html#index-0">fix qbmsst</a>
</dt>
<dt><a href="fix_qeq_comb.html#index-0">fix qeq/comb</a>
</dt>
<dt><a href="fix_qeq.html#index-0">fix qeq/point</a>
</dt>
<dt><a href="fix_qeq_reax.html#index-0">fix qeq/reax</a>
</dt>
<dt><a href="fix_qmmm.html#index-0">fix qmmm</a>
</dt>
<dt><a href="fix_qtb.html#index-0">fix qtb</a>
</dt>
<dt><a href="fix_reax_bonds.html#index-0">fix reax/bonds</a>
</dt>
<dt><a href="fix_reaxc_species.html#index-0">fix reax/c/species</a>
</dt>
<dt><a href="fix_recenter.html#index-0">fix recenter</a>
</dt>
<dt><a href="fix_restrain.html#index-0">fix restrain</a>
</dt>
<dt><a href="fix_rigid.html#index-0">fix rigid</a>
</dt>
<dt><a href="fix_saed_vtk.html#index-0">fix saed/vtk</a>
</dt>
<dt><a href="fix_setforce.html#index-0">fix setforce</a>
</dt>
<dt><a href="fix_shake.html#index-0">fix shake</a>
</dt>
<dt><a href="fix_smd.html#index-0">fix smd</a>
</dt>
<dt><a href="fix_smd_adjust_dt.html#index-0">fix smd/adjust_dt</a>
</dt>
<dt><a href="fix_smd_integrate_tlsph.html#index-0">fix smd/integrate_tlsph</a>
</dt>
<dt><a href="fix_smd_integrate_ulsph.html#index-0">fix smd/integrate_ulsph</a>
</dt>
<dt><a href="fix_smd_move_triangulated_surface.html#index-0">fix smd/move_tri_surf</a>
</dt>
<dt><a href="fix_smd_setvel.html#index-0">fix smd/setvel</a>
</dt>
<dt><a href="fix_smd_wall_surface.html#index-0">fix smd/wall_surface</a>
</dt>
<dt><a href="fix_spring.html#index-0">fix spring</a>
</dt>
<dt><a href="fix_spring_rg.html#index-0">fix spring/rg</a>
</dt>
<dt><a href="fix_spring_self.html#index-0">fix spring/self</a>
</dt>
<dt><a href="fix_srd.html#index-0">fix srd</a>
</dt>
<dt><a href="fix_store_force.html#index-0">fix store/force</a>
</dt>
<dt><a href="fix_store_state.html#index-0">fix store/state</a>
</dt>
<dt><a href="fix_temp_berendsen.html#index-0">fix temp/berendsen</a>
</dt>
<dt><a href="fix_temp_csvr.html#index-0">fix temp/csvr</a>
</dt>
<dt><a href="fix_temp_rescale.html#index-0">fix temp/rescale</a>
</dt>
<dt><a href="fix_temp_rescale_eff.html#index-0">fix temp/rescale/eff</a>
</dt>
<dt><a href="fix_tfmc.html#index-0">fix tfmc</a>
</dt>
<dt><a href="fix_thermal_conductivity.html#index-0">fix thermal/conductivity</a>
</dt>
<dt><a href="fix_ti_rs.html#index-0">fix ti/rs</a>
</dt>
<dt><a href="fix_ti_spring.html#index-0">fix ti/spring</a>
</dt>
<dt><a href="fix_tmd.html#index-0">fix tmd</a>
</dt>
<dt><a href="fix_ttm.html#index-0">fix ttm</a>
</dt>
<dt><a href="fix_tune_kspace.html#index-0">fix tune/kspace</a>
</dt>
<dt><a href="fix_vector.html#index-0">fix vector</a>
</dt>
<dt><a href="fix_viscosity.html#index-0">fix viscosity</a>
</dt>
<dt><a href="fix_viscous.html#index-0">fix viscous</a>
</dt>
<dt><a href="fix_wall_gran.html#index-0">fix wall/gran</a>
</dt>
<dt><a href="fix_wall.html#index-0">fix wall/lj93</a>
</dt>
<dt><a href="fix_wall_piston.html#index-0">fix wall/piston</a>
</dt>
<dt><a href="fix_wall_reflect.html#index-0">fix wall/reflect</a>
</dt>
<dt><a href="fix_wall_region.html#index-0">fix wall/region</a>
</dt>
<dt><a href="fix_wall_srd.html#index-0">fix wall/srd</a>
</dt>
<dt><a href="fix_modify.html#index-0">fix_modify</a>
</dt>
</dl></td>
</tr></table>
<h2 id="G">G</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="group.html#index-0">group</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="group2ndx.html#index-0">group2ndx</a>
</dt>
</dl></td>
</tr></table>
<h2 id="I">I</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="if.html#index-0">if</a>
</dt>
<dt><a href="improper_coeff.html#index-0">improper_coeff</a>
</dt>
<dt><a href="improper_style.html#index-0">improper_style</a>
</dt>
<dt><a href="improper_class2.html#index-0">improper_style class2</a>
</dt>
<dt><a href="improper_cossq.html#index-0">improper_style cossq</a>
</dt>
<dt><a href="improper_cvff.html#index-0">improper_style cvff</a>
</dt>
<dt><a href="improper_fourier.html#index-0">improper_style fourier</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="improper_harmonic.html#index-0">improper_style harmonic</a>
</dt>
<dt><a href="improper_hybrid.html#index-0">improper_style hybrid</a>
</dt>
<dt><a href="improper_none.html#index-0">improper_style none</a>
</dt>
<dt><a href="improper_ring.html#index-0">improper_style ring</a>
</dt>
<dt><a href="improper_umbrella.html#index-0">improper_style umbrella</a>
</dt>
<dt><a href="include.html#index-0">include</a>
</dt>
<dt><a href="info.html#index-0">info</a>
</dt>
</dl></td>
</tr></table>
<h2 id="J">J</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="jump.html#index-0">jump</a>
</dt>
</dl></td>
</tr></table>
<h2 id="K">K</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="kspace_modify.html#index-0">kspace_modify</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="kspace_style.html#index-0">kspace_style</a>
</dt>
</dl></td>
</tr></table>
<h2 id="L">L</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="label.html#index-0">label</a>
</dt>
<dt><a href="lattice.html#index-0">lattice</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="log.html#index-0">log</a>
</dt>
</dl></td>
</tr></table>
<h2 id="M">M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="mass.html#index-0">mass</a>
</dt>
<dt><a href="min_modify.html#index-0">min_modify</a>
</dt>
<dt><a href="min_style.html#index-0">min_style</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="minimize.html#index-0">minimize</a>
</dt>
<dt><a href="molecule.html#index-0">molecule</a>
</dt>
</dl></td>
</tr></table>
<h2 id="N">N</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="neb.html#index-0">neb</a>
</dt>
<dt><a href="neigh_modify.html#index-0">neigh_modify</a>
</dt>
<dt><a href="neighbor.html#index-0">neighbor</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="newton.html#index-0">newton</a>
</dt>
<dt><a href="next.html#index-0">next</a>
</dt>
</dl></td>
</tr></table>
<h2 id="P">P</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="package.html#index-0">package</a>
</dt>
<dt><a href="pair_coeff.html#index-0">pair_coeff</a>
</dt>
<dt><a href="pair_modify.html#index-0">pair_modify</a>
</dt>
<dt><a href="pair_style.html#index-0">pair_style</a>
</dt>
<dt><a href="pair_adp.html#index-0">pair_style adp</a>
</dt>
<dt><a href="pair_airebo.html#index-0">pair_style airebo</a>
</dt>
<dt><a href="pair_awpmd.html#index-0">pair_style awpmd/cut</a>
</dt>
<dt><a href="pair_beck.html#index-0">pair_style beck</a>
</dt>
<dt><a href="pair_body.html#index-0">pair_style body</a>
</dt>
<dt><a href="pair_bop.html#index-0">pair_style bop</a>
</dt>
<dt><a href="pair_born.html#index-0">pair_style born</a>
</dt>
<dt><a href="pair_cs.html#index-0">pair_style born/coul/long/cs</a>
</dt>
<dt><a href="pair_brownian.html#index-0">pair_style brownian</a>
</dt>
<dt><a href="pair_buck.html#index-0">pair_style buck</a>
</dt>
<dt><a href="pair_buck_long.html#index-0">pair_style buck/long/coul/long</a>
</dt>
<dt><a href="pair_colloid.html#index-0">pair_style colloid</a>
</dt>
<dt><a href="pair_comb.html#index-0">pair_style comb</a>
</dt>
<dt><a href="pair_coul.html#index-0">pair_style coul/cut</a>
</dt>
<dt><a href="pair_coul_diel.html#index-0">pair_style coul/diel</a>
</dt>
<dt><a href="pair_dpd.html#index-0">pair_style dpd</a>
</dt>
<dt><a href="pair_dsmc.html#index-0">pair_style dsmc</a>
</dt>
<dt><a href="pair_eam.html#index-0">pair_style eam</a>
</dt>
<dt><a href="pair_edip.html#index-0">pair_style edip</a>
</dt>
<dt><a href="pair_eff.html#index-0">pair_style eff/cut</a>
</dt>
<dt><a href="pair_eim.html#index-0">pair_style eim</a>
</dt>
<dt><a href="pair_gauss.html#index-0">pair_style gauss</a>
</dt>
<dt><a href="pair_gayberne.html#index-0">pair_style gayberne</a>
</dt>
<dt><a href="pair_gran.html#index-0">pair_style gran/hooke</a>
</dt>
<dt><a href="pair_hbond_dreiding.html#index-0">pair_style hbond/dreiding/lj</a>
</dt>
<dt><a href="pair_hybrid.html#index-0">pair_style hybrid</a>
</dt>
<dt><a href="pair_kim.html#index-0">pair_style kim</a>
</dt>
<dt><a href="pair_lcbop.html#index-0">pair_style lcbop</a>
</dt>
<dt><a href="pair_line_lj.html#index-0">pair_style line/lj</a>
</dt>
<dt><a href="pair_list.html#index-0">pair_style list</a>
</dt>
<dt><a href="pair_charmm.html#index-0">pair_style lj/charmm/coul/charmm</a>
</dt>
<dt><a href="pair_class2.html#index-0">pair_style lj/class2</a>
</dt>
<dt><a href="pair_lj_cubic.html#index-0">pair_style lj/cubic</a>
</dt>
<dt><a href="pair_lj.html#index-0">pair_style lj/cut</a>
</dt>
<dt><a href="pair_dipole.html#index-0">pair_style lj/cut/dipole/cut</a>
</dt>
<dt><a href="pair_lj_soft.html#index-0">pair_style lj/cut/soft</a>
</dt>
<dt><a href="pair_lj_expand.html#index-0">pair_style lj/expand</a>
</dt>
<dt><a href="pair_gromacs.html#index-0">pair_style lj/gromacs</a>
</dt>
<dt><a href="pair_lj_long.html#index-0">pair_style lj/long/coul/long</a>
</dt>
<dt><a href="pair_sdk.html#index-0">pair_style lj/sdk</a>
</dt>
<dt><a href="pair_lj_sf.html#index-0">pair_style lj/sf</a>
</dt>
<dt><a href="pair_lj_smooth.html#index-0">pair_style lj/smooth</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="pair_lj_smooth_linear.html#index-0">pair_style lj/smooth/linear</a>
</dt>
<dt><a href="pair_lj96.html#index-0">pair_style lj96/cut</a>
</dt>
<dt><a href="pair_lubricate.html#index-0">pair_style lubricate</a>
</dt>
<dt><a href="pair_lubricateU.html#index-0">pair_style lubricateU</a>
</dt>
<dt><a href="pair_meam.html#index-0">pair_style meam</a>
</dt>
<dt><a href="pair_mie.html#index-0">pair_style mie/cut</a>
</dt>
<dt><a href="pair_morse.html#index-0">pair_style morse</a>
</dt>
<dt><a href="pair_nb3b_harmonic.html#index-0">pair_style nb3b/harmonic</a>
</dt>
<dt><a href="pair_nm.html#index-0">pair_style nm/cut</a>
</dt>
<dt><a href="pair_none.html#index-0">pair_style none</a>
</dt>
<dt><a href="pair_peri.html#index-0">pair_style peri/pmb</a>
</dt>
<dt><a href="pair_polymorphic.html#index-0">pair_style polymorphic</a>
</dt>
<dt><a href="pair_quip.html#index-0">pair_style quip</a>
</dt>
<dt><a href="pair_reax.html#index-0">pair_style reax</a>
</dt>
<dt><a href="pair_reax_c.html#index-0">pair_style reax/c</a>
</dt>
<dt><a href="pair_resquared.html#index-0">pair_style resquared</a>
</dt>
<dt><a href="pair_smd_hertz.html#index-0">pair_style smd/hertz</a>
</dt>
<dt><a href="pair_smd_tlsph.html#index-0">pair_style smd/tlsph</a>
</dt>
<dt><a href="pair_smd_triangulated_surface.html#index-0">pair_style smd/tri_surface</a>
</dt>
<dt><a href="pair_smd_ulsph.html#index-0">pair_style smd/ulsph</a>
</dt>
<dt><a href="pair_snap.html#index-0">pair_style snap</a>
</dt>
<dt><a href="pair_soft.html#index-0">pair_style soft</a>
</dt>
<dt><a href="pair_sph_heatconduction.html#index-0">pair_style sph/heatconduction</a>
</dt>
<dt><a href="pair_sph_idealgas.html#index-0">pair_style sph/idealgas</a>
</dt>
<dt><a href="pair_sph_lj.html#index-0">pair_style sph/lj</a>
</dt>
<dt><a href="pair_sph_rhosum.html#index-0">pair_style sph/rhosum</a>
</dt>
<dt><a href="pair_sph_taitwater.html#index-0">pair_style sph/taitwater</a>
</dt>
<dt><a href="pair_sph_taitwater_morris.html#index-0">pair_style sph/taitwater/morris</a>
</dt>
<dt><a href="pair_srp.html#index-0">pair_style srp</a>
</dt>
<dt><a href="pair_sw.html#index-0">pair_style sw</a>
</dt>
<dt><a href="pair_table.html#index-0">pair_style table</a>
</dt>
<dt><a href="pair_tersoff.html#index-0">pair_style tersoff</a>
</dt>
<dt><a href="pair_tersoff_mod.html#index-0">pair_style tersoff/mod</a>
</dt>
<dt><a href="pair_tersoff_zbl.html#index-0">pair_style tersoff/zbl</a>
</dt>
<dt><a href="pair_thole.html#index-0">pair_style thole</a>
</dt>
<dt><a href="pair_tri_lj.html#index-0">pair_style tri/lj</a>
</dt>
+ <dt><a href="pair_vashishta.html#index-0">pair_style vashishta</a>
+ </dt>
+
+
<dt><a href="pair_yukawa.html#index-0">pair_style yukawa</a>
</dt>
<dt><a href="pair_yukawa_colloid.html#index-0">pair_style yukawa/colloid</a>
</dt>
<dt><a href="pair_zbl.html#index-0">pair_style zbl</a>
</dt>
<dt><a href="pair_write.html#index-0">pair_write</a>
</dt>
<dt><a href="partition.html#index-0">partition</a>
</dt>
<dt><a href="prd.html#index-0">prd</a>
</dt>
<dt><a href="print.html#index-0">print</a>
</dt>
<dt><a href="processors.html#index-0">processors</a>
</dt>
<dt><a href="python.html#index-0">python</a>
</dt>
</dl></td>
</tr></table>
<h2 id="Q">Q</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="quit.html#index-0">quit</a>
</dt>
</dl></td>
</tr></table>
<h2 id="R">R</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="read_data.html#index-0">read_data</a>
</dt>
<dt><a href="read_dump.html#index-0">read_dump</a>
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<dt><a href="region.html#index-0">region</a>
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</dt>
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<td style="width: 33%" valign="top"><dl>
<dt><a href="rerun.html#index-0">rerun</a>
</dt>
<dt><a href="reset_timestep.html#index-0">reset_timestep</a>
</dt>
<dt><a href="restart.html#index-0">restart</a>
</dt>
<dt><a href="run.html#index-0">run</a>
</dt>
<dt><a href="run_style.html#index-0">run_style</a>
</dt>
</dl></td>
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<h2 id="S">S</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="set.html#index-0">set</a>
</dt>
<dt><a href="shell.html#index-0">shell</a>
</dt>
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<td style="width: 33%" valign="top"><dl>
<dt><a href="special_bonds.html#index-0">special_bonds</a>
</dt>
<dt><a href="suffix.html#index-0">suffix</a>
</dt>
</dl></td>
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<h2 id="T">T</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="tad.html#index-0">tad</a>
</dt>
<dt><a href="temper.html#index-0">temper</a>
</dt>
<dt><a href="thermo.html#index-0">thermo</a>
</dt>
<dt><a href="thermo_modify.html#index-0">thermo_modify</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="thermo_style.html#index-0">thermo_style</a>
</dt>
<dt><a href="timer.html#index-0">timer</a>
</dt>
<dt><a href="timestep.html#index-0">timestep</a>
</dt>
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<td style="width: 33%" valign="top"><dl>
<dt><a href="uncompute.html#index-0">uncompute</a>
</dt>
<dt><a href="undump.html#index-0">undump</a>
</dt>
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<td style="width: 33%" valign="top"><dl>
<dt><a href="unfix.html#index-0">unfix</a>
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<dt><a href="units.html#index-0">units</a>
</dt>
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<td style="width: 33%" valign="top"><dl>
<dt><a href="variable.html#index-0">variable</a>
</dt>
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<td style="width: 33%" valign="top"><dl>
<dt><a href="velocity.html#index-0">velocity</a>
</dt>
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<td style="width: 33%" valign="top"><dl>
<dt><a href="write_data.html#index-0">write_data</a>
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diff --git a/doc/doc2/molecule.html b/doc/doc2/molecule.html
index 15f8df52c..120683933 100644
--- a/doc/doc2/molecule.html
+++ b/doc/doc2/molecule.html
@@ -1,444 +1,473 @@
<HTML>
<CENTER><<A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>molecule command
</H3>
<P><B>Syntax:</B>
</P>
-<PRE>molecule ID file1 file2 ... keyword values ...
+<PRE>molecule ID file1 keyword values ... file2 keyword values ... fileN ...
</PRE>
<UL><LI>ID = user-assigned name for the molecule template
<LI>file1,file2,... = names of files containing molecule descriptions
-<LI>zero or more keyword/value pairs may be appended
+<LI>zero or more keyword/value pairs may be appended after each file
-<LI>keyword = <I>offset</I>
+<LI>keyword = <I>offset</I> or <I>toff</I> or <I>boff</I> or <I>aoff</I> or <I>doff</I> or <I>ioff</I> or <I>scale</I>
-<PRE> <I>offset</I> values = toff boff aoff doff ioff
- toff = offset to add to atom types
- boff = offset to add to bond types
- aoff = offset to add to angle types
- doff = offset to add to dihedral types
- ioff = offset to add to improper types
+<PRE> <I>offset</I> values = Toff Boff Aoff Doff Ioff
+ Toff = offset to add to atom types
+ Boff = offset to add to bond types
+ Aoff = offset to add to angle types
+ Doff = offset to add to dihedral types
+ Ioff = offset to add to improper types
+ <I>toff</I> value = Toff
+ Toff = offset to add to atom types
+ <I>boff</I> value = Boff
+ Boff = offset to add to bond types
+ <I>aoff</I> value = Aoff
+ Aoff = offset to add to angle types
+ <I>doff</I> value = Doff
+ Doff = offset to add to dihedral types
+ <I>ioff</I> value = Ioff
+ Ioff = offset to add to improper types
+ <I>scale</I> value = sfactor
+ sfactor = scale factor to apply to the size and mass of the molecule
</PRE>
</UL>
<P><B>Examples:</B>
</P>
-<PRE>molecule 1 mymol
+<PRE>molecule 1 mymol.txt
molecule 1 co2.txt h2o.txt
-molecule CO2 co2.txt
-molecule 1 mymol offset 6 9 18 23 14
+molecule CO2 co2.txt boff 3 aoff 2
+molecule 1 mymol.txt offset 6 9 18 23 14
+molecule objects file.1 scale 1.5 file.1 scale 2.0 file.2 scale 1.3
+</PRE>
+<PRE>
</PRE>
<P><B>Description:</B>
</P>
<P>Define a molecule template that can be used as part of other LAMMPS
commands, typically to define a collection of particles as a bonded
molecule or a rigid body. Commands that currently use molecule
templates include:
</P>
<UL><LI><A HREF = "fix_deposit.html">fix deposit</A>
<LI><A HREF = "fix_pour.html">fix pour</A>
<LI><A HREF = "fix_rigid.html">fix rigid/small</A>
<LI><A HREF = "fix_shake.html">fix shake</A>
<LI><A HREF = "fix_gcmc.html">fix gcmc</A>
<LI><A HREF = "create_atoms.html">create_atoms</A>
<LI><A HREF = "atom_style.html">atom_style template</A>
</UL>
<P>The ID of a molecule template can only contain alphanumeric characters
and underscores.
</P>
<P>A single template can contain multiple molecules, listed one per file.
-Many of the commands listed above currently use only the first
+Some of the commands listed above currently use only the first
molecule in the template, and will issue a warning if the template
contains multiple molecules. The <A HREF = "atom_style.html">atom_style
template</A> command allows multiple-molecule templates
to define a system with more than one templated molecule.
</P>
-<P>The optional <I>offset</I> keyword adds the specified offset values to the
-atom types, bond types, angle types, dihedral types, and improper
-types as they are read from the molecule file. E.g. if <I>toff</I> = 2,
-and the file uses atom types 1,2,3, then each created molecule will
-have atom types 3,4,5. This is to make it easy to use the same
-molecule template file in different simulations. Note that the same
-offsets are applied to the molecules in all specified files. All five
-offset values must be speicified, but individual values will be
-ignored if the molecule template does not use that attribute (e.g. no
-bonds).
-</P>
-<P>IMPORTANT NOTE: This command can be used to define molecules with
-bonds, angles, dihedrals, imporopers, or special bond lists of
+<P>Each filename can be followed by optional keywords which are applied
+only to the molecule in the file as used in this template. This is to
+make it easy to use the same molecule file in different molecule
+templates or in different simulations. You can specify the same file
+multiple times with different optional keywords.
+</P>
+<P>The <I>offset</I>, <I>toff</I>, <I>aoff</I>, <I>doff</I>, <I>ioff</I> keywords add the
+specified offset values to the atom types, bond types, angle types,
+dihedral types, and/or improper types as they are read from the
+molecule file. E.g. if <I>toff</I> = 2, and the file uses atom types
+1,2,3, then each created molecule will have atom types 3,4,5. For the
+<I>offset</I> keyword, all five offset values must be specified, but
+individual values will be ignored if the molecule template does not
+use that attribute (e.g. no bonds).
+</P>
+<P>The <I>scale</I> keyword scales the size of the molecule. This can be
+useful for modeling polydisperse granular rigid bodies. The scale
+factor is applied to each of these properties in the molecule file, if
+they are defined: the individual particle coordinates (Coords
+section), the individual mass of each particle (Masses section), the
+individual diameters of each particle (Diameters section), the total
+mass of the molecule (header keyword = mass), the center-of-mass of
+the molecule (header keyword = com), and the moments of inertia of the
+molecule (header keyword = inertia).
+</P>
+<P>IMPORTANT NOTE: The molecule command can be used to define molecules
+with bonds, angles, dihedrals, imporopers, or special bond lists of
neighbors within a molecular topology, so that you can later add the
molecules to your simulation, via one or more of the commands listed
above. If such molecules do not already exist when LAMMPS creates the
simulation box, via the <A HREF = "create_box.html">create_box</A> or
<A HREF = "read_data.html">read_data</A> command, when you later add them you may
overflow the pre-allocated data structures which store molecular
topology information with each atom, and an error will be generated.
Both the <A HREF = "create_box.html">create_box</A> command and the data files read
by the <A HREF = "read_data.html">read_data</A> command have "extra" options which
insure space is allocated for storing topology info for molecules that
are added later.
</P>
<P>The format of an individual molecule file is similar to the data file
read by the <A HREF = "read_data.html">read_data</A> commands, and is as follows.
</P>
<P>A molecule file has a header and a body. The header appears first.
The first line of the header is always skipped; it typically contains
a description of the file. Then lines are read one at a time. Lines
can have a trailing comment starting with '#' that is ignored. If the
line is blank (only whitespace after comment is deleted), it is
skipped. If the line contains a header keyword, the corresponding
value(s) is read from the line. If it doesn't contain a header
keyword, the line begins the body of the file.
</P>
<P>The body of the file contains zero or more sections. The first line
of a section has only a keyword. The next line is skipped. The
remaining lines of the section contain values. The number of lines
depends on the section keyword as described below. Zero or more blank
lines can be used between sections. Sections can appear in any order,
with a few exceptions as noted below.
</P>
<P>These are the recognized header keywords. Header lines can come in
any order. The numeric value(s) are read from the beginning of the
line. The keyword should appear at the end of the line. All these
settings have default values, as explained below. A line need only
appear if the value(s) are different than the default.
</P>
<UL><LI>N <I>atoms</I> = # of atoms N in molecule, default = 0
<LI>Nb <I>bonds</I> = # of bonds Nb in molecule, default = 0
<LI>Na <I>angles</I> = # of angles Na in molecule, default = 0
<LI>Nd <I>dihedrals</I> = # of dihedrals Nd in molecule, default = 0
<LI>Ni <I>impropers</I> = # of impropers Ni in molecule, default = 0
<LI>Mtotal <I>mass</I> = total mass of molecule
<LI>Xc Yc Zc <I>com</I> = coordinates of center-of-mass of molecule
<LI>Ixx Iyy Izz Ixy Ixz Iyz <I>inertia</I> = 6 components of inertia tensor of molecule
</UL>
<P>For <I>mass</I>, <I>com</I>, and <I>inertia</I>, the default is for LAMMPS to
calculate this quantity itself if needed, assuming the molecules
consists of a set of point particles or finite-size particles (with a
non-zero diameter) that do not overlap. If finite-size particles in
the molecule do overlap, LAMMPS will not account for the overlap
effects when calculating any of these 3 quantities, so you should
pre-compute them yourself and list the values in the file.
</P>
<P>The mass and center-of-mass coordinates (Xc,Yc,Zc) are
self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)
should be the values consistent with the current orientation of the
rigid body around its center of mass. The values are with respect to
the simulation box XYZ axes, not with respect to the prinicpal axes of
the rigid body itself. LAMMPS performs the latter calculation
internally.
</P>
<P>These are the allowed section keywords for the body of the file.
</P>
<UL><LI><I>Coords, Types, Charges, Diameters, Masses</I> = atom-property sections
<LI><I>Bonds, Angles, Dihedrals, Impropers</I> = molecular topology sections
<LI><I>Special Bond Counts, Special Bonds</I> = special neighbor info
<LI><I>Shake Flags, Shake Atoms, Shake Bond Types</I> = SHAKE info
</UL>
<P>If a Bonds section is specified then the Special Bond Counts and
Special Bonds sections can also be used, if desired, to explicitly
list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see
details below). This is optional since if these sections are not
included, LAMMPS will auto-generate this information. Note that
LAMMPS uses this info to properly exclude or weight bonded pairwise
interactions between bonded atoms. See the
<A HREF = "special_bonds.html">special_bonds</A> command for more details. One
reason to list the special bond info explicitly is for the
<A HREF = "tutorial_drude.html">thermalized Drude oscillator model</A> which treats
the bonds between nuclear cores and Drude electrons in a different
manner.
</P>
<P>IMPORTANT NOTE: Whether a section is required depends on how the
molecule template is used by other LAMMPS commands. For example, to
add a molecule via the <A HREF = "fix_deposit.html">fix deposit</A> command, the
Coords and Types sections are required. To add a rigid body via the
<A HREF = "fix_pout.html">fix pour</A> command, the Bonds (Angles, etc) sections are
not required, since the molecule will be treated as a rigid body.
Some sections are optional. For example, the <A HREF = "fix_pour.html">fix pour</A>
command can be used to add "molecules" which are clusters of
finite-size granular particles. If the Diameters section is not
specified, each particle in the molecule will have a default diameter
of 1.0. See the doc pages for LAMMPS commands that use molecule
templates for more details.
</P>
<P>Each section is listed below in alphabetic order. The format of each
section is described including the number of lines it must contain and
rules (if any) for whether it can appear in the data file. In each
case the ID is ignored; it is simply included for readability, and
should be a number from 1 to Nlines for the section, indicating which
atom (or bond, etc) the entry applies to. The lines are assumed to be
listed in order from 1 to Nlines, but LAMMPS does not check for this.
</P>
<HR>
<P><I>Coords</I> section:
</P>
<UL><LI>one line per atom
<LI>line syntax: ID x y z
<LI>x,y,z = coordinate of atom
</UL>
<HR>
<P><I>Types</I> section:
</P>
<UL><LI>one line per atom
<LI>line syntax: ID type
<LI>type = atom type of atom
</UL>
<HR>
<P><I>Charges</I> section:
</P>
<UL><LI>one line per atom
<LI>line syntax: ID q
<LI>q = charge on atom
</UL>
<P>This section is only allowed for <A HREF = "atom_style.html">atom styles</A> that
support charge. If this section is not included, the default charge
on each atom in the molecule is 0.0.
</P>
<HR>
<P><I>Diameters</I> section:
</P>
<UL><LI>one line per atom
<LI>line syntax: ID diam
<LI>diam = diameter of atom
</UL>
<P>This section is only allowed for <A HREF = "atom_style.html">atom styles</A> that
support finite-size spherical particles, e.g. atom_style sphere. If
not listed, the default diameter of each atom in the molecule is 1.0.
</P>
<HR>
<P><I>Masses</I> section:
</P>
<UL><LI>one line per atom
<LI>line syntax: ID mass
<LI>mass = mass of atom
</UL>
<P>This section is only allowed for <A HREF = "atom_style.html">atom styles</A> that
support per-atom mass, as opposed to per-type mass. See the
<A HREF = "mass.html">mass</A> command for details. If this section is not
included, the default mass for each atom is derived from its volume
(see Diameters section) and a default density of 1.0, in
<A HREF = "units.html">units</A> of mass/volume.
</P>
<HR>
<P><I>Bonds</I> section:
</P>
<UL><LI>one line per bond
<LI>line syntax: ID type atom1 atom2
<LI>type = bond type (1-Nbondtype)
<LI>atom1,atom2 = IDs of atoms in bond
</UL>
<P>The IDs for the two atoms in each bond should be values
from 1 to Natoms, where Natoms = # of atoms in the molecule.
</P>
<HR>
<P><I>Angles</I> section:
</P>
<UL><LI>one line per angle
<LI>line syntax: ID type atom1 atom2 atom3
<LI>type = angle type (1-Nangletype)
<LI>atom1,atom2,atom3 = IDs of atoms in angle
</UL>
<P>The IDs for the three atoms in each angle should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule. The 3 atoms are
ordered linearly within the angle. Thus the central atom (around
which the angle is computed) is the atom2 in the list.
</P>
<HR>
<P><I>Dihedrals</I> section:
</P>
<UL><LI>one line per dihedral
<LI>line syntax: ID type atom1 atom2 atom3 atom4
<LI>type = dihedral type (1-Ndihedraltype)
<LI>atom1,atom2,atom3,atom4 = IDs of atoms in dihedral
</UL>
<P>The IDs for the four atoms in each dihedral should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule. The 4 atoms are
ordered linearly within the dihedral.
</P>
<HR>
<P><I>Impropers</I> section:
</P>
<UL><LI>one line per improper
<LI>line syntax: ID type atom1 atom2 atom3 atom4
<LI>type = improper type (1-Nimpropertype)
<LI>atom1,atom2,atom3,atom4 = IDs of atoms in improper
</UL>
<P>The IDs for the four atoms in each improper should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule. The ordering of
the 4 atoms determines the definition of the improper angle used in
the formula for the defined <A HREF = "improper_style.html">improper style</A>. See
the doc pages for individual styles for details.
</P>
<HR>
<P><I>Special Bond Counts</I> section:
</P>
<UL><LI>one line per atom
<LI>line syntax: ID N1 N2 N3
<LI>N1 = # of 1-2 bonds
<LI>N2 = # of 1-3 bonds
<LI>N3 = # of 1-4 bonds
</UL>
<P>N1, N2, N3 are the number of 1-2, 1-3, 1-4 neighbors respectively of
this atom within the topology of the molecule. See the
<A HREF = "special_bonds.html">special_bonds</A> doc page for more discussion of
1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds
section must also appear. If this section is not specied, the
atoms in the molecule will have no special bonds.
</P>
<HR>
<P><I>Special Bonds</I> section:
</P>
<UL><LI>one line per atom
<LI>line syntax: ID a b c d ...
<LI>a,b,c,d,... = IDs of atoms in N1+N2+N3 special bonds
</UL>
<P>A, b, c, d, etc are the IDs of the n1+n2+n3 atoms that are 1-2, 1-3,
1-4 neighbors of this atom. The IDs should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule. The first N1
values should be the 1-2 neighbors, the next N2 should be the 1-3
neighbors, the last N3 should be the 1-4 neighbors. No atom ID should
appear more than once. See the <A HREF = "special_bonds.html">special_bonds</A> doc
page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section
appears, the Special Bond Counts section must also appear. If this
section is not specied, the atoms in the molecule will have no special
bonds.
</P>
<HR>
<P><I>Shake Flags</I> section:
</P>
<UL><LI>one line per atom
<LI>line syntax: ID flag
<LI>flag = 0,1,2,3,4
</UL>
<P>This section is only needed when molecules created using the template
will be constrained by SHAKE via the "fix shake" command. The other
two Shake sections must also appear in the file, following this one.
</P>
<P>The meaning of the flag for each atom is as follows. See the <A HREF = "fix_shake.html">fix
shake</A> doc page for a further description of SHAKE
clusters.
</P>
<UL><LI>0 = not part of a SHAKE cluster
<LI>1 = part of a SHAKE angle cluster (two bonds and the angle they form)
<LI>2 = part of a 2-atom SHAKE cluster with a single bond
<LI>3 = part of a 3-atom SHAKE cluster with two bonds
<LI>4 = part of a 4-atom SHAKE cluster with three bonds
</UL>
<HR>
<P><I>Shake Atoms</I> section:
</P>
<UL><LI>one line per atom
<LI>line syntax: ID a b c d
<LI>a,b,c,d = IDs of atoms in cluster
</UL>
<P>This section is only needed when molecules created using the template
will be constrained by SHAKE via the "fix shake" command. The other
two Shake sections must also appear in the file.
</P>
<P>The a,b,c,d values are atom IDs (from 1 to Natoms) for all the atoms
in the SHAKE cluster that this atom belongs to. The number of values
that must appear is determined by the shake flag for the atom (see the
Shake Flags section above). All atoms in a particular cluster should
list their a,b,c,d values identically.
</P>
<P>If flag = 0, no a,b,c,d values are listed on the line, just the
(ignored) ID.
</P>
<P>If flag = 1, a,b,c are listed, where a = ID of central atom in the
angle, and b,c the other two atoms in the angle.
</P>
<P>If flag = 2, a,b are listed, where a = ID of atom in bond with the the
lowest ID, and b = ID of atom in bond with the highest ID.
</P>
<P>If flag = 3, a,b,c are listed, where a = ID of central atom,
and b,c = IDs of other two atoms bonded to the central atom.
</P>
<P>If flag = 4, a,b,c,d are listed, where a = ID of central atom,
and b,c,d = IDs of other three atoms bonded to the central atom.
</P>
<P>See the <A HREF = "fix_shake.html">fix shake</A> doc page for a further description
of SHAKE clusters.
</P>
<HR>
<P><I>Shake Bond Types</I> section:
</P>
<UL><LI>one line per atom
<LI>line syntax: ID a b c
<LI>a,b,c = bond types (or angle type) of bonds (or angle) in cluster
</UL>
<P>This section is only needed when molecules created using the template
will be constrained by SHAKE via the "fix shake" command. The other
two Shake sections must also appear in the file.
</P>
<P>The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds
in the SHAKE cluster that this atom belongs to. The number of values
that must appear is determined by the shake flag for the atom (see the
Shake Flags section above). All atoms in a particular cluster should
list their a,b,c values identically.
</P>
<P>If flag = 0, no a,b,c values are listed on the line, just the
(ignored) ID.
</P>
<P>If flag = 1, a,b,c are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), b = bondtype of the bond between the central atom and
the 2nd non-central atom (value c in the Shake Atoms section), and c =
the angle type (1 to Nangletypes) of the angle between the 3 atoms.
</P>
<P>If flag = 2, only a is listed, where a = bondtype of the bond between
the 2 atoms in the cluster.
</P>
<P>If flag = 3, a,b are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), and b = bondtype of the bond between the central atom
and the 2nd non-central atom (value c in the Shake Atoms section).
</P>
<P>If flag = 4, a,b,c are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), b = bondtype of the bond between the central atom and
the 2nd non-central atom (value c in the Shake Atoms section), and c =
bondtype of the bond between the central atom and the 3rd non-central
atom (value d in the Shake Atoms section).
</P>
<P>See the <A HREF = "fix_shake.html">fix shake</A> doc page for a further description
of SHAKE clusters.
</P>
<HR>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_deposit.html">fix deposit</A>, <A HREF = "fix_pour.html">fix pour</A>,
<A HREF = "fix_gcmc.html">fix_gcmc</A>
</P>
<P><B>Default:</B>
</P>
-<P>The default keyword value is offset 0 0 0 0 0.
+<P>The default keywords values are offset 0 0 0 0 0 and scale = 1.0.
</P>
</HTML>
diff --git a/doc/doc2/pair_hybrid.html b/doc/doc2/pair_hybrid.html
index 4782685fe..9815d08fb 100644
--- a/doc/doc2/pair_hybrid.html
+++ b/doc/doc2/pair_hybrid.html
@@ -1,387 +1,390 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style hybrid command
</H3>
<H3>pair_style hybrid/omp command
</H3>
<H3>pair_style hybrid/overlay command
</H3>
<H3>pair_style hybrid/overlay/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style hybrid style1 args style2 args ...
pair_style hybrid/overlay style1 args style2 args ...
</PRE>
<UL><LI>style1,style2 = list of one or more pair styles and their arguments
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0
pair_coeff 1*2 1*2 eam niu3
pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
pair_coeff 1*2 3 lj/cut 0.5 1.2
</PRE>
<PRE>pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0
pair_coeff * * lj/cut 1.0 1.0
pair_coeff * * coul/long
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>hybrid</I> and <I>hybrid/overlay</I> styles enable the use of multiple
pair styles in one simulation. With the <I>hybrid</I> style, exactly one
pair style is assigned to each pair of atom types. With the
<I>hybrid/overlay</I> style, one or more pair styles can be assigned to
each pair of atom types. The assignment of pair styles to type pairs
is made via the <A HREF = "pair_coeff.html">pair_coeff</A> command.
</P>
<P>Here are two examples of hybrid simulations. The <I>hybrid</I> style could
be used for a simulation of a metal droplet on a LJ surface. The
metal atoms interact with each other via an <I>eam</I> potential, the
surface atoms interact with each other via a <I>lj/cut</I> potential, and
the metal/surface interaction is also computed via a <I>lj/cut</I>
potential. The <I>hybrid/overlay</I> style could be used as in the 2nd
example above, where multiple potentials are superposed in an additive
fashion to compute the interaction between atoms. In this example,
using <I>lj/cut</I> and <I>coul/long</I> together gives the same result as if
the <I>lj/cut/coul/long</I> potential were used by itself. In this case,
it would be more efficient to use the single combined potential, but
in general any combination of pair potentials can be used together in
to produce an interaction that is not encoded in any single pair_style
file, e.g. adding Coulombic forces between granular particles.
</P>
<P>All pair styles that will be used are listed as "sub-styles" following
the <I>hybrid</I> or <I>hybrid/overlay</I> keyword, in any order. Each
sub-style's name is followed by its usual arguments, as illustrated in
the example above. See the doc pages of individual pair styles for a
listing and explanation of the appropriate arguments.
</P>
<P>Note that an individual pair style can be used multiple times as a
sub-style. For efficiency this should only be done if your model
requires it. E.g. if you have different regions of Si and C atoms and
wish to use a Tersoff potential for pure Si for one set of atoms, and
a Tersoff potetnial for pure C for the other set (presumably with some
3rd potential for Si-C interactions), then the sub-style <I>tersoff</I>
could be listed twice. But if you just want to use a Lennard-Jones or
other pairwise potential for several different atom type pairs in your
model, then you should just list the sub-style once and use the
pair_coeff command to assign parameters for the different type pairs.
</P>
-<P>IMPORTANT NOTE: An exception to this option to list an individual pair
-style multiple times are the pair styles implemented as Fortran
-libraries: <A HREF = "pair_meam.html">pair_style meam</A> and <A HREF = "pair_reax.html">pair_style
-reax</A> (<A HREF = "pair_reax_c.html">pair_style reax/c</A> is OK).
-This is because unlike a C++ class, they can not be instantiated
-multiple times, due to the manner in which they were coded in Fortran.
+<P>IMPORTANT NOTE: There are two exceptions to this option to list an
+individual pair style multiple times. The first is for pair styles
+implemented as Fortran libraries: <A HREF = "pair_meam.html">pair_style meam</A> and
+<A HREF = "pair_reax.html">pair_style reax</A> (<A HREF = "pair_reax_c.html">pair_style reax/c</A>
+is OK). This is because unlike a C++ class, they can not be
+instantiated multiple times, due to the manner in which they were
+coded in Fortran. The second is for GPU-enabled pair styles in the
+GPU package. This is b/c the GPU package also currently assumes that
+only one instance of a pair style is being used.
</P>
<P>In the pair_coeff commands, the name of a pair style must be added
after the I,J type specification, with the remaining coefficients
being those appropriate to that style. If the pair style is used
multiple times in the pair_style command, then an additional numeric
argument must also be specified which is a number from 1 to M where M
is the number of times the sub-style was listed in the pair style
command. The extra number indicates which instance of the sub-style
these coefficients apply to.
</P>
<P>For example, consider a simulation with 3 atom types: types 1 and 2
are Ni atoms, type 3 are LJ atoms with charges. The following
commands would set up a hybrid simulation:
</P>
<PRE>pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
pair_coeff * * eam/alloy nialhjea Ni Ni NULL
pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
pair_coeff 1*2 3 lj/cut 0.8 1.3
</PRE>
<P>As an example of using the same pair style multiple times, consider a
simulation with 2 atom types. Type 1 is Si, type 2 is C. The
following commands would model the Si atoms with Tersoff, the C atoms
with Tersoff, and the cross-interactions with Lennard-Jones:
</P>
<PRE>pair_style hybrid lj/cut 2.5 tersoff tersoff
pair_coeff * * tersoff 1 Si.tersoff Si NULL
pair_coeff * * tersoff 2 C.tersoff NULL C
pair_coeff 1 2 lj/cut 1.0 1.5
</PRE>
<P>If pair coefficients are specified in the data file read via the
<A HREF = "read_data.html">read_data</A> command, then the same rule applies.
E.g. "eam/alloy" or "lj/cut" must be added after the atom type, for
each line in the "Pair Coeffs" section, e.g.
</P>
<PRE>Pair Coeffs
</PRE>
<PRE>1 lj/cut/coul/cut 1.0 1.0
...
</PRE>
<P>Note that the pair_coeff command for some potentials such as
<A HREF = "pair_eam.html">pair_style eam/alloy</A> includes a mapping specification
of elements to all atom types, which in the hybrid case, can include
atom types not assigned to the <I>eam/alloy</I> potential. The NULL
keyword is used by many such potentials (eam/alloy, Tersoff, AIREBO,
etc), to denote an atom type that will be assigned to a different
sub-style.
</P>
<P>For the <I>hybrid</I> style, each atom type pair I,J is assigned to exactly
one sub-style. Just as with a simulation using a single pair style,
if you specify the same atom type pair in a second pair_coeff command,
the previous assignment will be overwritten.
</P>
<P>For the <I>hybrid/overlay</I> style, each atom type pair I,J can be
assigned to one or more sub-styles. If you specify the same atom type
pair in a second pair_coeff command with a new sub-style, then the
second sub-style is added to the list of potentials that will be
calculated for two interacting atoms of those types. If you specify
the same atom type pair in a second pair_coeff command with a
sub-style that has already been defined for that pair of atoms, then
the new pair coefficients simply override the previous ones, as in the
normal usage of the pair_coeff command. E.g. these two sets of
commands are the same:
</P>
<PRE>pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 2 2 1.5 0.8
</PRE>
<PRE>pair_style hybrid/overlay lj/cut 2.5
pair_coeff * * lj/cut 1.0 1.0
pair_coeff 2 2 lj/cut 1.5 0.8
</PRE>
<P>Coefficients must be defined for each pair of atoms types via the
<A HREF = "pair_coeff.html">pair_coeff</A> command as described above, or in the
data file or restart files read by the <A HREF = "read_data.html">read_data</A> or
<A HREF = "read_restart.html">read_restart</A> commands, or by mixing as described
below.
</P>
<P>For both the <I>hybrid</I> and <I>hybrid/overlay</I> styles, every atom type
pair I,J (where I <= J) must be assigned to at least one sub-style via
the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above, or
in the data file read by the <A HREF = "read_data.html">read_data</A>, or by mixing
as described below.
</P>
<P>If you want there to be no interactions between a particular pair of
atom types, you have 3 choices. You can assign the type pair to some
sub-style and use the <A HREF = "neigh_modify.html">neigh_modify exclude type</A>
command. You can assign it to some sub-style and set the coefficients
so that there is effectively no interaction (e.g. epsilon = 0.0 in a
LJ potential). Or, for <I>hybrid</I> and <I>hybrid/overlay</I> simulations, you
can use this form of the pair_coeff command in your input script:
</P>
<PRE>pair_coeff 2 3 none
</PRE>
<P>or this form in the "Pair Coeffs" section of the data file:
</P>
<PRE>3 none
</PRE>
<P>If an assignment to <I>none</I> is made in a simulation with the
<I>hybrid/overlay</I> pair style, it wipes out all previous assignments of
that atom type pair to sub-styles.
</P>
<P>Note that you may need to use an <A HREF = "atom_style.html">atom_style</A> hybrid
command in your input script, if atoms in the simulation will need
attributes from several atom styles, due to using multiple pair
potentials.
</P>
<HR>
<P>Different force fields (e.g. CHARMM vs AMBER) may have different rules
for applying weightings that change the strength of pairwise
interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4
neighbors in the molecular bond topology, as normally set by the
<A HREF = "special_bonds.html">special_bonds</A> command. Different weights can be
assigned to different pair hybrid sub-styles via the <A HREF = "pair_modify.html">pair_modify
special</A> command. This allows multiple force fields
to be used in a model of a hybrid system, however, there is no consistent
approach to determine parameters automatically for the interactions
between the two force fields, this is only recommended when particles
described by the different force fields do not mix.
</P>
<P>Here is an example for mixing CHARMM and AMBER: The global <I>amber</I>
setting sets the 1-4 interactions to non-zero scaling factors and
then overrides them with 0.0 only for CHARMM:
</P>
<PRE>special_bonds amber
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
</PRE>
<P>The this input achieves the same effect:
</P>
<PRE>special_bonds 0.0 0.0 0.1
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
</PRE>
<P>Here is an example for mixing Tersoff with OPLS/AA based on
a data file that defines bonds for all atoms where for the
Tersoff part of the system the force constants for the bonded
interactions have been set to 0. Note the global settings are
effectively <I>lj/coul 0.0 0.0 0.5</I> as required for OPLS/AA:
</P>
<PRE>special_bonds lj/coul 1e-20 1e-20 0.5
pair_hybrid tersoff lj/cut/coul/long 12.0
pair_modify pair tersoff special lj/coul 1.0 1.0 1.0
</PRE>
<P>See the <A HREF = "pair_modify.html">pair_modify</A> doc page for details on
the specific syntax, requirements and restrictions.
</P>
<HR>
<P>The potential energy contribution to the overall system due to an
individual sub-style can be accessed and output via the <A HREF = "compute_pair.html">compute
pair</A> command.
</P>
<HR>
<P>IMPORTANT: Several of the potentials defined via the pair_style
command in LAMMPS are really many-body potentials, such as Tersoff,
AIREBO, MEAM, ReaxFF, etc. The way to think about using these
potentials in a hybrid setting is as follows.
</P>
<P>A subset of atom types is assigned to the many-body potential with a
single <A HREF = "pair_coeff.html">pair_coeff</A> command, using "* *" to include
all types and the NULL keywords described above to exclude specific
types not assigned to that potential. If types 1,3,4 were assigned in
that way (but not type 2), this means that all many-body interactions
between all atoms of types 1,3,4 will be computed by that potential.
Pair_style hybrid allows interactions between type pairs 2-2, 1-2,
2-3, 2-4 to be specified for computation by other pair styles. You
could even add a second interaction for 1-1 to be computed by another
pair style, assuming pair_style hybrid/overlay is used.
</P>
<P>But you should not, as a general rule, attempt to exclude the
many-body interactions for some subset of the type pairs within the
set of 1,3,4 interactions, e.g. exclude 1-1 or 1-3 interactions. That
is not conceptually well-defined for many-body interactions, since the
potential will typically calculate energies and foces for small groups
of atoms, e.g. 3 or 4 atoms, using the neighbor lists of the atoms to
find the additional atoms in the group. It is typically non-physical
to think of excluding an interaction between a particular pair of
atoms when the potential computes 3-body or 4-body interactions.
</P>
<P>However, you can still use the pair_coeff none setting or the
<A HREF = "neigh_modify.html">neigh_modify exclude</A> command to exclude certain
type pairs from the neighbor list that will be passed to a manybody
sub-style. This will alter the calculations made by a many-body
potential, since it builds its list of 3-body, 4-body, etc
interactions from the pair list. You will need to think carefully as
to whether it produces a physically meaningful result for your model.
</P>
<P>For example, imagine you have two atom types in your model, type 1 for
atoms in one surface, and type 2 for atoms in the other, and you wish
to use a Tersoff potential to compute interactions within each
surface, but not between surfaces. Then either of these two command
sequences would implement that model:
</P>
<PRE>pair_style hybrid tersoff
pair_coeff * * tersoff SiC.tersoff C C
pair_coeff 1 2 none
</PRE>
<PRE>pair_style tersoff
pair_coeff * * SiC.tersoff C C
neigh_modify exclude type 1 2
</PRE>
<P>Either way, only neighbor lists with 1-1 or 2-2 interactions would be
passed to the Tersoff potential, which means it would compute no
3-body interactions containing both type 1 and 2 atoms.
</P>
<P>Here is another example, using hybrid/overlay, to use 2 many-body
potentials together, in an overlapping manner. Imagine you have CNT
(C atoms) on a Si surface. You want to use Tersoff for Si/Si and Si/C
interactions, and AIREBO for C/C interactions. Si atoms are type 1; C
atoms are type 2. Something like this will work:
</P>
<PRE>pair_style hybrid/overlay tersoff airebo 3.0
pair_coeff * * tersoff SiC.tersoff.custom Si C
pair_coeff * * airebo CH.airebo NULL C
</PRE>
<P>Note that to prevent the Tersoff potential from computing C/C
interactions, you would need to modify the SiC.tersoff file to turn
off C/C interaction, i.e. by setting the appropriate coefficients to
0.0.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual.
</P>
<P>Since the <I>hybrid</I> and <I>hybrid/overlay</I> styles delegate computation
to the individual sub-styles, the suffix versions of the <I>hybrid</I>
and <I>hybrid/overlay</I> styles are used to propagate the corresponding
suffix to all sub-styles, if those versions exist. Otherwise the
non-accelerated version will be used.
</P>
<P>The individual accelerated sub-styles are part of the USER-CUDA, GPU,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the
<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>Any pair potential settings made via the
<A HREF = "pair_modify.html">pair_modify</A> command are passed along to all
sub-styles of the hybrid potential.
</P>
<P>For atom type pairs I,J and I != J, if the sub-style assigned to I,I
and J,J is the same, and if the sub-style allows for mixing, then the
coefficients for I,J can be mixed. This means you do not have to
specify a pair_coeff command for I,J since the I,J type pair will be
assigned automatically to the sub-style defined for both I,I and J,J
and its coefficients generated by the mixing rule used by that
sub-style. For the <I>hybrid/overlay</I> style, there is an additional
requirement that both the I,I and J,J pairs are assigned to a single
sub-style. See the "pair_modify" command for details of mixing rules.
See the See the doc page for the sub-style to see if allows for
mixing.
</P>
<P>The hybrid pair styles supports the <A HREF = "pair_modify.html">pair_modify</A>
shift, table, and tail options for an I,J pair interaction, if the
associated sub-style supports it.
</P>
<P>For the hybrid pair styles, the list of sub-styles and their
respective settings are written to <A HREF = "restart.html">binary restart
files</A>, so a <A HREF = "pair_style.html">pair_style</A> command does
not need to specified in an input script that reads a restart file.
However, the coefficient information is not stored in the restart
file. Thus, pair_coeff commands need to be re-specified in the
restart input script.
</P>
<P>These pair styles support the use of the <I>inner</I>, <I>middle</I>, and
<I>outer</I> keywords of the <A HREF = "run_style.html">run_style respa</A> command, if
their sub-styles do.
</P>
<P><B>Restrictions:</B>
</P>
<P>When using a long-range Coulombic solver (via the
<A HREF = "kspace_style.html">kspace_style</A> command) with a hybrid pair_style,
one or more sub-styles will be of the "long" variety,
e.g. <I>lj/cut/coul/long</I> or <I>buck/coul/long</I>. You must insure that the
short-range Coulombic cutoff used by each of these long pair styles is
the same or else LAMMPS will generate an error.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/doc2/pair_reax.html b/doc/doc2/pair_reax.html
index bbd554e1b..3b7aa0894 100644
--- a/doc/doc2/pair_reax.html
+++ b/doc/doc2/pair_reax.html
@@ -1,216 +1,218 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style reax command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style reax hbcut hbnewflag tripflag precision
</PRE>
<UL><LI>hbcut = hydrogen-bond cutoff (optional) (distance units)
<LI>hbnewflag = use old or new hbond function style (0 or 1) (optional)
<LI>tripflag = apply stabilization to all triple bonds (0 or 1) (optional)
<LI>precision = precision for charge equilibration (optional)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style reax
pair_style reax 10.0 0 1 1.0e-5
pair_coeff * * ffield.reax 3 1 2 2
pair_coeff * * ffield.reax 3 NULL NULL 3
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>reax</I> computes the ReaxFF potential of van Duin, Goddard and
co-workers. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. There is more than one version of ReaxFF. The version
implemented in LAMMPS uses the functional forms documented in the
supplemental information of the following paper:
<A HREF = "#Chenoweth_2008">(Chenoweth)</A>. The version integrated into LAMMPS matches
the most up-to-date version of ReaxFF as of summer 2010.
</P>
-<P>The <I>reax</I> style differs from the <A HREF = "pair_reax_c.html">pair_style reax/c</A>
-command in the lo-level implementation details. The <I>reax</I> style is a
+<P>WARNING: pair style reax is now deprecated and will soon be retired. Users
+should switch to <A HREF = "pair_reax_c.html">pair_style reax/c</A>. The <I>reax</I> style
+differs from the <I>reax/c</I> style in the lo-level implementation details.
+The <I>reax</I> style is a
Fortran library, linked to LAMMPS. The <I>reax/c</I> style was initially
implemented as stand-alone C code and is now integrated into LAMMPS as
-a package.
+a package.
</P>
<P>LAMMPS requires that a file called ffield.reax be provided, containing
the ReaxFF parameters for each atom type, bond type, etc. The format
is identical to the ffield file used by van Duin and co-workers. The
filename is required as an argument in the pair_coeff command. Any
value other than "ffield.reax" will be rejected (see below).
</P>
<P>LAMMPS provides several different versions of ffield.reax in its
potentials dir, each called potentials/ffield.reax.label. These are
documented in potentials/README.reax. The default ffield.reax
contains parameterizations for the following elements: C, H, O, N, S.
</P>
<P>IMPORTANT NOTE: We do not distribute a wide variety of ReaxFF force
field files with LAMMPS. Adri van Duin's group at PSU is the central
repository for this kind of data as they are continuously deriving and
updating parameterizations for different classes of materials. You
can visit their WWW site at
<A HREF = "http://www.engr.psu.edu/adri">http://www.engr.psu.edu/adri</A>, register
as a "new user", and then submit a request to their group describing
material(s) you are interested in modeling with ReaxFF. They can tell
you what is currently available or what it would take to create a
suitable ReaxFF parameterization.
</P>
<P>The format of these files is identical to that used originally by van
Duin. We have tested the accuracy of <I>pair_style reax</I> potential
against the original ReaxFF code for the systems mentioned above. You
can use other ffield files for specific chemical systems that may be
available elsewhere (but note that their accuracy may not have been
tested).
</P>
<P>The <I>hbcut</I>, <I>hbnewflag</I>, <I>tripflag</I>, and <I>precision</I> settings are
optional arguments. If none are provided, default settings are used:
<I>hbcut</I> = 6 (which is Angstroms in real units), <I>hbnewflag</I> = 1 (use
new hbond function style), <I>tripflag</I> = 1 (apply stabilization to all
triple bonds), and <I>precision</I> = 1.0e-6 (one part in 10^6). If you
wish to override any of these defaults, then all of the settings must
be specified.
</P>
<P>Two examples using <I>pair_style reax</I> are provided in the examples/reax
sub-directory, along with corresponding examples for
<A HREF = "pair_reax_c.html">pair_style reax/c</A>.
</P>
<P>Use of this pair style requires that a charge be defined for every
atom since the <I>reax</I> pair style performs a charge equilibration (QEq)
calculation. See the <A HREF = "atom_style.html">atom_style</A> and
<A HREF = "read_data.html">read_data</A> commands for details on how to specify
charges.
</P>
<P>The thermo variable <I>evdwl</I> stores the sum of all the ReaxFF potential
energy contributions, with the exception of the Coulombic and charge
equilibration contributions which are stored in the thermo variable
<I>ecoul</I>. The output of these quantities is controlled by the
<A HREF = "thermo.html">thermo</A> command.
</P>
<P>This pair style tallies a breakdown of the total ReaxFF potential
energy into sub-categories, which can be accessed via the <A HREF = "compute_pair.html">compute
pair</A> command as a vector of values of length 14.
The 14 values correspond to the following sub-categories (the variable
names in italics match those used in the ReaxFF FORTRAN library):
</P>
<OL><LI><I>eb</I> = bond energy
<LI><I>ea</I> = atom energy
<LI><I>elp</I> = lone-pair energy
<LI><I>emol</I> = molecule energy (always 0.0)
<LI><I>ev</I> = valence angle energy
<LI><I>epen</I> = double-bond valence angle penalty
<LI><I>ecoa</I> = valence angle conjugation energy
<LI><I>ehb</I> = hydrogen bond energy
<LI><I>et</I> = torsion energy
<LI><I>eco</I> = conjugation energy
<LI><I>ew</I> = van der Waals energy
<LI><I>ep</I> = Coulomb energy
<LI><I>efi</I> = electric field energy (always 0.0)
<LI><I>eqeq</I> = charge equilibration energy
</OL>
<P>To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
</P>
<PRE>compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
...
variable eqeq equal c_reax[14]
thermo_style custom step temp epair v_eb v_ea ... v_eqeq
</PRE>
<P>Only a single pair_coeff command is used with the <I>reax</I> style which
specifies a ReaxFF potential file with parameters for all needed
elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
</P>
<UL><LI>filename
<LI>N indices = mapping of ReaxFF elements to atom types
</UL>
<P>The specification of the filename and the mapping of LAMMPS atom types
recognized by the ReaxFF is done differently than for other LAMMPS
potentials, due to the non-portable difficulty of passing character
strings (e.g. filename, element names) between C++ and Fortran.
</P>
<P>The filename has to be "ffield.reax" and it has to exist in the
directory you are running LAMMPS in. This means you cannot prepend a
path to the file in the potentials dir. Rather, you should copy that
file into the directory you are running from. If you wish to use
another ReaxFF potential file, then name it "ffield.reax" and put it
in the directory you run from.
</P>
<P>In the ReaxFF potential file, near the top, after the general
parameters, is the atomic parameters section that contains element
names, each with a couple dozen numeric parameters. If there are M
elements specified in the <I>ffield</I> file, think of these as numbered 1
to M. Each of the N indices you specify for the N atom types of LAMMPS
atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
be mapped to whatever element you specify as the first index value,
etc. If a mapping value is specified as NULL, the mapping is not
performed. This can be used when a ReaxFF potential is used as part
of the <I>hybrid</I> pair style. The NULL values are placeholders for atom
types that will be used with other potentials.
</P>
<P>IMPORTANT NOTE: Currently the reax pair style cannot be used as part
of the <I>hybrid</I> pair style. Some additional changes still need to be
made to enable this.
</P>
<P>As an example, say your LAMMPS simulation has 4 atom types and the
elements are ordered as C, H, O, N in the <I>ffield</I> file. If you want
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
H, you would use the following pair_coeff command:
</P>
<PRE>pair_coeff * * ffield.reax 1 1 4 2
</PRE>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
mix, shift, table, and tail options.
</P>
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<P><B>Restrictions:</B>
</P>
<P>The ReaxFF potential files provided with LAMMPS in the potentials
directory are parameterized for real <A HREF = "units.html">units</A>. You can use
the ReaxFF potential with any LAMMPS units, but you would need to
create your own potential file with coefficients listed in the
appropriate units if your simulation doesn't use "real" units.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_reax_c.html">pair_style reax/c</A>,
<A HREF = "fix_reax_bonds.html">fix_reax_bonds</A>
</P>
<P><B>Default:</B>
</P>
<P>The keyword defaults are <I>hbcut</I> = 6, <I>hbnewflag</I> = 1, <I>tripflag</I> = 1,
<I>precision</I> = 1.0e-6.
</P>
<HR>
<A NAME = "Chenoweth_2008"></A>
<P><B>(Chenoweth_2008)</B> Chenoweth, van Duin and Goddard,
Journal of Physical Chemistry A, 112, 1040-1053 (2008).
</P>
</HTML>
diff --git a/doc/doc2/pair_srp.html b/doc/doc2/pair_srp.html
index df195432b..173a2f55b 100644
--- a/doc/doc2/pair_srp.html
+++ b/doc/doc2/pair_srp.html
@@ -1,172 +1,176 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style srp command
</H3>
<P><B>Syntax:</B>
</P>
-<P>pair_style srp cutoff bond_type dist keyword value ...
+<P>pair_style srp cutoff btype dist keyword value ...
</P>
<UL><LI>cutoff = global cutoff for SRP interactions (distance units)
-<LI>bond_type = bond type to apply SRP interactions
+<LI>btype = bond type to apply SRP interactions to (can be wildcard, see below)
<LI>distance = <I>min</I> or <I>mid</I>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>exclude</I>
<PRE> <I>exclude</I> value = <I>yes</I> or <I>no</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
pair_coeff 1 1 dpd 60.0 4.5 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0 0.8
</PRE>
<PRE>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
pair_coeff 1 1 dpd 60.0 50 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp 40.0
</PRE>
<PRE>pair_style hybrid srp 0.8 2 mid
pair_coeff 1 1 none
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0 0.8
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>srp</I> computes a soft segmental repulsive potential (SRP) that
acts between pairs of bonds. This potential is useful for preventing
bonds from passing through one another when a soft non-bonded
potential acts between beads in, for example, DPD polymer chains. An
example input script that uses this command is provided in
examples/USER/srp.
</P>
-<P>Bonds of type <I>btype</I> interact with one another through a
+<P>Bonds of specified type <I>btype</I> interact with one another through a
bond-pairwise potential, such that the force on bond <I>i</I> due to bond
<I>j</I> is as follows
</P>
<CENTER><IMG SRC = "Eqs/pair_srp1.jpg">
</CENTER>
<P>where <I>r</I> and <I>rij</I> are the distance and unit vector between the two
-bonds. The bondtype can also be specified as an asterisk (*) and then
-this interaction applied to all bonds.
-The <I>mid</I> option computes <I>r</I> and <I>rij</I> from the midpoint
-distance between bonds. The <I>min</I> option computes <I>r</I> and <I>rij</I> from
-the minimum distance between bonds. The force acting on a bond is
-mapped onto the two bond atoms according to the lever rule,
+bonds. Note that <I>btype</I> can be specified as an asterisk "*", which
+case the interaction is applied to all bond types. The <I>mid</I> option
+computes <I>r</I> and <I>rij</I> from the midpoint distance between bonds. The
+<I>min</I> option computes <I>r</I> and <I>rij</I> from the minimum distance between
+bonds. The force acting on a bond is mapped onto the two bond atoms
+according to the lever rule,
</P>
<CENTER><IMG SRC = "Eqs/pair_srp2.jpg">
</CENTER>
<P>where <I>L</I> is the normalized distance from the atom to the point of
closest approach of bond <I>i</I> and <I>j</I>. The <I>mid</I> option takes <I>L</I> as
0.5 for each interaction as described in <A HREF = "#Sirk">(Sirk)</A>.
</P>
<P>The following coefficients must be defined via the
<A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above, or in
the data file or restart file read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI><I>C</I> (force units)
<LI><I>rc</I> (distance units)
</UL>
<P>The last coefficient is optional. If not specified, the global cutoff
is used.
</P>
-<P>IMPORTANT NOTE: Pair style srp considers each bond of type <I>btype</I> as
-a fictitious particle of type <I>bptype</I>, where <I>bptype</I> is the largest
-atom type in the system. These "bond particles" are inserted at the
-beginning of the run, and serve as placeholders that define the
-position of the bonds. This allows neighbor lists to be constructed
-and pairwise interactions to be computed in almost the same way as is
-done for point particles. Because bonds interact only with other
-bonds, <A HREF = "pair_hybrid.html">pair_style hybrid</A> should be used to turn off
-interactions between atom type <I>bptype</I> and all other types of atoms.
-An error will be flagged if <A HREF = "pair_hybrid.html">pair_style hybrid</A> is
-not used. Further, only bond particles should be given an atom type
-of <I>bptype</I>; a check is done at the beginning of the run to ensure
-there are no regular atoms of <I>bptype</I>.
+<P>IMPORTANT NOTE: Pair style srp considers each bond of type <I>btype</I> to
+be a fictitious "particle" of type <I>bptype</I>, where <I>bptype</I> is the
+largest atom type in the system. There cannot be any actual particles
+assigned to this atom type. This means you must specify the number of
+types in your system to be one larger would normally be the case,
+e.g. via the <A HREF = "create_box.html">create_box</A> or
+<A HREF = "read_data.html">read_data</A> commands. These ficitious "bond particles"
+are inserted at the beginning of the run, and serve as placeholders
+that define the position of the bonds. This allows neighbor lists to
+be constructed and pairwise interactions to be computed in almost the
+same way as is done for actual particles. Because bonds interact only
+with other bonds, <A HREF = "pair_hybrid.html">pair_style hybrid</A> should be used
+to turn off interactions between atom type <I>bptype</I> and all other
+types of atoms. An error will be flagged if <A HREF = "pair_hybrid.html">pair_style
+hybrid</A> is not used.
</P>
<P>The optional <I>exclude</I> keyword determines if forces are computed
between first neighbor (directly connected) bonds. For a setting of
-<I>no</I>, first neighbor forces are computed; for <I>yes</I> they are not computed. A setting of <I>no</I>
-cannot be used with the <I>min</I> option for distance calculation because the the minimum distance between
-directly connected bonds is zero.
+<I>no</I>, first neighbor forces are computed; for <I>yes</I> they are not
+computed. A setting of <I>no</I> cannot be used with the <I>min</I> option for
+distance calculation because the the minimum distance between directly
+connected bonds is zero.
</P>
<P>Pair style <I>srp</I> turns off normalization of thermodynamic properties
by particle number, as if the command <A HREF = "thermo_modify.html">thermo_modify norm
no</A> had been issued.
</P>
<P>The pairwise energy associated with style <I>srp</I> is shifted to be zero
at the cutoff distance <I>rc</I>.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>This pair styles does not support mixing.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift option for the energy of the pair interaction. Note that as
discussed above, the energy term is already shifted to be 0.0 at the
cutoff distance <I>rc</I>.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant for
this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure.
</P>
<P>This pair style writes global and per-atom information to <A HREF = "restart.html">binary
restart files</A>. Pair srp should be used with <A HREF = "pair_hybrid.html">pair_style
hybrid</A>, thus the pair_coeff commands need to be
specified in the input script when reading a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This pair style is part of the USER-MISC package. It is only enabled
if LAMMPS was built with that package. See the Making LAMMPS section
for more info.
</P>
-<P>This pair style must be used with <A HREF = "pair_hybrid.html">pair_style hybrid</A>.
+<P>This pair style must be used with <A HREF = "pair_hybrid.html">pair_style
+hybrid</A>.
</P>
<P>This pair style requires the <A HREF = "newton.html">newton</A> command to be <I>on</I>
for non-bonded interactions.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_hybrid.html">pair_style hybrid</A>, <A HREF = "pair_coeff.html">pair_coeff</A>,
<A HREF = "pair_dpd.html">pair dpd</A>
</P>
<P><B>Default:</B>
</P>
<P>The default keyword value is exclude = yes.
</P>
<HR>
<A NAME = "Sirk"></A>
<P><B>(Sirk)</B> Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J
Chem Phys, 136 (13) 134903, 2012.
</P>
</HTML>
diff --git a/doc/doc2/pair_style.html b/doc/doc2/pair_style.html
index 6cfd97335..95fd464b9 100644
--- a/doc/doc2/pair_style.html
+++ b/doc/doc2/pair_style.html
@@ -1,234 +1,235 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = one of the styles from the list below
<LI>args = arguments used by a particular style
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/cut 2.5
pair_style eam/alloy
pair_style hybrid lj/charmm/coul/long 10.0 eam
pair_style table linear 1000
pair_style none
</PRE>
<P><B>Description:</B>
</P>
<P>Set the formula(s) LAMMPS uses to compute pairwise interactions. In
LAMMPS, pair potentials are defined between pairs of atoms that are
within a cutoff distance and the set of active interactions typically
changes over time. See the <A HREF = "bond_style.html">bond_style</A> command to
define potentials between pairs of bonded atoms, which typically
remain in place for the duration of a simulation.
</P>
<P>In LAMMPS, pairwise force fields encompass a variety of interactions,
some of which include many-body effects, e.g. EAM, Stillinger-Weber,
Tersoff, REBO potentials. They are still classified as "pairwise"
potentials because the set of interacting atoms changes with time
(unlike molecular bonds) and thus a neighbor list is used to find
nearby interacting atoms.
</P>
<P>Hybrid models where specified pairs of atom types interact via
different pair potentials can be setup using the <I>hybrid</I> pair style.
</P>
<P>The coefficients associated with a pair style are typically set for
each pair of atom types, and are specified by the
<A HREF = "pair_coeff.html">pair_coeff</A> command or read from a file by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> command sets options for mixing of
type I-J interaction coefficients and adding energy offsets or tail
corrections to Lennard-Jones potentials. Details on these options as
they pertain to individual potentials are described on the doc page
for the potential. Likewise, info on whether the potential
information is stored in a <A HREF = "write_restart.html">restart file</A> is listed
on the potential doc page.
</P>
<P>In the formulas listed for each pair style, <I>E</I> is the energy of a
pairwise interaction between two atoms separated by a distance <I>r</I>.
The force between the atoms is the negative derivative of this
expression.
</P>
<P>If the pair_style command has a cutoff argument, it sets global
cutoffs for all pairs of atom types. The distance(s) can be smaller
or larger than the dimensions of the simulation box.
</P>
<P>Typically, the global cutoff value can be overridden for a specific
pair of atom types by the <A HREF = "pair_coeff.html">pair_coeff</A> command. The
pair style settings (including global cutoffs) can be changed by a
subsequent pair_style command using the same style. This will reset
the cutoffs for all atom type pairs, including those previously set
explicitly by a <A HREF = "pair_coeff.html">pair_coeff</A> command. The exceptions
to this are that pair_style <I>table</I> and <I>hybrid</I> settings cannot be
reset. A new pair_style command for these styles will wipe out all
previously specified pair_coeff values.
</P>
<HR>
<P>Here is an alphabetic list of pair styles defined in LAMMPS. They are
also given in more compact form in the pair section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<P>Click on the style to display the formula it computes, arguments
specified in the pair_style command, and coefficients specified by the
associated <A HREF = "pair_coeff.html">pair_coeff</A> command.
</P>
<P>There are also additional pair styles (not listed here) submitted by
users which are included in the LAMMPS distribution. The list of
these with links to the individual styles are given in the pair
section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
</P>
<P>There are also additional accelerated pair styles (not listed here)
included in the LAMMPS distribution for faster performance on CPUs and
GPUs. The list of these with links to the individual styles are given
in the pair section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
</P>
<UL><LI><A HREF = "pair_none.html">pair_style none</A> - turn off pairwise interactions
<LI><A HREF = "pair_hybrid.html">pair_style hybrid</A> - multiple styles of pairwise interactions
<LI><A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> - multiple styles of superposed pairwise interactions
</UL>
<UL><LI><A HREF = "pair_adp.html">pair_style adp</A> - angular dependent potential (ADP) of Mishin
<LI><A HREF = "pair_airebo.html">pair_style airebo</A> - AIREBO potential of Stuart
<LI><A HREF = "pair_beck.html">pair_style beck</A> - Beck potential
<LI><A HREF = "pair_body.html">pair_style body</A> - interactions between body particles
<LI><A HREF = "pair_bop.html">pair_style bop</A> - BOP potential of Pettifor
<LI><A HREF = "pair_born.html">pair_style born</A> - Born-Mayer-Huggins potential
<LI><A HREF = "pair_born.html">pair_style born/coul/long</A> - Born-Mayer-Huggins with long-range Coulombics
<LI><A HREF = "pair_born.html">pair_style born/coul/long/cs</A> - Born-Mayer-Huggins with long-range Coulombics and core/shell
<LI><A HREF = "pair_born.html">pair_style born/coul/msm</A> - Born-Mayer-Huggins with long-range MSM Coulombics
<LI><A HREF = "pair_born.html">pair_style born/coul/wolf</A> - Born-Mayer-Huggins with Coulombics via Wolf potential
<LI><A HREF = "pair_brownian.html">pair_style brownian</A> - Brownian potential for Fast Lubrication Dynamics
<LI><A HREF = "pair_brownian.html">pair_style brownian/poly</A> - Brownian potential for Fast Lubrication Dynamics with polydispersity
<LI><A HREF = "pair_buck.html">pair_style buck</A> - Buckingham potential
<LI><A HREF = "pair_buck.html">pair_style buck/coul/cut</A> - Buckingham with cutoff Coulomb
<LI><A HREF = "pair_buck.html">pair_style buck/coul/long</A> - Buckingham with long-range Coulombics
<LI><A HREF = "pair_buck.html">pair_style buck/coul/long/cs</A> - Buckingham with long-range Coulombics and core/shell
<LI><A HREF = "pair_buck.html">pair_style buck/coul/msm</A> - Buckingham long-range MSM Coulombics
<LI><A HREF = "pair_buck_long.html">pair_style buck/long/coul/long</A> - long-range Buckingham with long-range Coulombics
<LI><A HREF = "pair_colloid.html">pair_style colloid</A> - integrated colloidal potential
<LI><A HREF = "pair_comb.html">pair_style comb</A> - charge-optimized many-body (COMB) potential
<LI><A HREF = "pair_comb.html">pair_style comb3</A> - charge-optimized many-body (COMB3) potential
<LI><A HREF = "pair_coul.html">pair_style coul/cut</A> - cutoff Coulombic potential
<LI><A HREF = "pair_coul.html">pair_style coul/debye</A> - cutoff Coulombic potential with Debye screening
<LI><A HREF = "pair_coul.html">pair_style coul/dsf</A> - Coulombics via damped shifted forces
<LI><A HREF = "pair_coul.html">pair_style coul/long</A> - long-range Coulombic potential
<LI><A HREF = "pair_coul.html">pair_style coul/long/cs</A> - long-range Coulombic potential and core/shell
<LI><A HREF = "pair_coul.html">pair_style coul/msm</A> - long-range MSM Coulombics
<LI><A HREF = "pair_coul_streitz.html">pair_style coul/msm</A> - Coulombics via Streitz/Mintmire Slater orbitals
<LI><A HREF = "pair_coul.html">pair_style coul/wolf</A> - Coulombics via Wolf potential
<LI><A HREF = "pair_dpd.html">pair_style dpd</A> - dissipative particle dynamics (DPD)
<LI><A HREF = "pair_dpd.html">pair_style dpd/tstat</A> - DPD thermostatting
<LI><A HREF = "pair_dsmc.html">pair_style dsmc</A> - Direct Simulation Monte Carlo (DSMC)
<LI><A HREF = "pair_eam.html">pair_style eam</A> - embedded atom method (EAM)
<LI><A HREF = "pair_eam.html">pair_style eam/alloy</A> - alloy EAM
<LI><A HREF = "pair_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
<LI><A HREF = "pair_eim.html">pair_style eim</A> - embedded ion method (EIM)
<LI><A HREF = "pair_gauss.html">pair_style gauss</A> - Gaussian potential
<LI><A HREF = "pair_gayberne.html">pair_style gayberne</A> - Gay-Berne ellipsoidal potential
<LI><A HREF = "pair_gran.html">pair_style gran/hertz/history</A> - granular potential with Hertzian interactions
<LI><A HREF = "pair_gran.html">pair_style gran/hooke</A> - granular potential with history effects
<LI><A HREF = "pair_gran.html">pair_style gran/hooke/history</A> - granular potential without history effects
<LI><A HREF = "pair_hbond_dreiding.html">pair_style hbond/dreiding/lj</A> - DREIDING hydrogen bonding LJ potential
<LI><A HREF = "pair_hbond_dreiding.html">pair_style hbond/dreiding/morse</A> - DREIDING hydrogen bonding Morse potential
<LI><A HREF = "pair_kim.html">pair_style kim</A> - interface to potentials provided by KIM project
<LI><A HREF = "pair_lcbop.html">pair_style lcbop</A> - long-range bond-order potential (LCBOP)
<LI><A HREF = "pair_line_lj.html">pair_style line/lj</A> - LJ potential between line segments
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A> - CHARMM with long-range Coulomb
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/msm</A> - CHARMM with long-range MSM Coulombics
<LI><A HREF = "pair_class2.html">pair_style lj/class2</A> - COMPASS (class 2) force field with no Coulomb
<LI><A HREF = "pair_class2.html">pair_style lj/class2/coul/cut</A> - COMPASS with cutoff Coulomb
<LI><A HREF = "pair_class2.html">pair_style lj/class2/coul/long</A> - COMPASS with long-range Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut</A> - cutoff Lennard-Jones potential with no Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/cut</A> - LJ with cutoff Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/debye</A> - LJ with Debye screening added to Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/dsf</A> - LJ with Coulombics via damped shifted forces
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long</A> - LJ with long-range Coulombics
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/msm</A> - LJ with long-range MSM Coulombics
<LI><A HREF = "pair_dipole.html">pair_style lj/cut/dipole/cut</A> - point dipoles with cutoff
<LI><A HREF = "pair_dipole.html">pair_style lj/cut/dipole/long</A> - point dipoles with long-range Ewald
<LI><A HREF = "pair_lj.html">pair_style lj/cut/tip4p/cut</A> - LJ with cutoff Coulomb for TIP4P water
<LI><A HREF = "pair_lj.html">pair_style lj/cut/tip4p/long</A> - LJ with long-range Coulomb for TIP4P water
<LI><A HREF = "pair_lj_expand.html">pair_style lj/expand</A> - Lennard-Jones for variable size particles
<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs</A> - GROMACS-style Lennard-Jones potential
<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs/coul/gromacs</A> - GROMACS-style LJ and Coulombic potential
<LI><A HREF = "pair_lj_long.html">pair_style lj/long/coul/long</A> - long-range LJ and long-range Coulombics
<LI><A HREF = "pair_dipole.html">pair_style lj/long/dipole/long</A> - long-range LJ and long-range point dipoles
<LI><A HREF = "pair_lj_long.html">pair_style lj/long/tip4p/long</A> - long-range LJ and long-range Coulomb for TIP4P water
<LI><A HREF = "pair_lj_smooth.html">pair_style lj/smooth</A> - smoothed Lennard-Jones potential
<LI><A HREF = "pair_lj_smooth_linear.html">pair_style lj/smooth/linear</A> - linear smoothed Lennard-Jones potential
<LI><A HREF = "pair_lj96.html">pair_style lj96/cut</A> - Lennard-Jones 9/6 potential
<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A> - hydrodynamic lubrication forces
<LI><A HREF = "pair_lubricate.html">pair_style lubricate/poly</A> - hydrodynamic lubrication forces with polydispersity
<LI><A HREF = "pair_lubricateU.html">pair_style lubricateU</A> - hydrodynamic lubrication forces for Fast Lubrication Dynamics
<LI><A HREF = "pair_lubricateU.html">pair_style lubricateU/poly</A> - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
<LI><A HREF = "pair_meam.html">pair_style meam</A> - modified embedded atom method (MEAM)
<LI><A HREF = "pair_mie.html">pair_style mie/cut</A> - Mie potential
<LI><A HREF = "pair_morse.html">pair_style morse</A> - Morse potential
<LI><A HREF = "pair_nb3b_harmonic.html">pair_style nb3b/harmonic</A> - nonbonded 3-body harmonic potential
<LI><A HREF = "pair_nm.html">pair_style nm/cut</A> - N-M potential
<LI><A HREF = "pair_nm.html">pair_style nm/cut/coul/cut</A> - N-M potential with cutoff Coulomb
<LI><A HREF = "pair_nm.html">pair_style nm/cut/coul/long</A> - N-M potential with long-range Coulombics
<LI><A HREF = "pair_peri.html">pair_style peri/eps</A> - peridynamic EPS potential
<LI><A HREF = "pair_peri.html">pair_style peri/lps</A> - peridynamic LPS potential
<LI><A HREF = "pair_peri.html">pair_style peri/pmb</A> - peridynamic PMB potential
<LI><A HREF = "pair_peri.html">pair_style peri/ves</A> - peridynamic VES potential
<LI><A HREF = "pair_polymorphic.html">pair_style polymorphic</A> - polymorphic 3-body potential
<LI><A HREF = "pair_reax.html">pair_style reax</A> - ReaxFF potential
<LI><A HREF = "pair_airebo.html">pair_style rebo</A> - 2nd generation REBO potential of Brenner
<LI><A HREF = "pair_resquared.html">pair_style resquared</A> - Everaers RE-Squared ellipsoidal potential
<LI><A HREF = "pair_snap.html">pair_style snap</A> - SNAP quantum-accurate potential
<LI><A HREF = "pair_soft.html">pair_style soft</A> - Soft (cosine) potential
<LI><A HREF = "pair_sw.html">pair_style sw</A> - Stillinger-Weber 3-body potential
<LI><A HREF = "pair_table.html">pair_style table</A> - tabulated pair potential
<LI><A HREF = "pair_tersoff.html">pair_style tersoff</A> - Tersoff 3-body potential
<LI><A HREF = "pair_tersoff_mod.html">pair_style tersoff/mod</A> - modified Tersoff 3-body potential
<LI><A HREF = "pair_tersoff_zbl.html">pair_style tersoff/zbl</A> - Tersoff/ZBL 3-body potential
<LI><A HREF = "pair_coul.html">pair_style tip4p/cut</A> - Coulomb for TIP4P water w/out LJ
<LI><A HREF = "pair_coul.html">pair_style tip4p/long</A> - long-range Coulombics for TIP4P water w/out LJ
<LI><A HREF = "pair_tri_lj.html">pair_style tri/lj</A> - LJ potential between triangles
+<LI><A HREF = "pair_vahishta.html">pair_style vashishta</A> - Vashishta 2-body and 3-body potential
<LI><A HREF = "pair_yukawa.html">pair_style yukawa</A> - Yukawa potential
<LI><A HREF = "pair_yukawa_colloid.html">pair_style yukawa/colloid</A> - screened Yukawa potential for finite-size particles
<LI><A HREF = "pair_zbl.html">pair_style zbl</A> - Ziegler-Biersack-Littmark potential
</UL>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This command must be used before any coefficients are set by the
<A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "read_data.html">read_data</A>, or
<A HREF = "read_restart.html">read_restart</A> commands.
</P>
<P>Some pair styles are part of specific packages. They are only enabled
if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
The doc pages for individual pair potentials tell if it is part of a
package.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "read_data.html">read_data</A>,
<A HREF = "pair_modify.html">pair_modify</A>, <A HREF = "kspace_style.html">kspace_style</A>,
<A HREF = "dielectric.html">dielectric</A>, <A HREF = "pair_write.html">pair_write</A>
</P>
<P><B>Default:</B>
</P>
<PRE>pair_style none
</PRE>
</HTML>
diff --git a/doc/pair_vashishta.html b/doc/doc2/pair_vashishta.html
similarity index 87%
copy from doc/pair_vashishta.html
copy to doc/doc2/pair_vashishta.html
index f2b42588e..7a5832c68 100644
--- a/doc/pair_vashishta.html
+++ b/doc/doc2/pair_vashishta.html
@@ -1,211 +1,236 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style vashishta command
</H3>
+<H3>pair_style vashishta/omp command
+</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style vashishta
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style vashishta
pair_coeff * * SiC.vashishta Si C
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>vashishta</I> style computes the combined 2-body and 3-body
family of potentials developed in the group of Vashishta and
co-workers. By combining repulsive, screened Coulombic,
screened charge-dipole, and dispersion interactions with a
bond-angle energy based on the Stillinger-Weber potential,
this potential has been used to describe a variety of inorganic
compounds, including SiO2 <A HREF = "#Vashishta1990">Vashishta1990</A>,
SiC <A HREF = "#Vashishta2007">Vashishta2007</A>,
and InP <A HREF = "#Branicio2009">Branicio2009</A>.
</P>
<P>The potential for the energy U of a system of atoms is
</P>
<CENTER><IMG SRC = "Eqs/pair_vashishta.jpg">
</CENTER>
<P>where we follow the notation used in <A HREF = "#Branicio2009">Branicio2009</A>.
U2 is a two-body term and U3 is a three-body term. The
summation over two-body terms is over all neighbors J within
a cutoff distance = <I>rc</I>. The twobody terms are shifted and
tilted by a linear function so that the energy and force are
both zero at <I>rc</I>. The summation over three-body terms
is over all neighbors J and K within a cut-off distance = <I>r0</I>,
where the exponential screening function becomes zero.
</P>
<P>Only a single pair_coeff command is used with the <I>vashishta</I> style which
specifies a Vashishta potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
</P>
<UL><LI>filename
<LI>N element names = mapping of Vashishta elements to atom types
</UL>
<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
to specify the path for the potential file.
</P>
<P>As an example, imagine a file SiC.vashishta has parameters for
Si and C. If your LAMMPS simulation has 4 atoms types and you want
the 1st 3 to be Si, and the 4th to be C, you would use the following
pair_coeff command:
</P>
<PRE>pair_coeff * * SiC.vashishta Si Si Si C
</PRE>
<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
element in the file. The final C argument maps LAMMPS atom type 4
to the C element in the file. If a mapping value is specified as
NULL, the mapping is not performed. This can be used when a <I>vashishta</I>
potential is used as part of the <I>hybrid</I> pair style. The NULL values
are placeholders for atom types that will be used with other
potentials.
</P>
<P>Vashishta files in the <I>potentials</I> directory of the LAMMPS
distribution have a ".vashishta" suffix. Lines that are not blank or
comments (starting with #) define parameters for a triplet of
elements. The parameters in a single entry correspond to the two-body
and three-body coefficients in the formulae above:
</P>
<UL><LI>element 1 (the center atom in a 3-body interaction)
<LI>element 2
<LI>element 3
<LI>H (energy units)
<LI>eta
<LI>Zi (electron charge units)
<LI>Zj (electron charge units)
<LI>lambda1 (distance units)
<LI>D (energy units)
<LI>lambda4 (distance units)
<LI>W (energy units)
<LI>rc (distance units)
<LI>B (energy units)
<LI>gamma
<LI>r0 (distance units)
<LI>C
<LI>costheta0
</UL>
<P>The non-annotated parameters are unitless.
The Vashishta potential file must contain entries for all the
elements listed in the pair_coeff command. It can also contain
entries for additional elements not being used in a particular
simulation; LAMMPS ignores those entries.
For a single-element simulation, only a single entry is required
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
specify parameters for all permutations of the two elements
interacting in three-body configurations. Thus for 3 elements, 27
entries would be required, etc.
</P>
<P>Depending on the particular version of the Vashishta potential,
the values of these parameters may be keyed to the identities of
zero, one, two, or three elements.
In order to make the input file format unambiguous, general,
and simple to code,
LAMMPS uses a slightly confusing method for specifying parameters.
All parameters are divided into two classes: two-body and three-body.
Two-body and three-body parameters are handled differently,
as described below.
The two-body parameters are H, eta, lambda1, D, lambda4, W, rc, gamma, and r0.
They appear in the above formulae with two subscripts.
The parameters Zi and Zj are also classified as two-body parameters,
even though they only have 1 subscript.
The three-body parameters are B, C, costheta0.
They appear in the above formulae with three subscripts.
Two-body and three-body parameters are handled differently,
as described below.
</P>
<P>The first element in each entry is the center atom
in a three-body interaction, while the second and third elements
are two neighbor atoms. Three-body parameters for a central atom I
and two neighbors J and K are taken from the IJK entry.
Note that even though three-body parameters do not depend on the order of
J and K, LAMMPS stores three-body parameters for both IJK and IKJ.
The user must ensure that these values are equal.
Two-body parameters for an atom I interacting with atom J are taken from
the IJJ entry, where the 2nd and 3rd
elements are the same. Thus the two-body parameters
for Si interacting with C come from the SiCC entry. Note that even
though two-body parameters (except possibly gamma and r0 in U3)
do not depend on the order of the two elements,
LAMMPS will get the Si-C value from the SiCC entry
and the C-Si value from the CSiSi entry. The user must ensure
that these values are equal. Two-body parameters appearing
in entries where the 2nd and 3rd elements are different are
stored but never used. It is good practice to enter zero for
these values. Note that the three-body function U3 above
contains the two-body parameters gamma and r0. So U3 for a
central C atom bonded to an Si atom and a second C atom
will take three-body parameters from the CSiC entry, but
two-body parameters from the CCC and CSiSi entries.
</P>
<HR>
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+</P>
+<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
+more instructions on how to use the accelerated styles effectively.
+</P>
+<HR>
+
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift, table, and tail options.
</P>
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
</P>
<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
for pair interactions.
</P>
<P>The Vashishta potential files provided with LAMMPS (see the
potentials directory) are parameterized for metal <A HREF = "units.html">units</A>.
You can use the Vashishta potential with any LAMMPS units, but you would need
to create your own Vashishta potential file with coefficients listed in the
appropriate units if your simulation doesn't use "metal" units.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Vashishta1990"></A>
<P><B>(Vashishta1990)</B> P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B 41, 12197 (1990).
</P>
<A NAME = "Vashishta2007"></A>
<P><B>(Vashishta2007)</B> P. Vashishta, R. K. Kalia, A. Nakano, J. P. Rino. J. Appl. Phys. 101, 103515 (2007).
</P>
<A NAME = "Branicio2009"></A>
<P><B>(Branicio2009)</B> Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002
</P>
</HTML>
diff --git a/doc/fix_adapt.html b/doc/fix_adapt.html
index fe2d76637..14ac58eb4 100644
--- a/doc/fix_adapt.html
+++ b/doc/fix_adapt.html
@@ -1,462 +1,466 @@
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<div class="section" id="fix-adapt-command">
<span id="index-0"></span><h1>fix adapt command<a class="headerlink" href="#fix-adapt-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>fix ID group-ID adapt N attribute args ... keyword value ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
<li>adapt = style name of this fix command</li>
<li>N = adapt simulation settings every this many timesteps</li>
<li>one or more attribute/arg pairs may be appended</li>
<li>attribute = <em>pair</em> or <em>kspace</em> or <em>atom</em></li>
</ul>
<pre class="literal-block">
<em>pair</em> args = pstyle pparam I J v_name
pstyle = pair style name, e.g. lj/cut
pparam = parameter to adapt over time
I,J = type pair(s) to set parameter for
v_name = variable with name that calculates value of pparam
<em>kspace</em> arg = v_name
v_name = variable with name that calculates scale factor on K-space terms
<em>atom</em> args = aparam v_name
aparam = parameter to adapt over time
v_name = variable with name that calculates value of aparam
</pre>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>scale</em> or <em>reset</em></li>
</ul>
<pre class="literal-block">
<em>scale</em> value = <em>no</em> or <em>yes</em>
<em>no</em> = the variable value is the new setting
<em>yes</em> = the variable value multiplies the original setting
<em>reset</em> value = <em>no</em> or <em>yes</em>
<em>no</em> = values will remain altered at the end of a run
<em>yes</em> = reset altered values to their original values at the end of a run
</pre>
</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>fix 1 all adapt 1 pair soft a 1 1 v_prefactor
fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
fix 1 all adapt 10 atom diameter v_size
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Change or adapt one or more specific simulation attributes or settings
over time as a simulation runs. Pair potential and K-space and atom
attributes which can be varied by this fix are discussed below. Many
other fixes can also be used to time-vary simulation parameters,
e.g. the “fix deform” command will change the simulation box
size/shape and the “fix move” command will change atom positions and
velocities in a prescribed manner. Also note that many commands allow
variables as arguments for specific parameters, if described in that
manner on their doc pages. An equal-style variable can calculate a
time-dependent quantity, so this is another way to vary a simulation
parameter over time.</p>
<p>If <em>N</em> is specified as 0, the specified attributes are only changed
once, before the simulation begins. This is all that is needed if the
associated variables are not time-dependent. If <em>N</em> > 0, then changes
are made every <em>N</em> steps during the simulation, presumably with a
variable that is time-dependent.</p>
<p>Depending on the value of the <em>reset</em> keyword, attributes changed by
this fix will or will not be reset back to their original values at
the end of a simulation. Even if <em>reset</em> is specified as <em>yes</em>, a
restart file written during a simulation will contain the modified
settings.</p>
<p>If the <em>scale</em> keyword is set to <em>no</em>, then the value the parameter is
set to will be whatever the variable generates. If the <em>scale</em>
keyword is set to <em>yes</em>, then the value of the altered parameter will
be the initial value of that parameter multiplied by whatever the
variable generates. I.e. the variable is now a “scale factor” applied
in (presumably) a time-varying fashion to the parameter.</p>
<p>Note that whether scale is <em>no</em> or <em>yes</em>, internally, the parameters
themselves are actually altered by this fix. Make sure you use the
<em>reset yes</em> option if you want the parameters to be restored to their
initial values after the run.</p>
<hr class="docutils" />
<p>The <em>pair</em> keyword enables various parameters of potentials defined by
the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command to be changed, if the pair
style supports it. Note that the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> and
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> commands must be used in the usual manner
to specify these parameters initially; the fix adapt command simply
overrides the parameters.</p>
<p>The <em>pstyle</em> argument is the name of the pair style. If <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid or hybrid/overlay</em></a> is used, <em>pstyle</em> should be
-a sub-style name. For example, <em>pstyle</em> could be specified as “soft”
-or “lubricate”. The <em>pparam</em> argument is the name of the parameter to
-change. This is the current list of pair styles and parameters that
-can be varied by this fix. See the doc pages for individual pair
-styles and their energy formulas for the meaning of these parameters:</p>
+a sub-style name. If there are multiple sub-styles using the same
+pair style, then <em>pstyle</em> should be specified as “style:N” where N is
+which instance of the pair style you wish to adapt, e.g. the first,
+second, etc. For example, <em>pstyle</em> could be specified as “soft” or
+“lubricate” or “lj/cut:1” or “lj/cut:2”. The <em>pparam</em> argument is the
+name of the parameter to change. This is the current list of pair
+styles and parameters that can be varied by this fix. See the doc
+pages for individual pair styles and their energy formulas for the
+meaning of these parameters:</p>
<table border="1" class="docutils">
<colgroup>
<col width="51%" />
<col width="31%" />
<col width="18%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="pair_born.html"><em>born</em></a></td>
<td>a,b,c</td>
<td>type pairs</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_buck.html"><em>buck</em></a></td>
<td>a,c</td>
<td>type pairs</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><em>coul/cut</em></a></td>
<td>scale</td>
<td>type pairs</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_coul.html"><em>coul/debye</em></a></td>
<td>scale</td>
<td>type pairs</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><em>coul/long</em></a></td>
<td>scale</td>
<td>type pairs</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj.html"><em>lj/cut</em></a></td>
<td>epsilon,sigma</td>
<td>type pairs</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_expand.html"><em>lj/expand</em></a></td>
<td>epsilon,sigma,delta</td>
<td>type pairs</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lubricate.html"><em>lubricate</em></a></td>
<td>mu</td>
<td>global</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_gauss.html"><em>gauss</em></a></td>
<td>a</td>
<td>type pairs</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_morse.html"><em>morse</em></a></td>
<td>d0,r0,alpha</td>
<td>type pairs</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_soft.html"><em>soft</em></a></td>
<td>a</td>
<td>type pairs</td>
</tr>
</tbody>
</table>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">It is easy to add new potentials and their parameters
to this list. All it typically takes is adding an extract() method to
the pair_*.cpp file associated with the potential.</p>
</div>
<p>Some parameters are global settings for the pair style, e.g. the
viscosity setting “mu” for <a class="reference internal" href="pair_lubricate.html"><em>pair_style lubricate</em></a>.
Other parameters apply to atom type pairs within the pair style,
e.g. the prefactor “a” for <a class="reference internal" href="pair_soft.html"><em>pair_style soft</em></a>.</p>
<p>Note that for many of the potentials, the parameter that can be varied
is effectively a prefactor on the entire energy expression for the
potential, e.g. the lj/cut epsilon. The parameters listed as “scale”
are exactly that, since the energy expression for the
<a class="reference internal" href="pair_coul.html"><em>coul/cut</em></a> potential (for example) has no labeled
prefactor in its formula. To apply an effective prefactor to some
potentials, multiple parameters need to be altered. For example, the
<a class="reference internal" href="pair_buck.html"><em>Buckingham potential</em></a> needs both the A and C terms
altered together. To scale the Buckingham potential, you should thus
list the pair style twice, once for A and once for C.</p>
<p>If a type pair parameter is specified, the <em>I</em> and <em>J</em> settings should
be specified to indicate which type pairs to apply it to. If a global
parameter is specified, the <em>I</em> and <em>J</em> settings still need to be
specified, but are ignored.</p>
<p>Similar to the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff command</em></a>, I and J can be
specified in one of two ways. Explicit numeric values can be used for
each, as in the 1st example above. I <= J is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same values.</p>
<p>A wild-card asterisk can be used in place of or in conjunction with
the I,J arguments to set the coefficients for multiple pairs of atom
types. This takes the form “*” or “<em>n” or “n</em>” or “m*n”. If N = the
number of atom types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive). Note that only type pairs with I <= J are considered; if
asterisks imply type pairs where J < I, they are ignored.</p>
<p>IMPROTANT NOTE: If <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid or hybrid/overlay</em></a> is being used, then the <em>pstyle</em> will
be a sub-style name. You must specify I,J arguments that correspond
to type pair values defined (via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>
command) for that sub-style.</p>
<p>The <em>v_name</em> argument for keyword <em>pair</em> is the name of an
<a class="reference internal" href="variable.html"><em>equal-style variable</em></a> which will be evaluated each time
this fix is invoked to set the parameter to a new value. It should be
specified as v_name, where name is the variable name. Equal-style
variables can specify formulas with various mathematical functions,
and include <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command keywords for the
simulation box parameters and timestep and elapsed time. Thus it is
easy to specify parameters that change as a function of time or span
consecutive runs in a continuous fashion. For the latter, see the
<em>start</em> and <em>stop</em> keywords of the <a class="reference internal" href="run.html"><em>run</em></a> command and the
<em>elaplong</em> keyword of <a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> for
details.</p>
<p>For example, these commands would change the prefactor coefficient of
the <a class="reference internal" href="pair_soft.html"><em>pair_style soft</em></a> potential from 10.0 to 30.0 in a
linear fashion over the course of a simulation:</p>
<div class="highlight-python"><div class="highlight"><pre>variable prefactor equal ramp(10,30)
fix 1 all adapt 1 pair soft a * * v_prefactor
</pre></div>
</div>
<hr class="docutils" />
<p>The <em>kspace</em> keyword used the specified variable as a scale factor on
the energy, forces, virial calculated by whatever K-Space solver is
defined by the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command. If the
variable has a value of 1.0, then the solver is unaltered.</p>
<p>The <em>kspace</em> keyword works this way whether the <em>scale</em> keyword
is set to <em>no</em> or <em>yes</em>.</p>
<hr class="docutils" />
<p>The <em>atom</em> keyword enables various atom properties to be changed. The
<em>aparam</em> argument is the name of the parameter to change. This is the
current list of atom parameters that can be varied by this fix:</p>
<ul class="simple">
<li>charge = charge on particle</li>
<li>diameter = diameter of particle</li>
</ul>
<p>The <em>v_name</em> argument of the <em>atom</em> keyword is the name of an
<a class="reference internal" href="variable.html"><em>equal-style variable</em></a> which will be evaluated each time
this fix is invoked to set the parameter to a new value. It should be
specified as v_name, where name is the variable name. See the
discussion above describing the formulas associated with equal-style
variables. The new value is assigned to the corresponding attribute
for all atoms in the fix group.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The <em>atom</em> keyword works this way whether the <em>scale</em>
keyword is set to <em>no</em> or <em>yes</em>. I.e. the use of scale yes is not yet
supported by the <em>atom</em> keyword.</p>
</div>
<p>If the atom parameter is <em>diameter</em> and per-atom density and per-atom
mass are defined for particles (e.g. <a class="reference internal" href="atom_style.html"><em>atom_style granular</em></a>), then the mass of each particle is also
changed when the diameter changes (density is assumed to stay
constant).</p>
<p>For example, these commands would shrink the diameter of all granular
particles in the “center” group from 1.0 to 0.1 in a linear fashion
over the course of a 1000-step simulation:</p>
<div class="highlight-python"><div class="highlight"><pre>variable size equal ramp(1.0,0.1)
fix 1 center adapt 10 atom diameter v_size
</pre></div>
</div>
</div>
<hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. No parameter of this fix can
be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><em>run</em></a> command.
This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
<p>For <a class="reference internal" href="run_style.html"><em>rRESPA time integration</em></a>, this fix changes
parameters on the outermost rRESPA level.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div>none</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_ti.html"><em>compute ti</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
<p>The option defaults are scale = no, reset = no.</p>
</div>
</div>
</div>
</div>
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\ No newline at end of file
diff --git a/doc/fix_adapt.txt b/doc/fix_adapt.txt
index 14c7789cf..a13101257 100644
--- a/doc/fix_adapt.txt
+++ b/doc/fix_adapt.txt
@@ -1,247 +1,251 @@
"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
fix adapt command :h3
[Syntax:]
fix ID group-ID adapt N attribute args ... keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
adapt = style name of this fix command :l
N = adapt simulation settings every this many timesteps :l
one or more attribute/arg pairs may be appended :l
attribute = {pair} or {kspace} or {atom} :l
{pair} args = pstyle pparam I J v_name
pstyle = pair style name, e.g. lj/cut
pparam = parameter to adapt over time
I,J = type pair(s) to set parameter for
v_name = variable with name that calculates value of pparam
{kspace} arg = v_name
v_name = variable with name that calculates scale factor on K-space terms
{atom} args = aparam v_name
aparam = parameter to adapt over time
v_name = variable with name that calculates value of aparam :pre
zero or more keyword/value pairs may be appended :l
keyword = {scale} or {reset} :l
{scale} value = {no} or {yes}
{no} = the variable value is the new setting
{yes} = the variable value multiplies the original setting
{reset} value = {no} or {yes}
{no} = values will remain altered at the end of a run
{yes} = reset altered values to their original values at the end of a run :pre
:ule
[Examples:]
fix 1 all adapt 1 pair soft a 1 1 v_prefactor
fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
fix 1 all adapt 10 atom diameter v_size :pre
[Description:]
Change or adapt one or more specific simulation attributes or settings
over time as a simulation runs. Pair potential and K-space and atom
attributes which can be varied by this fix are discussed below. Many
other fixes can also be used to time-vary simulation parameters,
e.g. the "fix deform" command will change the simulation box
size/shape and the "fix move" command will change atom positions and
velocities in a prescribed manner. Also note that many commands allow
variables as arguments for specific parameters, if described in that
manner on their doc pages. An equal-style variable can calculate a
time-dependent quantity, so this is another way to vary a simulation
parameter over time.
If {N} is specified as 0, the specified attributes are only changed
once, before the simulation begins. This is all that is needed if the
associated variables are not time-dependent. If {N} > 0, then changes
are made every {N} steps during the simulation, presumably with a
variable that is time-dependent.
Depending on the value of the {reset} keyword, attributes changed by
this fix will or will not be reset back to their original values at
the end of a simulation. Even if {reset} is specified as {yes}, a
restart file written during a simulation will contain the modified
settings.
If the {scale} keyword is set to {no}, then the value the parameter is
set to will be whatever the variable generates. If the {scale}
keyword is set to {yes}, then the value of the altered parameter will
be the initial value of that parameter multiplied by whatever the
variable generates. I.e. the variable is now a "scale factor" applied
in (presumably) a time-varying fashion to the parameter.
Note that whether scale is {no} or {yes}, internally, the parameters
themselves are actually altered by this fix. Make sure you use the
{reset yes} option if you want the parameters to be restored to their
initial values after the run.
:line
The {pair} keyword enables various parameters of potentials defined by
the "pair_style"_pair_style.html command to be changed, if the pair
style supports it. Note that the "pair_style"_pair_style.html and
"pair_coeff"_pair_coeff.html commands must be used in the usual manner
to specify these parameters initially; the fix adapt command simply
overrides the parameters.
The {pstyle} argument is the name of the pair style. If "pair_style
hybrid or hybrid/overlay"_pair_hybrid.html is used, {pstyle} should be
-a sub-style name. For example, {pstyle} could be specified as "soft"
-or "lubricate". The {pparam} argument is the name of the parameter to
-change. This is the current list of pair styles and parameters that
-can be varied by this fix. See the doc pages for individual pair
-styles and their energy formulas for the meaning of these parameters:
+a sub-style name. If there are multiple sub-styles using the same
+pair style, then {pstyle} should be specified as "style:N" where N is
+which instance of the pair style you wish to adapt, e.g. the first,
+second, etc. For example, {pstyle} could be specified as "soft" or
+"lubricate" or "lj/cut:1" or "lj/cut:2". The {pparam} argument is the
+name of the parameter to change. This is the current list of pair
+styles and parameters that can be varied by this fix. See the doc
+pages for individual pair styles and their energy formulas for the
+meaning of these parameters:
"born"_pair_born.html: a,b,c: type pairs:
"buck"_pair_buck.html: a,c: type pairs:
"coul/cut"_pair_coul.html: scale: type pairs:
"coul/debye"_pair_coul.html: scale: type pairs:
"coul/long"_pair_coul.html: scale: type pairs:
"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
"lubricate"_pair_lubricate.html: mu: global:
"gauss"_pair_gauss.html: a: type pairs:
"morse"_pair_morse.html: d0,r0,alpha: type pairs:
"soft"_pair_soft.html: a: type pairs :tb(c=3,s=:)
IMPORTANT NOTE: It is easy to add new potentials and their parameters
to this list. All it typically takes is adding an extract() method to
the pair_*.cpp file associated with the potential.
Some parameters are global settings for the pair style, e.g. the
viscosity setting "mu" for "pair_style lubricate"_pair_lubricate.html.
Other parameters apply to atom type pairs within the pair style,
e.g. the prefactor "a" for "pair_style soft"_pair_soft.html.
Note that for many of the potentials, the parameter that can be varied
is effectively a prefactor on the entire energy expression for the
potential, e.g. the lj/cut epsilon. The parameters listed as "scale"
are exactly that, since the energy expression for the
"coul/cut"_pair_coul.html potential (for example) has no labeled
prefactor in its formula. To apply an effective prefactor to some
potentials, multiple parameters need to be altered. For example, the
"Buckingham potential"_pair_buck.html needs both the A and C terms
altered together. To scale the Buckingham potential, you should thus
list the pair style twice, once for A and once for C.
If a type pair parameter is specified, the {I} and {J} settings should
be specified to indicate which type pairs to apply it to. If a global
parameter is specified, the {I} and {J} settings still need to be
specified, but are ignored.
Similar to the "pair_coeff command"_pair_coeff.html, I and J can be
specified in one of two ways. Explicit numeric values can be used for
each, as in the 1st example above. I <= J is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same values.
A wild-card asterisk can be used in place of or in conjunction with
the I,J arguments to set the coefficients for multiple pairs of atom
types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
number of atom types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive). Note that only type pairs with I <= J are considered; if
asterisks imply type pairs where J < I, they are ignored.
IMPROTANT NOTE: If "pair_style hybrid or
hybrid/overlay"_pair_hybrid.html is being used, then the {pstyle} will
be a sub-style name. You must specify I,J arguments that correspond
to type pair values defined (via the "pair_coeff"_pair_coeff.html
command) for that sub-style.
The {v_name} argument for keyword {pair} is the name of an
"equal-style variable"_variable.html which will be evaluated each time
this fix is invoked to set the parameter to a new value. It should be
specified as v_name, where name is the variable name. Equal-style
variables can specify formulas with various mathematical functions,
and include "thermo_style"_thermo_style.html command keywords for the
simulation box parameters and timestep and elapsed time. Thus it is
easy to specify parameters that change as a function of time or span
consecutive runs in a continuous fashion. For the latter, see the
{start} and {stop} keywords of the "run"_run.html command and the
{elaplong} keyword of "thermo_style custom"_thermo_style.html for
details.
For example, these commands would change the prefactor coefficient of
the "pair_style soft"_pair_soft.html potential from 10.0 to 30.0 in a
linear fashion over the course of a simulation:
variable prefactor equal ramp(10,30)
fix 1 all adapt 1 pair soft a * * v_prefactor :pre
:line
The {kspace} keyword used the specified variable as a scale factor on
the energy, forces, virial calculated by whatever K-Space solver is
defined by the "kspace_style"_kspace_style.html command. If the
variable has a value of 1.0, then the solver is unaltered.
The {kspace} keyword works this way whether the {scale} keyword
is set to {no} or {yes}.
:line
The {atom} keyword enables various atom properties to be changed. The
{aparam} argument is the name of the parameter to change. This is the
current list of atom parameters that can be varied by this fix:
charge = charge on particle
diameter = diameter of particle :ul
The {v_name} argument of the {atom} keyword is the name of an
"equal-style variable"_variable.html which will be evaluated each time
this fix is invoked to set the parameter to a new value. It should be
specified as v_name, where name is the variable name. See the
discussion above describing the formulas associated with equal-style
variables. The new value is assigned to the corresponding attribute
for all atoms in the fix group.
IMPORTANT NOTE: The {atom} keyword works this way whether the {scale}
keyword is set to {no} or {yes}. I.e. the use of scale yes is not yet
supported by the {atom} keyword.
If the atom parameter is {diameter} and per-atom density and per-atom
mass are defined for particles (e.g. "atom_style
granular"_atom_style.html), then the mass of each particle is also
changed when the diameter changes (density is assumed to stay
constant).
For example, these commands would shrink the diameter of all granular
particles in the "center" group from 1.0 to 0.1 in a linear fashion
over the course of a 1000-step simulation:
variable size equal ramp(1.0,0.1)
fix 1 center adapt 10 atom diameter v_size :pre
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
For "rRESPA time integration"_run_style.html, this fix changes
parameters on the outermost rRESPA level.
[Restrictions:] none
[Related commands:]
"compute ti"_compute_ti.html
[Default:]
The option defaults are scale = no, reset = no.
diff --git a/doc/fix_ave_correlate.html b/doc/fix_ave_correlate.html
index d9a2b1234..4217690a7 100644
--- a/doc/fix_ave_correlate.html
+++ b/doc/fix_ave_correlate.html
@@ -1,479 +1,483 @@
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<div class="section" id="fix-ave-correlate-command">
<span id="index-0"></span><h1>fix ave/correlate command<a class="headerlink" href="#fix-ave-correlate-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>fix ID group-ID ave/correlate Nevery Nrepeat Nfreq value1 value2 ... keyword args ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
<li>ave/correlate = style name of this fix command</li>
<li>Nevery = use input values every this many timesteps</li>
<li>Nrepeat = # of correlation time windows to accumulate</li>
-<li>Nfreq = calculate tine window averages every this many timesteps</li>
+<li>Nfreq = calculate time window averages every this many timesteps</li>
<li>one or more input values can be listed</li>
<li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
</ul>
<div class="highlight-python"><div class="highlight"><pre>c_ID = global scalar calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID
f_ID = global scalar calculated by a fix with ID
f_ID[I] = Ith component of global vector calculated by a fix with ID
v_name = global value calculated by an equal-style variable with name
</pre></div>
</div>
<ul class="simple">
<li>zero or more keyword/arg pairs may be appended</li>
<li>keyword = <em>type</em> or <em>ave</em> or <em>start</em> or <em>prefactor</em> or <em>file</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
</ul>
<pre class="literal-block">
<em>type</em> arg = <em>auto</em> or <em>upper</em> or <em>lower</em> or <em>auto/upper</em> or <em>auto/lower</em> or <em>full</em>
auto = correlate each value with itself
upper = correlate each value with each succeeding value
lower = correlate each value with each preceding value
auto/upper = auto + upper
auto/lower = auto + lower
full = correlate each value with every other value, including itself = auto + upper + lower
<em>ave</em> args = <em>one</em> or <em>running</em>
one = zero the correlation accumulation every Nfreq steps
running = accumulate correlations continuously
<em>start</em> args = Nstart
Nstart = start accumulating correlations on this timestep
<em>prefactor</em> args = value
value = prefactor to scale all the correlation data by
<em>file</em> arg = filename
filename = name of file to output correlation data to
<em>overwrite</em> arg = none = overwrite output file with only latest output
<em>title1</em> arg = string
string = text to print as 1st line of output file
<em>title2</em> arg = string
string = text to print as 2nd line of output file
<em>title3</em> arg = string
string = text to print as 3rd line of output file
</pre>
</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>fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
fix 1 all ave/correlate 1 50 10000 &
c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
type upper ave running title1 "My correlation data"
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Use one or more global scalar values as inputs every few timesteps,
calculate time correlations bewteen them at varying time intervals,
and average the correlation data over longer timescales. The
resulting correlation values can be time integrated by
-<a class="reference internal" href="variable.html"><em>variables</em></a> or used by other <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a> such as <a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a>, and can also be written to a file.</p>
+<a class="reference internal" href="variable.html"><em>variables</em></a> or used by other <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a> such as <a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a>, and can also be written to a file. See the
+<a class="reference internal" href="fix_ave_correlate_long.html"><em>fix ave/correlate/long</em></a> command for an
+alternate method for computing correlation functions efficiently over
+very long time windows.</p>
<p>The group specified with this command is ignored. However, note that
specified values may represent calculations performed by computes and
fixes which store their own “group” definitions.</p>
<p>Each listed value can be the result of a <a class="reference internal" href="compute.html"><em>compute</em></a> or
<a class="reference internal" href="fix.html"><em>fix</em></a> or the evaluation of an equal-style
<a class="reference internal" href="variable.html"><em>variable</em></a>. In each case, the compute, fix, or variable
must produce a global quantity, not a per-atom or local quantity. If
you wish to spatial- or time-average or histogram per-atom quantities
from a compute, fix, or variable, then see the <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a>, <a class="reference internal" href="fix_ave_atom.html"><em>fix ave/atom</em></a>,
or <a class="reference internal" href="fix_ave_histo.html"><em>fix ave/histo</em></a> commands. If you wish to sum a
per-atom quantity into a single global quantity, see the <a class="reference internal" href="compute_reduce.html"><em>compute reduce</em></a> command.</p>
<p><a class="reference internal" href="compute.html"><em>Computes</em></a> that produce global quantities are those which
do not have the word <em>atom</em> in their style name. Only a few
<a class="reference internal" href="fix.html"><em>fixes</em></a> produce global quantities. See the doc pages for
individual fixes for info on which ones produce such values.
<a class="reference internal" href="variable.html"><em>Variables</em></a> of style <em>equal</em> are the only ones that can
be used with this fix. Variables of style <em>atom</em> cannot be used,
since they produce per-atom values.</p>
<p>The input values must either be all scalars. What kinds of
correlations between input values are calculated is determined by the
<em>type</em> keyword as discussed below.</p>
<hr class="docutils" />
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
timesteps the input values will be used to calculate correlation data.
The input values are sampled every <em>Nevery</em> timesteps. The
correlation data for the preceding samples is computed on timesteps
that are a multiple of <em>Nfreq</em>. Consider a set of samples from some
initial time up to an output timestep. The initial time could be the
beginning of the simulation or the last output time; see the <em>ave</em>
keyword for options. For the set of samples, the correlation value
Cij is calculated as:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">Cij</span><span class="p">(</span><span class="n">delta</span><span class="p">)</span> <span class="o">=</span> <span class="n">ave</span><span class="p">(</span><span class="n">Vi</span><span class="p">(</span><span class="n">t</span><span class="p">)</span><span class="o">*</span><span class="n">Vj</span><span class="p">(</span><span class="n">t</span><span class="o">+</span><span class="n">delta</span><span class="p">))</span>
</pre></div>
</div>
<p>which is the correlation value between input values Vi and Vj,
separated by time delta. Note that the second value Vj in the pair is
always the one sampled at the later time. The ave() represents an
average over every pair of samples in the set that are separated by
time delta. The maximum delta used is of size (<em>Nrepeat</em>-1)**Nevery*.
Thus the correlation between a pair of input values yields <em>Nrepeat</em>
correlation datums:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">Cij</span><span class="p">(</span><span class="mi">0</span><span class="p">),</span> <span class="n">Cij</span><span class="p">(</span><span class="n">Nevery</span><span class="p">),</span> <span class="n">Cij</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">Nevery</span><span class="p">),</span> <span class="o">...</span><span class="p">,</span> <span class="n">Cij</span><span class="p">((</span><span class="n">Nrepeat</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="n">Nevery</span><span class="p">)</span>
</pre></div>
</div>
<p>For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on
timesteps 0,5,10,15,...,100 will be used to compute the final averages
on timestep 100. Six averages will be computed: Cij(0), Cij(5),
Cij(10), Cij(15), Cij(20), and Cij(25). Cij(10) on timestep 100 will
be the average of 19 samples, namely Vi(0)*Vj(10), Vi(5)*Vj(15),
Vi(10)*V j20), Vi(15)*Vj(25), ..., Vi(85)*Vj(95), Vi(90)*Vj(100).</p>
<p><em>Nfreq</em> must be a multiple of <em>Nevery</em>; <em>Nevery</em> and <em>Nrepeat</em> must be
non-zero. Also, if the <em>ave</em> keyword is set to <em>one</em> which is the
default, then <em>Nfreq</em> >= (<em>Nrepeat</em>-1)**Nevery* is required.</p>
<hr class="docutils" />
<p>If a value begins with “<a href="#id3"><span class="problematic" id="id4">c_</span></a>”, a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the compute is used. If a
bracketed term is appended, the Ith element of the global vector
calculated by the compute is used.</p>
<p>Note that there is a <a class="reference internal" href="compute_reduce.html"><em>compute reduce</em></a> command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix ave/correlate. Or it can be a compute
defined not in your input script, but by <a class="reference internal" href="thermo_style.html"><em>thermodynamic output</em></a> or other fixes such as <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>
or <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a>. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><em>add them to LAMMPS</em></a>.</p>
<p>If a value begins with “<a href="#id5"><span class="problematic" id="id6">f_</span></a>”, a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the fix is used. If a
bracketed term is appended, the Ith element of the global vector
calculated by the fix is used.</p>
<p>Note that some fixes only produce their values on certain timesteps,
which must be compatible with <em>Nevery</em>, else an error will result.
Users can also write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><em>add them to LAMMPS</em></a>.</p>
<p>If a value begins with “<a href="#id7"><span class="problematic" id="id8">v_</span></a>”, a variable name must follow which has
been previously defined in the input script. Only equal-style
variables can be referenced. See the <a class="reference internal" href="variable.html"><em>variable</em></a> command
for details. Note that variables of style <em>equal</em> define a formula
which can reference individual atom properties or thermodynamic
keywords, or they can invoke other computes, fixes, or variables when
they are evaluated, so this is a very general means of specifying
quantities to time correlate.</p>
<hr class="docutils" />
<p>Additional optional keywords also affect the operation of this fix.</p>
<p>The <em>type</em> keyword determines which pairs of input values are
correlated with each other. For N input values Vi, for i = 1 to N,
let the number of pairs = Npair. Note that the second value in the
pair Vi(t)*Vj(t+delta) is always the one sampled at the later time.</p>
<ul class="simple">
<li>If <em>type</em> is set to <em>auto</em> then each input value is correlated with
itself. I.e. Cii = Vi*Vi, for i = 1 to N, so Npair = N.</li>
<li>If <em>type</em> is set
to <em>upper</em> then each input value is correlated with every succeeding
value. I.e. Cij = Vi*Vj, for i < j, so Npair = N*(N-1)/2.</li>
<li>If <em>type</em> is set
to <em>lower</em> then each input value is correlated with every preceeding
value. I.e. Cij = Vi*Vj, for i > j, so Npair = N*(N-1)/2.</li>
<li>If <em>type</em> is set to <em>auto/upper</em> then each input value is correlated
with itself and every succeeding value. I.e. Cij = Vi*Vj, for i >= j,
so Npair = N*(N+1)/2.</li>
<li>If <em>type</em> is set to <em>auto/lower</em> then each input value is correlated
with itself and every preceding value. I.e. Cij = Vi*Vj, for i <= j,
so Npair = N*(N+1)/2.</li>
<li>If <em>type</em> is set to <em>full</em> then each input value is correlated with
itself and every other value. I.e. Cij = Vi*Vj, for i,j = 1,N so
Npair = N^2.</li>
</ul>
<p>The <em>ave</em> keyword determines what happens to the accumulation of
correlation samples every <em>Nfreq</em> timesteps. If the <em>ave</em> setting is
<em>one</em>, then the accumulation is restarted or zeroed every <em>Nfreq</em>
timesteps. Thus the outputs on successive <em>Nfreq</em> timesteps are
essentially independent of each other. The exception is that the
Cij(0) = Vi(T)*Vj(T) value at a timestep T, where T is a multiple of
<em>Nfreq</em>, contributes to the correlation output both at time T and at
time T+Nfreq.</p>
<p>If the <em>ave</em> setting is <em>running</em>, then the accumulation is never
zeroed. Thus the output of correlation data at any timestep is the
average over samples accumulated every <em>Nevery</em> steps since the fix
was defined. it can only be restarted by deleting the fix via the
<a class="reference internal" href="unfix.html"><em>unfix</em></a> command, or by re-defining the fix by re-specifying
it.</p>
<p>The <em>start</em> keyword specifies what timestep the accumulation of
correlation samples will begin on. The default is step 0. Setting it
to a larger value can avoid adding non-equilibrated data to the
correlation averages.</p>
<p>The <em>prefactor</em> keyword specifies a constant which will be used as a
multiplier on the correlation data after it is averaged. It is
effectively a scale factor on Vi*Vj, which can be used to account for
the size of the time window or other unit conversions.</p>
<p>The <em>file</em> keyword allows a filename to be specified. Every <em>Nfreq</em>
steps, an array of correlation data is written to the file. The
number of rows is <em>Nrepeat</em>, as described above. The number of
columns is the Npair+2, also as described above. Thus the file ends
up to be a series of these array sections.</p>
<p>The <em>overwrite</em> keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of
output. This option can only be used with the <em>ave running</em> setting.</p>
<p>The <em>title1</em> and <em>title2</em> and <em>title3</em> keywords allow specification of
the strings that will be printed as the first 3 lines of the output
file, assuming the <em>file</em> keyword was used. LAMMPS uses default
values for each of these, so they do not need to be specified.</p>
<p>By default, these header lines are as follows:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># Time-correlated data for fix ID</span>
<span class="c"># TimeStep Number-of-time-windows</span>
<span class="c"># Index TimeDelta Ncount valueI*valueJ valueI*valueJ ...</span>
</pre></div>
</div>
<p>In the first line, ID is replaced with the fix-ID. The second line
describes the two values that are printed at the first of each section
of output. In the third line the value pairs are replaced with the
appropriate fields from the fix ave/correlate command.</p>
<hr class="docutils" />
<p>Let Sij = a set of time correlation data for input values I and J,
namely the <em>Nrepeat</em> values:</p>
<div class="highlight-python"><div class="highlight"><pre>Sij = Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij(*Nrepeat-1)*Nevery)
</pre></div>
</div>
<p>As explained below, these datums are output as one column of a global
array, which is effectively the correlation matrix.</p>
<p>The <em>trap</em> function defined for <a class="reference internal" href="variable.html"><em>equal-style variables</em></a>
can be used to perform a time integration of this vector of datums,
using a trapezoidal rule. This is useful for calculating various
quantities which can be derived from time correlation data. If a
normalization factor is needed for the time integration, it can be
included in the variable formula or via the <em>prefactor</em> keyword.</p>
</div>
<hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options
are relevant to this fix.</p>
<p>This fix computes a global array of values which can be accessed by
various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The values can
only be accessed on timesteps that are multiples of <em>Nfreq</em> since that
is when averaging is performed. The global array has # of rows =
<em>Nrepeat</em> and # of columns = Npair+2. The first column has the time
delta (in timesteps) between the pairs of input values used to
calculate the correlation, as described above. The 2nd column has the
number of samples contributing to the correlation average, as
described above. The remaining Npair columns are for I,J pairs of the
N input values, as determined by the <em>type</em> keyword, as described
above.</p>
<ul class="simple">
<li>For <em>type</em> = <em>auto</em>, the Npair = N columns are ordered: C11, C22, ...,
CNN.</li>
<li>For <em>type</em> = <em>upper</em>, the Npair = N*(N-1)/2 columns are ordered: C12,
C13, ..., C1N, C23, ..., C2N, C34, ..., CN-1N.</li>
<li>For <em>type</em> = <em>lower</em>, the Npair = N*(N-1)/2 columns are ordered: C21,
C31, C32, C41, C42, C43, ..., CN1, CN2, ..., CNN-1.</li>
<li>For <em>type</em> = <em>auto/upper</em>, the Npair = N*(N+1)/2 columns are ordered:
C11, C12, C13, ..., C1N, C22, C23, ..., C2N, C33, C34, ..., CN-1N,
CNN.</li>
<li>For <em>type</em> = <em>auto/lower</em>, the Npair = N*(N+1)/2 columns are ordered:
C11, C21, C22, C31, C32, C33, C41, ..., C44, CN1, CN2, ..., CNN-1,
CNN.</li>
<li>For <em>type</em> = <em>full</em>, the Npair = N^2 columns are ordered: C11, C12,
..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1,
CNN.</li>
</ul>
<p>The array values calculated by this fix are treated as “intensive”.
If you need to divide them by the number of atoms, you must do this in
a later processing step, e.g. when using them in a
<a class="reference internal" href="variable.html"><em>variable</em></a>.</p>
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
the <a class="reference internal" href="run.html"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div>none</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.html"><em>compute</em></a>, <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>, <a class="reference internal" href="fix_ave_atom.html"><em>fix ave/atom</em></a>, <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a>,
+<p><a class="reference internal" href="fix_ave_correlate_long.html"><em>fix ave/correlate/long</em></a>,
+<a class="reference internal" href="compute.html"><em>compute</em></a>, <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>, <a class="reference internal" href="fix_ave_atom.html"><em>fix ave/atom</em></a>, <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a>,
<a class="reference internal" href="fix_ave_histo.html"><em>fix ave/histo</em></a>, <a class="reference internal" href="variable.html"><em>variable</em></a></p>
<p><strong>Default:</strong> none</p>
<p>The option defaults are ave = one, type = auto, start = 0, no file
output, title 1,2,3 = strings as described above, and prefactor = 1.0.</p>
</div>
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diff --git a/doc/fix_ave_correlate.txt b/doc/fix_ave_correlate.txt
index 47036af03..6ad218c46 100644
--- a/doc/fix_ave_correlate.txt
+++ b/doc/fix_ave_correlate.txt
@@ -1,334 +1,338 @@
"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
fix ave/correlate command :h3
[Syntax:]
fix ID group-ID ave/correlate Nevery Nrepeat Nfreq value1 value2 ... keyword args ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
ave/correlate = style name of this fix command :l
Nevery = use input values every this many timesteps :l
Nrepeat = # of correlation time windows to accumulate :l
-Nfreq = calculate tine window averages every this many timesteps :l
+Nfreq = calculate time window averages every this many timesteps :l
one or more input values can be listed :l
value = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
c_ID = global scalar calculated by a compute with ID
c_ID\[I\] = Ith component of global vector calculated by a compute with ID
f_ID = global scalar calculated by a fix with ID
f_ID\[I\] = Ith component of global vector calculated by a fix with ID
v_name = global value calculated by an equal-style variable with name :pre
zero or more keyword/arg pairs may be appended :l
keyword = {type} or {ave} or {start} or {prefactor} or {file} or {overwrite} or {title1} or {title2} or {title3} :l
{type} arg = {auto} or {upper} or {lower} or {auto/upper} or {auto/lower} or {full}
auto = correlate each value with itself
upper = correlate each value with each succeeding value
lower = correlate each value with each preceding value
auto/upper = auto + upper
auto/lower = auto + lower
full = correlate each value with every other value, including itself = auto + upper + lower
{ave} args = {one} or {running}
one = zero the correlation accumulation every Nfreq steps
running = accumulate correlations continuously
{start} args = Nstart
Nstart = start accumulating correlations on this timestep
{prefactor} args = value
value = prefactor to scale all the correlation data by
{file} arg = filename
filename = name of file to output correlation data to
{overwrite} arg = none = overwrite output file with only latest output
{title1} arg = string
string = text to print as 1st line of output file
{title2} arg = string
string = text to print as 2nd line of output file
{title3} arg = string
string = text to print as 3rd line of output file :pre
:ule
[Examples:]
fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
fix 1 all ave/correlate 1 50 10000 &
c_thermo_press\[1\] c_thermo_press\[2\] c_thermo_press\[3\] &
type upper ave running title1 "My correlation data" :pre
[Description:]
Use one or more global scalar values as inputs every few timesteps,
calculate time correlations bewteen them at varying time intervals,
and average the correlation data over longer timescales. The
resulting correlation values can be time integrated by
"variables"_variable.html or used by other "output
commands"_Section_howto.html#howto_15 such as "thermo_style
-custom"_thermo_style.html, and can also be written to a file.
+custom"_thermo_style.html, and can also be written to a file. See the
+"fix ave/correlate/long"_fix_ave_correlate_long.html command for an
+alternate method for computing correlation functions efficiently over
+very long time windows.
The group specified with this command is ignored. However, note that
specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
Each listed value can be the result of a "compute"_compute.html or
"fix"_fix.html or the evaluation of an equal-style
"variable"_variable.html. In each case, the compute, fix, or variable
must produce a global quantity, not a per-atom or local quantity. If
you wish to spatial- or time-average or histogram per-atom quantities
from a compute, fix, or variable, then see the "fix
ave/spatial"_fix_ave_spatial.html, "fix ave/atom"_fix_ave_atom.html,
or "fix ave/histo"_fix_ave_histo.html commands. If you wish to sum a
per-atom quantity into a single global quantity, see the "compute
reduce"_compute_reduce.html command.
"Computes"_compute.html that produce global quantities are those which
do not have the word {atom} in their style name. Only a few
"fixes"_fix.html produce global quantities. See the doc pages for
individual fixes for info on which ones produce such values.
"Variables"_variable.html of style {equal} are the only ones that can
be used with this fix. Variables of style {atom} cannot be used,
since they produce per-atom values.
The input values must either be all scalars. What kinds of
correlations between input values are calculated is determined by the
{type} keyword as discussed below.
:line
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
timesteps the input values will be used to calculate correlation data.
The input values are sampled every {Nevery} timesteps. The
correlation data for the preceding samples is computed on timesteps
that are a multiple of {Nfreq}. Consider a set of samples from some
initial time up to an output timestep. The initial time could be the
beginning of the simulation or the last output time; see the {ave}
keyword for options. For the set of samples, the correlation value
Cij is calculated as:
Cij(delta) = ave(Vi(t)*Vj(t+delta)) :pre
which is the correlation value between input values Vi and Vj,
separated by time delta. Note that the second value Vj in the pair is
always the one sampled at the later time. The ave() represents an
average over every pair of samples in the set that are separated by
time delta. The maximum delta used is of size ({Nrepeat}-1)*{Nevery}.
Thus the correlation between a pair of input values yields {Nrepeat}
correlation datums:
Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij((Nrepeat-1)*Nevery) :pre
For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on
timesteps 0,5,10,15,...,100 will be used to compute the final averages
on timestep 100. Six averages will be computed: Cij(0), Cij(5),
Cij(10), Cij(15), Cij(20), and Cij(25). Cij(10) on timestep 100 will
be the average of 19 samples, namely Vi(0)*Vj(10), Vi(5)*Vj(15),
Vi(10)*V j20), Vi(15)*Vj(25), ..., Vi(85)*Vj(95), Vi(90)*Vj(100).
{Nfreq} must be a multiple of {Nevery}; {Nevery} and {Nrepeat} must be
non-zero. Also, if the {ave} keyword is set to {one} which is the
default, then {Nfreq} >= ({Nrepeat}-1)*{Nevery} is required.
:line
If a value begins with "c_", a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the compute is used. If a
bracketed term is appended, the Ith element of the global vector
calculated by the compute is used.
Note that there is a "compute reduce"_compute_reduce.html command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix ave/correlate. Or it can be a compute
defined not in your input script, but by "thermodynamic
output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html
or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and "add them to
LAMMPS"_Section_modify.html.
If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the fix is used. If a
bracketed term is appended, the Ith element of the global vector
calculated by the fix is used.
Note that some fixes only produce their values on certain timesteps,
which must be compatible with {Nevery}, else an error will result.
Users can also write code for their own fix styles and "add them to
LAMMPS"_Section_modify.html.
If a value begins with "v_", a variable name must follow which has
been previously defined in the input script. Only equal-style
variables can be referenced. See the "variable"_variable.html command
for details. Note that variables of style {equal} define a formula
which can reference individual atom properties or thermodynamic
keywords, or they can invoke other computes, fixes, or variables when
they are evaluated, so this is a very general means of specifying
quantities to time correlate.
:line
Additional optional keywords also affect the operation of this fix.
The {type} keyword determines which pairs of input values are
correlated with each other. For N input values Vi, for i = 1 to N,
let the number of pairs = Npair. Note that the second value in the
pair Vi(t)*Vj(t+delta) is always the one sampled at the later time.
If {type} is set to {auto} then each input value is correlated with
itself. I.e. Cii = Vi*Vi, for i = 1 to N, so Npair = N. :ulb,l
If {type} is set
to {upper} then each input value is correlated with every succeeding
value. I.e. Cij = Vi*Vj, for i < j, so Npair = N*(N-1)/2. :l
If {type} is set
to {lower} then each input value is correlated with every preceeding
value. I.e. Cij = Vi*Vj, for i > j, so Npair = N*(N-1)/2. :l
If {type} is set to {auto/upper} then each input value is correlated
with itself and every succeeding value. I.e. Cij = Vi*Vj, for i >= j,
so Npair = N*(N+1)/2. :l
If {type} is set to {auto/lower} then each input value is correlated
with itself and every preceding value. I.e. Cij = Vi*Vj, for i <= j,
so Npair = N*(N+1)/2. :l
If {type} is set to {full} then each input value is correlated with
itself and every other value. I.e. Cij = Vi*Vj, for i,j = 1,N so
Npair = N^2. :l,ule
The {ave} keyword determines what happens to the accumulation of
correlation samples every {Nfreq} timesteps. If the {ave} setting is
{one}, then the accumulation is restarted or zeroed every {Nfreq}
timesteps. Thus the outputs on successive {Nfreq} timesteps are
essentially independent of each other. The exception is that the
Cij(0) = Vi(T)*Vj(T) value at a timestep T, where T is a multiple of
{Nfreq}, contributes to the correlation output both at time T and at
time T+Nfreq.
If the {ave} setting is {running}, then the accumulation is never
zeroed. Thus the output of correlation data at any timestep is the
average over samples accumulated every {Nevery} steps since the fix
was defined. it can only be restarted by deleting the fix via the
"unfix"_unfix.html command, or by re-defining the fix by re-specifying
it.
The {start} keyword specifies what timestep the accumulation of
correlation samples will begin on. The default is step 0. Setting it
to a larger value can avoid adding non-equilibrated data to the
correlation averages.
The {prefactor} keyword specifies a constant which will be used as a
multiplier on the correlation data after it is averaged. It is
effectively a scale factor on Vi*Vj, which can be used to account for
the size of the time window or other unit conversions.
The {file} keyword allows a filename to be specified. Every {Nfreq}
steps, an array of correlation data is written to the file. The
number of rows is {Nrepeat}, as described above. The number of
columns is the Npair+2, also as described above. Thus the file ends
up to be a series of these array sections.
The {overwrite} keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of
output. This option can only be used with the {ave running} setting.
The {title1} and {title2} and {title3} keywords allow specification of
the strings that will be printed as the first 3 lines of the output
file, assuming the {file} keyword was used. LAMMPS uses default
values for each of these, so they do not need to be specified.
By default, these header lines are as follows:
# Time-correlated data for fix ID
# TimeStep Number-of-time-windows
# Index TimeDelta Ncount valueI*valueJ valueI*valueJ ... :pre
In the first line, ID is replaced with the fix-ID. The second line
describes the two values that are printed at the first of each section
of output. In the third line the value pairs are replaced with the
appropriate fields from the fix ave/correlate command.
:line
Let Sij = a set of time correlation data for input values I and J,
namely the {Nrepeat} values:
Sij = Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij(*Nrepeat-1)*Nevery) :pre
As explained below, these datums are output as one column of a global
array, which is effectively the correlation matrix.
The {trap} function defined for "equal-style variables"_variable.html
can be used to perform a time integration of this vector of datums,
using a trapezoidal rule. This is useful for calculating various
quantities which can be derived from time correlation data. If a
normalization factor is needed for the time integration, it can be
included in the variable formula or via the {prefactor} keyword.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global array of values which can be accessed by
various "output commands"_Section_howto.html#howto_15. The values can
only be accessed on timesteps that are multiples of {Nfreq} since that
is when averaging is performed. The global array has # of rows =
{Nrepeat} and # of columns = Npair+2. The first column has the time
delta (in timesteps) between the pairs of input values used to
calculate the correlation, as described above. The 2nd column has the
number of samples contributing to the correlation average, as
described above. The remaining Npair columns are for I,J pairs of the
N input values, as determined by the {type} keyword, as described
above.
For {type} = {auto}, the Npair = N columns are ordered: C11, C22, ...,
CNN. :ulb,l
For {type} = {upper}, the Npair = N*(N-1)/2 columns are ordered: C12,
C13, ..., C1N, C23, ..., C2N, C34, ..., CN-1N. :l
For {type} = {lower}, the Npair = N*(N-1)/2 columns are ordered: C21,
C31, C32, C41, C42, C43, ..., CN1, CN2, ..., CNN-1. :l
For {type} = {auto/upper}, the Npair = N*(N+1)/2 columns are ordered:
C11, C12, C13, ..., C1N, C22, C23, ..., C2N, C33, C34, ..., CN-1N,
CNN. :l
For {type} = {auto/lower}, the Npair = N*(N+1)/2 columns are ordered:
C11, C21, C22, C31, C32, C33, C41, ..., C44, CN1, CN2, ..., CNN-1,
CNN. :l
For {type} = {full}, the Npair = N^2 columns are ordered: C11, C12,
..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1,
CNN. :l,ule
The array values calculated by this fix are treated as "intensive".
If you need to divide them by the number of atoms, you must do this in
a later processing step, e.g. when using them in a
"variable"_variable.html.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:]
+"fix ave/correlate/long"_fix_ave_correlate_long.html,
"compute"_compute.html, "fix ave/time"_fix_ave_time.html, "fix
ave/atom"_fix_ave_atom.html, "fix ave/spatial"_fix_ave_spatial.html,
"fix ave/histo"_fix_ave_histo.html, "variable"_variable.html
[Default:] none
The option defaults are ave = one, type = auto, start = 0, no file
output, title 1,2,3 = strings as described above, and prefactor = 1.0.
diff --git a/doc/fix_ave_correlate_long.html b/doc/fix_ave_correlate_long.html
new file mode 100644
index 000000000..f1c8bf529
--- /dev/null
+++ b/doc/fix_ave_correlate_long.html
@@ -0,0 +1,317 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
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+ <title>fix ave/correlate/long command — LAMMPS 15 May 2015 version documentation</title>
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+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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+
+ <div class="section" id="fix-ave-correlate-long-command">
+<span id="index-0"></span><h1>fix ave/correlate/long command<a class="headerlink" href="#fix-ave-correlate-long-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>fix ID group-ID ave/correlate/long Nevery Nfreq value1 value2 ... keyword args ...
+</pre></div>
+</div>
+<ul class="simple">
+<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
+<li>ave/correlate/long = style name of this fix command</li>
+<li>Nevery = use input values every this many timesteps</li>
+<li>Nfreq = save state of the time correlation functions every this many timesteps</li>
+<li>one or more input values can be listed</li>
+<li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
+</ul>
+<div class="highlight-python"><div class="highlight"><pre>c_ID = global scalar calculated by a compute with ID
+c_ID[I] = Ith component of global vector calculated by a compute with ID
+f_ID = global scalar calculated by a fix with ID
+f_ID[I] = Ith component of global vector calculated by a fix with ID
+v_name = global value calculated by an equal-style variable with name
+</pre></div>
+</div>
+<ul class="simple">
+<li>zero or more keyword/arg pairs may be appended</li>
+<li>keyword = <em>type</em> or <em>start</em> or <em>file</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>ncorr</em> or <em>p</em> or <em>m</em></li>
+</ul>
+<pre class="literal-block">
+<em>type</em> arg = <em>auto</em> or <em>upper</em> or <em>lower</em> or <em>auto/upper</em> or <em>auto/lower</em> or <em>full</em>
+ auto = correlate each value with itself
+ upper = correlate each value with each succeeding value
+ lower = correlate each value with each preceding value
+ auto/upper = auto + upper
+ auto/lower = auto + lower
+ full = correlate each value with every other value, including itself = auto + upper + lower
+<em>start</em> args = Nstart
+ Nstart = start accumulating correlations on this timestep
+<em>file</em> arg = filename
+ filename = name of file to output correlation data to
+<em>overwrite</em> arg = none = overwrite output file with only latest output
+<em>title1</em> arg = string
+ string = text to print as 1st line of output file
+<em>title2</em> arg = string
+ string = text to print as 2nd line of output file
+<em>ncorr</em> arg = Ncorrelators
+ Ncorrelators = number of correlators to store
+<em>nlen</em> args = Nlen
+ Nlen = length of each correlator
+<em>ncount</em> args = Ncount
+ Ncount = number of values over which succesive correlators are averaged
+</pre>
+</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>fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
+fix 1 all ave/correlate/long 1 10000 &
+ c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
+ type upper title1 "My correlation data" nlen 15 ncount 3
+</pre></div>
+</div>
+</div>
+<div class="section" id="description">
+<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
+<p>This fix is similar in spirit and syntax to the <a class="reference internal" href="fix_ave_correlate.html"><em>fix ave/correlate</em></a>. However, this fix allows the
+efficient calculation of time correlation functions on the fly over
+extremely long time windows without too much CPU overhead, using a
+multiple-tau method <a class="reference internal" href="#ramirez"><span>(Ramirez)</span></a> that decreases the resolution
+of the stored correlation function with time.</p>
+<p>The group specified with this command is ignored. However, note that
+specified values may represent calculations performed by computes and
+fixes which store their own “group” definitions.</p>
+<p>Each listed value can be the result of a compute or fix or the
+evaluation of an equal-style variable. See the <a class="reference internal" href="fix_ave_correlate.html"><em>fix ave/correlate</em></a> doc page for details.</p>
+<p>The <em>Nevery</em> and <em>Nfreq</em> arguments specify on what timesteps the input
+values will be used to calculate correlation data, and the frequency
+with which the time correlation functions will be output to a file.
+Note that there is no <em>Nrepeat</em> argument, unlike the <a class="reference internal" href="fix_ave_correlate.html"><em>fix ave/correlate</em></a> command.</p>
+<p>The optional keywords <em>ncorr</em>, <em>nlen</em>, and <em>ncount</em> are unique to this
+command and determine the number of correlation points calculated and
+the memory and CPU overhead used by this calculation. <em>Nlen</em> and
+<em>ncount</em> determine the amount of averaging done at longer correlation
+times. The default values <em>nlen=16</em>, <em>ncount=2</em> ensure that the
+systematic error of the multiple-tau correlator is always below the
+level of the statistical error of a typical simulation (which depends
+on the ensemble size and the simulation length).</p>
+<p>The maximum correlation time (in time steps) that can be reached is
+given by the formula (nlen-1) * ncount^(ncorr-1). Longer correlation
+times are discarded and not calculated. With the default values of
+the parameters (ncorr=20, nlen=16 and ncount=2), this corresponds to
+7864320 time steps. If longer correlation times are needed, the value
+of ncorr should be increased. Using nlen=16 and ncount=2, with
+ncorr=30, the maximum number of steps that can be correlated is
+80530636808. If ncorr=40, correlation times in excess of 8e12 time
+steps can be calculated.</p>
+<p>The total memory needed for each correlation pair is roughly
+4*ncorr*nlen*8 bytes. With the default values of the parameters, this
+corresponds to about 10 KB.</p>
+<p>For the meaning of the additional optional keywords, see the <a class="reference internal" href="fix_ave_correlate.html"><em>fix ave/correlate</em></a> doc page.</p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
+<p>Since this fix in intended for the calculation of time correlation
+functions over very long MD simulations, the information about this
+fix is written automatically to binary restart files, so that the time
+correlation calculation can continue in subsequent simulations. None
+of the fix_modify options are relevant to this fix.</p>
+<p>No parameter of this fix can be used with the start/stop keywords of
+the run command. This fix is not invoked during energy minimization.</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-MISC 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_ave_correlate.html"><em>fix ave/correlate</em></a></p>
+<p><strong>Default:</strong> none</p>
+<p>The option defaults for keywords that are also keywords for the <a class="reference internal" href="fix_ave_correlate.html"><em>fix ave/correlate</em></a> command are as follows: type =
+auto, start = 0, no file output, title 1,2 = strings as described on
+the <a class="reference internal" href="fix_ave_correlate.html"><em>fix ave/correlate</em></a> doc page.</p>
+<p>The option defaults for keywords unique to this command are as
+follows: ncorr=20, nlen=16, ncount=2.</p>
+<hr class="docutils" />
+<p id="ramirez"><strong>(Ramirez)</strong> J. Ramirez, S.K. Sukumaran, B. Vorselaars and
+A.E. Likhtman, J. Chem. Phys. 133, 154103 (2010).</p>
+</div>
+</div>
+
+
+ </div>
+ </div>
+ <footer>
+
+
+ <hr/>
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+ <div role="contentinfo">
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+ <script type="text/javascript">
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\ No newline at end of file
diff --git a/doc/fix_ave_correlate_long.txt b/doc/fix_ave_correlate_long.txt
new file mode 100644
index 000000000..e744ad4cb
--- /dev/null
+++ b/doc/fix_ave_correlate_long.txt
@@ -0,0 +1,144 @@
+"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
+
+fix ave/correlate/long command :h3
+
+[Syntax:]
+
+fix ID group-ID ave/correlate/long Nevery Nfreq value1 value2 ... keyword args ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+ave/correlate/long = style name of this fix command :l
+Nevery = use input values every this many timesteps :l
+Nfreq = save state of the time correlation functions every this many timesteps :l
+one or more input values can be listed :l
+value = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
+ c_ID = global scalar calculated by a compute with ID
+ c_ID\[I\] = Ith component of global vector calculated by a compute with ID
+ f_ID = global scalar calculated by a fix with ID
+ f_ID\[I\] = Ith component of global vector calculated by a fix with ID
+ v_name = global value calculated by an equal-style variable with name :pre
+
+zero or more keyword/arg pairs may be appended :l
+keyword = {type} or {start} or {file} or {overwrite} or {title1} or {title2} or {ncorr} or {p} or {m} :l
+ {type} arg = {auto} or {upper} or {lower} or {auto/upper} or {auto/lower} or {full}
+ auto = correlate each value with itself
+ upper = correlate each value with each succeeding value
+ lower = correlate each value with each preceding value
+ auto/upper = auto + upper
+ auto/lower = auto + lower
+ full = correlate each value with every other value, including itself = auto + upper + lower
+ {start} args = Nstart
+ Nstart = start accumulating correlations on this timestep
+ {file} arg = filename
+ filename = name of file to output correlation data to
+ {overwrite} arg = none = overwrite output file with only latest output
+ {title1} arg = string
+ string = text to print as 1st line of output file
+ {title2} arg = string
+ string = text to print as 2nd line of output file
+ {ncorr} arg = Ncorrelators
+ Ncorrelators = number of correlators to store
+ {nlen} args = Nlen
+ Nlen = length of each correlator
+ {ncount} args = Ncount
+ Ncount = number of values over which succesive correlators are averaged :pre
+:ule
+
+[Examples:]
+
+fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
+fix 1 all ave/correlate/long 1 10000 &
+ c_thermo_press\[1\] c_thermo_press\[2\] c_thermo_press\[3\] &
+ type upper title1 "My correlation data" nlen 15 ncount 3 :pre
+
+[Description:]
+
+This fix is similar in spirit and syntax to the "fix
+ave/correlate"_fix_ave_correlate.html. However, this fix allows the
+efficient calculation of time correlation functions on the fly over
+extremely long time windows without too much CPU overhead, using a
+multiple-tau method "(Ramirez)"_#Ramirez that decreases the resolution
+of the stored correlation function with time.
+
+The group specified with this command is ignored. However, note that
+specified values may represent calculations performed by computes and
+fixes which store their own "group" definitions.
+
+Each listed value can be the result of a compute or fix or the
+evaluation of an equal-style variable. See the "fix
+ave/correlate"_fix_ave_correlate.html doc page for details.
+
+The {Nevery} and {Nfreq} arguments specify on what timesteps the input
+values will be used to calculate correlation data, and the frequency
+with which the time correlation functions will be output to a file.
+Note that there is no {Nrepeat} argument, unlike the "fix
+ave/correlate"_fix_ave_correlate.html command.
+
+The optional keywords {ncorr}, {nlen}, and {ncount} are unique to this
+command and determine the number of correlation points calculated and
+the memory and CPU overhead used by this calculation. {Nlen} and
+{ncount} determine the amount of averaging done at longer correlation
+times. The default values {nlen=16}, {ncount=2} ensure that the
+systematic error of the multiple-tau correlator is always below the
+level of the statistical error of a typical simulation (which depends
+on the ensemble size and the simulation length).
+
+The maximum correlation time (in time steps) that can be reached is
+given by the formula (nlen-1) * ncount^(ncorr-1). Longer correlation
+times are discarded and not calculated. With the default values of
+the parameters (ncorr=20, nlen=16 and ncount=2), this corresponds to
+7864320 time steps. If longer correlation times are needed, the value
+of ncorr should be increased. Using nlen=16 and ncount=2, with
+ncorr=30, the maximum number of steps that can be correlated is
+80530636808. If ncorr=40, correlation times in excess of 8e12 time
+steps can be calculated.
+
+The total memory needed for each correlation pair is roughly
+4*ncorr*nlen*8 bytes. With the default values of the parameters, this
+corresponds to about 10 KB.
+
+For the meaning of the additional optional keywords, see the "fix
+ave/correlate"_fix_ave_correlate.html doc page.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+Since this fix in intended for the calculation of time correlation
+functions over very long MD simulations, the information about this
+fix is written automatically to binary restart files, so that the time
+correlation calculation can continue in subsequent simulations. None
+of the fix_modify options are relevant to this fix.
+
+No parameter of this fix can be used with the start/stop keywords of
+the run command. This fix is not invoked during energy minimization.
+
+[Restrictions:]
+
+This compute is part of the USER-MISC 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:]
+
+"fix ave/correlate"_fix_ave_correlate.html
+
+[Default:] none
+
+The option defaults for keywords that are also keywords for the "fix
+ave/correlate"_fix_ave_correlate.html command are as follows: type =
+auto, start = 0, no file output, title 1,2 = strings as described on
+the "fix ave/correlate"_fix_ave_correlate.html doc page.
+
+The option defaults for keywords unique to this command are as
+follows: ncorr=20, nlen=16, ncount=2.
+
+:line
+
+:link(Ramirez)
+[(Ramirez)] J. Ramirez, S.K. Sukumaran, B. Vorselaars and
+A.E. Likhtman, J. Chem. Phys. 133, 154103 (2010).
diff --git a/doc/fix_gcmc.html b/doc/fix_gcmc.html
index 21864923c..84b770acf 100644
--- a/doc/fix_gcmc.html
+++ b/doc/fix_gcmc.html
@@ -1,369 +1,505 @@
-<HTML>
-<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
-</CENTER>
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+ <meta charset="utf-8">
+
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+ <title>fix gcmc command — LAMMPS 15 May 2015 version documentation</title>
+
+
+
+
+
+
+
-<HR>
+
-<H3>fix gcmc command
-</H3>
-<P><B>Syntax:</B>
-</P>
-<PRE>fix ID group-ID gcmc N X M type seed T mu displace keyword values ...
-</PRE>
-<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+
+ <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+
-<LI>gcmc = style name of this fix command
+
+ <link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
+
-<LI>N = invoke this fix every N steps
+
+ <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
-<LI>X = average number of GCMC exchanges to attempt every N steps
+
+ <script src="_static/js/modernizr.min.js"></script>
-<LI>M = average number of MC moves to attempt every N steps
+</head>
-<LI>type = atom type for inserted atoms (must be 0 if mol keyword used)
+<body class="wy-body-for-nav" role="document">
-<LI>seed = random # seed (positive integer)
+ <div class="wy-grid-for-nav">
-<LI>T = temperature of the ideal gas reservoir (temperature units)
+
+ <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+ <div class="wy-side-nav-search">
+
-<LI>mu = chemical potential of the ideal gas reservoir (energy units)
+
+ <a href="Manual.html" class="icon icon-home"> LAMMPS
+
-<LI>translate = maximum Monte Carlo translation distance (length units)
+
+ </a>
-<LI>zero or more keyword/value pairs may be appended to args
+
+<div role="search">
+ <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+ <input type="text" name="q" placeholder="Search docs" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+</div>
-<PRE>keyword = <I>mol</I>, <I>region</I>, <I>maxangle</I>, <I>pressure</I>, <I>fugacity_coeff</I>, <I>full_energy</I>, <I>charge</I>, <I>group</I>, <I>grouptype</I>, <I>intra_energy</I>, or <I>tfac_insert</I>
- <I>mol</I> value = template-ID
- template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
- <I>shake</I> value = fix-ID
- fix-ID = ID of <A HREF = "fix_shake.html">fix shake</A> command
- <I>region</I> value = region-ID
- region-ID = ID of region where MC moves are allowed
- <I>maxangle</I> value = maximum molecular rotation angle (degrees)
- <I>pressure</I> value = pressure of the gas reservoir (pressure units)
- <I>fugacity_coeff</I> value = fugacity coefficient of the gas reservoir (unitless)
- <I>full_energy</I> = compute the entire system energy when performing MC moves
- <I>charge</I> value = charge of inserted atoms (charge units)
- <I>group</I> value = group-ID
+
+ </div>
+
+ <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+
+
+
+ <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+</ul>
+
+
+
+ </div>
+
+ </nav>
+
+ <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
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+ <div role="navigation" aria-label="breadcrumbs navigation">
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+ <a href="Section_commands.html#comm">Commands</a>
+
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+ </ul>
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+</div>
+ <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+ <div itemprop="articleBody">
+
+ <div class="section" id="fix-gcmc-command">
+<span id="index-0"></span><h1>fix gcmc command<a class="headerlink" href="#fix-gcmc-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>fix ID group-ID gcmc N X M type seed T mu displace keyword values ...
+</pre></div>
+</div>
+<ul class="simple">
+<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
+<li>gcmc = style name of this fix command</li>
+<li>N = invoke this fix every N steps</li>
+<li>X = average number of GCMC exchanges to attempt every N steps</li>
+<li>M = average number of MC moves to attempt every N steps</li>
+<li>type = atom type for inserted atoms (must be 0 if mol keyword used)</li>
+<li>seed = random # seed (positive integer)</li>
+<li>T = temperature of the ideal gas reservoir (temperature units)</li>
+<li>mu = chemical potential of the ideal gas reservoir (energy units)</li>
+<li>translate = maximum Monte Carlo translation distance (length units)</li>
+<li>zero or more keyword/value pairs may be appended to args</li>
+</ul>
+<pre class="literal-block">
+keyword = <em>mol</em>, <em>region</em>, <em>maxangle</em>, <em>pressure</em>, <em>fugacity_coeff</em>, <em>full_energy</em>, <em>charge</em>, <em>group</em>, <em>grouptype</em>, <em>intra_energy</em>, or <em>tfac_insert</em>
+ <em>mol</em> value = template-ID
+ template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
+ <em>shake</em> value = fix-ID
+ fix-ID = ID of <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command
+ <em>region</em> value = region-ID
+ region-ID = ID of region where MC moves are allowed
+ <em>maxangle</em> value = maximum molecular rotation angle (degrees)
+ <em>pressure</em> value = pressure of the gas reservoir (pressure units)
+ <em>fugacity_coeff</em> value = fugacity coefficient of the gas reservoir (unitless)
+ <em>full_energy</em> = compute the entire system energy when performing MC moves
+ <em>charge</em> value = charge of inserted atoms (charge units)
+ <em>group</em> value = group-ID
group-ID = group-ID for inserted atoms (string)
- <I>grouptype</I> values = type group-ID
+ <em>grouptype</em> values = type group-ID
type = atom type (int)
group-ID = group-ID for inserted atoms (string)
- <I>intra_energy</I> value = intramolecular energy (energy units)
- <I>tfac_insert</I> value = scale up/down temperature of inserted atoms (unitless)
-</PRE>
-
-</UL>
-<P><B>Examples:</B>
-</P>
-<PRE>fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
+ <em>intra_energy</em> value = intramolecular energy (energy units)
+ <em>tfac_insert</em> value = scale up/down temperature of inserted atoms (unitless)
+</pre>
+</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>fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
-fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
-</PRE>
-<P><B>Description:</B>
-</P>
-<P>This fix performs grand canonical Monte Carlo (GCMC) exchanges of
+fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
+</pre></div>
+</div>
+</div>
+<div class="section" id="description">
+<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
+<p>This fix performs grand canonical Monte Carlo (GCMC) exchanges of
atoms or molecules of the given type with an imaginary ideal gas reservoir at
the specified T and chemical potential (mu) as discussed in
-<A HREF = "#Frenkel">(Frenkel)</A>. If used with the <A HREF = "fix_nh.html">fix nvt</A> command,
+<a class="reference internal" href="#frenkel"><span>(Frenkel)</span></a>. If used with the <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a> command,
simulations in the grand canonical ensemble (muVT, constant chemical
potential, constant volume, and constant temperature) can be
performed. Specific uses include computing isotherms in microporous
-materials, or computing vapor-liquid coexistence curves.
-</P>
-<P>Every N timesteps the fix attempts a number of GCMC exchanges (insertions
+materials, or computing vapor-liquid coexistence curves.</p>
+<p>Every N timesteps the fix attempts a number of GCMC exchanges (insertions
or deletions) of gas atoms or molecules of
the given type between the simulation cell and the imaginary
reservoir. It also attempts a number of Monte Carlo
moves (translations and molecule rotations) of gas of the given type
-within the simulation cell or region. The average number of
+within the simulation cell or region. The average number of
attempted GCMC exchanges is X. The average number of attempted MC moves is M.
M should typically be chosen to be
approximately equal to the expected number of gas atoms or molecules
-of the given type within the simulation cell or region,
+of the given type within the simulation cell or region,
which will result in roughly one
-MC translation per atom or molecule per MC cycle.
-</P>
-<P>For MC moves of molecular gasses, rotations and translations are each
+MC translation per atom or molecule per MC cycle.</p>
+<p>For MC moves of molecular gasses, rotations and translations are each
attempted with 50% probability. For MC moves of atomic gasses,
translations are attempted 100% of the time. For MC exchanges of
either molecular or atomic gasses, deletions and insertions are each
-attempted with 50% probability.
-</P>
-<P>All inserted particles are always assigned to two groups: the default group
-"all" and the group specified in the fix gcmc command (which can also
-be "all"). In addition, particles are also added to any groups specified
-by the <I>group</I> and <I>grouptype</I> keywords.
+attempted with 50% probability.</p>
+<p>All inserted particles are always assigned to two groups: the default group
+“all” and the group specified in the fix gcmc command (which can also
+be “all”). In addition, particles are also added to any groups specified
+by the <em>group</em> and <em>grouptype</em> keywords.
If inserted particles are individual atoms, they are
-assigned the atom type given by the type argument. If they are molecules,
-the type argument has no effect and must be set to zero. Instead,
-the type of each atom in the inserted molecule is specified
-in the file read by the <A HREF = "molecule.html">molecule</A> command.
-</P>
-<P>This fix cannot be used to perform MC insertions of gas atoms or
+assigned the atom type given by the type argument. If they are molecules,
+the type argument has no effect and must be set to zero. Instead,
+the type of each atom in the inserted molecule is specified
+in the file read by the <a class="reference internal" href="molecule.html"><em>molecule</em></a> command.</p>
+<p>This fix cannot be used to perform MC insertions of gas atoms or
molecules other than the exchanged type, but MC deletions,
translations, and rotations can be performed on any atom/molecule in
the fix group. All atoms in the simulation cell can be moved using
regular time integration translations, e.g. via
-<A HREF = "fix_nvt.html">fix_nvt</A>, resulting in a hybrid GCMC+MD simulation. A
+<code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>, resulting in a hybrid GCMC+MD simulation. A
smaller-than-usual timestep size may be needed when running such a
hybrid simulation, especially if the inserted molecules are not well
-equilibrated.
-</P>
-<P>This command may optionally use the <I>region</I> keyword to define an
-exchange and move volume. The specified region must have been
-previously defined with a <A HREF = "region.html">region</A> command. It must be
-defined with side = <I>in</I>. Insertion attempts occur only within the
-specified region. For non-rectangular regions, random trial
+equilibrated.</p>
+<p>This command may optionally use the <em>region</em> keyword to define an
+exchange and move volume. The specified region must have been
+previously defined with a <a class="reference internal" href="region.html"><em>region</em></a> command. It must be
+defined with side = <em>in</em>. Insertion attempts occur only within the
+specified region. For non-rectangular regions, random trial
points are generated within the rectangular bounding box until a point is found
that lies inside the region. If no valid point is generated after 1000 trials,
no insertion is performed, but it is counted as an attempted insertion.
-Move and deletion attempt candidates are selected
+Move and deletion attempt candidates are selected
from gas atoms or molecules within the region. If there are no candidates,
no move or deletion is performed, but it is counted as an attempt move
-or deletion. If an attempted move places the atom or molecule center-of-mass outside
-the specified region, a new attempted move is generated. This process is repeated
-until the atom or molecule center-of-mass is inside the specified region.
-</P>
-<P>If used with <A HREF = "fix_nvt.html">fix_nvt</A>, the temperature of the imaginary
+or deletion. If an attempted move places the atom or molecule center-of-mass outside
+the specified region, a new attempted move is generated. This process is repeated
+until the atom or molecule center-of-mass is inside the specified region.</p>
+<p>If used with <code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>, the temperature of the imaginary
reservoir, T, should be set to be equivalent to the target temperature
-used in <A HREF = "fix_nvt.html">fix_nvt</A>. Otherwise, the imaginary reservoir
+used in <code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>. Otherwise, the imaginary reservoir
will not be in thermal equilibrium with the simulation cell. Also,
it is important that the temperature used by fix nvt be dynamic,
-which can be achieved as follows:
-</P>
-<PRE>compute mdtemp mdatoms temp
+which can be achieved as follows:</p>
+<div class="highlight-python"><div class="highlight"><pre>compute mdtemp mdatoms temp
compute_modify mdtemp dynamic yes
fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
-fix_modify mdnvt temp mdtemp
-</PRE>
-<P>Note that neighbor lists are re-built every timestep that this fix is
+fix_modify mdnvt temp mdtemp
+</pre></div>
+</div>
+<p>Note that neighbor lists are re-built every timestep that this fix is
invoked, so you should not set N to be too small. However, periodic
rebuilds are necessary in order to avoid dangerous rebuilds and missed
interactions. Specifically, avoid performing so many MC translations
per timestep that atoms can move beyond the neighbor list skin
-distance. See the <A HREF = "neighbor.html">neighbor</A> command for details.
-</P>
-<P>When an atom or molecule is to be inserted, its
+distance. See the <a class="reference internal" href="neighbor.html"><em>neighbor</em></a> command for details.</p>
+<p>When an atom or molecule is to be inserted, its
coordinates are chosen at a random position within the current
simulation cell or region, and new atom velocities are randomly chosen from
the specified temperature distribution given by T. The effective
temperature for new atom velocities can be increased or decreased
-using the optional keyword <I>tfac_insert</I> (see below). Relative
+using the optional keyword <em>tfac_insert</em> (see below). Relative
coordinates for atoms in a molecule are taken from the template
molecule provided by the user. The center of mass of the molecule
is placed at the insertion point. The orientation of the molecule
-is chosen at random by rotating about this point.
-</P>
-<P>Individual atoms are inserted, unless the <I>mol</I> keyword is used. It
-specifies a <I>template-ID</I> previously defined using the
-<A HREF = "molecule.html">molecule</A> command, which reads a file that defines the
+is chosen at random by rotating about this point.</p>
+<p>Individual atoms are inserted, unless the <em>mol</em> keyword is used. It
+specifies a <em>template-ID</em> previously defined using the
+<a class="reference internal" href="molecule.html"><em>molecule</em></a> command, which reads a file that defines the
molecule. The coordinates, atom types, charges, etc, as well as any
bond/angle/etc and special neighbor information for the molecule can
-be specified in the molecule file. See the <A HREF = "molecule.html">molecule</A>
+be specified in the molecule file. See the <a class="reference internal" href="molecule.html"><em>molecule</em></a>
command for details. The only settings required to be in this file
-are the coordinates and types of atoms in the molecule.
-</P>
-<P>When not using the <I>mol</I> keyword, you should ensure you do not delete
+are the coordinates and types of atoms in the molecule.</p>
+<p>When not using the <em>mol</em> keyword, you should ensure you do not delete
atoms that are bonded to other atoms, or LAMMPS will
soon generate an error when it tries to find bonded neighbors. LAMMPS will
warn you if any of the atoms eligible for deletion have a non-zero
-molecule ID, but does not check for this at the time of deletion.
-</P>
-<P>If you wish to insert molecules via the <I>mol</I> keyword, that will have
-their bonds or angles constrained via SHAKE, use the <I>shake</I> keyword,
-specifying as its value the ID of a separate <A HREF = "fix_shake.html">fix
-shake</A> command which also appears in your input script.
-</P>
-<P>Optionally, users may specify the maximum rotation angle for
-molecular rotations using the <I>maxangle</I> keyword and specifying
+molecule ID, but does not check for this at the time of deletion.</p>
+<p>If you wish to insert molecules via the <em>mol</em> keyword, that will have
+their bonds or angles constrained via SHAKE, use the <em>shake</em> keyword,
+specifying as its value the ID of a separate <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command which also appears in your input script.</p>
+<p>Optionally, users may specify the maximum rotation angle for
+molecular rotations using the <em>maxangle</em> keyword and specifying
the angle in degrees. Rotations are performed by generating a random
point on the unit sphere and a random rotation angle on the
range [0,maxangle). The molecule is then rotated by that angle about an
-axis passing through the molecule center of mass. The axis is parallel
-to the unit vector defined by the point on the unit sphere.
+axis passing through the molecule center of mass. The axis is parallel
+to the unit vector defined by the point on the unit sphere.
The same procedure is used for randomly rotating molecules when they
-are inserted, except that the maximum angle is 360 degrees.
-</P>
-<P>Note that fix GCMC does not use configurational bias
-MC or any other kind of sampling of intramolecular degrees of freedom.
-Inserted molecules can have different orientations, but they will all
-have the same intramolecular configuration,
-which was specified in the molecule command input.
-</P>
-<P>For atomic gasses, inserted atoms have the specified atom type, but
-deleted atoms are any atoms that have been inserted or that belong
-to the user-specified fix group. For molecular gasses, exchanged
-molecules use the same atom types as in the template molecule
+are inserted, except that the maximum angle is 360 degrees.</p>
+<p>Note that fix GCMC does not use configurational bias
+MC or any other kind of sampling of intramolecular degrees of freedom.
+Inserted molecules can have different orientations, but they will all
+have the same intramolecular configuration,
+which was specified in the molecule command input.</p>
+<p>For atomic gasses, inserted atoms have the specified atom type, but
+deleted atoms are any atoms that have been inserted or that belong
+to the user-specified fix group. For molecular gasses, exchanged
+molecules use the same atom types as in the template molecule
supplied by the user. In both cases, exchanged
-atoms/molecules are assigned to two groups: the default group "all"
-and the group specified in the fix gcmc command (which can also be
-"all").
-</P>
-<P>The gas reservoir pressure can be specified using the <I>pressure</I>
-keyword, in which case the user-specified chemical potential is
-ignored. For non-ideal gas reservoirs, the user may also specify the
-fugacity coefficient using the <I>fugacity_coeff</I> keyword.
-</P>
-<P>The <I>full_energy</I> option means that fix GCMC will compute the total
+atoms/molecules are assigned to two groups: the default group “all”
+and the group specified in the fix gcmc command (which can also be
+“all”).</p>
+<p>The gas reservoir pressure can be specified using the <em>pressure</em>
+keyword, in which case the user-specified chemical potential is
+ignored. For non-ideal gas reservoirs, the user may also specify the
+fugacity coefficient using the <em>fugacity_coeff</em> keyword.</p>
+<p>The <em>full_energy</em> option means that fix GCMC will compute the total
potential energy of the entire simulated system. The total system
energy before and after the proposed GCMC move is then used in the
-Metropolis criterion to determine whether or not to accept the
+Metropolis criterion to determine whether or not to accept the
proposed GCMC move. By default, this option is off, in which case
only partial energies are computed to determine the difference in
-energy that would be caused by the proposed GCMC move.
-</P>
-<P>The <I>full_energy</I> option is needed for systems with complicated
-potential energy calculations, including the following:
-</P>
-<UL><LI> long-range electrostatics (kspace)
-<LI> many-body pair styles
-<LI> hybrid pair styles
-<LI> eam pair styles
-<LI> triclinic systems
-<LI> need to include potential energy contributions from other fixes
-</UL>
-<P>In these cases, LAMMPS will automatically apply the <I>full_energy</I>
-keyword and issue a warning message.
-</P>
-<P>When the <I>mol</I> keyword is used, the <I>full_energy</I> option also includes
-the intramolecular energy of inserted and deleted molecules. If this
-is not desired, the <I>intra_energy</I> keyword can be used to define an
+energy that would be caused by the proposed GCMC move.</p>
+<p>The <em>full_energy</em> option is needed for systems with complicated
+potential energy calculations, including the following:</p>
+<ul class="simple">
+<li>long-range electrostatics (kspace)</li>
+<li>many-body pair styles</li>
+<li>hybrid pair styles</li>
+<li>eam pair styles</li>
+<li>triclinic systems</li>
+<li>need to include potential energy contributions from other fixes</li>
+</ul>
+<p>In these cases, LAMMPS will automatically apply the <em>full_energy</em>
+keyword and issue a warning message.</p>
+<p>When the <em>mol</em> keyword is used, the <em>full_energy</em> option also includes
+the intramolecular energy of inserted and deleted molecules. If this
+is not desired, the <em>intra_energy</em> keyword can be used to define an
amount of energy that is subtracted from the final energy when a molecule
is inserted, and added to the initial energy when a molecule is
deleted. For molecules that have a non-zero intramolecular energy, this
-will ensure roughly the same behavior whether or not the <I>full_energy</I>
-option is used.
-</P>
-<P>Inserted atoms and molecules are assigned random velocities based on the
+will ensure roughly the same behavior whether or not the <em>full_energy</em>
+option is used.</p>
+<p>Inserted atoms and molecules are assigned random velocities based on the
specified temperature T. Because the relative velocity of
all atoms in the molecule is zero, this may result in inserted molecules
that are systematically too cold. In addition, the intramolecular potential
energy of the inserted molecule may cause the kinetic energy
-of the molecule to quickly increase or decrease after insertion.
-The <I>tfac_insert</I> keyword allows the user to counteract these effects
-by changing the temperature used to assign velocities to
+of the molecule to quickly increase or decrease after insertion.
+The <em>tfac_insert</em> keyword allows the user to counteract these effects
+by changing the temperature used to assign velocities to
inserted atoms and molecules by a constant factor. For a
particular application, some experimentation may be required
-to find a value of <I>tfac_insert</I> that results in inserted molecules that
-equilibrate quickly to the correct temperature.
-</P>
-<P>Some fixes have an associated potential energy. Examples of such fixes
-include: <A HREF = "fix_efield.html">efield</A>, <A HREF = "fix_gravity.html">gravity</A>,
-<A HREF = "fix_addforce.html">addforce</A>, <A HREF = "fix_langevin.html">langevin</A>,
-<A HREF = "fix_restrain.html">restrain</A>, <A HREF = "fix_temp_berendsen.html">temp/berendsen</A>,
-<A HREF = "fix_temp_rescale.html">temp/rescale</A>, and <A HREF = "fix_wall.html">wall fixes</A>.
-For that energy to be included in the total potential energy of the
+to find a value of <em>tfac_insert</em> that results in inserted molecules that
+equilibrate quickly to the correct temperature.</p>
+<p>Some fixes have an associated potential energy. Examples of such fixes
+include: <a class="reference internal" href="fix_efield.html"><em>efield</em></a>, <a class="reference internal" href="fix_gravity.html"><em>gravity</em></a>,
+<a class="reference internal" href="fix_addforce.html"><em>addforce</em></a>, <a class="reference internal" href="fix_langevin.html"><em>langevin</em></a>,
+<a class="reference internal" href="fix_restrain.html"><em>restrain</em></a>, <a class="reference internal" href="fix_temp_berendsen.html"><em>temp/berendsen</em></a>,
+<a class="reference internal" href="fix_temp_rescale.html"><em>temp/rescale</em></a>, and <a class="reference internal" href="fix_wall.html"><em>wall fixes</em></a>.
+For that energy to be included in the total potential energy of the
system (the quantity used when performing GCMC moves),
-you MUST enable the <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for
-that fix. The doc pages for individual <A HREF = "fix.html">fix</A> commands
-specify if this should be done.
-</P>
-<P>Use the <I>charge</I> option to insert atoms with a user-specified point
-charge. Note that doing so will cause the system to become non-neutral.
-LAMMPS issues a warning when using long-range electrostatics (kspace)
-with non-neutral systems. See the
-<A HREF = "compute_group_group.html">compute_group_group</A> documentation for more
-details about simulating non-neutral systems with kspace on.
-</P>
-<P>Use of this fix typically will cause the number of atoms to fluctuate,
+you MUST enable the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> option for
+that fix. The doc pages for individual <a class="reference internal" href="fix.html"><em>fix</em></a> commands
+specify if this should be done.</p>
+<p>Use the <em>charge</em> option to insert atoms with a user-specified point
+charge. Note that doing so will cause the system to become non-neutral.
+LAMMPS issues a warning when using long-range electrostatics (kspace)
+with non-neutral systems. See the
+<a class="reference internal" href="compute_group_group.html"><em>compute_group_group</em></a> documentation for more
+details about simulating non-neutral systems with kspace on.</p>
+<p>Use of this fix typically will cause the number of atoms to fluctuate,
therefore, you will want to use the
-<A HREF = "compute_modify.html">compute_modify</A> command to insure that the
+<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command to insure that the
current number of atoms is used as a normalizing factor each time
-temperature is computed. Here is the necessary command:
-</P>
-<PRE>compute_modify thermo_temp dynamic yes
-</PRE>
-<P>If LJ units are used, note that a value of 0.18292026 is used by this
-fix as the reduced value for Planck's constant. This value was
+temperature is computed. Here is the necessary command:</p>
+<div class="highlight-python"><div class="highlight"><pre>compute_modify thermo_temp dynamic yes
+</pre></div>
+</div>
+<p>If LJ units are used, note that a value of 0.18292026 is used by this
+fix as the reduced value for Planck’s constant. This value was
derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 *
epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
-mass = 39.948 amu.
-</P>
-<P>The <I>group</I> keyword assigns all inserted atoms to the <A HREF = "group.html">group</A>
-of the group-ID value. The <I>grouptype</I> keyword assigns all
-inserted atoms of the specified type to the <A HREF = "group.html">group</A>
-of the group-ID value.
-</P>
-<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
-</P>
-<P>This fix writes the state of the fix to <A HREF = "restart.html">binary restart
-files</A>. This includes information about the random
+mass = 39.948 amu.</p>
+<p>The <em>group</em> keyword assigns all inserted atoms to the <a class="reference internal" href="group.html"><em>group</em></a>
+of the group-ID value. The <em>grouptype</em> keyword assigns all
+inserted atoms of the specified type to the <a class="reference internal" href="group.html"><em>group</em></a>
+of the group-ID value.</p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
+<p>This fix writes the state of the fix to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. This includes information about the random
number generator seed, the next timestep for MC exchanges, etc. See
-the <A HREF = "read_restart.html">read_restart</A> command for info on how to
+the <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command for info on how to
re-specify a fix in an input script that reads a restart file, so that
-the operation of the fix continues in an uninterrupted fashion.
-</P>
-<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
-fix.
-</P>
-<P>This fix computes a global vector of length 8, which can be accessed
-by various <A HREF = "Section_howto.html#howto_15">output commands</A>. The vector
-values are the following global cumulative quantities:
-</P>
-<UL><LI>1 = translation attempts
-<LI>2 = translation successes
-<LI>3 = insertion attempts
-<LI>4 = insertion successes
-<LI>5 = deletion attempts
-<LI>6 = deletion successes
-<LI>7 = rotation attempts
-<LI>8 = rotation successes
-</UL>
-<P>The vector values calculated by this fix are "extensive".
-</P>
-<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
-the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
-minimization</A>.
-</P>
-<P><B>Restrictions:</B>
-</P>
-<P>This fix is part of the MC package. It is only enabled if LAMMPS was
-built with that package. See the <A HREF = "Section_start.html#start_3">Making
-LAMMPS</A> section for more info.
-</P>
-<P>Do not set "neigh_modify once yes" or else this fix will never be
-called. Reneighboring is required.
-</P>
-<P>Can be run in parallel, but aspects of the GCMC part will not scale
-well in parallel. Only usable for 3D simulations.
-</P>
-<P>Note that very lengthy simulations involving insertions/deletions of
+the operation of the fix continues in an uninterrupted fashion.</p>
+<p>None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options are relevant to this
+fix.</p>
+<p>This fix computes a global vector of length 8, which can be accessed
+by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The vector
+values are the following global cumulative quantities:</p>
+<ul class="simple">
+<li>1 = translation attempts</li>
+<li>2 = translation successes</li>
+<li>3 = insertion attempts</li>
+<li>4 = insertion successes</li>
+<li>5 = deletion attempts</li>
+<li>6 = deletion successes</li>
+<li>7 = rotation attempts</li>
+<li>8 = rotation successes</li>
+</ul>
+<p>The vector values calculated by this fix are “extensive”.</p>
+<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
+the <a class="reference internal" href="run.html"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</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 fix is part of the MC 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>Do not set “neigh_modify once yes” or else this fix will never be
+called. Reneighboring is required.</p>
+<p>Can be run in parallel, but aspects of the GCMC part will not scale
+well in parallel. Only usable for 3D simulations.</p>
+<p>Note that very lengthy simulations involving insertions/deletions of
billions of gas molecules may run out of atom or molecule IDs and
-trigger an error, so it is better to run multiple shorter-duration
+trigger an error, so it is better to run multiple shorter-duration
simulations. Likewise, very large molecules have not been tested
-and may turn out to be problematic.
-</P>
-<P>Use of multiple fix gcmc commands in the same input script can be
-problematic if using a template molecule. The issue is that the
+and may turn out to be problematic.</p>
+<p>Use of multiple fix gcmc commands in the same input script can be
+problematic if using a template molecule. The issue is that the
user-referenced template molecule in the second fix gcmc command
may no longer exist since it might have been deleted by the first
fix gcmc command. An existing template molecule will need to be
-referenced by the user for each subsequent fix gcmc command.
-</P>
-<P><B>Related commands:</B>
-</P>
-<P><A HREF = "fix_atom_swap.html">fix atom/swap</A>,
-<A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "neighbor.html">neighbor</A>,
-<A HREF = "fix_deposit.html">fix deposit</A>, <A HREF = "fix_evaporate.html">fix evaporate</A>,
-<A HREF = "delete_atoms.html">delete_atoms</A>
-</P>
-<P><B>Default:</B>
-</P>
-<P>The option defaults are mol = no, maxangle = 10, full_energy = no,
+referenced by the user for each subsequent fix gcmc command.</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_atom_swap.html"><em>fix atom/swap</em></a>,
+<code class="xref doc docutils literal"><span class="pre">fix</span> <span class="pre">nvt</span></code>, <a class="reference internal" href="neighbor.html"><em>neighbor</em></a>,
+<a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a>, <a class="reference internal" href="fix_evaporate.html"><em>fix evaporate</em></a>,
+<a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a></p>
+</div>
+<div class="section" id="default">
+<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
+<p>The option defaults are mol = no, maxangle = 10, full_energy = no,
except for the situations where full_energy is required, as
-listed above.
-</P>
-<HR>
+listed above.</p>
+<hr class="docutils" />
+<p id="frenkel"><strong>(Frenkel)</strong> Frenkel and Smit, Understanding Molecular Simulation,
+Academic Press, London, 2002.</p>
+</div>
+</div>
+
+
+ </div>
+ </div>
+ <footer>
+
+
+ <hr/>
+
+ <div role="contentinfo">
+ <p>
+ © Copyright .
+ </p>
+ </div>
+ Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
+
+ </div>
+ </div>
+
+ </section>
+
+ </div>
+
+
+
+
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT:'./',
+ VERSION:'15 May 2015 version',
+ COLLAPSE_INDEX:false,
+ FILE_SUFFIX:'.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+ <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
+ <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
+ <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
+
+
+
+
+
+ <script type="text/javascript" src="_static/js/theme.js"></script>
+
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+
+
+ <script type="text/javascript">
+ jQuery(function () {
+ SphinxRtdTheme.StickyNav.enable();
+ });
+ </script>
+
-<P><B>(Frenkel)</B> Frenkel and Smit, Understanding Molecular Simulation,
-Academic Press, London, 2002.
-</P>
-</HTML>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/genindex.html b/doc/genindex.html
index 7ef4cf69a..36d13dad4 100644
--- a/doc/genindex.html
+++ b/doc/genindex.html
@@ -1,2220 +1,2228 @@
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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_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<h1 id="index">Index</h1>
<div class="genindex-jumpbox">
<a href="#A"><strong>A</strong></a>
| <a href="#B"><strong>B</strong></a>
| <a href="#C"><strong>C</strong></a>
| <a href="#D"><strong>D</strong></a>
| <a href="#E"><strong>E</strong></a>
| <a href="#F"><strong>F</strong></a>
| <a href="#G"><strong>G</strong></a>
| <a href="#I"><strong>I</strong></a>
| <a href="#J"><strong>J</strong></a>
| <a href="#K"><strong>K</strong></a>
| <a href="#L"><strong>L</strong></a>
| <a href="#M"><strong>M</strong></a>
| <a href="#N"><strong>N</strong></a>
| <a href="#P"><strong>P</strong></a>
| <a href="#Q"><strong>Q</strong></a>
| <a href="#R"><strong>R</strong></a>
| <a href="#S"><strong>S</strong></a>
| <a href="#T"><strong>T</strong></a>
| <a href="#U"><strong>U</strong></a>
| <a href="#V"><strong>V</strong></a>
| <a href="#W"><strong>W</strong></a>
</div>
<h2 id="A">A</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="angle_coeff.html#index-0">angle_coeff</a>
</dt>
<dt><a href="angle_style.html#index-0">angle_style</a>
</dt>
<dt><a href="angle_charmm.html#index-0">angle_style charmm</a>
</dt>
<dt><a href="angle_class2.html#index-0">angle_style class2</a>
</dt>
<dt><a href="angle_cosine.html#index-0">angle_style cosine</a>
</dt>
<dt><a href="angle_cosine_delta.html#index-0">angle_style cosine/delta</a>
</dt>
<dt><a href="angle_cosine_periodic.html#index-0">angle_style cosine/periodic</a>
</dt>
<dt><a href="angle_cosine_shift.html#index-0">angle_style cosine/shift</a>
</dt>
<dt><a href="angle_cosine_shift_exp.html#index-0">angle_style cosine/shift/exp</a>
</dt>
<dt><a href="angle_cosine_squared.html#index-0">angle_style cosine/squared</a>
</dt>
<dt><a href="angle_dipole.html#index-0">angle_style dipole</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="angle_fourier.html#index-0">angle_style fourier</a>
</dt>
<dt><a href="angle_fourier_simple.html#index-0">angle_style fourier/simple</a>
</dt>
<dt><a href="angle_harmonic.html#index-0">angle_style harmonic</a>
</dt>
<dt><a href="angle_hybrid.html#index-0">angle_style hybrid</a>
</dt>
<dt><a href="angle_none.html#index-0">angle_style none</a>
</dt>
<dt><a href="angle_quartic.html#index-0">angle_style quartic</a>
</dt>
<dt><a href="angle_sdk.html#index-0">angle_style sdk</a>
</dt>
<dt><a href="angle_table.html#index-0">angle_style table</a>
</dt>
<dt><a href="atom_modify.html#index-0">atom_modify</a>
</dt>
<dt><a href="atom_style.html#index-0">atom_style</a>
</dt>
</dl></td>
</tr></table>
<h2 id="B">B</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="balance.html#index-0">balance</a>
</dt>
<dt><a href="bond_coeff.html#index-0">bond_coeff</a>
</dt>
<dt><a href="bond_style.html#index-0">bond_style</a>
</dt>
<dt><a href="bond_class2.html#index-0">bond_style class2</a>
</dt>
<dt><a href="bond_fene.html#index-0">bond_style fene</a>
</dt>
<dt><a href="bond_fene_expand.html#index-0">bond_style fene/expand</a>
</dt>
<dt><a href="bond_harmonic.html#index-0">bond_style harmonic</a>
</dt>
<dt><a href="bond_harmonic_shift.html#index-0">bond_style harmonic/shift</a>
</dt>
<dt><a href="bond_harmonic_shift_cut.html#index-0">bond_style harmonic/shift/cut</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="bond_hybrid.html#index-0">bond_style hybrid</a>
</dt>
<dt><a href="bond_morse.html#index-0">bond_style morse</a>
</dt>
<dt><a href="bond_none.html#index-0">bond_style none</a>
</dt>
<dt><a href="bond_nonlinear.html#index-0">bond_style nonlinear</a>
</dt>
<dt><a href="bond_quartic.html#index-0">bond_style quartic</a>
</dt>
<dt><a href="bond_table.html#index-0">bond_style table</a>
</dt>
<dt><a href="boundary.html#index-0">boundary</a>
</dt>
<dt><a href="box.html#index-0">box</a>
</dt>
</dl></td>
</tr></table>
<h2 id="C">C</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="change_box.html#index-0">change_box</a>
</dt>
<dt><a href="clear.html#index-0">clear</a>
</dt>
<dt><a href="comm_modify.html#index-0">comm_modify</a>
</dt>
<dt><a href="comm_style.html#index-0">comm_style</a>
</dt>
<dt><a href="compute.html#index-0">compute</a>
</dt>
<dt><a href="compute_ackland_atom.html#index-0">compute ackland/atom</a>
</dt>
<dt><a href="compute_angle_local.html#index-0">compute angle/local</a>
</dt>
<dt><a href="compute_angmom_chunk.html#index-0">compute angmom/chunk</a>
</dt>
<dt><a href="compute_basal_atom.html#index-0">compute basal/atom</a>
</dt>
<dt><a href="compute_body_local.html#index-0">compute body/local</a>
</dt>
<dt><a href="compute_bond_local.html#index-0">compute bond/local</a>
</dt>
<dt><a href="compute_centro_atom.html#index-0">compute centro/atom</a>
</dt>
<dt><a href="compute_chunk_atom.html#index-0">compute chunk/atom</a>
</dt>
<dt><a href="compute_cluster_atom.html#index-0">compute cluster/atom</a>
</dt>
<dt><a href="compute_cna_atom.html#index-0">compute cna/atom</a>
</dt>
<dt><a href="compute_com.html#index-0">compute com</a>
</dt>
<dt><a href="compute_com_chunk.html#index-0">compute com/chunk</a>
</dt>
<dt><a href="compute_contact_atom.html#index-0">compute contact/atom</a>
</dt>
<dt><a href="compute_coord_atom.html#index-0">compute coord/atom</a>
</dt>
<dt><a href="compute_damage_atom.html#index-0">compute damage/atom</a>
</dt>
<dt><a href="compute_dihedral_local.html#index-0">compute dihedral/local</a>
</dt>
<dt><a href="compute_dilatation_atom.html#index-0">compute dilatation/atom</a>
</dt>
<dt><a href="compute_displace_atom.html#index-0">compute displace/atom</a>
</dt>
<dt><a href="compute_erotate_asphere.html#index-0">compute erotate/asphere</a>
</dt>
<dt><a href="compute_erotate_rigid.html#index-0">compute erotate/rigid</a>
</dt>
<dt><a href="compute_erotate_sphere.html#index-0">compute erotate/sphere</a>
</dt>
<dt><a href="compute_erotate_sphere_atom.html#index-0">compute erotate/sphere/atom</a>
</dt>
<dt><a href="compute_event_displace.html#index-0">compute event/displace</a>
</dt>
<dt><a href="compute_fep.html#index-0">compute fep</a>
</dt>
<dt><a href="compute_tally.html#index-0">compute force/tally</a>
</dt>
<dt><a href="compute_group_group.html#index-0">compute group/group</a>
</dt>
<dt><a href="compute_gyration.html#index-0">compute gyration</a>
</dt>
<dt><a href="compute_gyration_chunk.html#index-0">compute gyration/chunk</a>
</dt>
<dt><a href="compute_heat_flux.html#index-0">compute heat/flux</a>
</dt>
<dt><a href="compute_improper_local.html#index-0">compute improper/local</a>
</dt>
<dt><a href="compute_inertia_chunk.html#index-0">compute inertia/chunk</a>
</dt>
<dt><a href="compute_ke.html#index-0">compute ke</a>
</dt>
<dt><a href="compute_ke_atom.html#index-0">compute ke/atom</a>
</dt>
<dt><a href="compute_ke_atom_eff.html#index-0">compute ke/atom/eff</a>
</dt>
<dt><a href="compute_ke_eff.html#index-0">compute ke/eff</a>
</dt>
<dt><a href="compute_ke_rigid.html#index-0">compute ke/rigid</a>
</dt>
<dt><a href="compute_meso_e_atom.html#index-0">compute meso_e/atom</a>
</dt>
<dt><a href="compute_meso_rho_atom.html#index-0">compute meso_rho/atom</a>
</dt>
<dt><a href="compute_meso_t_atom.html#index-0">compute meso_t/atom</a>
</dt>
<dt><a href="compute_msd.html#index-0">compute msd</a>
</dt>
<dt><a href="compute_msd_chunk.html#index-0">compute msd/chunk</a>
</dt>
<dt><a href="compute_msd_nongauss.html#index-0">compute msd/nongauss</a>
</dt>
<dt><a href="compute_omega_chunk.html#index-0">compute omega/chunk</a>
</dt>
<dt><a href="compute_pair.html#index-0">compute pair</a>
</dt>
<dt><a href="compute_pair_local.html#index-0">compute pair/local</a>
</dt>
<dt><a href="compute_pe.html#index-0">compute pe</a>
</dt>
<dt><a href="compute_pe_atom.html#index-0">compute pe/atom</a>
</dt>
<dt><a href="compute_plasticity_atom.html#index-0">compute plasticity/atom</a>
</dt>
<dt><a href="compute_pressure.html#index-0">compute pressure</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="compute_property_atom.html#index-0">compute property/atom</a>
</dt>
<dt><a href="compute_property_chunk.html#index-0">compute property/chunk</a>
</dt>
<dt><a href="compute_property_local.html#index-0">compute property/local</a>
</dt>
<dt><a href="compute_rdf.html#index-0">compute rdf</a>
</dt>
<dt><a href="compute_reduce.html#index-0">compute reduce</a>
</dt>
<dt><a href="compute_saed.html#index-0">compute saed</a>
</dt>
<dt><a href="compute_slice.html#index-0">compute slice</a>
</dt>
<dt><a href="compute_smd_contact_radius.html#index-0">compute smd/contact_radius</a>
</dt>
<dt><a href="compute_smd_damage.html#index-0">compute smd/damage</a>
</dt>
<dt><a href="compute_smd_hourglass_error.html#index-0">compute smd/hourglass_error</a>
</dt>
<dt><a href="compute_smd_internal_energy.html#index-0">compute smd/internal_energy</a>
</dt>
<dt><a href="compute_smd_plastic_strain.html#index-0">compute smd/plastic_strain</a>
</dt>
<dt><a href="compute_smd_plastic_strain_rate.html#index-0">compute smd/plastic_strain_rate</a>
</dt>
<dt><a href="compute_smd_rho.html#index-0">compute smd/rho</a>
</dt>
<dt><a href="compute_smd_tlsph_defgrad.html#index-0">compute smd/tlsph_defgrad</a>
</dt>
<dt><a href="compute_smd_tlsph_dt.html#index-0">compute smd/tlsph_dt</a>
</dt>
<dt><a href="compute_smd_tlsph_num_neighs.html#index-0">compute smd/tlsph_num_neighs</a>
</dt>
<dt><a href="compute_smd_tlsph_shape.html#index-0">compute smd/tlsph_shape</a>
</dt>
<dt><a href="compute_smd_tlsph_strain.html#index-0">compute smd/tlsph_strain</a>
</dt>
<dt><a href="compute_smd_tlsph_strain_rate.html#index-0">compute smd/tlsph_strain_rate</a>
</dt>
<dt><a href="compute_smd_tlsph_stress.html#index-0">compute smd/tlsph_stress</a>
</dt>
<dt><a href="compute_smd_ulsph_num_neighs.html#index-0">compute smd/ulsph_num_neighs</a>
</dt>
<dt><a href="compute_smd_ulsph_strain.html#index-0">compute smd/ulsph_strain</a>
</dt>
<dt><a href="compute_smd_ulsph_strain_rate.html#index-0">compute smd/ulsph_strain_rate</a>
</dt>
<dt><a href="compute_smd_ulsph_stress.html#index-0">compute smd/ulsph_stress</a>
</dt>
<dt><a href="compute_smd_vol.html#index-0">compute smd/vol</a>
</dt>
<dt><a href="compute_sna_atom.html#index-0">compute sna/atom</a>
</dt>
<dt><a href="compute_stress_atom.html#index-0">compute stress/atom</a>
</dt>
<dt><a href="compute_temp.html#index-0">compute temp</a>
</dt>
<dt><a href="compute_temp_asphere.html#index-0">compute temp/asphere</a>
</dt>
<dt><a href="compute_temp_chunk.html#index-0">compute temp/chunk</a>
</dt>
<dt><a href="compute_temp_com.html#index-0">compute temp/com</a>
</dt>
<dt><a href="compute_temp_cs.html#index-0">compute temp/cs</a>
</dt>
<dt><a href="compute_temp_deform.html#index-0">compute temp/deform</a>
</dt>
<dt><a href="compute_temp_deform_eff.html#index-0">compute temp/deform/eff</a>
</dt>
<dt><a href="compute_temp_drude.html#index-0">compute temp/drude</a>
</dt>
<dt><a href="compute_temp_eff.html#index-0">compute temp/eff</a>
</dt>
<dt><a href="compute_temp_partial.html#index-0">compute temp/partial</a>
</dt>
<dt><a href="compute_temp_profile.html#index-0">compute temp/profile</a>
</dt>
<dt><a href="compute_temp_ramp.html#index-0">compute temp/ramp</a>
</dt>
<dt><a href="compute_temp_region.html#index-0">compute temp/region</a>
</dt>
<dt><a href="compute_temp_region_eff.html#index-0">compute temp/region/eff</a>
</dt>
<dt><a href="compute_temp_rotate.html#index-0">compute temp/rotate</a>
</dt>
<dt><a href="compute_temp_sphere.html#index-0">compute temp/sphere</a>
</dt>
<dt><a href="compute_ti.html#index-0">compute ti</a>
</dt>
<dt><a href="compute_torque_chunk.html#index-0">compute torque/chunk</a>
</dt>
<dt><a href="compute_vacf.html#index-0">compute vacf</a>
</dt>
<dt><a href="compute_vcm_chunk.html#index-0">compute vcm/chunk</a>
</dt>
<dt><a href="compute_voronoi_atom.html#index-0">compute voronoi/atom</a>
</dt>
<dt><a href="compute_xrd.html#index-0">compute xrd</a>
</dt>
<dt><a href="compute_modify.html#index-0">compute_modify</a>
</dt>
<dt><a href="create_atoms.html#index-0">create_atoms</a>
</dt>
<dt><a href="create_bonds.html#index-0">create_bonds</a>
</dt>
<dt><a href="create_box.html#index-0">create_box</a>
</dt>
</dl></td>
</tr></table>
<h2 id="D">D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="delete_atoms.html#index-0">delete_atoms</a>
</dt>
<dt><a href="delete_bonds.html#index-0">delete_bonds</a>
</dt>
<dt><a href="dielectric.html#index-0">dielectric</a>
</dt>
<dt><a href="dihedral_coeff.html#index-0">dihedral_coeff</a>
</dt>
<dt><a href="dihedral_style.html#index-0">dihedral_style</a>
</dt>
<dt><a href="dihedral_charmm.html#index-0">dihedral_style charmm</a>
</dt>
<dt><a href="dihedral_class2.html#index-0">dihedral_style class2</a>
</dt>
<dt><a href="dihedral_cosine_shift_exp.html#index-0">dihedral_style cosine/shift/exp</a>
</dt>
<dt><a href="dihedral_fourier.html#index-0">dihedral_style fourier</a>
</dt>
<dt><a href="dihedral_harmonic.html#index-0">dihedral_style harmonic</a>
</dt>
<dt><a href="dihedral_helix.html#index-0">dihedral_style helix</a>
</dt>
<dt><a href="dihedral_hybrid.html#index-0">dihedral_style hybrid</a>
</dt>
<dt><a href="dihedral_multi_harmonic.html#index-0">dihedral_style multi/harmonic</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="dihedral_nharmonic.html#index-0">dihedral_style nharmonic</a>
</dt>
<dt><a href="dihedral_none.html#index-0">dihedral_style none</a>
</dt>
<dt><a href="dihedral_opls.html#index-0">dihedral_style opls</a>
</dt>
<dt><a href="dihedral_quadratic.html#index-0">dihedral_style quadratic</a>
</dt>
<dt><a href="dihedral_table.html#index-0">dihedral_style table</a>
</dt>
<dt><a href="dimension.html#index-0">dimension</a>
</dt>
<dt><a href="displace_atoms.html#index-0">displace_atoms</a>
</dt>
<dt><a href="dump.html#index-0">dump</a>
</dt>
<dt><a href="dump_h5md.html#index-0">dump h5md</a>
</dt>
<dt><a href="dump_image.html#index-0">dump image</a>
</dt>
<dt><a href="dump_molfile.html#index-0">dump molfile</a>
</dt>
<dt><a href="dump_modify.html#index-0">dump_modify</a>
</dt>
</dl></td>
</tr></table>
<h2 id="E">E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="echo.html#index-0">echo</a>
</dt>
</dl></td>
</tr></table>
<h2 id="F">F</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="fix.html#index-0">fix</a>
</dt>
<dt><a href="fix_adapt.html#index-0">fix adapt</a>
</dt>
<dt><a href="fix_adapt_fep.html#index-0">fix adapt/fep</a>
</dt>
<dt><a href="fix_addforce.html#index-0">fix addforce</a>
</dt>
<dt><a href="fix_addtorque.html#index-0">fix addtorque</a>
</dt>
<dt><a href="fix_append_atoms.html#index-0">fix append/atoms</a>
</dt>
<dt><a href="fix_atc.html#index-0">fix atc</a>
</dt>
<dt><a href="fix_atom_swap.html#index-0">fix atom/swap</a>
</dt>
<dt><a href="fix_ave_atom.html#index-0">fix ave/atom</a>
</dt>
<dt><a href="fix_ave_chunk.html#index-0">fix ave/chunk</a>
</dt>
<dt><a href="fix_ave_correlate.html#index-0">fix ave/correlate</a>
</dt>
+ <dt><a href="fix_ave_correlate_long.html#index-0">fix ave/correlate/long</a>
+ </dt>
+
+
<dt><a href="fix_ave_histo.html#index-0">fix ave/histo</a>
</dt>
<dt><a href="fix_ave_spatial.html#index-0">fix ave/spatial</a>
</dt>
<dt><a href="fix_ave_spatial_sphere.html#index-0">fix ave/spatial/sphere</a>
</dt>
<dt><a href="fix_ave_time.html#index-0">fix ave/time</a>
</dt>
<dt><a href="fix_aveforce.html#index-0">fix aveforce</a>
</dt>
<dt><a href="fix_balance.html#index-0">fix balance</a>
</dt>
<dt><a href="fix_bond_break.html#index-0">fix bond/break</a>
</dt>
<dt><a href="fix_bond_create.html#index-0">fix bond/create</a>
</dt>
<dt><a href="fix_bond_swap.html#index-0">fix bond/swap</a>
</dt>
<dt><a href="fix_box_relax.html#index-0">fix box/relax</a>
</dt>
<dt><a href="fix_colvars.html#index-0">fix colvars</a>
</dt>
<dt><a href="fix_deform.html#index-0">fix deform</a>
</dt>
<dt><a href="fix_deposit.html#index-0">fix deposit</a>
</dt>
<dt><a href="fix_drag.html#index-0">fix drag</a>
</dt>
<dt><a href="fix_drude.html#index-0">fix drude</a>
</dt>
<dt><a href="fix_drude_transform.html#index-0">fix drude/transform/direct</a>
</dt>
<dt><a href="fix_dt_reset.html#index-0">fix dt/reset</a>
</dt>
<dt><a href="fix_efield.html#index-0">fix efield</a>
</dt>
<dt><a href="fix_enforce2d.html#index-0">fix enforce2d</a>
</dt>
<dt><a href="fix_evaporate.html#index-0">fix evaporate</a>
</dt>
<dt><a href="fix_external.html#index-0">fix external</a>
</dt>
<dt><a href="fix_freeze.html#index-0">fix freeze</a>
</dt>
<dt><a href="fix_gcmc.html#index-0">fix gcmc</a>
</dt>
<dt><a href="fix_gld.html#index-0">fix gld</a>
</dt>
<dt><a href="fix_gle.html#index-0">fix gle</a>
</dt>
<dt><a href="fix_gravity.html#index-0">fix gravity</a>
</dt>
<dt><a href="fix_heat.html#index-0">fix heat</a>
</dt>
<dt><a href="fix_imd.html#index-0">fix imd</a>
</dt>
<dt><a href="fix_indent.html#index-0">fix indent</a>
</dt>
<dt><a href="fix_ipi.html#index-0">fix ipi</a>
</dt>
<dt><a href="fix_langevin.html#index-0">fix langevin</a>
</dt>
<dt><a href="fix_langevin_drude.html#index-0">fix langevin/drude</a>
</dt>
<dt><a href="fix_langevin_eff.html#index-0">fix langevin/eff</a>
</dt>
<dt><a href="fix_lb_fluid.html#index-0">fix lb/fluid</a>
</dt>
<dt><a href="fix_lb_momentum.html#index-0">fix lb/momentum</a>
</dt>
<dt><a href="fix_lb_pc.html#index-0">fix lb/pc</a>
</dt>
<dt><a href="fix_lb_rigid_pc_sphere.html#index-0">fix lb/rigid/pc/sphere</a>
</dt>
<dt><a href="fix_lb_viscous.html#index-0">fix lb/viscous</a>
</dt>
<dt><a href="fix_lineforce.html#index-0">fix lineforce</a>
</dt>
<dt><a href="fix_meso.html#index-0">fix meso</a>
</dt>
<dt><a href="fix_meso_stationary.html#index-0">fix meso/stationary</a>
</dt>
<dt><a href="fix_momentum.html#index-0">fix momentum</a>
</dt>
<dt><a href="fix_move.html#index-0">fix move</a>
</dt>
<dt><a href="fix_msst.html#index-0">fix msst</a>
</dt>
<dt><a href="fix_neb.html#index-0">fix neb</a>
</dt>
<dt><a href="fix_nph_asphere.html#index-0">fix nph/asphere</a>
</dt>
<dt><a href="fix_nph_sphere.html#index-0">fix nph/sphere</a>
</dt>
<dt><a href="fix_nphug.html#index-0">fix nphug</a>
</dt>
<dt><a href="fix_npt_asphere.html#index-0">fix npt/asphere</a>
</dt>
<dt><a href="fix_npt_sphere.html#index-0">fix npt/sphere</a>
</dt>
<dt><a href="fix_nve.html#index-0">fix nve</a>
</dt>
<dt><a href="fix_nve_asphere.html#index-0">fix nve/asphere</a>
</dt>
<dt><a href="fix_nve_asphere_noforce.html#index-0">fix nve/asphere/noforce</a>
</dt>
<dt><a href="fix_nve_body.html#index-0">fix nve/body</a>
</dt>
<dt><a href="fix_nve_eff.html#index-0">fix nve/eff</a>
</dt>
<dt><a href="fix_nve_limit.html#index-0">fix nve/limit</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="fix_nve_line.html#index-0">fix nve/line</a>
</dt>
<dt><a href="fix_nve_noforce.html#index-0">fix nve/noforce</a>
</dt>
<dt><a href="fix_nve_sphere.html#index-0">fix nve/sphere</a>
</dt>
<dt><a href="fix_nve_tri.html#index-0">fix nve/tri</a>
</dt>
<dt><a href="fix_nh.html#index-0">fix nvt</a>
</dt>
<dt><a href="fix_nvt_asphere.html#index-0">fix nvt/asphere</a>
</dt>
<dt><a href="fix_nh_eff.html#index-0">fix nvt/eff</a>
</dt>
<dt><a href="fix_nvt_sllod.html#index-0">fix nvt/sllod</a>
</dt>
<dt><a href="fix_nvt_sllod_eff.html#index-0">fix nvt/sllod/eff</a>
</dt>
<dt><a href="fix_nvt_sphere.html#index-0">fix nvt/sphere</a>
</dt>
<dt><a href="fix_oneway.html#index-0">fix oneway</a>
</dt>
<dt><a href="fix_orient_fcc.html#index-0">fix orient/fcc</a>
</dt>
<dt><a href="fix_phonon.html#index-0">fix phonon</a>
</dt>
<dt><a href="fix_pimd.html#index-0">fix pimd</a>
</dt>
<dt><a href="fix_planeforce.html#index-0">fix planeforce</a>
</dt>
<dt><a href="fix_pour.html#index-0">fix pour</a>
</dt>
<dt><a href="fix_press_berendsen.html#index-0">fix press/berendsen</a>
</dt>
<dt><a href="fix_print.html#index-0">fix print</a>
</dt>
<dt><a href="fix_property_atom.html#index-0">fix property/atom</a>
</dt>
<dt><a href="fix_qbmsst.html#index-0">fix qbmsst</a>
</dt>
<dt><a href="fix_qeq_comb.html#index-0">fix qeq/comb</a>
</dt>
<dt><a href="fix_qeq.html#index-0">fix qeq/point</a>
</dt>
<dt><a href="fix_qeq_reax.html#index-0">fix qeq/reax</a>
</dt>
<dt><a href="fix_qmmm.html#index-0">fix qmmm</a>
</dt>
<dt><a href="fix_qtb.html#index-0">fix qtb</a>
</dt>
<dt><a href="fix_reax_bonds.html#index-0">fix reax/bonds</a>
</dt>
<dt><a href="fix_reaxc_species.html#index-0">fix reax/c/species</a>
</dt>
<dt><a href="fix_recenter.html#index-0">fix recenter</a>
</dt>
<dt><a href="fix_restrain.html#index-0">fix restrain</a>
</dt>
<dt><a href="fix_rigid.html#index-0">fix rigid</a>
</dt>
<dt><a href="fix_saed_vtk.html#index-0">fix saed/vtk</a>
</dt>
<dt><a href="fix_setforce.html#index-0">fix setforce</a>
</dt>
<dt><a href="fix_shake.html#index-0">fix shake</a>
</dt>
<dt><a href="fix_smd.html#index-0">fix smd</a>
</dt>
<dt><a href="fix_smd_adjust_dt.html#index-0">fix smd/adjust_dt</a>
</dt>
<dt><a href="fix_smd_integrate_tlsph.html#index-0">fix smd/integrate_tlsph</a>
</dt>
<dt><a href="fix_smd_integrate_ulsph.html#index-0">fix smd/integrate_ulsph</a>
</dt>
<dt><a href="fix_smd_move_triangulated_surface.html#index-0">fix smd/move_tri_surf</a>
</dt>
<dt><a href="fix_smd_setvel.html#index-0">fix smd/setvel</a>
</dt>
<dt><a href="fix_smd_wall_surface.html#index-0">fix smd/wall_surface</a>
</dt>
<dt><a href="fix_spring.html#index-0">fix spring</a>
</dt>
<dt><a href="fix_spring_rg.html#index-0">fix spring/rg</a>
</dt>
<dt><a href="fix_spring_self.html#index-0">fix spring/self</a>
</dt>
<dt><a href="fix_srd.html#index-0">fix srd</a>
</dt>
<dt><a href="fix_store_force.html#index-0">fix store/force</a>
</dt>
<dt><a href="fix_store_state.html#index-0">fix store/state</a>
</dt>
<dt><a href="fix_temp_berendsen.html#index-0">fix temp/berendsen</a>
</dt>
<dt><a href="fix_temp_csvr.html#index-0">fix temp/csvr</a>
</dt>
<dt><a href="fix_temp_rescale.html#index-0">fix temp/rescale</a>
</dt>
<dt><a href="fix_temp_rescale_eff.html#index-0">fix temp/rescale/eff</a>
</dt>
<dt><a href="fix_tfmc.html#index-0">fix tfmc</a>
</dt>
<dt><a href="fix_thermal_conductivity.html#index-0">fix thermal/conductivity</a>
</dt>
<dt><a href="fix_ti_rs.html#index-0">fix ti/rs</a>
</dt>
<dt><a href="fix_ti_spring.html#index-0">fix ti/spring</a>
</dt>
<dt><a href="fix_tmd.html#index-0">fix tmd</a>
</dt>
<dt><a href="fix_ttm.html#index-0">fix ttm</a>
</dt>
<dt><a href="fix_tune_kspace.html#index-0">fix tune/kspace</a>
</dt>
<dt><a href="fix_vector.html#index-0">fix vector</a>
</dt>
<dt><a href="fix_viscosity.html#index-0">fix viscosity</a>
</dt>
<dt><a href="fix_viscous.html#index-0">fix viscous</a>
</dt>
<dt><a href="fix_wall_gran.html#index-0">fix wall/gran</a>
</dt>
<dt><a href="fix_wall.html#index-0">fix wall/lj93</a>
</dt>
<dt><a href="fix_wall_piston.html#index-0">fix wall/piston</a>
</dt>
<dt><a href="fix_wall_reflect.html#index-0">fix wall/reflect</a>
</dt>
<dt><a href="fix_wall_region.html#index-0">fix wall/region</a>
</dt>
<dt><a href="fix_wall_srd.html#index-0">fix wall/srd</a>
</dt>
<dt><a href="fix_modify.html#index-0">fix_modify</a>
</dt>
</dl></td>
</tr></table>
<h2 id="G">G</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="group.html#index-0">group</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="group2ndx.html#index-0">group2ndx</a>
</dt>
</dl></td>
</tr></table>
<h2 id="I">I</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="if.html#index-0">if</a>
</dt>
<dt><a href="improper_coeff.html#index-0">improper_coeff</a>
</dt>
<dt><a href="improper_style.html#index-0">improper_style</a>
</dt>
<dt><a href="improper_class2.html#index-0">improper_style class2</a>
</dt>
<dt><a href="improper_cossq.html#index-0">improper_style cossq</a>
</dt>
<dt><a href="improper_cvff.html#index-0">improper_style cvff</a>
</dt>
<dt><a href="improper_fourier.html#index-0">improper_style fourier</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="improper_harmonic.html#index-0">improper_style harmonic</a>
</dt>
<dt><a href="improper_hybrid.html#index-0">improper_style hybrid</a>
</dt>
<dt><a href="improper_none.html#index-0">improper_style none</a>
</dt>
<dt><a href="improper_ring.html#index-0">improper_style ring</a>
</dt>
<dt><a href="improper_umbrella.html#index-0">improper_style umbrella</a>
</dt>
<dt><a href="include.html#index-0">include</a>
</dt>
<dt><a href="info.html#index-0">info</a>
</dt>
</dl></td>
</tr></table>
<h2 id="J">J</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="jump.html#index-0">jump</a>
</dt>
</dl></td>
</tr></table>
<h2 id="K">K</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="kspace_modify.html#index-0">kspace_modify</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="kspace_style.html#index-0">kspace_style</a>
</dt>
</dl></td>
</tr></table>
<h2 id="L">L</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="label.html#index-0">label</a>
</dt>
<dt><a href="lattice.html#index-0">lattice</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="log.html#index-0">log</a>
</dt>
</dl></td>
</tr></table>
<h2 id="M">M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="mass.html#index-0">mass</a>
</dt>
<dt><a href="min_modify.html#index-0">min_modify</a>
</dt>
<dt><a href="min_style.html#index-0">min_style</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="minimize.html#index-0">minimize</a>
</dt>
<dt><a href="molecule.html#index-0">molecule</a>
</dt>
</dl></td>
</tr></table>
<h2 id="N">N</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
<dt><a href="neb.html#index-0">neb</a>
</dt>
<dt><a href="neigh_modify.html#index-0">neigh_modify</a>
</dt>
<dt><a href="neighbor.html#index-0">neighbor</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="newton.html#index-0">newton</a>
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diff --git a/doc/molecule.html b/doc/molecule.html
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<div class="section" id="molecule-command">
<span id="index-0"></span><h1>molecule command<a class="headerlink" href="#molecule-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>molecule ID file1 file2 ... keyword values ...
+<div class="highlight-python"><div class="highlight"><pre>molecule ID file1 keyword values ... file2 keyword values ... fileN ...
</pre></div>
</div>
<ul class="simple">
<li>ID = user-assigned name for the molecule template</li>
<li>file1,file2,... = names of files containing molecule descriptions</li>
-<li>zero or more keyword/value pairs may be appended</li>
-<li>keyword = <em>offset</em></li>
+<li>zero or more keyword/value pairs may be appended after each file</li>
+<li>keyword = <em>offset</em> or <em>toff</em> or <em>boff</em> or <em>aoff</em> or <em>doff</em> or <em>ioff</em> or <em>scale</em></li>
</ul>
<pre class="literal-block">
-<em>offset</em> values = toff boff aoff doff ioff
- toff = offset to add to atom types
- boff = offset to add to bond types
- aoff = offset to add to angle types
- doff = offset to add to dihedral types
- ioff = offset to add to improper types
+<em>offset</em> values = Toff Boff Aoff Doff Ioff
+ Toff = offset to add to atom types
+ Boff = offset to add to bond types
+ Aoff = offset to add to angle types
+ Doff = offset to add to dihedral types
+ Ioff = offset to add to improper types
+<em>toff</em> value = Toff
+ Toff = offset to add to atom types
+<em>boff</em> value = Boff
+ Boff = offset to add to bond types
+<em>aoff</em> value = Aoff
+ Aoff = offset to add to angle types
+<em>doff</em> value = Doff
+ Doff = offset to add to dihedral types
+<em>ioff</em> value = Ioff
+ Ioff = offset to add to improper types
+<em>scale</em> value = sfactor
+ sfactor = scale factor to apply to the size and mass of the molecule
</pre>
</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>molecule 1 mymol
+<div class="highlight-python"><div class="highlight"><pre>molecule 1 mymol.txt
molecule 1 co2.txt h2o.txt
-molecule CO2 co2.txt
-molecule 1 mymol offset 6 9 18 23 14
+molecule CO2 co2.txt boff 3 aoff 2
+molecule 1 mymol.txt offset 6 9 18 23 14
+molecule objects file.1 scale 1.5 file.1 scale 2.0 file.2 scale 1.3
</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 molecule template that can be used as part of other LAMMPS
commands, typically to define a collection of particles as a bonded
molecule or a rigid body. Commands that currently use molecule
templates include:</p>
<ul class="simple">
<li><a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a></li>
<li><a class="reference internal" href="fix_pour.html"><em>fix pour</em></a></li>
<li><a class="reference internal" href="fix_rigid.html"><em>fix rigid/small</em></a></li>
<li><a class="reference internal" href="fix_shake.html"><em>fix shake</em></a></li>
<li><a class="reference internal" href="fix_gcmc.html"><em>fix gcmc</em></a></li>
<li><a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a></li>
<li><a class="reference internal" href="atom_style.html"><em>atom_style template</em></a></li>
</ul>
<p>The ID of a molecule template can only contain alphanumeric characters
and underscores.</p>
<p>A single template can contain multiple molecules, listed one per file.
-Many of the commands listed above currently use only the first
+Some of the commands listed above currently use only the first
molecule in the template, and will issue a warning if the template
contains multiple molecules. The <a class="reference internal" href="atom_style.html"><em>atom_style template</em></a> command allows multiple-molecule templates
to define a system with more than one templated molecule.</p>
-<p>The optional <em>offset</em> keyword adds the specified offset values to the
-atom types, bond types, angle types, dihedral types, and improper
-types as they are read from the molecule file. E.g. if <em>toff</em> = 2,
-and the file uses atom types 1,2,3, then each created molecule will
-have atom types 3,4,5. This is to make it easy to use the same
-molecule template file in different simulations. Note that the same
-offsets are applied to the molecules in all specified files. All five
-offset values must be speicified, but individual values will be
-ignored if the molecule template does not use that attribute (e.g. no
-bonds).</p>
+<p>Each filename can be followed by optional keywords which are applied
+only to the molecule in the file as used in this template. This is to
+make it easy to use the same molecule file in different molecule
+templates or in different simulations. You can specify the same file
+multiple times with different optional keywords.</p>
+<p>The <em>offset</em>, <em>toff</em>, <em>aoff</em>, <em>doff</em>, <em>ioff</em> keywords add the
+specified offset values to the atom types, bond types, angle types,
+dihedral types, and/or improper types as they are read from the
+molecule file. E.g. if <em>toff</em> = 2, and the file uses atom types
+1,2,3, then each created molecule will have atom types 3,4,5. For the
+<em>offset</em> keyword, all five offset values must be specified, but
+individual values will be ignored if the molecule template does not
+use that attribute (e.g. no bonds).</p>
+<p>The <em>scale</em> keyword scales the size of the molecule. This can be
+useful for modeling polydisperse granular rigid bodies. The scale
+factor is applied to each of these properties in the molecule file, if
+they are defined: the individual particle coordinates (Coords
+section), the individual mass of each particle (Masses section), the
+individual diameters of each particle (Diameters section), the total
+mass of the molecule (header keyword = mass), the center-of-mass of
+the molecule (header keyword = com), and the moments of inertia of the
+molecule (header keyword = inertia).</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
-<p class="last">This command can be used to define molecules with
-bonds, angles, dihedrals, imporopers, or special bond lists of
+<p class="last">The molecule command can be used to define molecules
+with bonds, angles, dihedrals, imporopers, or special bond lists of
neighbors within a molecular topology, so that you can later add the
molecules to your simulation, via one or more of the commands listed
above. If such molecules do not already exist when LAMMPS creates the
simulation box, via the <a class="reference internal" href="create_box.html"><em>create_box</em></a> or
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command, when you later add them you may
overflow the pre-allocated data structures which store molecular
topology information with each atom, and an error will be generated.
Both the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command and the data files read
by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command have “extra” options which
insure space is allocated for storing topology info for molecules that
are added later.</p>
</div>
<p>The format of an individual molecule file is similar to the data file
read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> commands, and is as follows.</p>
<p>A molecule file has a header and a body. The header appears first.
The first line of the header is always skipped; it typically contains
a description of the file. Then lines are read one at a time. Lines
can have a trailing comment starting with ‘#’ that is ignored. If the
line is blank (only whitespace after comment is deleted), it is
skipped. If the line contains a header keyword, the corresponding
value(s) is read from the line. If it doesn’t contain a header
keyword, the line begins the body of the file.</p>
<p>The body of the file contains zero or more sections. The first line
of a section has only a keyword. The next line is skipped. The
remaining lines of the section contain values. The number of lines
depends on the section keyword as described below. Zero or more blank
lines can be used between sections. Sections can appear in any order,
with a few exceptions as noted below.</p>
<p>These are the recognized header keywords. Header lines can come in
any order. The numeric value(s) are read from the beginning of the
line. The keyword should appear at the end of the line. All these
settings have default values, as explained below. A line need only
appear if the value(s) are different than the default.</p>
<ul class="simple">
<li>N <em>atoms</em> = # of atoms N in molecule, default = 0</li>
<li>Nb <em>bonds</em> = # of bonds Nb in molecule, default = 0</li>
<li>Na <em>angles</em> = # of angles Na in molecule, default = 0</li>
<li>Nd <em>dihedrals</em> = # of dihedrals Nd in molecule, default = 0</li>
<li>Ni <em>impropers</em> = # of impropers Ni in molecule, default = 0</li>
<li>Mtotal <em>mass</em> = total mass of molecule</li>
<li>Xc Yc Zc <em>com</em> = coordinates of center-of-mass of molecule</li>
<li>Ixx Iyy Izz Ixy Ixz Iyz <em>inertia</em> = 6 components of inertia tensor of molecule</li>
</ul>
<p>For <em>mass</em>, <em>com</em>, and <em>inertia</em>, the default is for LAMMPS to
calculate this quantity itself if needed, assuming the molecules
consists of a set of point particles or finite-size particles (with a
non-zero diameter) that do not overlap. If finite-size particles in
the molecule do overlap, LAMMPS will not account for the overlap
effects when calculating any of these 3 quantities, so you should
pre-compute them yourself and list the values in the file.</p>
<p>The mass and center-of-mass coordinates (Xc,Yc,Zc) are
self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)
should be the values consistent with the current orientation of the
rigid body around its center of mass. The values are with respect to
the simulation box XYZ axes, not with respect to the prinicpal axes of
the rigid body itself. LAMMPS performs the latter calculation
internally.</p>
<p>These are the allowed section keywords for the body of the file.</p>
<ul class="simple">
<li><em>Coords, Types, Charges, Diameters, Masses</em> = atom-property sections</li>
<li><em>Bonds, Angles, Dihedrals, Impropers</em> = molecular topology sections</li>
<li><em>Special Bond Counts, Special Bonds</em> = special neighbor info</li>
<li><em>Shake Flags, Shake Atoms, Shake Bond Types</em> = SHAKE info</li>
</ul>
<p>If a Bonds section is specified then the Special Bond Counts and
Special Bonds sections can also be used, if desired, to explicitly
list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see
details below). This is optional since if these sections are not
included, LAMMPS will auto-generate this information. Note that
LAMMPS uses this info to properly exclude or weight bonded pairwise
interactions between bonded atoms. See the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command for more details. One
reason to list the special bond info explicitly is for the
<a class="reference internal" href="tutorial_drude.html"><em>thermalized Drude oscillator model</em></a> which treats
the bonds between nuclear cores and Drude electrons in a different
manner.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Whether a section is required depends on how the
molecule template is used by other LAMMPS commands. For example, to
add a molecule via the <a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a> command, the
Coords and Types sections are required. To add a rigid body via the
<code class="xref doc docutils literal"><span class="pre">fix</span> <span class="pre">pour</span></code> command, the Bonds (Angles, etc) sections are
not required, since the molecule will be treated as a rigid body.
Some sections are optional. For example, the <a class="reference internal" href="fix_pour.html"><em>fix pour</em></a>
command can be used to add “molecules” which are clusters of
finite-size granular particles. If the Diameters section is not
specified, each particle in the molecule will have a default diameter
of 1.0. See the doc pages for LAMMPS commands that use molecule
templates for more details.</p>
</div>
<p>Each section is listed below in alphabetic order. The format of each
section is described including the number of lines it must contain and
rules (if any) for whether it can appear in the data file. In each
case the ID is ignored; it is simply included for readability, and
should be a number from 1 to Nlines for the section, indicating which
atom (or bond, etc) the entry applies to. The lines are assumed to be
listed in order from 1 to Nlines, but LAMMPS does not check for this.</p>
<hr class="docutils" />
<p><em>Coords</em> section:</p>
<ul class="simple">
<li>one line per atom</li>
<li>line syntax: ID x y z</li>
<li>x,y,z = coordinate of atom</li>
</ul>
<hr class="docutils" />
<p><em>Types</em> section:</p>
<ul class="simple">
<li>one line per atom</li>
<li>line syntax: ID type</li>
<li>type = atom type of atom</li>
</ul>
<hr class="docutils" />
<p><em>Charges</em> section:</p>
<ul class="simple">
<li>one line per atom</li>
<li>line syntax: ID q</li>
<li>q = charge on atom</li>
</ul>
<p>This section is only allowed for <a class="reference internal" href="atom_style.html"><em>atom styles</em></a> that
support charge. If this section is not included, the default charge
on each atom in the molecule is 0.0.</p>
<hr class="docutils" />
<p><em>Diameters</em> section:</p>
<ul class="simple">
<li>one line per atom</li>
<li>line syntax: ID diam</li>
<li>diam = diameter of atom</li>
</ul>
<p>This section is only allowed for <a class="reference internal" href="atom_style.html"><em>atom styles</em></a> that
support finite-size spherical particles, e.g. atom_style sphere. If
not listed, the default diameter of each atom in the molecule is 1.0.</p>
<hr class="docutils" />
<p><em>Masses</em> section:</p>
<ul class="simple">
<li>one line per atom</li>
<li>line syntax: ID mass</li>
<li>mass = mass of atom</li>
</ul>
<p>This section is only allowed for <a class="reference internal" href="atom_style.html"><em>atom styles</em></a> that
support per-atom mass, as opposed to per-type mass. See the
<a class="reference internal" href="mass.html"><em>mass</em></a> command for details. If this section is not
included, the default mass for each atom is derived from its volume
(see Diameters section) and a default density of 1.0, in
<a class="reference internal" href="units.html"><em>units</em></a> of mass/volume.</p>
<hr class="docutils" />
<p><em>Bonds</em> section:</p>
<ul class="simple">
<li>one line per bond</li>
<li>line syntax: ID type atom1 atom2</li>
<li>type = bond type (1-Nbondtype)</li>
<li>atom1,atom2 = IDs of atoms in bond</li>
</ul>
<p>The IDs for the two atoms in each bond should be values
from 1 to Natoms, where Natoms = # of atoms in the molecule.</p>
<hr class="docutils" />
<p><em>Angles</em> section:</p>
<ul class="simple">
<li>one line per angle</li>
<li>line syntax: ID type atom1 atom2 atom3</li>
<li>type = angle type (1-Nangletype)</li>
<li>atom1,atom2,atom3 = IDs of atoms in angle</li>
</ul>
<p>The IDs for the three atoms in each angle should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule. The 3 atoms are
ordered linearly within the angle. Thus the central atom (around
which the angle is computed) is the atom2 in the list.</p>
<hr class="docutils" />
<p><em>Dihedrals</em> section:</p>
<ul class="simple">
<li>one line per dihedral</li>
<li>line syntax: ID type atom1 atom2 atom3 atom4</li>
<li>type = dihedral type (1-Ndihedraltype)</li>
<li>atom1,atom2,atom3,atom4 = IDs of atoms in dihedral</li>
</ul>
<p>The IDs for the four atoms in each dihedral should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule. The 4 atoms are
ordered linearly within the dihedral.</p>
<hr class="docutils" />
<p><em>Impropers</em> section:</p>
<ul class="simple">
<li>one line per improper</li>
<li>line syntax: ID type atom1 atom2 atom3 atom4</li>
<li>type = improper type (1-Nimpropertype)</li>
<li>atom1,atom2,atom3,atom4 = IDs of atoms in improper</li>
</ul>
<p>The IDs for the four atoms in each improper should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule. The ordering of
the 4 atoms determines the definition of the improper angle used in
the formula for the defined <a class="reference internal" href="improper_style.html"><em>improper style</em></a>. See
the doc pages for individual styles for details.</p>
<hr class="docutils" />
<p><em>Special Bond Counts</em> section:</p>
<ul class="simple">
<li>one line per atom</li>
<li>line syntax: ID N1 N2 N3</li>
<li>N1 = # of 1-2 bonds</li>
<li>N2 = # of 1-3 bonds</li>
<li>N3 = # of 1-4 bonds</li>
</ul>
<p>N1, N2, N3 are the number of 1-2, 1-3, 1-4 neighbors respectively of
this atom within the topology of the molecule. See the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> doc page for more discussion of
1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds
section must also appear. If this section is not specied, the
atoms in the molecule will have no special bonds.</p>
<hr class="docutils" />
<p><em>Special Bonds</em> section:</p>
<ul class="simple">
<li>one line per atom</li>
<li>line syntax: ID a b c d ...</li>
<li>a,b,c,d,... = IDs of atoms in N1+N2+N3 special bonds</li>
</ul>
<p>A, b, c, d, etc are the IDs of the n1+n2+n3 atoms that are 1-2, 1-3,
1-4 neighbors of this atom. The IDs should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule. The first N1
values should be the 1-2 neighbors, the next N2 should be the 1-3
neighbors, the last N3 should be the 1-4 neighbors. No atom ID should
appear more than once. See the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> doc
page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section
appears, the Special Bond Counts section must also appear. If this
section is not specied, the atoms in the molecule will have no special
bonds.</p>
<hr class="docutils" />
<p><em>Shake Flags</em> section:</p>
<ul class="simple">
<li>one line per atom</li>
<li>line syntax: ID flag</li>
<li>flag = 0,1,2,3,4</li>
</ul>
<p>This section is only needed when molecules created using the template
will be constrained by SHAKE via the “fix shake” command. The other
two Shake sections must also appear in the file, following this one.</p>
<p>The meaning of the flag for each atom is as follows. See the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> doc page for a further description of SHAKE
clusters.</p>
<ul class="simple">
<li>0 = not part of a SHAKE cluster</li>
<li>1 = part of a SHAKE angle cluster (two bonds and the angle they form)</li>
<li>2 = part of a 2-atom SHAKE cluster with a single bond</li>
<li>3 = part of a 3-atom SHAKE cluster with two bonds</li>
<li>4 = part of a 4-atom SHAKE cluster with three bonds</li>
</ul>
<hr class="docutils" />
<p><em>Shake Atoms</em> section:</p>
<ul class="simple">
<li>one line per atom</li>
<li>line syntax: ID a b c d</li>
<li>a,b,c,d = IDs of atoms in cluster</li>
</ul>
<p>This section is only needed when molecules created using the template
will be constrained by SHAKE via the “fix shake” command. The other
two Shake sections must also appear in the file.</p>
<p>The a,b,c,d values are atom IDs (from 1 to Natoms) for all the atoms
in the SHAKE cluster that this atom belongs to. The number of values
that must appear is determined by the shake flag for the atom (see the
Shake Flags section above). All atoms in a particular cluster should
list their a,b,c,d values identically.</p>
<p>If flag = 0, no a,b,c,d values are listed on the line, just the
(ignored) ID.</p>
<p>If flag = 1, a,b,c are listed, where a = ID of central atom in the
angle, and b,c the other two atoms in the angle.</p>
<p>If flag = 2, a,b are listed, where a = ID of atom in bond with the the
lowest ID, and b = ID of atom in bond with the highest ID.</p>
<p>If flag = 3, a,b,c are listed, where a = ID of central atom,
and b,c = IDs of other two atoms bonded to the central atom.</p>
<p>If flag = 4, a,b,c,d are listed, where a = ID of central atom,
and b,c,d = IDs of other three atoms bonded to the central atom.</p>
<p>See the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> doc page for a further description
of SHAKE clusters.</p>
<hr class="docutils" />
<p><em>Shake Bond Types</em> section:</p>
<ul class="simple">
<li>one line per atom</li>
<li>line syntax: ID a b c</li>
<li>a,b,c = bond types (or angle type) of bonds (or angle) in cluster</li>
</ul>
<p>This section is only needed when molecules created using the template
will be constrained by SHAKE via the “fix shake” command. The other
two Shake sections must also appear in the file.</p>
<p>The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds
in the SHAKE cluster that this atom belongs to. The number of values
that must appear is determined by the shake flag for the atom (see the
Shake Flags section above). All atoms in a particular cluster should
list their a,b,c values identically.</p>
<p>If flag = 0, no a,b,c values are listed on the line, just the
(ignored) ID.</p>
<p>If flag = 1, a,b,c are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), b = bondtype of the bond between the central atom and
the 2nd non-central atom (value c in the Shake Atoms section), and c =
the angle type (1 to Nangletypes) of the angle between the 3 atoms.</p>
<p>If flag = 2, only a is listed, where a = bondtype of the bond between
the 2 atoms in the cluster.</p>
<p>If flag = 3, a,b are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), and b = bondtype of the bond between the central atom
and the 2nd non-central atom (value c in the Shake Atoms section).</p>
<p>If flag = 4, a,b,c are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), b = bondtype of the bond between the central atom and
the 2nd non-central atom (value c in the Shake Atoms section), and c =
bondtype of the bond between the central atom and the 3rd non-central
atom (value d in the Shake Atoms section).</p>
<p>See the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> doc page for a further description
of SHAKE clusters.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div>none</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="fix_deposit.html"><em>fix deposit</em></a>, <a class="reference internal" href="fix_pour.html"><em>fix pour</em></a>,
<a class="reference internal" href="fix_gcmc.html"><em>fix_gcmc</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
-<p>The default keyword value is offset 0 0 0 0 0.</p>
+<p>The default keywords values are offset 0 0 0 0 0 and scale = 1.0.</p>
</div>
</div>
</div>
</div>
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\ No newline at end of file
diff --git a/doc/molecule.txt b/doc/molecule.txt
index 3aedbc8e1..41c11ae24 100644
--- a/doc/molecule.txt
+++ b/doc/molecule.txt
@@ -1,434 +1,463 @@
<"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
molecule command :h3
[Syntax:]
-molecule ID file1 file2 ... keyword values ... :pre
+molecule ID file1 keyword values ... file2 keyword values ... fileN ... :pre
ID = user-assigned name for the molecule template :ulb,l
file1,file2,... = names of files containing molecule descriptions :l
-zero or more keyword/value pairs may be appended :l
-keyword = {offset} :l
- {offset} values = toff boff aoff doff ioff
- toff = offset to add to atom types
- boff = offset to add to bond types
- aoff = offset to add to angle types
- doff = offset to add to dihedral types
- ioff = offset to add to improper types :pre
+zero or more keyword/value pairs may be appended after each file :l
+keyword = {offset} or {toff} or {boff} or {aoff} or {doff} or {ioff} or {scale} :l
+ {offset} values = Toff Boff Aoff Doff Ioff
+ Toff = offset to add to atom types
+ Boff = offset to add to bond types
+ Aoff = offset to add to angle types
+ Doff = offset to add to dihedral types
+ Ioff = offset to add to improper types
+ {toff} value = Toff
+ Toff = offset to add to atom types
+ {boff} value = Boff
+ Boff = offset to add to bond types
+ {aoff} value = Aoff
+ Aoff = offset to add to angle types
+ {doff} value = Doff
+ Doff = offset to add to dihedral types
+ {ioff} value = Ioff
+ Ioff = offset to add to improper types
+ {scale} value = sfactor
+ sfactor = scale factor to apply to the size and mass of the molecule :pre
:ule
[Examples:]
-molecule 1 mymol
+molecule 1 mymol.txt
molecule 1 co2.txt h2o.txt
-molecule CO2 co2.txt
-molecule 1 mymol offset 6 9 18 23 14 :pre
+molecule CO2 co2.txt boff 3 aoff 2
+molecule 1 mymol.txt offset 6 9 18 23 14
+molecule objects file.1 scale 1.5 file.1 scale 2.0 file.2 scale 1.3 :pre
+
+:pre
[Description:]
Define a molecule template that can be used as part of other LAMMPS
commands, typically to define a collection of particles as a bonded
molecule or a rigid body. Commands that currently use molecule
templates include:
"fix deposit"_fix_deposit.html
"fix pour"_fix_pour.html
"fix rigid/small"_fix_rigid.html
"fix shake"_fix_shake.html
"fix gcmc"_fix_gcmc.html
"create_atoms"_create_atoms.html
"atom_style template"_atom_style.html :ul
The ID of a molecule template can only contain alphanumeric characters
and underscores.
A single template can contain multiple molecules, listed one per file.
-Many of the commands listed above currently use only the first
+Some of the commands listed above currently use only the first
molecule in the template, and will issue a warning if the template
contains multiple molecules. The "atom_style
template"_atom_style.html command allows multiple-molecule templates
to define a system with more than one templated molecule.
-The optional {offset} keyword adds the specified offset values to the
-atom types, bond types, angle types, dihedral types, and improper
-types as they are read from the molecule file. E.g. if {toff} = 2,
-and the file uses atom types 1,2,3, then each created molecule will
-have atom types 3,4,5. This is to make it easy to use the same
-molecule template file in different simulations. Note that the same
-offsets are applied to the molecules in all specified files. All five
-offset values must be speicified, but individual values will be
-ignored if the molecule template does not use that attribute (e.g. no
-bonds).
-
-IMPORTANT NOTE: This command can be used to define molecules with
-bonds, angles, dihedrals, imporopers, or special bond lists of
+Each filename can be followed by optional keywords which are applied
+only to the molecule in the file as used in this template. This is to
+make it easy to use the same molecule file in different molecule
+templates or in different simulations. You can specify the same file
+multiple times with different optional keywords.
+
+The {offset}, {toff}, {aoff}, {doff}, {ioff} keywords add the
+specified offset values to the atom types, bond types, angle types,
+dihedral types, and/or improper types as they are read from the
+molecule file. E.g. if {toff} = 2, and the file uses atom types
+1,2,3, then each created molecule will have atom types 3,4,5. For the
+{offset} keyword, all five offset values must be specified, but
+individual values will be ignored if the molecule template does not
+use that attribute (e.g. no bonds).
+
+The {scale} keyword scales the size of the molecule. This can be
+useful for modeling polydisperse granular rigid bodies. The scale
+factor is applied to each of these properties in the molecule file, if
+they are defined: the individual particle coordinates (Coords
+section), the individual mass of each particle (Masses section), the
+individual diameters of each particle (Diameters section), the total
+mass of the molecule (header keyword = mass), the center-of-mass of
+the molecule (header keyword = com), and the moments of inertia of the
+molecule (header keyword = inertia).
+
+IMPORTANT NOTE: The molecule command can be used to define molecules
+with bonds, angles, dihedrals, imporopers, or special bond lists of
neighbors within a molecular topology, so that you can later add the
molecules to your simulation, via one or more of the commands listed
above. If such molecules do not already exist when LAMMPS creates the
simulation box, via the "create_box"_create_box.html or
"read_data"_read_data.html command, when you later add them you may
overflow the pre-allocated data structures which store molecular
topology information with each atom, and an error will be generated.
Both the "create_box"_create_box.html command and the data files read
by the "read_data"_read_data.html command have "extra" options which
insure space is allocated for storing topology info for molecules that
are added later.
The format of an individual molecule file is similar to the data file
read by the "read_data"_read_data.html commands, and is as follows.
A molecule file has a header and a body. The header appears first.
The first line of the header is always skipped; it typically contains
a description of the file. Then lines are read one at a time. Lines
can have a trailing comment starting with '#' that is ignored. If the
line is blank (only whitespace after comment is deleted), it is
skipped. If the line contains a header keyword, the corresponding
value(s) is read from the line. If it doesn't contain a header
keyword, the line begins the body of the file.
The body of the file contains zero or more sections. The first line
of a section has only a keyword. The next line is skipped. The
remaining lines of the section contain values. The number of lines
depends on the section keyword as described below. Zero or more blank
lines can be used between sections. Sections can appear in any order,
with a few exceptions as noted below.
These are the recognized header keywords. Header lines can come in
any order. The numeric value(s) are read from the beginning of the
line. The keyword should appear at the end of the line. All these
settings have default values, as explained below. A line need only
appear if the value(s) are different than the default.
N {atoms} = # of atoms N in molecule, default = 0
Nb {bonds} = # of bonds Nb in molecule, default = 0
Na {angles} = # of angles Na in molecule, default = 0
Nd {dihedrals} = # of dihedrals Nd in molecule, default = 0
Ni {impropers} = # of impropers Ni in molecule, default = 0
Mtotal {mass} = total mass of molecule
Xc Yc Zc {com} = coordinates of center-of-mass of molecule
Ixx Iyy Izz Ixy Ixz Iyz {inertia} = 6 components of inertia tensor of molecule :ul
For {mass}, {com}, and {inertia}, the default is for LAMMPS to
calculate this quantity itself if needed, assuming the molecules
consists of a set of point particles or finite-size particles (with a
non-zero diameter) that do not overlap. If finite-size particles in
the molecule do overlap, LAMMPS will not account for the overlap
effects when calculating any of these 3 quantities, so you should
pre-compute them yourself and list the values in the file.
The mass and center-of-mass coordinates (Xc,Yc,Zc) are
self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)
should be the values consistent with the current orientation of the
rigid body around its center of mass. The values are with respect to
the simulation box XYZ axes, not with respect to the prinicpal axes of
the rigid body itself. LAMMPS performs the latter calculation
internally.
These are the allowed section keywords for the body of the file.
{Coords, Types, Charges, Diameters, Masses} = atom-property sections
{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections
{Special Bond Counts, Special Bonds} = special neighbor info
{Shake Flags, Shake Atoms, Shake Bond Types} = SHAKE info :ul
If a Bonds section is specified then the Special Bond Counts and
Special Bonds sections can also be used, if desired, to explicitly
list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see
details below). This is optional since if these sections are not
included, LAMMPS will auto-generate this information. Note that
LAMMPS uses this info to properly exclude or weight bonded pairwise
interactions between bonded atoms. See the
"special_bonds"_special_bonds.html command for more details. One
reason to list the special bond info explicitly is for the
"thermalized Drude oscillator model"_tutorial_drude.html which treats
the bonds between nuclear cores and Drude electrons in a different
manner.
IMPORTANT NOTE: Whether a section is required depends on how the
molecule template is used by other LAMMPS commands. For example, to
add a molecule via the "fix deposit"_fix_deposit.html command, the
Coords and Types sections are required. To add a rigid body via the
"fix pour"_fix_pout.html command, the Bonds (Angles, etc) sections are
not required, since the molecule will be treated as a rigid body.
Some sections are optional. For example, the "fix pour"_fix_pour.html
command can be used to add "molecules" which are clusters of
finite-size granular particles. If the Diameters section is not
specified, each particle in the molecule will have a default diameter
of 1.0. See the doc pages for LAMMPS commands that use molecule
templates for more details.
Each section is listed below in alphabetic order. The format of each
section is described including the number of lines it must contain and
rules (if any) for whether it can appear in the data file. In each
case the ID is ignored; it is simply included for readability, and
should be a number from 1 to Nlines for the section, indicating which
atom (or bond, etc) the entry applies to. The lines are assumed to be
listed in order from 1 to Nlines, but LAMMPS does not check for this.
:line
{Coords} section:
one line per atom
line syntax: ID x y z
x,y,z = coordinate of atom :ul
:line
{Types} section:
one line per atom
line syntax: ID type
type = atom type of atom :ul
:line
{Charges} section:
one line per atom
line syntax: ID q
q = charge on atom :ul
This section is only allowed for "atom styles"_atom_style.html that
support charge. If this section is not included, the default charge
on each atom in the molecule is 0.0.
:line
{Diameters} section:
one line per atom
line syntax: ID diam
diam = diameter of atom :ul
This section is only allowed for "atom styles"_atom_style.html that
support finite-size spherical particles, e.g. atom_style sphere. If
not listed, the default diameter of each atom in the molecule is 1.0.
:line
{Masses} section:
one line per atom
line syntax: ID mass
mass = mass of atom :ul
This section is only allowed for "atom styles"_atom_style.html that
support per-atom mass, as opposed to per-type mass. See the
"mass"_mass.html command for details. If this section is not
included, the default mass for each atom is derived from its volume
(see Diameters section) and a default density of 1.0, in
"units"_units.html of mass/volume.
:line
{Bonds} section:
one line per bond
line syntax: ID type atom1 atom2
type = bond type (1-Nbondtype)
atom1,atom2 = IDs of atoms in bond :ul
The IDs for the two atoms in each bond should be values
from 1 to Natoms, where Natoms = # of atoms in the molecule.
:line
{Angles} section:
one line per angle
line syntax: ID type atom1 atom2 atom3
type = angle type (1-Nangletype)
atom1,atom2,atom3 = IDs of atoms in angle :ul
The IDs for the three atoms in each angle should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule. The 3 atoms are
ordered linearly within the angle. Thus the central atom (around
which the angle is computed) is the atom2 in the list.
:line
{Dihedrals} section:
one line per dihedral
line syntax: ID type atom1 atom2 atom3 atom4
type = dihedral type (1-Ndihedraltype)
atom1,atom2,atom3,atom4 = IDs of atoms in dihedral :ul
The IDs for the four atoms in each dihedral should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule. The 4 atoms are
ordered linearly within the dihedral.
:line
{Impropers} section:
one line per improper
line syntax: ID type atom1 atom2 atom3 atom4
type = improper type (1-Nimpropertype)
atom1,atom2,atom3,atom4 = IDs of atoms in improper :ul
The IDs for the four atoms in each improper should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule. The ordering of
the 4 atoms determines the definition of the improper angle used in
the formula for the defined "improper style"_improper_style.html. See
the doc pages for individual styles for details.
:line
{Special Bond Counts} section:
one line per atom
line syntax: ID N1 N2 N3
N1 = # of 1-2 bonds
N2 = # of 1-3 bonds
N3 = # of 1-4 bonds :ul
N1, N2, N3 are the number of 1-2, 1-3, 1-4 neighbors respectively of
this atom within the topology of the molecule. See the
"special_bonds"_special_bonds.html doc page for more discussion of
1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds
section must also appear. If this section is not specied, the
atoms in the molecule will have no special bonds.
:line
{Special Bonds} section:
one line per atom
line syntax: ID a b c d ...
a,b,c,d,... = IDs of atoms in N1+N2+N3 special bonds :ul
A, b, c, d, etc are the IDs of the n1+n2+n3 atoms that are 1-2, 1-3,
1-4 neighbors of this atom. The IDs should be values from 1 to
Natoms, where Natoms = # of atoms in the molecule. The first N1
values should be the 1-2 neighbors, the next N2 should be the 1-3
neighbors, the last N3 should be the 1-4 neighbors. No atom ID should
appear more than once. See the "special_bonds"_special_bonds.html doc
page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section
appears, the Special Bond Counts section must also appear. If this
section is not specied, the atoms in the molecule will have no special
bonds.
:line
{Shake Flags} section:
one line per atom
line syntax: ID flag
flag = 0,1,2,3,4 :ul
This section is only needed when molecules created using the template
will be constrained by SHAKE via the "fix shake" command. The other
two Shake sections must also appear in the file, following this one.
The meaning of the flag for each atom is as follows. See the "fix
shake"_fix_shake.html doc page for a further description of SHAKE
clusters.
0 = not part of a SHAKE cluster
1 = part of a SHAKE angle cluster (two bonds and the angle they form)
2 = part of a 2-atom SHAKE cluster with a single bond
3 = part of a 3-atom SHAKE cluster with two bonds
4 = part of a 4-atom SHAKE cluster with three bonds :ul
:line
{Shake Atoms} section:
one line per atom
line syntax: ID a b c d
a,b,c,d = IDs of atoms in cluster :ul
This section is only needed when molecules created using the template
will be constrained by SHAKE via the "fix shake" command. The other
two Shake sections must also appear in the file.
The a,b,c,d values are atom IDs (from 1 to Natoms) for all the atoms
in the SHAKE cluster that this atom belongs to. The number of values
that must appear is determined by the shake flag for the atom (see the
Shake Flags section above). All atoms in a particular cluster should
list their a,b,c,d values identically.
If flag = 0, no a,b,c,d values are listed on the line, just the
(ignored) ID.
If flag = 1, a,b,c are listed, where a = ID of central atom in the
angle, and b,c the other two atoms in the angle.
If flag = 2, a,b are listed, where a = ID of atom in bond with the the
lowest ID, and b = ID of atom in bond with the highest ID.
If flag = 3, a,b,c are listed, where a = ID of central atom,
and b,c = IDs of other two atoms bonded to the central atom.
If flag = 4, a,b,c,d are listed, where a = ID of central atom,
and b,c,d = IDs of other three atoms bonded to the central atom.
See the "fix shake"_fix_shake.html doc page for a further description
of SHAKE clusters.
:line
{Shake Bond Types} section:
one line per atom
line syntax: ID a b c
a,b,c = bond types (or angle type) of bonds (or angle) in cluster :ul
This section is only needed when molecules created using the template
will be constrained by SHAKE via the "fix shake" command. The other
two Shake sections must also appear in the file.
The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds
in the SHAKE cluster that this atom belongs to. The number of values
that must appear is determined by the shake flag for the atom (see the
Shake Flags section above). All atoms in a particular cluster should
list their a,b,c values identically.
If flag = 0, no a,b,c values are listed on the line, just the
(ignored) ID.
If flag = 1, a,b,c are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), b = bondtype of the bond between the central atom and
the 2nd non-central atom (value c in the Shake Atoms section), and c =
the angle type (1 to Nangletypes) of the angle between the 3 atoms.
If flag = 2, only a is listed, where a = bondtype of the bond between
the 2 atoms in the cluster.
If flag = 3, a,b are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), and b = bondtype of the bond between the central atom
and the 2nd non-central atom (value c in the Shake Atoms section).
If flag = 4, a,b,c are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), b = bondtype of the bond between the central atom and
the 2nd non-central atom (value c in the Shake Atoms section), and c =
bondtype of the bond between the central atom and the 3rd non-central
atom (value d in the Shake Atoms section).
See the "fix shake"_fix_shake.html doc page for a further description
of SHAKE clusters.
:line
[Restrictions:] none
[Related commands:]
"fix deposit"_fix_deposit.html, "fix pour"_fix_pour.html,
"fix_gcmc"_fix_gcmc.html
[Default:]
-The default keyword value is offset 0 0 0 0 0.
+The default keywords values are offset 0 0 0 0 0 and scale = 1.0.
diff --git a/doc/pair_hybrid.html b/doc/pair_hybrid.html
index 7c116747d..329c77fec 100644
--- a/doc/pair_hybrid.html
+++ b/doc/pair_hybrid.html
@@ -1,539 +1,543 @@
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<div class="section" id="pair-style-hybrid-command">
<span id="index-0"></span><h1>pair_style hybrid command<a class="headerlink" href="#pair-style-hybrid-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-hybrid-omp-command">
<h1>pair_style hybrid/omp command<a class="headerlink" href="#pair-style-hybrid-omp-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-hybrid-overlay-command">
<h1>pair_style hybrid/overlay command<a class="headerlink" href="#pair-style-hybrid-overlay-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-hybrid-overlay-omp-command">
<h1>pair_style hybrid/overlay/omp command<a class="headerlink" href="#pair-style-hybrid-overlay-omp-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>pair_style hybrid style1 args style2 args ...
pair_style hybrid/overlay style1 args style2 args ...
</pre></div>
</div>
<ul class="simple">
<li>style1,style2 = list of one or more pair styles and their arguments</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>pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0
pair_coeff 1*2 1*2 eam niu3
pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
pair_coeff 1*2 3 lj/cut 0.5 1.2
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0
pair_coeff * * lj/cut 1.0 1.0
pair_coeff * * coul/long
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>The <em>hybrid</em> and <em>hybrid/overlay</em> styles enable the use of multiple
pair styles in one simulation. With the <em>hybrid</em> style, exactly one
pair style is assigned to each pair of atom types. With the
<em>hybrid/overlay</em> style, one or more pair styles can be assigned to
each pair of atom types. The assignment of pair styles to type pairs
is made via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command.</p>
<p>Here are two examples of hybrid simulations. The <em>hybrid</em> style could
be used for a simulation of a metal droplet on a LJ surface. The
metal atoms interact with each other via an <em>eam</em> potential, the
surface atoms interact with each other via a <em>lj/cut</em> potential, and
the metal/surface interaction is also computed via a <em>lj/cut</em>
potential. The <em>hybrid/overlay</em> style could be used as in the 2nd
example above, where multiple potentials are superposed in an additive
fashion to compute the interaction between atoms. In this example,
using <em>lj/cut</em> and <em>coul/long</em> together gives the same result as if
the <em>lj/cut/coul/long</em> potential were used by itself. In this case,
it would be more efficient to use the single combined potential, but
in general any combination of pair potentials can be used together in
to produce an interaction that is not encoded in any single pair_style
file, e.g. adding Coulombic forces between granular particles.</p>
<p>All pair styles that will be used are listed as “sub-styles” following
the <em>hybrid</em> or <em>hybrid/overlay</em> keyword, in any order. Each
sub-style’s name is followed by its usual arguments, as illustrated in
the example above. See the doc pages of individual pair styles for a
listing and explanation of the appropriate arguments.</p>
<p>Note that an individual pair style can be used multiple times as a
sub-style. For efficiency this should only be done if your model
requires it. E.g. if you have different regions of Si and C atoms and
wish to use a Tersoff potential for pure Si for one set of atoms, and
a Tersoff potetnial for pure C for the other set (presumably with some
3rd potential for Si-C interactions), then the sub-style <em>tersoff</em>
could be listed twice. But if you just want to use a Lennard-Jones or
other pairwise potential for several different atom type pairs in your
model, then you should just list the sub-style once and use the
pair_coeff command to assign parameters for the different type pairs.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
-<p class="last">An exception to this option to list an individual pair
-style multiple times are the pair styles implemented as Fortran
-libraries: <a class="reference internal" href="pair_meam.html"><em>pair_style meam</em></a> and <a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a> (<a class="reference internal" href="pair_reax_c.html"><em>pair_style reax/c</em></a> is OK).
-This is because unlike a C++ class, they can not be instantiated
-multiple times, due to the manner in which they were coded in Fortran.</p>
+<p class="last">There are two exceptions to this option to list an
+individual pair style multiple times. The first is for pair styles
+implemented as Fortran libraries: <a class="reference internal" href="pair_meam.html"><em>pair_style meam</em></a> and
+<a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a> (<a class="reference internal" href="pair_reax_c.html"><em>pair_style reax/c</em></a>
+is OK). This is because unlike a C++ class, they can not be
+instantiated multiple times, due to the manner in which they were
+coded in Fortran. The second is for GPU-enabled pair styles in the
+GPU package. This is b/c the GPU package also currently assumes that
+only one instance of a pair style is being used.</p>
</div>
<p>In the pair_coeff commands, the name of a pair style must be added
after the I,J type specification, with the remaining coefficients
being those appropriate to that style. If the pair style is used
multiple times in the pair_style command, then an additional numeric
argument must also be specified which is a number from 1 to M where M
is the number of times the sub-style was listed in the pair style
command. The extra number indicates which instance of the sub-style
these coefficients apply to.</p>
<p>For example, consider a simulation with 3 atom types: types 1 and 2
are Ni atoms, type 3 are LJ atoms with charges. The following
commands would set up a hybrid simulation:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
pair_coeff * * eam/alloy nialhjea Ni Ni NULL
pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
pair_coeff 1*2 3 lj/cut 0.8 1.3
</pre></div>
</div>
<p>As an example of using the same pair style multiple times, consider a
simulation with 2 atom types. Type 1 is Si, type 2 is C. The
following commands would model the Si atoms with Tersoff, the C atoms
with Tersoff, and the cross-interactions with Lennard-Jones:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid lj/cut 2.5 tersoff tersoff
pair_coeff * * tersoff 1 Si.tersoff Si NULL
pair_coeff * * tersoff 2 C.tersoff NULL C
pair_coeff 1 2 lj/cut 1.0 1.5
</pre></div>
</div>
<p>If pair coefficients are specified in the data file read via the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command, then the same rule applies.
E.g. “eam/alloy” or “lj/cut” must be added after the atom type, for
each line in the “Pair Coeffs” section, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>Pair Coeffs
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>1 lj/cut/coul/cut 1.0 1.0
...
</pre></div>
</div>
<p>Note that the pair_coeff command for some potentials such as
<a class="reference internal" href="pair_eam.html"><em>pair_style eam/alloy</em></a> includes a mapping specification
of elements to all atom types, which in the hybrid case, can include
atom types not assigned to the <em>eam/alloy</em> potential. The NULL
keyword is used by many such potentials (eam/alloy, Tersoff, AIREBO,
etc), to denote an atom type that will be assigned to a different
sub-style.</p>
<p>For the <em>hybrid</em> style, each atom type pair I,J is assigned to exactly
one sub-style. Just as with a simulation using a single pair style,
if you specify the same atom type pair in a second pair_coeff command,
the previous assignment will be overwritten.</p>
<p>For the <em>hybrid/overlay</em> style, each atom type pair I,J can be
assigned to one or more sub-styles. If you specify the same atom type
pair in a second pair_coeff command with a new sub-style, then the
second sub-style is added to the list of potentials that will be
calculated for two interacting atoms of those types. If you specify
the same atom type pair in a second pair_coeff command with a
sub-style that has already been defined for that pair of atoms, then
the new pair coefficients simply override the previous ones, as in the
normal usage of the pair_coeff command. E.g. these two sets of
commands are the same:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 2 2 1.5 0.8
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid/overlay lj/cut 2.5
pair_coeff * * lj/cut 1.0 1.0
pair_coeff 2 2 lj/cut 1.5 0.8
</pre></div>
</div>
<p>Coefficients must be defined for each pair of atoms types via the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as described above, or in the
data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> or
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands, or by mixing as described
below.</p>
<p>For both the <em>hybrid</em> and <em>hybrid/overlay</em> styles, every atom type
pair I,J (where I <= J) must be assigned to at least one sub-style via
the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above, or
in the data file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>, or by mixing
as described below.</p>
<p>If you want there to be no interactions between a particular pair of
atom types, you have 3 choices. You can assign the type pair to some
sub-style and use the <a class="reference internal" href="neigh_modify.html"><em>neigh_modify exclude type</em></a>
command. You can assign it to some sub-style and set the coefficients
so that there is effectively no interaction (e.g. epsilon = 0.0 in a
LJ potential). Or, for <em>hybrid</em> and <em>hybrid/overlay</em> simulations, you
can use this form of the pair_coeff command in your input script:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff 2 3 none
</pre></div>
</div>
<p>or this form in the “Pair Coeffs” section of the data file:</p>
<div class="highlight-python"><div class="highlight"><pre>3 none
</pre></div>
</div>
<p>If an assignment to <em>none</em> is made in a simulation with the
<em>hybrid/overlay</em> pair style, it wipes out all previous assignments of
that atom type pair to sub-styles.</p>
<p>Note that you may need to use an <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> hybrid
command in your input script, if atoms in the simulation will need
attributes from several atom styles, due to using multiple pair
potentials.</p>
<hr class="docutils" />
<p>Different force fields (e.g. CHARMM vs AMBER) may have different rules
for applying weightings that change the strength of pairwise
interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4
neighbors in the molecular bond topology, as normally set by the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command. Different weights can be
assigned to different pair hybrid sub-styles via the <a class="reference internal" href="pair_modify.html"><em>pair_modify special</em></a> command. This allows multiple force fields
to be used in a model of a hybrid system, however, there is no consistent
approach to determine parameters automatically for the interactions
between the two force fields, this is only recommended when particles
described by the different force fields do not mix.</p>
<p>Here is an example for mixing CHARMM and AMBER: The global <em>amber</em>
setting sets the 1-4 interactions to non-zero scaling factors and
then overrides them with 0.0 only for CHARMM:</p>
<div class="highlight-python"><div class="highlight"><pre>special_bonds amber
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
</pre></div>
</div>
<p>The this input achieves the same effect:</p>
<div class="highlight-python"><div class="highlight"><pre>special_bonds 0.0 0.0 0.1
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
</pre></div>
</div>
<p>Here is an example for mixing Tersoff with OPLS/AA based on
a data file that defines bonds for all atoms where for the
Tersoff part of the system the force constants for the bonded
interactions have been set to 0. Note the global settings are
effectively <em>lj/coul 0.0 0.0 0.5</em> as required for OPLS/AA:</p>
<div class="highlight-python"><div class="highlight"><pre>special_bonds lj/coul 1e-20 1e-20 0.5
pair_hybrid tersoff lj/cut/coul/long 12.0
pair_modify pair tersoff special lj/coul 1.0 1.0 1.0
</pre></div>
</div>
<p>See the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> doc page for details on
the specific syntax, requirements and restrictions.</p>
<hr class="docutils" />
<p>The potential energy contribution to the overall system due to an
individual sub-style can be accessed and output via the <a class="reference internal" href="compute_pair.html"><em>compute pair</em></a> command.</p>
<hr class="docutils" />
<p>IMPORTANT: Several of the potentials defined via the pair_style
command in LAMMPS are really many-body potentials, such as Tersoff,
AIREBO, MEAM, ReaxFF, etc. The way to think about using these
potentials in a hybrid setting is as follows.</p>
<p>A subset of atom types is assigned to the many-body potential with a
single <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command, using “* <a href="#id1"><span class="problematic" id="id2">*</span></a>” to include
all types and the NULL keywords described above to exclude specific
types not assigned to that potential. If types 1,3,4 were assigned in
that way (but not type 2), this means that all many-body interactions
between all atoms of types 1,3,4 will be computed by that potential.
Pair_style hybrid allows interactions between type pairs 2-2, 1-2,
2-3, 2-4 to be specified for computation by other pair styles. You
could even add a second interaction for 1-1 to be computed by another
pair style, assuming pair_style hybrid/overlay is used.</p>
<p>But you should not, as a general rule, attempt to exclude the
many-body interactions for some subset of the type pairs within the
set of 1,3,4 interactions, e.g. exclude 1-1 or 1-3 interactions. That
is not conceptually well-defined for many-body interactions, since the
potential will typically calculate energies and foces for small groups
of atoms, e.g. 3 or 4 atoms, using the neighbor lists of the atoms to
find the additional atoms in the group. It is typically non-physical
to think of excluding an interaction between a particular pair of
atoms when the potential computes 3-body or 4-body interactions.</p>
<p>However, you can still use the pair_coeff none setting or the
<a class="reference internal" href="neigh_modify.html"><em>neigh_modify exclude</em></a> command to exclude certain
type pairs from the neighbor list that will be passed to a manybody
sub-style. This will alter the calculations made by a many-body
potential, since it builds its list of 3-body, 4-body, etc
interactions from the pair list. You will need to think carefully as
to whether it produces a physically meaningful result for your model.</p>
<p>For example, imagine you have two atom types in your model, type 1 for
atoms in one surface, and type 2 for atoms in the other, and you wish
to use a Tersoff potential to compute interactions within each
surface, but not between surfaces. Then either of these two command
sequences would implement that model:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid tersoff
pair_coeff * * tersoff SiC.tersoff C C
pair_coeff 1 2 none
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style tersoff
pair_coeff * * SiC.tersoff C C
neigh_modify exclude type 1 2
</pre></div>
</div>
<p>Either way, only neighbor lists with 1-1 or 2-2 interactions would be
passed to the Tersoff potential, which means it would compute no
3-body interactions containing both type 1 and 2 atoms.</p>
<p>Here is another example, using hybrid/overlay, to use 2 many-body
potentials together, in an overlapping manner. Imagine you have CNT
(C atoms) on a Si surface. You want to use Tersoff for Si/Si and Si/C
interactions, and AIREBO for C/C interactions. Si atoms are type 1; C
atoms are type 2. Something like this will work:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid/overlay tersoff airebo 3.0
pair_coeff * * tersoff SiC.tersoff.custom Si C
pair_coeff * * airebo CH.airebo NULL C
</pre></div>
</div>
<p>Note that to prevent the Tersoff potential from computing C/C
interactions, you would need to modify the SiC.tersoff file to turn
off C/C interaction, i.e. by setting the appropriate coefficients to
0.0.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
of the manual.</p>
<p>Since the <em>hybrid</em> and <em>hybrid/overlay</em> styles delegate computation
to the individual sub-styles, the suffix versions of the <em>hybrid</em>
and <em>hybrid/overlay</em> styles are used to propagate the corresponding
suffix to all sub-styles, if those versions exist. Otherwise the
non-accelerated version will be used.</p>
<p>The individual accelerated sub-styles are part of the USER-CUDA, GPU,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the
<a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>Any pair potential settings made via the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> command are passed along to all
sub-styles of the hybrid potential.</p>
<p>For atom type pairs I,J and I != J, if the sub-style assigned to I,I
and J,J is the same, and if the sub-style allows for mixing, then the
coefficients for I,J can be mixed. This means you do not have to
specify a pair_coeff command for I,J since the I,J type pair will be
assigned automatically to the sub-style defined for both I,I and J,J
and its coefficients generated by the mixing rule used by that
sub-style. For the <em>hybrid/overlay</em> style, there is an additional
requirement that both the I,I and J,J pairs are assigned to a single
sub-style. See the “pair_modify” command for details of mixing rules.
See the See the doc page for the sub-style to see if allows for
mixing.</p>
<p>The hybrid pair styles supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options for an I,J pair interaction, if the
associated sub-style supports it.</p>
<p>For the hybrid pair styles, the list of sub-styles and their
respective settings are written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so a <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command does
not need to specified in an input script that reads a restart file.
However, the coefficient information is not stored in the restart
file. Thus, pair_coeff commands need to be re-specified in the
restart input script.</p>
<p>These pair styles support the use of the <em>inner</em>, <em>middle</em>, and
<em>outer</em> keywords of the <a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command, if
their sub-styles do.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>When using a long-range Coulombic solver (via the
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command) with a hybrid pair_style,
one or more sub-styles will be of the “long” variety,
e.g. <em>lj/cut/coul/long</em> or <em>buck/coul/long</em>. You must insure that the
short-range Coulombic cutoff used by each of these long pair styles is
the same or else LAMMPS will generate an error.</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="pair_coeff.html"><em>pair_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
</div>
</div>
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\ No newline at end of file
diff --git a/doc/pair_hybrid.txt b/doc/pair_hybrid.txt
index 103a7bd16..34c09f392 100644
--- a/doc/pair_hybrid.txt
+++ b/doc/pair_hybrid.txt
@@ -1,378 +1,381 @@
"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
pair_style hybrid command :h3
pair_style hybrid/omp command :h3
pair_style hybrid/overlay command :h3
pair_style hybrid/overlay/omp command :h3
[Syntax:]
pair_style hybrid style1 args style2 args ...
pair_style hybrid/overlay style1 args style2 args ... :pre
style1,style2 = list of one or more pair styles and their arguments :ul
[Examples:]
pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0
pair_coeff 1*2 1*2 eam niu3
pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
pair_coeff 1*2 3 lj/cut 0.5 1.2 :pre
pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0
pair_coeff * * lj/cut 1.0 1.0
pair_coeff * * coul/long :pre
[Description:]
The {hybrid} and {hybrid/overlay} styles enable the use of multiple
pair styles in one simulation. With the {hybrid} style, exactly one
pair style is assigned to each pair of atom types. With the
{hybrid/overlay} style, one or more pair styles can be assigned to
each pair of atom types. The assignment of pair styles to type pairs
is made via the "pair_coeff"_pair_coeff.html command.
Here are two examples of hybrid simulations. The {hybrid} style could
be used for a simulation of a metal droplet on a LJ surface. The
metal atoms interact with each other via an {eam} potential, the
surface atoms interact with each other via a {lj/cut} potential, and
the metal/surface interaction is also computed via a {lj/cut}
potential. The {hybrid/overlay} style could be used as in the 2nd
example above, where multiple potentials are superposed in an additive
fashion to compute the interaction between atoms. In this example,
using {lj/cut} and {coul/long} together gives the same result as if
the {lj/cut/coul/long} potential were used by itself. In this case,
it would be more efficient to use the single combined potential, but
in general any combination of pair potentials can be used together in
to produce an interaction that is not encoded in any single pair_style
file, e.g. adding Coulombic forces between granular particles.
All pair styles that will be used are listed as "sub-styles" following
the {hybrid} or {hybrid/overlay} keyword, in any order. Each
sub-style's name is followed by its usual arguments, as illustrated in
the example above. See the doc pages of individual pair styles for a
listing and explanation of the appropriate arguments.
Note that an individual pair style can be used multiple times as a
sub-style. For efficiency this should only be done if your model
requires it. E.g. if you have different regions of Si and C atoms and
wish to use a Tersoff potential for pure Si for one set of atoms, and
a Tersoff potetnial for pure C for the other set (presumably with some
3rd potential for Si-C interactions), then the sub-style {tersoff}
could be listed twice. But if you just want to use a Lennard-Jones or
other pairwise potential for several different atom type pairs in your
model, then you should just list the sub-style once and use the
pair_coeff command to assign parameters for the different type pairs.
-IMPORTANT NOTE: An exception to this option to list an individual pair
-style multiple times are the pair styles implemented as Fortran
-libraries like "pair_style meam"_pair_meam.html
+IMPORTANT NOTE: There are two exceptions to this option to list an
+individual pair style multiple times. The first is for pair styles
+implemented as Fortran libraries: "pair_style meam"_pair_meam.html.
This is because unlike a C++ class, they can not be instantiated
multiple times, due to the manner in which they were coded in Fortran.
+The second is for GPU-enabled pair styles in the GPU package.
+This is b/c the GPU package also currently assumes that only one
+instance of a pair style is being used.
In the pair_coeff commands, the name of a pair style must be added
after the I,J type specification, with the remaining coefficients
being those appropriate to that style. If the pair style is used
multiple times in the pair_style command, then an additional numeric
argument must also be specified which is a number from 1 to M where M
is the number of times the sub-style was listed in the pair style
command. The extra number indicates which instance of the sub-style
these coefficients apply to.
For example, consider a simulation with 3 atom types: types 1 and 2
are Ni atoms, type 3 are LJ atoms with charges. The following
commands would set up a hybrid simulation:
pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
pair_coeff * * eam/alloy nialhjea Ni Ni NULL
pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
pair_coeff 1*2 3 lj/cut 0.8 1.3 :pre
As an example of using the same pair style multiple times, consider a
simulation with 2 atom types. Type 1 is Si, type 2 is C. The
following commands would model the Si atoms with Tersoff, the C atoms
with Tersoff, and the cross-interactions with Lennard-Jones:
pair_style hybrid lj/cut 2.5 tersoff tersoff
pair_coeff * * tersoff 1 Si.tersoff Si NULL
pair_coeff * * tersoff 2 C.tersoff NULL C
pair_coeff 1 2 lj/cut 1.0 1.5 :pre
If pair coefficients are specified in the data file read via the
"read_data"_read_data.html command, then the same rule applies.
E.g. "eam/alloy" or "lj/cut" must be added after the atom type, for
each line in the "Pair Coeffs" section, e.g.
Pair Coeffs :pre
1 lj/cut/coul/cut 1.0 1.0
... :pre
Note that the pair_coeff command for some potentials such as
"pair_style eam/alloy"_pair_eam.html includes a mapping specification
of elements to all atom types, which in the hybrid case, can include
atom types not assigned to the {eam/alloy} potential. The NULL
keyword is used by many such potentials (eam/alloy, Tersoff, AIREBO,
etc), to denote an atom type that will be assigned to a different
sub-style.
For the {hybrid} style, each atom type pair I,J is assigned to exactly
one sub-style. Just as with a simulation using a single pair style,
if you specify the same atom type pair in a second pair_coeff command,
the previous assignment will be overwritten.
For the {hybrid/overlay} style, each atom type pair I,J can be
assigned to one or more sub-styles. If you specify the same atom type
pair in a second pair_coeff command with a new sub-style, then the
second sub-style is added to the list of potentials that will be
calculated for two interacting atoms of those types. If you specify
the same atom type pair in a second pair_coeff command with a
sub-style that has already been defined for that pair of atoms, then
the new pair coefficients simply override the previous ones, as in the
normal usage of the pair_coeff command. E.g. these two sets of
commands are the same:
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 2 2 1.5 0.8 :pre
pair_style hybrid/overlay lj/cut 2.5
pair_coeff * * lj/cut 1.0 1.0
pair_coeff 2 2 lj/cut 1.5 0.8 :pre
Coefficients must be defined for each pair of atoms types via the
"pair_coeff"_pair_coeff.html command as described above, or in the
data file or restart files read by the "read_data"_read_data.html or
"read_restart"_read_restart.html commands, or by mixing as described
below.
For both the {hybrid} and {hybrid/overlay} styles, every atom type
pair I,J (where I <= J) must be assigned to at least one sub-style via
the "pair_coeff"_pair_coeff.html command as in the examples above, or
in the data file read by the "read_data"_read_data.html, or by mixing
as described below.
If you want there to be no interactions between a particular pair of
atom types, you have 3 choices. You can assign the type pair to some
sub-style and use the "neigh_modify exclude type"_neigh_modify.html
command. You can assign it to some sub-style and set the coefficients
so that there is effectively no interaction (e.g. epsilon = 0.0 in a
LJ potential). Or, for {hybrid} and {hybrid/overlay} simulations, you
can use this form of the pair_coeff command in your input script:
pair_coeff 2 3 none :pre
or this form in the "Pair Coeffs" section of the data file:
3 none :pre
If an assignment to {none} is made in a simulation with the
{hybrid/overlay} pair style, it wipes out all previous assignments of
that atom type pair to sub-styles.
Note that you may need to use an "atom_style"_atom_style.html hybrid
command in your input script, if atoms in the simulation will need
attributes from several atom styles, due to using multiple pair
potentials.
:line
Different force fields (e.g. CHARMM vs AMBER) may have different rules
for applying weightings that change the strength of pairwise
interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4
neighbors in the molecular bond topology, as normally set by the
"special_bonds"_special_bonds.html command. Different weights can be
assigned to different pair hybrid sub-styles via the "pair_modify
special"_pair_modify.html command. This allows multiple force fields
to be used in a model of a hybrid system, however, there is no consistent
approach to determine parameters automatically for the interactions
between the two force fields, this is only recommended when particles
described by the different force fields do not mix.
Here is an example for mixing CHARMM and AMBER: The global {amber}
setting sets the 1-4 interactions to non-zero scaling factors and
then overrides them with 0.0 only for CHARMM:
special_bonds amber
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0 :pre
The this input achieves the same effect:
special_bonds 0.0 0.0 0.1
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0 :pre
Here is an example for mixing Tersoff with OPLS/AA based on
a data file that defines bonds for all atoms where for the
Tersoff part of the system the force constants for the bonded
interactions have been set to 0. Note the global settings are
effectively {lj/coul 0.0 0.0 0.5} as required for OPLS/AA:
special_bonds lj/coul 1e-20 1e-20 0.5
pair_hybrid tersoff lj/cut/coul/long 12.0
pair_modify pair tersoff special lj/coul 1.0 1.0 1.0 :pre
See the "pair_modify"_pair_modify.html doc page for details on
the specific syntax, requirements and restrictions.
:line
The potential energy contribution to the overall system due to an
individual sub-style can be accessed and output via the "compute
pair"_compute_pair.html command.
:line
IMPORTANT: Several of the potentials defined via the pair_style
command in LAMMPS are really many-body potentials, such as Tersoff,
AIREBO, MEAM, ReaxFF, etc. The way to think about using these
potentials in a hybrid setting is as follows.
A subset of atom types is assigned to the many-body potential with a
single "pair_coeff"_pair_coeff.html command, using "* *" to include
all types and the NULL keywords described above to exclude specific
types not assigned to that potential. If types 1,3,4 were assigned in
that way (but not type 2), this means that all many-body interactions
between all atoms of types 1,3,4 will be computed by that potential.
Pair_style hybrid allows interactions between type pairs 2-2, 1-2,
2-3, 2-4 to be specified for computation by other pair styles. You
could even add a second interaction for 1-1 to be computed by another
pair style, assuming pair_style hybrid/overlay is used.
But you should not, as a general rule, attempt to exclude the
many-body interactions for some subset of the type pairs within the
set of 1,3,4 interactions, e.g. exclude 1-1 or 1-3 interactions. That
is not conceptually well-defined for many-body interactions, since the
potential will typically calculate energies and foces for small groups
of atoms, e.g. 3 or 4 atoms, using the neighbor lists of the atoms to
find the additional atoms in the group. It is typically non-physical
to think of excluding an interaction between a particular pair of
atoms when the potential computes 3-body or 4-body interactions.
However, you can still use the pair_coeff none setting or the
"neigh_modify exclude"_neigh_modify.html command to exclude certain
type pairs from the neighbor list that will be passed to a manybody
sub-style. This will alter the calculations made by a many-body
potential, since it builds its list of 3-body, 4-body, etc
interactions from the pair list. You will need to think carefully as
to whether it produces a physically meaningful result for your model.
For example, imagine you have two atom types in your model, type 1 for
atoms in one surface, and type 2 for atoms in the other, and you wish
to use a Tersoff potential to compute interactions within each
surface, but not between surfaces. Then either of these two command
sequences would implement that model:
pair_style hybrid tersoff
pair_coeff * * tersoff SiC.tersoff C C
pair_coeff 1 2 none :pre
pair_style tersoff
pair_coeff * * SiC.tersoff C C
neigh_modify exclude type 1 2 :pre
Either way, only neighbor lists with 1-1 or 2-2 interactions would be
passed to the Tersoff potential, which means it would compute no
3-body interactions containing both type 1 and 2 atoms.
Here is another example, using hybrid/overlay, to use 2 many-body
potentials together, in an overlapping manner. Imagine you have CNT
(C atoms) on a Si surface. You want to use Tersoff for Si/Si and Si/C
interactions, and AIREBO for C/C interactions. Si atoms are type 1; C
atoms are type 2. Something like this will work:
pair_style hybrid/overlay tersoff airebo 3.0
pair_coeff * * tersoff SiC.tersoff.custom Si C
pair_coeff * * airebo CH.airebo NULL C :pre
Note that to prevent the Tersoff potential from computing C/C
interactions, you would need to modify the SiC.tersoff file to turn
off C/C interaction, i.e. by setting the appropriate coefficients to
0.0.
:line
Styles with a {cuda}, {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section_accelerate"_Section_accelerate.html
of the manual.
Since the {hybrid} and {hybrid/overlay} styles delegate computation
to the individual sub-styles, the suffix versions of the {hybrid}
and {hybrid/overlay} styles are used to propagate the corresponding
suffix to all sub-styles, if those versions exist. Otherwise the
non-accelerated version will be used.
The individual accelerated sub-styles are part of the USER-CUDA, GPU,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the
"Making LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
Any pair potential settings made via the
"pair_modify"_pair_modify.html command are passed along to all
sub-styles of the hybrid potential.
For atom type pairs I,J and I != J, if the sub-style assigned to I,I
and J,J is the same, and if the sub-style allows for mixing, then the
coefficients for I,J can be mixed. This means you do not have to
specify a pair_coeff command for I,J since the I,J type pair will be
assigned automatically to the sub-style defined for both I,I and J,J
and its coefficients generated by the mixing rule used by that
sub-style. For the {hybrid/overlay} style, there is an additional
requirement that both the I,I and J,J pairs are assigned to a single
sub-style. See the "pair_modify" command for details of mixing rules.
See the See the doc page for the sub-style to see if allows for
mixing.
The hybrid pair styles supports the "pair_modify"_pair_modify.html
shift, table, and tail options for an I,J pair interaction, if the
associated sub-style supports it.
For the hybrid pair styles, the list of sub-styles and their
respective settings are written to "binary restart
files"_restart.html, so a "pair_style"_pair_style.html command does
not need to specified in an input script that reads a restart file.
However, the coefficient information is not stored in the restart
file. Thus, pair_coeff commands need to be re-specified in the
restart input script.
These pair styles support the use of the {inner}, {middle}, and
{outer} keywords of the "run_style respa"_run_style.html command, if
their sub-styles do.
[Restrictions:]
When using a long-range Coulombic solver (via the
"kspace_style"_kspace_style.html command) with a hybrid pair_style,
one or more sub-styles will be of the "long" variety,
e.g. {lj/cut/coul/long} or {buck/coul/long}. You must insure that the
short-range Coulombic cutoff used by each of these long pair styles is
the same or else LAMMPS will generate an error.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
diff --git a/doc/pair_srp.html b/doc/pair_srp.html
index 4e926a94c..38b3f4f56 100644
--- a/doc/pair_srp.html
+++ b/doc/pair_srp.html
@@ -1,326 +1,328 @@
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<div class="section" id="pair-style-srp-command">
<span id="index-0"></span><h1>pair_style srp command<a class="headerlink" href="#pair-style-srp-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>
-<p>pair_style srp cutoff bond_type dist keyword value ...</p>
+<p>pair_style srp cutoff btype dist keyword value ...</p>
<ul class="simple">
<li>cutoff = global cutoff for SRP interactions (distance units)</li>
-<li>bond_type = bond type to apply SRP interactions</li>
+<li>btype = bond type to apply SRP interactions to (can be wildcard, see below)</li>
<li>distance = <em>min</em> or <em>mid</em></li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>exclude</em></li>
</ul>
<pre class="literal-block">
<em>exclude</em> value = <em>yes</em> or <em>no</em>
</pre>
</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>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
pair_coeff 1 1 dpd 60.0 4.5 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0 0.8
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
pair_coeff 1 1 dpd 60.0 50 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp 40.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid srp 0.8 2 mid
pair_coeff 1 1 none
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0 0.8
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Style <em>srp</em> computes a soft segmental repulsive potential (SRP) that
acts between pairs of bonds. This potential is useful for preventing
bonds from passing through one another when a soft non-bonded
potential acts between beads in, for example, DPD polymer chains. An
example input script that uses this command is provided in
examples/USER/srp.</p>
-<p>Bonds of type <em>btype</em> interact with one another through a
+<p>Bonds of specified type <em>btype</em> interact with one another through a
bond-pairwise potential, such that the force on bond <em>i</em> due to bond
<em>j</em> is as follows</p>
<img alt="_images/pair_srp1.jpg" class="align-center" src="_images/pair_srp1.jpg" />
<p>where <em>r</em> and <em>rij</em> are the distance and unit vector between the two
-bonds. The bondtype can also be specified as an asterisk (*) and then
-this interaction applied to all bonds.
-The <em>mid</em> option computes <em>r</em> and <em>rij</em> from the midpoint
-distance between bonds. The <em>min</em> option computes <em>r</em> and <em>rij</em> from
-the minimum distance between bonds. The force acting on a bond is
-mapped onto the two bond atoms according to the lever rule,</p>
+bonds. Note that <em>btype</em> can be specified as an asterisk “*”, which
+case the interaction is applied to all bond types. The <em>mid</em> option
+computes <em>r</em> and <em>rij</em> from the midpoint distance between bonds. The
+<em>min</em> option computes <em>r</em> and <em>rij</em> from the minimum distance between
+bonds. The force acting on a bond is mapped onto the two bond atoms
+according to the lever rule,</p>
<img alt="_images/pair_srp2.jpg" class="align-center" src="_images/pair_srp2.jpg" />
<p>where <em>L</em> is the normalized distance from the atom to the point of
closest approach of bond <em>i</em> and <em>j</em>. The <em>mid</em> option takes <em>L</em> as
0.5 for each interaction as described in <a class="reference internal" href="#sirk"><span>(Sirk)</span></a>.</p>
<p>The following coefficients must be defined via the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above, or in
the data file or restart file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li><em>C</em> (force units)</li>
<li><em>rc</em> (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global cutoff
is used.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
-<p class="last">Pair style srp considers each bond of type <em>btype</em> as
-a fictitious particle of type <em>bptype</em>, where <em>bptype</em> is the largest
-atom type in the system. These “bond particles” are inserted at the
-beginning of the run, and serve as placeholders that define the
-position of the bonds. This allows neighbor lists to be constructed
-and pairwise interactions to be computed in almost the same way as is
-done for point particles. Because bonds interact only with other
-bonds, <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> should be used to turn off
-interactions between atom type <em>bptype</em> and all other types of atoms.
-An error will be flagged if <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> is
-not used. Further, only bond particles should be given an atom type
-of <em>bptype</em>; a check is done at the beginning of the run to ensure
-there are no regular atoms of <em>bptype</em>.</p>
+<p class="last">Pair style srp considers each bond of type <em>btype</em> to
+be a fictitious “particle” of type <em>bptype</em>, where <em>bptype</em> is the
+largest atom type in the system. There cannot be any actual particles
+assigned to this atom type. This means you must specify the number of
+types in your system to be one larger would normally be the case,
+e.g. via the <a class="reference internal" href="create_box.html"><em>create_box</em></a> or
+<a class="reference internal" href="read_data.html"><em>read_data</em></a> commands. These ficitious “bond particles”
+are inserted at the beginning of the run, and serve as placeholders
+that define the position of the bonds. This allows neighbor lists to
+be constructed and pairwise interactions to be computed in almost the
+same way as is done for actual particles. Because bonds interact only
+with other bonds, <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> should be used
+to turn off interactions between atom type <em>bptype</em> and all other
+types of atoms. An error will be flagged if <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> is not used.</p>
</div>
<p>The optional <em>exclude</em> keyword determines if forces are computed
between first neighbor (directly connected) bonds. For a setting of
-<em>no</em>, first neighbor forces are computed; for <em>yes</em> they are not computed. A setting of <em>no</em>
-cannot be used with the <em>min</em> option for distance calculation because the the minimum distance between
-directly connected bonds is zero.</p>
+<em>no</em>, first neighbor forces are computed; for <em>yes</em> they are not
+computed. A setting of <em>no</em> cannot be used with the <em>min</em> option for
+distance calculation because the the minimum distance between directly
+connected bonds is zero.</p>
<p>Pair style <em>srp</em> turns off normalization of thermodynamic properties
by particle number, as if the command <a class="reference internal" href="thermo_modify.html"><em>thermo_modify norm no</em></a> had been issued.</p>
<p>The pairwise energy associated with style <em>srp</em> is shifted to be zero
at the cutoff distance <em>rc</em>.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair styles does not support mixing.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option for the energy of the pair interaction. Note that as
discussed above, the energy term is already shifted to be 0.0 at the
cutoff distance <em>rc</em>.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant for
this pair style.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
tail option for adding long-range tail corrections to energy and
pressure.</p>
<p>This pair style writes global and per-atom information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. Pair srp should be used with <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a>, thus the pair_coeff commands need to be
specified in the input script when reading a restart file.</p>
<p>This pair style can only be used via the <em>pair</em> keyword of the
<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>This pair style is part of the USER-MISC package. It is only enabled
if LAMMPS was built with that package. See the Making LAMMPS section
for more info.</p>
<p>This pair style must be used with <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a>.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><em>newton</em></a> command to be <em>on</em>
for non-bonded interactions.</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="pair_hybrid.html"><em>pair_style hybrid</em></a>, <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>,
<a class="reference internal" href="pair_dpd.html"><em>pair dpd</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
<p>The default keyword value is exclude = yes.</p>
<hr class="docutils" />
<p id="sirk"><strong>(Sirk)</strong> Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J
Chem Phys, 136 (13) 134903, 2012.</p>
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diff --git a/doc/pair_srp.txt b/doc/pair_srp.txt
index 05a89fde6..02e3f8383 100644
--- a/doc/pair_srp.txt
+++ b/doc/pair_srp.txt
@@ -1,160 +1,164 @@
"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
pair_style srp command :h3
[Syntax:]
-pair_style srp cutoff bond_type dist keyword value ...
+pair_style srp cutoff btype dist keyword value ...
cutoff = global cutoff for SRP interactions (distance units) :ulb,l
-bond_type = bond type to apply SRP interactions :l
+btype = bond type to apply SRP interactions to (can be wildcard, see below) :l
distance = {min} or {mid} :l
zero or more keyword/value pairs may be appended :l
keyword = {exclude} :l
{exclude} value = {yes} or {no} :pre
:ule
[Examples:]
pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
pair_coeff 1 1 dpd 60.0 4.5 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0 0.8 :pre
pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
pair_coeff 1 1 dpd 60.0 50 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp 40.0 :pre
pair_style hybrid srp 0.8 2 mid
pair_coeff 1 1 none
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0 0.8 :pre
[Description:]
Style {srp} computes a soft segmental repulsive potential (SRP) that
acts between pairs of bonds. This potential is useful for preventing
bonds from passing through one another when a soft non-bonded
potential acts between beads in, for example, DPD polymer chains. An
example input script that uses this command is provided in
examples/USER/srp.
-Bonds of type {btype} interact with one another through a
+Bonds of specified type {btype} interact with one another through a
bond-pairwise potential, such that the force on bond {i} due to bond
{j} is as follows
:c,image(Eqs/pair_srp1.jpg)
where {r} and {rij} are the distance and unit vector between the two
-bonds. The bondtype can also be specified as an asterisk (*) and then
-this interaction applied to all bonds.
-The {mid} option computes {r} and {rij} from the midpoint
-distance between bonds. The {min} option computes {r} and {rij} from
-the minimum distance between bonds. The force acting on a bond is
-mapped onto the two bond atoms according to the lever rule,
+bonds. Note that {btype} can be specified as an asterisk "*", which
+case the interaction is applied to all bond types. The {mid} option
+computes {r} and {rij} from the midpoint distance between bonds. The
+{min} option computes {r} and {rij} from the minimum distance between
+bonds. The force acting on a bond is mapped onto the two bond atoms
+according to the lever rule,
:c,image(Eqs/pair_srp2.jpg)
where {L} is the normalized distance from the atom to the point of
closest approach of bond {i} and {j}. The {mid} option takes {L} as
0.5 for each interaction as described in "(Sirk)"_#Sirk.
The following coefficients must be defined via the
"pair_coeff"_pair_coeff.html command as in the examples above, or in
the data file or restart file read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
{C} (force units)
{rc} (distance units) :ul
The last coefficient is optional. If not specified, the global cutoff
is used.
-IMPORTANT NOTE: Pair style srp considers each bond of type {btype} as
-a fictitious particle of type {bptype}, where {bptype} is the largest
-atom type in the system. These "bond particles" are inserted at the
-beginning of the run, and serve as placeholders that define the
-position of the bonds. This allows neighbor lists to be constructed
-and pairwise interactions to be computed in almost the same way as is
-done for point particles. Because bonds interact only with other
-bonds, "pair_style hybrid"_pair_hybrid.html should be used to turn off
-interactions between atom type {bptype} and all other types of atoms.
-An error will be flagged if "pair_style hybrid"_pair_hybrid.html is
-not used. Further, only bond particles should be given an atom type
-of {bptype}; a check is done at the beginning of the run to ensure
-there are no regular atoms of {bptype}.
+IMPORTANT NOTE: Pair style srp considers each bond of type {btype} to
+be a fictitious "particle" of type {bptype}, where {bptype} is the
+largest atom type in the system. There cannot be any actual particles
+assigned to this atom type. This means you must specify the number of
+types in your system to be one larger would normally be the case,
+e.g. via the "create_box"_create_box.html or
+"read_data"_read_data.html commands. These ficitious "bond particles"
+are inserted at the beginning of the run, and serve as placeholders
+that define the position of the bonds. This allows neighbor lists to
+be constructed and pairwise interactions to be computed in almost the
+same way as is done for actual particles. Because bonds interact only
+with other bonds, "pair_style hybrid"_pair_hybrid.html should be used
+to turn off interactions between atom type {bptype} and all other
+types of atoms. An error will be flagged if "pair_style
+hybrid"_pair_hybrid.html is not used.
The optional {exclude} keyword determines if forces are computed
between first neighbor (directly connected) bonds. For a setting of
-{no}, first neighbor forces are computed; for {yes} they are not computed. A setting of {no}
-cannot be used with the {min} option for distance calculation because the the minimum distance between
-directly connected bonds is zero.
+{no}, first neighbor forces are computed; for {yes} they are not
+computed. A setting of {no} cannot be used with the {min} option for
+distance calculation because the the minimum distance between directly
+connected bonds is zero.
Pair style {srp} turns off normalization of thermodynamic properties
by particle number, as if the command "thermo_modify norm
no"_thermo_modify.html had been issued.
The pairwise energy associated with style {srp} is shifted to be zero
at the cutoff distance {rc}.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This pair styles does not support mixing.
This pair style does not support the "pair_modify"_pair_modify.html
shift option for the energy of the pair interaction. Note that as
discussed above, the energy term is already shifted to be 0.0 at the
cutoff distance {rc}.
The "pair_modify"_pair_modify.html table option is not relevant for
this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
This pair style writes global and per-atom information to "binary
restart files"_restart.html. Pair srp should be used with "pair_style
hybrid"_pair_hybrid.html, thus the pair_coeff commands need to be
specified in the input script when reading a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
This pair style is part of the USER-MISC package. It is only enabled
if LAMMPS was built with that package. See the Making LAMMPS section
for more info.
-This pair style must be used with "pair_style hybrid"_pair_hybrid.html.
+This pair style must be used with "pair_style
+hybrid"_pair_hybrid.html.
This pair style requires the "newton"_newton.html command to be {on}
for non-bonded interactions.
[Related commands:]
"pair_style hybrid"_pair_hybrid.html, "pair_coeff"_pair_coeff.html,
"pair dpd"_pair_dpd.html
[Default:]
The default keyword value is exclude = yes.
:line
:link(Sirk)
[(Sirk)] Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J
Chem Phys, 136 (13) 134903, 2012.
diff --git a/doc/pair_style.html b/doc/pair_style.html
index 4396eb0b2..761e22141 100644
--- a/doc/pair_style.html
+++ b/doc/pair_style.html
@@ -1,404 +1,405 @@
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<div class="section" id="pair-style-command">
<span id="index-0"></span><h1>pair_style command<a class="headerlink" href="#pair-style-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>pair_style style args
</pre></div>
</div>
<ul class="simple">
<li>style = one of the styles from the list below</li>
<li>args = arguments used by a particular style</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>pair_style lj/cut 2.5
pair_style eam/alloy
pair_style hybrid lj/charmm/coul/long 10.0 eam
pair_style table linear 1000
pair_style none
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Set the formula(s) LAMMPS uses to compute pairwise interactions. In
LAMMPS, pair potentials are defined between pairs of atoms that are
within a cutoff distance and the set of active interactions typically
changes over time. See the <a class="reference internal" href="bond_style.html"><em>bond_style</em></a> command to
define potentials between pairs of bonded atoms, which typically
remain in place for the duration of a simulation.</p>
<p>In LAMMPS, pairwise force fields encompass a variety of interactions,
some of which include many-body effects, e.g. EAM, Stillinger-Weber,
Tersoff, REBO potentials. They are still classified as “pairwise”
potentials because the set of interacting atoms changes with time
(unlike molecular bonds) and thus a neighbor list is used to find
nearby interacting atoms.</p>
<p>Hybrid models where specified pairs of atom types interact via
different pair potentials can be setup using the <em>hybrid</em> pair style.</p>
<p>The coefficients associated with a pair style are typically set for
each pair of atom types, and are specified by the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command or read from a file by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> command sets options for mixing of
type I-J interaction coefficients and adding energy offsets or tail
corrections to Lennard-Jones potentials. Details on these options as
they pertain to individual potentials are described on the doc page
for the potential. Likewise, info on whether the potential
information is stored in a <a class="reference internal" href="write_restart.html"><em>restart file</em></a> is listed
on the potential doc page.</p>
<p>In the formulas listed for each pair style, <em>E</em> is the energy of a
pairwise interaction between two atoms separated by a distance <em>r</em>.
The force between the atoms is the negative derivative of this
expression.</p>
<p>If the pair_style command has a cutoff argument, it sets global
cutoffs for all pairs of atom types. The distance(s) can be smaller
or larger than the dimensions of the simulation box.</p>
<p>Typically, the global cutoff value can be overridden for a specific
pair of atom types by the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command. The
pair style settings (including global cutoffs) can be changed by a
subsequent pair_style command using the same style. This will reset
the cutoffs for all atom type pairs, including those previously set
explicitly by a <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command. The exceptions
to this are that pair_style <em>table</em> and <em>hybrid</em> settings cannot be
reset. A new pair_style command for these styles will wipe out all
previously specified pair_coeff values.</p>
<hr class="docutils" />
<p>Here is an alphabetic list of pair styles defined in LAMMPS. They are
also given in more compact form in the pair section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<p>Click on the style to display the formula it computes, arguments
specified in the pair_style command, and coefficients specified by the
associated <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command.</p>
<p>There are also additional pair styles (not listed here) submitted by
users which are included in the LAMMPS distribution. The list of
these with links to the individual styles are given in the pair
section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<p>There are also additional accelerated pair styles (not listed here)
included in the LAMMPS distribution for faster performance on CPUs and
GPUs. The list of these with links to the individual styles are given
in the pair section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<ul class="simple">
<li><a class="reference internal" href="pair_none.html"><em>pair_style none</em></a> - turn off pairwise interactions</li>
<li><a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> - multiple styles of pairwise interactions</li>
<li><a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a> - multiple styles of superposed pairwise interactions</li>
<li><a class="reference internal" href="pair_adp.html"><em>pair_style adp</em></a> - angular dependent potential (ADP) of Mishin</li>
<li><a class="reference internal" href="pair_airebo.html"><em>pair_style airebo</em></a> - AIREBO potential of Stuart</li>
<li><a class="reference internal" href="pair_beck.html"><em>pair_style beck</em></a> - Beck potential</li>
<li><a class="reference internal" href="pair_body.html"><em>pair_style body</em></a> - interactions between body particles</li>
<li><a class="reference internal" href="pair_bop.html"><em>pair_style bop</em></a> - BOP potential of Pettifor</li>
<li><a class="reference internal" href="pair_born.html"><em>pair_style born</em></a> - Born-Mayer-Huggins potential</li>
<li><a class="reference internal" href="pair_born.html"><em>pair_style born/coul/long</em></a> - Born-Mayer-Huggins with long-range Coulombics</li>
<li><a class="reference internal" href="pair_born.html"><em>pair_style born/coul/long/cs</em></a> - Born-Mayer-Huggins with long-range Coulombics and core/shell</li>
<li><a class="reference internal" href="pair_born.html"><em>pair_style born/coul/msm</em></a> - Born-Mayer-Huggins with long-range MSM Coulombics</li>
<li><a class="reference internal" href="pair_born.html"><em>pair_style born/coul/wolf</em></a> - Born-Mayer-Huggins with Coulombics via Wolf potential</li>
<li><a class="reference internal" href="pair_brownian.html"><em>pair_style brownian</em></a> - Brownian potential for Fast Lubrication Dynamics</li>
<li><a class="reference internal" href="pair_brownian.html"><em>pair_style brownian/poly</em></a> - Brownian potential for Fast Lubrication Dynamics with polydispersity</li>
<li><a class="reference internal" href="pair_buck.html"><em>pair_style buck</em></a> - Buckingham potential</li>
<li><a class="reference internal" href="pair_buck.html"><em>pair_style buck/coul/cut</em></a> - Buckingham with cutoff Coulomb</li>
<li><a class="reference internal" href="pair_buck.html"><em>pair_style buck/coul/long</em></a> - Buckingham with long-range Coulombics</li>
<li><a class="reference internal" href="pair_buck.html"><em>pair_style buck/coul/long/cs</em></a> - Buckingham with long-range Coulombics and core/shell</li>
<li><a class="reference internal" href="pair_buck.html"><em>pair_style buck/coul/msm</em></a> - Buckingham long-range MSM Coulombics</li>
<li><a class="reference internal" href="pair_buck_long.html"><em>pair_style buck/long/coul/long</em></a> - long-range Buckingham with long-range Coulombics</li>
<li><a class="reference internal" href="pair_colloid.html"><em>pair_style colloid</em></a> - integrated colloidal potential</li>
<li><a class="reference internal" href="pair_comb.html"><em>pair_style comb</em></a> - charge-optimized many-body (COMB) potential</li>
<li><a class="reference internal" href="pair_comb.html"><em>pair_style comb3</em></a> - charge-optimized many-body (COMB3) potential</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style coul/cut</em></a> - cutoff Coulombic potential</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style coul/debye</em></a> - cutoff Coulombic potential with Debye screening</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style coul/dsf</em></a> - Coulombics via damped shifted forces</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style coul/long</em></a> - long-range Coulombic potential</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style coul/long/cs</em></a> - long-range Coulombic potential and core/shell</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style coul/msm</em></a> - long-range MSM Coulombics</li>
<li><code class="xref doc docutils literal"><span class="pre">pair_style</span> <span class="pre">coul/msm</span></code> - Coulombics via Streitz/Mintmire Slater orbitals</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style coul/wolf</em></a> - Coulombics via Wolf potential</li>
<li><a class="reference internal" href="pair_dpd.html"><em>pair_style dpd</em></a> - dissipative particle dynamics (DPD)</li>
<li><a class="reference internal" href="pair_dpd.html"><em>pair_style dpd/tstat</em></a> - DPD thermostatting</li>
<li><a class="reference internal" href="pair_dsmc.html"><em>pair_style dsmc</em></a> - Direct Simulation Monte Carlo (DSMC)</li>
<li><a class="reference internal" href="pair_eam.html"><em>pair_style eam</em></a> - embedded atom method (EAM)</li>
<li><a class="reference internal" href="pair_eam.html"><em>pair_style eam/alloy</em></a> - alloy EAM</li>
<li><a class="reference internal" href="pair_eam.html"><em>pair_style eam/fs</em></a> - Finnis-Sinclair EAM</li>
<li><a class="reference internal" href="pair_eim.html"><em>pair_style eim</em></a> - embedded ion method (EIM)</li>
<li><a class="reference internal" href="pair_gauss.html"><em>pair_style gauss</em></a> - Gaussian potential</li>
<li><a class="reference internal" href="pair_gayberne.html"><em>pair_style gayberne</em></a> - Gay-Berne ellipsoidal potential</li>
<li><a class="reference internal" href="pair_gran.html"><em>pair_style gran/hertz/history</em></a> - granular potential with Hertzian interactions</li>
<li><a class="reference internal" href="pair_gran.html"><em>pair_style gran/hooke</em></a> - granular potential with history effects</li>
<li><a class="reference internal" href="pair_gran.html"><em>pair_style gran/hooke/history</em></a> - granular potential without history effects</li>
<li><a class="reference internal" href="pair_hbond_dreiding.html"><em>pair_style hbond/dreiding/lj</em></a> - DREIDING hydrogen bonding LJ potential</li>
<li><a class="reference internal" href="pair_hbond_dreiding.html"><em>pair_style hbond/dreiding/morse</em></a> - DREIDING hydrogen bonding Morse potential</li>
<li><a class="reference internal" href="pair_kim.html"><em>pair_style kim</em></a> - interface to potentials provided by KIM project</li>
<li><a class="reference internal" href="pair_lcbop.html"><em>pair_style lcbop</em></a> - long-range bond-order potential (LCBOP)</li>
<li><a class="reference internal" href="pair_line_lj.html"><em>pair_style line/lj</em></a> - LJ potential between line segments</li>
<li><a class="reference internal" href="pair_charmm.html"><em>pair_style lj/charmm/coul/charmm</em></a> - CHARMM potential with cutoff Coulomb</li>
<li><a class="reference internal" href="pair_charmm.html"><em>pair_style lj/charmm/coul/charmm/implicit</em></a> - CHARMM for implicit solvent</li>
<li><a class="reference internal" href="pair_charmm.html"><em>pair_style lj/charmm/coul/long</em></a> - CHARMM with long-range Coulomb</li>
<li><a class="reference internal" href="pair_charmm.html"><em>pair_style lj/charmm/coul/msm</em></a> - CHARMM with long-range MSM Coulombics</li>
<li><a class="reference internal" href="pair_class2.html"><em>pair_style lj/class2</em></a> - COMPASS (class 2) force field with no Coulomb</li>
<li><a class="reference internal" href="pair_class2.html"><em>pair_style lj/class2/coul/cut</em></a> - COMPASS with cutoff Coulomb</li>
<li><a class="reference internal" href="pair_class2.html"><em>pair_style lj/class2/coul/long</em></a> - COMPASS with long-range Coulomb</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut</em></a> - cutoff Lennard-Jones potential with no Coulomb</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/cut</em></a> - LJ with cutoff Coulomb</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/debye</em></a> - LJ with Debye screening added to Coulomb</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/dsf</em></a> - LJ with Coulombics via damped shifted forces</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/long</em></a> - LJ with long-range Coulombics</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/msm</em></a> - LJ with long-range MSM Coulombics</li>
<li><a class="reference internal" href="pair_dipole.html"><em>pair_style lj/cut/dipole/cut</em></a> - point dipoles with cutoff</li>
<li><a class="reference internal" href="pair_dipole.html"><em>pair_style lj/cut/dipole/long</em></a> - point dipoles with long-range Ewald</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/tip4p/cut</em></a> - LJ with cutoff Coulomb for TIP4P water</li>
<li><a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/tip4p/long</em></a> - LJ with long-range Coulomb for TIP4P water</li>
<li><a class="reference internal" href="pair_lj_expand.html"><em>pair_style lj/expand</em></a> - Lennard-Jones for variable size particles</li>
<li><a class="reference internal" href="pair_gromacs.html"><em>pair_style lj/gromacs</em></a> - GROMACS-style Lennard-Jones potential</li>
<li><a class="reference internal" href="pair_gromacs.html"><em>pair_style lj/gromacs/coul/gromacs</em></a> - GROMACS-style LJ and Coulombic potential</li>
<li><a class="reference internal" href="pair_lj_long.html"><em>pair_style lj/long/coul/long</em></a> - long-range LJ and long-range Coulombics</li>
<li><a class="reference internal" href="pair_dipole.html"><em>pair_style lj/long/dipole/long</em></a> - long-range LJ and long-range point dipoles</li>
<li><a class="reference internal" href="pair_lj_long.html"><em>pair_style lj/long/tip4p/long</em></a> - long-range LJ and long-range Coulomb for TIP4P water</li>
<li><a class="reference internal" href="pair_lj_smooth.html"><em>pair_style lj/smooth</em></a> - smoothed Lennard-Jones potential</li>
<li><a class="reference internal" href="pair_lj_smooth_linear.html"><em>pair_style lj/smooth/linear</em></a> - linear smoothed Lennard-Jones potential</li>
<li><a class="reference internal" href="pair_lj96.html"><em>pair_style lj96/cut</em></a> - Lennard-Jones 9/6 potential</li>
<li><a class="reference internal" href="pair_lubricate.html"><em>pair_style lubricate</em></a> - hydrodynamic lubrication forces</li>
<li><a class="reference internal" href="pair_lubricate.html"><em>pair_style lubricate/poly</em></a> - hydrodynamic lubrication forces with polydispersity</li>
<li><a class="reference internal" href="pair_lubricateU.html"><em>pair_style lubricateU</em></a> - hydrodynamic lubrication forces for Fast Lubrication Dynamics</li>
<li><a class="reference internal" href="pair_lubricateU.html"><em>pair_style lubricateU/poly</em></a> - hydrodynamic lubrication forces for Fast Lubrication with polydispersity</li>
<li><a class="reference internal" href="pair_meam.html"><em>pair_style meam</em></a> - modified embedded atom method (MEAM)</li>
<li><a class="reference internal" href="pair_mie.html"><em>pair_style mie/cut</em></a> - Mie potential</li>
<li><a class="reference internal" href="pair_morse.html"><em>pair_style morse</em></a> - Morse potential</li>
<li><a class="reference internal" href="pair_nb3b_harmonic.html"><em>pair_style nb3b/harmonic</em></a> - nonbonded 3-body harmonic potential</li>
<li><a class="reference internal" href="pair_nm.html"><em>pair_style nm/cut</em></a> - N-M potential</li>
<li><a class="reference internal" href="pair_nm.html"><em>pair_style nm/cut/coul/cut</em></a> - N-M potential with cutoff Coulomb</li>
<li><a class="reference internal" href="pair_nm.html"><em>pair_style nm/cut/coul/long</em></a> - N-M potential with long-range Coulombics</li>
<li><a class="reference internal" href="pair_peri.html"><em>pair_style peri/eps</em></a> - peridynamic EPS potential</li>
<li><a class="reference internal" href="pair_peri.html"><em>pair_style peri/lps</em></a> - peridynamic LPS potential</li>
<li><a class="reference internal" href="pair_peri.html"><em>pair_style peri/pmb</em></a> - peridynamic PMB potential</li>
<li><a class="reference internal" href="pair_peri.html"><em>pair_style peri/ves</em></a> - peridynamic VES potential</li>
<li><a class="reference internal" href="pair_polymorphic.html"><em>pair_style polymorphic</em></a> - polymorphic 3-body potential</li>
<li><a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a> - ReaxFF potential</li>
<li><a class="reference internal" href="pair_airebo.html"><em>pair_style rebo</em></a> - 2nd generation REBO potential of Brenner</li>
<li><a class="reference internal" href="pair_resquared.html"><em>pair_style resquared</em></a> - Everaers RE-Squared ellipsoidal potential</li>
<li><a class="reference internal" href="pair_snap.html"><em>pair_style snap</em></a> - SNAP quantum-accurate potential</li>
<li><a class="reference internal" href="pair_soft.html"><em>pair_style soft</em></a> - Soft (cosine) potential</li>
<li><a class="reference internal" href="pair_sw.html"><em>pair_style sw</em></a> - Stillinger-Weber 3-body potential</li>
<li><a class="reference internal" href="pair_table.html"><em>pair_style table</em></a> - tabulated pair potential</li>
<li><a class="reference internal" href="pair_tersoff.html"><em>pair_style tersoff</em></a> - Tersoff 3-body potential</li>
<li><a class="reference internal" href="pair_tersoff_mod.html"><em>pair_style tersoff/mod</em></a> - modified Tersoff 3-body potential</li>
<li><a class="reference internal" href="pair_tersoff_zbl.html"><em>pair_style tersoff/zbl</em></a> - Tersoff/ZBL 3-body potential</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style tip4p/cut</em></a> - Coulomb for TIP4P water w/out LJ</li>
<li><a class="reference internal" href="pair_coul.html"><em>pair_style tip4p/long</em></a> - long-range Coulombics for TIP4P water w/out LJ</li>
<li><a class="reference internal" href="pair_tri_lj.html"><em>pair_style tri/lj</em></a> - LJ potential between triangles</li>
+<li><code class="xref doc docutils literal"><span class="pre">pair_style</span> <span class="pre">vashishta</span></code> - Vashishta 2-body and 3-body potential</li>
<li><a class="reference internal" href="pair_yukawa.html"><em>pair_style yukawa</em></a> - Yukawa potential</li>
<li><a class="reference internal" href="pair_yukawa_colloid.html"><em>pair_style yukawa/colloid</em></a> - screened Yukawa potential for finite-size particles</li>
<li><a class="reference internal" href="pair_zbl.html"><em>pair_style zbl</em></a> - Ziegler-Biersack-Littmark potential</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>This command must be used before any coefficients are set by the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="read_data.html"><em>read_data</em></a>, or
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands.</p>
<p>Some pair styles are part of specific packages. They are 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 on packages.
The doc pages for individual pair potentials tell if it is part of a
package.</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="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="read_data.html"><em>read_data</em></a>,
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>, <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a>,
<a class="reference internal" href="dielectric.html"><em>dielectric</em></a>, <a class="reference internal" href="pair_write.html"><em>pair_write</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style none
</pre></div>
</div>
</div>
</div>
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diff --git a/doc/pair_vashishta.html b/doc/pair_vashishta.html
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-<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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-<H3>pair_style vashishta command
-</H3>
-<P><B>Syntax:</B>
-</P>
-<PRE>pair_style vashishta
-</PRE>
-<P><B>Examples:</B>
-</P>
-<PRE>pair_style vashishta
-pair_coeff * * SiC.vashishta Si C
-</PRE>
-<P><B>Description:</B>
-</P>
-<P>The <I>vashishta</I> style computes the combined 2-body and 3-body
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+ <div class="section" id="pair-style-vashishta-command">
+<span id="index-0"></span><h1>pair_style vashishta command<a class="headerlink" href="#pair-style-vashishta-command" title="Permalink to this headline">¶</a></h1>
+</div>
+<div class="section" id="pair-style-vashishta-omp-command">
+<h1>pair_style vashishta/omp command<a class="headerlink" href="#pair-style-vashishta-omp-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>pair_style vashishta
+</pre></div>
+</div>
+</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>pair_style vashishta
+pair_coeff * * SiC.vashishta Si C
+</pre></div>
+</div>
+</div>
+<div class="section" id="description">
+<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
+<p>The <em>vashishta</em> style computes the combined 2-body and 3-body
family of potentials developed in the group of Vashishta and
-co-workers. By combining repulsive, screened Coulombic,
-screened charge-dipole, and dispersion interactions with a
-bond-angle energy based on the Stillinger-Weber potential,
+co-workers. By combining repulsive, screened Coulombic,
+screened charge-dipole, and dispersion interactions with a
+bond-angle energy based on the Stillinger-Weber potential,
this potential has been used to describe a variety of inorganic
-compounds, including SiO2 <A HREF = "#Vashishta1990">Vashishta1990</A>,
-SiC <A HREF = "#Vashishta2007">Vashishta2007</A>,
-and InP <A HREF = "#Branicio2009">Branicio2009</A>.
-</P>
-<P>The potential for the energy U of a system of atoms is
-</P>
-<CENTER><IMG SRC = "Eqs/pair_vashishta.jpg">
-</CENTER>
-<P>where we follow the notation used in <A HREF = "#Branicio2009">Branicio2009</A>.
+compounds, including SiO2 <a class="reference internal" href="#vashishta1990"><span>Vashishta1990</span></a>,
+SiC <a class="reference internal" href="#vashishta2007"><span>Vashishta2007</span></a>,
+and InP <a class="reference internal" href="#branicio2009"><span>Branicio2009</span></a>.</p>
+<p>The potential for the energy U of a system of atoms is</p>
+<img alt="_images/pair_vashishta.jpg" class="align-center" src="_images/pair_vashishta.jpg" />
+<p>where we follow the notation used in <a class="reference internal" href="#branicio2009"><span>Branicio2009</span></a>.
U2 is a two-body term and U3 is a three-body term. The
summation over two-body terms is over all neighbors J within
-a cutoff distance = <I>rc</I>. The twobody terms are shifted and
-tilted by a linear function so that the energy and force are
-both zero at <I>rc</I>. The summation over three-body terms
-is over all neighbors J and K within a cut-off distance = <I>r0</I>,
-where the exponential screening function becomes zero.
-</P>
-<P>Only a single pair_coeff command is used with the <I>vashishta</I> style which
+a cutoff distance = <em>rc</em>. The twobody terms are shifted and
+tilted by a linear function so that the energy and force are
+both zero at <em>rc</em>. The summation over three-body terms
+is over all neighbors J and K within a cut-off distance = <em>r0</em>,
+where the exponential screening function becomes zero.</p>
+<p>Only a single pair_coeff command is used with the <em>vashishta</em> style which
specifies a Vashishta potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
-where N is the number of LAMMPS atom types:
-</P>
-<UL><LI>filename
-<LI>N element names = mapping of Vashishta elements to atom types
-</UL>
-<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
-to specify the path for the potential file.
-</P>
-<P>As an example, imagine a file SiC.vashishta has parameters for
+where N is the number of LAMMPS atom types:</p>
+<ul class="simple">
+<li>filename</li>
+<li>N element names = mapping of Vashishta elements to atom types</li>
+</ul>
+<p>See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc page for alternate ways
+to specify the path for the potential file.</p>
+<p>As an example, imagine a file SiC.vashishta has parameters for
Si and C. If your LAMMPS simulation has 4 atoms types and you want
the 1st 3 to be Si, and the 4th to be C, you would use the following
-pair_coeff command:
-</P>
-<PRE>pair_coeff * * SiC.vashishta Si Si Si C
-</PRE>
-<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+pair_coeff command:</p>
+<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * SiC.vashishta Si Si Si C
+</pre></div>
+</div>
+<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
element in the file. The final C argument maps LAMMPS atom type 4
to the C element in the file. If a mapping value is specified as
-NULL, the mapping is not performed. This can be used when a <I>vashishta</I>
-potential is used as part of the <I>hybrid</I> pair style. The NULL values
+NULL, the mapping is not performed. This can be used when a <em>vashishta</em>
+potential is used as part of the <em>hybrid</em> pair style. The NULL values
are placeholders for atom types that will be used with other
-potentials.
-</P>
-<P>Vashishta files in the <I>potentials</I> directory of the LAMMPS
-distribution have a ".vashishta" suffix. Lines that are not blank or
+potentials.</p>
+<p>Vashishta files in the <em>potentials</em> directory of the LAMMPS
+distribution have a ”.vashishta” suffix. Lines that are not blank or
comments (starting with #) define parameters for a triplet of
elements. The parameters in a single entry correspond to the two-body
-and three-body coefficients in the formulae above:
-</P>
-<UL><LI>element 1 (the center atom in a 3-body interaction)
-<LI>element 2
-<LI>element 3
-<LI>H (energy units)
-<LI>eta
-<LI>Zi (electron charge units)
-<LI>Zj (electron charge units)
-<LI>lambda1 (distance units)
-<LI>D (energy units)
-<LI>lambda4 (distance units)
-<LI>W (energy units)
-<LI>rc (distance units)
-<LI>B (energy units)
-<LI>gamma
-<LI>r0 (distance units)
-<LI>C
-<LI>costheta0
-</UL>
-<P>The non-annotated parameters are unitless.
+and three-body coefficients in the formulae above:</p>
+<ul class="simple">
+<li>element 1 (the center atom in a 3-body interaction)</li>
+<li>element 2</li>
+<li>element 3</li>
+<li>H (energy units)</li>
+<li>eta</li>
+<li>Zi (electron charge units)</li>
+<li>Zj (electron charge units)</li>
+<li>lambda1 (distance units)</li>
+<li>D (energy units)</li>
+<li>lambda4 (distance units)</li>
+<li>W (energy units)</li>
+<li>rc (distance units)</li>
+<li>B (energy units)</li>
+<li>gamma</li>
+<li>r0 (distance units)</li>
+<li>C</li>
+<li>costheta0</li>
+</ul>
+<p>The non-annotated parameters are unitless.
The Vashishta potential file must contain entries for all the
elements listed in the pair_coeff command. It can also contain
entries for additional elements not being used in a particular
simulation; LAMMPS ignores those entries.
For a single-element simulation, only a single entry is required
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
specify parameters for all permutations of the two elements
interacting in three-body configurations. Thus for 3 elements, 27
-entries would be required, etc.
-</P>
-<P>Depending on the particular version of the Vashishta potential,
+entries would be required, etc.</p>
+<p>Depending on the particular version of the Vashishta potential,
the values of these parameters may be keyed to the identities of
zero, one, two, or three elements.
In order to make the input file format unambiguous, general,
and simple to code,
LAMMPS uses a slightly confusing method for specifying parameters.
All parameters are divided into two classes: two-body and three-body.
Two-body and three-body parameters are handled differently,
as described below.
The two-body parameters are H, eta, lambda1, D, lambda4, W, rc, gamma, and r0.
They appear in the above formulae with two subscripts.
The parameters Zi and Zj are also classified as two-body parameters,
even though they only have 1 subscript.
The three-body parameters are B, C, costheta0.
They appear in the above formulae with three subscripts.
Two-body and three-body parameters are handled differently,
-as described below.
-</P>
-<P>The first element in each entry is the center atom
+as described below.</p>
+<p>The first element in each entry is the center atom
in a three-body interaction, while the second and third elements
are two neighbor atoms. Three-body parameters for a central atom I
and two neighbors J and K are taken from the IJK entry.
Note that even though three-body parameters do not depend on the order of
J and K, LAMMPS stores three-body parameters for both IJK and IKJ.
-The user must ensure that these values are equal.
+The user must ensure that these values are equal.
Two-body parameters for an atom I interacting with atom J are taken from
the IJJ entry, where the 2nd and 3rd
-elements are the same. Thus the two-body parameters
+elements are the same. Thus the two-body parameters
for Si interacting with C come from the SiCC entry. Note that even
-though two-body parameters (except possibly gamma and r0 in U3)
-do not depend on the order of the two elements,
+though two-body parameters (except possibly gamma and r0 in U3)
+do not depend on the order of the two elements,
LAMMPS will get the Si-C value from the SiCC entry
and the C-Si value from the CSiSi entry. The user must ensure
that these values are equal. Two-body parameters appearing
in entries where the 2nd and 3rd elements are different are
stored but never used. It is good practice to enter zero for
-these values. Note that the three-body function U3 above
-contains the two-body parameters gamma and r0. So U3 for a
+these values. Note that the three-body function U3 above
+contains the two-body parameters gamma and r0. So U3 for a
central C atom bonded to an Si atom and a second C atom
will take three-body parameters from the CSiC entry, but
-two-body parameters from the CCC and CSiSi entries.
-</P>
-<HR>
-
-<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
-</P>
-<P>For atom type pairs I,J and I != J, where types I and J correspond to
+two-body parameters from the CCC and CSiSi entries.</p>
+<hr class="docutils" />
+<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
+of the manual. The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.</p>
+<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively. They are only
+enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
+<p>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
+use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
+<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
+more instructions on how to use the accelerated styles effectively.</p>
+<hr class="docutils" />
+<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
+<p>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
-described above from values in the potential file.
-</P>
-<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
-shift, table, and tail options.
-</P>
-<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
-files</A>, since it is stored in potential files. Thus, you
+described above from values in the potential file.</p>
+<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
+shift, table, and tail options.</p>
+<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
-script that reads a restart file.
-</P>
-<P>This pair style can only be used via the <I>pair</I> keyword of the
-<A HREF = "run_style.html">run_style respa</A> command. It does not support the
-<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
-</P>
-<HR>
-
-<P><B>Restrictions:</B>
-</P>
-<P>This pair style is part of the MANYBODY package. It is only enabled
+script that reads a restart file.</p>
+<p>This pair style can only be used via the <em>pair</em> keyword of the
+<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command. It does not support the
+<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
+</div>
+<hr class="docutils" />
+<div class="section" id="restrictions">
+<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
+<p>This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
-the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
-</P>
-<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
-for pair interactions.
-</P>
-<P>The Vashishta potential files provided with LAMMPS (see the
-potentials directory) are parameterized for metal <A HREF = "units.html">units</A>.
+the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
+<p>This pair style requires the <a class="reference internal" href="newton.html"><em>newton</em></a> setting to be “on”
+for pair interactions.</p>
+<p>The Vashishta potential files provided with LAMMPS (see the
+potentials directory) are parameterized for metal <a class="reference internal" href="units.html"><em>units</em></a>.
You can use the Vashishta potential with any LAMMPS units, but you would need
to create your own Vashishta potential file with coefficients listed in the
-appropriate units if your simulation doesn't use "metal" units.
-</P>
-<P><B>Related commands:</B>
-</P>
-<P><A HREF = "pair_coeff.html">pair_coeff</A>
-</P>
-<P><B>Default:</B> none
-</P>
-<HR>
-
-<A NAME = "Vashishta1990"></A>
-
-<P><B>(Vashishta1990)</B> P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B 41, 12197 (1990).
-</P>
-<A NAME = "Vashishta2007"></A>
-
-<P><B>(Vashishta2007)</B> P. Vashishta, R. K. Kalia, A. Nakano, J. P. Rino. J. Appl. Phys. 101, 103515 (2007).
-</P>
-<A NAME = "Branicio2009"></A>
-
-<P><B>(Branicio2009)</B> Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002
-</P>
-</HTML>
+appropriate units if your simulation doesn’t use “metal” units.</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="pair_coeff.html"><em>pair_coeff</em></a></p>
+<p><strong>Default:</strong> none</p>
+<hr class="docutils" />
+<p id="vashishta1990"><strong>(Vashishta1990)</strong> P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B 41, 12197 (1990).</p>
+<p id="vashishta2007"><strong>(Vashishta2007)</strong> P. Vashishta, R. K. Kalia, A. Nakano, J. P. Rino. J. Appl. Phys. 101, 103515 (2007).</p>
+<p id="branicio2009"><strong>(Branicio2009)</strong> Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002</p>
+</div>
+</div>
+
+
+ </div>
+ </div>
+ <footer>
+
+
+ <hr/>
+
+ <div role="contentinfo">
+ <p>
+ © Copyright .
+ </p>
+ </div>
+ Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
+
+ </div>
+ </div>
+
+ </section>
+
+ </div>
+
+
+
+
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT:'./',
+ VERSION:'15 May 2015 version',
+ COLLAPSE_INDEX:false,
+ FILE_SUFFIX:'.html',
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+ jQuery(function () {
+ SphinxRtdTheme.StickyNav.enable();
+ });
+ </script>
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+</body>
+</html>
\ No newline at end of file
diff --git a/doc/searchindex.js b/doc/searchindex.js
index 1a5074045..b13413c7a 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
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384,385,386,387,393,394,395,406,407,408,409,410,411,415,419,421,422,429,439,441,442,443,451,453,455,456,457,458,459,461,462,464,466,468,470,473,474,477,481,482,483,484,485,486],afterrun:464,afterward:3,afterword:41,ag1:164,ag2:164,again:[6,11,12,17,62,140,145,147,151,159,188,191,216,231,278,333,346,357,407,408,451,453,454,456,458,463,470,472,482,484],against:[11,12,13,64,217,357,421,422],aggreg:[6,12,65,68,69,79,92,108,115,231,247,290,292,305,451,483],aggress:[231,470],agilio:[9,13],agre:[3,8,185,355,364,395,422],agreement:[5,7],ahd:392,ahead:326,aidan:[0,5,7,9,13,350],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:190,akohlmei:[7,9,13,192,232],aktulga:[7,9,285,422],al2o3_001:[118,293],al3:164,ala:238,alain:9,alat:[273,409],alb:[419,441,443],albeit:291,albert:9,alchem:[87,159],alcohol:322,alcu:[363,368],alcu_eam:419,alderton:381,alejandr:[251,252],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,191,200,210,213,216,238,240,241,263,275,292,295,314,315,319,322,327,353,354,355,359,362,386,408,426,428,451,453,470],alia:12,alias:[1,348],aliceblu:191,align:[6,12,29,41,71,167,185,206,210,233,350,456,459,477],alkali:386,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,153,158,159,160,161,162,163,164,165,166,167,168,169,171,173,178,184,185,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,244,246,247,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,303,304,306,307,308,309,310,311,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332,333,334,337,342,345,346,347,348,349,350,352,355,356,357,358,359,361,362,363,364,365,367,368,369,371,372,373,374,375,377,378,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,402,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,450,451,453,454,455,456,457,458,459,460,461,463,464,465,466,467,468,469,470,471,473,474,475,477,481,482,483,484,485,486],allen:[29,87,381,389],allentildeslei:87,allign:3,allindex:331,alloc:[3,5,6,8,9,11,12,60,225,321,356,358,362,417,422,456,464],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,142,144,145,158,163,164,165,167,173,184,185,188,190,191,192,194,195,197,199,200,201,203,204,205,206,207,208,210,212,213,214,215,216,217,221,222,225,227,228,229,230,232,235,238,241,242,246,248,251,252,273,277,279,280,281,282,286,292,293,295,296,298,299,303,307,314,315,316,317,319,320,321,322,323,324,330,332,334,342,347,348,350,355,356,357,358,361,362,365,368,369,370,371,372,373,378,384,386,390,391,392,393,398,402,407,408,413,419,422,423,426,428,437,446,448,451,454,456,458,459,460,461,462,463,466,468,469,470,473,474,482,483],almost:[2,3,12,60,233,282,319,348,359,362,437],alo:378,alon:[6,7,213,288,421,422,454],alond:13,along:[6,8,9,12,29,40,87,118,164,165,187,188,190,213,233,238,239,243,248,250,282,292,295,296,300,304,305,314,318,319,325,328,330,350,353,354,355,357,378,381,390,393,396,398,402,409,421,422,440,456,459,466,467,482],alonso:[410,411],alpha:[6,12,51,195,238,274,282,287,355,363,366,369,378,382,384,385,387,392,397,398,409,414,418,442,444,474,477],alpha_:444,alpha_c:406,alpha_i:[429,444],alpha_ialpha_j:444,alpha_lj:406,alphabet:[2,3,22,37,44,55,63,173,184,194,334,342,356,375,438,456],alphanumer:[3,63,194,281,289,332,356,482],alreadi:[3,7,8,12,42,165,166,168,189,199,203,206,207,210,212,216,242,280,282,307,330,356,357,382,391,393,400,408,437,446,449,452,456,457,461,466,482],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,149,151,152,153,154,155,157,158,159,160,161,162,163,165,166,167,168,169,171,173,184,185,186,188,189,190,191,192,194,195,196,197,199,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,222,225,226,227,228,229,231,232,235,236,237,238,248,249,251,252,253,254,255,256,257,262,265,266,268,269,270,271,273,274,275,277,278,279,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,300,301,304,305,307,310,311,312,313,314,318,319,320,321,323,325,328,330,332,334,339,342,345,347,348,350,351,352,355,356,357,358,359,361,362,368,372,373,375,379,380,381,382,384,385,386,389,390,392,393,394,402,406,407,409,413,415,417,418,419,420,423,424,426,432,433,435,436,437,438,439,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460],co2:[40,164,295,356],coars:[7,9,29,36,40,54,177,277,292,307,391,424,468],coarser:[348,482],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,171,172,173,178,333,334,339,375,393,397,413,426,428,430,456,458],coeffcient:456,coeffici:[],coefficienct:382,coefficient0:384,coefficient1:384,coeffieci:[6,366],coeffincientn:384,coexist:[9,227,386],cohes:[6,387,409],coincid:[122,328,373,407,408,451],colberg:189,cold:[6,150,231,358,477],coldest:315,coleman8:9,coleman:[9,118,164,293],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,145,153,160,162,165,188,191,203,215,241,247,277,287,290,292,330,347,356,358,376,396,456,463,469,475,486],collid:[221,307,329],colliex:164,collinear:[3,277],collis:[3,238,307,325,329,383,390,449],colllis:307,colloid:[],colombo:39,colon:[192,330,457],color1:191,color2:191,color:[3,9,41,188,190,191,210,228,282,287],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,145,153,160,162,163,164,185,188,191,194,202,203,204,205,206,207,208,241,248,249,282,292,308,309,319,329,388,392,421,422,457,471,473,482],colvar:[],colvarmodul:12,com:[],comamnd:216,comand:[213,458],comannd:362,comb3:[],comb:[],comb_1:284,comb_2:284,combiant:379,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,144,158,188,190,200,205,232,241,251,275,281,311,320,328,331,333,347,348,350,354,362,376,378,379,386,387,393,405,406,429,439,441,443,448,459,464,469,477,482],come:[],comfort:[12,13],comm:[0,3,12,61,73,189,232,234,235,348,357,362,382,413,418,440],comm_modifi:[],comm_modift:61,comm_styl:[],command:[],comment:[2,7,11,12,38,56,171,185,188,236,292,319,356,357,363,384,385,387,397,409,415,422,429,439,440,441,442,443,453,454,456,477,482],commerci:7,commmand:[3,6,12,59,107,270,450,451,453,470,485],common:[],commonli:[3,6,12,17,25,57,59,105,167,188,190,192,343,391,400,429,441,443,456,459,468],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,169,190,191,210,211,212,214,215,216,232,234,238,240,241,242,251,274,281,283,284,285,292,307,319,330,345,347,358,359,360,362,383,417,453,454,458,465,466,482,484,486],communc:347,comp:[7,189,234,235,295,348,357,386,413,418,423,436,440,442],compact:[63,194,375,438],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,148,163,164,173,184,191,220,283,330,332,347,348,355,357,409,451,470,471,477,481],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,172,173,184,333,334,342,374,438],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,176,188,192,196,202,203,204,205,206,207,208,210,274,286,311,314,321,324,327,347,362,394,413,440,453,454,482],compens:[6,211,212,290,358,386],compet:318,competit:348,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,163,188,189,190,192,232,318,348,362,456,457,461,482],compl:17,complain:[12,17],complement:409,complementari:[7,378,398],complet:[3,6,9,12,15,41,59,71,191,206,210,215,241,275,278,281,307,318,320,332,346,357,362,387,426,428,445,451,456,461,464,468,470,473,477,482],complex:[6,8,11,12,13,25,40,42,62,140,142,153,165,166,238,303,328,345,357,386,440,454,456,459,482],compli:[314,318],complic:[6,7,9,12,13,201,227,454],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,160,161,162,188,190,191,197,198,202,203,204,205,206,207,208,209,213,214,216,217,222,225,230,234,235,238,241,243,247,248,250,251,252,255,256,257,268,269,271,272,274,275,276,279,290,292,294,295,296,300,301,304,307,310,311,312,314,321,322,327,328,329,347,350,354,355,356,357,362,382,386,390,407,408,426,428,429,456,457,466,474,482,483],componenet:6,composit:[6,201,238,384],compound:[377,386,387],compres:[71,114,203],compress:[3,6,9,12,59,71,114,168,188,190,191,203,216,249,255,279,282],compris:[40,328,396,423,445],compton:[118,164],comptu:[3,6],compuat:348,comput:[],computation:[3,6,211,212,319,368],computational:477,compute_arrai:8,compute_fep:[196,406],compute_group_group:227,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,293],compute_scalar:8,compute_temp:8,compute_ti:196,compute_vector:8,compute_xrd:164,concaten:[2,3,485],concav:328,concentr:384,concept:[6,145,155,203,465],conceptu:[3,6,71,153,214,216,357,378,393,409,461],concern:[6,73,87,189,228],concis:[11,318],conclud:12,concret:8,concurr:[9,16,348,482],conden:[319,441,443],condens:[6,147,319,364,380,384,398],condit:[],conducit:6,conduct:[],cone:459,confid:[3,470],config:[12,188,453],configfil:215,configur:[1,2,6,12,15,17,38,59,122,167,185,187,188,190,194,214,215,216,217,221,227,234,235,263,275,283,318,345,355,357,364,368,385,409,439,441,443,451,456,458,459,470],confin:[456,470],conflict:[3,12,40,413,454],conform:[3,6,13,59,213,214,250,291,296,318,341,357,386,468],confus:3,conjuct:382,conjug:[7,8,235,354,386,421,422],conjunct:[6,7,71,86,87,114,148,153,159,165,169,191,195,196,235,238,242,263,278,279,283,284,285,287,292,307,315,322,327,347,348,357,369,371,375,378,382,386,392,398,413,416,424,444,456,459,463,477,486],connect:[3,6,87,150,168,213,232,277,292,295,304,357,379,390,437,443,453,454,460,477],conput:3,consecut:[3,11,12,39,71,165,191,195,196,217,232,233,378,398,402,451,457,459],consequ:[1,6,201,319,397,470],conserv:[3,194,201,213,220,221,228,231,235,237,238,242,247,249,251,263,292,295,310,311,315,322,323,327,357,381,382,390,404,465,470],consid:[6,9,70,71,78,87,115,147,150,151,168,188,191,195,196,202,204,206,210,212,213,217,239,252,274,292,314,315,318,319,322,348,375,386,393,422,423,437,451,452,454,457,458,459,461,464,466,474,477,482],consider:[6,8,235,236,310,311,312,362,465],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,145,148,150,165,177,187,192,197,198,203,216,217,220,222,225,228,235,236,237,248,251,253,254,255,256,257,258,259,261,262,263,264,266,267,268,269,270,271,279,282,287,289,291,292,310,311,312,313,323,347,348,350,356,357,362,364,368,370,376,378,386,389,393,407,408,409,413,423,426,428,440,446,454,456,457,459,460,461,468,477,482],consistent_fe_initi:200,consit:292,constant:[],constitu:[3,6,241,292,324,328,376,423],constitut:[426,428],constrain:[3,6,8,143,144,145,146,148,151,152,153,154,155,157,158,194,203,217,227,228,233,241,245,277,278,290,292,295,305,315,322,355,356,386,461,468,477],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,164,214,251,274,291,328,358,362,381,413,437,439,440,459,460,475,482],constructor:8,consult:422,consum:[1,287,417,482],consumpt:345,contact:[],contact_stiff:[425,427],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,145,153,163,164,165,167,171,173,184,185,188,190,191,192,194,195,196,200,202,203,204,205,206,207,208,210,215,217,222,229,233,234,235,236,238,249,263,273,274,277,278,280,282,285,289,292,293,297,307,314,318,319,328,329,332,346,348,356,357,360,361,363,364,365,368,377,378,381,384,385,386,393,394,409,415,419,420,421,422,429,439,440,441,442,443,444,451,452,453,454,456,457,458,459,461,463,465,468,470,473,474,477,482,484,486],content:[12,18,422,472,474],context:[3,6,8,12,17,117,191,211,212,217,277,289,323,354,448,456,463,472,481,482,483],contibut:70,contigu:453,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,161,191,194,195,196,201,203,204,205,206,207,208,210,213,214,215,216,217,227,228,229,231,232,233,235,236,237,243,248,249,251,253,254,255,256,257,268,269,270,271,276,278,281,282,292,293,296,306,307,309,316,317,319,325,328,332,346,361,362,368,382,383,400,403,421,422,423,426,428,442,451,454,456,458,459,464,470,473,474,482,484],continuum:[6,7,9,200,319,426,428],contour_integr:200,contract:[59,214,216,251,279,292],contradictori:3,contrain:295,contraint:263,contrari:[229,236],contrast:[1,6,42,55,64,150,216,330,426,428,448,485],contrib:319,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,196,201,202,203,204,205,206,207,208,214,227,235,238,241,242,246,252,269,270,277,278,286,289,292,293,295,321,347,355,357,365,382,383,384,386,393,407,408,413,421,422,468,474,477],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,174,188,190,194,200,201,210,214,215,216,231,232,235,236,251,253,254,255,256,257,279,284,292,298,299,310,311,312,319,323,345,347,359,386,389,421,422,425,427,439,443,451,453,465,471,472],control_typ:200,controlfil:422,convect:91,conveni:[6,12,29,188,192,208,293,350,429,482],convent:[3,8,9,29,176,183,184,191,291,304,331,384,386,482],converg:[3,6,41,88,188,190,192,197,210,213,214,222,225,255,282,284,287,291,295,353,354,355,357,377,378,398,451,463,470],convers:[3,8,140,190,191,201,204,279,347,378,379,380,386,398,402,406,416,454,470,481],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,165,172,188,190,191,208,249,330,333,335,338,341,350,357,363,384,441,443,449,454,456,457,458,463,473,477,481,482,484,486],convex:328,convinc:[7,12],cook:9,cooki:7,cool:[7,155,231,290],cooordin:188,cooper:[5,7],coord123:114,coord1:[3,114,203,206,207],coord2:[3,114,203,206,207],coord3:[3,114,203,206,207],coord:[],coordiat:355,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,148,154,160,162,163,165,169,187,188,189,190,191,192,194,197,202,203,205,206,207,210,211,212,213,214,215,216,217,220,222,223,225,227,230,231,232,233,234,235,236,248,250,251,253,254,256,257,269,272,273,274,277,278,279,289,290,292,294,295,296,301,304,305,306,307,309,317,318,319,326,327,329,330,350,355,356,357,362,363,364,367,385,451,456,457,459,461,464,466,470,477,482,483],coordn:[114,203],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,190,319,357,375,421,454],copper:449,coproccesor:16,coprocessor:[1,4,7,9,16,17,362,469],coproprocessor:17,copy_arrai:8,copyright:[7,8,277],coral:191,core:[],core_shel:147,coreshel:[6,9,371,378,380],cornel:[6,171,468],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,190,328,329,350,445,456],cornflowerblu:191,cornsilk:191,corpor:16,corr:377,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,147,152,159,190,216,229,235,251,252,269,277,279,282,318,324,328,347,357,363,364,365,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,445,447,448,449,456,471,474,477],correction_max_iter:200,correctli:[3,8,9,11,17,71,81,102,103,143,144,146,148,150,151,152,153,154,157,158,161,188,191,197,217,222,225,236,245,251,252,285,292,295,304,306,325,328,357,358,362,380,408,453,454,456,466,481,483],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,143,144,152,159,164,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,203,205,206,207,209,212,214,216,223,225,226,230,235,238,239,247,248,249,251,253,254,255,256,257,258,263,266,268,269,271,274,275,279,284,292,294,295,310,312,314,323,324,325,327,328,329,331,333,334,335,336,337,338,341,343,348,352,354,356,357,363,364,366,369,370,371,372,373,374,375,376,377,378,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,409,410,413,414,415,416,418,419,421,422,423,424,429,430,439,440,441,442,443,445,447,448,449,451,453,454,456,457,459,469,470,471,473,474,477,482],correspondingli:[407,408,465],cosin:[],cosineshift:27,cosmo:[229,234],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,164,190,191,203,206,207,210,211,212,224,251,284,319,347,348,360,378,398,402,413,439,453,465],costheta0:[439,441,443],costheta:419,costli:[11,88,229,358],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,145,155,160,162,178,188,190,191,195,196,203,204,206,210,216,225,234,281,282,283,287,290,292,294,307,308,314,318,319,320,324,328,330,332,339,344,346,353,355,358,362,365,388,392,393,421,422,452,453,454,456,458,460,463,464,472,477,482,483],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,116,141,166,170,283,285,320,347,348,355,362,369,371,372,373,374,377,378,379,380,381,386,390,391,393,398,402,406,413,416,421,422,424,438,443,444,448,461,468,474,477,481],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,41,63,68,77,91,114,116,117,153,163,169,197,198,201,203,205,206,207,209,210,217,222,224,227,233,251,263,278,295,310,311,328,348,355,356,357,359,362,388,392,413,474,482],counter:[325,451,462,464,470],counterbal:231,counterpart:[188,292,451],counterproduct:18,coupl:[],courant:297,cours:[3,8,126,128,159,188,195,196,228,291,304,318,324,326,327,329,330,348,407,430,453,456,469,477,482,484],courtesi:350,coval:[6,29,386,409,477],covari:229,cover:[6,71,185,191,200,238,386,396,445],coverag:[71,206],cpc:234,cpp:[1,3,6,8,9,11,12,13,87,188,195,196,225,295],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,191,194,220,236,320,345,348,362,375,438,451,469,470,473,474,475,482],cpuremain:474,cr2:164,cr3:164,crack:[4,358],crada:[5,7],crai:[5,7,13,18,188],crash:[3,12,358,477],craympi:362,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:200,create_faceset:200,create_group:189,create_nodeset:200,createatom:[],creation:[],crimson:191,critchlei:277,criteria:[3,116,166,190,191,211,212,213,246,355,418,445,458,461,482],criterion:[12,41,121,163,165,168,201,210,213,227,263,284,297,325,330,355,357,377,386,390,461,470,471],criterioni:470,critic:[48,49,249,314,319,355],cross:[3,12,22,71,89,144,173,188,190,202,206,212,216,248,250,269,292,300,304,306,315,322,334,350,357,373,382,383,384,391,392,393,398,400,402,419,424,426,428,441,443,449,456,460,466,484],crossov:1,crossterm:456,crozier:[0,7,13],crucial:282,crystal:[4,6,13,73,273,274,317,350,358,460,474,477],crystallin:[6,274,350,442,477],crystallis:314,crystallogr:[118,164],crystallograph:[350,474],crystallographi:[118,164,350],cs1:164,cs_chunk:6,cs_im:[40,456],cs_re:[40,456],csanyi:[140,420,429],cscl:409,csequ:6,csh:[11,12,375],cshrc:[11,12],csic:[385,439,441,443],csinfo:6,csisi:[385,439,441,443],csld:[],cst:384,cstherm:6,cstyle:453,csvr:[],ctcm:[363,384],ctemp_cor:220,cterm:296,ctr:9,ctype:11,cu1:164,cu2:164,cu3au:409,cube:[6,41,163,168,210,220,328,350,477],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:368,cummul:[3,6,208,211,212,213,215,224,229,235,237,307,310,311,312,313,315,322,392,474],cumul:[6,201,203,205,206,207,221,227,235,249,251,255,263,292,293,357],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,145,153,155,161,163,166,169,188,189,190,191,192,195,196,200,203,206,207,208,210,211,212,213,214,215,216,217,221,222,225,227,229,232,233,235,241,248,251,252,256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220,227,229,230,235,236,241,251,252,255,256,257,268,269,271,275,277,291,292,295,310,311,312,317,333,335,338,341,343,355,381,384,392,466,474,477,483],degress:[145,203],del:470,delai:[3,6,12,358,383,474],deleg:393,delet:[2,3,7,8,12,54,57,60,63,163,168,169,194,203,204,205,206,207,208,211,213,224,227,251,293,310,311,330,332,346,356,358,361,413,456,457,459,467,468,473,478,480,482,483],delete_atom:[],delete_bond:[],delete_el:200,deli:187,delimit:[454,482],deloc:[252,386],delr:409,delt_lo:470,delta:[],delta_1:368,delta_3:368,delta_7:368,delta_conf:3,delta_ij:[409,419],delta_mu:3,delta_pi:368,delta_r:419,delta_sigma:368,delx:187,delz:187,demand:287,demo:11,demon:272,demonstr:[282,409],den:278,dendrim:392,denniston:[9,238,240,241,242,274],denomin:[7,170],denot:[118,220,236,274,285,287,378,391,393,422,426,428],dens:[71,213,386],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,151,163,165,195,196,200,203,206,207,210,216,225,238,241,244,245,274,278,279,283,319,324,350,352,356,363,368,384,409,410,411,419,423,432,434,435,436,456,465,466,474,481],density_continu:428,density_summ:428,depart:[0,7],departur:[249,282],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,143,148,152,153,159,165,166,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,190,191,194,195,196,197,198,201,203,205,206,208,209,210,212,214,216,222,223,226,229,230,231,233,235,236,238,240,241,248,251,253,254,255,256,257,258,266,268,269,271,273,284,287,289,292,294,295,301,307,310,311,312,314,316,318,319,321,323,324,327,328,329,330,332,333,334,335,336,337,338,341,343,348,350,355,356,358,359,360,362,363,364,366,367,368,369,370,371,372,373,374,375,376,377,378,379,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,409,410,412,414,415,416,418,419,421,422,423,424,429,430,438,439,440,441,442,443,444,445,447,448,449,451,453,456,458,459,462,466,468,470,473,474,476,482,483],dependend:6,depflag:12,dephas:[451,470],depos:217,deposit:[],deprec:283,depth:[51,144,190,319,389,423],dequidt:9,der:[87,107,376,377,406,421,422,448,477],deriv:[6,7,8,38,56,63,87,140,159,185,204,214,216,227,235,248,251,253,254,255,256,257,273,279,283,287,316,317,319,324,325,328,354,356,364,368,376,381,386,387,391,400,404,405,409,421,422,438,440,448,477],derjagin:448,derlet:273,descend:191,descent:[7,354],descib:[40,283],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,144,145,149,150,153,156,158,159,163,164,165,167,168,177,182,185,188,189,194,195,196,203,204,205,206,207,208,210,213,214,215,216,217,219,220,228,229,232,233,234,235,236,237,238,240,241,242,246,250,251,252,255,262,270,273,275,280,281,282,283,284,285,292,296,304,307,308,309,310,311,312,313,314,315,316,317,322,324,325,327,332,347,348,350,353,354,355,356,357,361,364,365,367,369,370,371,373,374,375,376,377,378,381,384,386,387,389,390,391,393,398,399,400,401,402,403,404,405,406,407,408,409,412,418,419,420,421,422,423,424,429,430,437,438,439,440,441,442,443,444,447,448,449,451,453,454,456,457,459,460,466,469,470,473,482,483,484],descript:[],descriptor:[140,188,394],deserno:348,design:[0,3,6,7,8,9,11,13,14,15,17,118,147,150,164,200,213,219,220,251,252,273,274,293,314,319,365,366,367,370,373,378,380,386,406,407,408,410,411,419,422,440,465],desir:[2,3,6,7,11,12,14,15,16,18,33,40,50,59,71,88,91,112,117,141,147,165,178,187,203,208,214,216,225,227,228,235,236,237,241,251,269,277,278,279,280,283,287,292,295,307,310,311,312,313,318,325,339,344,347,348,350,353,355,356,357,382,384,392,407,408,439,441,443,452,453,454,456,460,465,470,471,473,474,482,483,484],desk:7,desktop:[4,6,7,10,12,17,190],despit:477,destabil:368,destre:341,destroi:[11,39,211,212],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,143,144,145,148,158,159,160,162,165,166,169,170,173,184,188,190,191,194,195,196,200,203,204,205,206,208,210,212,213,214,215,216,217,225,227,228,229,230,232,233,235,237,238,242,248,249,250,251,252,253,254,255,256,257,261,263,268,269,270,271,274,277,278,279,281,282,284,285,286,292,295,307,310,311,312,313,314,315,317,318,319,320,321,322,323,330,332,334,342,347,348,351,355,356,358,359,362,363,364,365,367,368,370,372,373,374,375,376,377,378,381,382,386,387,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,408,409,412,413,418,421,422,423,429,430,438,445,447,448,454,456,457,458,459,461,462,465,466,468,471,474,475,482,483,486],detect:[2,3,12,61,63,86,226,278,318,357,377,392,397,451,453,456,467,470,482],determ:362,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,153,154,163,164,165,187,188,190,191,192,193,197,198,199,202,203,204,205,206,207,208,209,210,214,216,217,220,222,227,230,231,233,235,236,241,246,248,249,251,256,257,268,269,271,273,275,279,282,289,290,291,292,293,294,297,299,301,307,310,311,312,314,320,321,324,325,326,327,328,329,330,342,347,348,350,356,358,359,362,364,365,372,377,381,383,384,388,390,393,394,402,409,413,422,423,437,440,444,448,453,456,457,459,461,463,466,470,472,473,475,481,482,483],detil:108,devan:[9,424],devanathan:443,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,232,255,277,282,283,286,364,368,386,411,458],devemi:9,deviat:[249,255,273,388],deviator:9,devic:[1,3,12,15,17,232,362],device_typ:362,devin:[284,377],devis:411,dfactor:190,dff:477,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,348],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,286],dhi:[59,187,216,278],dhug:[249,282],dhugoniot:[249,282],dia:409,diagnost:[],diagon:[3,6,83,140,141,142,214,251,279,292,322,426,428],diagonalstyl:429,diagram:[41,118,164,184,210,275],diallo:392,diam:[190,191,278,356],diamet:[3,6,40,113,165,188,190,191,195,196,235,278,292,307,323,325,356,376,389,390,396,400,423,445,448,456,457,466],diamond:[350,386,409],diamter:[40,278],dick:6,dicsuss:248,dictat:[201,249],did:[3,12,355,382,383,384,390,413,441,443,464],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,161,321,347],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,143,144,145,146,148,151,152,153,154,155,157,158,159,165,166,168,173,184,185,187,188,190,191,194,196,199,201,203,205,210,211,212,213,214,215,216,220,226,227,228,229,230,231,232,235,236,238,248,251,252,253,254,256,257,259,261,264,266,267,268,271,273,275,277,279,282,283,284,287,290,292,295,296,304,305,307,310,311,312,315,316,317,319,322,323,324,325,328,332,333,342,344,346,347,348,350,351,353,354,356,357,359,360,361,362,363,364,368,372,373,375,376,377,382,384,386,389,390,391,393,396,398,399,401,402,409,410,411,412,413,415,419,421,422,423,424,425,426,428,429,430,438,439,440,441,443,445,448,450,451,453,454,456,458,459,460,461,464,465,466,468,470,471,473,474,475,477,481,482,483,484],differenti:[1,3,6,29,185,347,378,419,442],difficult:[214,275,362,392,465],difficulti:[295,421],diffract:[],diffus:[],digit:[2,3,191,332],dih_table1:185,dih_table2:185,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:212,dihydrid:386,dij:295,dilat:[],dim1:3,dim2:3,dim:[3,59,71,143,146,147,148,151,152,153,154,155,157,165,187,206,216,233,325,350,409,459,481,482,483],dimdim:482,dimems:274,dimens:[],dimension:[3,39,112,118,140,143,145,146,147,148,151,152,153,154,155,157,164,186,203,206,250,274,319,350,353,357,419,456,466],dimensionless:[105,121,122,124,127,129,131,136,140,319,348,429,448],dimentionless:135,dimer:[6,292,409],dimgrai:191,dimstr:[41,210],dinola:[279,310],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,188,309,477],dir1:467,dir2:467,dir:[1,3,4,8,11,12,249,273,282,306,419,421,422,454,467,482],dirac:140,direc:419,direct:[],directli:[3,6,8,9,11,12,87,113,140,142,188,189,190,197,222,229,233,238,274,293,311,323,325,326,327,328,350,354,362,363,364,369,371,372,378,381,384,386,398,402,413,416,424,437,454,466,467,468,474,482],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,60,192,215,234,277,283,286,303,307,316,317,357,361,363,364,368,375,377,378,384,385,387,394,395,406,409,410,411,415,419,420,421,422,429,439,441,442,443,454,456,457,458,467,482],disabl:[3,12,16,319,397,454,469,482],disadvantag:[6,210],disallow:[188,216,251],disappear:458,discard:[2,3,41,71,206,210,320,328,453,458,459],discontinu:[9,185,355,404],discourag:409,discov:[13,320],discret:[6,8,40,42,190,191,235,238],discuss:[],disk:[6,84,85,158,186,217,227,278,454],disloc:70,disord:[39,70],disp:[],dispar:423,disperion:[381,402],dispers:[3,6,7,9,163,274,347,348,372,381,402,407,413,422,440],displac:[],displace_atom:[],displace_box:59,displacemet:459,displai:[11,13,22,37,44,55,173,184,188,190,334,342,375,438],dispters:3,dissip:[6,228,235,274,316,317,370,382,390,407,408,438],dissolut:211,dist:[6,69,91,108,117,188,275,291,383,437,451,483],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,154,160,163,165,166,167,168,172,187,188,190,191,199,203,206,207,211,212,213,214,216,217,218,221,227,233,238,248,249,250,251,255,263,273,274,278,282,283,290,291,292,295,296,300,304,305,306,307,314,315,317,318,319,322,324,325,326,327,328,329,333,347,348,350,353,355,357,358,359,362,365,366,367,368,369,370,371,372,373,374,376,378,379,380,381,382,383,384,385,386,388,389,390,391,392,396,397,398,399,400,401,402,403,404,405,406,407,408,409,412,413,414,415,416,417,418,419,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,454,456,459,465,466,470,474,477,481,483],distinct:[6,220,289,347,423],distinguish:[6,86,140,241,386,455],distort:363,distrbut:363,distribut:[],distro:[111,375,418,419],ditto:[8,11,12,14,15,16,17,18,115,212,449,454],div:8,divd:117,diverg:[3,12,39,292,317,458,477,484],divid:[3,6,16,41,91,112,117,126,128,141,162,163,173,184,191,203,204,205,210,216,273,315,322,327,347,355,357,387,422,465,473,482],divis:[6,238,368,396,406,453,456,474,482],dl_poli:7,dlambda:159,dlammps_async_imd:232,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,190],dlammps_gzip:[3,12,188,190,318,456,457,461],dlammps_jpeg:[3,12,190],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,190],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,188],dlen:466,dlmp_intel_offload:[12,16],dlo:[59,187,216,278],dlopen:6,dlvo:[7,376,448],dm_lb:238,dmax:[307,353],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,144,145,158,160,162,165,166,167,173,184,188,189,190,191,192,194,195,196,201,202,203,204,205,206,207,208,217,227,235,236,246,251,252,256,257,261,268,269,270,271,278,281,292,304,307,310,311,312,321,325,328,330,332,334,342,346,355,356,357,362,363,364,367,375,377,378,384,385,387,392,393,395,396,409,410,411,413,415,418,419,420,429,438,439,441,443,445,454,456,457,458,459,461,464,465,466,473,474,482,483,484,485],docuement:423,dodgerblu:191,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,116,117,118,142,144,145,147,148,153,155,159,164,165,166,167,169,171,173,178,184,185,187,188,189,190,191,194,200,201,203,206,209,210,212,213,214,216,220,222,224,227,228,231,233,235,236,238,241,247,251,252,253,254,256,257,268,269,270,271,279,280,281,285,287,290,292,307,310,312,314,315,319,322,323,324,327,328,329,330,335,336,338,339,341,346,347,348,349,350,356,357,358,363,364,365,366,367,368,370,372,373,374,376,377,378,379,381,382,383,384,385,386,388,389,390,391,393,394,395,396,397,400,401,403,404,405,407,408,409,410,411,413,419,420,421,422,423,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,443,444,445,447,448,449,451,452,453,454,456,457,458,459,460,463,464,466,467,468,469,470,473,474,477,482,486],doegenomestolif:7,doesn:[3,7,8,12,165,188,201,206,207,304,356,358,362,364,377,385,395,421,422,439,441,442,443,456,458],dof:[3,8,112,144,145,158,203,292,483],dof_per_atom:[145,203],dof_per_chunk:[145,203],doff:[356,456],doi:[6,215],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,154,164,167,187,189,190,191,194,201,210,214,216,217,231,234,238,251,252,275,287,292,319,324,325,347,348,357,362,383,413,451,453,456,460,473],domin:[1,386,470],don:[0,8,11,12,13,116,168,197,222,236,281,328,409,454,456],donadio:311,done:[1,3,6,7,8,12,14,15,16,17,18,19,38,39,41,56,59,62,71,159,162,165,168,185,188,190,191,200,201,203,205,206,207,208,210,211,212,213,214,216,217,225,227,232,233,235,236,243,251,256,257,268,269,271,272,274,275,276,281,289,292,293,295,307,310,311,312,314,316,317,330,332,346,347,348,355,357,358,361,362,364,372,384,393,394,395,402,408,409,413,421,437,440,445,451,452,453,454,457,460,461,464,474,475,477,482,483],donor:392,dot:[141,161,197,222,230,250],doti:[368,419],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,216,225,280,328,332,346,348,361,362,368,387,391,421,422,452,456,460,464,469,482,483],dover:200,down:[3,6,7,8,11,39,71,214,235,307,323,362,386,413,455,475],downhil:[353,354],download:[5,7,8,9,11,12,13,17,232,394,420],downsid:6,downward:289,dozen:[8,12,107,194,421,422],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:244,dproduct:365,dr_ewald:[118,293],drag:[],dragforc:238,drai:[249,282],drain:[231,323,355],dramat:[59,187,211,212,213,214,216,251,307,310,311,348,362,413,453],drautz:368,draw:190,drawback:281,drawn:[188,190,191,228,451],drayleigh:[249,282],dreid:[],drfourth:105,drho:[113,363,384],drift:[6,103,105,228,229,235,236,247,290,307,465,473,477],drive:[11,12,198,214,216,230,251,273,279,292,326,357],driven:[6,177],driver:[6,12,14,15,194,225,232],drop:[3,191,382],droplet:393,drsquar:105,drude:[],dry:224,dsecriptor:394,dsf:[],dsmc:[],dstyle:278,dt_collis:238,dt_lb:238,dt_md:238,dt_srd:307,dtilt:[59,216],dtneb:470,dtqm:282,dtype:[115,212],dual:[17,307,362],dudarev:164,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,105,106,110,116,118,126,140,141,143,144,146,148,151,152,153,154,155,157,158,160,164,165,168,169,188,190,194,197,198,205,209,211,212,213,214,215,216,217,222,223,224,225,228,229,232,233,235,236,237,238,241,242,243,247,248,249,250,251,255,263,273,276,278,290,291,292,294,304,306,307,308,310,311,312,313,314,316,317,319,323,324,326,327,328,330,348,353,355,357,358,359,379,382,384,388,389,393,407,408,413,419,421,423,424,437,440,441,443,446,448,449,451,453,456,457,458,465,470,473,474,475,477,482,483],duffi:319,duin:[9,283,288,421,422],duke:348,dummi:[12,29,442],dump1:461,dump2:461,dump2vtk_tri:134,dump:[],dump_atom:8,dump_custom:8,dump_h5md:189,dump_modifi:[],dumpcustom:8,dumptimestep:461,dunbrack:[6,20,171,373,468],dunweg:[235,237],duplic:[2,3,14,15,16,17,18,19,41,42,166,210,229,273,456,481],dupont:[5,7,13],durat:[37,55,143,144,146,147,148,150,151,152,153,154,157,158,184,191,203,227,287,319,342,390,438],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,126,128,142,147,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415,416,418,419,421,422,423,424,429,430,431,432,437,438,439,440,441,442,443,445,446,447,448,449,451,454,456,461,465,466,468,470,472,473,474,477,481,482,485],energy_update_freq:422,enforc:[6,57,58,104,187,188,189,190,192,194,201,213,216,251,272,274,284,292,295,332,347,398,453,482,483],enforce2d:[],eng:[11,65,69,108,188,225,330,332,377,411],eng_previ:332,engin:[200,216,277,296,316,384,410],engr:[421,422],enhanc:[196,200,451],enlarg:[59,190],enough:[3,40,61,86,165,166,168,210,236,278,282,287,292,320,324,325,328,358,362,378,417,456,460,461],enpub:384,enrti:[],ensembl:[],ensight:6,ensur:[3,6,140,188,201,214,227,228,251,297,318,348,368,383,406,437,439],enter:[57,155,387,470],enthalpi:[123,253,254,384,473,474,482],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,141,145,164,165,191,194,195,196,203,206,207,210,213,215,224,227,228,231,235,236,247,251,253,254,255,256,257,273,275,277,290,292,305,319,321,332,362,381,402,413,440,456,464,465],entireti:[396,445],entiti:[6,8,40,42,188,292],entri:[3,8,12,38,42,56,65,69,79,92,108,115,118,127,130,131,132,133,134,136,137,138,163,185,191,205,206,207,215,282,330,356,368,385,409,415,422,429,439,440,441,442,443,482],entropi:470,entry1:[38,56,191,375,440],entry2:191,entryn:191,enumer:[166,188],enumuer:6,env:362,environ:[1,3,6,11,12,16,17,18,190,229,234,273,362,363,368,375,377,385,386,419,441,453,467,482],epair:[107,191,388,392,421,422,474],epen:[421,422],epfl:[229,234],epp:381,epq:381,eps0:448,eps14:406,epsilon0:443,epsilon:[3,6,36,45,46,50,53,54,87,171,195,196,227,292,307,324,328,353,355,367,373,374,376,378,379,380,381,389,391,392,393,396,397,398,399,400,401,402,403,404,405,406,412,416,423,424,433,439,445,447,448,465,477,481],epsilon_0:449,epsilon_14:373,epsilon_:423,epsilon_d:379,epsilon_i:[389,413,423],epsilon_i_:423,epsilon_i_a:[389,423],epsilon_i_b:[389,423],epsilon_i_c:[389,423],epsilon_ij:413,epsilon_j:[389,413,423],epsilon_j_:423,epsilon_j_a:[389,423],epsilon_j_b:[389,423],epsilon_j_c:[389,423],epsilon_lj:423,epton:418,eqch:160,eqeq:[421,422],eqp:381,eqq:381,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,144,159,161,165,190,191,194,195,196,197,198,201,204,205,208,209,210,214,216,217,222,227,228,230,231,233,235,236,238,241,242,248,249,255,265,273,275,278,280,282,283,284,287,289,291,292,294,296,301,303,310,311,312,315,316,317,319,321,322,324,327,329,330,332,346,350,355,357,358,359,361,362,377,382,388,389,392,407,412,419,421,422,423,425,426,427,429,430,440,445,449,452,453,454,456,458,459,463,464,467,470,472,474,482,483],equat:[3,6,7,8,9,91,112,118,164,173,184,194,214,220,221,229,235,236,238,241,249,250,251,252,255,269,273,275,282,283,287,295,307,315,319,322,324,325,327,329,341,347,348,376,381,382,386,387,390,395,407,408,409,413,423,426,428,432,433,435,436,444,449,477],equi:252,equidist:250,equil:[3,283,351,463,486],equilater:466,equilibr:[3,4,5,6,7,9,59,91,165,194,201,204,213,214,227,249,251,252,269,270,282,283,284,285,315,316,317,322,377,378,421,422,452,466],equilibria:322,equilibribum:[211,212],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,148,149,172,174,214,216,227,228,229,236,238,251,255,269,282,287,291,295,296,304,307,314,315,317,322,333,335,338,341,377,409,415,477],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:200,equival:[6,12,13,59,61,124,125,133,138,163,167,191,205,208,214,216,227,235,251,269,279,291,292,327,382,386,441,443,456,459,464,465,474,477],equlibrium:6,equliibr:[283,285],er3:164,eradiu:[40,113,386,456],eras:[294,316],erat:[216,408],erc:378,erfc:[378,398,413],erforc:113,erg:481,erhart:[201,384,441,443],ermscal:365,ernst:9,eror:3,eros:409,erose_form:409,erot:[],errata:[441,443],erratum:324,erron:3,error:[],erta:390,ervel:[113,456],escap:[217,477],especi:[8,11,16,153,165,194,201,210,227,282,287,290,291,362,453],espresso:[9,286],essenti:[8,11,12,27,88,128,146,147,148,151,152,153,154,155,157,174,204,255,274,323,348,364,378,398,443,461,474],essex:29,establish:[87,231],estim:[1,3,6,10,12,38,41,56,91,141,200,210,221,249,307,314,347,348,353,413,422,440,470,474],esu:481,esub:409,eta:[6,238,251,282,283,285,323,385,387,389,419,442,481],eta_dot:251,eta_ij:419,eta_ji:387,etag:[40,456],etail:474,etap:251,etap_dot:251,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,17,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,143,145,146,147,148,149,151,152,153,154,155,157,159,165,167,168,169,178,188,190,191,194,200,201,202,203,205,206,207,208,211,212,216,217,225,227,228,235,251,278,289,293,319,320,328,332,346,347,355,356,357,358,360,384,385,393,406,408,417,421,422,439,441,443,451,454,456,457,458,463,465,466,470,472,473,474,475,477,481,482,484,486],ethernet:18,etol:[355,357,451,470],etot0:282,etot:[6,94,96,97,110,141,151,191,220,236,249,282,473,474],eu2:164,eu3:164,euler:[355,357],eulerian:200,euqat:431,europhi:238,ev_tal:8,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,140,142,145,155,163,165,188,190,191,195,196,197,198,200,202,203,204,205,206,207,208,209,216,222,228,230,231,233,234,235,236,274,280,283,294,297,301,310,311,312,321,324,327,329,330,332,347,348,353,355,362,413,419,425,427,440,451,452,454,458,459,461,463,464,465,466,470,472,474,482,483],evalut:[332,454],evan:[153,269],evanseck:[6,20,171,373,468],evapor:[],evaul:[8,355],evdwl:[107,421,422,474],even:[3,6,8,12,15,16,17,18,34,39,41,52,57,59,61,63,70,71,119,166,167,181,185,188,191,194,195,196,201,202,203,205,206,207,208,210,211,212,214,216,217,220,233,236,249,251,252,274,287,289,292,293,303,307,315,319,322,324,328,330,340,347,353,355,357,362,367,386,387,390,393,413,423,446,456,457,459,461,462,463,465,466,468,471,473,474,475,477,486],evenli:[3,41,141,185,210,238,396,446,456],event:[],eventu:[3,6,12,15,167,283,470],ever:[54,56,234,307],evera:[376,389,423,438],everi:[0,1,2,3,6,8,11,12,15,16,39,41,71,72,91,113,119,128,153,168,188,189,190,191,192,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,221,224,225,227,229,231,232,233,238,239,247,251,252,255,272,273,274,278,279,280,281,282,283,284,285,287,289,290,292,293,295,296,307,309,310,311,312,313,314,315,318,319,320,321,322,330,332,346,348,357,358,359,362,382,383,393,406,421,422,434,450,451,452,456,458,460,461,463,464,465,470,471,472,474,482,486],everyth:[8,107],everywher:[116,400],eviri:386,evolut:[229,238,275,451],evolv:[238,275,320],ewald:[2,3,5,6,7,8,12,88,110,118,141,320,347,348,355,369,371,372,378,381,386,398,402,416,424,438,440,458],ewald_disp:381,ewalddisp:3,exact:[22,41,44,71,122,159,168,173,210,213,228,229,235,236,237,278,287,288,307,319,334,347,375,458,463,470,482,484,486],exactli:[3,6,12,14,17,38,41,56,59,71,91,116,144,149,156,165,185,195,196,205,210,216,221,228,235,236,237,252,262,263,270,274,282,307,312,313,326,362,375,382,384,390,393,396,407,413,440,458,459,466,470,482],exager:477,examin:[6,8,9,213,274],examp:[454,482],exampl:[],exce:[3,6,16,17,18,41,58,71,167,203,206,207,210,214,216,221,224,251,274,298,299,307,355,362,456,482],exceed:[3,41,59,210,216,251,307,464],excel:386,except:[1,2,5,6,8,11,14,16,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,191,194,197,203,204,205,209,210,214,216,223,226,227,230,233,235,237,251,252,253,254,255,256,257,258,262,263,266,268,269,270,271,275,284,285,292,294,295,304,307,310,312,313,319,323,327,330,332,333,334,335,336,337,338,341,342,343,347,348,350,352,356,357,358,360,361,362,363,364,366,369,370,371,372,373,374,375,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,408,410,414,415,416,418,421,422,423,424,430,438,439,440,441,442,443,445,447,448,449,451,453,454,456,458,459,461,464,465,466,467,468,470,474,477,481,482,483,485],excess:386,exchang:[2,3,6,8,9,61,62,194,200,201,227,235,284,292,315,319,322,347,362,386,471],exchange:347,excit:[9,386],exclud:[3,6,9,12,16,17,63,71,112,140,145,152,153,169,188,203,206,211,212,239,247,277,290,292,314,325,330,355,356,358,370,390,393,407,408,413,437,468],exclus:[1,3,9,12,16,87,362,377,413,465,475],excurs:451,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,166,190,232,286,332,346,349,361,452,454,464,467,470,482],exemplari:228,exemplifi:386,exert:[6,233,236,287,326,327,328,348],exhaust:[200,361,482],exhibit:[251,354,386,465],exist:[3,6,7,8,11,12,13,37,55,59,68,70,122,165,166,184,189,190,191,194,199,209,212,214,217,227,277,278,280,330,333,335,336,338,342,351,356,362,393,421,446,452,454,456,457,458,467,468,469,482,483,484],exit:[2,3,11,12,41,57,188,210,346,361,454,455,464,473,482],exlanatori:3,exp:[],expand:[],expans:[12,140,188,467,482],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,146,157,163,185,210,222,227,229,248,273,279,281,282,287,292,330,348,358,375,409,413,451,454,456,458,461,465,470,482],expens:[6,10,71,191,273,277,292,319,330,347,348,358,362,454],experi:[6,13,15,17,209,217,232,241,250,279,291,292,353,357,382,413,465,470],experienc:[6,12,240,241],experiment:[347,362,470],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,145,153,185,188,190,191,194,203,204,208,210,212,214,216,251,273,281,292,304,330,332,346,347,350,356,357,361,367,384,396,430,445,454,457,458,461,463,466,477,482,486],explan:[3,6,59,113,140,188,203,250,273,393,450,453,454,456,465],explanatori:[3,8,117,188,202,203,205,206,207,292,356,453,482],explantori:[3,288],explic:412,explicit:[6,9,11,22,44,77,87,113,116,159,173,195,196,216,298,299,334,352,364,365,368,373,375,384,386,397,407,444,450,453,457,460],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,143,152,155,163,165,171,172,174,175,176,177,179,180,182,183,185,188,191,197,206,209,216,223,226,228,230,235,251,253,254,255,256,257,258,266,268,269,271,281,282,284,292,294,295,310,312,313,319,323,327,333,335,336,337,338,341,343,356,362,363,364,366,369,370,371,372,373,374,375,376,377,378,379,381,382,383,384,385,387,388,389,390,391,392,393,396,397,398,399,400,401,402,403,404,405,406,407,410,413,414,415,416,418,423,424,430,431,432,433,434,435,436,438,439,440,441,442,443,444,445,447,448,449,456,458,465,466,468,469,475,477],explictli:[16,469],exploit:[9,15,17,275],explor:[118,164],expon:[3,283,285,384,389,392,406,412,424],exponenti:[87,419,439,449,470,482],expos:11,exposit:[200,382,383],express:[6,140,151,165,195,196,214,248,273,283,319,325,332,368,384,386,400,409,429,438,482],expressiont:368,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,194,197,198,201,208,209,215,218,222,225,226,227,229,230,231,233,235,237,249,251,255,263,273,274,290,291,292,294,296,301,304,306,310,311,312,313,314,316,317,319,321,324,328,329,389,409,422,423,429,473,474],extent:[1,3,41,45,57,71,163,167,188,199,206,210,233,326,329,347,350,364,425,427,440,453,456,459],exterior:[3,6,328],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,143,144,146,148,151,152,153,154,155,157,158,164,165,166,167,171,191,205,210,212,251,280,281,282,292,307,355,356,359,360,381,390,393,396,409,413,453,454,456,459,468,477,482],extract:[3,6,11,13,36,63,87,107,115,117,119,195,196,285,357,378,387,409,429,454,461,473],extract_atom:11,extract_comput:[11,454],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,190,214,216,251,317,386,442,477],extrema:406,extrins:200,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[161,321],f_a:[441,442,443],f_ave:117,f_c:442,f_f:443,f_fix_id:282,f_harm:317,f_i:419,f_id:[6,71,117,119,188,194,202,203,204,205,206,207,208,246,309,321,474,482],f_ij:419,f_indent:208,f_int:316,f_jj:91,f_k:419,f_langevin:319,f_max:[282,287],f_msst:249,f_r:[236,441,442,443],f_sigma:368,f_solid:317,f_ss:6,f_temp:236,face:[3,6,57,59,71,153,163,167,199,206,207,324,326,327,328,329,350,389,409,423,456,459],face_threshold:163,facet:163,facil:[0,12],facilit:[6,13],fact:[6,8,16,229,307,317,390,468],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,116,118,140,159,164,167,171,182,188,190,191,195,196,204,210,214,216,217,227,232,235,237,238,249,251,252,255,275,279,291,295,297,299,307,311,315,322,323,324,328,338,348,350,362,364,365,368,369,371,373,378,379,380,382,386,390,393,397,398,409,413,415,416,422,424,430,439,444,453,456,459,460,465,468,470,471,474,477,481,482],factori:[3,454],factoriz:347,fail:[3,11,12,59,169,214,217,347,355,357,380,422,454],failur:[121,426,455,482],fairli:[11,413,465,470],faken:73,falcon:232,fall:[3,6,191,205,278,454,482],fals:[86,330,332,482],fame:8,famili:453,familiar:[0,11],fan:419,far:[3,6,12,17,57,59,61,86,188,191,192,210,211,212,214,217,251,273,291,292,307,324,335,338,353,357,358,445,454,456,461,474],farago:235,farrel:[441,443],farther:188,fashion:[6,8,41,71,165,191,194,195,196,201,206,210,212,217,227,229,233,248,249,251,253,254,255,256,257,265,268,269,270,271,281,282,284,292,296,300,306,309,317,319,323,324,325,327,329,357,393,407,459,468,482,485],fasolino:395,fast:[6,7,9,12,13,17,39,188,260,282,320,347,348,370,407,408,438,440,458,463,465,474,483,486],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,143,152,171,172,174,175,176,177,179,180,182,183,185,188,191,194,197,209,210,216,223,226,230,234,235,251,253,254,255,256,257,258,266,268,269,271,279,283,284,292,294,295,307,310,312,314,316,319,323,327,333,335,336,337,338,341,343,347,348,359,360,362,363,364,366,368,369,370,371,372,373,374,375,376,377,378,381,382,384,385,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,410,414,415,416,418,423,424,430,438,439,440,441,442,443,445,447,448,449,451,465,469,477],fastest:[6,14,17,153,206,319,320,362,453],fatal:[3,473],fault:[70,422],faulti:12,fava:389,favor:213,favorit:7,fbmc:314,fcc:[],fcm:[265,482],fdirect:220,fdotr:394,fdti:87,fe2:164,fe3:164,fe_md_boundari:200,featu:8,featur:[],fecr:384,feedback:[7,232],feel:[7,232,233,241,273,328,330,357,413],felling:411,felt:328,femtosecond:481,fene:[],fennel:[378,398],fep:[],ferguson:[6,171,468],fermi:[1,12,15,151,362,443],fermion:[9,386],ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,17,18,39,192,202,203,204,205,206,207,208,236,251,278,281,283,295,321,347,355,356,357,364,453,456,461,465,467,475,482,484],fewer:[1,3,11,15,16,61,241,465],fewest:3,fextern:225,feynman:275,fff:454,ffield:[377,387,421,422],ffmpeg:[3,12,190],ffplai:190,fft:[1,3,7,12,14,15,88,109,110,141,274,347,348,465],fft_inc:[12,348],fft_lib:12,fft_path:12,fftbench:[347,475],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,197,198,222,225,229,275,291,378,398,402,437],field1:[457,461],field2:457,field:[],fifth:[304,415],figur:[1,3,8,11,12,282,453,454],fij:381,file0:273,file1:[11,13,273,318,332,356,461,463,467],file2:[11,13,318,332,356,461,463,467],file:[],file_from:189,filenam:[3,12,13,38,41,56,185,188,190,191,192,200,203,204,205,206,207,208,210,215,273,277,280,283,284,285,288,289,292,293,318,319,344,345,346,357,363,364,368,378,384,385,387,395,409,410,411,415,419,420,421,422,429,439,440,441,442,443,452,453,454,457,458,463,467,474,482,484,485,486],filennam:463,filep:[3,188,191,458,463,486],filepo:289,fill:[7,165,190,278,319,350,358,368,422,459],filter:[191,200],final_integr:8,final_integrate_respa:8,finchham:[6,147,380],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,168,185,192,201,213,214,224,227,250,273,279,287,291,353,355,357,358,378,393,398,402,409,438,440,477,482],find_custom:8,fine:[16,17,169,197,222,317,358,362,482],finer:[140,165,482],finest:347,finger:[165,187,248,459],finish:[6,11,41,210,332,344,346,347,359,361,362,445,461,482,483],finit:[],finni:[7,384,438],finvers:220,fiorin:[9,215],fire:[353,354,355,357,470],firebrick:191,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,150,153,159,161,163,164,166,167,168,172,185,188,189,190,191,192,194,203,204,205,206,207,208,210,213,216,227,228,233,238,248,249,250,251,273,275,280,281,282,284,289,292,295,296,304,305,307,308,309,316,317,318,319,321,325,330,332,333,339,350,355,356,357,358,361,362,363,364,367,368,369,371,373,375,377,378,384,386,387,390,391,394,395,397,398,402,407,408,409,411,413,415,419,421,422,429,437,439,440,441,442,443,449,451,452,453,454,456,457,458,461,463,465,468,469,470,473,474,477,482,483,484,486],fischer:[6,9,19,20,171,373,468],fit:[3,6,9,12,38,56,185,291,307,364,368,395,409,413,433,440,442,464,482],five:[73,151,282,356,368,410,456,470],fix:[],fix_adapt:[159,196,406],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,201,278],fix_evapor:201,fix_flux:200,fix_gcmc:[201,356],fix_gl:229,fix_gld:229,fix_grav:278,fix_id:[3,214,249,251,253,254,255,256,257,279,282],fix_modifi:[],fix_mov:[187,325],fix_nh:8,fix_npt:229,fix_nvt:[201,227],fix_poem:[3,6],fix_pour:[3,217],fix_qbmsst:9,fix_qeq:[3,377],fix_rattl:295,fix_reax_bond:421,fix_rigid:[241,367],fix_saed_vtk:293,fix_setforc:8,fix_shak:295,fix_srd:3,fix_styl:255,fix_temp_rescal:313,fixedpoint:[214,251],fixextern:225,fixid:200,fji:381,flag1:[219,360],flag2:[219,360],flag:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,160,164,168,188,190,191,192,208,213,215,219,232,235,239,241,247,248,274,281,292,304,306,307,314,318,327,330,345,348,356,360,361,362,364,392,397,409,437,451,453,454,456,457,458,460,461,462,466,482],flag_buck:372,flag_coul:[372,381,402],flag_lj:[381,402],flagfld:[370,407,408],flaghi:[3,370,407,408],flaglog:[370,407,408],flagn:219,flagvf:[370,407,408],flat:[6,319,324,325,329],flavor:[2,7,12],fld:[9,324,370,407,408],flen:365,flex_press:365,flexibl:[3,6,8,166,190,203,206,215,229,252,315,322,386,442,474],flip:[3,6,216,251,326,327],floor:482,flop:12,floralwhit:191,flow:[],fluctuat:[6,64,87,214,227,228,235,238,251,255,273,274,317,319,341],fluid:[],fluid_veloc:242,flush:[3,191,473],flux:[],flv:190,fly:[7,9,12,41,190,194,200,217,220,292,295,320,368,474,477],fmackai:9,fmag:218,fmass:275,fmax:[355,474],fmomentum:220,fmsec:[2,191,235,236,248,251,279,292,310,311,465,476,481,483],fname:346,fno:12,fnorm:[355,474],fnpt:220,fnvt:220,foce:393,fock:365,focu:295,fogarti:[9,285,422],foil:[140,273,429],fold:[305,465],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,144,145,151,153,158,161,163,165,166,171,174,175,176,177,179,180,182,183,185,188,189,190,191,194,200,201,202,203,204,205,206,207,208,210,215,216,217,220,221,225,227,228,229,232,234,235,236,238,241,249,251,255,256,257,268,269,271,274,275,277,280,281,282,283,285,287,289,291,292,293,295,309,310,311,312,315,316,317,318,319,321,322,330,331,335,336,337,338,341,343,345,350,352,355,356,357,362,363,364,365,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,426,428,429,430,431,432,433,434,435,436,437,439,440,441,442,443,444,445,447,448,449,451,453,454,456,457,458,459,461,463,464,465,468,470,471,472,477,482,483,485],foo:[4,8,11,12,188,190,225,454,467,482],foot:6,footprint:[12,362],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:241,forcefield:[291,392],forcegroup:238,forcezero:353,ford:381,forestgreen:191,forev:71,forget:[236,477],forgiv:251,fork:[12,188],form:[2,3,6,8,12,16,19,22,44,54,63,66,74,75,77,81,87,89,90,93,103,104,106,116,140,141,159,160,169,173,191,194,195,196,212,228,229,235,237,241,248,269,274,285,287,291,292,319,324,328,333,334,341,352,354,356,357,364,365,368,375,384,386,388,392,393,397,409,411,415,416,419,421,422,423,429,430,438,440,441,442,443,448,450,453,454,456,461,466,473,477,482],formal:[6,78,80,91,228,229,235,251,275,307,315],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,173,185,188,189,190,191,192,203,205,206,207,208,210,212,274,277,281,283,285,288,292,293,303,318,319,330,331,334,352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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":211,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,145,153,154,158,164,165,168,170,184,186,187,188,190,191,192,193,195,196,197,199,200,201,203,206,207,208,211,212,214,215,216,217,221,224,227,228,233,235,236,237,238,239,241,246,249,251,252,255,269,270,274,275,278,279,280,281,282,284,287,289,290,292,293,307,309,314,315,316,317,320,322,324,326,330,342,345,347,348,350,351,353,354,356,358,359,360,362,365,368,370,386,407,408,413,421,422,437,438,451,452,453,456,457,459,461,463,464,465,468,470,472,473,474,475,476,481,483,484,485],"function":482,"long":[369,371,372,373,374,378,380,381,398,402,406,416,424],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[195,196],addforc:197,addit:[12,13],addtorqu:198,adiabat:6,adjust_dt:297,adp:363,airebo:364,alloi:384,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:199,arrai:6,aspher:[6,82,144,253,256,259,260,268],atc:[9,200],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,163,199,201,202,281,482],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:209,awpmd:[9,365],balanc:[41,210],barostat:6,basal:67,beck:366,berendsen:[279,310],between:6,binary2txt:13,bodi:[6,8,42,68,261,367],bond:[8,13,69,211,212,213,288],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:368,born:[369,380],boundari:[7,57],box:[6,58,214],brownian:370,buck:[371,372,380],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,171,373,406],chunk:[6,66,71,75,90,93,104,106,114,145,160,162,203],citat:7,class2:[21,43,172,333,374],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[324,376,448],colvar:[9,13,215],com:[74,75,146],comb3:377,comb:[284,377],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,483,484,485,486],common:3,comparison:1,compos:6,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,482],compute_modifi:102,condit:7,conduct:[6,315],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:204,cosin:[23,24,25,26,27,28,174],cossq:335,coul:[369,371,372,373,374,378,379,380,391,398,402,406,416,424],coupl:6,creat:212,create_atom:165,create_bond:166,create_box:167,createatom:13,creation:7,csld:311,csvr:311,cubic:400,cuda:[9,14,109,112,143,152,197,209,223,226,230,251,258,294,295,310,312,323,369,371,373,374,384,390,391,398,399,401,404,414,439,441],custom:8,cut:[49,365,371,374,378,381,386,388,398,399,406,412,416],cvff:336,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[378,398],deform:[148,149,216],delete_atom:168,delete_bond:169,delta:24,deposit:217,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92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,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329,464],run_styl:465,scalabl:10,scalar:6,screen:12,script:[2,6,8,11,12],sdk:[36,424],self:306,serial:11,set:[6,466],setforc:294,setvel:301,shake:295,share:[11,12],shell:[6,467],shield:283,shift:[26,27,48,49,174],simpl:31,simul:6,size:6,slater:283,slice:119,sllod:[269,270],small:292,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,296,297,298,299,300,301,303,425,426,427,428],smooth:[404,405],sna:140,snad:140,snap:429,snapshot:6,snav:140,soft:[406,430],solver:2,sourc:7,spatial:[206,207],spc:6,speci:289,special:[7,413,482],special_bond:468,sph:[9,431,432,433,434,435,436],sphere:[84,85,158,207,241,254,257,266,271],spheric:6,spline:[410,411],spring:[304,305,306,317],squar:28,srd:[307,329],srp:437,standard:9,start:[12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],state:309,stationari:245,stop:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],store:[308,309],strategi:1,streitz:378,stress:[141,142],structur:2,style:[1,2,6,8],submit:8,suffix:469,summari:6,swap:[201,213],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,483,484,485,486],system:6,tabl:[0,6,38,56,185,440,441],tad:470,taitwat:[435,436],talli:142,temp:[143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,310,311,312,313],temper:471,temperatur:6,tersoff:[441,442,443],test:11,tfmc:314,thermal:[6,315],thermo:[6,472],thermo_modifi:473,thermo_styl:474,thermodynam:[6,8],thermostat:6,thole:444,time:[6,208],timer:475,timestep:476,tip3p:6,tip4p:[6,378,398,402,406],tip:12,tlsph:426,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:318,tool:13,torqu:160,transform:220,tri:[267,445],tri_surfac:427,triangle_mesh_vertic:134,triclin:6,tstat:382,ttm:319,tune:320,type:7,ulsph:428,ulsph_num_neigh:135,ulsph_strain:136,ulsph_strain_r:137,ulsph_stress:138,umbrella:343,uncomput:478,u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\ No newline at end of file
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283,291,293,296,304,309,311,312,313,315,316,317,318,319,323,325,327,331,334,335,340,347,353,354,356,357,359,361,362,363,364,365,369,376,378,385,386,387,388,394,395,396,407,408,409,410,411,412,416,420,422,423,430,440,442,443,444,447,453,455,457,458,459,460,461,463,464,466,468,470,472,475,476,479,483,484,485,486,487,488],afterrun:466,afterward:3,afterword:41,ag1:164,ag2:164,again:[6,11,12,16,17,62,140,145,151,159,188,191,217,232,279,334,347,358,408,409,453,455,456,458,460,465,472,474,484,486],against:[11,12,13,64,218,358,422,423],aggreg:[6,12,65,68,69,79,92,108,115,232,248,291,293,306,453,485],aggress:[232,472],agilio:[9,13],agre:[3,8,185,356,365,396,423],agreement:[5,7],ahd:393,ahead:327,aidan:[0,5,7,9,13,351],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:190,akohlmei:[7,9,13,192,233],aktulga:[7,9,286,423],al2o3_001:[118,294],al3:164,ala:239,alain:9,alat:[274,410],alb:[420,442,444],albeit:292,albert:9,alchem:[87,159],alcohol:323,alcu:[364,369],alcu_eam:420,alderton:382,alejandr:[252,253],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,191,200,211,214,217,239,241,242,264,276,293,296,315,316,320,323,328,354,355,356,360,363,387,409,427,429,453,455,472],alia:[12,16],alias:[1,349],aliceblu:191,align:[6,12,29,41,71,167,185,207,211,234,351,458,461,479],alkali:387,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,153,158,159,160,161,162,163,164,165,166,167,168,169,171,173,178,184,185,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,245,247,248,250,252,253,254,255,256,257,258,259,260,261,262,263,264,265,267,268,269,270,271,272,273,274,275,276,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,304,305,307,308,309,310,311,312,315,316,317,318,319,320,321,322,323,325,326,327,328,329,330,331,332,333,334,335,338,343,346,347,348,349,350,351,353,356,357,358,359,360,362,363,364,365,366,368,369,370,372,373,374,375,376,378,379,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,403,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,423,424,425,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,450,451,452,453,455,456,457,458,459,460,461,462,463,465,466,467,468,469,470,471,472,473,475,476,477,479,483,484,485,486,487,488],allen:[29,87,382,390],allentildeslei:87,allign:3,allindex:332,alloc:[3,5,6,8,9,11,12,60,226,322,357,359,363,418,423,458,466],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,142,144,145,158,163,164,165,167,173,184,185,188,190,191,192,194,195,197,199,200,201,203,204,205,206,207,208,209,211,213,214,215,216,217,218,222,223,226,228,229,230,231,233,236,239,242,243,247,249,252,253,274,278,280,281,282,283,287,293,294,296,297,299,300,304,308,315,316,317,318,320,321,322,323,324,325,331,333,335,343,348,349,351,356,357,358,359,362,363,366,369,370,371,372,373,374,379,385,387,391,392,393,394,399,403,408,409,414,420,423,424,427,429,438,448,450,453,456,458,460,461,462,463,464,465,468,470,471,472,475,476,484,485],almost:[2,3,12,60,234,283,320,349,360,363,438],alo:379,alon:[6,7,214,289,422,423,456],alond:13,along:[6,8,9,12,29,40,87,118,164,165,187,188,190,214,234,239,240,244,249,251,283,293,296,297,301,305,306,315,319,320,326,329,331,351,354,355,356,358,379,382,391,394,397,399,403,410,422,423,441,458,461,468,469,484],alonso:[411,412],alpha:[6,12,51,195,239,275,283,288,356,364,367,370,379,383,385,386,388,393,398,399,410,415,419,443,445,476,479],alpha_:445,alpha_c:407,alpha_i:[430,445],alpha_ialpha_j:445,alpha_lj:407,alphabet:[2,3,22,37,44,55,63,173,184,194,335,343,357,376,439,458],alphanumer:[3,63,194,282,290,333,357,484],alreadi:[3,7,8,9,12,16,17,18,42,165,166,168,189,199,203,207,208,211,213,217,243,281,283,308,331,357,358,383,392,394,401,409,438,448,451,454,458,459,463,468,484],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,149,151,152,153,154,155,157,158,159,160,161,162,163,165,166,167,168,169,171,173,184,185,186,188,189,190,191,192,194,195,196,197,199,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,223,226,227,228,229,230,232,233,236,237,238,239,249,250,252,253,254,255,256,257,258,263,266,267,269,270,271,272,274,275,276,278,279,280,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,301,302,305,306,308,311,312,313,314,315,319,320,321,322,324,326,329,331,333,335,340,343,346,348,349,351,352,3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,363,365,369,379,380,410,414,426,428,444,462,468,479,481],closer:[3,41,116,163,187,188,211,215,219,317,358],closest:[213,274,293,323,390,424,438,448],cloud:479,clovertown:18,clsuter:72,clump1:[278,293],clump2:[278,293],clump3:[278,293],clump:293,cluster:[],clutter:[3,9],cmap:458,cmatrix:230,cmax:410,cmd:[11,12,276,469],cmin:410,cmm:[],cn1:204,cn2:204,cna:[],cnn:204,cnr:[9,13],cnt:[394,462],co2:[40,164,296,357],coars:[7,9,29,36,40,54,177,278,293,308,392,425,470],coarser:[349,484],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,171,172,173,178,334,335,340,376,394,398,414,427,429,431,458,460],coeffcient:458,coeffici:[],coefficienct:383,coefficient0:385,coefficient1:385,coeffieci:[6,367],coeffincientn:385,coexist:[9,228,387],cohes:[6,388,410],coincid:[122,329,374,408,409,453],colberg:189,cold:[6,150,228,232,359,479],coldest:316,coleman8:9,coleman:[9,118,164,294],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,145,153,160,162,165,188,191,203,216,242,248,278,288,291,293,331,348,357,359,377,397,458,465,471,477,488],collid:[222,308,330],colliex:164,collinear:[3,278],collis:[3,239,308,326,330,384,391,451],colllis:308,colloid:[],colombo:39,colon:[192,331,459],color1:191,color2:191,color:[3,9,41,188,190,191,211,229,283,288],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,145,153,160,162,163,164,185,188,191,194,202,203,204,206,207,208,209,242,249,250,283,293,309,310,320,330,389,393,422,423,459,473,475,484],colvar:[],colvarmodul:12,com:[],comamnd:217,comand:[214,460],comannd:363,comb3:[],comb:[],comb_1:285,comb_2:285,combiant:380,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,144,158,188,190,200,206,233,242,252,276,282,312,321,329,332,334,348,349,351,355,363,377,379,380,387,388,394,406,407,430,440,442,444,447,450,461,466,471,479,484],come:[],comfort:[12,13],comm:[0,3,12,61,73,189,233,235,236,349,358,363,383,414,419,441],comm_modifi:[],comm_modift:61,comm_styl:[],command:[],comment:[2,7,11,12,38,56,171,185,188,237,293,320,357,358,364,385,386,388,398,410,416,423,430,440,441,442,443,444,447,455,456,458,479,484],commerci:7,commmand:[3,6,12,59,107,271,452,453,455,472,487],common:[],commonli:[3,6,12,17,25,57,59,105,167,188,190,192,344,392,401,430,442,444,458,461,470],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,169,190,191,211,212,213,215,216,217,233,235,239,241,242,243,252,275,282,284,285,286,293,308,320,331,346,348,359,360,361,363,384,418,455,456,460,467,468,484,486,488],communc:348,comp:[7,189,235,236,296,349,358,387,414,419,424,437,441,443],compact:[63,194,376,439],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,148,163,164,173,184,191,221,284,331,333,348,349,356,358,410,453,472,473,479,483],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,172,173,184,334,335,343,375,439],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,176,188,192,196,202,203,204,206,207,208,209,211,275,287,312,315,322,325,328,348,363,395,414,441,455,456,484],compens:[6,212,213,291,359,387],compet:319,competit:349,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,163,188,189,190,192,233,319,349,363,458,459,463,484],compl:17,complain:[12,17],complement:410,complementari:[7,379,399],complet:[3,6,9,12,15,41,59,71,191,207,211,216,242,276,279,282,308,319,321,333,347,358,363,388,427,429,446,453,458,463,466,470,472,475,479,484],complex:[6,8,11,12,13,25,40,42,62,140,142,153,165,166,239,304,329,346,358,387,441,456,458,461,484],compli:[315,319],complic:[6,7,9,12,13,201,228,456],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,160,161,162,188,190,191,197,198,202,203,204,205,206,207,208,209,210,214,215,217,218,223,226,231,235,236,239,242,244,248,249,251,252,253,256,257,258,269,270,272,273,275,276,277,280,291,293,295,296,297,301,302,305,308,311,312,313,315,322,323,328,329,330,348,351,355,356,357,358,363,383,387,391,408,409,427,429,430,458,459,468,476,484,485],componenet:6,composit:[6,201,239,385],compound:[378,387,388,447],compres:[71,114,203],compress:[3,59,71,114,168,188,190,191,203,217,250,256,280,283],compris:[40,329,397,424,446],compton:[118,164],comptu:3,compuat:349,comput:[],computation:[3,6,212,213,320,369],computational:479,compute_arrai:8,compute_fep:[196,407],compute_group_group:228,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,294],compute_scalar:8,compute_temp:8,compute_ti:196,compute_vector:8,compute_xrd:164,concaten:[2,3,487],concav:329,concentr:385,concept:[6,145,155,203,467],conceptu:[3,6,71,153,215,217,358,379,394,410,463],concern:[6,73,87,189,229],concis:[11,319],conclud:12,concret:8,concurr:[9,16,349,484],conden:[320,442,444],condens:[6,147,320,365,381,385,399,447],condit:[],conducit:6,conduct:[],cone:461,confid:[3,472],config:[12,188,455],configfil:216,configur:[1,2,6,12,15,17,38,59,122,167,185,187,188,190,194,215,216,217,218,222,228,235,236,264,276,284,319,346,356,358,365,369,386,410,440,442,444,447,453,458,460,461,472],confin:[458,472],conflict:[3,12,40,414,456],conform:[3,6,13,59,214,215,251,292,297,319,342,358,387,470],confus:[3,447],conjuct:383,conjug:[7,8,236,355,387,422,423],conjunct:[6,7,71,86,87,114,148,153,159,165,169,191,195,196,236,239,243,264,279,280,284,285,286,288,293,308,316,323,328,348,349,358,370,372,376,379,383,387,393,399,414,417,425,445,458,461,465,479,488],connect:[3,6,87,150,168,214,233,278,293,296,305,358,380,391,438,444,455,456,462,479],conput:3,consecut:[3,11,12,39,71,165,191,195,196,218,233,234,379,399,403,453,459,461],consequ:[1,6,201,320,398,472],conserv:[3,194,201,214,221,222,229,232,236,238,239,243,248,250,252,264,293,296,311,312,316,323,324,328,358,382,383,391,405,467,472],consid:[6,9,70,71,78,87,115,147,150,151,168,188,191,195,196,202,204,207,211,213,214,218,240,253,275,293,315,316,319,320,323,349,376,387,394,423,424,438,453,454,456,459,460,461,463,466,468,476,479,484],consider:[6,8,236,237,311,312,313,363,467],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,145,148,150,165,177,187,192,197,198,203,217,218,221,223,226,229,236,237,238,249,252,254,255,256,257,258,259,260,262,263,264,265,267,268,269,270,271,272,280,283,288,290,292,293,311,312,313,314,324,348,349,351,357,358,363,365,369,371,377,379,387,390,394,408,409,410,414,424,427,429,441,448,456,458,459,461,462,463,470,479,484],consistent_fe_initi:200,consit:293,constant:[],constitu:[3,6,242,293,325,329,377,424],constitut:[427,429],constrain:[3,6,8,143,144,145,146,148,151,152,153,154,155,157,158,194,203,218,228,229,234,242,246,278,279,291,293,296,306,316,323,356,357,387,463,470,479],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,164,215,252,275,292,329,359,363,382,414,438,440,441,461,462,477,484],constructor:8,consult:423,consum:[1,288,418,484],consumpt:346,contact:[],contact_stiff:[426,428],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,145,153,163,164,165,167,171,173,184,185,188,190,191,192,194,195,196,200,202,203,204,206,207,208,209,211,216,218,223,230,234,235,236,237,239,250,264,274,275,278,279,281,283,286,290,293,294,298,308,315,319,320,329,330,333,347,349,357,358,361,362,364,365,366,369,378,379,382,385,386,387,394,395,410,416,420,421,422,423,430,440,441,442,443,444,445,447,453,454,455,456,458,459,460,461,463,465,467,470,472,475,476,479,484,486,488],content:[12,18,423,474,476],context:[3,6,8,12,17,117,191,212,213,218,278,290,324,355,450,458,465,474,483,484,485],contibut:70,contigu:455,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,161,191,194,195,196,201,203,204,205,206,207,208,209,211,214,215,216,217,218,228,229,230,232,233,234,236,237,238,244,249,250,252,254,255,256,257,258,269,270,271,272,277,279,282,283,293,294,297,307,308,310,317,318,320,326,329,333,347,362,363,369,383,384,401,404,422,423,424,427,429,443,453,456,458,460,461,466,472,475,476,484,486],continuum:[6,7,9,200,320,427,429],contour_integr:200,contract:[59,215,217,252,280,293],contradictori:3,contrain:296,contraint:264,contrari:[230,237],contrast:[1,6,42,55,64,147,150,217,331,427,429,450,487],contrib:320,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,196,201,202,203,204,206,207,208,209,215,228,236,239,242,243,247,253,270,271,278,279,287,290,293,294,296,322,348,356,358,366,383,384,385,387,394,408,409,414,422,423,470,476,479],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,174,188,190,194,200,201,211,215,216,217,232,233,236,237,252,254,255,256,257,258,280,285,293,299,300,311,312,313,320,324,346,348,360,387,390,422,423,426,428,440,444,453,455,467,473,474],control_typ:200,controlfil:423,convect:91,conveni:[6,12,29,188,192,209,294,351,430,484],convent:[3,8,9,29,176,183,184,191,292,305,332,385,387,484],converg:[3,6,41,88,188,190,192,197,211,214,215,223,226,256,283,285,288,292,296,354,355,356,358,378,379,399,453,465,472],convers:[3,8,140,190,191,201,204,280,348,379,380,381,387,399,403,407,417,456,472,483],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,165,172,188,190,191,209,250,331,334,336,339,342,351,358,364,385,442,444,451,456,458,459,460,465,475,479,483,484,486,488],convex:329,convinc:[7,12],cook:9,cooki:7,cool:[7,155,232,291],cooordin:188,cooper:[5,7],coord123:114,coord1:[3,114,203,207,208],coord2:[3,114,203,207,208],coord3:[3,114,203,207,208],coord:[],coordiat:356,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,148,154,160,162,163,165,169,187,188,189,190,191,192,194,197,202,203,206,207,208,211,212,213,214,215,216,217,218,221,223,224,226,228,231,232,233,234,235,236,237,249,251,252,254,255,257,258,270,273,274,275,278,279,280,290,291,293,295,296,297,302,305,306,307,308,310,318,319,320,327,328,330,331,351,356,357,358,363,364,365,368,386,453,458,459,461,463,466,468,472,479,484,485],coordn:[114,203],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,190,320,358,376,422,456],copper:451,coproccesor:16,coprocessor:[1,4,7,9,16,17,363,471],coproprocessor:17,copy_arrai:8,copyright:[7,8,278],coral:191,core:[],core_shel:147,coreshel:[6,9,372,379,381],cornel:[6,171,470],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,190,329,330,351,446,458],cornflowerblu:191,cornsilk:191,corpor:16,corr:378,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,147,152,159,190,217,228,230,236,252,253,270,278,280,283,319,325,329,348,358,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,417,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,446,447,449,450,451,458,473,476,479],correction_max_iter:200,correctli:[3,8,9,11,17,71,81,102,103,143,144,146,148,150,151,152,153,154,157,158,161,188,191,197,218,223,226,237,246,252,253,286,293,296,305,307,326,329,358,359,363,381,409,455,456,458,468,483,485],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,143,144,152,159,164,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,203,205,206,207,208,210,213,215,217,224,226,227,231,236,239,240,248,249,250,252,254,255,256,257,258,259,264,267,269,270,272,275,276,280,285,293,295,296,311,313,315,324,325,326,328,329,330,332,334,335,336,337,338,339,342,344,349,353,355,357,358,364,365,367,370,371,372,373,374,375,376,377,378,379,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,414,415,416,417,419,420,422,423,424,425,430,431,440,441,442,443,444,446,447,449,450,451,453,455,456,458,459,461,471,472,473,475,476,479,484],correspondingli:[408,409,467],cosin:[],cosineshift:27,cosmo:[230,235],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,164,190,191,203,207,208,211,212,213,225,252,285,320,348,349,361,379,399,403,414,440,455,467],costheta0:[440,442,444,447],costheta:420,costli:[11,88,230,359],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,145,155,160,162,178,188,190,191,195,196,203,204,207,211,217,226,235,282,283,284,288,291,293,295,308,309,315,319,320,321,325,329,331,333,340,345,347,354,356,359,363,366,389,393,394,422,423,454,455,456,458,460,462,465,466,474,479,484,485],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,116,141,166,170,284,286,321,348,349,356,363,370,372,373,374,375,378,379,380,381,382,387,391,392,394,399,403,407,414,417,422,423,425,439,444,445,447,450,463,470,476,479,483],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,114,116,117,153,163,169,197,198,201,203,206,207,208,210,211,218,223,225,228,234,252,264,279,296,311,312,329,349,356,357,358,360,363,389,393,414,476,484],counter:[326,453,464,466,472],counteract:228,counterbal:232,counterpart:[188,293,453],counterproduct:18,coupl:[],courant:298,cours:[3,8,126,128,159,188,195,196,229,292,305,319,325,327,328,330,331,349,408,431,455,458,471,479,484,486],courtesi:351,coval:[6,29,387,410,479],covari:230,cover:[6,71,185,191,200,239,387,397,446],coverag:[71,207],cpc:235,cpp:[1,3,6,8,9,11,12,13,87,188,195,196,226,296],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,191,194,205,221,237,321,346,349,363,376,439,453,471,472,475,476,477,484],cpuremain:476,cr2:164,cr3:164,crack:[4,359],crada:[5,7],crai:[5,7,13,18,188],crash:[3,12,359,479],craympi:363,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:200,create_faceset:200,create_group:189,create_nodeset:200,createatom:[],creation:[],crimson:191,critchlei:278,criteria:[3,116,166,190,191,212,213,214,247,356,419,446,460,463,484],criterion:[12,41,121,163,165,168,201,211,214,228,264,285,298,326,331,356,358,378,387,391,463,472,473],criterioni:472,critic:[6,48,49,250,315,320,356],cross:[3,12,22,71,89,144,173,188,190,202,207,213,217,249,251,270,293,301,305,307,316,323,335,351,358,374,383,384,385,392,393,394,399,401,403,420,425,427,429,442,444,451,458,462,468,486],crossov:1,crossterm:458,crozier:[0,7,13],crucial:283,crystal:[4,6,13,73,274,275,318,351,359,462,476,479],crystallin:[6,275,351,443,479],crystallis:315,crystallogr:[118,164],crystallograph:[351,476],crystallographi:[118,164,351],cs1:164,cs_chunk:6,cs_im:[40,458],cs_re:[40,458],csanyi:[140,421,430],cscl:410,csequ:6,csh:[11,12,376],cshrc:[11,12],csic:[386,440,442,444,447],csinfo:6,csisi:[386,440,442,444,447],csld:[],cst:385,cstherm:6,cstyle:455,csvr:[],ctcm:[364,385],ctemp_cor:221,cterm:297,ctr:9,ctype:11,cu1:164,cu2:164,cu3au:410,cube:[6,41,163,168,211,221,329,351,479],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:369,cummul:[3,6,209,212,213,214,216,225,230,236,238,308,311,312,313,314,316,323,393,476],cumul:[6,201,203,206,207,208,222,228,236,250,252,256,264,293,294,358],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,145,153,155,161,163,166,169,188,189,190,191,192,195,196,200,203,207,208,209,211,212,213,214,215,216,217,218,222,223,226,228,230,233,234,236,242,249,252,253,257,258,264,269,270,272,278,284,285,287,290,291,292,293,296,297,298,299,300,301,302,304,306,307,308,311,312,313,319,320,323,324,325,326,327,328,330,331,333,346,347,348,349,352,353,355,356,357,358,363,369,376,378,382,385,387,388,391,394,395,398,408,409,410,411,412,414,420,422,423,426,427,428,429,431,442,444,445,448,453,454,455,456,458,459,460,461,462,464,465,466,468,470,472,473,475,476,484,485,486,487,488],curv:[6,165,228,275],curvatur:[390,424,451],custom:[],cut0:456,cut1:467,cut2:467,cut:[],cuthi:[274,286],cutinn:[371,408,409],cutlo:[274,286],cutmax:420,cutoff1:[375,382,399,403,407,417,425],cutoff2:[370,372,373,375,381,382,399,403,407,417,425],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,163,166,168,213,214,219,274,283,284,286,288,290,293,308,321,325,329,331,346,348,349,356,359,360,361,363,364,365,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,383,384,385,386,387,388,389,390,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,422,423,424,425,430,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,456,460,463,467,479,484],cutoffa:386,cutoffc:386,cuu3:385,cval:164,cvd:315,cvel:297,cvff:[],cwiggl:[3,249,325,328,330,484],cyan:[2,190,191],cycl:[3,228,250,252,253,256],cyclic:[3,185],cygwin:12,cylind:[3,4,190,234,279,326,329,461],cylindr:[6,234,305,326],cypress:363,cyrot:369,cyrstal:275,d3q15:239,d3q19:239,d_double_doubl:15,d_e:320,d_flag2:282,d_flag:282,d_name:[113,188,282,310,468],d_single_doubl:15,d_single_singl:15,d_sx:282,d_sy:282,d_sz:282,daan:318,dai:12,daili:12,daivi:270,damag:[],dammak:288,damp:[3,6,194,199,236,237,238,243,252,253,256,280,283,288,293,311,312,324,326,327,355,356,358,370,372,374,379,382,387,391,399,407,417,425,439,445,472,479],damp_com:237,damp_drud:237,dampen:[293,479],dampflag:[326,391],dan:17,danger:[3,12,228,331,383,476],dangl:168,daniel:9,darden:[349,382],darkblu:191,darkcyan:191,darken:190,darkgoldenrod:191,darkgrai:191,darkgreen:191,darkkhaki:191,darkmagenta:191,darkolivegreen:191,darkorang:191,darkorchid:191,darkr:191,darksalmon:191,darkseagreen:191,darkslateblu:191,darkslategrai:191,darkturquois:191,darkviolet:191,dasgupta:284,dash:[391,475],dat:[6,91,185,200,454],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,294],dataset:294,datatyp:3,date:[0,6,12,13,422,423,484],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,188,204],davi:325,david:[9,19,348,349,442,444],daw:[385,420],dbg:14,dcd:[3,6,7,188,189,190,191,192,276,459,463],ddim:187,deactiv:407,dealt:235,debug:[6,7,11,12,13,14,17,118,122,164,165,276,281,346,348,363,395,414,448,456,457,460,465,468,475,484],deby:[],decai:[379,451],decid:[3,6,12,16,71,249,282,293,321,473],decipher:351,declar:189,declin:308,decod:190,decompos:[87,430],decomposit:[3,5,7,18,62,200,276],decoupl:[6,479],decreas:[3,188,197,198,205,214,217,223,226,228,236,319,348],decrement:297,deepli:345,deeppink:191,deepskyblu:191,def:[12,13,456],defaul:61,defect:[6,70,163],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,171,172,173,174,175,176,177,179,180,182,183,184,185,186,187,188,189,190,191,194,195,196,197,198,199,200,201,202,203,204,206,207,208,209,210,211,212,213,214,215,217,218,221,222,223,226,227,228,231,234,235,236,237,238,239,247,249,251,252,253,254,255,256,257,258,260,261,262,265,267,268,269,270,271,272,274,275,276,278,279,280,282,284,286,291,293,294,295,296,298,302,306,308,310,311,312,313,314,316,317,318,320,322,323,325,326,327,328,329,330,331,333,334,335,336,337,338,339,342,343,344,346,348,349,351,353,355,356,357,358,359,360,361,362,363,365,366,367,368,370,371,372,373,374,375,376,377,379,380,382,383,384,386,387,389,390,391,392,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,413,414,415,416,417,419,420,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,455,456,458,459,461,462,463,464,467,468,469,470,472,473,475,476,479,480,481,482,483,484,485],definit:[2,3,6,8,12,13,78,80,116,140,191,203,204,205,206,207,208,209,217,234,256,294,310,322,325,328,330,332,343,346,357,366,369,377,387,397,420,427,429,430,446,456,458,460,467,469,483,484],defint:476,deform:[],deg2theta:164,deg:479,degener:[3,278],degrad:[8,18,275,349,467],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,164,165,171,172,175,176,183,185,187,190,203,214,221,228,230,231,236,237,242,252,253,256,257,258,269,270,272,276,278,292,293,296,311,312,313,318,334,336,339,342,344,356,382,385,393,468,476,479,485],degress:[145,203],del:472,delai:[3,6,12,359,384,476],deleg:394,delet:[2,3,7,8,12,54,57,60,63,163,168,169,194,203,204,206,207,208,209,212,214,225,228,252,294,311,312,331,333,347,357,359,362,414,458,459,461,469,470,475,480,482,484,485],delete_atom:[],delete_bond:[],delete_el:200,deli:187,delimit:[456,484],deloc:[253,387],delr:410,delt_lo:472,delta:[],delta_1:369,delta_3:369,delta_7:369,delta_conf:3,delta_ij:[410,420],delta_mu:3,delta_pi:369,delta_r:420,delta_sigma:369,delx:187,delz:187,demand:288,demo:11,demon:273,demonstr:[283,410],den:279,dendrim:393,denniston:[9,239,241,242,243,275],denomin:[7,170],denot:[118,221,237,275,286,288,379,392,394,423,427,429],dens:[71,214,387],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,151,163,165,195,196,200,203,207,208,211,217,226,239,242,245,246,275,279,280,284,320,325,351,353,357,364,369,385,410,411,412,420,424,433,435,436,437,458,467,468,476,483],density_continu:429,density_summ:429,depart:[0,7],departur:[250,283],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,143,148,152,153,159,165,166,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,190,191,194,195,196,197,198,201,203,205,206,207,209,210,211,213,215,217,223,224,227,230,231,232,234,236,237,239,241,242,249,252,254,255,256,257,258,259,267,269,270,272,274,285,288,290,293,295,296,302,308,311,312,313,315,317,319,320,322,324,325,328,329,330,331,333,334,335,336,337,338,339,342,344,349,351,356,357,359,360,361,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,410,411,413,415,416,417,419,420,422,423,424,425,430,431,439,440,441,442,443,444,445,446,447,449,450,451,453,455,458,460,461,464,468,470,472,475,476,478,484,485],dependend:6,depflag:12,dephas:[453,472],depos:218,deposit:[],deprec:[284,422],depth:[51,144,190,320,390,424],dequidt:9,der:[87,107,377,378,407,422,423,450,479],deriv:[6,7,8,9,38,56,63,87,140,159,185,204,215,217,228,236,249,252,254,255,256,257,258,274,280,284,288,317,318,320,325,326,329,355,357,365,369,377,382,387,388,392,401,405,406,410,422,423,439,441,450,479],derjagin:450,derlet:274,descend:191,descent:[7,355],descib:[40,284],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,144,145,149,150,153,156,158,159,163,164,165,167,168,177,182,185,188,189,194,195,196,203,204,205,206,207,208,209,211,214,215,216,217,218,220,221,229,230,233,234,235,236,237,238,239,241,242,243,247,251,252,253,256,263,271,274,276,281,282,283,284,285,286,293,297,305,308,309,310,311,312,313,314,315,316,317,318,323,325,326,328,333,348,349,351,354,355,356,357,358,362,365,366,368,370,371,372,374,375,376,377,378,379,382,385,387,388,390,391,392,394,399,400,401,402,403,404,405,406,407,408,409,410,413,419,420,421,422,423,424,425,430,431,438,439,440,441,442,443,444,445,447,449,450,451,453,455,456,458,459,461,462,468,471,472,475,484,485,486],descript:[],descriptor:[140,188,395],deserno:349,design:[0,3,6,7,8,9,11,13,14,15,17,118,147,150,164,200,214,220,221,252,253,274,275,294,315,320,366,367,368,371,374,379,381,387,407,408,409,411,412,420,423,441,467],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,112,117,141,147,165,178,187,203,209,215,217,226,228,229,236,237,238,242,252,270,278,279,280,281,284,288,293,296,308,311,312,313,314,319,326,340,345,348,349,351,354,356,357,358,383,385,393,408,409,440,442,444,454,455,456,458,462,467,472,473,475,476,484,485,486],desk:7,desktop:[4,6,7,10,12,190],despit:479,destabil:369,destre:342,destroi:[11,39,212,213],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,143,144,145,148,158,159,160,162,165,166,169,170,173,184,188,190,191,194,195,196,200,203,204,205,206,207,209,211,213,214,215,216,217,218,226,228,229,230,231,233,234,236,238,239,243,249,250,251,252,253,254,255,256,257,258,262,264,269,270,271,272,275,278,279,280,282,283,285,286,287,293,296,308,311,312,313,314,315,316,318,319,320,321,322,323,324,331,333,335,343,348,349,352,356,357,359,360,363,364,365,366,368,369,371,373,374,375,376,377,378,379,382,383,387,388,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,410,413,414,419,422,423,424,430,431,439,446,449,450,456,458,459,460,461,463,464,467,468,470,473,476,477,484,485,488],detect:[2,3,12,61,63,86,227,279,319,358,378,393,398,453,455,458,469,472,484],determ:363,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,153,154,163,164,165,187,188,190,191,192,193,197,198,199,202,203,204,205,206,207,208,209,210,211,215,217,218,221,223,228,231,232,234,236,237,242,247,249,250,252,257,258,269,270,272,274,276,280,283,290,291,292,293,294,295,298,300,302,308,311,312,313,315,321,322,325,326,327,328,329,330,331,343,348,349,351,357,359,360,363,365,366,373,378,382,384,385,389,391,394,395,403,410,414,423,424,438,441,445,450,455,458,459,461,463,465,468,472,474,475,477,483,484,485],detil:108,devan:[9,425],devanathan:444,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,233,256,278,283,284,287,365,369,387,412,447,460],devemi:9,deviat:[250,256,274,389],deviator:9,devic:[1,3,12,15,17,233,363],device_typ:363,devin:[285,378],devis:412,dfactor:190,dff:479,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,349],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,287],dhi:[59,187,217,279],dhug:[250,283],dhugoniot:[250,283],dia:410,diagnost:[],diagon:[3,6,83,140,141,142,215,252,280,293,323,427,429],diagonalstyl:430,diagram:[41,118,164,184,211,276],diallo:393,diam:[190,191,279,357],diamet:[3,6,40,113,165,188,190,191,195,196,236,279,293,308,324,326,357,377,390,391,397,401,424,446,450,458,459,468],diamond:[351,387,410],diamter:[40,279],dick:6,dicsuss:249,dictat:[201,250],did:[3,12,356,383,384,385,391,414,442,444,466],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,161,322,348],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,143,144,145,146,148,151,152,153,154,155,157,158,159,165,166,168,173,184,185,187,188,190,191,194,196,199,201,203,206,211,212,213,214,215,216,217,221,227,228,229,230,231,232,233,236,237,239,249,252,253,254,255,257,258,260,262,265,267,268,269,272,274,276,278,280,283,284,285,288,291,293,296,297,305,306,308,311,312,313,316,317,318,320,323,324,325,326,329,333,334,343,345,347,348,349,351,352,354,355,357,358,360,361,362,363,364,365,369,373,374,376,377,378,383,385,387,390,391,392,394,397,399,400,402,403,410,411,412,413,414,416,420,422,423,424,425,426,427,429,430,431,439,440,441,442,444,446,447,450,452,453,455,456,458,460,461,462,463,466,467,468,470,472,473,475,476,477,479,483,484,485,486],differenti:[1,3,6,29,185,348,379,420,443],difficult:[215,276,363,393,467],difficulti:[296,422],diffract:[],diffus:[],digit:[2,3,191,333],dih_table1:185,dih_table2:185,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:213,dihydrid:387,dij:296,dilat:[],dim1:3,dim2:3,dim:[3,59,71,143,146,147,148,151,152,153,154,155,157,165,187,207,217,234,326,351,410,461,483,484,485],dimdim:484,dimems:275,dimens:[],dimension:[3,39,112,118,140,143,145,146,147,148,151,152,153,154,155,157,164,186,203,207,251,275,320,351,354,358,420,458,468],dimensionless:[105,121,122,124,127,129,131,136,140,320,349,430,450],dimentionless:135,dimer:[6,293,410],dimgrai:191,dimstr:[41,211],dinola:[280,311],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,188,310,479],dir1:469,dir2:469,dir:[1,3,4,8,9,11,12,250,274,283,307,420,422,423,456,469,484],dirac:140,direc:420,direct:[],directli:[3,6,8,9,11,12,87,113,140,142,188,189,190,197,223,230,234,239,275,294,312,324,326,327,328,329,351,355,363,364,365,370,372,373,379,382,385,387,399,403,414,417,425,438,456,468,469,470,476,484],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,192,216,235,278,284,287,304,308,317,318,358,362,364,365,369,376,378,379,385,386,388,395,396,407,410,411,412,416,420,421,422,423,430,440,442,443,444,447,456,458,459,460,469,484],disabl:[3,12,16,320,398,456,471,484],disadvantag:[6,211],disallow:[188,217,252],disappear:460,discard:[2,3,41,71,205,207,211,321,329,455,460,461],discontinu:[9,185,356,405],discourag:410,discov:[13,321],discret:[6,8,40,42,190,191,236,239],discuss:[],disk:[6,84,85,158,186,218,228,279,456],disloc:70,disord:[39,70],disp:[],dispar:424,disperion:[382,403],dispers:[3,6,7,9,163,275,348,349,373,382,403,408,414,423,441,447],displac:[],displace_atom:[],displace_box:59,displacemet:461,displai:[11,13,22,37,44,55,173,184,188,190,335,343,376,439],dispters:3,dissip:[6,229,236,275,317,318,371,383,391,408,409,439],dissolut:212,dist:[6,69,91,108,117,188,276,292,384,438,453,485],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,154,160,163,165,166,167,168,172,187,188,190,191,199,203,207,208,212,213,214,215,217,218,219,222,228,234,239,249,250,251,252,256,264,274,275,279,283,284,291,292,293,296,297,301,305,306,307,308,315,316,318,319,320,323,325,326,327,328,329,330,334,348,349,351,354,356,358,359,360,363,366,367,368,369,370,371,372,373,374,375,377,379,380,381,382,38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54,155,157,159,165,167,168,169,178,188,190,191,194,195,200,201,202,203,206,207,208,209,212,213,217,218,226,228,229,236,252,279,290,294,320,321,329,333,347,348,356,357,358,359,361,385,386,394,407,409,418,422,423,440,442,444,447,453,456,458,459,460,465,467,468,472,474,475,476,477,479,483,484,486,488],ethernet:18,etol:[356,358,453,472],etot0:283,etot:[6,94,96,97,110,141,151,191,221,237,250,283,475,476],eu2:164,eu3:164,euler:[356,358],eulerian:200,euqat:432,europhi:239,ev_tal:8,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,140,142,145,155,163,165,188,190,191,195,196,197,198,200,202,203,204,205,206,207,208,209,210,217,223,229,231,232,234,235,236,237,275,281,284,295,298,302,311,312,313,322,325,328,330,331,333,348,349,354,356,363,414,420,426,428,441,453,454,456,460,461,463,465,466,467,468,472,474,476,484,485],evalut:[333,456],evan:[153,270],evanseck:[6,20,171,374,470],evapor:[],evaul:[8,356],evdwl:[107,422,423,476],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,119,166,167,181,185,188,191,194,195,196,201,202,203,206,207,208,209,211,212,213,215,217,218,221,234,237,250,252,253,275,288,290,293,294,304,308,316,320,323,325,329,331,341,348,354,356,358,363,368,387,388,391,394,414,424,447,448,458,459,461,463,464,465,467,468,470,473,475,476,477,479,488],evenli:[3,41,141,185,211,239,397,448,458],event:[],eventu:[3,6,12,15,167,284,472],ever:[54,56,235,308],evera:[377,390,424,439],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,113,119,128,153,168,188,189,190,191,192,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,222,225,226,228,230,232,233,234,239,240,248,252,253,256,273,274,275,279,280,281,282,283,284,285,286,288,290,291,293,294,296,297,308,310,311,312,313,314,315,316,319,320,321,322,323,331,333,347,349,358,359,360,363,383,384,394,407,422,423,435,452,453,454,458,460,462,463,465,466,467,472,473,474,476,484,488],everyth:[8,107],everywher:[116,401],eviri:387,evolut:[230,239,276,453],evolv:[239,276,321],ewald:[2,3,5,6,7,8,12,88,110,118,141,321,348,349,356,370,372,373,379,382,387,399,403,417,425,439,441,460],ewald_disp:382,ewalddisp:3,exact:[22,41,44,71,122,159,168,173,211,214,229,230,236,237,238,279,288,289,308,320,335,348,376,460,465,472,484,486,488],exactli:[3,6,12,14,17,38,41,56,59,71,91,116,144,149,156,165,185,195,196,206,211,217,222,229,236,237,238,253,263,264,271,275,283,308,313,314,327,363,376,383,385,391,394,397,408,414,441,460,461,468,472,484],exager:479,examin:[6,8,9,17,214,275],examp:[456,484],exampl:[],exce:[3,6,16,17,18,41,58,71,167,203,207,208,211,215,217,222,225,252,275,299,300,308,356,363,458,484],exceed:[3,41,59,211,217,252,308,466],excel:387,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,191,194,197,203,204,206,210,211,215,217,224,227,228,231,234,236,238,252,253,254,255,256,257,258,259,263,264,267,269,270,271,272,276,285,286,293,295,296,305,308,311,313,314,320,324,328,331,333,334,335,336,337,338,339,342,343,344,348,349,351,353,357,358,359,361,362,363,364,365,367,370,371,372,373,374,375,376,377,378,379,381,382,383,385,386,387,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,409,411,415,416,417,419,422,423,424,425,431,439,440,441,442,443,444,446,447,449,450,451,453,455,456,458,460,461,463,466,467,468,469,470,472,476,479,483,484,485,487],excess:[205,387],exchang:[2,3,6,8,9,61,62,194,200,201,228,236,285,293,316,320,323,348,363,387,473],exchange:348,excit:[9,387],exclud:[3,6,9,12,16,17,63,71,112,140,145,152,153,169,188,203,207,212,213,240,248,278,291,293,315,326,331,356,357,359,371,391,394,408,409,414,438,470],exclus:[1,3,9,12,16,87,363,378,414,467,477],excurs:453,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,166,190,233,287,333,347,350,362,454,456,466,469,472,484],exemplari:229,exemplifi:387,exert:[6,234,237,288,327,328,329,349],exhaust:[200,362,484],exhibit:[252,355,387,467],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,122,165,166,184,189,190,191,194,199,210,213,215,218,228,278,279,281,331,334,336,337,339,343,352,357,363,394,422,448,454,456,458,459,460,469,470,471,484,485,486],exit:[2,3,11,12,41,57,188,211,347,362,456,457,466,475,484],exlanatori:3,exp:[],expand:[],expans:[12,140,188,469,484],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,146,157,163,185,211,223,228,230,249,274,280,282,283,288,293,331,349,359,376,410,414,453,456,458,460,463,467,472,484],expens:[6,10,71,191,274,278,293,320,331,348,349,359,363,456],experi:[6,13,15,17,210,218,233,242,251,280,292,293,354,358,383,414,467,472],experienc:[6,12,241,242],experiment:[228,348,363,472],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,145,153,185,188,190,191,194,203,204,209,211,213,215,217,252,274,282,293,305,331,333,347,348,351,357,358,362,368,385,397,431,446,456,459,460,463,465,468,479,484,488],explan:[3,6,59,113,140,188,203,251,274,394,452,455,456,458,467],explanatori:[3,8,117,188,202,203,206,207,208,293,357,455,484],explantori:[3,289],explic:413,explicit:[6,9,11,22,44,77,87,113,116,159,173,195,196,217,299,300,335,353,365,366,369,374,376,385,387,398,408,445,452,455,459,462],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,143,152,155,163,165,171,172,174,175,176,177,179,180,182,183,185,188,191,197,207,210,217,224,227,229,231,236,252,254,255,256,257,258,259,267,269,270,272,282,283,285,293,295,296,311,313,314,320,324,328,334,336,337,338,339,342,344,357,363,364,365,367,370,371,372,373,374,375,376,377,378,379,380,382,383,384,385,386,388,389,390,391,392,393,394,397,398,399,400,401,402,403,404,405,406,407,408,411,414,415,416,417,419,424,425,431,432,433,434,435,436,437,439,440,441,442,443,444,445,446,447,449,450,451,458,460,467,468,470,471,477,479],explictli:[16,471],exploit:[9,15,17,276],explor:[118,164],expon:[3,284,286,385,390,393,407,413,425],exponenti:[87,420,440,447,451,472,484],expos:11,exposit:[200,383,384],express:[6,140,151,165,195,196,215,249,274,284,320,326,333,369,385,387,401,410,430,439,484],expressiont:369,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,194,197,198,201,209,210,216,219,223,226,227,228,230,231,232,234,236,238,250,252,256,264,274,275,291,292,293,295,297,302,305,307,311,312,313,314,315,317,318,320,322,325,329,330,390,410,423,424,430,475,476],extent:[1,3,41,45,57,71,163,167,188,199,207,211,234,327,330,348,351,365,426,428,441,455,458,461],exterior:[3,6,329],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,143,144,146,148,151,152,153,154,155,157,158,164,165,166,167,171,191,206,211,213,252,281,282,283,293,308,356,357,360,361,382,391,394,397,410,414,455,456,458,461,470,479,484],extract:[3,6,11,13,36,63,87,107,115,117,119,195,196,286,358,379,388,410,430,456,463,475],extract_atom:11,extract_comput:[11,456],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,190,205,215,217,252,318,387,443,479],extrema:407,extrins:200,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[161,322],f_a:[442,443,444],f_ave:117,f_c:443,f_f:444,f_fix_id:283,f_harm:318,f_i:420,f_id:[6,71,117,119,188,194,202,203,204,205,206,207,208,209,247,310,322,476,484],f_ij:420,f_indent:209,f_int:317,f_jj:91,f_k:420,f_langevin:320,f_max:[283,288],f_msst:250,f_r:[237,442,443,444],f_sigma:369,f_solid:318,f_ss:6,f_temp:237,face:[3,6,57,59,71,153,163,167,199,207,208,325,327,328,329,330,351,390,410,424,458,461],face_threshold:163,facet:163,facil:[0,12],facilit:[6,13],fact:[6,8,16,230,308,318,391,470],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,116,118,140,159,164,167,171,182,188,190,191,195,196,204,211,215,217,218,228,233,236,238,239,250,252,253,256,276,280,292,296,298,300,308,312,316,323,324,325,329,339,349,351,357,363,365,366,369,370,372,374,379,380,381,383,387,391,394,398,399,410,414,416,417,423,425,431,440,445,455,458,461,462,467,470,472,473,476,479,483,484],factori:[3,456],factoriz:348,fail:[3,11,12,59,169,215,218,348,356,358,381,423,456],failur:[121,427,457,484],fairli:[11,414,467,472],faken:73,falcon:233,fall:[3,6,191,206,279,456,484],fals:[86,331,333,484],fame:8,famili:[447,455],familiar:[0,11],fan:420,far:[3,6,12,17,57,59,61,86,188,191,192,211,212,213,215,218,252,274,292,293,308,325,336,339,354,358,359,446,456,458,463,476],farago:236,farrel:[442,444],farther:188,fashion:[6,8,41,71,165,191,194,195,196,201,207,211,213,218,228,230,234,249,250,252,254,255,256,257,258,266,269,270,271,272,282,283,285,293,297,301,307,310,318,320,324,325,326,328,330,358,394,408,461,470,484,487],fasolino:396,fast:[6,7,9,12,13,17,39,188,261,283,321,348,349,371,408,409,439,441,460,465,467,476,485,488],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,143,152,171,172,174,175,176,177,179,180,182,183,185,188,191,194,197,210,211,217,224,227,231,235,236,252,254,255,256,257,258,259,267,269,270,272,280,284,285,293,295,296,308,311,313,315,317,320,324,328,334,336,337,338,339,342,344,348,349,360,361,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,382,383,385,386,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,411,415,416,417,419,424,425,431,439,440,441,442,443,444,446,447,449,450,451,453,467,471,479],fastest:[1,6,14,17,153,207,320,321,363,455],fatal:[3,475],fault:[70,423],faulti:12,fava:390,favor:214,favorit:7,fbmc:315,fcc:[],fcm:[266,484],fdirect:221,fdotr:395,fdti:87,fe2:164,fe3:164,fe_md_boundari:200,featu:8,featur:[],fecr:385,feedback:[7,233],feel:[7,233,234,242,274,329,331,358,414],felling:412,felt:329,femtosecond:483,fene:[],fennel:[379,399],fep:[],ferguson:[6,171,470],fermi:[1,12,15,151,363,444],fermion:[9,387],ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,192,202,203,204,206,207,208,209,237,252,279,282,284,296,322,348,356,357,358,365,455,458,463,467,469,477,484,486],fewer:[1,3,11,15,16,61,242,467],fewest:3,fextern:226,feynman:276,fff:456,ffield:[378,388,422,423],ffmpeg:[3,12,190],ffplai:190,fft:[1,3,7,12,14,15,88,109,110,141,275,348,349,467],fft_inc:[12,349],fft_lib:12,fft_path:12,fftbench:[348,477],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:438,fictiti:[6,197,198,223,226,230,276,292,379,399,403,438],field1:[459,463],field2:459,field:[],fifth:[305,416],figur:[1,3,8,11,12,283,455,456],fij:382,file0:274,file1:[11,13,274,319,333,357,463,465,469],file2:[11,13,319,333,357,463,465,469],file:[],file_from:189,filen:357,filenam:[3,12,13,38,41,56,185,188,190,191,192,200,203,204,205,206,207,208,209,211,216,274,278,281,284,285,286,289,290,293,294,319,320,345,346,347,357,358,364,365,369,379,385,386,388,396,410,411,412,416,420,421,422,423,430,440,441,442,443,444,447,454,455,456,459,460,465,469,476,484,486,487,488],filennam:465,filep:[3,188,191,460,465,488],filepo:290,fill:[7,165,190,279,320,351,359,369,423,461],filter:[191,200],final_integr:8,final_integrate_respa:8,finchham:[6,147,381],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,168,185,192,201,214,215,225,228,251,274,280,288,292,354,356,358,359,379,394,399,403,410,439,441,479,484],find_custom:8,fine:[16,17,169,197,223,318,359,363,484],finer:[140,165,484],finest:348,finger:[165,187,249,461],finish:[6,11,41,211,333,345,347,348,360,362,363,446,463,484,485],finit:[],finni:[7,385,439],finvers:221,fiorin:[9,216],fire:[354,355,356,358,472],firebrick:191,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,150,153,159,161,163,164,166,167,168,172,185,188,189,190,191,192,194,195,203,204,206,207,208,209,211,214,217,228,229,234,239,249,250,251,252,274,276,281,282,283,285,290,293,296,297,305,306,308,309,310,317,318,319,320,322,326,331,333,334,340,351,356,357,358,359,362,363,364,365,368,369,370,372,374,376,378,379,385,387,388,391,392,394,395,396,398,399,403,408,409,410,412,414,416,420,422,423,430,438,440,441,442,443,444,447,451,453,454,455,456,458,459,460,463,465,467,470,471,472,475,476,479,484,485,486,488],fischer:[6,9,19,20,171,374,470],fit:[3,6,9,12,38,56,185,292,308,365,369,396,410,414,434,441,443,466,484],five:[73,151,283,357,369,411,458,472],fix:[],fix_adapt:[159,196,407],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,201,279],fix_evapor:201,fix_flux:200,fix_gcmc:[201,357],fix_gl:230,fix_gld:230,fix_grav:279,fix_id:[3,215,250,252,254,255,256,257,258,280,283],fix_modifi:[],fix_mov:[187,326],fix_nh:8,fix_npt:230,fix_nvt:[201,228],fix_poem:[3,6],fix_pour:[3,218],fix_qbmsst:9,fix_qeq:[3,378],fix_rattl:296,fix_reax_bond:422,fix_rigid:[242,368],fix_saed_vtk:294,fix_setforc:8,fix_shak:296,fix_srd:3,fix_styl:256,fix_temp_rescal:314,fixedpoint:[215,252],fixextern:226,fixid:200,fji:382,flag1:[220,361],flag2:[220,361],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,93,103,104,106,118,160,164,168,188,190,191,192,209,214,216,220,233,236,240,242,248,249,275,282,293,305,307,308,315,319,328,331,346,349,357,361,362,363,365,393,398,410,438,453,455,456,458,459,460,462,463,464,468,484],flag_buck:373,flag_coul:[373,382,403],flag_lj:[382,403],flagfld:[371,408,409],flaghi:[3,371,408,409],flaglog:[371,408,409],flagn:220,flagvf:[371,408,409],flat:[6,320,325,326,330],flavor:[2,7,12],fld:[9,325,371,408,409],flen:366,flex_press:366,flexibl:[3,6,8,166,190,203,207,216,230,253,316,323,387,443,476],flip:[3,6,217,252,327,328],floor:484,flop:12,floralwhit:191,flow:[],fluctuat:[6,64,87,215,228,229,236,239,252,256,274,275,318,320,342],fluid:[],fluid_veloc:243,flush:[3,191,475],flux:[],flv:190,fly:[7,9,12,41,190,194,200,205,218,221,293,296,321,369,476,479],fmackai:9,fmag:219,fmass:276,fmax:[356,476],fmomentum:221,fmsec:[2,191,236,237,249,252,280,293,311,312,467,478,483,485],fname:347,fno:[12,16],fnorm:[356,476],fnpt:221,fnvt:221,foce:394,fock:366,focu:296,fogarti:[9,286,423],foil:[140,274,430],fold:[306,467],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,144,145,151,153,158,161,163,165,166,171,174,175,176,177,179,180,182,183,185,188,189,190,191,194,200,201,202,203,204,205,206,207,208,209,211,216,217,218,221,222,226,228,229,230,233,235,236,237,239,242,250,252,256,257,258,269,270,272,275,276,278,281,282,283,284,286,288,290,292,293,294,296,310,311,312,313,316,317,318,319,320,322,323,331,332,336,337,338,339,342,344,346,351,353,356,357,358,363,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,423,424,425,427,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,447,449,450,451,453,455,456,458,459,460,461,463,465,466,467,470,472,473,474,479,484,485,487],foo:[4,8,11,12,188,1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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":212,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,145,153,154,158,164,165,168,170,184,186,187,188,190,191,192,193,195,196,197,199,200,201,203,207,208,209,212,213,215,216,217,218,222,225,228,229,234,236,237,238,239,240,242,247,250,252,253,256,270,271,275,276,279,280,281,282,283,285,288,290,291,293,294,308,310,315,316,317,318,321,323,325,327,331,343,346,348,349,351,352,354,355,357,359,360,361,363,366,369,371,387,408,409,414,422,423,438,439,453,454,455,458,459,461,463,465,466,467,470,472,474,475,476,477,478,483,485,486,487],"function":484,"long":[205,370,372,373,374,375,379,381,382,399,403,407,417,425],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[195,196],addforc:197,addit:[12,13],addtorqu:198,adiabat:6,adjust_dt:298,adp:364,airebo:365,alloi:385,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:199,arrai:6,aspher:[6,82,144,254,257,260,261,269],atc:[9,200],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,163,199,201,202,282,484],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:210,awpmd:[9,366],balanc:[41,211],barostat:6,basal:67,beck:367,berendsen:[280,311],between:6,binary2txt:13,bodi:[6,8,42,68,262,368],bond:[8,13,69,212,213,214,289],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:369,born:[370,381],boundari:[7,57],box:[6,58,215],brownian:371,buck:[372,373,381],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,171,374,407],chunk:[6,66,71,75,90,93,104,106,114,145,160,162,203],citat:7,class2:[21,43,172,334,375],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[325,377,450],colvar:[9,13,216],com:[74,75,146],comb3:378,comb:[285,378],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,484],compute_modifi:102,condit:7,conduct:[6,316],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:[204,205],cosin:[23,24,25,26,27,28,174],cossq:336,coul:[370,372,373,374,375,379,380,381,392,399,403,407,417,425],coupl:6,creat:213,create_atom:165,create_bond:166,create_box:167,createatom:13,creation:7,csld:312,csvr:312,cubic:401,cuda:[9,14,109,112,143,152,197,210,224,227,231,252,259,295,296,311,313,324,370,372,374,375,385,391,392,399,400,402,405,415,440,442],custom:8,cut:[49,366,372,375,379,382,387,389,399,400,407,413,417],cvff:337,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[379,399],deform:[148,149,217],delete_atom:168,delete_bond:169,delta:24,deposit:218,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488],diagnost:7,diel:380,dielectr:170,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:173,dihedral_styl:[2,171,172,174,175,176,177,178,179,180,181,182,183,184,185],dilat:80,dimens:186,dipol:[6,29,382],direct:221,discuss:6,disp:6,displac:[81,86],displace_atom:187,distribut:[7,12],document:0,dpd:383,drag:219,dreid:[6,393],drude:[6,9,150,220,221,237],dsf:[379,399],dsmc:384,dump:[6,8,188,189,190,192],dump_modifi:191,dynam:284,eam:[13,385],echo:193,edip:386,eff:[9,13,96,97,149,151,156,238,253,263,271,314,387],efield:223,eim:388,elast:6,emac:13,enforce2d:224,ensembl:7,erot:[82,83,84,85],error:3,evapor:225,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488],exp:[27,174],expand:[46,402],extend:[8,11],extern:226,fcc:274,featur:[7,8,484],fene:[45,46],fep:[9,13,87,196],field:[6,7],file:6,finit:6,fix:[2,6,8,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,484],fix_modifi:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330],flow:6,fluid:239,flux:[91,142],forc:[6,7,142,309],fourier:[30,31,175,338],freez:227,from:[6,11],futur:5,gauss:389,gaybern:390,gcmc:228,gener:[1,6,7,13],get:12,gld:229,gle:230,global:6,gpu:[9,15,367,370,372,374,375,377,379,382,383,385,389,390,392,399,400,401,402,413,415,424,425,431,440,441,442,449,450,451],gran:[326,391],granular:6,graviti:231,gromac:392,group2ndx:332,group:[88,331,484],gyrat:[89,90],h5md:[9,188,189],harmon:[32,47,48,49,176,179,325,339,416],hbond:393,heat:[91,142,232],heatconduct:432,helix:177,hertz:[391,426],histo:206,histori:[5,391],hook:391,hourglass_error:122,how:6,hybrid:[33,50,178,340,394],idealga:433,imag:[188,190],imd:233,implicit:374,improp:[8,92],improper_coeff:335,improper_styl:[2,334,336,337,338,339,340,341,342,343,344],includ:345,inclus:8,indent:234,indic:0,individu:2,induc:6,inertia:93,info:[0,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,346],input:[2,6,8],instal:11,instruct:9,integr:[6,7],integrate_tlsph:299,integrate_ulsph:300,intel:[9,16,374,390,399,440],interfac:[6,11],internal_energi:123,introduct:7,invers:221,ipi:235,ipp:13,jul:[],jump:347,kate:13,keyword:414,kim:[9,395],kokko:[9,17],kspace:[2,8,9,321],kspace_modifi:348,kspace_styl:[6,349],label:350,lammp:[0,1,2,6,7,8,11,12],langevin:[236,237,238],lattic:351,lcbop:396,librari:[6,11,12],limit:[264,313],line:[12,265,397],linear:406,lineforc:244,list:[2,398],lj1043:325,lj126:325,lj93:325,lj96:400,lmp2arc:13,lmp2cfg:13,lmp2vmd:13,local:[6,65,68,69,79,92,108,115],log:352,lubric:408,lubricateu:409,make:12,mass:353,math:484,matlab:13,meam:[9,410,411,412],measur:1,meso:[245,246],meso_:99,meso_rho:100,meso_t:101,messag:3,micelle2d:13,mie:413,min_modifi:354,min_styl:355,minim:[8,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,356],misc:9,mod:[320,443],model:[6,7],modifi:8,molecul:357,molfil:[9,188,192],moltempl:13,momentum:[240,248],morri:437,mors:[51,393,415],move:249,move_tri_surf:301,movi:[188,190],mpi:11,msd:[103,104,105],msi2lmp:13,msm:[370,372,374,379,399],msst:250,multi:[6,7,179],multipl:6,nb3b:416,neb:[251,358],neigh_modifi:359,neighbor:360,nemd:6,newton:361,next:362,nharmon:180,noforc:[261,266],non:[6,7],none:[34,52,181,341,418],nongauss:105,nonlinear:53,nph:[252,253,254,255,293],nphug:256,npt:[252,253,257,258,293],nve:[259,260,261,262,263,264,265,266,267,268,293],nvt:[252,253,269,270,271,272,293],omega:106,omp:[9,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,43,45,46,47,48,49,51,53,54,56,171,172,174,175,176,177,179,180,182,183,185,231,252,254,255,256,257,258,259,267,269,270,272,285,334,336,337,338,339,342,344,364,365,367,370,371,372,373,374,375,377,378,379,380,382,383,385,388,389,390,391,392,393,394,397,399,400,401,402,403,404,405,406,407,408,411,412,415,416,417,419,424,425,431,440,441,442,443,444,446,447,449,450,451],onewai:273,open:7,oper:484,opl:182,opt:[19,374,385,399,403,415],optim:1,option:[6,8,12],orient:274,orthogon:6,other:6,output:[6,7,8,12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330],overlai:394,overview:11,packag:[1,9,12,14,15,16,17,18,19,363],pair:[6,107,108],pair_coeff:376,pair_modifi:414,pair_styl:[2,364,365,366,367,368,369,370,371,372,373,374,375,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,450,451],pair_writ:448,pairwis:8,parallel:11,paramet:6,pars:2,partial:152,particl:[6,7,42],partit:452,past:5,per:6,perform:[1,10],peri:419,period:25,phonon:[9,13,275],pimd:276,piston:327,planeforc:277,plastic:111,plastic_strain:124,plastic_strain_r:125,pmb:419,poem:[9,278],point:284,polariz:6,poli:[371,408,409],polym:13,polymorph:420,post:7,potenti:[2,6,8],pour:279,pppm:6,prd:453,pre:7,press:280,pressur:112,previou:12,print:[281,454],problem:[3,4],process:[6,7],processor:455,profil:153,properti:[6,113,114,115,282],pymol_aspher:13,python:[9,11,13,456],qbmsst:283,qeq:[284,285,286],qmmm:[9,287],qtb:[9,288],quadrat:183,quantiti:6,quartic:[35,54],quip:421,quit:457,ramp:154,rattl:296,rdf:116,read_data:458,read_dump:459,read_restart:460,reax:[9,13,286,289,290,422,423],reaxc:9,rebo:365,recent:291,reduc:117,refer:484,reflect:328,region:[8,117,155,156,329,461,484],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,227,228,229,230,231,232,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,288,289,290,291,293,294,295,297,298,299,300,301,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,342,343,344,345,346,347,348,349,351,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,463,464,465,466,467,468,470,471,472,473,474,475,476,477,478,480,481,482,484,485,486,487,488],relax:215,replic:462,replica:[6,7],report:3,requir:12,rerun:463,rescal:[313,314],reset:222,reset_timestep:464,resquar:424,restart2data:13,restart:[6,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,465],restrain:292,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488],rho:126,rhosum:435,rigid:[6,83,98,242,293],ring:342,rotat:157,rule:2,run:[6,11,12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,466],run_styl:467,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,425],self:307,serial:11,set:[6,468],setforc:295,setvel:302,shake:296,share:[11,12],shell:[6,469],shield:284,shift:[26,27,48,49,174],simpl:31,simul:6,size:6,slater:284,slice:119,sllod:[270,271],small:293,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,297,298,299,300,301,302,304,426,427,428,429],smooth:[405,406],sna:140,snad:140,snap:430,snapshot:6,snav:140,soft:[407,431],solver:2,sourc:7,spatial:[207,208],spc:6,speci:290,special:[7,414,484],special_bond:470,sph:[9,432,433,434,435,436,437],sphere:[84,85,158,208,242,255,258,267,272],spheric:6,spline:[411,412],spring:[305,306,307,318],squar:28,srd:[308,330],srp:438,standard:9,start:[12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330],state:310,stationari:246,stop:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330],store:[309,310],strategi:1,streitz:379,stress:[141,142],structur:2,style:[1,2,6,8],submit:8,suffix:471,summari:6,swap:[201,214],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,480,481,482,483,484,485,486,487,488],system:6,tabl:[0,6,38,56,185,441,442],tad:472,taitwat:[436,437],talli:142,temp:[143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,311,312,313,314],temper:473,temperatur:6,tersoff:[442,443,444],test:11,tfmc:315,thermal:[6,316],thermo:[6,474],thermo_modifi:475,thermo_styl:476,thermodynam:[6,8],thermostat:6,thole:445,time:[6,209],timer:477,timestep:478,tip3p:6,tip4p:[6,379,399,403,407],tip:12,tlsph:427,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:319,tool:[12,13],torqu:160,transform:221,tri:[268,446],tri_surfac:428,triangle_mesh_vertic:134,triclin:6,tstat:383,ttm:320,tune:321,type:7,ulsph:429,ulsph_num_neigh:135,ulsph_strain:136,ulsph_strain_r:137,ulsph_stress:138,umbrella:344,uncomput:480,undump:481,unfix:482,unit:483,user:[9,12,14,16,18],vacf:161,valu:[6,484],variabl:[6,8,484],variou:1,vashishta:447,vcm:162,vector:[6,322,484],veloc:485,version:[0,5,12],via:12,vim:13,viscos:[6,323],viscou:[243,324],visual:6,vol:139,voronoi:[9,163],vtk:294,wall:[6,325,326,327,328,329,330],wall_surfac:304,warn:3,water:6,weight:206,what:[7,12],wolf:[370,379],wrapper:11,write:6,write_data:486,write_dump:487,write_restart:488,xmgrace:13,xmovi:13,xrd:164,xtc:9,yukawa:[449,450],zbl:[444,451]}})
\ No newline at end of file
diff --git a/examples/USER/lb/polymer/in.polymer b/examples/USER/lb/polymer/in.polymer_default_gamma
similarity index 75%
copy from examples/USER/lb/polymer/in.polymer
copy to examples/USER/lb/polymer/in.polymer_default_gamma
index 932ce989b..4344dc0ef 100755
--- a/examples/USER/lb/polymer/in.polymer
+++ b/examples/USER/lb/polymer/in.polymer_default_gamma
@@ -1,105 +1,107 @@
#===========================================================================#
# polymer test #
# #
# Run consists of a lone 32-bead coarse-grained polymer #
# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
# #
# Here, gamma (used in the calculation of the monomer-fluid interaction #
# force) is set by the user (gamma = 0.03 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# Sample output from this run can be found in the file: #
# 'dump.polymer.lammpstrj' #
# and viewed using, e.g., the VMD software. #
# #
-# Santtu Ollila #
-# santtu.ollila@aalto.fi #
-# Aalto University #
-# August 14, 2013 #
#===========================================================================#
units nano
dimension 3
boundary p p p
atom_style hybrid molecular
special_bonds fene
read_data data.polymer
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
#----------------------------------------------------------------------------
neighbor 0.5 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# each monomer (use a truncated and shifted Lennard-Jones potential).
#----------------------------------------------------------------------------
bond_style fene
bond_coeff 1 60.0 2.25 4.14195 1.5
pair_style lj/cut 1.68369
pair_coeff 1 1 4.14195 1.5 1.68369
pair_coeff 1 2 4.14195 1.5 1.68369
pair_coeff 2 2 0 1.0
mass * 0.000000771064
timestep 0.00003
#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each monomer which
# do not interact with the fluid, but are used to implement the hard-sphere
# interactions.
# FluidAtoms are the particles representing the surface of the monomer
-# which do interact with the fluid.
+# which do interact with the fluid. Monomer surface is shell of radius 0.7
#----------------------------------------------------------------------------
group ForceAtoms type 1
group FluidAtoms type 2
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicity apply a force back on to these
-# particles. This is accomplished through the use of the rigid_pc_sphere
+# particles. This is accomplished through the use of the lb/viscous
# fix).
-# Use the LB integration scheme of Ollila et. al. (for stability reasons,
-# this integration scheme should be used when a large user set value for
-# gamma is specified), a fluid viscosity = 0.023333333,
-# fluid density= 0.0000166368,
-# value for gamma=0.03, lattice spacing dx=1.0, and mass unit, dm=0.0000166368.
+# Uses the standard LB integration scheme, fluid viscosity = 0.023333333,
+# fluid density= 0.0000166368, lattice spacing dx=1.0, and mass unit,
+# dm=0.0000166368.
+# Use the default method to calculate the interaction force between the
+# particles and the fluid. This calculation requires the surface area
+# of the composite object represented by each particle node. By default
+# this area is assumed equal to dx*dx; however, since this is not the case
+# here, it is input through the setArea keyword (i.e. particles of type 2
+# correspond to a surface area of 0.2025=4 Pi R^2/N ).
+# Use the trilinear interpolation stencil to distribute the force from
+# a given particle onto the fluid mesh (results in a smaller hydrodynamic
+# radius than if the Peskin stencil is used).
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=15003). This enables the particles to undergo Brownian motion in
# the fluid.
#----------------------------------------------------------------------------
-fix 1 FluidAtoms lb/fluid 5 1 0.023333333 0.0000166368 setGamma 0.03 dx 1.0 dm 0.0000166368 noise 300.0 15003
+fix 1 FluidAtoms lb/fluid 3 1 0.023333333 0.0000166368 setArea 2 0.20525 dx 1.0 dm 0.0000166368 noise 300.0 15003
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid
# spherical object.
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
# shell) should move and rotate together, this fix is applied to all of
# the atoms in the system. However, since the central atoms should not
-# feel a force due to the fluid, they are excluded from the force
-# calculation through the use of the 'innerNodes' keyword.
-# NOTE: This fix should only be used when the user specifies a value for
-# gamma (through the setGamma keyword) in the lb_fluid fix.
+# feel a force due to the fluid, they are excluded from the fluid force
+# calculation.
#----------------------------------------------------------------------------
-fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms
+fix 2 FluidAtoms lb/viscous
+fix 3 all rigid molecule
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 10000 timesteps to zero out the
# total (particle plus fluid) momentum in the system.
#----------------------------------------------------------------------------
-fix 3 all lb/momentum 10000 linear 1 1 1
+fix 4 all lb/momentum 10000 linear 1 1 1
#----------------------------------------------------------------------------
# Write position and velocity coordinates into a file every 2000 time steps.
#----------------------------------------------------------------------------
-dump 1 ForceAtoms custom 2000 dump.polymer.lammpstrj id x y z vx vy vz
+dump 1 ForceAtoms custom 2000 dump.polymer_default_gamma.lammpstrj id x y z vx vy vz
run 2000001
diff --git a/examples/USER/lb/polymer/in.polymer b/examples/USER/lb/polymer/in.polymer_setgamma
similarity index 96%
rename from examples/USER/lb/polymer/in.polymer
rename to examples/USER/lb/polymer/in.polymer_setgamma
index 932ce989b..b5108a60f 100755
--- a/examples/USER/lb/polymer/in.polymer
+++ b/examples/USER/lb/polymer/in.polymer_setgamma
@@ -1,105 +1,105 @@
#===========================================================================#
# polymer test #
# #
# Run consists of a lone 32-bead coarse-grained polymer #
# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
# #
# Here, gamma (used in the calculation of the monomer-fluid interaction #
# force) is set by the user (gamma = 0.03 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# Sample output from this run can be found in the file: #
# 'dump.polymer.lammpstrj' #
# and viewed using, e.g., the VMD software. #
# #
# Santtu Ollila #
# santtu.ollila@aalto.fi #
# Aalto University #
# August 14, 2013 #
#===========================================================================#
units nano
dimension 3
boundary p p p
atom_style hybrid molecular
special_bonds fene
read_data data.polymer
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
#----------------------------------------------------------------------------
neighbor 0.5 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# each monomer (use a truncated and shifted Lennard-Jones potential).
#----------------------------------------------------------------------------
bond_style fene
bond_coeff 1 60.0 2.25 4.14195 1.5
pair_style lj/cut 1.68369
pair_coeff 1 1 4.14195 1.5 1.68369
pair_coeff 1 2 4.14195 1.5 1.68369
pair_coeff 2 2 0 1.0
mass * 0.000000771064
timestep 0.00003
#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each monomer which
# do not interact with the fluid, but are used to implement the hard-sphere
# interactions.
# FluidAtoms are the particles representing the surface of the monomer
# which do interact with the fluid.
#----------------------------------------------------------------------------
group ForceAtoms type 1
group FluidAtoms type 2
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicity apply a force back on to these
# particles. This is accomplished through the use of the rigid_pc_sphere
# fix).
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for
# gamma is specified), a fluid viscosity = 0.023333333,
# fluid density= 0.0000166368,
# value for gamma=0.03, lattice spacing dx=1.0, and mass unit, dm=0.0000166368.
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=15003). This enables the particles to undergo Brownian motion in
# the fluid.
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 5 1 0.023333333 0.0000166368 setGamma 0.03 dx 1.0 dm 0.0000166368 noise 300.0 15003
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid
# spherical object.
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
# shell) should move and rotate together, this fix is applied to all of
# the atoms in the system. However, since the central atoms should not
# feel a force due to the fluid, they are excluded from the force
# calculation through the use of the 'innerNodes' keyword.
# NOTE: This fix should only be used when the user specifies a value for
# gamma (through the setGamma keyword) in the lb_fluid fix.
#----------------------------------------------------------------------------
fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 10000 timesteps to zero out the
# total (particle plus fluid) momentum in the system.
#----------------------------------------------------------------------------
fix 3 all lb/momentum 10000 linear 1 1 1
#----------------------------------------------------------------------------
# Write position and velocity coordinates into a file every 2000 time steps.
#----------------------------------------------------------------------------
-dump 1 ForceAtoms custom 2000 dump.polymer.lammpstrj id x y z vx vy vz
+dump 1 ForceAtoms custom 2000 dump.polymer_setgamma.lammpstrj id x y z vx vy vz
run 2000001
diff --git a/examples/USER/lb/polymer/out.polymer b/examples/USER/lb/polymer/out.polymer
deleted file mode 100755
index 91a1c4d60..000000000
--- a/examples/USER/lb/polymer/out.polymer
+++ /dev/null
@@ -1,19 +0,0 @@
-LAMMPS (22 Feb 2013)
-Scanning data file ...
- 1 = max bonds/atom
-Reading data file ...
- orthogonal box = (0 0 0) to (40 40 40)
- 2 by 2 by 2 MPI processor grid
- 992 atoms
- 31 bonds
-Finding 1-2 1-3 1-4 neighbors ...
- 2 = max # of 1-2 neighbors
- 2 = max # of special neighbors
-32 atoms in group ForceAtoms
-960 atoms in group FluidAtoms
-Using a lattice-Boltzmann grid of 40 by 40 by 40 total grid points. (fix_lb_fluid.cpp:354)
-32 rigid bodies with 992 atoms
-Setting up run ...
-Memory usage per processor = 0.539707 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0 -8.2758489 2790.7741 2782.4982 1.8503717e-20
diff --git a/examples/USER/lb/polymer/out.polymer_default_gamma b/examples/USER/lb/polymer/out.polymer_default_gamma
new file mode 100644
index 000000000..438e1c2ca
--- /dev/null
+++ b/examples/USER/lb/polymer/out.polymer_default_gamma
@@ -0,0 +1,83 @@
+LAMMPS (10 Aug 2015)
+Reading data file ...
+ orthogonal box = (0 0 0) to (40 40 40)
+ 2 by 2 by 4 MPI processor grid
+ reading atoms ...
+ 992 atoms
+ scanning bonds ...
+ 1 = max bonds/atom
+ reading bonds ...
+ 31 bonds
+Finding 1-2 1-3 1-4 neighbors ...
+ Special bond factors lj: 0 1 1
+ Special bond factors coul: 0 1 1
+ 2 = max # of 1-2 neighbors
+ 2 = max # of special neighbors
+32 atoms in group ForceAtoms
+960 atoms in group FluidAtoms
+Using a lattice-Boltzmann grid of 40 by 40 by 40 total grid points. (../fix_lb_fluid.cpp:385)
+32 rigid bodies with 992 atoms
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ master list distance cutoff = 2.18369
+ ghost atom cutoff = 2.18369
+Setting up Verlet run ...
+ Unit style : nano
+ Current step: 0
+ Time step : 3e-05
+Memory usage per processor = 0.111926 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -8.2758489 2790.7741 2782.4982 1.9081958e-20
+ 2000001 4.3017148 0 2792.6037 2798.2163 -0.00077006865
+Loop time of 51900 on 16 procs for 2000001 steps with 992 atoms
+
+Pair time (%) = 4.33729 (0.00835701)
+Bond time (%) = 3.33134 (0.00641876)
+Neigh time (%) = 35.1247 (0.0676777)
+Comm time (%) = 61.528 (0.118551)
+Outpt time (%) = 0.361813 (0.000697135)
+Other time (%) = 51795.3 (99.7983)
+
+Nlocal: 62 ave 465 max 0 min
+Histogram: 11 0 3 1 0 0 0 0 0 1
+Nghost: 94.8125 ave 340 max 0 min
+Histogram: 9 0 0 0 4 0 0 1 0 2
+Neighs: 0.25 ave 2 max 0 min
+Histogram: 13 0 0 0 0 2 0 0 0 1
+
+Total # of neighbors = 4
+Ave neighs/atom = 0.00403226
+Ave special neighs/atom = 0.0625
+Neighbor list builds = 23853
+Dangerous builds = 0
+
+------------------------------------------------------------
+Sender: LSF System <lsfadmin@lsfhost.localdomain>
+Subject: Job 883849: </opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer_default_gamma> Done
+
+Job </opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer_default_gamma> was submitted from host <req770> by user <colin>.
+Job was executed on host(s) <16*lsfhost.localdomain>, in queue <mpi>, as user <colin>.
+</home/colin> was used as the home directory.
+</home/colin/lammps-10Aug15/examples/USER/lb/tested/polymer_default> was used as the working directory.
+Started at Mon Aug 24 11:13:12 2015
+Results reported at Tue Aug 25 01:38:50 2015
+
+Your job looked like:
+
+------------------------------------------------------------
+# LSBATCH: User input
+/opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer_default_gamma
+------------------------------------------------------------
+
+Successfully completed.
+
+Resource usage summary:
+
+ CPU time : 829343.88 sec.
+ Max Memory : 43 MB
+ Max Swap : 805 MB
+
+
+The output (if any) is above this job summary.
+
diff --git a/examples/USER/lb/polymer/out.polymer_setgamma b/examples/USER/lb/polymer/out.polymer_setgamma
new file mode 100644
index 000000000..5dc141c08
--- /dev/null
+++ b/examples/USER/lb/polymer/out.polymer_setgamma
@@ -0,0 +1,83 @@
+LAMMPS (10 Aug 2015)
+Reading data file ...
+ orthogonal box = (0 0 0) to (40 40 40)
+ 2 by 2 by 4 MPI processor grid
+ reading atoms ...
+ 992 atoms
+ scanning bonds ...
+ 1 = max bonds/atom
+ reading bonds ...
+ 31 bonds
+Finding 1-2 1-3 1-4 neighbors ...
+ Special bond factors lj: 0 1 1
+ Special bond factors coul: 0 1 1
+ 2 = max # of 1-2 neighbors
+ 2 = max # of special neighbors
+32 atoms in group ForceAtoms
+960 atoms in group FluidAtoms
+Using a lattice-Boltzmann grid of 40 by 40 by 40 total grid points. (../fix_lb_fluid.cpp:385)
+32 rigid bodies with 992 atoms
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ master list distance cutoff = 2.18369
+ ghost atom cutoff = 2.18369
+Setting up Verlet run ...
+ Unit style : nano
+ Current step: 0
+ Time step : 3e-05
+Memory usage per processor = 0.108554 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -8.2758489 2790.7741 2782.4982 -0.00085093693
+ 2000001 0.5548925 0 2792.3403 2803.7286 -0.0037777326
+Loop time of 50862.3 on 16 procs for 2000001 steps with 992 atoms
+
+Pair time (%) = 4.10128 (0.0080635)
+Bond time (%) = 3.29621 (0.00648066)
+Neigh time (%) = 40.0195 (0.0786822)
+Comm time (%) = 89.3201 (0.175612)
+Outpt time (%) = 1.05399 (0.00207224)
+Other time (%) = 50724.5 (99.7291)
+
+Nlocal: 62 ave 501 max 0 min
+Histogram: 14 0 0 0 0 0 0 0 0 2
+Nghost: 29 ave 259 max 0 min
+Histogram: 14 0 0 0 0 0 0 1 0 1
+Neighs: 0.375 ave 3 max 0 min
+Histogram: 14 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 6
+Ave neighs/atom = 0.00604839
+Ave special neighs/atom = 0.0625
+Neighbor list builds = 30671
+Dangerous builds = 0
+
+------------------------------------------------------------
+Sender: LSF System <lsfadmin@lsfhost.localdomain>
+Subject: Job 883848: </opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer> Done
+
+Job </opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer> was submitted from host <req770> by user <colin>.
+Job was executed on host(s) <16*lsfhost.localdomain>, in queue <mpi>, as user <colin>.
+</home/colin> was used as the home directory.
+</home/colin/lammps-10Aug15/examples/USER/lb/tested/polymer> was used as the working directory.
+Started at Mon Aug 24 11:12:37 2015
+Results reported at Tue Aug 25 01:20:46 2015
+
+Your job looked like:
+
+------------------------------------------------------------
+# LSBATCH: User input
+/opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer
+------------------------------------------------------------
+
+Successfully completed.
+
+Resource usage summary:
+
+ CPU time : 812767.44 sec.
+ Max Memory : 44 MB
+ Max Swap : 812 MB
+
+
+The output (if any) is above this job summary.
+
diff --git a/src/CORESHELL/compute_temp_cs.cpp b/src/CORESHELL/compute_temp_cs.cpp
index cd577291f..8714b5201 100644
--- a/src/CORESHELL/compute_temp_cs.cpp
+++ b/src/CORESHELL/compute_temp_cs.cpp
@@ -1,499 +1,489 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Hendrik Heenen (Technical University of Munich)
(hendrik.heenen at mytum.com)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "stdlib.h"
#include "string.h"
#include "math.h"
#include "compute_temp_cs.h"
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "update.h"
#include "force.h"
#include "group.h"
#include "modify.h"
#include "fix.h"
#include "fix_store.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 5) error->all(FLERR,"Illegal compute temp/cs command");
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Compute temp/cs used when bonds are not allowed");
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 1;
extarray = 0;
// find and define groupbits for core and shell groups
cgroup = group->find(arg[3]);
if (cgroup == -1)
error->all(FLERR,"Cannot find specified group ID for core particles");
groupbit_c = group->bitmask[cgroup];
sgroup = group->find(arg[4]);
if (sgroup == -1)
error->all(FLERR,"Cannot find specified group ID for shell particles");
groupbit_s = group->bitmask[sgroup];
// create a new fix STORE style
// id = compute-ID + COMPUTE_STORE, fix group = compute group
int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
id_fix = new char[n];
strcpy(id_fix,id);
strcat(id_fix,"_COMPUTE_STORE");
char **newarg = new char*[5];
newarg[0] = id_fix;
newarg[1] = group->names[igroup];
newarg[2] = (char *) "STORE";
newarg[3] = (char *) "0";
newarg[4] = (char *) "1";
modify->add_fix(5,newarg);
fix = (FixStore *) modify->fix[modify->nfix-1];
delete [] newarg;
// set fix store values = 0 for now
// fill them in via setup() once Comm::borders() has been called
// skip if resetting from restart file
if (fix->restart_reset) {
fix->restart_reset = 0;
firstflag = 0;
} else {
double *partner = fix->vstore;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) partner[i] = ubuf(0).d;
firstflag = 1;
}
// allocate memory
vector = new double[6];
maxatom = 0;
vint = NULL;
// set comm size needed by this Compute
comm_reverse = 1;
}
/* ---------------------------------------------------------------------- */
ComputeTempCS::~ComputeTempCS()
{
// check nfix in case all fixes have already been deleted
if (modify->nfix) modify->delete_fix(id_fix);
delete [] id_fix;
delete [] vector;
memory->destroy(vint);
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::init()
{
if (comm->ghost_velocity == 0)
error->all(FLERR,"Compute temp/cs requires ghost atoms store velocity");
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::setup()
{
if (firstflag) {
firstflag = 0;
// insure # of core atoms = # of shell atoms
int ncores = group->count(cgroup);
nshells = group->count(sgroup);
if (ncores != nshells)
error->all(FLERR,"Number of core atoms != number of shell atoms");
// for each C/S pair:
// set partner IDs of both atoms if this atom stores bond between them
// will set partner IDs for ghost atoms if needed by another proc
// nall loop insures all ghost atom partner IDs are set before reverse comm
int *num_bond = atom->num_bond;
tagint **bond_atom = atom->bond_atom;
tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *partner = fix->vstore;
tagint partnerID;
int nall = nlocal + atom->nghost;
for (int i = nlocal; i < nall; i++) partner[i] = ubuf(0).d;
int i,j,m,match;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit_c || mask[i] & groupbit_s) {
for (m = 0; m < num_bond[i]; m++) {
partnerID = bond_atom[i][m];
j = atom->map(partnerID);
if (j == -1) error->one(FLERR,"Core/shell partner atom not found");
match = 0;
if (mask[i] & groupbit_c && mask[j] & groupbit_s) match = 1;
if (mask[i] & groupbit_s && mask[j] & groupbit_c) match = 1;
if (match) {
partner[i] = ubuf(partnerID).d;
partner[j] = ubuf(tag[i]).d;
}
}
}
}
// reverse comm to acquire unknown partner IDs from ghost atoms
// only needed if newton_bond = on
if (force->newton_bond) comm->reverse_comm_compute(this);
// check that all C/S partners were found
int flag = 0;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit_c || mask[i] & groupbit_s) {
partnerID = (tagint) ubuf(partner[i]).i;
if (partnerID == 0) flag = 1;
}
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) error->all(FLERR,"Core/shell partners were not all found");
}
// calculate DOF for temperature
dof_compute();
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::dof_compute()
{
adjust_dof_fix();
int nper = domain->dimension;
natoms_temp = group->count(igroup);
dof = nper * natoms_temp;
dof -= nper * nshells;
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
}
/* ---------------------------------------------------------------------- */
double ComputeTempCS::compute_scalar()
{
double vthermal[3];
invoked_scalar = update->ntimestep;
vcm_pairs();
// calculate thermal scalar in respect to atom velocities as center-of-mass
// velocities of its according core/shell pairs
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double t = 0.0;
for (int i = 0; i < nlocal; i++){
if (mask[i] & groupbit) {
vthermal[0] = v[i][0] - vint[i][0];
vthermal[1] = v[i][1] - vint[i][1];
vthermal[2] = v[i][2] - vint[i][2];
if (rmass)
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * rmass[i];
else
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * mass[type[i]];
}
}
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::compute_vector()
{
- double vthermal[3];
-
invoked_vector = update->ntimestep;
- vcm_pairs();
-
- // calculate thermal vector in respect to atom velocities as center-of-mass
- // velocities of its according C/S pairs
-
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double massone;
double t[6];
for (int i = 0; i < 6; i++) t[i] = 0.0;
for (int i = 0; i < nlocal; i++){
if (mask[i] & groupbit) {
- vthermal[0] = v[i][0] - vint[i][0];
- vthermal[1] = v[i][1] - vint[i][1];
- vthermal[2] = v[i][2] - vint[i][2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
- t[0] += massone * vthermal[0]*vthermal[0];
- t[1] += massone * vthermal[1]*vthermal[1];
- t[2] += massone * vthermal[2]*vthermal[2];
- t[3] += massone * vthermal[0]*vthermal[1];
- t[4] += massone * vthermal[0]*vthermal[2];
- t[5] += massone * vthermal[1]*vthermal[2];
+ t[0] += massone * v[i][0]*v[i][0];
+ t[1] += massone * v[i][1]*v[i][1];
+ t[2] += massone * v[i][2]*v[i][2];
+ t[3] += massone * v[i][0]*v[i][1];
+ t[4] += massone * v[i][0]*v[i][2];
+ t[5] += massone * v[i][1]*v[i][2];
}
}
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::vcm_pairs()
{
int i,j;
double massone,masstwo;
double vcm[3];
// reallocate vint if necessary
int nlocal = atom->nlocal;
if (nlocal > maxatom) {
memory->destroy(vint);
maxatom = atom->nmax;
memory->create(vint,maxatom,3,"temp/cs:vint");
}
// vcm = COM velocity of each CS pair
// vint = internal velocity of each C/S atom, used as bias
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
double *partner = fix->vstore;
tagint partnerID;
for (i = 0; i < nlocal; i++) {
if ((mask[i] & groupbit) &&
(mask[i] & groupbit_c || mask[i] & groupbit_s)) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
vcm[0] = v[i][0]*massone;
vcm[1] = v[i][1]*massone;
vcm[2] = v[i][2]*massone;
partnerID = (tagint) ubuf(partner[i]).i;
j = atom->map(partnerID);
if (j == -1) error->one(FLERR,"Core/shell partner atom not found");
if (rmass) masstwo = rmass[j];
else masstwo = mass[type[j]];
vcm[0] += v[j][0]*masstwo;
vcm[1] += v[j][1]*masstwo;
vcm[2] += v[j][2]*masstwo;
vcm[0] /= (massone + masstwo);
vcm[1] /= (massone + masstwo);
vcm[2] /= (massone + masstwo);
vint[i][0] = v[i][0] - vcm[0];
vint[i][1] = v[i][1] - vcm[1];
vint[i][2] = v[i][2] - vcm[2];
} else vint[i][0] = vint[i][1] = vint[i][2] = 0.0;
}
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
thermal velocity in this case is COM velocity of C/S pair
------------------------------------------------------------------------- */
void ComputeTempCS::remove_bias(int i, double *v)
{
v[0] -= vint[i][0];
v[1] -= vint[i][1];
v[2] -= vint[i][2];
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
thermal velocity in this case is COM velocity of C/S pair
------------------------------------------------------------------------- */
void ComputeTempCS::remove_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] -= vint[i][0];
v[i][1] -= vint[i][1];
v[i][2] -= vint[i][2];
}
}
/* ----------------------------------------------------------------------
reset thermal velocity of all atoms to be consistent with bias
called from velocity command after it creates thermal velocities
this resets each atom's velocity to COM velocity of C/S pair
------------------------------------------------------------------------- */
void ComputeTempCS::reapply_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// recalculate current COM velocities
vcm_pairs();
// zero vint after using ti so that Velocity call to restore_bias_all()
// will not further alter the velocities within a C/S pair
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] -= vint[i][0];
v[i][1] -= vint[i][1];
v[i][2] -= vint[i][2];
vint[i][0] = 0.0;
vint[i][1] = 0.0;
vint[i][2] = 0.0;
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempCS::restore_bias(int i, double *v)
{
v[0] += vint[i][0];
v[1] += vint[i][1];
v[2] += vint[i][2];
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTempCS::restore_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] += vint[i][0];
v[i][1] += vint[i][1];
v[i][2] += vint[i][2];
}
}
/* ---------------------------------------------------------------------- */
int ComputeTempCS::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
double *partner = fix->vstore;
m = 0;
last = first + n;
for (i = first; i < last; i++) buf[m++] = partner[i];
return m;
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
double *partner = fix->vstore;
tagint partnerID;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
partnerID = (tagint) ubuf(buf[m++]).i;
if (partnerID) partner[j] = ubuf(partnerID).d;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeTempCS::memory_usage()
{
double bytes = (bigint) maxatom * 3 * sizeof(double);
return bytes;
}
diff --git a/src/MAKE/MINE/Makefile.intel b/src/MAKE/MINE/Makefile.intel
new file mode 100755
index 000000000..3acf37769
--- /dev/null
+++ b/src/MAKE/MINE/Makefile.intel
@@ -0,0 +1,115 @@
+# serial = g++ compiler, no MPI, internal FFT
+
+SHELL = /bin/sh
+
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC = icpc
+CCFLAGS = -g -O3
+SHFLAGS = -fPIC
+DEPFLAGS = -M
+
+LINK = icpc
+LINKFLAGS = -g -O -static-intel
+LIB =
+SIZE = size
+
+ARCHIVE = ar
+ARFLAGS = -rc
+SHLIBFLAGS = -shared
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings, all OPTIONAL
+# specify settings for LAMMPS features you will use
+# if you change any -D setting, do full re-compile after "make clean"
+
+# LAMMPS ifdef settings
+# see possible settings in Section 2.2 (step 4) of manual
+
+LMP_INC = -DLAMMPS_GZIP
+
+# MPI library
+# see discussion in Section 2.2 (step 5) of manual
+# MPI wrapper compiler/linker can provide this info
+# can point to dummy MPI library in src/STUBS as in Makefile.serial
+# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -I../STUBS
+MPI_PATH = -L../STUBS
+MPI_LIB = -lmpi_stubs
+
+# FFT library
+# see discussion in Section 2.2 (step 6) of manaul
+# can be left blank to use provided KISS FFT library
+# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC =
+FFT_PATH =
+FFT_LIB =
+
+# JPEG and/or PNG library
+# see discussion in Section 2.2 (step 7) of manual
+# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
+# INC = path(s) for jpeglib.h and/or png.h
+# PATH = path(s) for JPEG library and/or PNG library
+# LIB = name(s) of JPEG library and/or PNG library
+
+JPG_INC =
+JPG_PATH =
+JPG_LIB =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# do not edit this section
+
+include Makefile.package.settings
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
+EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
+EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)
+
+# Path to src files
+
+vpath %.cpp ..
+vpath %.h ..
+
+# Link target
+
+$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+ $(SIZE) $(EXE)
+
+# Library targets
+
+lib: $(OBJ) $(EXTRA_LINK_DEPENDS)
+ $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
+shlib: $(OBJ) $(EXTRA_LINK_DEPENDS)
+ $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
+ $(OBJ) $(EXTRA_LIB) $(LIB)
+
+# Compilation rules
+
+%.o:%.cpp $(EXTRA_CPP_DEPENDS)
+ $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+%.d:%.cpp $(EXTRA_CPP_DEPENDS)
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
+
+%.o:%.cu $(EXTRA_CPP_DEPENDS)
+ $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+# Individual dependencies
+
+DEPENDS = $(OBJ:.o=.d)
+sinclude $(DEPENDS)
diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp
index 6e050f720..bede607d7 100644
--- a/src/MC/fix_bond_break.cpp
+++ b/src/MC/fix_bond_break.cpp
@@ -1,858 +1,858 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "math.h"
#include "mpi.h"
#include "string.h"
#include "stdlib.h"
#include "fix_bond_break.h"
#include "update.h"
#include "respa.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define DELTA 16
/* ---------------------------------------------------------------------- */
FixBondBreak::FixBondBreak(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 6) error->all(FLERR,"Illegal fix bond/break command");
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal fix bond/break command");
force_reneighbor = 1;
next_reneighbor = -1;
vector_flag = 1;
size_vector = 2;
global_freq = 1;
extvector = 0;
btype = force->inumeric(FLERR,arg[4]);
cutoff = force->numeric(FLERR,arg[5]);
if (btype < 1 || btype > atom->nbondtypes)
error->all(FLERR,"Invalid bond type in fix bond/break command");
if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/break command");
cutsq = cutoff*cutoff;
// optional keywords
fraction = 1.0;
int seed = 12345;
int iarg = 6;
while (iarg < narg) {
if (strcmp(arg[iarg],"prob") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/break command");
fraction = force->numeric(FLERR,arg[iarg+1]);
seed = force->inumeric(FLERR,arg[iarg+2]);
if (fraction < 0.0 || fraction > 1.0)
error->all(FLERR,"Illegal fix bond/break command");
if (seed <= 0) error->all(FLERR,"Illegal fix bond/break command");
iarg += 3;
} else error->all(FLERR,"Illegal fix bond/break command");
}
// error check
if (atom->molecular != 1)
error->all(FLERR,"Cannot use fix bond/break with non-molecular systems");
// initialize Marsaglia RNG with processor-unique seed
random = new RanMars(lmp,seed + me);
// set comm sizes needed by this fix
// forward is big due to comm of broken bonds and 1-2 neighbors
comm_forward = MAX(2,2+atom->maxspecial);
comm_reverse = 2;
// allocate arrays local to this fix
nmax = 0;
partner = finalpartner = NULL;
distsq = NULL;
maxbreak = 0;
broken = NULL;
// copy = special list for one atom
// size = ms^2 + ms is sufficient
- // b/c in recreate_special() neighs of all 1-2s are added,
+ // b/c in rebuild_special_one() neighs of all 1-2s are added,
// then a dedup(), then neighs of all 1-3s are added, then final dedup()
// this means intermediate size cannot exceed ms^2 + ms
int maxspecial = atom->maxspecial;
copy = new tagint[maxspecial*maxspecial + maxspecial];
// zero out stats
breakcount = 0;
breakcounttotal = 0;
}
/* ---------------------------------------------------------------------- */
FixBondBreak::~FixBondBreak()
{
delete random;
// delete locally stored arrays
memory->destroy(partner);
memory->destroy(finalpartner);
memory->destroy(distsq);
memory->destroy(broken);
delete [] copy;
}
/* ---------------------------------------------------------------------- */
int FixBondBreak::setmask()
{
int mask = 0;
mask |= POST_INTEGRATE;
mask |= POST_INTEGRATE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::init()
{
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
// enable angle/dihedral/improper breaking if any defined
if (atom->nangles) angleflag = 1;
else angleflag = 0;
if (atom->ndihedrals) dihedralflag = 1;
else dihedralflag = 0;
if (atom->nimpropers) improperflag = 1;
else improperflag = 0;
if (force->improper) {
if (force->improper_match("class2") || force->improper_match("ring"))
error->all(FLERR,"Cannot yet use fix bond/break with this "
"improper style");
}
lastcheck = -1;
// DEBUG
//print_bb();
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::post_integrate()
{
int i,j,k,m,n,i1,i2,n1,n3,type;
double delx,dely,delz,rsq;
tagint *slist;
if (update->ntimestep % nevery) return;
// check that all procs have needed ghost atoms within ghost cutoff
// only if neighbor list has changed since last check
if (lastcheck < neighbor->lastcall) check_ghosts();
// acquire updated ghost atom positions
// necessary b/c are calling this after integrate, but before Verlet comm
comm->forward_comm();
// resize bond partner list and initialize it
// probability array overlays distsq array
// needs to be atom->nmax in length
if (atom->nmax > nmax) {
memory->destroy(partner);
memory->destroy(finalpartner);
memory->destroy(distsq);
nmax = atom->nmax;
memory->create(partner,nmax,"bond/break:partner");
memory->create(finalpartner,nmax,"bond/break:finalpartner");
memory->create(distsq,nmax,"bond/break:distsq");
probability = distsq;
}
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
for (i = 0; i < nall; i++) {
partner[i] = 0;
finalpartner[i] = 0;
distsq[i] = 0.0;
}
// loop over bond list
// setup possible partner list of bonds to break
double **x = atom->x;
tagint *tag = atom->tag;
int *mask = atom->mask;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
for (n = 0; n < nbondlist; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
if (!(mask[i1] & groupbit)) continue;
if (!(mask[i2] & groupbit)) continue;
if (type != btype) continue;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutsq) continue;
if (rsq > distsq[i1]) {
partner[i1] = tag[i2];
distsq[i1] = rsq;
}
if (rsq > distsq[i2]) {
partner[i2] = tag[i1];
distsq[i2] = rsq;
}
}
// reverse comm of partner info
if (force->newton_bond) comm->reverse_comm_fix(this);
// each atom now knows its winning partner
// for prob check, generate random value for each atom with a bond partner
// forward comm of partner and random value, so ghosts have it
if (fraction < 1.0) {
for (i = 0; i < nlocal; i++)
if (partner[i]) probability[i] = random->uniform();
}
commflag = 1;
comm->forward_comm_fix(this,2);
// break bonds
// if both atoms list each other as winning bond partner
// and probability constraint is satisfied
int **bond_type = atom->bond_type;
tagint **bond_atom = atom->bond_atom;
int *num_bond = atom->num_bond;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
nbreak = 0;
for (i = 0; i < nlocal; i++) {
if (partner[i] == 0) continue;
j = atom->map(partner[i]);
if (partner[j] != tag[i]) continue;
// apply probability constraint using RN for atom with smallest ID
if (fraction < 1.0) {
if (tag[i] < tag[j]) {
if (probability[i] >= fraction) continue;
} else {
if (probability[j] >= fraction) continue;
}
}
// delete bond from atom I if I stores it
// atom J will also do this
for (m = 0; m < num_bond[i]; m++) {
if (bond_atom[i][m] == partner[i]) {
for (k = m; k < num_bond[i]-1; k++) {
bond_atom[i][k] = bond_atom[i][k+1];
bond_type[i][k] = bond_type[i][k+1];
}
num_bond[i]--;
break;
}
}
// remove J from special bond list for atom I
// atom J will also do this, whatever proc it is on
slist = special[i];
n1 = nspecial[i][0];
for (m = 0; m < n1; m++)
if (slist[m] == partner[i]) break;
n3 = nspecial[i][2];
for (; m < n3-1; m++) slist[m] = slist[m+1];
nspecial[i][0]--;
nspecial[i][1]--;
nspecial[i][2]--;
// store final broken bond partners and count the broken bond once
finalpartner[i] = tag[j];
finalpartner[j] = tag[i];
if (tag[i] < tag[j]) nbreak++;
}
// tally stats
MPI_Allreduce(&nbreak,&breakcount,1,MPI_INT,MPI_SUM,world);
breakcounttotal += breakcount;
atom->nbonds -= breakcount;
// trigger reneighboring if any bonds were broken
// this insures neigh lists will immediately reflect the topology changes
// done if no bonds broken
if (breakcount) next_reneighbor = update->ntimestep;
if (!breakcount) return;
// communicate final partner and 1-2 special neighbors
// 1-2 neighs already reflect broken bonds
commflag = 2;
comm->forward_comm_fix(this);
// create list of broken bonds that influence my owned atoms
// even if between owned-ghost or ghost-ghost atoms
// finalpartner is now set for owned and ghost atoms so loop over nall
// OK if duplicates in broken list due to ghosts duplicating owned atoms
// check J < 0 to insure a broken bond to unknown atom is included
// i.e. bond partner outside of cutoff length
nbreak = 0;
for (i = 0; i < nall; i++) {
if (finalpartner[i] == 0) continue;
j = atom->map(finalpartner[i]);
if (j < 0 || tag[i] < tag[j]) {
if (nbreak == maxbreak) {
maxbreak += DELTA;
memory->grow(broken,maxbreak,2,"bond/break:broken");
}
broken[nbreak][0] = tag[i];
broken[nbreak][1] = finalpartner[i];
nbreak++;
}
}
// update special neigh lists of all atoms affected by any broken bond
// also remove angles/dihedrals/impropers broken by broken bonds
update_topology();
// DEBUG
// print_bb();
}
/* ----------------------------------------------------------------------
insure all atoms 2 hops away from owned atoms are in ghost list
this allows dihedral 1-2-3-4 to be properly deleted
and special list of 1 to be properly updated
if I own atom 1, but not 2,3,4, and bond 3-4 is deleted
then 2,3 will be ghosts and 3 will store 4 as its finalpartner
------------------------------------------------------------------------- */
void FixBondBreak::check_ghosts()
{
int i,j,n;
tagint *slist;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int nlocal = atom->nlocal;
int flag = 0;
for (i = 0; i < nlocal; i++) {
slist = special[i];
n = nspecial[i][1];
for (j = 0; j < n; j++)
if (atom->map(slist[j]) < 0) flag = 1;
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall)
error->all(FLERR,"Fix bond/break needs ghost atoms from further away");
lastcheck = update->ntimestep;
}
/* ----------------------------------------------------------------------
double loop over my atoms and broken bonds
influenced = 1 if atom's topology is affected by any broken bond
yes if is one of 2 atoms in bond
yes if both atom IDs appear in atom's special list
else no
if influenced:
check for angles/dihedrals/impropers to break due to specific broken bonds
rebuild the atom's special list of 1-2,1-3,1-4 neighs
------------------------------------------------------------------------- */
void FixBondBreak::update_topology()
{
int i,j,k,n,influence,influenced,found;
tagint id1,id2;
tagint *slist;
tagint *tag = atom->tag;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int nlocal = atom->nlocal;
nangles = 0;
ndihedrals = 0;
nimpropers = 0;
//printf("NBREAK %d: ",nbreak);
//for (i = 0; i < nbreak; i++)
// printf(" %d %d,",broken[i][0],broken[i][1]);
//printf("\n");
for (i = 0; i < nlocal; i++) {
influenced = 0;
slist = special[i];
for (j = 0; j < nbreak; j++) {
id1 = broken[j][0];
id2 = broken[j][1];
influence = 0;
if (tag[i] == id1 || tag[i] == id2) influence = 1;
else {
n = nspecial[i][2];
found = 0;
for (k = 0; k < n; k++)
if (slist[k] == id1 || slist[k] == id2) found++;
if (found == 2) influence = 1;
}
if (!influence) continue;
influenced = 1;
if (angleflag) break_angles(i,id1,id2);
if (dihedralflag) break_dihedrals(i,id1,id2);
if (improperflag) break_impropers(i,id1,id2);
}
- if (influenced) recreate_special(i);
+ if (influenced) rebuild_special_one(i);
}
int newton_bond = force->newton_bond;
int all;
if (angleflag) {
MPI_Allreduce(&nangles,&all,1,MPI_INT,MPI_SUM,world);
if (!newton_bond) all /= 3;
atom->nangles -= all;
}
if (dihedralflag) {
MPI_Allreduce(&ndihedrals,&all,1,MPI_INT,MPI_SUM,world);
if (!newton_bond) all /= 4;
atom->ndihedrals -= all;
}
if (improperflag) {
MPI_Allreduce(&nimpropers,&all,1,MPI_INT,MPI_SUM,world);
if (!newton_bond) all /= 4;
atom->nimpropers -= all;
}
}
/* ----------------------------------------------------------------------
re-build special list of atom M
does not affect 1-2 neighs (already include effects of new bond)
affects 1-3 and 1-4 neighs due to other atom's augmented 1-2 neighs
------------------------------------------------------------------------- */
-void FixBondBreak::recreate_special(int m)
+void FixBondBreak::rebuild_special_one(int m)
{
int i,j,n,n1,cn1,cn2,cn3;
tagint *slist;
tagint *tag = atom->tag;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
// existing 1-2 neighs of atom M
slist = special[m];
n1 = nspecial[m][0];
cn1 = 0;
for (i = 0; i < n1; i++)
copy[cn1++] = slist[i];
// new 1-3 neighs of atom M, based on 1-2 neighs of 1-2 neighs
// exclude self
// remove duplicates after adding all possible 1-3 neighs
cn2 = cn1;
for (i = 0; i < cn1; i++) {
n = atom->map(copy[i]);
slist = special[n];
n1 = nspecial[n][0];
for (j = 0; j < n1; j++)
if (slist[j] != tag[m]) copy[cn2++] = slist[j];
}
cn2 = dedup(cn1,cn2,copy);
// new 1-4 neighs of atom M, based on 1-2 neighs of 1-3 neighs
// exclude self
// remove duplicates after adding all possible 1-4 neighs
cn3 = cn2;
for (i = cn1; i < cn2; i++) {
n = atom->map(copy[i]);
slist = special[n];
n1 = nspecial[n][0];
for (j = 0; j < n1; j++)
if (slist[j] != tag[m]) copy[cn3++] = slist[j];
}
cn3 = dedup(cn2,cn3,copy);
// store new special list with atom M
nspecial[m][0] = cn1;
nspecial[m][1] = cn2;
nspecial[m][2] = cn3;
memcpy(special[m],copy,cn3*sizeof(int));
}
/* ----------------------------------------------------------------------
break any angles owned by atom M that include atom IDs 1 and 2
angle is broken if ID1-ID2 is one of 2 bonds in angle (I-J,J-K)
------------------------------------------------------------------------- */
void FixBondBreak::break_angles(int m, tagint id1, tagint id2)
{
int j,found;
int num_angle = atom->num_angle[m];
int *angle_type = atom->angle_type[m];
tagint *angle_atom1 = atom->angle_atom1[m];
tagint *angle_atom2 = atom->angle_atom2[m];
tagint *angle_atom3 = atom->angle_atom3[m];
int i = 0;
while (i < num_angle) {
found = 0;
if (angle_atom1[i] == id1 && angle_atom2[i] == id2) found = 1;
else if (angle_atom2[i] == id1 && angle_atom3[i] == id2) found = 1;
else if (angle_atom1[i] == id2 && angle_atom2[i] == id1) found = 1;
else if (angle_atom2[i] == id2 && angle_atom3[i] == id1) found = 1;
if (!found) i++;
else {
for (j = i; j < num_angle-1; j++) {
angle_type[j] = angle_type[j+1];
angle_atom1[j] = angle_atom1[j+1];
angle_atom2[j] = angle_atom2[j+1];
angle_atom3[j] = angle_atom3[j+1];
}
num_angle--;
nangles++;
}
}
atom->num_angle[m] = num_angle;
}
/* ----------------------------------------------------------------------
break any dihedrals owned by atom M that include atom IDs 1 and 2
dihedral is broken if ID1-ID2 is one of 3 bonds in dihedral (I-J,J-K.K-L)
------------------------------------------------------------------------- */
void FixBondBreak::break_dihedrals(int m, tagint id1, tagint id2)
{
int j,found;
int num_dihedral = atom->num_dihedral[m];
int *dihedral_type = atom->dihedral_type[m];
tagint *dihedral_atom1 = atom->dihedral_atom1[m];
tagint *dihedral_atom2 = atom->dihedral_atom2[m];
tagint *dihedral_atom3 = atom->dihedral_atom3[m];
tagint *dihedral_atom4 = atom->dihedral_atom4[m];
int i = 0;
while (i < num_dihedral) {
found = 0;
if (dihedral_atom1[i] == id1 && dihedral_atom2[i] == id2) found = 1;
else if (dihedral_atom2[i] == id1 && dihedral_atom3[i] == id2) found = 1;
else if (dihedral_atom3[i] == id1 && dihedral_atom4[i] == id2) found = 1;
else if (dihedral_atom1[i] == id2 && dihedral_atom2[i] == id1) found = 1;
else if (dihedral_atom2[i] == id2 && dihedral_atom3[i] == id1) found = 1;
else if (dihedral_atom3[i] == id2 && dihedral_atom4[i] == id1) found = 1;
if (!found) i++;
else {
for (j = i; j < num_dihedral-1; j++) {
dihedral_type[j] = dihedral_type[j+1];
dihedral_atom1[j] = dihedral_atom1[j+1];
dihedral_atom2[j] = dihedral_atom2[j+1];
dihedral_atom3[j] = dihedral_atom3[j+1];
dihedral_atom4[j] = dihedral_atom4[j+1];
}
num_dihedral--;
ndihedrals++;
}
}
atom->num_dihedral[m] = num_dihedral;
}
/* ----------------------------------------------------------------------
break any impropers owned by atom M that include atom IDs 1 and 2
improper is broken if ID1-ID2 is one of 3 bonds in improper (I-J,I-K,I-L)
------------------------------------------------------------------------- */
void FixBondBreak::break_impropers(int m, tagint id1, tagint id2)
{
int j,found;
int num_improper = atom->num_improper[m];
int *improper_type = atom->improper_type[m];
tagint *improper_atom1 = atom->improper_atom1[m];
tagint *improper_atom2 = atom->improper_atom2[m];
tagint *improper_atom3 = atom->improper_atom3[m];
tagint *improper_atom4 = atom->improper_atom4[m];
int i = 0;
while (i < num_improper) {
found = 0;
if (improper_atom1[i] == id1 && improper_atom2[i] == id2) found = 1;
else if (improper_atom1[i] == id1 && improper_atom3[i] == id2) found = 1;
else if (improper_atom1[i] == id1 && improper_atom4[i] == id2) found = 1;
else if (improper_atom1[i] == id2 && improper_atom2[i] == id1) found = 1;
else if (improper_atom1[i] == id2 && improper_atom3[i] == id1) found = 1;
else if (improper_atom1[i] == id2 && improper_atom4[i] == id1) found = 1;
if (!found) i++;
else {
for (j = i; j < num_improper-1; j++) {
improper_type[j] = improper_type[j+1];
improper_atom1[j] = improper_atom1[j+1];
improper_atom2[j] = improper_atom2[j+1];
improper_atom3[j] = improper_atom3[j+1];
improper_atom4[j] = improper_atom4[j+1];
}
num_improper--;
nimpropers++;
}
}
atom->num_improper[m] = num_improper;
}
/* ----------------------------------------------------------------------
remove all ID duplicates in copy from Nstart:Nstop-1
compare to all previous values in copy
return N decremented by any discarded duplicates
------------------------------------------------------------------------- */
int FixBondBreak::dedup(int nstart, int nstop, tagint *copy)
{
int i;
int m = nstart;
while (m < nstop) {
for (i = 0; i < m; i++)
if (copy[i] == copy[m]) {
copy[m] = copy[nstop-1];
nstop--;
break;
}
if (i == m) m++;
}
return nstop;
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::post_integrate_respa(int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_integrate();
}
/* ---------------------------------------------------------------------- */
int FixBondBreak::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,k,m,ns;
if (commflag == 1) {
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(partner[j]).d;
buf[m++] = probability[j];
}
return m;
}
int **nspecial = atom->nspecial;
tagint **special = atom->special;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(finalpartner[j]).d;
ns = nspecial[j][0];
buf[m++] = ubuf(ns).d;
for (k = 0; k < ns; k++)
buf[m++] = ubuf(special[j][k]).d;
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::unpack_forward_comm(int n, int first, double *buf)
{
int i,j,m,ns,last;
if (commflag == 1) {
m = 0;
last = first + n;
for (i = first; i < last; i++) {
partner[i] = (tagint) ubuf(buf[m++]).i;
probability[i] = buf[m++];
}
} else {
int **nspecial = atom->nspecial;
tagint **special = atom->special;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
finalpartner[i] = (tagint) ubuf(buf[m++]).i;
ns = (int) ubuf(buf[m++]).i;
nspecial[i][0] = ns;
for (j = 0; j < ns; j++)
special[i][j] = (tagint) ubuf(buf[m++]).i;
}
}
}
/* ---------------------------------------------------------------------- */
int FixBondBreak::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = ubuf(partner[i]).d;
buf[m++] = distsq[i];
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
if (buf[m+1] > distsq[j]) {
partner[j] = (tagint) ubuf(buf[m++]).i;
distsq[j] = buf[m++];
} else m += 2;
}
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::print_bb()
{
for (int i = 0; i < atom->nlocal; i++) {
printf("TAG " TAGINT_FORMAT ": %d nbonds: ",atom->tag[i],atom->num_bond[i]);
for (int j = 0; j < atom->num_bond[i]; j++) {
printf(" %d",atom->bond_atom[i][j]);
}
printf("\n");
printf("TAG " TAGINT_FORMAT ": %d nangles: ",atom->tag[i],atom->num_angle[i]);
for (int j = 0; j < atom->num_angle[i]; j++) {
printf(" %d %d %d,",atom->angle_atom1[i][j],
atom->angle_atom2[i][j],atom->angle_atom3[i][j]);
}
printf("\n");
printf("TAG " TAGINT_FORMAT ": %d ndihedrals: ",atom->tag[i],atom->num_dihedral[i]);
for (int j = 0; j < atom->num_dihedral[i]; j++) {
printf(" %d %d %d %d,",atom->dihedral_atom1[i][j],
atom->dihedral_atom2[i][j],atom->dihedral_atom3[i][j],
atom->dihedral_atom4[i][j]);
}
printf("\n");
printf("TAG " TAGINT_FORMAT ": %d %d %d nspecial: ",atom->tag[i],
atom->nspecial[i][0],atom->nspecial[i][1],atom->nspecial[i][2]);
for (int j = 0; j < atom->nspecial[i][2]; j++) {
printf(" %d",atom->special[i][j]);
}
printf("\n");
}
}
/* ---------------------------------------------------------------------- */
void FixBondBreak::print_copy(const char *str, tagint m,
int n1, int n2, int n3, int *v)
{
printf("%s %i: %d %d %d nspecial: ",str,m,n1,n2,n3);
for (int j = 0; j < n3; j++) printf(" %d",v[j]);
printf("\n");
}
/* ---------------------------------------------------------------------- */
double FixBondBreak::compute_vector(int n)
{
if (n == 0) return (double) breakcount;
return (double) breakcounttotal;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixBondBreak::memory_usage()
{
int nmax = atom->nmax;
double bytes = 2*nmax * sizeof(tagint);
bytes += nmax * sizeof(double);
return bytes;
}
diff --git a/src/MC/fix_bond_break.h b/src/MC/fix_bond_break.h
old mode 100644
new mode 100755
index 3cf24acce..51f926ce9
--- a/src/MC/fix_bond_break.h
+++ b/src/MC/fix_bond_break.h
@@ -1,113 +1,113 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(bond/break,FixBondBreak)
#else
#ifndef LMP_FIX_BOND_BREAK_H
#define LMP_FIX_BOND_BREAK_H
#include "fix.h"
namespace LAMMPS_NS {
class FixBondBreak : public Fix {
public:
FixBondBreak(class LAMMPS *, int, char **);
~FixBondBreak();
int setmask();
void init();
void post_integrate();
void post_integrate_respa(int,int);
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
double compute_vector(int);
double memory_usage();
private:
int me,nprocs;
int btype,seed;
double cutoff,cutsq,fraction;
int angleflag,dihedralflag,improperflag;
bigint lastcheck;
int breakcount,breakcounttotal;
int nmax;
tagint *partner,*finalpartner;
double *distsq,*probability;
int nbreak,maxbreak;
tagint **broken;
tagint *copy;
class RanMars *random;
int nlevels_respa;
int commflag;
int nbroken;
int nangles,ndihedrals,nimpropers;
void check_ghosts();
void update_topology();
void break_angles(int, tagint, tagint);
void break_dihedrals(int, tagint, tagint);
void break_impropers(int, tagint, tagint);
- void recreate_special(int);
+ void rebuild_special_one(int);
int dedup(int, int, tagint *);
// DEBUG
void print_bb();
void print_copy(const char *, tagint, int, int, int, int *);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Invalid bond type in fix bond/break command
Self-explanatory.
E: Cannot use fix bond/break with non-molecular systems
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify.
E: Cannot yet use fix bond/break with this improper style
This is a current restriction in LAMMPS.
E: Fix bond/break needs ghost atoms from further away
This is because the fix needs to walk bonds to a certain distance to
acquire needed info, The comm_modify cutoff command can be used to
extend the communication range.
*/
diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp
index 1d8ecfb7c..7b4e8a03d 100644
--- a/src/MC/fix_bond_create.cpp
+++ b/src/MC/fix_bond_create.cpp
@@ -1,1444 +1,1444 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "math.h"
#include "mpi.h"
#include "string.h"
#include "stdlib.h"
#include "fix_bond_create.h"
#include "update.h"
#include "respa.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define BIG 1.0e20
#define DELTA 16
/* ---------------------------------------------------------------------- */
FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 8) error->all(FLERR,"Illegal fix bond/create command");
MPI_Comm_rank(world,&me);
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal fix bond/create command");
force_reneighbor = 1;
next_reneighbor = -1;
vector_flag = 1;
size_vector = 2;
global_freq = 1;
extvector = 0;
iatomtype = force->inumeric(FLERR,arg[4]);
jatomtype = force->inumeric(FLERR,arg[5]);
double cutoff = force->numeric(FLERR,arg[6]);
btype = force->inumeric(FLERR,arg[7]);
if (iatomtype < 1 || iatomtype > atom->ntypes ||
jatomtype < 1 || jatomtype > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix bond/create command");
if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/create command");
if (btype < 1 || btype > atom->nbondtypes)
error->all(FLERR,"Invalid bond type in fix bond/create command");
cutsq = cutoff*cutoff;
// optional keywords
imaxbond = 0;
inewtype = iatomtype;
jmaxbond = 0;
jnewtype = jatomtype;
fraction = 1.0;
int seed = 12345;
atype = dtype = itype = 0;
int iarg = 8;
while (iarg < narg) {
if (strcmp(arg[iarg],"iparam") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/create command");
imaxbond = force->inumeric(FLERR,arg[iarg+1]);
inewtype = force->inumeric(FLERR,arg[iarg+2]);
if (imaxbond < 0) error->all(FLERR,"Illegal fix bond/create command");
if (inewtype < 1 || inewtype > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix bond/create command");
iarg += 3;
} else if (strcmp(arg[iarg],"jparam") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/create command");
jmaxbond = force->inumeric(FLERR,arg[iarg+1]);
jnewtype = force->inumeric(FLERR,arg[iarg+2]);
if (jmaxbond < 0) error->all(FLERR,"Illegal fix bond/create command");
if (jnewtype < 1 || jnewtype > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix bond/create command");
iarg += 3;
} else if (strcmp(arg[iarg],"prob") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/create command");
fraction = force->numeric(FLERR,arg[iarg+1]);
seed = force->inumeric(FLERR,arg[iarg+2]);
if (fraction < 0.0 || fraction > 1.0)
error->all(FLERR,"Illegal fix bond/create command");
if (seed <= 0) error->all(FLERR,"Illegal fix bond/create command");
iarg += 3;
} else if (strcmp(arg[iarg],"atype") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/create command");
atype = force->inumeric(FLERR,arg[iarg+1]);
if (atype < 0) error->all(FLERR,"Illegal fix bond/create command");
iarg += 2;
} else if (strcmp(arg[iarg],"dtype") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/create command");
dtype = force->inumeric(FLERR,arg[iarg+1]);
if (dtype < 0) error->all(FLERR,"Illegal fix bond/create command");
iarg += 2;
} else if (strcmp(arg[iarg],"itype") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/create command");
itype = force->inumeric(FLERR,arg[iarg+1]);
if (itype < 0) error->all(FLERR,"Illegal fix bond/create command");
iarg += 2;
} else error->all(FLERR,"Illegal fix bond/create command");
}
// error check
if (atom->molecular != 1)
error->all(FLERR,"Cannot use fix bond/create with non-molecular systems");
if (iatomtype == jatomtype &&
((imaxbond != jmaxbond) || (inewtype != jnewtype)))
error->all(FLERR,
"Inconsistent iparam/jparam values in fix bond/create command");
// initialize Marsaglia RNG with processor-unique seed
random = new RanMars(lmp,seed + me);
// perform initial allocation of atom-based arrays
// register with Atom class
// bondcount values will be initialized in setup()
bondcount = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
countflag = 0;
// set comm sizes needed by this fix
// forward is big due to comm of broken bonds and 1-2 neighbors
comm_forward = MAX(2,2+atom->maxspecial);
comm_reverse = 2;
// allocate arrays local to this fix
nmax = 0;
partner = finalpartner = NULL;
distsq = NULL;
maxcreate = 0;
created = NULL;
// copy = special list for one atom
// size = ms^2 + ms is sufficient
- // b/c in recreate_special() neighs of all 1-2s are added,
+ // b/c in rebuild_special_one() neighs of all 1-2s are added,
// then a dedup(), then neighs of all 1-3s are added, then final dedup()
// this means intermediate size cannot exceed ms^2 + ms
int maxspecial = atom->maxspecial;
copy = new tagint[maxspecial*maxspecial + maxspecial];
// zero out stats
createcount = 0;
createcounttotal = 0;
}
/* ---------------------------------------------------------------------- */
FixBondCreate::~FixBondCreate()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
delete random;
// delete locally stored arrays
memory->destroy(bondcount);
memory->destroy(partner);
memory->destroy(finalpartner);
memory->destroy(distsq);
memory->destroy(created);
delete [] copy;
}
/* ---------------------------------------------------------------------- */
int FixBondCreate::setmask()
{
int mask = 0;
mask |= POST_INTEGRATE;
mask |= POST_INTEGRATE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::init()
{
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
// check cutoff for iatomtype,jatomtype
if (force->pair == NULL || cutsq > force->pair->cutsq[iatomtype][jatomtype])
error->all(FLERR,"Fix bond/create cutoff is longer than pairwise cutoff");
// enable angle/dihedral/improper creation if atype/dtype/itype
// option was used and a force field has been specified
if (atype && force->angle) {
angleflag = 1;
if (atype > atom->nangletypes)
error->all(FLERR,"Fix bond/create angle type is invalid");
} else angleflag = 0;
if (dtype && force->dihedral) {
dihedralflag = 1;
if (dtype > atom->ndihedraltypes)
error->all(FLERR,"Fix bond/create dihedral type is invalid");
} else dihedralflag = 0;
if (itype && force->improper) {
improperflag = 1;
if (itype > atom->nimpropertypes)
error->all(FLERR,"Fix bond/create improper type is invalid");
} else improperflag = 0;
if (force->improper) {
if (force->improper_match("class2") || force->improper_match("ring"))
error->all(FLERR,"Cannot yet use fix bond/create with this "
"improper style");
}
// need a half neighbor list, built every Nevery steps
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->occasional = 1;
lastcheck = -1;
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::setup(int vflag)
{
int i,j,m;
// compute initial bondcount if this is first run
// can't do this earlier, in constructor or init, b/c need ghost info
if (countflag) return;
countflag = 1;
// count bonds stored with each bond I own
// if newton bond is not set, just increment count on atom I
// if newton bond is set, also increment count on atom J even if ghost
// bondcount is long enough to tally ghost atom counts
int *num_bond = atom->num_bond;
int **bond_type = atom->bond_type;
tagint **bond_atom = atom->bond_atom;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
int nall = nlocal + nghost;
int newton_bond = force->newton_bond;
for (i = 0; i < nall; i++) bondcount[i] = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_bond[i]; j++) {
if (bond_type[i][j] == btype) {
bondcount[i]++;
if (newton_bond) {
m = atom->map(bond_atom[i][j]);
if (m < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms "
"from further away");
bondcount[m]++;
}
}
}
// if newton_bond is set, need to sum bondcount
commflag = 1;
if (newton_bond) comm->reverse_comm_fix(this,1);
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::post_integrate()
{
int i,j,k,m,n,ii,jj,inum,jnum,itype,jtype,n1,n2,n3,possible;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
tagint *slist;
if (update->ntimestep % nevery) return;
// check that all procs have needed ghost atoms within ghost cutoff
// only if neighbor list has changed since last check
// needs to be <= test b/c neighbor list could have been re-built in
// same timestep as last post_integrate() call, but afterwards
// NOTE: no longer think is needed, due to error tests on atom->map()
// NOTE: if delete, can also delete lastcheck and check_ghosts()
//if (lastcheck <= neighbor->lastcall) check_ghosts();
// acquire updated ghost atom positions
// necessary b/c are calling this after integrate, but before Verlet comm
comm->forward_comm();
// forward comm of bondcount, so ghosts have it
commflag = 1;
comm->forward_comm_fix(this,1);
// resize bond partner list and initialize it
// probability array overlays distsq array
// needs to be atom->nmax in length
if (atom->nmax > nmax) {
memory->destroy(partner);
memory->destroy(finalpartner);
memory->destroy(distsq);
nmax = atom->nmax;
memory->create(partner,nmax,"bond/create:partner");
memory->create(finalpartner,nmax,"bond/create:finalpartner");
memory->create(distsq,nmax,"bond/create:distsq");
probability = distsq;
}
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
for (i = 0; i < nall; i++) {
partner[i] = 0;
finalpartner[i] = 0;
distsq[i] = BIG;
}
// loop over neighbors of my atoms
// each atom sets one closest eligible partner atom ID to bond with
double **x = atom->x;
tagint *tag = atom->tag;
tagint **bond_atom = atom->bond_atom;
int *num_bond = atom->num_bond;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int *mask = atom->mask;
int *type = atom->type;
neighbor->build_one(list,1);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (!(mask[i] & groupbit)) continue;
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
if (!(mask[j] & groupbit)) continue;
jtype = type[j];
possible = 0;
if (itype == iatomtype && jtype == jatomtype) {
if ((imaxbond == 0 || bondcount[i] < imaxbond) &&
(jmaxbond == 0 || bondcount[j] < jmaxbond))
possible = 1;
} else if (itype == jatomtype && jtype == iatomtype) {
if ((jmaxbond == 0 || bondcount[i] < jmaxbond) &&
(imaxbond == 0 || bondcount[j] < imaxbond))
possible = 1;
}
if (!possible) continue;
// do not allow a duplicate bond to be created
// check 1-2 neighbors of atom I
for (k = 0; k < nspecial[i][0]; k++)
if (special[i][k] == tag[j]) possible = 0;
if (!possible) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq >= cutsq) continue;
if (rsq < distsq[i]) {
partner[i] = tag[j];
distsq[i] = rsq;
}
if (rsq < distsq[j]) {
partner[j] = tag[i];
distsq[j] = rsq;
}
}
}
// reverse comm of distsq and partner
// not needed if newton_pair off since I,J pair was seen by both procs
commflag = 2;
if (force->newton_pair) comm->reverse_comm_fix(this);
// each atom now knows its winning partner
// for prob check, generate random value for each atom with a bond partner
// forward comm of partner and random value, so ghosts have it
if (fraction < 1.0) {
for (i = 0; i < nlocal; i++)
if (partner[i]) probability[i] = random->uniform();
}
commflag = 2;
comm->forward_comm_fix(this,2);
// create bonds for atoms I own
// only if both atoms list each other as winning bond partner
// and probability constraint is satisfied
// if other atom is owned by another proc, it should do same thing
int **bond_type = atom->bond_type;
int newton_bond = force->newton_bond;
ncreate = 0;
for (i = 0; i < nlocal; i++) {
if (partner[i] == 0) continue;
j = atom->map(partner[i]);
if (partner[j] != tag[i]) continue;
// apply probability constraint using RN for atom with smallest ID
if (fraction < 1.0) {
if (tag[i] < tag[j]) {
if (probability[i] >= fraction) continue;
} else {
if (probability[j] >= fraction) continue;
}
}
// if newton_bond is set, only store with I or J
// if not newton_bond, store bond with both I and J
// atom J will also do this consistently, whatever proc it is on
if (!newton_bond || tag[i] < tag[j]) {
if (num_bond[i] == atom->bond_per_atom)
error->one(FLERR,"New bond exceeded bonds per atom in fix bond/create");
bond_type[i][num_bond[i]] = btype;
bond_atom[i][num_bond[i]] = tag[j];
num_bond[i]++;
}
// add a 1-2 neighbor to special bond list for atom I
// atom J will also do this, whatever proc it is on
// need to first remove tag[j] from later in list if it appears
- // prevents list from overflowing, will be rebuilt in recreate_special()
+ // prevents list from overflowing, will be rebuilt in rebuild_special_one()
slist = special[i];
n1 = nspecial[i][0];
n2 = nspecial[i][1];
n3 = nspecial[i][2];
for (m = n1; m < n3; m++)
if (slist[m] == tag[j]) break;
if (m < n3) {
for (n = m; n < n3-1; n++) slist[n] = slist[n+1];
n3--;
if (m < n2) n2--;
}
if (n3 == atom->maxspecial)
error->one(FLERR,
"New bond exceeded special list size in fix bond/create");
for (m = n3; m > n1; m--) slist[m] = slist[m-1];
slist[n1] = tag[j];
nspecial[i][0] = n1+1;
nspecial[i][1] = n2+1;
nspecial[i][2] = n3+1;
// increment bondcount, convert atom to new type if limit reached
// atom J will also do this, whatever proc it is on
bondcount[i]++;
if (type[i] == iatomtype) {
if (bondcount[i] == imaxbond) type[i] = inewtype;
} else {
if (bondcount[i] == jmaxbond) type[i] = jnewtype;
}
// store final created bond partners and count the created bond once
finalpartner[i] = tag[j];
finalpartner[j] = tag[i];
if (tag[i] < tag[j]) ncreate++;
}
// tally stats
MPI_Allreduce(&ncreate,&createcount,1,MPI_INT,MPI_SUM,world);
createcounttotal += createcount;
atom->nbonds += createcount;
// trigger reneighboring if any bonds were formed
// this insures neigh lists will immediately reflect the topology changes
// done if any bonds created
if (createcount) next_reneighbor = update->ntimestep;
if (!createcount) return;
// communicate final partner and 1-2 special neighbors
// 1-2 neighs already reflect created bonds
commflag = 3;
comm->forward_comm_fix(this);
// create list of broken bonds that influence my owned atoms
// even if between owned-ghost or ghost-ghost atoms
// finalpartner is now set for owned and ghost atoms so loop over nall
// OK if duplicates in broken list due to ghosts duplicating owned atoms
// check J < 0 to insure a broken bond to unknown atom is included
// i.e. a bond partner outside of cutoff length
ncreate = 0;
for (i = 0; i < nall; i++) {
if (finalpartner[i] == 0) continue;
j = atom->map(finalpartner[i]);
if (j < 0 || tag[i] < tag[j]) {
if (ncreate == maxcreate) {
maxcreate += DELTA;
memory->grow(created,maxcreate,2,"bond/create:created");
}
created[ncreate][0] = tag[i];
created[ncreate][1] = finalpartner[i];
ncreate++;
}
}
// update special neigh lists of all atoms affected by any created bond
// also add angles/dihedrals/impropers induced by created bonds
update_topology();
// DEBUG
//print_bb();
}
/* ----------------------------------------------------------------------
insure all atoms 2 hops away from owned atoms are in ghost list
this allows dihedral 1-2-3-4 to be properly created
and special list of 1 to be properly updated
if I own atom 1, but not 2,3,4, and bond 3-4 is added
then 2,3 will be ghosts and 3 will store 4 as its finalpartner
------------------------------------------------------------------------- */
void FixBondCreate::check_ghosts()
{
int i,j,n;
tagint *slist;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int nlocal = atom->nlocal;
int flag = 0;
for (i = 0; i < nlocal; i++) {
slist = special[i];
n = nspecial[i][1];
for (j = 0; j < n; j++)
if (atom->map(slist[j]) < 0) flag = 1;
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall)
error->all(FLERR,"Fix bond/create needs ghost atoms from further away");
lastcheck = update->ntimestep;
}
/* ----------------------------------------------------------------------
double loop over my atoms and created bonds
influenced = 1 if atom's topology is affected by any created bond
yes if is one of 2 atoms in bond
yes if either atom ID appears in as 1-2 or 1-3 in atom's special list
else no
if influenced by any created bond:
rebuild the atom's special list of 1-2,1-3,1-4 neighs
check for angles/dihedrals/impropers to create due modified special list
------------------------------------------------------------------------- */
void FixBondCreate::update_topology()
{
int i,j,k,n,influence,influenced;
tagint id1,id2;
tagint *slist;
tagint *tag = atom->tag;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int nlocal = atom->nlocal;
nangles = 0;
ndihedrals = 0;
nimpropers = 0;
overflow = 0;
//printf("NCREATE %d: ",ncreate);
//for (i = 0; i < ncreate; i++)
// printf(" %d %d,",created[i][0],created[i][1]);
//printf("\n");
for (i = 0; i < nlocal; i++) {
influenced = 0;
slist = special[i];
for (j = 0; j < ncreate; j++) {
id1 = created[j][0];
id2 = created[j][1];
influence = 0;
if (tag[i] == id1 || tag[i] == id2) influence = 1;
else {
n = nspecial[i][1];
for (k = 0; k < n; k++)
if (slist[k] == id1 || slist[k] == id2) {
influence = 1;
break;
}
}
if (!influence) continue;
influenced = 1;
}
- // recreate_special first, since used by create_angles, etc
+ // rebuild_special_one() first, since used by create_angles, etc
if (influenced) {
- recreate_special(i);
+ rebuild_special_one(i);
if (angleflag) create_angles(i);
if (dihedralflag) create_dihedrals(i);
if (improperflag) create_impropers(i);
}
}
int overflowall;
MPI_Allreduce(&overflow,&overflowall,1,MPI_INT,MPI_SUM,world);
if (overflowall) error->all(FLERR,"Fix bond/create induced too many "
"angles/dihedrals/impropers per atom");
int newton_bond = force->newton_bond;
int all;
if (angleflag) {
MPI_Allreduce(&nangles,&all,1,MPI_INT,MPI_SUM,world);
if (!newton_bond) all /= 3;
atom->nangles += all;
}
if (dihedralflag) {
MPI_Allreduce(&ndihedrals,&all,1,MPI_INT,MPI_SUM,world);
if (!newton_bond) all /= 4;
atom->ndihedrals += all;
}
if (improperflag) {
MPI_Allreduce(&nimpropers,&all,1,MPI_INT,MPI_SUM,world);
if (!newton_bond) all /= 4;
atom->nimpropers += all;
}
}
/* ----------------------------------------------------------------------
re-build special list of atom M
does not affect 1-2 neighs (already include effects of new bond)
affects 1-3 and 1-4 neighs due to other atom's augmented 1-2 neighs
------------------------------------------------------------------------- */
-void FixBondCreate::recreate_special(int m)
+void FixBondCreate::rebuild_special_one(int m)
{
int i,j,n,n1,cn1,cn2,cn3;
tagint *slist;
tagint *tag = atom->tag;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
// existing 1-2 neighs of atom M
slist = special[m];
n1 = nspecial[m][0];
cn1 = 0;
for (i = 0; i < n1; i++)
copy[cn1++] = slist[i];
// new 1-3 neighs of atom M, based on 1-2 neighs of 1-2 neighs
// exclude self
// remove duplicates after adding all possible 1-3 neighs
cn2 = cn1;
for (i = 0; i < cn1; i++) {
n = atom->map(copy[i]);
if (n < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
slist = special[n];
n1 = nspecial[n][0];
for (j = 0; j < n1; j++)
if (slist[j] != tag[m]) copy[cn2++] = slist[j];
}
cn2 = dedup(cn1,cn2,copy);
if (cn2 > atom->maxspecial)
error->one(FLERR,"Special list size exceeded in fix bond/create");
// new 1-4 neighs of atom M, based on 1-2 neighs of 1-3 neighs
// exclude self
// remove duplicates after adding all possible 1-4 neighs
cn3 = cn2;
for (i = cn1; i < cn2; i++) {
n = atom->map(copy[i]);
if (n < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
slist = special[n];
n1 = nspecial[n][0];
for (j = 0; j < n1; j++)
if (slist[j] != tag[m]) copy[cn3++] = slist[j];
}
cn3 = dedup(cn2,cn3,copy);
if (cn3 > atom->maxspecial)
error->one(FLERR,"Special list size exceeded in fix bond/create");
// store new special list with atom M
nspecial[m][0] = cn1;
nspecial[m][1] = cn2;
nspecial[m][2] = cn3;
memcpy(special[m],copy,cn3*sizeof(int));
}
/* ----------------------------------------------------------------------
create any angles owned by atom M induced by newly created bonds
walk special list to find all possible angles to create
only add an angle if a new bond is one of its 2 bonds (I-J,J-K)
for newton_bond on, atom M is central atom
for newton_bond off, atom M is any of 3 atoms in angle
------------------------------------------------------------------------- */
void FixBondCreate::create_angles(int m)
{
int i,j,n,i2local,n1,n2;
tagint i1,i2,i3;
tagint *s1list,*s2list;
tagint *tag = atom->tag;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int num_angle = atom->num_angle[m];
int *angle_type = atom->angle_type[m];
tagint *angle_atom1 = atom->angle_atom1[m];
tagint *angle_atom2 = atom->angle_atom2[m];
tagint *angle_atom3 = atom->angle_atom3[m];
// atom M is central atom in angle
// double loop over 1-2 neighs
// avoid double counting by 2nd loop as j = i+1,N not j = 1,N
// consider all angles, only add if:
// a new bond is in the angle and atom types match
i2 = tag[m];
n2 = nspecial[m][0];
s2list = special[m];
for (i = 0; i < n2; i++) {
i1 = s2list[i];
for (j = i+1; j < n2; j++) {
i3 = s2list[j];
// angle = i1-i2-i3
for (n = 0; n < ncreate; n++) {
if (created[n][0] == i1 && created[n][1] == i2) break;
if (created[n][0] == i2 && created[n][1] == i1) break;
if (created[n][0] == i2 && created[n][1] == i3) break;
if (created[n][0] == i3 && created[n][1] == i2) break;
}
if (n == ncreate) continue;
// NOTE: this is place to check atom types of i1,i2,i3
if (num_angle < atom->angle_per_atom) {
angle_type[num_angle] = atype;
angle_atom1[num_angle] = i1;
angle_atom2[num_angle] = i2;
angle_atom3[num_angle] = i3;
num_angle++;
nangles++;
} else overflow = 1;
}
}
atom->num_angle[m] = num_angle;
if (force->newton_bond) return;
// for newton_bond off, also consider atom M as atom 1 in angle
i1 = tag[m];
n1 = nspecial[m][0];
s1list = special[m];
for (i = 0; i < n1; i++) {
i2 = s1list[i];
i2local = atom->map(i2);
if (i2local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s2list = special[i2local];
n2 = nspecial[i2local][0];
for (j = 0; j < n2; j++) {
i3 = s2list[j];
if (i3 == i1) continue;
// angle = i1-i2-i3
for (n = 0; n < ncreate; n++) {
if (created[n][0] == i1 && created[n][1] == i2) break;
if (created[n][0] == i2 && created[n][1] == i1) break;
if (created[n][0] == i2 && created[n][1] == i3) break;
if (created[n][0] == i3 && created[n][1] == i2) break;
}
if (n == ncreate) continue;
// NOTE: this is place to check atom types of i1,i2,i3
if (num_angle < atom->angle_per_atom) {
angle_type[num_angle] = atype;
angle_atom1[num_angle] = i1;
angle_atom2[num_angle] = i2;
angle_atom3[num_angle] = i3;
num_angle++;
nangles++;
} else overflow = 1;
}
}
atom->num_angle[m] = num_angle;
}
/* ----------------------------------------------------------------------
create any dihedrals owned by atom M induced by newly created bonds
walk special list to find all possible dihedrals to create
only add a dihedral if a new bond is one of its 3 bonds (I-J,J-K,K-L)
for newton_bond on, atom M is central atom
for newton_bond off, atom M is any of 4 atoms in dihedral
------------------------------------------------------------------------- */
void FixBondCreate::create_dihedrals(int m)
{
int i,j,k,n,i1local,i2local,i3local,n1,n2,n3;
tagint i1,i2,i3,i4;
tagint *s1list,*s2list,*s3list;
tagint *tag = atom->tag;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int num_dihedral = atom->num_dihedral[m];
int *dihedral_type = atom->dihedral_type[m];
tagint *dihedral_atom1 = atom->dihedral_atom1[m];
tagint *dihedral_atom2 = atom->dihedral_atom2[m];
tagint *dihedral_atom3 = atom->dihedral_atom3[m];
tagint *dihedral_atom4 = atom->dihedral_atom4[m];
// atom M is 2nd atom in dihedral
// double loop over 1-2 neighs
// two triple loops: one over neighs at each end of triplet
// avoid double counting by 2nd loop as j = i+1,N not j = 1,N
// avoid double counting due to another atom being 2nd atom in same dihedral
// by requiring ID of 2nd atom < ID of 3rd atom
// don't do this if newton bond off since want to double count
// consider all dihedrals, only add if:
// a new bond is in the dihedral and atom types match
i2 = tag[m];
n2 = nspecial[m][0];
s2list = special[m];
for (i = 0; i < n2; i++) {
i1 = s2list[i];
for (j = i+1; j < n2; j++) {
i3 = s2list[j];
if (force->newton_bond && i2 > i3) continue;
i3local = atom->map(i3);
if (i3local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s3list = special[i3local];
n3 = nspecial[i3local][0];
for (k = 0; k < n3; k++) {
i4 = s3list[k];
if (i4 == i1 || i4 == i2 || i4 == i3) continue;
// dihedral = i1-i2-i3-i4
for (n = 0; n < ncreate; n++) {
if (created[n][0] == i1 && created[n][1] == i2) break;
if (created[n][0] == i2 && created[n][1] == i1) break;
if (created[n][0] == i2 && created[n][1] == i3) break;
if (created[n][0] == i3 && created[n][1] == i2) break;
if (created[n][0] == i3 && created[n][1] == i4) break;
if (created[n][0] == i4 && created[n][1] == i3) break;
}
if (n < ncreate) {
// NOTE: this is place to check atom types of i3,i2,i1,i4
if (num_dihedral < atom->dihedral_per_atom) {
dihedral_type[num_dihedral] = dtype;
dihedral_atom1[num_dihedral] = i1;
dihedral_atom2[num_dihedral] = i2;
dihedral_atom3[num_dihedral] = i3;
dihedral_atom4[num_dihedral] = i4;
num_dihedral++;
ndihedrals++;
} else overflow = 1;
}
}
}
}
for (i = 0; i < n2; i++) {
i1 = s2list[i];
if (force->newton_bond && i2 > i1) continue;
i1local = atom->map(i1);
if (i1local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s3list = special[i1local];
n3 = nspecial[i1local][0];
for (j = i+1; j < n2; j++) {
i3 = s2list[j];
for (k = 0; k < n3; k++) {
i4 = s3list[k];
if (i4 == i1 || i4 == i2 || i4 == i3) continue;
// dihedral = i3-i2-i1-i4
for (n = 0; n < ncreate; n++) {
if (created[n][0] == i3 && created[n][1] == i2) break;
if (created[n][0] == i2 && created[n][1] == i3) break;
if (created[n][0] == i2 && created[n][1] == i1) break;
if (created[n][0] == i1 && created[n][1] == i2) break;
if (created[n][0] == i1 && created[n][1] == i4) break;
if (created[n][0] == i4 && created[n][1] == i1) break;
}
if (n < ncreate) {
// NOTE: this is place to check atom types of i3,i2,i1,i4
if (num_dihedral < atom->dihedral_per_atom) {
dihedral_type[num_dihedral] = dtype;
dihedral_atom1[num_dihedral] = i3;
dihedral_atom2[num_dihedral] = i2;
dihedral_atom3[num_dihedral] = i1;
dihedral_atom4[num_dihedral] = i4;
num_dihedral++;
ndihedrals++;
} else overflow = 1;
}
}
}
}
atom->num_dihedral[m] = num_dihedral;
if (force->newton_bond) return;
// for newton_bond off, also consider atom M as atom 1 in dihedral
i1 = tag[m];
n1 = nspecial[m][0];
s1list = special[m];
for (i = 0; i < n1; i++) {
i2 = s1list[i];
i2local = atom->map(i2);
if (i2local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s2list = special[i2local];
n2 = nspecial[i2local][0];
for (j = 0; j < n2; j++) {
i3 = s2list[j];
if (i3 == i1) continue;
i3local = atom->map(i3);
if (i3local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s3list = special[i3local];
n3 = nspecial[i3local][0];
for (k = 0; k < n3; k++) {
i4 = s3list[k];
if (i4 == i1 || i4 == i2 || i4 == i3) continue;
// dihedral = i1-i2-i3-i4
for (n = 0; n < ncreate; n++) {
if (created[n][0] == i1 && created[n][1] == i2) break;
if (created[n][0] == i2 && created[n][1] == i1) break;
if (created[n][0] == i2 && created[n][1] == i3) break;
if (created[n][0] == i3 && created[n][1] == i2) break;
if (created[n][0] == i3 && created[n][1] == i4) break;
if (created[n][0] == i4 && created[n][1] == i3) break;
}
if (n < ncreate) {
// NOTE: this is place to check atom types of i3,i2,i1,i4
if (num_dihedral < atom->dihedral_per_atom) {
dihedral_type[num_dihedral] = dtype;
dihedral_atom1[num_dihedral] = i1;
dihedral_atom2[num_dihedral] = i2;
dihedral_atom3[num_dihedral] = i3;
dihedral_atom4[num_dihedral] = i4;
num_dihedral++;
ndihedrals++;
} else overflow = 1;
}
}
}
}
}
/* ----------------------------------------------------------------------
create any impropers owned by atom M induced by newly created bonds
walk special list to find all possible impropers to create
only add an improper if a new bond is one of its 3 bonds (I-J,I-K,I-L)
for newton_bond on, atom M is central atom
for newton_bond off, atom M is any of 4 atoms in improper
------------------------------------------------------------------------- */
void FixBondCreate::create_impropers(int m)
{
int i,j,k,n,i1local,n1,n2;
tagint i1,i2,i3,i4;
tagint *s1list,*s2list;
tagint *tag = atom->tag;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int num_improper = atom->num_improper[m];
int *improper_type = atom->improper_type[m];
tagint *improper_atom1 = atom->improper_atom1[m];
tagint *improper_atom2 = atom->improper_atom2[m];
tagint *improper_atom3 = atom->improper_atom3[m];
tagint *improper_atom4 = atom->improper_atom4[m];
// atom M is central atom in improper
// triple loop over 1-2 neighs
// avoid double counting by 2nd loop as j = i+1,N not j = 1,N
// consider all impropers, only add if:
// a new bond is in the improper and atom types match
i1 = tag[m];
n1 = nspecial[m][0];
s1list = special[m];
for (i = 0; i < n1; i++) {
i2 = s1list[i];
for (j = i+1; j < n1; j++) {
i3 = s1list[j];
for (k = j+1; k < n1; k++) {
i4 = s1list[k];
// improper = i1-i2-i3-i4
for (n = 0; n < ncreate; n++) {
if (created[n][0] == i1 && created[n][1] == i2) break;
if (created[n][0] == i2 && created[n][1] == i1) break;
if (created[n][0] == i1 && created[n][1] == i3) break;
if (created[n][0] == i3 && created[n][1] == i1) break;
if (created[n][0] == i1 && created[n][1] == i4) break;
if (created[n][0] == i4 && created[n][1] == i1) break;
}
if (n == ncreate) continue;
// NOTE: this is place to check atom types of i1,i2,i3,i4
if (num_improper < atom->improper_per_atom) {
improper_type[num_improper] = itype;
improper_atom1[num_improper] = i1;
improper_atom2[num_improper] = i2;
improper_atom3[num_improper] = i3;
improper_atom4[num_improper] = i4;
num_improper++;
nimpropers++;
} else overflow = 1;
}
}
}
atom->num_improper[m] = num_improper;
if (force->newton_bond) return;
// for newton_bond off, also consider atom M as atom 2 in improper
i2 = tag[m];
n2 = nspecial[m][0];
s2list = special[m];
for (i = 0; i < n2; i++) {
i1 = s2list[i];
i1local = atom->map(i1);
if (i1local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s1list = special[i1local];
n1 = nspecial[i1local][0];
for (j = 0; j < n1; j++) {
i3 = s1list[j];
if (i3 == i1 || i3 == i2) continue;
for (k = j+1; k < n1; k++) {
i4 = s1list[k];
if (i4 == i1 || i4 == i2) continue;
// improper = i1-i2-i3-i4
for (n = 0; n < ncreate; n++) {
if (created[n][0] == i1 && created[n][1] == i2) break;
if (created[n][0] == i2 && created[n][1] == i1) break;
if (created[n][0] == i1 && created[n][1] == i3) break;
if (created[n][0] == i3 && created[n][1] == i1) break;
if (created[n][0] == i1 && created[n][1] == i4) break;
if (created[n][0] == i4 && created[n][1] == i1) break;
}
if (n < ncreate) {
// NOTE: this is place to check atom types of i3,i2,i1,i4
if (num_improper < atom->improper_per_atom) {
improper_type[num_improper] = itype;
improper_atom1[num_improper] = i1;
improper_atom2[num_improper] = i2;
improper_atom3[num_improper] = i3;
improper_atom4[num_improper] = i4;
num_improper++;
nimpropers++;
} else overflow = 1;
}
}
}
}
}
/* ----------------------------------------------------------------------
remove all ID duplicates in copy from Nstart:Nstop-1
compare to all previous values in copy
return N decremented by any discarded duplicates
------------------------------------------------------------------------- */
int FixBondCreate::dedup(int nstart, int nstop, tagint *copy)
{
int i;
int m = nstart;
while (m < nstop) {
for (i = 0; i < m; i++)
if (copy[i] == copy[m]) {
copy[m] = copy[nstop-1];
nstop--;
break;
}
if (i == m) m++;
}
return nstop;
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::post_integrate_respa(int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_integrate();
}
/* ---------------------------------------------------------------------- */
int FixBondCreate::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,k,m,ns;
m = 0;
if (commflag == 1) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(bondcount[j]).d;
}
return m;
}
if (commflag == 2) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(partner[j]).d;
buf[m++] = probability[j];
}
return m;
}
int **nspecial = atom->nspecial;
tagint **special = atom->special;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(finalpartner[j]).d;
ns = nspecial[j][0];
buf[m++] = ubuf(ns).d;
for (k = 0; k < ns; k++)
buf[m++] = ubuf(special[j][k]).d;
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::unpack_forward_comm(int n, int first, double *buf)
{
int i,j,m,ns,last;
m = 0;
last = first + n;
if (commflag == 1) {
for (i = first; i < last; i++)
bondcount[i] = (int) ubuf(buf[m++]).i;
} else if (commflag == 2) {
for (i = first; i < last; i++) {
partner[i] = (tagint) ubuf(buf[m++]).i;
probability[i] = buf[m++];
}
} else {
int **nspecial = atom->nspecial;
tagint **special = atom->special;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
finalpartner[i] = (tagint) ubuf(buf[m++]).i;
ns = (int) ubuf(buf[m++]).i;
nspecial[i][0] = ns;
for (j = 0; j < ns; j++)
special[i][j] = (tagint) ubuf(buf[m++]).i;
}
}
}
/* ---------------------------------------------------------------------- */
int FixBondCreate::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
if (commflag == 1) {
for (i = first; i < last; i++)
buf[m++] = ubuf(bondcount[i]).d;
return m;
}
for (i = first; i < last; i++) {
buf[m++] = ubuf(partner[i]).d;
buf[m++] = distsq[i];
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
if (commflag == 1) {
for (i = 0; i < n; i++) {
j = list[i];
bondcount[j] += (int) ubuf(buf[m++]).i;
}
} else {
for (i = 0; i < n; i++) {
j = list[i];
if (buf[m+1] < distsq[j]) {
partner[j] = (tagint) ubuf(buf[m++]).i;
distsq[j] = buf[m++];
} else m += 2;
}
}
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixBondCreate::grow_arrays(int nmax)
{
memory->grow(bondcount,nmax,"bond/create:bondcount");
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixBondCreate::copy_arrays(int i, int j, int delflag)
{
bondcount[j] = bondcount[i];
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixBondCreate::pack_exchange(int i, double *buf)
{
buf[0] = bondcount[i];
return 1;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixBondCreate::unpack_exchange(int nlocal, double *buf)
{
bondcount[nlocal] = static_cast<int> (buf[0]);
return 1;
}
/* ---------------------------------------------------------------------- */
double FixBondCreate::compute_vector(int n)
{
if (n == 0) return (double) createcount;
return (double) createcounttotal;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixBondCreate::memory_usage()
{
int nmax = atom->nmax;
double bytes = nmax * sizeof(int);
bytes = 2*nmax * sizeof(tagint);
bytes += nmax * sizeof(double);
return bytes;
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::print_bb()
{
for (int i = 0; i < atom->nlocal; i++) {
printf("TAG " TAGINT_FORMAT ": %d nbonds: ",atom->tag[i],atom->num_bond[i]);
for (int j = 0; j < atom->num_bond[i]; j++) {
printf(" " TAGINT_FORMAT,atom->bond_atom[i][j]);
}
printf("\n");
printf("TAG " TAGINT_FORMAT ": %d nangles: ",atom->tag[i],atom->num_angle[i]);
for (int j = 0; j < atom->num_angle[i]; j++) {
printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT ",",
atom->angle_atom1[i][j], atom->angle_atom2[i][j],
atom->angle_atom3[i][j]);
}
printf("\n");
printf("TAG " TAGINT_FORMAT ": %d ndihedrals: ",atom->tag[i],atom->num_dihedral[i]);
for (int j = 0; j < atom->num_dihedral[i]; j++) {
printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT ",", atom->dihedral_atom1[i][j],
atom->dihedral_atom2[i][j],atom->dihedral_atom3[i][j],
atom->dihedral_atom4[i][j]);
}
printf("\n");
printf("TAG " TAGINT_FORMAT ": %d nimpropers: ",atom->tag[i],atom->num_improper[i]);
for (int j = 0; j < atom->num_improper[i]; j++) {
printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT ",",atom->improper_atom1[i][j],
atom->improper_atom2[i][j],atom->improper_atom3[i][j],
atom->improper_atom4[i][j]);
}
printf("\n");
printf("TAG " TAGINT_FORMAT ": %d %d %d nspecial: ",atom->tag[i],
atom->nspecial[i][0],atom->nspecial[i][1],atom->nspecial[i][2]);
for (int j = 0; j < atom->nspecial[i][2]; j++) {
printf(" " TAGINT_FORMAT,atom->special[i][j]);
}
printf("\n");
}
}
/* ---------------------------------------------------------------------- */
void FixBondCreate::print_copy(const char *str, tagint m,
int n1, int n2, int n3, int *v)
{
printf("%s " TAGINT_FORMAT ": %d %d %d nspecial: ",str,m,n1,n2,n3);
for (int j = 0; j < n3; j++) printf(" %d",v[j]);
printf("\n");
}
diff --git a/src/MC/fix_bond_create.h b/src/MC/fix_bond_create.h
old mode 100644
new mode 100755
index 95c7b4327..707b75406
--- a/src/MC/fix_bond_create.h
+++ b/src/MC/fix_bond_create.h
@@ -1,173 +1,173 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(bond/create,FixBondCreate)
#else
#ifndef LMP_FIX_BOND_CREATE_H
#define LMP_FIX_BOND_CREATE_H
#include "fix.h"
namespace LAMMPS_NS {
class FixBondCreate : public Fix {
public:
FixBondCreate(class LAMMPS *, int, char **);
~FixBondCreate();
int setmask();
void init();
void init_list(int, class NeighList *);
void setup(int);
void post_integrate();
void post_integrate_respa(int, int);
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
void grow_arrays(int);
void copy_arrays(int, int, int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
double compute_vector(int);
double memory_usage();
private:
int me;
int iatomtype,jatomtype;
int btype,seed;
int imaxbond,jmaxbond;
int inewtype,jnewtype;
double cutsq,fraction;
int atype,dtype,itype;
int angleflag,dihedralflag,improperflag;
int overflow;
tagint lastcheck;
int *bondcount;
int createcount,createcounttotal;
int nmax;
tagint *partner,*finalpartner;
double *distsq,*probability;
int ncreate,maxcreate;
tagint **created;
tagint *copy;
class RanMars *random;
class NeighList *list;
int countflag,commflag;
int nlevels_respa;
int nangles,ndihedrals,nimpropers;
void check_ghosts();
void update_topology();
- void recreate_special(int);
+ void rebuild_special_one(int);
void create_angles(int);
void create_dihedrals(int);
void create_impropers(int);
int dedup(int, int, tagint *);
// DEBUG
void print_bb();
void print_copy(const char *, tagint, int, int, int, int *);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Invalid atom type in fix bond/create command
Self-explanatory.
E: Invalid bond type in fix bond/create command
Self-explanatory.
E: Cannot use fix bond/create with non-molecular systems
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify.
E: Inconsistent iparam/jparam values in fix bond/create command
If itype and jtype are the same, then their maxbond and newtype
settings must also be the same.
E: Fix bond/create cutoff is longer than pairwise cutoff
This is not allowed because bond creation is done using the
pairwise neighbor list.
E: Fix bond/create angle type is invalid
Self-explanatory.
E: Fix bond/create dihedral type is invalid
Self-explanatory.
E: Fix bond/create improper type is invalid
Self-explanatory.
E: Cannot yet use fix bond/create with this improper style
This is a current restriction in LAMMPS.
E: Fix bond/create needs ghost atoms from further away
This is because the fix needs to walk bonds to a certain distance to
acquire needed info, The comm_modify cutoff command can be used to
extend the communication range.
E: New bond exceeded bonds per atom in fix bond/create
See the read_data command for info on setting the "extra bond per
atom" header value to allow for additional bonds to be formed.
E: New bond exceeded special list size in fix bond/create
See the special_bonds extra command for info on how to leave space in
the special bonds list to allow for additional bonds to be formed.
E: Fix bond/create induced too many angles/dihedrals/impropers per atom
See the read_data command for info on setting the "extra angle per
atom", etc header values to allow for additional angles, etc to be
formed.
E: Special list size exceeded in fix bond/create
See the read_data command for info on setting the "extra special per
atom" header value to allow for additional special values to be
stored.
*/
diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp
index 192e888dc..d82445560 100644
--- a/src/RIGID/fix_shake.cpp
+++ b/src/RIGID/fix_shake.cpp
@@ -1,2706 +1,2707 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "stdio.h"
#include "fix_shake.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "update.h"
#include "respa.h"
#include "modify.h"
#include "domain.h"
#include "force.h"
#include "bond.h"
#include "angle.h"
#include "comm.h"
#include "group.h"
#include "fix_respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
// allocate space for static class variable
FixShake *FixShake::fsptr;
#define BIG 1.0e20
#define MASSDELTA 0.1
/* ---------------------------------------------------------------------- */
FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
virial_flag = 1;
create_attribute = 1;
dof_flag = 1;
// error check
molecular = atom->molecular;
if (molecular == 0)
error->all(FLERR,"Cannot use fix shake with non-molecular system");
// perform initial allocation of atom-based arrays
// register with Atom class
shake_flag = NULL;
shake_atom = NULL;
shake_type = NULL;
xshake = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
// set comm size needed by this fix
comm_forward = 3;
// parse SHAKE args
if (narg < 8) error->all(FLERR,"Illegal fix shake command");
tolerance = force->numeric(FLERR,arg[3]);
max_iter = force->inumeric(FLERR,arg[4]);
output_every = force->inumeric(FLERR,arg[5]);
// parse SHAKE args for bond and angle types
// will be used by find_clusters
// store args for "b" "a" "t" as flags in (1:n) list for fast access
// store args for "m" in list of length nmass for looping over
// for "m" verify that atom masses have been set
bond_flag = new int[atom->nbondtypes+1];
for (int i = 1; i <= atom->nbondtypes; i++) bond_flag[i] = 0;
angle_flag = new int[atom->nangletypes+1];
for (int i = 1; i <= atom->nangletypes; i++) angle_flag[i] = 0;
type_flag = new int[atom->ntypes+1];
for (int i = 1; i <= atom->ntypes; i++) type_flag[i] = 0;
mass_list = new double[atom->ntypes];
nmass = 0;
char mode = '\0';
int next = 6;
while (next < narg) {
if (strcmp(arg[next],"b") == 0) mode = 'b';
else if (strcmp(arg[next],"a") == 0) mode = 'a';
else if (strcmp(arg[next],"t") == 0) mode = 't';
else if (strcmp(arg[next],"m") == 0) {
mode = 'm';
atom->check_mass();
// break if keyword that is not b,a,t,m
} else if (isalpha(arg[next][0])) break;
// read numeric args of b,a,t,m
else if (mode == 'b') {
int i = force->inumeric(FLERR,arg[next]);
if (i < 1 || i > atom->nbondtypes)
error->all(FLERR,"Invalid bond type index for fix shake");
bond_flag[i] = 1;
} else if (mode == 'a') {
int i = force->inumeric(FLERR,arg[next]);
if (i < 1 || i > atom->nangletypes)
error->all(FLERR,"Invalid angle type index for fix shake");
angle_flag[i] = 1;
} else if (mode == 't') {
int i = force->inumeric(FLERR,arg[next]);
if (i < 1 || i > atom->ntypes)
error->all(FLERR,"Invalid atom type index for fix shake");
type_flag[i] = 1;
} else if (mode == 'm') {
double massone = force->numeric(FLERR,arg[next]);
if (massone == 0.0) error->all(FLERR,"Invalid atom mass for fix shake");
if (nmass == atom->ntypes)
error->all(FLERR,"Too many masses for fix shake");
mass_list[nmass++] = massone;
} else error->all(FLERR,"Illegal fix shake command");
next++;
}
// parse optional args
onemols = NULL;
int iarg = next;
while (iarg < narg) {
if (strcmp(arg[next],"mol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix shake command");
int imol = atom->find_molecule(arg[iarg+1]);
if (imol == -1)
error->all(FLERR,"Molecule template ID for fix shake does not exist");
if (atom->molecules[imol]->nset > 1 && comm->me == 0)
error->warning(FLERR,"Molecule template for "
"fix shake has multiple molecules");
onemols = &atom->molecules[imol];
nmol = onemols[0]->nset;
iarg += 2;
} else error->all(FLERR,"Illegal fix shake command");
}
// error check for Molecule template
if (onemols) {
for (int i = 0; i < nmol; i++)
if (onemols[i]->shakeflag == 0)
error->all(FLERR,"Fix shake molecule template must have shake info");
}
// allocate bond and angle distance arrays, indexed from 1 to n
bond_distance = new double[atom->nbondtypes+1];
angle_distance = new double[atom->nangletypes+1];
// allocate statistics arrays
if (output_every) {
int nb = atom->nbondtypes + 1;
b_count = new int[nb];
b_count_all = new int[nb];
b_ave = new double[nb];
b_ave_all = new double[nb];
b_max = new double[nb];
b_max_all = new double[nb];
b_min = new double[nb];
b_min_all = new double[nb];
int na = atom->nangletypes + 1;
a_count = new int[na];
a_count_all = new int[na];
a_ave = new double[na];
a_ave_all = new double[na];
a_max = new double[na];
a_max_all = new double[na];
a_min = new double[na];
a_min_all = new double[na];
}
// SHAKE vs RATTLE
rattle = 0;
vflag_post_force = 0;
// identify all SHAKE clusters
find_clusters();
// initialize list of SHAKE clusters to constrain
maxlist = 0;
list = NULL;
}
/* ---------------------------------------------------------------------- */
FixShake::~FixShake()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
// set bond_type and angle_type back to positive for SHAKE clusters
// must set for all SHAKE bonds and angles stored by each atom
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i] == 0) continue;
else if (shake_flag[i] == 1) {
bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],1);
bondtype_findset(i,shake_atom[i][0],shake_atom[i][2],1);
angletype_findset(i,shake_atom[i][1],shake_atom[i][2],1);
} else if (shake_flag[i] == 2) {
bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],1);
} else if (shake_flag[i] == 3) {
bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],1);
bondtype_findset(i,shake_atom[i][0],shake_atom[i][2],1);
} else if (shake_flag[i] == 4) {
bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],1);
bondtype_findset(i,shake_atom[i][0],shake_atom[i][2],1);
bondtype_findset(i,shake_atom[i][0],shake_atom[i][3],1);
}
}
// delete locally stored arrays
memory->destroy(shake_flag);
memory->destroy(shake_atom);
memory->destroy(shake_type);
memory->destroy(xshake);
delete [] bond_flag;
delete [] angle_flag;
delete [] type_flag;
delete [] mass_list;
delete [] bond_distance;
delete [] angle_distance;
if (output_every) {
delete [] b_count;
delete [] b_count_all;
delete [] b_ave;
delete [] b_ave_all;
delete [] b_max;
delete [] b_max_all;
delete [] b_min;
delete [] b_min_all;
delete [] a_count;
delete [] a_count_all;
delete [] a_ave;
delete [] a_ave_all;
delete [] a_max;
delete [] a_max_all;
delete [] a_min;
delete [] a_min_all;
}
memory->destroy(list);
}
/* ---------------------------------------------------------------------- */
int FixShake::setmask()
{
int mask = 0;
mask |= PRE_NEIGHBOR;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
return mask;
}
/* ----------------------------------------------------------------------
set bond and angle distances
this init must happen after force->bond and force->angle inits
------------------------------------------------------------------------- */
void FixShake::init()
{
int i,m,flag,flag_all,type1,type2,bond1_type,bond2_type;
double rsq,angle;
// error if more than one shake fix
int count = 0;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"shake") == 0) count++;
if (count > 1) error->all(FLERR,"More than one fix shake");
// cannot use with minimization since SHAKE turns off bonds
// that should contribute to potential energy
if (update->whichflag == 2)
error->all(FLERR,"Fix shake cannot be used with minimization");
// error if npt,nph fix comes before shake fix
for (i = 0; i < modify->nfix; i++) {
if (strcmp(modify->fix[i]->style,"npt") == 0) break;
if (strcmp(modify->fix[i]->style,"nph") == 0) break;
}
if (i < modify->nfix) {
for (int j = i; j < modify->nfix; j++)
if (strcmp(modify->fix[j]->style,"shake") == 0)
error->all(FLERR,"Shake fix must come before NPT/NPH fix");
}
// if rRESPA, find associated fix that must exist
// could have changed locations in fix list since created
// set ptrs to rRESPA variables
if (strstr(update->integrate_style,"respa")) {
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"RESPA") == 0) ifix_respa = i;
nlevels_respa = ((Respa *) update->integrate)->nlevels;
loop_respa = ((Respa *) update->integrate)->loop;
step_respa = ((Respa *) update->integrate)->step;
}
// set equilibrium bond distances
if (force->bond == NULL)
error->all(FLERR,"Bond potential must be defined for SHAKE");
for (i = 1; i <= atom->nbondtypes; i++)
bond_distance[i] = force->bond->equilibrium_distance(i);
// set equilibrium angle distances
int nlocal = atom->nlocal;
-
+
for (i = 1; i <= atom->nangletypes; i++) {
if (angle_flag[i] == 0) continue;
if (force->angle == NULL)
error->all(FLERR,"Angle potential must be defined for SHAKE");
// scan all atoms for a SHAKE angle cluster
// extract bond types for the 2 bonds in the cluster
// bond types must be same in all clusters of this angle type,
// else set error flag
flag = 0;
bond1_type = bond2_type = 0;
for (m = 0; m < nlocal; m++) {
if (shake_flag[m] != 1) continue;
if (shake_type[m][2] != i) continue;
type1 = MIN(shake_type[m][0],shake_type[m][1]);
type2 = MAX(shake_type[m][0],shake_type[m][1]);
if (bond1_type > 0) {
if (type1 != bond1_type || type2 != bond2_type) {
flag = 1;
break;
}
}
bond1_type = type1;
bond2_type = type2;
}
// error check for any bond types that are not the same
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_MAX,world);
if (flag_all) error->all(FLERR,"Shake angles have different bond types");
// insure all procs have bond types
MPI_Allreduce(&bond1_type,&flag_all,1,MPI_INT,MPI_MAX,world);
bond1_type = flag_all;
MPI_Allreduce(&bond2_type,&flag_all,1,MPI_INT,MPI_MAX,world);
bond2_type = flag_all;
// if bond types are 0, no SHAKE angles of this type exist
// just skip this angle
if (bond1_type == 0) {
angle_distance[i] = 0.0;
continue;
}
// compute the angle distance as a function of 2 bond distances
+ // formula is now correct for bonds of same or different lengths (Oct15)
angle = force->angle->equilibrium_angle(i);
const double b1 = bond_distance[bond1_type];
const double b2 = bond_distance[bond2_type];
rsq = b1*b1 + b2*b2 - 2.0*b1*b2*cos(angle);
angle_distance[i] = sqrt(rsq);
}
}
/* ----------------------------------------------------------------------
SHAKE as pre-integrator constraint
------------------------------------------------------------------------- */
void FixShake::setup(int vflag)
{
pre_neighbor();
if (output_every) stats();
// setup SHAKE output
bigint ntimestep = update->ntimestep;
if (output_every) {
next_output = ntimestep + output_every;
if (ntimestep % output_every != 0)
next_output = (ntimestep/output_every)*output_every + output_every;
} else next_output = -1;
// half timestep constraint on pre-step, full timestep thereafter
if (strstr(update->integrate_style,"verlet")) {
respa = 0;
dtv = update->dt;
dtfsq = 0.5 * update->dt * update->dt * force->ftm2v;
FixShake::post_force(vflag);
if (!rattle) dtfsq = update->dt * update->dt * force->ftm2v;
} else {
respa = 1;
dtv = step_respa[0];
dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v;
dtf_inner = dtf_innerhalf;
// apply correction to all rRESPA levels
for (int ilevel = 0; ilevel < nlevels_respa; ilevel++) {
((Respa *) update->integrate)->copy_flevel_f(ilevel);
FixShake::post_force_respa(vflag,ilevel,loop_respa[ilevel]-1);
((Respa *) update->integrate)->copy_f_flevel(ilevel);
}
if (!rattle) dtf_inner = step_respa[0] * force->ftm2v;
}
}
/* ----------------------------------------------------------------------
build list of SHAKE clusters to constrain
if one or more atoms in cluster are on this proc,
this proc lists the cluster exactly once
------------------------------------------------------------------------- */
void FixShake::pre_neighbor()
{
int atom1,atom2,atom3,atom4;
// local copies of atom quantities
// used by SHAKE until next re-neighboring
x = atom->x;
v = atom->v;
f = atom->f;
mass = atom->mass;
rmass = atom->rmass;
type = atom->type;
nlocal = atom->nlocal;
// extend size of SHAKE list if necessary
if (nlocal > maxlist) {
maxlist = nlocal;
memory->destroy(list);
memory->create(list,maxlist,"shake:list");
}
// build list of SHAKE clusters I compute
nlist = 0;
for (int i = 0; i < nlocal; i++)
if (shake_flag[i]) {
if (shake_flag[i] == 2) {
atom1 = atom->map(shake_atom[i][0]);
atom2 = atom->map(shake_atom[i][1]);
if (atom1 == -1 || atom2 == -1) {
char str[128];
sprintf(str,"Shake atoms " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],me,update->ntimestep);
error->one(FLERR,str);
}
if (i <= atom1 && i <= atom2) list[nlist++] = i;
} else if (shake_flag[i] % 2 == 1) {
atom1 = atom->map(shake_atom[i][0]);
atom2 = atom->map(shake_atom[i][1]);
atom3 = atom->map(shake_atom[i][2]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
char str[128];
sprintf(str,"Shake atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],shake_atom[i][2],
me,update->ntimestep);
error->one(FLERR,str);
}
if (i <= atom1 && i <= atom2 && i <= atom3) list[nlist++] = i;
} else {
atom1 = atom->map(shake_atom[i][0]);
atom2 = atom->map(shake_atom[i][1]);
atom3 = atom->map(shake_atom[i][2]);
atom4 = atom->map(shake_atom[i][3]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
char str[128];
sprintf(str,"Shake atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],
shake_atom[i][2],shake_atom[i][3],
me,update->ntimestep);
error->one(FLERR,str);
}
if (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)
list[nlist++] = i;
}
}
}
/* ----------------------------------------------------------------------
compute the force adjustment for SHAKE constraint
------------------------------------------------------------------------- */
void FixShake::post_force(int vflag)
{
if (update->ntimestep == next_output) stats();
// xshake = unconstrained move with current v,f
// communicate results if necessary
unconstrained_update();
if (nprocs > 1) comm->forward_comm_fix(this);
// virial setup
if (vflag) v_setup(vflag);
else evflag = 0;
// loop over clusters to add constraint forces
int m;
for (int i = 0; i < nlist; i++) {
m = list[i];
if (shake_flag[m] == 2) shake(m);
else if (shake_flag[m] == 3) shake3(m);
else if (shake_flag[m] == 4) shake4(m);
else shake3angle(m);
}
// store vflag for coordinate_constraints_end_of_step()
vflag_post_force = vflag;
}
/* ----------------------------------------------------------------------
enforce SHAKE constraints from rRESPA
xshake prediction portion is different than Verlet
------------------------------------------------------------------------- */
void FixShake::post_force_respa(int vflag, int ilevel, int iloop)
{
// call stats only on outermost level
if (ilevel == nlevels_respa-1 && update->ntimestep == next_output) stats();
// might be OK to skip enforcing SHAKE constraings
// on last iteration of inner levels if pressure not requested
// however, leads to slightly different trajectories
//if (ilevel < nlevels_respa-1 && iloop == loop_respa[ilevel]-1 && !vflag)
// return;
// xshake = unconstrained move with current v,f as function of level
// communicate results if necessary
unconstrained_update_respa(ilevel);
if (nprocs > 1) comm->forward_comm_fix(this);
// virial setup only needed on last iteration of innermost level
// and if pressure is requested
// virial accumulation happens via evflag at last iteration of each level
if (ilevel == 0 && iloop == loop_respa[ilevel]-1 && vflag) v_setup(vflag);
if (iloop == loop_respa[ilevel]-1) evflag = 1;
else evflag = 0;
// loop over clusters to add constraint forces
int m;
for (int i = 0; i < nlist; i++) {
m = list[i];
if (shake_flag[m] == 2) shake(m);
else if (shake_flag[m] == 3) shake3(m);
else if (shake_flag[m] == 4) shake4(m);
else shake3angle(m);
}
// store vflag for coordinate_constraints_end_of_step()
vflag_post_force = vflag;
}
/* ----------------------------------------------------------------------
count # of degrees-of-freedom removed by SHAKE for atoms in igroup
------------------------------------------------------------------------- */
int FixShake::dof(int igroup)
{
int groupbit = group->bitmask[igroup];
int *mask = atom->mask;
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
// count dof in a cluster if and only if
// the central atom is in group and atom i is the central atom
int n = 0;
for (int i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
if (shake_flag[i] == 0) continue;
if (shake_atom[i][0] != tag[i]) continue;
if (shake_flag[i] == 1) n += 3;
else if (shake_flag[i] == 2) n += 1;
else if (shake_flag[i] == 3) n += 2;
else if (shake_flag[i] == 4) n += 3;
}
int nall;
MPI_Allreduce(&n,&nall,1,MPI_INT,MPI_SUM,world);
return nall;
}
/* ----------------------------------------------------------------------
identify whether each atom is in a SHAKE cluster
only include atoms in fix group and those bonds/angles specified in input
test whether all clusters are valid
set shake_flag, shake_atom, shake_type values
set bond,angle types negative so will be ignored in neighbor lists
------------------------------------------------------------------------- */
void FixShake::find_clusters()
{
int i,j,m,n,imol,iatom;
int flag,flag_all,nbuf,size;
tagint tagprev;
double massone;
tagint *buf;
if (me == 0 && screen) {
if (!rattle) fprintf(screen,"Finding SHAKE clusters ...\n");
else fprintf(screen,"Finding RATTLE clusters ...\n");
}
atommols = atom->avec->onemols;
tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double *mass = atom->mass;
double *rmass = atom->rmass;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
int nlocal = atom->nlocal;
int angles_allow = atom->avec->angles_allow;
// setup ring of procs
int next = me + 1;
int prev = me -1;
if (next == nprocs) next = 0;
if (prev < 0) prev = nprocs - 1;
// -----------------------------------------------------
// allocate arrays for self (1d) and bond partners (2d)
// max = max # of bond partners for owned atoms = 2nd dim of partner arrays
// npartner[i] = # of bonds attached to atom i
// nshake[i] = # of SHAKE bonds attached to atom i
// partner_tag[i][] = global IDs of each partner
// partner_mask[i][] = mask of each partner
// partner_type[i][] = type of each partner
// partner_massflag[i][] = 1 if partner meets mass criterion, 0 if not
// partner_bondtype[i][] = type of bond attached to each partner
// partner_shake[i][] = 1 if SHAKE bonded to partner, 0 if not
// partner_nshake[i][] = nshake value for each partner
// -----------------------------------------------------
int max = 0;
if (molecular == 1) {
for (i = 0; i < nlocal; i++) max = MAX(max,nspecial[i][0]);
} else {
for (i = 0; i < nlocal; i++) {
imol = molindex[i];
if (imol < 0) continue;
iatom = molatom[i];
max = MAX(max,atommols[imol]->nspecial[iatom][0]);
}
}
int *npartner;
memory->create(npartner,nlocal,"shake:npartner");
memory->create(nshake,nlocal,"shake:nshake");
tagint **partner_tag;
int **partner_mask,**partner_type,**partner_massflag;
int **partner_bondtype,**partner_shake,**partner_nshake;
memory->create(partner_tag,nlocal,max,"shake:partner_tag");
memory->create(partner_mask,nlocal,max,"shake:partner_mask");
memory->create(partner_type,nlocal,max,"shake:partner_type");
memory->create(partner_massflag,nlocal,max,"shake:partner_massflag");
memory->create(partner_bondtype,nlocal,max,"shake:partner_bondtype");
memory->create(partner_shake,nlocal,max,"shake:partner_shake");
memory->create(partner_nshake,nlocal,max,"shake:partner_nshake");
// -----------------------------------------------------
// set npartner and partner_tag from special arrays
// -----------------------------------------------------
if (molecular == 1) {
for (i = 0; i < nlocal; i++) {
npartner[i] = nspecial[i][0];
for (j = 0; j < npartner[i]; j++)
partner_tag[i][j] = special[i][j];
}
} else {
for (i = 0; i < nlocal; i++) {
imol = molindex[i];
if (imol < 0) continue;
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
npartner[i] = atommols[imol]->nspecial[iatom][0];
for (j = 0; j < npartner[i]; j++)
partner_tag[i][j] = atommols[imol]->special[iatom][j] + tagprev;;
}
}
// -----------------------------------------------------
// set partner_mask, partner_type, partner_massflag, partner_bondtype
// for bonded partners
// requires communication for off-proc partners
// -----------------------------------------------------
// fill in mask, type, massflag, bondtype if own bond partner
// info to store in buf for each off-proc bond = nper = 6
// 2 atoms IDs in bond, space for mask, type, massflag, bondtype
// nbufmax = largest buffer needed to hold info from any proc
int nper = 6;
nbuf = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < npartner[i]; j++) {
partner_mask[i][j] = 0;
partner_type[i][j] = 0;
partner_massflag[i][j] = 0;
partner_bondtype[i][j] = 0;
m = atom->map(partner_tag[i][j]);
if (m >= 0 && m < nlocal) {
partner_mask[i][j] = mask[m];
partner_type[i][j] = type[m];
if (nmass) {
if (rmass) massone = rmass[m];
else massone = mass[type[m]];
partner_massflag[i][j] = masscheck(massone);
}
n = bondtype_findset(i,tag[i],partner_tag[i][j],0);
if (n) partner_bondtype[i][j] = n;
else {
n = bondtype_findset(m,tag[i],partner_tag[i][j],0);
if (n) partner_bondtype[i][j] = n;
}
} else nbuf += nper;
}
}
memory->create(buf,nbuf,"shake:buf");
// fill buffer with info
size = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < npartner[i]; j++) {
m = atom->map(partner_tag[i][j]);
if (m < 0 || m >= nlocal) {
buf[size] = tag[i];
buf[size+1] = partner_tag[i][j];
buf[size+2] = 0;
buf[size+3] = 0;
buf[size+4] = 0;
n = bondtype_findset(i,tag[i],partner_tag[i][j],0);
if (n) buf[size+5] = n;
else buf[size+5] = 0;
size += nper;
}
}
}
// cycle buffer around ring of procs back to self
fsptr = this;
comm->ring(size,sizeof(tagint),buf,1,ring_bonds,buf);
// store partner info returned to me
m = 0;
while (m < size) {
i = atom->map(buf[m]);
for (j = 0; j < npartner[i]; j++)
if (buf[m+1] == partner_tag[i][j]) break;
partner_mask[i][j] = buf[m+2];
partner_type[i][j] = buf[m+3];
partner_massflag[i][j] = buf[m+4];
partner_bondtype[i][j] = buf[m+5];
m += nper;
}
memory->destroy(buf);
// error check for unfilled partner info
// if partner_type not set, is an error
// partner_bondtype may not be set if special list is not consistent
// with bondatom (e.g. due to delete_bonds command)
// this is OK if one or both atoms are not in fix group, since
// bond won't be SHAKEn anyway
// else it's an error
flag = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < npartner[i]; j++) {
if (partner_type[i][j] == 0) flag = 1;
if (!(mask[i] & groupbit)) continue;
if (!(partner_mask[i][j] & groupbit)) continue;
if (partner_bondtype[i][j] == 0) flag = 1;
}
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all(FLERR,"Did not find fix shake partner info");
// -----------------------------------------------------
// identify SHAKEable bonds
// set nshake[i] = # of SHAKE bonds attached to atom i
// set partner_shake[i][] = 1 if SHAKE bonded to partner, 0 if not
// both atoms must be in group, bondtype must be > 0
// check if bondtype is in input bond_flag
// check if type of either atom is in input type_flag
// check if mass of either atom is in input mass_list
// -----------------------------------------------------
int np;
for (i = 0; i < nlocal; i++) {
nshake[i] = 0;
np = npartner[i];
for (j = 0; j < np; j++) {
partner_shake[i][j] = 0;
if (!(mask[i] & groupbit)) continue;
if (!(partner_mask[i][j] & groupbit)) continue;
if (partner_bondtype[i][j] <= 0) continue;
if (bond_flag[partner_bondtype[i][j]]) {
partner_shake[i][j] = 1;
nshake[i]++;
continue;
}
if (type_flag[type[i]] || type_flag[partner_type[i][j]]) {
partner_shake[i][j] = 1;
nshake[i]++;
continue;
}
if (nmass) {
if (partner_massflag[i][j]) {
partner_shake[i][j] = 1;
nshake[i]++;
continue;
} else {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
if (masscheck(massone)) {
partner_shake[i][j] = 1;
nshake[i]++;
continue;
}
}
}
}
}
// -----------------------------------------------------
// set partner_nshake for bonded partners
// requires communication for off-proc partners
// -----------------------------------------------------
// fill in partner_nshake if own bond partner
// info to store in buf for each off-proc bond =
// 2 atoms IDs in bond, space for nshake value
// nbufmax = largest buffer needed to hold info from any proc
nbuf = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < npartner[i]; j++) {
m = atom->map(partner_tag[i][j]);
if (m >= 0 && m < nlocal) partner_nshake[i][j] = nshake[m];
else nbuf += 3;
}
}
memory->create(buf,nbuf,"shake:buf");
// fill buffer with info
size = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < npartner[i]; j++) {
m = atom->map(partner_tag[i][j]);
if (m < 0 || m >= nlocal) {
buf[size] = tag[i];
buf[size+1] = partner_tag[i][j];
size += 3;
}
}
}
// cycle buffer around ring of procs back to self
fsptr = this;
comm->ring(size,sizeof(tagint),buf,2,ring_nshake,buf);
// store partner info returned to me
m = 0;
while (m < size) {
i = atom->map(buf[m]);
for (j = 0; j < npartner[i]; j++)
if (buf[m+1] == partner_tag[i][j]) break;
partner_nshake[i][j] = buf[m+2];
m += 3;
}
memory->destroy(buf);
// -----------------------------------------------------
// error checks
// no atom with nshake > 3
// no connected atoms which both have nshake > 1
// -----------------------------------------------------
flag = 0;
for (i = 0; i < nlocal; i++) if (nshake[i] > 3) flag = 1;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all(FLERR,"Shake cluster of more than 4 atoms");
flag = 0;
for (i = 0; i < nlocal; i++) {
if (nshake[i] <= 1) continue;
for (j = 0; j < npartner[i]; j++)
if (partner_shake[i][j] && partner_nshake[i][j] > 1) flag = 1;
}
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all(FLERR,"Shake clusters are connected");
// -----------------------------------------------------
// set SHAKE arrays that are stored with atoms & add angle constraints
// zero shake arrays for all owned atoms
// if I am central atom set shake_flag & shake_atom & shake_type
// for 2-atom clusters, I am central atom if my atom ID < partner ID
// for 3-atom clusters, test for angle constraint
// angle will be stored by this atom if it exists
// if angle type matches angle_flag, then it is angle-constrained
// shake_flag[] = 0 if atom not in SHAKE cluster
// 2,3,4 = size of bond-only cluster
// 1 = 3-atom angle cluster
// shake_atom[][] = global IDs of 2,3,4 atoms in cluster
// central atom is 1st
// for 2-atom cluster, lowest ID is 1st
// shake_type[][] = bondtype of each bond in cluster
// for 3-atom angle cluster, 3rd value is angletype
// -----------------------------------------------------
for (i = 0; i < nlocal; i++) {
shake_flag[i] = 0;
shake_atom[i][0] = 0;
shake_atom[i][1] = 0;
shake_atom[i][2] = 0;
shake_atom[i][3] = 0;
shake_type[i][0] = 0;
shake_type[i][1] = 0;
shake_type[i][2] = 0;
if (nshake[i] == 1) {
for (j = 0; j < npartner[i]; j++)
if (partner_shake[i][j]) break;
if (partner_nshake[i][j] == 1 && tag[i] < partner_tag[i][j]) {
shake_flag[i] = 2;
shake_atom[i][0] = tag[i];
shake_atom[i][1] = partner_tag[i][j];
shake_type[i][0] = partner_bondtype[i][j];
}
}
if (nshake[i] > 1) {
shake_flag[i] = 1;
shake_atom[i][0] = tag[i];
for (j = 0; j < npartner[i]; j++)
if (partner_shake[i][j]) {
m = shake_flag[i];
shake_atom[i][m] = partner_tag[i][j];
shake_type[i][m-1] = partner_bondtype[i][j];
shake_flag[i]++;
}
}
if (nshake[i] == 2 && angles_allow) {
n = angletype_findset(i,shake_atom[i][1],shake_atom[i][2],0);
if (n <= 0) continue;
if (angle_flag[n]) {
shake_flag[i] = 1;
shake_type[i][2] = n;
}
}
}
// -----------------------------------------------------
// set shake_flag,shake_atom,shake_type for non-central atoms
// requires communication for off-proc atoms
// -----------------------------------------------------
// fill in shake arrays for each bond partner I own
// info to store in buf for each off-proc bond =
// all values from shake_flag, shake_atom, shake_type
// nbufmax = largest buffer needed to hold info from any proc
nbuf = 0;
for (i = 0; i < nlocal; i++) {
if (shake_flag[i] == 0) continue;
for (j = 0; j < npartner[i]; j++) {
if (partner_shake[i][j] == 0) continue;
m = atom->map(partner_tag[i][j]);
if (m >= 0 && m < nlocal) {
shake_flag[m] = shake_flag[i];
shake_atom[m][0] = shake_atom[i][0];
shake_atom[m][1] = shake_atom[i][1];
shake_atom[m][2] = shake_atom[i][2];
shake_atom[m][3] = shake_atom[i][3];
shake_type[m][0] = shake_type[i][0];
shake_type[m][1] = shake_type[i][1];
shake_type[m][2] = shake_type[i][2];
} else nbuf += 9;
}
}
memory->create(buf,nbuf,"shake:buf");
// fill buffer with info
size = 0;
for (i = 0; i < nlocal; i++) {
if (shake_flag[i] == 0) continue;
for (j = 0; j < npartner[i]; j++) {
if (partner_shake[i][j] == 0) continue;
m = atom->map(partner_tag[i][j]);
if (m < 0 || m >= nlocal) {
buf[size] = partner_tag[i][j];
buf[size+1] = shake_flag[i];
buf[size+2] = shake_atom[i][0];
buf[size+3] = shake_atom[i][1];
buf[size+4] = shake_atom[i][2];
buf[size+5] = shake_atom[i][3];
buf[size+6] = shake_type[i][0];
buf[size+7] = shake_type[i][1];
buf[size+8] = shake_type[i][2];
size += 9;
}
}
}
// cycle buffer around ring of procs back to self
fsptr = this;
comm->ring(size,sizeof(tagint),buf,3,ring_shake,NULL);
memory->destroy(buf);
// -----------------------------------------------------
// free local memory
// -----------------------------------------------------
memory->destroy(npartner);
memory->destroy(nshake);
memory->destroy(partner_tag);
memory->destroy(partner_mask);
memory->destroy(partner_type);
memory->destroy(partner_massflag);
memory->destroy(partner_bondtype);
memory->destroy(partner_shake);
memory->destroy(partner_nshake);
// -----------------------------------------------------
// set bond_type and angle_type negative for SHAKE clusters
// must set for all SHAKE bonds and angles stored by each atom
// -----------------------------------------------------
for (i = 0; i < nlocal; i++) {
if (shake_flag[i] == 0) continue;
else if (shake_flag[i] == 1) {
bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],-1);
bondtype_findset(i,shake_atom[i][0],shake_atom[i][2],-1);
angletype_findset(i,shake_atom[i][1],shake_atom[i][2],-1);
} else if (shake_flag[i] == 2) {
bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],-1);
} else if (shake_flag[i] == 3) {
bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],-1);
bondtype_findset(i,shake_atom[i][0],shake_atom[i][2],-1);
} else if (shake_flag[i] == 4) {
bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],-1);
bondtype_findset(i,shake_atom[i][0],shake_atom[i][2],-1);
bondtype_findset(i,shake_atom[i][0],shake_atom[i][3],-1);
}
}
// -----------------------------------------------------
// print info on SHAKE clusters
// -----------------------------------------------------
int count1,count2,count3,count4;
count1 = count2 = count3 = count4 = 0;
for (i = 0; i < nlocal; i++) {
if (shake_flag[i] == 1) count1++;
else if (shake_flag[i] == 2) count2++;
else if (shake_flag[i] == 3) count3++;
else if (shake_flag[i] == 4) count4++;
}
int tmp;
tmp = count1;
MPI_Allreduce(&tmp,&count1,1,MPI_INT,MPI_SUM,world);
tmp = count2;
MPI_Allreduce(&tmp,&count2,1,MPI_INT,MPI_SUM,world);
tmp = count3;
MPI_Allreduce(&tmp,&count3,1,MPI_INT,MPI_SUM,world);
tmp = count4;
MPI_Allreduce(&tmp,&count4,1,MPI_INT,MPI_SUM,world);
if (me == 0) {
if (screen) {
fprintf(screen," %d = # of size 2 clusters\n",count2/2);
fprintf(screen," %d = # of size 3 clusters\n",count3/3);
fprintf(screen," %d = # of size 4 clusters\n",count4/4);
fprintf(screen," %d = # of frozen angles\n",count1/3);
}
if (logfile) {
fprintf(logfile," %d = # of size 2 clusters\n",count2/2);
fprintf(logfile," %d = # of size 3 clusters\n",count3/3);
fprintf(logfile," %d = # of size 4 clusters\n",count4/4);
fprintf(logfile," %d = # of frozen angles\n",count1/3);
}
}
}
/* ----------------------------------------------------------------------
when receive buffer, scan bond partner IDs for atoms I own
if I own partner:
fill in mask and type and massflag
search for bond with 1st atom and fill in bondtype
------------------------------------------------------------------------- */
void FixShake::ring_bonds(int ndatum, char *cbuf)
{
Atom *atom = fsptr->atom;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
int nmass = fsptr->nmass;
tagint *buf = (tagint *) cbuf;
int m,n;
double massone;
for (int i = 0; i < ndatum; i += 6) {
m = atom->map(buf[i+1]);
if (m >= 0 && m < nlocal) {
buf[i+2] = mask[m];
buf[i+3] = type[m];
if (nmass) {
if (rmass) massone = rmass[m];
else massone = mass[type[m]];
buf[i+4] = fsptr->masscheck(massone);
}
if (buf[i+5] == 0) {
n = fsptr->bondtype_findset(m,buf[i],buf[i+1],0);
if (n) buf[i+5] = n;
}
}
}
}
/* ----------------------------------------------------------------------
when receive buffer, scan bond partner IDs for atoms I own
if I own partner, fill in nshake value
------------------------------------------------------------------------- */
void FixShake::ring_nshake(int ndatum, char *cbuf)
{
Atom *atom = fsptr->atom;
int nlocal = atom->nlocal;
int *nshake = fsptr->nshake;
tagint *buf = (tagint *) cbuf;
int m;
for (int i = 0; i < ndatum; i += 3) {
m = atom->map(buf[i+1]);
if (m >= 0 && m < nlocal) buf[i+2] = nshake[m];
}
}
/* ----------------------------------------------------------------------
when receive buffer, scan bond partner IDs for atoms I own
if I own partner, fill in nshake value
------------------------------------------------------------------------- */
void FixShake::ring_shake(int ndatum, char *cbuf)
{
Atom *atom = fsptr->atom;
int nlocal = atom->nlocal;
int *shake_flag = fsptr->shake_flag;
tagint **shake_atom = fsptr->shake_atom;
int **shake_type = fsptr->shake_type;
tagint *buf = (tagint *) cbuf;
int m;
for (int i = 0; i < ndatum; i += 9) {
m = atom->map(buf[i]);
if (m >= 0 && m < nlocal) {
shake_flag[m] = buf[i+1];
shake_atom[m][0] = buf[i+2];
shake_atom[m][1] = buf[i+3];
shake_atom[m][2] = buf[i+4];
shake_atom[m][3] = buf[i+5];
shake_type[m][0] = buf[i+6];
shake_type[m][1] = buf[i+7];
shake_type[m][2] = buf[i+8];
}
}
}
/* ----------------------------------------------------------------------
check if massone is within MASSDELTA of any mass in mass_list
return 1 if yes, 0 if not
------------------------------------------------------------------------- */
int FixShake::masscheck(double massone)
{
for (int i = 0; i < nmass; i++)
if (fabs(mass_list[i]-massone) <= MASSDELTA) return 1;
return 0;
}
/* ----------------------------------------------------------------------
update the unconstrained position of each atom
only for SHAKE clusters, else set to 0.0
assumes NVE update, seems to be accurate enough for NVT,NPT,NPH as well
------------------------------------------------------------------------- */
void FixShake::unconstrained_update()
{
double dtfmsq;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
dtfmsq = dtfsq / rmass[i];
xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
} else {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
dtfmsq = dtfsq / mass[type[i]];
xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
}
}
/* ----------------------------------------------------------------------
update the unconstrained position of each atom in a rRESPA step
only for SHAKE clusters, else set to 0.0
assumes NVE update, seems to be accurate enough for NVT,NPT,NPH as well
------------------------------------------------------------------------- */
void FixShake::unconstrained_update_respa(int ilevel)
{
// xshake = atom coords after next x update in innermost loop
// depends on rRESPA level
// for levels > 0 this includes more than one velocity update
// xshake = predicted position from call to this routine at level N =
// x + dt0 (v + dtN/m fN + 1/2 dt(N-1)/m f(N-1) + ... + 1/2 dt0/m f0)
// also set dtfsq = dt0*dtN so that shake,shake3,etc can use it
double ***f_level = ((FixRespa *) modify->fix[ifix_respa])->f_level;
dtfsq = dtf_inner * step_respa[ilevel];
double invmass,dtfmsq;
int jlevel;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
invmass = 1.0 / rmass[i];
dtfmsq = dtfsq * invmass;
xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
for (jlevel = 0; jlevel < ilevel; jlevel++) {
dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
}
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
} else {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
invmass = 1.0 / mass[type[i]];
dtfmsq = dtfsq * invmass;
xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
for (jlevel = 0; jlevel < ilevel; jlevel++) {
dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
}
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
}
}
/* ---------------------------------------------------------------------- */
void FixShake::shake(int m)
{
int nlist,list[2];
double v[6];
double invmass0,invmass1;
// local atom IDs and constraint distances
int i0 = atom->map(shake_atom[m][0]);
int i1 = atom->map(shake_atom[m][1]);
double bond1 = bond_distance[shake_type[m][0]];
// r01 = distance vec between atoms, with PBC
double r01[3];
r01[0] = x[i0][0] - x[i1][0];
r01[1] = x[i0][1] - x[i1][1];
r01[2] = x[i0][2] - x[i1][2];
domain->minimum_image(r01);
// s01 = distance vec after unconstrained update, with PBC
double s01[3];
s01[0] = xshake[i0][0] - xshake[i1][0];
s01[1] = xshake[i0][1] - xshake[i1][1];
s01[2] = xshake[i0][2] - xshake[i1][2];
domain->minimum_image(s01);
// scalar distances between atoms
double r01sq = r01[0]*r01[0] + r01[1]*r01[1] + r01[2]*r01[2];
double s01sq = s01[0]*s01[0] + s01[1]*s01[1] + s01[2]*s01[2];
// a,b,c = coeffs in quadratic equation for lamda
if (rmass) {
invmass0 = 1.0/rmass[i0];
invmass1 = 1.0/rmass[i1];
} else {
invmass0 = 1.0/mass[type[i0]];
invmass1 = 1.0/mass[type[i1]];
}
double a = (invmass0+invmass1)*(invmass0+invmass1) * r01sq;
double b = 2.0 * (invmass0+invmass1) *
(s01[0]*r01[0] + s01[1]*r01[1] + s01[2]*r01[2]);
double c = s01sq - bond1*bond1;
// error check
double determ = b*b - 4.0*a*c;
if (determ < 0.0) {
error->warning(FLERR,"Shake determinant < 0.0",0);
determ = 0.0;
}
// exact quadratic solution for lamda
double lamda,lamda1,lamda2;
lamda1 = (-b+sqrt(determ)) / (2.0*a);
lamda2 = (-b-sqrt(determ)) / (2.0*a);
if (fabs(lamda1) <= fabs(lamda2)) lamda = lamda1;
else lamda = lamda2;
// update forces if atom is owned by this processor
lamda /= dtfsq;
if (i0 < nlocal) {
f[i0][0] += lamda*r01[0];
f[i0][1] += lamda*r01[1];
f[i0][2] += lamda*r01[2];
}
if (i1 < nlocal) {
f[i1][0] -= lamda*r01[0];
f[i1][1] -= lamda*r01[1];
f[i1][2] -= lamda*r01[2];
}
if (evflag) {
nlist = 0;
if (i0 < nlocal) list[nlist++] = i0;
if (i1 < nlocal) list[nlist++] = i1;
v[0] = lamda*r01[0]*r01[0];
v[1] = lamda*r01[1]*r01[1];
v[2] = lamda*r01[2]*r01[2];
v[3] = lamda*r01[0]*r01[1];
v[4] = lamda*r01[0]*r01[2];
v[5] = lamda*r01[1]*r01[2];
v_tally(nlist,list,2.0,v);
}
}
/* ---------------------------------------------------------------------- */
void FixShake::shake3(int m)
{
int nlist,list[3];
double v[6];
double invmass0,invmass1,invmass2;
// local atom IDs and constraint distances
int i0 = atom->map(shake_atom[m][0]);
int i1 = atom->map(shake_atom[m][1]);
int i2 = atom->map(shake_atom[m][2]);
double bond1 = bond_distance[shake_type[m][0]];
double bond2 = bond_distance[shake_type[m][1]];
// r01,r02 = distance vec between atoms, with PBC
double r01[3];
r01[0] = x[i0][0] - x[i1][0];
r01[1] = x[i0][1] - x[i1][1];
r01[2] = x[i0][2] - x[i1][2];
domain->minimum_image(r01);
double r02[3];
r02[0] = x[i0][0] - x[i2][0];
r02[1] = x[i0][1] - x[i2][1];
r02[2] = x[i0][2] - x[i2][2];
domain->minimum_image(r02);
// s01,s02 = distance vec after unconstrained update, with PBC
double s01[3];
s01[0] = xshake[i0][0] - xshake[i1][0];
s01[1] = xshake[i0][1] - xshake[i1][1];
s01[2] = xshake[i0][2] - xshake[i1][2];
domain->minimum_image(s01);
double s02[3];
s02[0] = xshake[i0][0] - xshake[i2][0];
s02[1] = xshake[i0][1] - xshake[i2][1];
s02[2] = xshake[i0][2] - xshake[i2][2];
domain->minimum_image(s02);
// scalar distances between atoms
double r01sq = r01[0]*r01[0] + r01[1]*r01[1] + r01[2]*r01[2];
double r02sq = r02[0]*r02[0] + r02[1]*r02[1] + r02[2]*r02[2];
double s01sq = s01[0]*s01[0] + s01[1]*s01[1] + s01[2]*s01[2];
double s02sq = s02[0]*s02[0] + s02[1]*s02[1] + s02[2]*s02[2];
// matrix coeffs and rhs for lamda equations
if (rmass) {
invmass0 = 1.0/rmass[i0];
invmass1 = 1.0/rmass[i1];
invmass2 = 1.0/rmass[i2];
} else {
invmass0 = 1.0/mass[type[i0]];
invmass1 = 1.0/mass[type[i1]];
invmass2 = 1.0/mass[type[i2]];
}
double a11 = 2.0 * (invmass0+invmass1) *
(s01[0]*r01[0] + s01[1]*r01[1] + s01[2]*r01[2]);
double a12 = 2.0 * invmass0 *
(s01[0]*r02[0] + s01[1]*r02[1] + s01[2]*r02[2]);
double a21 = 2.0 * invmass0 *
(s02[0]*r01[0] + s02[1]*r01[1] + s02[2]*r01[2]);
double a22 = 2.0 * (invmass0+invmass2) *
(s02[0]*r02[0] + s02[1]*r02[1] + s02[2]*r02[2]);
// inverse of matrix
double determ = a11*a22 - a12*a21;
if (determ == 0.0) error->one(FLERR,"Shake determinant = 0.0");
double determinv = 1.0/determ;
double a11inv = a22*determinv;
double a12inv = -a12*determinv;
double a21inv = -a21*determinv;
double a22inv = a11*determinv;
// quadratic correction coeffs
double r0102 = (r01[0]*r02[0] + r01[1]*r02[1] + r01[2]*r02[2]);
double quad1_0101 = (invmass0+invmass1)*(invmass0+invmass1) * r01sq;
double quad1_0202 = invmass0*invmass0 * r02sq;
double quad1_0102 = 2.0 * (invmass0+invmass1)*invmass0 * r0102;
double quad2_0202 = (invmass0+invmass2)*(invmass0+invmass2) * r02sq;
double quad2_0101 = invmass0*invmass0 * r01sq;
double quad2_0102 = 2.0 * (invmass0+invmass2)*invmass0 * r0102;
// iterate until converged
double lamda01 = 0.0;
double lamda02 = 0.0;
int niter = 0;
int done = 0;
double quad1,quad2,b1,b2,lamda01_new,lamda02_new;
while (!done && niter < max_iter) {
quad1 = quad1_0101 * lamda01*lamda01 + quad1_0202 * lamda02*lamda02 +
quad1_0102 * lamda01*lamda02;
quad2 = quad2_0101 * lamda01*lamda01 + quad2_0202 * lamda02*lamda02 +
quad2_0102 * lamda01*lamda02;
b1 = bond1*bond1 - s01sq - quad1;
b2 = bond2*bond2 - s02sq - quad2;
lamda01_new = a11inv*b1 + a12inv*b2;
lamda02_new = a21inv*b1 + a22inv*b2;
done = 1;
if (fabs(lamda01_new-lamda01) > tolerance) done = 0;
if (fabs(lamda02_new-lamda02) > tolerance) done = 0;
lamda01 = lamda01_new;
lamda02 = lamda02_new;
niter++;
}
// update forces if atom is owned by this processor
lamda01 = lamda01/dtfsq;
lamda02 = lamda02/dtfsq;
if (i0 < nlocal) {
f[i0][0] += lamda01*r01[0] + lamda02*r02[0];
f[i0][1] += lamda01*r01[1] + lamda02*r02[1];
f[i0][2] += lamda01*r01[2] + lamda02*r02[2];
}
if (i1 < nlocal) {
f[i1][0] -= lamda01*r01[0];
f[i1][1] -= lamda01*r01[1];
f[i1][2] -= lamda01*r01[2];
}
if (i2 < nlocal) {
f[i2][0] -= lamda02*r02[0];
f[i2][1] -= lamda02*r02[1];
f[i2][2] -= lamda02*r02[2];
}
if (evflag) {
nlist = 0;
if (i0 < nlocal) list[nlist++] = i0;
if (i1 < nlocal) list[nlist++] = i1;
if (i2 < nlocal) list[nlist++] = i2;
v[0] = lamda01*r01[0]*r01[0] + lamda02*r02[0]*r02[0];
v[1] = lamda01*r01[1]*r01[1] + lamda02*r02[1]*r02[1];
v[2] = lamda01*r01[2]*r01[2] + lamda02*r02[2]*r02[2];
v[3] = lamda01*r01[0]*r01[1] + lamda02*r02[0]*r02[1];
v[4] = lamda01*r01[0]*r01[2] + lamda02*r02[0]*r02[2];
v[5] = lamda01*r01[1]*r01[2] + lamda02*r02[1]*r02[2];
v_tally(nlist,list,3.0,v);
}
}
/* ---------------------------------------------------------------------- */
void FixShake::shake4(int m)
{
int nlist,list[4];
double v[6];
double invmass0,invmass1,invmass2,invmass3;
// local atom IDs and constraint distances
int i0 = atom->map(shake_atom[m][0]);
int i1 = atom->map(shake_atom[m][1]);
int i2 = atom->map(shake_atom[m][2]);
int i3 = atom->map(shake_atom[m][3]);
double bond1 = bond_distance[shake_type[m][0]];
double bond2 = bond_distance[shake_type[m][1]];
double bond3 = bond_distance[shake_type[m][2]];
// r01,r02,r03 = distance vec between atoms, with PBC
double r01[3];
r01[0] = x[i0][0] - x[i1][0];
r01[1] = x[i0][1] - x[i1][1];
r01[2] = x[i0][2] - x[i1][2];
domain->minimum_image(r01);
double r02[3];
r02[0] = x[i0][0] - x[i2][0];
r02[1] = x[i0][1] - x[i2][1];
r02[2] = x[i0][2] - x[i2][2];
domain->minimum_image(r02);
double r03[3];
r03[0] = x[i0][0] - x[i3][0];
r03[1] = x[i0][1] - x[i3][1];
r03[2] = x[i0][2] - x[i3][2];
domain->minimum_image(r03);
// s01,s02,s03 = distance vec after unconstrained update, with PBC
double s01[3];
s01[0] = xshake[i0][0] - xshake[i1][0];
s01[1] = xshake[i0][1] - xshake[i1][1];
s01[2] = xshake[i0][2] - xshake[i1][2];
domain->minimum_image(s01);
double s02[3];
s02[0] = xshake[i0][0] - xshake[i2][0];
s02[1] = xshake[i0][1] - xshake[i2][1];
s02[2] = xshake[i0][2] - xshake[i2][2];
domain->minimum_image(s02);
double s03[3];
s03[0] = xshake[i0][0] - xshake[i3][0];
s03[1] = xshake[i0][1] - xshake[i3][1];
s03[2] = xshake[i0][2] - xshake[i3][2];
domain->minimum_image(s03);
// scalar distances between atoms
double r01sq = r01[0]*r01[0] + r01[1]*r01[1] + r01[2]*r01[2];
double r02sq = r02[0]*r02[0] + r02[1]*r02[1] + r02[2]*r02[2];
double r03sq = r03[0]*r03[0] + r03[1]*r03[1] + r03[2]*r03[2];
double s01sq = s01[0]*s01[0] + s01[1]*s01[1] + s01[2]*s01[2];
double s02sq = s02[0]*s02[0] + s02[1]*s02[1] + s02[2]*s02[2];
double s03sq = s03[0]*s03[0] + s03[1]*s03[1] + s03[2]*s03[2];
// matrix coeffs and rhs for lamda equations
if (rmass) {
invmass0 = 1.0/rmass[i0];
invmass1 = 1.0/rmass[i1];
invmass2 = 1.0/rmass[i2];
invmass3 = 1.0/rmass[i3];
} else {
invmass0 = 1.0/mass[type[i0]];
invmass1 = 1.0/mass[type[i1]];
invmass2 = 1.0/mass[type[i2]];
invmass3 = 1.0/mass[type[i3]];
}
double a11 = 2.0 * (invmass0+invmass1) *
(s01[0]*r01[0] + s01[1]*r01[1] + s01[2]*r01[2]);
double a12 = 2.0 * invmass0 *
(s01[0]*r02[0] + s01[1]*r02[1] + s01[2]*r02[2]);
double a13 = 2.0 * invmass0 *
(s01[0]*r03[0] + s01[1]*r03[1] + s01[2]*r03[2]);
double a21 = 2.0 * invmass0 *
(s02[0]*r01[0] + s02[1]*r01[1] + s02[2]*r01[2]);
double a22 = 2.0 * (invmass0+invmass2) *
(s02[0]*r02[0] + s02[1]*r02[1] + s02[2]*r02[2]);
double a23 = 2.0 * invmass0 *
(s02[0]*r03[0] + s02[1]*r03[1] + s02[2]*r03[2]);
double a31 = 2.0 * invmass0 *
(s03[0]*r01[0] + s03[1]*r01[1] + s03[2]*r01[2]);
double a32 = 2.0 * invmass0 *
(s03[0]*r02[0] + s03[1]*r02[1] + s03[2]*r02[2]);
double a33 = 2.0 * (invmass0+invmass3) *
(s03[0]*r03[0] + s03[1]*r03[1] + s03[2]*r03[2]);
// inverse of matrix;
double determ = a11*a22*a33 + a12*a23*a31 + a13*a21*a32 -
a11*a23*a32 - a12*a21*a33 - a13*a22*a31;
if (determ == 0.0) error->one(FLERR,"Shake determinant = 0.0");
double determinv = 1.0/determ;
double a11inv = determinv * (a22*a33 - a23*a32);
double a12inv = -determinv * (a12*a33 - a13*a32);
double a13inv = determinv * (a12*a23 - a13*a22);
double a21inv = -determinv * (a21*a33 - a23*a31);
double a22inv = determinv * (a11*a33 - a13*a31);
double a23inv = -determinv * (a11*a23 - a13*a21);
double a31inv = determinv * (a21*a32 - a22*a31);
double a32inv = -determinv * (a11*a32 - a12*a31);
double a33inv = determinv * (a11*a22 - a12*a21);
// quadratic correction coeffs
double r0102 = (r01[0]*r02[0] + r01[1]*r02[1] + r01[2]*r02[2]);
double r0103 = (r01[0]*r03[0] + r01[1]*r03[1] + r01[2]*r03[2]);
double r0203 = (r02[0]*r03[0] + r02[1]*r03[1] + r02[2]*r03[2]);
double quad1_0101 = (invmass0+invmass1)*(invmass0+invmass1) * r01sq;
double quad1_0202 = invmass0*invmass0 * r02sq;
double quad1_0303 = invmass0*invmass0 * r03sq;
double quad1_0102 = 2.0 * (invmass0+invmass1)*invmass0 * r0102;
double quad1_0103 = 2.0 * (invmass0+invmass1)*invmass0 * r0103;
double quad1_0203 = 2.0 * invmass0*invmass0 * r0203;
double quad2_0101 = invmass0*invmass0 * r01sq;
double quad2_0202 = (invmass0+invmass2)*(invmass0+invmass2) * r02sq;
double quad2_0303 = invmass0*invmass0 * r03sq;
double quad2_0102 = 2.0 * (invmass0+invmass2)*invmass0 * r0102;
double quad2_0103 = 2.0 * invmass0*invmass0 * r0103;
double quad2_0203 = 2.0 * (invmass0+invmass2)*invmass0 * r0203;
double quad3_0101 = invmass0*invmass0 * r01sq;
double quad3_0202 = invmass0*invmass0 * r02sq;
double quad3_0303 = (invmass0+invmass3)*(invmass0+invmass3) * r03sq;
double quad3_0102 = 2.0 * invmass0*invmass0 * r0102;
double quad3_0103 = 2.0 * (invmass0+invmass3)*invmass0 * r0103;
double quad3_0203 = 2.0 * (invmass0+invmass3)*invmass0 * r0203;
// iterate until converged
double lamda01 = 0.0;
double lamda02 = 0.0;
double lamda03 = 0.0;
int niter = 0;
int done = 0;
double quad1,quad2,quad3,b1,b2,b3,lamda01_new,lamda02_new,lamda03_new;
while (!done && niter < max_iter) {
quad1 = quad1_0101 * lamda01*lamda01 +
quad1_0202 * lamda02*lamda02 +
quad1_0303 * lamda03*lamda03 +
quad1_0102 * lamda01*lamda02 +
quad1_0103 * lamda01*lamda03 +
quad1_0203 * lamda02*lamda03;
quad2 = quad2_0101 * lamda01*lamda01 +
quad2_0202 * lamda02*lamda02 +
quad2_0303 * lamda03*lamda03 +
quad2_0102 * lamda01*lamda02 +
quad2_0103 * lamda01*lamda03 +
quad2_0203 * lamda02*lamda03;
quad3 = quad3_0101 * lamda01*lamda01 +
quad3_0202 * lamda02*lamda02 +
quad3_0303 * lamda03*lamda03 +
quad3_0102 * lamda01*lamda02 +
quad3_0103 * lamda01*lamda03 +
quad3_0203 * lamda02*lamda03;
b1 = bond1*bond1 - s01sq - quad1;
b2 = bond2*bond2 - s02sq - quad2;
b3 = bond3*bond3 - s03sq - quad3;
lamda01_new = a11inv*b1 + a12inv*b2 + a13inv*b3;
lamda02_new = a21inv*b1 + a22inv*b2 + a23inv*b3;
lamda03_new = a31inv*b1 + a32inv*b2 + a33inv*b3;
done = 1;
if (fabs(lamda01_new-lamda01) > tolerance) done = 0;
if (fabs(lamda02_new-lamda02) > tolerance) done = 0;
if (fabs(lamda03_new-lamda03) > tolerance) done = 0;
lamda01 = lamda01_new;
lamda02 = lamda02_new;
lamda03 = lamda03_new;
niter++;
}
// update forces if atom is owned by this processor
lamda01 = lamda01/dtfsq;
lamda02 = lamda02/dtfsq;
lamda03 = lamda03/dtfsq;
if (i0 < nlocal) {
f[i0][0] += lamda01*r01[0] + lamda02*r02[0] + lamda03*r03[0];
f[i0][1] += lamda01*r01[1] + lamda02*r02[1] + lamda03*r03[1];
f[i0][2] += lamda01*r01[2] + lamda02*r02[2] + lamda03*r03[2];
}
if (i1 < nlocal) {
f[i1][0] -= lamda01*r01[0];
f[i1][1] -= lamda01*r01[1];
f[i1][2] -= lamda01*r01[2];
}
if (i2 < nlocal) {
f[i2][0] -= lamda02*r02[0];
f[i2][1] -= lamda02*r02[1];
f[i2][2] -= lamda02*r02[2];
}
if (i3 < nlocal) {
f[i3][0] -= lamda03*r03[0];
f[i3][1] -= lamda03*r03[1];
f[i3][2] -= lamda03*r03[2];
}
if (evflag) {
nlist = 0;
if (i0 < nlocal) list[nlist++] = i0;
if (i1 < nlocal) list[nlist++] = i1;
if (i2 < nlocal) list[nlist++] = i2;
if (i3 < nlocal) list[nlist++] = i3;
v[0] = lamda01*r01[0]*r01[0]+lamda02*r02[0]*r02[0]+lamda03*r03[0]*r03[0];
v[1] = lamda01*r01[1]*r01[1]+lamda02*r02[1]*r02[1]+lamda03*r03[1]*r03[1];
v[2] = lamda01*r01[2]*r01[2]+lamda02*r02[2]*r02[2]+lamda03*r03[2]*r03[2];
v[3] = lamda01*r01[0]*r01[1]+lamda02*r02[0]*r02[1]+lamda03*r03[0]*r03[1];
v[4] = lamda01*r01[0]*r01[2]+lamda02*r02[0]*r02[2]+lamda03*r03[0]*r03[2];
v[5] = lamda01*r01[1]*r01[2]+lamda02*r02[1]*r02[2]+lamda03*r03[1]*r03[2];
v_tally(nlist,list,4.0,v);
}
}
/* ---------------------------------------------------------------------- */
void FixShake::shake3angle(int m)
{
int nlist,list[3];
double v[6];
double invmass0,invmass1,invmass2;
// local atom IDs and constraint distances
int i0 = atom->map(shake_atom[m][0]);
int i1 = atom->map(shake_atom[m][1]);
int i2 = atom->map(shake_atom[m][2]);
double bond1 = bond_distance[shake_type[m][0]];
double bond2 = bond_distance[shake_type[m][1]];
double bond12 = angle_distance[shake_type[m][2]];
// r01,r02,r12 = distance vec between atoms, with PBC
double r01[3];
r01[0] = x[i0][0] - x[i1][0];
r01[1] = x[i0][1] - x[i1][1];
r01[2] = x[i0][2] - x[i1][2];
domain->minimum_image(r01);
double r02[3];
r02[0] = x[i0][0] - x[i2][0];
r02[1] = x[i0][1] - x[i2][1];
r02[2] = x[i0][2] - x[i2][2];
domain->minimum_image(r02);
double r12[3];
r12[0] = x[i1][0] - x[i2][0];
r12[1] = x[i1][1] - x[i2][1];
r12[2] = x[i1][2] - x[i2][2];
domain->minimum_image(r12);
// s01,s02,s12 = distance vec after unconstrained update, with PBC
double s01[3];
s01[0] = xshake[i0][0] - xshake[i1][0];
s01[1] = xshake[i0][1] - xshake[i1][1];
s01[2] = xshake[i0][2] - xshake[i1][2];
domain->minimum_image(s01);
double s02[3];
s02[0] = xshake[i0][0] - xshake[i2][0];
s02[1] = xshake[i0][1] - xshake[i2][1];
s02[2] = xshake[i0][2] - xshake[i2][2];
domain->minimum_image(s02);
double s12[3];
s12[0] = xshake[i1][0] - xshake[i2][0];
s12[1] = xshake[i1][1] - xshake[i2][1];
s12[2] = xshake[i1][2] - xshake[i2][2];
domain->minimum_image(s12);
// scalar distances between atoms
double r01sq = r01[0]*r01[0] + r01[1]*r01[1] + r01[2]*r01[2];
double r02sq = r02[0]*r02[0] + r02[1]*r02[1] + r02[2]*r02[2];
double r12sq = r12[0]*r12[0] + r12[1]*r12[1] + r12[2]*r12[2];
double s01sq = s01[0]*s01[0] + s01[1]*s01[1] + s01[2]*s01[2];
double s02sq = s02[0]*s02[0] + s02[1]*s02[1] + s02[2]*s02[2];
double s12sq = s12[0]*s12[0] + s12[1]*s12[1] + s12[2]*s12[2];
// matrix coeffs and rhs for lamda equations
if (rmass) {
invmass0 = 1.0/rmass[i0];
invmass1 = 1.0/rmass[i1];
invmass2 = 1.0/rmass[i2];
} else {
invmass0 = 1.0/mass[type[i0]];
invmass1 = 1.0/mass[type[i1]];
invmass2 = 1.0/mass[type[i2]];
}
double a11 = 2.0 * (invmass0+invmass1) *
(s01[0]*r01[0] + s01[1]*r01[1] + s01[2]*r01[2]);
double a12 = 2.0 * invmass0 *
(s01[0]*r02[0] + s01[1]*r02[1] + s01[2]*r02[2]);
double a13 = - 2.0 * invmass1 *
(s01[0]*r12[0] + s01[1]*r12[1] + s01[2]*r12[2]);
double a21 = 2.0 * invmass0 *
(s02[0]*r01[0] + s02[1]*r01[1] + s02[2]*r01[2]);
double a22 = 2.0 * (invmass0+invmass2) *
(s02[0]*r02[0] + s02[1]*r02[1] + s02[2]*r02[2]);
double a23 = 2.0 * invmass2 *
(s02[0]*r12[0] + s02[1]*r12[1] + s02[2]*r12[2]);
double a31 = - 2.0 * invmass1 *
(s12[0]*r01[0] + s12[1]*r01[1] + s12[2]*r01[2]);
double a32 = 2.0 * invmass2 *
(s12[0]*r02[0] + s12[1]*r02[1] + s12[2]*r02[2]);
double a33 = 2.0 * (invmass1+invmass2) *
(s12[0]*r12[0] + s12[1]*r12[1] + s12[2]*r12[2]);
// inverse of matrix
double determ = a11*a22*a33 + a12*a23*a31 + a13*a21*a32 -
a11*a23*a32 - a12*a21*a33 - a13*a22*a31;
if (determ == 0.0) error->one(FLERR,"Shake determinant = 0.0");
double determinv = 1.0/determ;
double a11inv = determinv * (a22*a33 - a23*a32);
double a12inv = -determinv * (a12*a33 - a13*a32);
double a13inv = determinv * (a12*a23 - a13*a22);
double a21inv = -determinv * (a21*a33 - a23*a31);
double a22inv = determinv * (a11*a33 - a13*a31);
double a23inv = -determinv * (a11*a23 - a13*a21);
double a31inv = determinv * (a21*a32 - a22*a31);
double a32inv = -determinv * (a11*a32 - a12*a31);
double a33inv = determinv * (a11*a22 - a12*a21);
// quadratic correction coeffs
double r0102 = (r01[0]*r02[0] + r01[1]*r02[1] + r01[2]*r02[2]);
double r0112 = (r01[0]*r12[0] + r01[1]*r12[1] + r01[2]*r12[2]);
double r0212 = (r02[0]*r12[0] + r02[1]*r12[1] + r02[2]*r12[2]);
double quad1_0101 = (invmass0+invmass1)*(invmass0+invmass1) * r01sq;
double quad1_0202 = invmass0*invmass0 * r02sq;
double quad1_1212 = invmass1*invmass1 * r12sq;
double quad1_0102 = 2.0 * (invmass0+invmass1)*invmass0 * r0102;
double quad1_0112 = - 2.0 * (invmass0+invmass1)*invmass1 * r0112;
double quad1_0212 = - 2.0 * invmass0*invmass1 * r0212;
double quad2_0101 = invmass0*invmass0 * r01sq;
double quad2_0202 = (invmass0+invmass2)*(invmass0+invmass2) * r02sq;
double quad2_1212 = invmass2*invmass2 * r12sq;
double quad2_0102 = 2.0 * (invmass0+invmass2)*invmass0 * r0102;
double quad2_0112 = 2.0 * invmass0*invmass2 * r0112;
double quad2_0212 = 2.0 * (invmass0+invmass2)*invmass2 * r0212;
double quad3_0101 = invmass1*invmass1 * r01sq;
double quad3_0202 = invmass2*invmass2 * r02sq;
double quad3_1212 = (invmass1+invmass2)*(invmass1+invmass2) * r12sq;
double quad3_0102 = - 2.0 * invmass1*invmass2 * r0102;
double quad3_0112 = - 2.0 * (invmass1+invmass2)*invmass1 * r0112;
double quad3_0212 = 2.0 * (invmass1+invmass2)*invmass2 * r0212;
// iterate until converged
double lamda01 = 0.0;
double lamda02 = 0.0;
double lamda12 = 0.0;
int niter = 0;
int done = 0;
double quad1,quad2,quad3,b1,b2,b3,lamda01_new,lamda02_new,lamda12_new;
while (!done && niter < max_iter) {
quad1 = quad1_0101 * lamda01*lamda01 +
quad1_0202 * lamda02*lamda02 +
quad1_1212 * lamda12*lamda12 +
quad1_0102 * lamda01*lamda02 +
quad1_0112 * lamda01*lamda12 +
quad1_0212 * lamda02*lamda12;
quad2 = quad2_0101 * lamda01*lamda01 +
quad2_0202 * lamda02*lamda02 +
quad2_1212 * lamda12*lamda12 +
quad2_0102 * lamda01*lamda02 +
quad2_0112 * lamda01*lamda12 +
quad2_0212 * lamda02*lamda12;
quad3 = quad3_0101 * lamda01*lamda01 +
quad3_0202 * lamda02*lamda02 +
quad3_1212 * lamda12*lamda12 +
quad3_0102 * lamda01*lamda02 +
quad3_0112 * lamda01*lamda12 +
quad3_0212 * lamda02*lamda12;
b1 = bond1*bond1 - s01sq - quad1;
b2 = bond2*bond2 - s02sq - quad2;
b3 = bond12*bond12 - s12sq - quad3;
lamda01_new = a11inv*b1 + a12inv*b2 + a13inv*b3;
lamda02_new = a21inv*b1 + a22inv*b2 + a23inv*b3;
lamda12_new = a31inv*b1 + a32inv*b2 + a33inv*b3;
done = 1;
if (fabs(lamda01_new-lamda01) > tolerance) done = 0;
if (fabs(lamda02_new-lamda02) > tolerance) done = 0;
if (fabs(lamda12_new-lamda12) > tolerance) done = 0;
lamda01 = lamda01_new;
lamda02 = lamda02_new;
lamda12 = lamda12_new;
niter++;
}
// update forces if atom is owned by this processor
lamda01 = lamda01/dtfsq;
lamda02 = lamda02/dtfsq;
lamda12 = lamda12/dtfsq;
if (i0 < nlocal) {
f[i0][0] += lamda01*r01[0] + lamda02*r02[0];
f[i0][1] += lamda01*r01[1] + lamda02*r02[1];
f[i0][2] += lamda01*r01[2] + lamda02*r02[2];
}
if (i1 < nlocal) {
f[i1][0] -= lamda01*r01[0] - lamda12*r12[0];
f[i1][1] -= lamda01*r01[1] - lamda12*r12[1];
f[i1][2] -= lamda01*r01[2] - lamda12*r12[2];
}
if (i2 < nlocal) {
f[i2][0] -= lamda02*r02[0] + lamda12*r12[0];
f[i2][1] -= lamda02*r02[1] + lamda12*r12[1];
f[i2][2] -= lamda02*r02[2] + lamda12*r12[2];
}
if (evflag) {
nlist = 0;
if (i0 < nlocal) list[nlist++] = i0;
if (i1 < nlocal) list[nlist++] = i1;
if (i2 < nlocal) list[nlist++] = i2;
v[0] = lamda01*r01[0]*r01[0]+lamda02*r02[0]*r02[0]+lamda12*r12[0]*r12[0];
v[1] = lamda01*r01[1]*r01[1]+lamda02*r02[1]*r02[1]+lamda12*r12[1]*r12[1];
v[2] = lamda01*r01[2]*r01[2]+lamda02*r02[2]*r02[2]+lamda12*r12[2]*r12[2];
v[3] = lamda01*r01[0]*r01[1]+lamda02*r02[0]*r02[1]+lamda12*r12[0]*r12[1];
v[4] = lamda01*r01[0]*r01[2]+lamda02*r02[0]*r02[2]+lamda12*r12[0]*r12[2];
v[5] = lamda01*r01[1]*r01[2]+lamda02*r02[1]*r02[2]+lamda12*r12[1]*r12[2];
v_tally(nlist,list,3.0,v);
}
}
/* ----------------------------------------------------------------------
print-out bond & angle statistics
------------------------------------------------------------------------- */
void FixShake::stats()
{
int i,j,m,n,iatom,jatom,katom;
double delx,dely,delz;
double r,r1,r2,r3,angle;
// zero out accumulators
int nb = atom->nbondtypes + 1;
int na = atom->nangletypes + 1;
for (i = 0; i < nb; i++) {
b_count[i] = 0;
b_ave[i] = b_max[i] = 0.0;
b_min[i] = BIG;
}
for (i = 0; i < na; i++) {
a_count[i] = 0;
a_ave[i] = a_max[i] = 0.0;
a_min[i] = BIG;
}
// log stats for each bond & angle
// OK to double count since are just averaging
double **x = atom->x;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (shake_flag[i] == 0) continue;
// bond stats
n = shake_flag[i];
if (n == 1) n = 3;
iatom = atom->map(shake_atom[i][0]);
for (j = 1; j < n; j++) {
jatom = atom->map(shake_atom[i][j]);
delx = x[iatom][0] - x[jatom][0];
dely = x[iatom][1] - x[jatom][1];
delz = x[iatom][2] - x[jatom][2];
domain->minimum_image(delx,dely,delz);
r = sqrt(delx*delx + dely*dely + delz*delz);
m = shake_type[i][j-1];
b_count[m]++;
b_ave[m] += r;
b_max[m] = MAX(b_max[m],r);
b_min[m] = MIN(b_min[m],r);
}
// angle stats
if (shake_flag[i] == 1) {
iatom = atom->map(shake_atom[i][0]);
jatom = atom->map(shake_atom[i][1]);
katom = atom->map(shake_atom[i][2]);
delx = x[iatom][0] - x[jatom][0];
dely = x[iatom][1] - x[jatom][1];
delz = x[iatom][2] - x[jatom][2];
domain->minimum_image(delx,dely,delz);
r1 = sqrt(delx*delx + dely*dely + delz*delz);
delx = x[iatom][0] - x[katom][0];
dely = x[iatom][1] - x[katom][1];
delz = x[iatom][2] - x[katom][2];
domain->minimum_image(delx,dely,delz);
r2 = sqrt(delx*delx + dely*dely + delz*delz);
delx = x[jatom][0] - x[katom][0];
dely = x[jatom][1] - x[katom][1];
delz = x[jatom][2] - x[katom][2];
domain->minimum_image(delx,dely,delz);
r3 = sqrt(delx*delx + dely*dely + delz*delz);
angle = acos((r1*r1 + r2*r2 - r3*r3) / (2.0*r1*r2));
angle *= 180.0/MY_PI;
m = shake_type[i][2];
a_count[m]++;
a_ave[m] += angle;
a_max[m] = MAX(a_max[m],angle);
a_min[m] = MIN(a_min[m],angle);
}
}
// sum across all procs
MPI_Allreduce(b_count,b_count_all,nb,MPI_INT,MPI_SUM,world);
MPI_Allreduce(b_ave,b_ave_all,nb,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(b_max,b_max_all,nb,MPI_DOUBLE,MPI_MAX,world);
MPI_Allreduce(b_min,b_min_all,nb,MPI_DOUBLE,MPI_MIN,world);
MPI_Allreduce(a_count,a_count_all,na,MPI_INT,MPI_SUM,world);
MPI_Allreduce(a_ave,a_ave_all,na,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(a_max,a_max_all,na,MPI_DOUBLE,MPI_MAX,world);
MPI_Allreduce(a_min,a_min_all,na,MPI_DOUBLE,MPI_MIN,world);
// print stats only for non-zero counts
if (me == 0) {
if (screen) {
fprintf(screen,
"SHAKE stats (type/ave/delta) on step " BIGINT_FORMAT "\n",
update->ntimestep);
for (i = 1; i < nb; i++)
if (b_count_all[i])
fprintf(screen," %d %g %g %d\n",i,
b_ave_all[i]/b_count_all[i],b_max_all[i]-b_min_all[i],
b_count_all[i]);
for (i = 1; i < na; i++)
if (a_count_all[i])
fprintf(screen," %d %g %g\n",i,
a_ave_all[i]/a_count_all[i],a_max_all[i]-a_min_all[i]);
}
if (logfile) {
fprintf(logfile,
"SHAKE stats (type/ave/delta) on step " BIGINT_FORMAT "\n",
update->ntimestep);
for (i = 0; i < nb; i++)
if (b_count_all[i])
fprintf(logfile," %d %g %g\n",i,
b_ave_all[i]/b_count_all[i],b_max_all[i]-b_min_all[i]);
for (i = 0; i < na; i++)
if (a_count_all[i])
fprintf(logfile," %d %g %g\n",i,
a_ave_all[i]/a_count_all[i],a_max_all[i]-a_min_all[i]);
}
}
// next timestep for stats
next_output += output_every;
}
/* ----------------------------------------------------------------------
find a bond between global atom IDs n1 and n2 stored with local atom i
if find it:
if setflag = 0, return bond type
if setflag = -1/1, set bond type to negative/positive and return 0
if do not find it, return 0
------------------------------------------------------------------------- */
int FixShake::bondtype_findset(int i, tagint n1, tagint n2, int setflag)
{
int m,nbonds;
int *btype;
if (molecular == 1) {
tagint *tag = atom->tag;
tagint **bond_atom = atom->bond_atom;
nbonds = atom->num_bond[i];
for (m = 0; m < nbonds; m++) {
if (n1 == tag[i] && n2 == bond_atom[i][m]) break;
if (n1 == bond_atom[i][m] && n2 == tag[i]) break;
}
} else {
int imol = atom->molindex[i];
int iatom = atom->molatom[i];
tagint *tag = atom->tag;
tagint tagprev = tag[i] - iatom - 1;
tagint *batom = atommols[imol]->bond_atom[iatom];
btype = atommols[imol]->bond_type[iatom];
nbonds = atommols[imol]->num_bond[iatom];
for (m = 0; m < nbonds; m++) {
if (n1 == tag[i] && n2 == batom[m]+tagprev) break;
if (n1 == batom[m]+tagprev && n2 == tag[i]) break;
}
}
if (m < nbonds) {
if (setflag == 0) {
if (molecular == 1) return atom->bond_type[i][m];
else return btype[m];
}
if (molecular == 1) {
if ((setflag < 0 && atom->bond_type[i][m] > 0) ||
(setflag > 0 && atom->bond_type[i][m] < 0))
atom->bond_type[i][m] = -atom->bond_type[i][m];
} else {
if ((setflag < 0 && btype[m] > 0) ||
(setflag > 0 && btype[m] < 0)) btype[m] = -btype[m];
}
}
return 0;
}
/* ----------------------------------------------------------------------
find an angle with global end atom IDs n1 and n2 stored with local atom i
if find it:
if setflag = 0, return angle type
if setflag = -1/1, set angle type to negative/positive and return 0
if do not find it, return 0
------------------------------------------------------------------------- */
int FixShake::angletype_findset(int i, tagint n1, tagint n2, int setflag)
{
int m,nangles;
int *atype;
if (molecular == 1) {
tagint **angle_atom1 = atom->angle_atom1;
tagint **angle_atom3 = atom->angle_atom3;
nangles = atom->num_angle[i];
for (m = 0; m < nangles; m++) {
if (n1 == angle_atom1[i][m] && n2 == angle_atom3[i][m]) break;
if (n1 == angle_atom3[i][m] && n2 == angle_atom1[i][m]) break;
}
} else {
int imol = atom->molindex[i];
int iatom = atom->molatom[i];
tagint *tag = atom->tag;
tagint tagprev = tag[i] - iatom - 1;
tagint *aatom1 = atommols[imol]->angle_atom1[iatom];
tagint *aatom3 = atommols[imol]->angle_atom3[iatom];
atype = atommols[imol]->angle_type[iatom];
nangles = atommols[imol]->num_angle[iatom];
for (m = 0; m < nangles; m++) {
if (n1 == aatom1[m]+tagprev && n2 == aatom3[m]+tagprev) break;
if (n1 == aatom3[m]+tagprev && n2 == aatom1[m]+tagprev) break;
}
}
if (m < nangles) {
if (setflag == 0) {
if (molecular == 1) return atom->angle_type[i][m];
else return atype[m];
}
if (molecular == 1) {
if ((setflag < 0 && atom->angle_type[i][m] > 0) ||
(setflag > 0 && atom->angle_type[i][m] < 0))
atom->angle_type[i][m] = -atom->angle_type[i][m];
} else {
if ((setflag < 0 && atype[m] > 0) ||
(setflag > 0 && atype[m] < 0)) atype[m] = -atype[m];
}
}
return 0;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixShake::memory_usage()
{
int nmax = atom->nmax;
double bytes = nmax * sizeof(int);
bytes += nmax*4 * sizeof(int);
bytes += nmax*3 * sizeof(int);
bytes += nmax*3 * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixShake::grow_arrays(int nmax)
{
memory->grow(shake_flag,nmax,"shake:shake_flag");
memory->grow(shake_atom,nmax,4,"shake:shake_atom");
memory->grow(shake_type,nmax,3,"shake:shake_type");
memory->destroy(xshake);
memory->create(xshake,nmax,3,"shake:xshake");
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixShake::copy_arrays(int i, int j, int delflag)
{
int flag = shake_flag[j] = shake_flag[i];
if (flag == 1) {
shake_atom[j][0] = shake_atom[i][0];
shake_atom[j][1] = shake_atom[i][1];
shake_atom[j][2] = shake_atom[i][2];
shake_type[j][0] = shake_type[i][0];
shake_type[j][1] = shake_type[i][1];
shake_type[j][2] = shake_type[i][2];
} else if (flag == 2) {
shake_atom[j][0] = shake_atom[i][0];
shake_atom[j][1] = shake_atom[i][1];
shake_type[j][0] = shake_type[i][0];
} else if (flag == 3) {
shake_atom[j][0] = shake_atom[i][0];
shake_atom[j][1] = shake_atom[i][1];
shake_atom[j][2] = shake_atom[i][2];
shake_type[j][0] = shake_type[i][0];
shake_type[j][1] = shake_type[i][1];
} else if (flag == 4) {
shake_atom[j][0] = shake_atom[i][0];
shake_atom[j][1] = shake_atom[i][1];
shake_atom[j][2] = shake_atom[i][2];
shake_atom[j][3] = shake_atom[i][3];
shake_type[j][0] = shake_type[i][0];
shake_type[j][1] = shake_type[i][1];
shake_type[j][2] = shake_type[i][2];
}
}
/* ----------------------------------------------------------------------
initialize one atom's array values, called when atom is created
------------------------------------------------------------------------- */
void FixShake::set_arrays(int i)
{
shake_flag[i] = 0;
}
/* ----------------------------------------------------------------------
update one atom's array values
called when molecule is created from fix gcmc
------------------------------------------------------------------------- */
void FixShake::update_arrays(int i, int atom_offset)
{
int flag = shake_flag[i];
if (flag == 1) {
shake_atom[i][0] += atom_offset;
shake_atom[i][1] += atom_offset;
shake_atom[i][2] += atom_offset;
} else if (flag == 2) {
shake_atom[i][0] += atom_offset;
shake_atom[i][1] += atom_offset;
} else if (flag == 3) {
shake_atom[i][0] += atom_offset;
shake_atom[i][1] += atom_offset;
shake_atom[i][2] += atom_offset;
} else if (flag == 4) {
shake_atom[i][0] += atom_offset;
shake_atom[i][1] += atom_offset;
shake_atom[i][2] += atom_offset;
shake_atom[i][3] += atom_offset;
}
}
/* ----------------------------------------------------------------------
initialize a molecule inserted by another fix, e.g. deposit or pour
called when molecule is created
nlocalprev = # of atoms on this proc before molecule inserted
tagprev = atom ID previous to new atoms in the molecule
xgeom,vcm,quat ignored
------------------------------------------------------------------------- */
void FixShake::set_molecule(int nlocalprev, tagint tagprev, int imol,
double *xgeom, double *vcm, double *quat)
{
int m,flag;
int nlocal = atom->nlocal;
if (nlocalprev == nlocal) return;
tagint *tag = atom->tag;
tagint **mol_shake_atom = onemols[imol]->shake_atom;
int **mol_shake_type = onemols[imol]->shake_type;
for (int i = nlocalprev; i < nlocal; i++) {
m = tag[i] - tagprev-1;
flag = shake_flag[i] = onemols[imol]->shake_flag[m];
if (flag == 1) {
shake_atom[i][0] = mol_shake_atom[m][0] + tagprev;
shake_atom[i][1] = mol_shake_atom[m][1] + tagprev;
shake_atom[i][2] = mol_shake_atom[m][2] + tagprev;
shake_type[i][0] = mol_shake_type[m][0];
shake_type[i][1] = mol_shake_type[m][1];
shake_type[i][2] = mol_shake_type[m][2];
} else if (flag == 2) {
shake_atom[i][0] = mol_shake_atom[m][0] + tagprev;
shake_atom[i][1] = mol_shake_atom[m][1] + tagprev;
shake_type[i][0] = mol_shake_type[m][0];
} else if (flag == 3) {
shake_atom[i][0] = mol_shake_atom[m][0] + tagprev;
shake_atom[i][1] = mol_shake_atom[m][1] + tagprev;
shake_atom[i][2] = mol_shake_atom[m][2] + tagprev;
shake_type[i][0] = mol_shake_type[m][0];
shake_type[i][1] = mol_shake_type[m][1];
} else if (flag == 4) {
shake_atom[i][0] = mol_shake_atom[m][0] + tagprev;
shake_atom[i][1] = mol_shake_atom[m][1] + tagprev;
shake_atom[i][2] = mol_shake_atom[m][2] + tagprev;
shake_atom[i][3] = mol_shake_atom[m][3] + tagprev;
shake_type[i][0] = mol_shake_type[m][0];
shake_type[i][1] = mol_shake_type[m][1];
shake_type[i][2] = mol_shake_type[m][2];
}
}
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixShake::pack_exchange(int i, double *buf)
{
int m = 0;
buf[m++] = shake_flag[i];
int flag = shake_flag[i];
if (flag == 1) {
buf[m++] = shake_atom[i][0];
buf[m++] = shake_atom[i][1];
buf[m++] = shake_atom[i][2];
buf[m++] = shake_type[i][0];
buf[m++] = shake_type[i][1];
buf[m++] = shake_type[i][2];
} else if (flag == 2) {
buf[m++] = shake_atom[i][0];
buf[m++] = shake_atom[i][1];
buf[m++] = shake_type[i][0];
} else if (flag == 3) {
buf[m++] = shake_atom[i][0];
buf[m++] = shake_atom[i][1];
buf[m++] = shake_atom[i][2];
buf[m++] = shake_type[i][0];
buf[m++] = shake_type[i][1];
} else if (flag == 4) {
buf[m++] = shake_atom[i][0];
buf[m++] = shake_atom[i][1];
buf[m++] = shake_atom[i][2];
buf[m++] = shake_atom[i][3];
buf[m++] = shake_type[i][0];
buf[m++] = shake_type[i][1];
buf[m++] = shake_type[i][2];
}
return m;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixShake::unpack_exchange(int nlocal, double *buf)
{
int m = 0;
int flag = shake_flag[nlocal] = static_cast<int> (buf[m++]);
if (flag == 1) {
shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
shake_atom[nlocal][2] = static_cast<tagint> (buf[m++]);
shake_type[nlocal][0] = static_cast<int> (buf[m++]);
shake_type[nlocal][1] = static_cast<int> (buf[m++]);
shake_type[nlocal][2] = static_cast<int> (buf[m++]);
} else if (flag == 2) {
shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
shake_type[nlocal][0] = static_cast<int> (buf[m++]);
} else if (flag == 3) {
shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
shake_atom[nlocal][2] = static_cast<tagint> (buf[m++]);
shake_type[nlocal][0] = static_cast<int> (buf[m++]);
shake_type[nlocal][1] = static_cast<int> (buf[m++]);
} else if (flag == 4) {
shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
shake_atom[nlocal][2] = static_cast<tagint> (buf[m++]);
shake_atom[nlocal][3] = static_cast<tagint> (buf[m++]);
shake_type[nlocal][0] = static_cast<int> (buf[m++]);
shake_type[nlocal][1] = static_cast<int> (buf[m++]);
shake_type[nlocal][2] = static_cast<int> (buf[m++]);
}
return m;
}
/* ---------------------------------------------------------------------- */
int FixShake::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = xshake[j][0];
buf[m++] = xshake[j][1];
buf[m++] = xshake[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = xshake[j][0] + dx;
buf[m++] = xshake[j][1] + dy;
buf[m++] = xshake[j][2] + dz;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixShake::unpack_forward_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
xshake[i][0] = buf[m++];
xshake[i][1] = buf[m++];
xshake[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void FixShake::reset_dt()
{
if (strstr(update->integrate_style,"verlet")) {
dtv = update->dt;
if (rattle) dtfsq = 0.5 * update->dt * update->dt * force->ftm2v;
else dtfsq = update->dt * update->dt * force->ftm2v;
} else {
dtv = step_respa[0];
dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v;
if (rattle) dtf_inner = dtf_innerhalf;
else dtf_inner = step_respa[0] * force->ftm2v;
}
}
/* ----------------------------------------------------------------------
extract Molecule ptr
------------------------------------------------------------------------- */
void *FixShake::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str,"onemol") == 0) {
return onemols;
}
return NULL;
}
/* ----------------------------------------------------------------------
wrapper method for end_of_step fixes which modify the coordinates
------------------------------------------------------------------------- */
void FixShake::coordinate_constraints_end_of_step() {
if (!respa) {
dtfsq = 0.5 * update->dt * update->dt * force->ftm2v;
FixShake::post_force(vflag_post_force);
if (!rattle) dtfsq = update->dt * update->dt * force->ftm2v;
}
else {
dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v;
dtf_inner = dtf_innerhalf;
// apply correction to all rRESPA levels
for (int ilevel = 0; ilevel < nlevels_respa; ilevel++) {
((Respa *) update->integrate)->copy_flevel_f(ilevel);
FixShake::post_force_respa(vflag_post_force,ilevel,loop_respa[ilevel]-1);
((Respa *) update->integrate)->copy_f_flevel(ilevel);
}
if (!rattle) dtf_inner = step_respa[0] * force->ftm2v;
}
}
diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/USER-DRUDE/fix_drude.cpp
index 9b95c1506..46b49707d 100644
--- a/src/USER-DRUDE/fix_drude.cpp
+++ b/src/USER-DRUDE/fix_drude.cpp
@@ -1,496 +1,497 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "fix_drude.h"
#include "atom.h"
#include "comm.h"
#include "modify.h"
#include "error.h"
#include "memory.h"
#include <set>
#include <vector>
using namespace LAMMPS_NS;
using namespace FixConst;
FixDrude *FixDrude::sptr = NULL;
/* ---------------------------------------------------------------------- */
FixDrude::FixDrude(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 3 + atom->ntypes) error->all(FLERR,"Illegal fix drude command");
comm_border = 1; // drudeid
special_alter_flag = 1;
create_attribute = 1;
memory->create(drudetype, atom->ntypes+1, "fix_drude::drudetype");
for (int i=3; i<narg; i++) {
if (arg[i][0] == 'n' || arg[i][0] == 'N' || arg[i][0] == '0')
drudetype[i-2] = NOPOL_TYPE;
else if (arg[i][0] == 'c' || arg[i][0] == 'C' || arg[i][0] == '1')
drudetype[i-2] = CORE_TYPE;
else if (arg[i][0] == 'd' || arg[i][0] == 'D' || arg[i][0] == '2')
drudetype[i-2] = DRUDE_TYPE;
else
error->all(FLERR, "Illegal fix drude command");
}
drudeid = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
atom->add_callback(1);
atom->add_callback(2);
// one-time assignment of Drude partners
build_drudeid();
// set rebuildflag = 0 to indicate special lists have never been rebuilt
rebuildflag = 0;
}
/* ---------------------------------------------------------------------- */
FixDrude::~FixDrude()
{
atom->delete_callback(id,2);
atom->delete_callback(id,1);
atom->delete_callback(id,0);
memory->destroy(drudetype);
memory->destroy(drudeid);
}
/* ---------------------------------------------------------------------- */
void FixDrude::init()
{
int count = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"drude") == 0) count++;
if (count > 1) error->all(FLERR,"More than one fix drude");
if (!rebuildflag) rebuild_special();
}
/* ---------------------------------------------------------------------- */
int FixDrude::setmask()
{
int mask = 0;
return mask;
}
/* ----------------------------------------------------------------------
look in bond lists for Drude partner tags and fill drudeid
------------------------------------------------------------------------- */
void FixDrude::build_drudeid(){
int nlocal = atom->nlocal;
int *type = atom->type;
std::vector<tagint> drude_vec; // list of my Drudes' tags
std::vector<tagint> core_drude_vec;
partner_set = new std::set<tagint>[nlocal]; // Temporary sets of bond partner tags
sptr = this;
// Build list of my atoms' bond partners
for (int i=0; i<nlocal; i++){
if (drudetype[type[i]] == NOPOL_TYPE) continue;
drudeid[i] = 0;
for (int k=0; k<atom->num_bond[i]; k++){
core_drude_vec.push_back(atom->tag[i]);
core_drude_vec.push_back(atom->bond_atom[i][k]);
}
}
// Loop on procs to fill my atoms' sets of bond partners
comm->ring(core_drude_vec.size(), sizeof(tagint),
(char *) core_drude_vec.data(),
4, ring_build_partner, NULL, 1);
// Build the list of my Drudes' tags
// The only bond partners of a Drude particle is its core,
// so fill drudeid for my Drudes.
for (int i=0; i<nlocal; i++){
if (drudetype[type[i]] == DRUDE_TYPE){
drude_vec.push_back(atom->tag[i]);
drudeid[i] = *partner_set[i].begin(); // only one 1-2 neighbor, the core
}
}
// At this point each of my Drudes knows its core.
// Send my list of Drudes to other procs and myself
// so that each core finds its Drude.
comm->ring(drude_vec.size(), sizeof(tagint),
(char *) drude_vec.data(),
3, ring_search_drudeid, NULL, 1);
delete [] partner_set;
}
/* ----------------------------------------------------------------------
* when receive buffer, build the set of received Drude tags.
* Look in my cores' bond partner tags if there is a Drude tag.
* If so fill this core's dureid.
------------------------------------------------------------------------- */
void FixDrude::ring_search_drudeid(int size, char *cbuf){
// Search for the drude partner of my cores
Atom *atom = sptr->atom;
int nlocal = atom->nlocal;
int *type = atom->type;
std::set<tagint> *partner_set = sptr->partner_set;
tagint *drudeid = sptr->drudeid;
int *drudetype = sptr->drudetype;
tagint *first = (tagint *) cbuf;
tagint *last = first + size;
std::set<tagint> drude_set(first, last);
std::set<tagint>::iterator it;
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] != CORE_TYPE || drudeid[i] > 0) continue;
for (it = partner_set[i].begin(); it != partner_set[i].end(); it++) { // Drude-core are 1-2 neighbors
if (drude_set.count(*it) > 0){
drudeid[i] = *it;
break;
}
}
}
}
/* ----------------------------------------------------------------------
* buffer contains bond partners. Look for my atoms and add their partner's
* tag in its set of bond partners.
------------------------------------------------------------------------- */
void FixDrude::ring_build_partner(int size, char *cbuf){
// Add partners from incoming list
Atom *atom = sptr->atom;
int nlocal = atom->nlocal;
std::set<tagint> *partner_set = sptr->partner_set;
tagint *it = (tagint *) cbuf;
tagint *last = it + size;
while (it < last) {
int j = atom->map(*it);
if (j >= 0 && j < nlocal)
partner_set[j].insert(*(it+1));
j = atom->map(*(it+1));
if (j >= 0 && j < nlocal)
partner_set[j].insert(*it);
it += 2;
}
}
/* ----------------------------------------------------------------------
allocate atom-based array for drudeid
------------------------------------------------------------------------- */
void FixDrude::grow_arrays(int nmax)
{
memory->grow(drudeid,nmax,"fix_drude:drudeid");
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixDrude::copy_arrays(int i, int j, int delflag)
{
drudeid[j] = drudeid[i];
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixDrude::pack_exchange(int i, double *buf)
{
int m = 0;
buf[m++] = ubuf(drudeid[i]).d;
return m;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixDrude::unpack_exchange(int nlocal, double *buf)
{
int m = 0;
drudeid[nlocal] = (tagint) ubuf(buf[m++]).i;
return m;
}
/* ----------------------------------------------------------------------
pack values for border communication at re-neighboring
------------------------------------------------------------------------- */
int FixDrude::pack_border(int n, int *list, double *buf)
{
int m = 0;
for (int i=0; i<n; i++){
int j = list[i];
buf[m++] = ubuf(drudeid[j]).d;
}
return m;
}
/* ----------------------------------------------------------------------
unpack values for border communication at re-neighboring
------------------------------------------------------------------------- */
int FixDrude::unpack_border(int n, int first, double *buf)
{
int m = 0;
for (int i=first; i<first+n; i++){
drudeid[i] = (tagint) ubuf(buf[m++]).i;
}
return m;
}
/* ----------------------------------------------------------------------
Rebuild the list of special neighbors if atom_style is Drude
so that each Drude particle is equivalent to its core atom.
------------------------------------------------------------------------- */
+
void FixDrude::rebuild_special(){
rebuildflag = 1;
int nlocal = atom->nlocal;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int *type = atom->type;
// Make sure that drude partners know each other
//build_drudeid();
// Log info
if (comm->me == 0) {
if (screen) fprintf(screen, "Rebuild special list taking Drude particles into account\n");
if (logfile) fprintf(logfile, "Rebuild special list taking Drude particles into account\n");
}
int nspecmax, nspecmax_old, nspecmax_loc;
nspecmax_loc = 0;
for (int i=0; i<nlocal; i++) {
if (nspecmax_loc < nspecial[i][2]) nspecmax_loc = nspecial[i][2];
}
MPI_Allreduce(&nspecmax_loc, &nspecmax_old, 1, MPI_INT, MPI_MAX, world);
if (comm->me == 0) {
if (screen) fprintf(screen, "Old max number of 1-2 to 1-4 neighbors: %d\n", nspecmax_old);
if (logfile) fprintf(logfile, "Old max number of 1-2 to 1-4 neighbors: %d\n", nspecmax_old);
}
// Build lists of drude and core-drude pairs
std::vector<tagint> drude_vec, core_drude_vec, core_special_vec;
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] == DRUDE_TYPE) {
drude_vec.push_back(atom->tag[i]);
} else if (drudetype[type[i]] == CORE_TYPE){
core_drude_vec.push_back(atom->tag[i]);
core_drude_vec.push_back(drudeid[i]);
}
}
// Remove Drude particles from the special lists of each proc
comm->ring(drude_vec.size(), sizeof(tagint),
(char *) drude_vec.data(),
9, ring_remove_drude, NULL, 1);
// Add back Drude particles in the lists just after their core
comm->ring(core_drude_vec.size(), sizeof(tagint),
(char *) core_drude_vec.data(),
10, ring_add_drude, NULL, 1);
// Check size of special list
nspecmax_loc = 0;
for (int i=0; i<nlocal; i++) {
if (nspecmax_loc < nspecial[i][2]) nspecmax_loc = nspecial[i][2];
}
MPI_Allreduce(&nspecmax_loc, &nspecmax, 1, MPI_INT, MPI_MAX, world);
if (comm->me == 0) {
if (screen) fprintf(screen, "New max number of 1-2 to 1-4 neighbors: %d (+%d)\n", nspecmax, nspecmax - nspecmax_old);
if (logfile) fprintf(logfile, "New max number of 1-2 to 1-4 neighbors: %d (+%d)\n", nspecmax, nspecmax - nspecmax_old);
}
if (atom->maxspecial < nspecmax) {
char str[1024];
sprintf(str, "Not enough space in special: special_bonds extra should be at least %d", nspecmax - nspecmax_old);
error->all(FLERR, str);
}
// Build list of cores' special lists to communicate to ghost drude particles
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] != CORE_TYPE) continue;
core_special_vec.push_back(atom->tag[i]);
core_special_vec.push_back((tagint) nspecial[i][0]);
core_special_vec.push_back((tagint) nspecial[i][1]);
core_special_vec.push_back((tagint) nspecial[i][2]);
for (int j=1; j<nspecial[i][2]; j++)
core_special_vec.push_back(special[i][j]);
}
// Copy core's list into their drude list
comm->ring(core_special_vec.size(), sizeof(tagint),
(char *) core_special_vec.data(),
11, ring_copy_drude, NULL, 1);
}
/* ----------------------------------------------------------------------
* When receive buffer, build a set of drude tags, look into my atoms'
* special list if some tags are drude particles. If so, remove it.
------------------------------------------------------------------------- */
void FixDrude::ring_remove_drude(int size, char *cbuf){
// Remove all drude particles from special list
Atom *atom = sptr->atom;
int nlocal = atom->nlocal;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int *type = atom->type;
tagint *first = (tagint *) cbuf;
tagint *last = first + size;
std::set<tagint> drude_set(first, last);
int *drudetype = sptr->drudetype;
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] == DRUDE_TYPE) continue;
for (int j=0; j<nspecial[i][2]; j++) {
if (drude_set.count(special[i][j]) > 0) { // I identify a drude in my special list, remove it
// left shift
nspecial[i][2]--;
for (int k=j; k<nspecial[i][2]; k++)
special[i][k] = special[i][k+1];
if (j < nspecial[i][1]) {
nspecial[i][1]--;
if (j < nspecial[i][0]) nspecial[i][0]--;
}
j--;
}
}
}
}
/* ----------------------------------------------------------------------
* When receive buffer, build a map core tag -> drude tag.
* Loop on my atoms' special list to find core tags. Insert their Drude
* particle if they have one.
------------------------------------------------------------------------- */
void FixDrude::ring_add_drude(int size, char *cbuf){
// Assume special array size is big enough
// Add all particle just after their core in the special list
Atom *atom = sptr->atom;
int nlocal = atom->nlocal;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int *type = atom->type;
tagint *drudeid = sptr->drudeid;
int *drudetype = sptr->drudetype;
tagint *first = (tagint *) cbuf;
tagint *last = first + size;
std::map<tagint, tagint> core_drude_map;
tagint *it = first;
while (it < last) {
tagint core_tag = *it;
it++;
core_drude_map[core_tag] = *it;
it++;
}
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] == DRUDE_TYPE) continue;
if (core_drude_map.count(atom->tag[i]) > 0) { // I identify myself as a core, add my own drude
// right shift
for (int k=nspecial[i][2]-1; k>=0; k--)
special[i][k+1] = special[i][k];
special[i][0] = drudeid[i];
nspecial[i][0]++;
nspecial[i][1]++;
nspecial[i][2]++;
}
for (int j=0; j<nspecial[i][2]; j++) {
if (core_drude_map.count(special[i][j]) > 0) { // I identify a core in my special list, add his drude
// right shift
for (int k=nspecial[i][2]-1; k>j; k--)
special[i][k+1] = special[i][k];
special[i][j+1] = core_drude_map[special[i][j]];
nspecial[i][2]++;
if (j < nspecial[i][1]) {
nspecial[i][1]++;
if (j < nspecial[i][0]) nspecial[i][0]++;
}
j++;
}
}
}
}
/* ----------------------------------------------------------------------
* When receive buffer, build a map core tag -> pointer to special info
* in the buffer. Loop on my Drude particles and copy their special
* info from that of their core if the latter is found in the map.
------------------------------------------------------------------------- */
void FixDrude::ring_copy_drude(int size, char *cbuf){
// Copy special list of drude from its core (except itself)
Atom *atom = sptr->atom;
int nlocal = atom->nlocal;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int *type = atom->type;
tagint *drudeid = sptr->drudeid;
int *drudetype = sptr->drudetype;
tagint *first = (tagint *) cbuf;
tagint *last = first + size;
std::map<tagint, tagint*> core_special_map;
tagint *it = first;
while (it < last) {
tagint core_tag = *it;
it++;
core_special_map[core_tag] = it;
it += 2;
it += (int) *it;
}
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] != DRUDE_TYPE) continue;
if (core_special_map.count(drudeid[i]) > 0) { // My core is in this list, copy its special info
it = core_special_map[drudeid[i]];
nspecial[i][0] = (int) *it;
it++;
nspecial[i][1] = (int) *it;
it++;
nspecial[i][2] = (int) *it;
it++;
special[i][0] = drudeid[i];
for (int k=1; k<nspecial[i][2]; k++) {
special[i][k] = *it;
it++;
}
}
}
}
/* ----------------------------------------------------------------------
* Set drudeid when a new atom is created,
* special list must be up-to-date
* ----------------------------------------------------------------------*/
void FixDrude::set_arrays(int i){
if (drudetype[atom->type[i]] != NOPOL_TYPE){
if (atom->nspecial[i] ==0) error->all(FLERR, "Polarizable atoms cannot be inserted with special lists info from the molecule template");
drudeid[i] = atom->special[i][0]; // Drude partner should be at first place in the special list
} else {
drudeid[i] = 0;
}
}
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index a67eb58b6..9bd1a632c 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -1,800 +1,803 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: W. Michael Brown (Intel)
Anupama Kurpad (Intel) - Host Affinitization
------------------------------------------------------------------------- */
#include "comm.h"
#include "error.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "pair.h"
#include "pair_hybrid.h"
#include "pair_hybrid_overlay.h"
#include "timer.h"
#include "universe.h"
#include "update.h"
#include "fix_intel.h"
#include <string.h>
#include <stdlib.h>
#include <stdio.h>
#ifdef _LMP_INTEL_OFFLOAD
#ifndef INTEL_OFFLOAD_NOAFFINITY
#include <unistd.h>
#endif
#endif
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#ifdef __INTEL_OFFLOAD
#ifndef _LMP_INTEL_OFFLOAD
#warning "Not building Intel package with Xeon Phi offload support."
#endif
#endif
enum{NSQ,BIN,MULTI};
/* ---------------------------------------------------------------------- */
FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal package intel command");
int ncops = force->inumeric(FLERR,arg[3]);
_precision_mode = PREC_MODE_MIXED;
_offload_balance = 1.0;
_overflow_flag[LMP_OVERFLOW] = 0;
_off_overflow_flag[LMP_OVERFLOW] = 0;
_offload_affinity_balanced = 0;
_offload_threads = 0;
_offload_tpc = 4;
#ifdef _LMP_INTEL_OFFLOAD
if (ncops < 0) error->all(FLERR,"Illegal package intel command");
_offload_affinity_set = 0;
_off_force_array_s = 0;
_off_force_array_m = 0;
_off_force_array_d = 0;
_off_ev_array_s = 0;
_off_ev_array_d = 0;
_balance_fixed = 0.0;
_cop = 0;
#endif
// optional keywords
int nomp = 0, no_affinity = 0;
_allow_separate_buffers = 1;
_offload_ghost = -1;
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"omp") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
nomp = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"mode") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
if (strcmp(arg[iarg+1],"single") == 0)
_precision_mode = PREC_MODE_SINGLE;
else if (strcmp(arg[iarg+1],"mixed") == 0)
_precision_mode = PREC_MODE_MIXED;
else if (strcmp(arg[iarg+1],"double") == 0)
_precision_mode = PREC_MODE_DOUBLE;
else error->all(FLERR,"Illegal package intel command");
iarg += 2;
} else if (strcmp(arg[iarg],"balance") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
_offload_balance = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg], "ghost") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
if (strcmp(arg[iarg+1],"yes") == 0) _offload_ghost = 1;
else if (strcmp(arg[iarg+1],"no") == 0) _offload_ghost = 0;
else error->all(FLERR,"Illegal package intel command");
iarg += 2;
} else if (strcmp(arg[iarg], "tpc") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
_offload_tpc = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"tptask") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
_offload_threads = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"no_affinity") == 0) {
no_affinity = 1;
iarg++;
}
// undocumented options
else if (strcmp(arg[iarg],"offload_affinity_balanced") == 0) {
_offload_affinity_balanced = 1;
iarg++;
} else if (strcmp(arg[iarg],"buffers") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
_allow_separate_buffers = atoi(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal package intel command");
}
// if ncops is zero, just run on the cpu
if (ncops < 1) {
ncops = -1;
_offload_balance = 0.0;
}
// error check
if (_offload_balance > 1.0 || _offload_threads < 0 ||
_offload_tpc <= 0 || _offload_tpc > 4 || nomp < 0)
error->all(FLERR,"Illegal package intel command");
#ifdef _LMP_INTEL_OFFLOAD
_ncops = ncops;
if (_offload_balance != 0.0) {
_real_space_comm = MPI_COMM_WORLD;
if (no_affinity == 0)
if (set_host_affinity(nomp) != 0)
error->all(FLERR,"Could not set host affinity for offload tasks");
}
int max_offload_threads = 0, offload_cores = 0;
if (_offload_balance != 0.0) {
#pragma offload target(mic:_cop) mandatory \
out(max_offload_threads,offload_cores)
{
offload_cores = omp_get_num_procs();
omp_set_num_threads(offload_cores);
max_offload_threads = omp_get_max_threads();
}
_max_offload_threads = max_offload_threads;
_offload_cores = offload_cores;
if (_offload_threads == 0) _offload_threads = offload_cores;
}
#endif
// set OpenMP threads
// nomp is user setting, default = 0
#if defined(_OPENMP)
+ #if defined(__INTEL_COMPILER)
+ kmp_set_blocktime(0);
+ #endif
if (nomp != 0) {
omp_set_num_threads(nomp);
comm->nthreads = nomp;
} else {
int nthreads;
#pragma omp parallel default(none) shared(nthreads)
nthreads = omp_get_num_threads();
comm->nthreads = nthreads;
}
#endif
// set offload params
#ifdef _LMP_INTEL_OFFLOAD
if (_offload_balance < 0.0) {
_balance_neighbor = 0.9;
_balance_pair = 0.9;
} else {
_balance_neighbor = _offload_balance;
_balance_pair = _offload_balance;
}
_tscreen = screen;
zero_timers();
_setup_time_cleared = false;
_timers_allocated = false;
#else
_offload_balance = 0.0;
#endif
// set precision
if (_precision_mode == PREC_MODE_SINGLE)
_single_buffers = new IntelBuffers<float,float>(lmp);
else if (_precision_mode == PREC_MODE_MIXED)
_mixed_buffers = new IntelBuffers<float,double>(lmp);
else
_double_buffers = new IntelBuffers<double,double>(lmp);
}
/* ---------------------------------------------------------------------- */
FixIntel::~FixIntel()
{
#ifdef _LMP_INTEL_OFFLOAD
output_timing_data();
if (_timers_allocated) {
double *time1 = off_watch_pair();
double *time2 = off_watch_neighbor();
int *overflow = get_off_overflow_flag();
if (_offload_balance != 0.0 && time1 != NULL && time2 != NULL &&
overflow != NULL) {
#pragma offload_transfer target(mic:_cop) \
nocopy(time1,time2,overflow:alloc_if(0) free_if(1))
}
}
#endif
if (_precision_mode == PREC_MODE_SINGLE)
delete _single_buffers;
else if (_precision_mode == PREC_MODE_MIXED)
delete _mixed_buffers;
else
delete _double_buffers;
}
/* ---------------------------------------------------------------------- */
int FixIntel::setmask()
{
int mask = 0;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixIntel::init()
{
#ifdef _LMP_INTEL_OFFLOAD
output_timing_data();
#endif
int nstyles = 0;
if (force->pair_match("hybrid", 1) != NULL) {
PairHybrid *hybrid = (PairHybrid *) force->pair;
for (int i = 0; i < hybrid->nstyles; i++)
if (strstr(hybrid->keywords[i], "/intel") != NULL)
nstyles++;
} else if (force->pair_match("hybrid/overlay", 1) != NULL) {
PairHybridOverlay *hybrid = (PairHybridOverlay *) force->pair;
for (int i = 0; i < hybrid->nstyles; i++)
if (strstr(hybrid->keywords[i], "/intel") != NULL)
nstyles++;
else
force->pair->no_virial_fdotr_compute = 1;
}
if (nstyles > 1)
error->all(FLERR,
"Currently, cannot use more than one intel style with hybrid.");
neighbor->fix_intel = (void *)this;
check_neighbor_intel();
if (_precision_mode == PREC_MODE_SINGLE)
_single_buffers->zero_ev();
else if (_precision_mode == PREC_MODE_MIXED)
_mixed_buffers->zero_ev();
else
_double_buffers->zero_ev();
}
/* ---------------------------------------------------------------------- */
void FixIntel::setup(int vflag)
{
if (neighbor->style != BIN)
error->all(FLERR,
"Currently, neighbor style BIN must be used with Intel package.");
if (neighbor->exclude_setting() != 0)
error->all(FLERR,
"Currently, cannot use neigh_modify exclude with Intel package.");
}
/* ---------------------------------------------------------------------- */
void FixIntel::pair_init_check()
{
#ifdef INTEL_VMASK
atom->sortfreq = 1;
#endif
#ifdef _LMP_INTEL_OFFLOAD
if (_offload_balance != 0.0) atom->sortfreq = 1;
if (force->newton_pair == 0)
_offload_noghost = 0;
else if (_offload_ghost == 0)
_offload_noghost = 1;
set_offload_affinity();
if (!_timers_allocated) {
double *time1 = off_watch_pair();
double *time2 = off_watch_neighbor();
int *overflow = get_off_overflow_flag();
if (_offload_balance !=0.0 && time1 != NULL && time2 != NULL &&
overflow != NULL) {
#pragma offload_transfer target(mic:_cop) \
nocopy(time1,time2:length(1) alloc_if(1) free_if(0)) \
in(overflow:length(5) alloc_if(1) free_if(0))
}
_timers_allocated = true;
}
if (update->whichflag == 2 && _offload_balance != 0.0) {
if (_offload_balance == 1.0 && _offload_noghost == 0)
_sync_at_pair = 1;
else
_sync_at_pair = 2;
} else {
_sync_at_pair = 0;
if (strstr(update->integrate_style,"intel") == 0)
error->all(FLERR,
"Specified run_style does not support the Intel package.");
}
#endif
_nthreads = comm->nthreads;
if (_offload_balance != 0.0 && comm->me == 0) {
#ifndef __INTEL_COMPILER_BUILD_DATE
error->warning(FLERR, "Unknown Intel Compiler Version\n");
#else
if (__INTEL_COMPILER_BUILD_DATE != 20131008 &&
__INTEL_COMPILER_BUILD_DATE < 20141023)
error->warning(FLERR, "Unsupported Intel Compiler.");
#endif
#if !defined(__INTEL_COMPILER)
error->warning(FLERR, "Unsupported Intel Compiler.");
#endif
}
int need_tag = 0;
if (atom->molecular) need_tag = 1;
// Clear buffers used for pair style
char kmode[80];
if (_precision_mode == PREC_MODE_SINGLE) {
strcpy(kmode, "single");
get_single_buffers()->free_all_nbor_buffers();
get_single_buffers()->need_tag(need_tag);
} else if (_precision_mode == PREC_MODE_MIXED) {
strcpy(kmode, "mixed");
get_mixed_buffers()->free_all_nbor_buffers();
get_mixed_buffers()->need_tag(need_tag);
} else {
strcpy(kmode, "double");
get_double_buffers()->free_all_nbor_buffers();
get_double_buffers()->need_tag(need_tag);
}
#ifdef _LMP_INTEL_OFFLOAD
set_offload_affinity();
#endif
if (comm->me == 0) {
if (screen) {
fprintf(screen,
"----------------------------------------------------------\n");
if (_offload_balance != 0.0) {
fprintf(screen,"Using Intel Coprocessor with %d threads per core, ",
_offload_tpc);
fprintf(screen,"%d threads per task\n",_offload_threads);
} else {
fprintf(screen,"Using Intel Package without Coprocessor.\n");
}
fprintf(screen,"Precision: %s\n",kmode);
fprintf(screen,
"----------------------------------------------------------\n");
}
}
}
/* ---------------------------------------------------------------------- */
void FixIntel::check_neighbor_intel()
{
#ifdef _LMP_INTEL_OFFLOAD
_full_host_list = 0;
#endif
const int nrequest = neighbor->nrequest;
for (int i = 0; i < nrequest; ++i) {
#ifdef _LMP_INTEL_OFFLOAD
if (_offload_balance != 0.0 && neighbor->requests[i]->intel == 0) {
_full_host_list = 1;
_offload_noghost = 0;
}
#endif
if (neighbor->requests[i]->skip)
error->all(FLERR, "Cannot yet use hybrid styles with Intel package.");
}
}
/* ---------------------------------------------------------------------- */
void FixIntel::sync_coprocessor()
{
#ifdef _LMP_INTEL_OFFLOAD
if (_offload_balance != 0.0) {
if (_off_force_array_m != 0) {
add_off_results(_off_force_array_m, _off_ev_array_d);
_off_force_array_m = 0;
} else if (_off_force_array_d != 0) {
add_off_results(_off_force_array_d, _off_ev_array_d);
_off_force_array_d = 0;
} else if (_off_force_array_s != 0) {
add_off_results(_off_force_array_s, _off_ev_array_s);
_off_force_array_s = 0;
}
}
#endif
}
/* ---------------------------------------------------------------------- */
double FixIntel::memory_usage()
{
double bytes;
if (_precision_mode == PREC_MODE_SINGLE)
bytes = _single_buffers->memory_usage(_nthreads);
else if (_precision_mode == PREC_MODE_MIXED)
bytes = _mixed_buffers->memory_usage(_nthreads);
else
bytes = _double_buffers->memory_usage(_nthreads);
return bytes;
}
/* ---------------------------------------------------------------------- */
#ifdef _LMP_INTEL_OFFLOAD
void FixIntel::output_timing_data() {
if (_im_real_space_task == 0 || _offload_affinity_set == 0) return;
double timer_total = 0.0;
int size, rank;
double timers[NUM_ITIMERS];
MPI_Comm_size(_real_space_comm, &size);
MPI_Comm_rank(_real_space_comm, &rank);
MPI_Allreduce(&_timers, &timers, NUM_ITIMERS, MPI_DOUBLE, MPI_SUM,
_real_space_comm);
for (int i=0; i < NUM_ITIMERS; i++) {
timers[i] /= size;
timer_total += timers[i];
}
#ifdef TIME_BALANCE
double timers_min[NUM_ITIMERS], timers_max[NUM_ITIMERS];
MPI_Allreduce(&_timers, &timers_max, NUM_ITIMERS, MPI_DOUBLE, MPI_MAX,
_real_space_comm);
MPI_Allreduce(&_timers, &timers_min, NUM_ITIMERS, MPI_DOUBLE, MPI_MIN,
_real_space_comm);
#endif
if (timer_total > 0.0) {
double balance_out[2], balance_in[2];
balance_out[0] = _balance_pair;
balance_out[1] = _balance_neighbor;
MPI_Reduce(balance_out, balance_in, 2, MPI_DOUBLE, MPI_SUM,
0, _real_space_comm);
balance_in[0] /= size;
balance_in[1] /= size;
if (rank == 0 && _tscreen) {
fprintf(_tscreen, "\n------------------------------------------------\n");
fprintf(_tscreen, " Offload Timing Data\n");
fprintf(_tscreen, "------------------------------------------------\n");
fprintf(_tscreen, " Data Pack/Cast Seconds %f\n",
timers[TIME_PACK]);
if (_offload_balance != 0.0) {
fprintf(_tscreen, " Host Neighbor Seconds %f\n",
timers[TIME_HOST_NEIGHBOR]);
fprintf(_tscreen, " Host Pair Seconds %f\n",
timers[TIME_HOST_PAIR]);
fprintf(_tscreen, " Offload Neighbor Seconds %f\n",
timers[TIME_OFFLOAD_NEIGHBOR]);
fprintf(_tscreen, " Offload Pair Seconds %f\n",
timers[TIME_OFFLOAD_PAIR]);
fprintf(_tscreen, " Offload Wait Seconds %f\n",
timers[TIME_OFFLOAD_WAIT]);
fprintf(_tscreen, " Offload Latency Seconds %f\n",
timers[TIME_OFFLOAD_LATENCY]);
fprintf(_tscreen, " Offload Neighbor Balance %f\n",
balance_in[1]);
fprintf(_tscreen, " Offload Pair Balance %f\n",
balance_in[0]);
fprintf(_tscreen, " Offload Ghost Atoms ");
if (_offload_noghost) fprintf(_tscreen,"No\n");
else fprintf(_tscreen,"Yes\n");
#ifdef TIME_BALANCE
fprintf(_tscreen, " Offload Imbalance Seconds %f\n",
timers[TIME_IMBALANCE]);
fprintf(_tscreen, " Offload Min/Max Seconds ");
for (int i = 0; i < NUM_ITIMERS; i++)
fprintf(_tscreen, "[%f, %f] ",timers_min[i],timers_max[i]);
fprintf(_tscreen, "\n");
#endif
double ht = timers[TIME_HOST_NEIGHBOR] + timers[TIME_HOST_PAIR] +
timers[TIME_OFFLOAD_WAIT];
double ct = timers[TIME_OFFLOAD_NEIGHBOR] +
timers[TIME_OFFLOAD_PAIR];
double tt = MAX(ht,ct);
if (timers[TIME_OFFLOAD_LATENCY] / tt > 0.07 && _separate_coi == 0)
error->warning(FLERR,
"Leaving a core free can improve performance for offload");
}
fprintf(_tscreen, "------------------------------------------------\n");
}
zero_timers();
_setup_time_cleared = false;
}
}
/* ---------------------------------------------------------------------- */
int FixIntel::get_ppn(int &node_rank) {
int nprocs;
int rank;
MPI_Comm_size(_real_space_comm, &nprocs);
MPI_Comm_rank(_real_space_comm, &rank);
int name_length;
char node_name[MPI_MAX_PROCESSOR_NAME];
MPI_Get_processor_name(node_name,&name_length);
node_name[name_length] = '\0';
char *node_names = new char[MPI_MAX_PROCESSOR_NAME*nprocs];
MPI_Allgather(node_name, MPI_MAX_PROCESSOR_NAME, MPI_CHAR, node_names,
MPI_MAX_PROCESSOR_NAME, MPI_CHAR, _real_space_comm);
int ppn = 0;
node_rank = 0;
for (int i = 0; i < nprocs; i++) {
if (strcmp(node_name, node_names + i * MPI_MAX_PROCESSOR_NAME) == 0) {
ppn++;
if (i < rank)
node_rank++;
}
}
return ppn;
}
/* ---------------------------------------------------------------------- */
void FixIntel::set_offload_affinity()
{
_separate_buffers = 0;
if (_allow_separate_buffers)
if (_offload_balance != 0.0 && _offload_balance < 1.0)
_separate_buffers = 1;
_im_real_space_task = 1;
if (strncmp(update->integrate_style,"verlet/split",12) == 0) {
_real_space_comm = world;
if (universe->iworld != 0) {
_im_real_space_task = 0;
return;
}
} else
_real_space_comm = universe->uworld;
if (_offload_balance == 0.0) _cop = -1;
if (_offload_balance == 0.0 || _offload_affinity_set == 1)
return;
_offload_affinity_set = 1;
int node_rank;
int ppn = get_ppn(node_rank);
if (ppn % _ncops != 0)
error->all(FLERR, "MPI tasks per node must be multiple of offload_cards");
ppn = ppn / _ncops;
_cop = node_rank / ppn;
node_rank = node_rank % ppn;
int max_threads_per_task = _offload_cores / 4 * _offload_tpc / ppn;
if (_offload_threads > max_threads_per_task)
_offload_threads = max_threads_per_task;
if (_offload_threads > _max_offload_threads)
_offload_threads = _max_offload_threads;
int offload_threads = _offload_threads;
int offload_tpc = _offload_tpc;
int offload_affinity_balanced = _offload_affinity_balanced;
#pragma offload target(mic:_cop) mandatory \
in(node_rank,offload_threads,offload_tpc,offload_affinity_balanced)
{
omp_set_num_threads(offload_threads);
#pragma omp parallel
{
int tnum = omp_get_thread_num();
kmp_affinity_mask_t mask;
kmp_create_affinity_mask(&mask);
int proc;
if (offload_affinity_balanced) {
proc = offload_threads * node_rank + tnum;
proc = proc * 4 - (proc / 60) * 240 + proc / 60 + 1;
} else {
proc = offload_threads * node_rank + tnum;
proc += (proc / 4) * (4 - offload_tpc) + 1;
}
kmp_set_affinity_mask_proc(proc, &mask);
if (kmp_set_affinity(&mask) != 0)
printf("Could not set affinity on rank %d thread %d to %d\n",
node_rank, tnum, proc);
}
}
if (_precision_mode == PREC_MODE_SINGLE)
_single_buffers->set_off_params(offload_threads, _cop, _separate_buffers);
else if (_precision_mode == PREC_MODE_MIXED)
_mixed_buffers->set_off_params(offload_threads, _cop, _separate_buffers);
else
_double_buffers->set_off_params(offload_threads, _cop, _separate_buffers);
}
/* ---------------------------------------------------------------------- */
int FixIntel::set_host_affinity(const int nomp)
{
#ifndef INTEL_OFFLOAD_NOAFFINITY
_separate_coi = 1;
int rank = comm->me;
int node_rank;
int ppn = get_ppn(node_rank);
int cop = node_rank / (ppn / _ncops);
// Get a sorted list of logical cores
int proc_list[INTEL_MAX_HOST_CORE_COUNT];
int ncores;
FILE *p;
char cmd[512];
char readbuf[INTEL_MAX_HOST_CORE_COUNT*5];
sprintf(cmd, "lscpu -p=cpu,core,socket | grep -v '#' |"
"sort -t, -k 3,3n -k 2,2n | awk -F, '{print $1}'");
p = popen(cmd, "r");
if (p == NULL) return -1;
ncores = 0;
while(fgets(readbuf, 512, p)) {
proc_list[ncores] = atoi(readbuf);
ncores++;
}
pclose(p);
// Sanity checks for core list
if (ncores < 2) return -1;
int nzero = 0;
for (int i = 0; i < ncores; i++) {
if (proc_list[i] == 0) nzero++;
if (proc_list[i] < 0 || proc_list[i] >= ncores) return -1;
}
if (nzero > 1) return -1;
// Determine the OpenMP/MPI configuration
char *estring;
int nthreads = nomp;
if (nthreads == 0) {
estring = getenv("OMP_NUM_THREADS");
if (estring != NULL) {
nthreads = atoi(estring);
if (nthreads < 2) nthreads = 1;
} else
nthreads = 1;
}
// Determine how many logical cores for COI and MPI tasks
int coi_cores = 0, mpi_cores;
int subscription = nthreads * ppn;
if (subscription > ncores) {
if (rank == 0)
error->warning(FLERR,
"More MPI tasks/OpenMP threads than available cores");
return 0;
}
if (subscription == ncores)
_separate_coi = 0;
if (subscription > ncores / 2) {
coi_cores = ncores - subscription;
if (coi_cores > INTEL_MAX_COI_CORES) coi_cores = INTEL_MAX_COI_CORES;
}
mpi_cores = (ncores - coi_cores) / ppn;
// Get ids of all LWPs that COI spawned and affinitize
int lwp = 0, plwp = 0, nlwp = 0, mlwp = 0, fail = 0;
cpu_set_t cpuset;
pid_t pid = getpid();
if (coi_cores) {
sprintf(cmd, "ps -Lp %d -o lwp | awk ' (NR > 2) {print}'", pid);
p = popen(cmd, "r");
if (p == NULL) return -1;
while(fgets(readbuf, 512, p)) {
lwp = atoi(readbuf);
int first = coi_cores + node_rank * mpi_cores;
CPU_ZERO(&cpuset);
for (int i = first; i < first + mpi_cores; i++)
CPU_SET(proc_list[i], &cpuset);
if (sched_setaffinity(lwp, sizeof(cpu_set_t), &cpuset)) {
fail = 1;
break;
}
plwp++;
}
pclose(p);
// Do async offload to create COI threads
int sig1, sig2;
float *buf1;
int pragma_size = 1024;
buf1 = (float*) malloc(sizeof(float)*pragma_size);
#pragma offload target (mic:0) mandatory \
in(buf1:length(pragma_size) alloc_if(1) free_if(0)) \
signal(&sig1)
{ buf1[0] = 0.0; }
#pragma offload_wait target(mic:0) wait(&sig1)
#pragma offload target (mic:0) mandatory \
out(buf1:length(pragma_size) alloc_if(0) free_if(1)) \
signal(&sig2)
{ buf1[0] = 1.0; }
#pragma offload_wait target(mic:0) wait(&sig2)
free(buf1);
p = popen(cmd, "r");
if (p == NULL) return -1;
while(fgets(readbuf, 512, p)) {
lwp = atoi(readbuf);
nlwp++;
if (nlwp <= plwp) continue;
CPU_ZERO(&cpuset);
for(int i=0; i<coi_cores; i++)
CPU_SET(proc_list[i], &cpuset);
if (sched_setaffinity(lwp, sizeof(cpu_set_t), &cpuset)) {
fail = 1;
break;
}
}
pclose(p);
nlwp -= plwp;
// Get stats on the number of LWPs per process
MPI_Reduce(&nlwp, &mlwp, 1, MPI_INT, MPI_MAX, 0, MPI_COMM_WORLD);
}
if (screen && rank == 0) {
if (coi_cores)
fprintf(screen,"Intel Package: Affinitizing %d Offload Threads to %d Cores\n",
mlwp, coi_cores);
fprintf(screen,"Intel Package: Affinitizing MPI Tasks to %d Cores Each\n",mpi_cores);
}
if (fail) return -1;
// Affinitize MPI Ranks
CPU_ZERO(&cpuset);
int first = coi_cores + node_rank * mpi_cores;
for (int i = first; i < first+mpi_cores; i++)
CPU_SET(proc_list[i], &cpuset);
if (sched_setaffinity(pid, sizeof(cpu_set_t), &cpuset))
return -1;
#endif
return 0;
}
#endif
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index a4b13967b..c8ca571b4 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -1,61 +1,61 @@
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 (*.cpp and *.h).
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:
doc/Section_commands.html, subsection 3.5
User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections.
The list of features and author of each is given below.
You should contact the author directly if you have specific questions
about the feature or its coding.
------------------------------------------------------------
angle_style cosine/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
angle_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
angle_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
angle_style fourier/simple, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
angle_style dipole, Mario Orsi, orsimario at gmail.com, 10 Jan 12
angle_style quartic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
bond_style harmonic/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
bond_style harmonic/shift/cut, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007
compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013
compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
dihedral_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
dihedral_style nharmonic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
dihedral_style quadratic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12
fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
fix ave/spatial/sphere, Niall Jackson (Imperial College), niall.jackson at gmail.com, 18 Nov 14
-fix correlator, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 28 Sep 2015
+fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015
fix gle, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014
fix imd, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 2009
fix ipi, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014
fix pimd, Yuxing Peng (U Chicago), yuxing at uchicago.edu, 24 Nov 2014
fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008
fix ti/rs, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013
fix ti/spring, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013
fix ttm/mod, Sergey Starikov and Vasily Pisarev (JIHT), pisarevvv at gmail.com, 2 Feb 2015
improper_style cossq, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12
improper_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
improper_style ring, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12
pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11
pair_style eam/cd, Alexander Stukowski, stukowski at mm.tu-darmstadt.de, 7 Nov 09
pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
pair_style list, Axel Kohlmeyer (Temple U), akohlmey at gmail.com, 1 Jun 13
pair_style lj/sf, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12
pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12
pair_style srp, Tim Sirk, tim.sirk at us.army.mil, 21 Nov 14
pair_style tersoff/table, Luca Ferraro, luca.ferraro@caspur.it, 1 Dec 11
diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp
new file mode 100644
index 000000000..03fdd1367
--- /dev/null
+++ b/src/USER-MISC/fix_ave_correlate_long.cpp
@@ -0,0 +1,785 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing authors:
+ Jorge Ramirez (jorge.ramirez@upm.es, Universidad Politecnica de Madrid),
+ Alexei Likhtman (University of Reading)
+ Structure and syntax of fix inspired by fix_ave_correlate
+ Scalar Correlator f(tau)=<A(t)A(t+tau)> and
+ Cross-correlator f(tau)=<A(t)B(t+tau)>
+ see J. Chem. Phys. 133, 154103 (2010)
+------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "stdlib.h"
+#include "string.h"
+#include "unistd.h"
+#include "fix_ave_correlate_long.h"
+#include "update.h"
+#include "modify.h"
+#include "compute.h"
+#include "input.h"
+#include "variable.h"
+#include "memory.h"
+#include "error.h"
+#include "force.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+enum{COMPUTE,FIX,VARIABLE};
+enum{AUTO,UPPER,LOWER,AUTOUPPER,AUTOLOWER,FULL};
+
+#define INVOKED_SCALAR 1
+#define INVOKED_VECTOR 2
+#define INVOKED_ARRAY 4
+
+/* ---------------------------------------------------------------------- */
+
+FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
+ Fix (lmp, narg, arg)
+{
+ // At least nevery nfrez and one value are needed
+ if (narg < 6) error->all(FLERR,"Illegal fix ave/correlate/long command");
+
+ MPI_Comm_rank(world,&me);
+
+ nevery = force->inumeric(FLERR,arg[3]);
+ nfreq = force->inumeric(FLERR,arg[4]);
+
+ restart_global = 1;
+ global_freq = nfreq;
+
+ // parse values until one isn't recognized
+
+ which = new int[narg-5];
+ argindex = new int[narg-5];
+ ids = new char*[narg-5];
+ value2index = new int[narg-5];
+ nvalues = 0;
+
+ int iarg = 5;
+ while (iarg < narg) {
+ if (strncmp(arg[iarg],"c_",2) == 0 ||
+ strncmp(arg[iarg],"f_",2) == 0 ||
+ strncmp(arg[iarg],"v_",2) == 0) {
+ if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
+ else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
+ else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
+
+ int n = strlen(arg[iarg]);
+ char *suffix = new char[n];
+ strcpy(suffix,&arg[iarg][2]);
+
+ char *ptr = strchr(suffix,'[');
+ if (ptr) {
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Illegal fix ave/correlate/long command");
+ argindex[nvalues] = atoi(ptr+1);
+ *ptr = '\0';
+ } else argindex[nvalues] = 0;
+
+ n = strlen(suffix) + 1;
+ ids[nvalues] = new char[n];
+ strcpy(ids[nvalues],suffix);
+ delete [] suffix;
+
+ nvalues++;
+ iarg++;
+ } else break;
+ }
+
+ // optional args
+
+ type = AUTO;
+ startstep = 0;
+ fp = NULL;
+ overwrite = 0;
+ numcorrelators=20;
+ p = 16;
+ m = 2;
+ char *title1 = NULL;
+ char *title2 = NULL;
+
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"type") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal fix ave/correlate/long command");
+ if (strcmp(arg[iarg+1],"auto") == 0) type = AUTO;
+ else if (strcmp(arg[iarg+1],"upper") == 0) type = UPPER;
+ else if (strcmp(arg[iarg+1],"lower") == 0) type = LOWER;
+ else if (strcmp(arg[iarg+1],"auto/upper") == 0) type = AUTOUPPER;
+ else if (strcmp(arg[iarg+1],"auto/lower") == 0) type = AUTOLOWER;
+ else if (strcmp(arg[iarg+1],"full") == 0) type = FULL;
+ else error->all(FLERR,"Illegal fix ave/correlate/long command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"start") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal fix ave/correlate/long command");
+ startstep = force->inumeric(FLERR,arg[iarg+1]);
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"ncorr") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal fix ave/correlate/long command");
+ numcorrelators = force->inumeric(FLERR,arg[iarg+1]);
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"nlen") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal fix ave/correlate/long command");
+ p = force->inumeric(FLERR,arg[iarg+1]);
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"ncount") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal fix ave/correlate/long command");
+ m = force->inumeric(FLERR,arg[iarg+1]);
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"file") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal fix ave/correlate/long command");
+ if (me == 0) {
+ fp = fopen(arg[iarg+1],"w");
+ if (fp == NULL) {
+ char str[128];
+ sprintf(str,"Cannot open fix ave/correlate/long file %s",arg[iarg+1]);
+ error->one(FLERR,str);
+ }
+ }
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"overwrite") == 0) {
+ overwrite = 1;
+ iarg += 1;
+ } else if (strcmp(arg[iarg],"title1") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal fix ave/correlate/long command");
+ delete [] title1;
+ int n = strlen(arg[iarg+1]) + 1;
+ title1 = new char[n];
+ strcpy(title1,arg[iarg+1]);
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"title2") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal fix ave/correlate/long command");
+ delete [] title2;
+ int n = strlen(arg[iarg+1]) + 1;
+ title2 = new char[n];
+ strcpy(title2,arg[iarg+1]);
+ iarg += 2;
+ } else error->all(FLERR,"Illegal fix ave/correlate/long command");
+ }
+
+ if (p % m != 0) error->all(FLERR,"fix_correlator: p mod m must be 0");
+ dmin = p/m;
+ length = numcorrelators*p;
+ npcorr = 0;
+ kmax = 0;
+
+ // setup and error check
+ // for fix inputs, check that fix frequency is acceptable
+
+ if (nevery <= 0 || nfreq <= 0)
+ error->all(FLERR,"Illegal fix ave/correlate/long command");
+ if (nfreq % nevery)
+ error->all(FLERR,"Illegal fix ave/correlate/long command");
+
+ for (int i = 0; i < nvalues; i++) {
+ if (which[i] == COMPUTE) {
+ int icompute = modify->find_compute(ids[i]);
+ if (icompute < 0)
+ error->all(FLERR,"Compute ID for fix ave/correlate/long does not exist");
+ if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0)
+ error->all(FLERR,
+ "Fix ave/correlate/long compute does not calculate a scalar");
+ if (argindex[i] && modify->compute[icompute]->vector_flag == 0)
+ error->all(FLERR,
+ "Fix ave/correlate/long compute does not calculate a vector");
+ if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector)
+ error->all(FLERR,"Fix ave/correlate/long compute vector "
+ "is accessed out-of-range");
+
+ } else if (which[i] == FIX) {
+ int ifix = modify->find_fix(ids[i]);
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for fix ave/correlate/long does not exist");
+ if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
+ error->all(FLERR,"Fix ave/correlate/long fix does not calculate a scalar");
+ if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
+ error->all(FLERR,"Fix ave/correlate/long fix does not calculate a vector");
+ if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector)
+ error->all(FLERR,
+ "Fix ave/correlate/long fix vector is accessed out-of-range");
+ if (nevery % modify->fix[ifix]->global_freq)
+ error->all(FLERR,"Fix for fix ave/correlate/long "
+ "not computed at compatible time");
+
+ } else if (which[i] == VARIABLE) {
+ int ivariable = input->variable->find(ids[i]);
+ if (ivariable < 0)
+ error->all(FLERR,"Variable name for fix ave/correlate/long does not exist");
+ if (input->variable->equalstyle(ivariable) == 0)
+ error->all(FLERR,
+ "Fix ave/correlate/long variable is not equal-style variable");
+ }
+ }
+
+ // npair = # of correlation pairs to calculate
+ if (type == AUTO) npair = nvalues;
+ if (type == UPPER || type == LOWER) npair = nvalues*(nvalues-1)/2;
+ if (type == AUTOUPPER || type == AUTOLOWER) npair = nvalues*(nvalues+1)/2;
+ if (type == FULL) npair = nvalues*nvalues;
+
+ // print file comment lines
+ if (fp && me == 0) {
+ if (title1) fprintf(fp,"%s\n",title1);
+ else fprintf(fp,"# Time-correlated data for fix %s\n",id);
+ if (title2) fprintf(fp,"%s\n",title2);
+ else {
+ fprintf(fp,"# Time");
+ if (type == AUTO)
+ for (int i = 0; i < nvalues; i++)
+ fprintf(fp," %s*%s",arg[5+i],arg[5+i]);
+ else if (type == UPPER)
+ for (int i = 0; i < nvalues; i++)
+ for (int j = i+1; j < nvalues; j++)
+ fprintf(fp," %s*%s",arg[5+i],arg[5+j]);
+ else if (type == LOWER)
+ for (int i = 0; i < nvalues; i++)
+ for (int j = 0; j < i-1; j++)
+ fprintf(fp," %s*%s",arg[5+i],arg[5+j]);
+ else if (type == AUTOUPPER)
+ for (int i = 0; i < nvalues; i++)
+ for (int j = i; j < nvalues; j++)
+ fprintf(fp," %s*%s",arg[5+i],arg[5+j]);
+ else if (type == AUTOLOWER)
+ for (int i = 0; i < nvalues; i++)
+ for (int j = 0; j < i; j++)
+ fprintf(fp," %s*%s",arg[5+i],arg[5+j]);
+ else if (type == FULL)
+ for (int i = 0; i < nvalues; i++)
+ for (int j = 0; j < nvalues; j++)
+ fprintf(fp," %s*%s",arg[5+i],arg[5+j]);
+ fprintf(fp,"\n");
+ }
+ filepos = ftell(fp);
+ }
+
+ delete [] title1;
+ delete [] title2;
+
+ // allocate and initialize memory for calculated values and correlators
+
+ memory->create(values,nvalues,"correlator:values");
+ memory->create(shift,npair,numcorrelators,p,"correlator:shift");
+ memory->create(shift2,npair,numcorrelators,p,"correlator:shift2"); //NOT OPTMAL
+ memory->create(correlation,npair,numcorrelators,p,"correlator:correlation");
+ memory->create(accumulator,npair,numcorrelators,"correlator:accumulator");
+ memory->create(accumulator2,npair,numcorrelators,"correlator:accumulator2"); // NOT OPTIMAL
+
+ memory->create(ncorrelation,numcorrelators,p,"correlator:ncorrelation");
+ memory->create(naccumulator,numcorrelators,"correlator:naccumulator");
+ memory->create(insertindex,numcorrelators,"correlator:insertindex");
+ memory->create(t,length,"correlator:t");
+ memory->create(f,npair,length,"correlator:f");
+
+ for (int i=0;i<npair;i++)
+ for (int j=0;j<numcorrelators;j++) {
+ for (int k=0;k<p;k++) {
+ shift[i][j][k]=-2E10;
+ shift2[i][j][k]=0.0;
+ correlation[i][j][k]=0.0;
+ }
+ accumulator[i][j]=0.0;
+ accumulator2[i][j]=0.0;
+ }
+
+ for (int i=0;i<numcorrelators;i++) {
+ for (int j=0;j<p;j++) ncorrelation[i][j]=0;
+ naccumulator[i]=0;
+ insertindex[i]=0;
+ }
+
+ for (int i=0;i<length;i++) t[i]=0.0;
+ for (int i=0;i<npair;i++)
+ for (int j=0;j<length;j++) f[i][j]=0.0;
+
+
+ // nvalid = next step on which end_of_step does something
+ // add nvalid to all computes that store invocation times
+ // since don't know a priori which are invoked by this fix
+ // once in end_of_step() can set timestep for ones actually invoked
+
+ nvalid_last = -1;
+ nvalid = nextvalid();
+ modify->addstep_compute_all(nvalid);
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixAveCorrelateLong::~FixAveCorrelateLong()
+{
+ delete [] which;
+ delete [] argindex;
+ delete [] value2index;
+ for (int i = 0; i < nvalues; i++) delete [] ids[i];
+ delete [] ids;
+
+ memory->destroy(values);
+ memory->destroy(shift);
+ memory->destroy(shift2);
+ memory->destroy(correlation);
+ memory->destroy(accumulator);
+ memory->destroy(accumulator2);
+ memory->destroy(ncorrelation);
+ memory->destroy(naccumulator);
+ memory->destroy(insertindex);
+ memory->destroy(t);
+ memory->destroy(f);
+
+ if (fp && me == 0) fclose(fp);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixAveCorrelateLong::setmask()
+{
+ int mask = 0;
+ mask |= END_OF_STEP;
+ return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixAveCorrelateLong::init()
+{
+ // set current indices for all computes,fixes,variables
+
+ for (int i = 0; i < nvalues; i++) {
+ if (which[i] == COMPUTE) {
+ int icompute = modify->find_compute(ids[i]);
+ if (icompute < 0)
+ error->all(FLERR,"Compute ID for fix ave/correlate/long does not exist");
+ value2index[i] = icompute;
+
+ } else if (which[i] == FIX) {
+ int ifix = modify->find_fix(ids[i]);
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for fix ave/correlate/long does not exist");
+ value2index[i] = ifix;
+
+ } else if (which[i] == VARIABLE) {
+ int ivariable = input->variable->find(ids[i]);
+ if (ivariable < 0)
+ error->all(FLERR,"Variable name for fix ave/correlate/long does not exist");
+ value2index[i] = ivariable;
+ }
+ }
+
+ // need to reset nvalid if nvalid < ntimestep b/c minimize was performed
+
+ if (nvalid < update->ntimestep) {
+ nvalid = nextvalid();
+ modify->addstep_compute_all(nvalid);
+ }
+}
+
+/* ----------------------------------------------------------------------
+ only does something if nvalid = current timestep
+------------------------------------------------------------------------- */
+
+void FixAveCorrelateLong::setup(int vflag)
+{
+ end_of_step();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixAveCorrelateLong::end_of_step()
+{
+ int i,m;
+ double scalar;
+
+ // skip if not step which requires doing something
+ // error check if timestep was reset in an invalid manner
+
+ bigint ntimestep = update->ntimestep;
+ if (ntimestep < nvalid_last || ntimestep > nvalid)
+ error->all(FLERR,"Invalid timestep reset for fix ave/correlate/long");
+ if (ntimestep != nvalid) return;
+ nvalid_last = nvalid;
+
+ // accumulate results of computes,fixes,variables to origin
+ // compute/fix/variable may invoke computes so wrap with clear/add
+
+ modify->clearstep_compute();
+
+ for (i = 0; i < nvalues; i++) {
+ m = value2index[i];
+
+ // invoke compute if not previously invoked
+
+ if (which[i] == COMPUTE) {
+ Compute *compute = modify->compute[m];
+
+ if (argindex[i] == 0) {
+ if (!(compute->invoked_flag & INVOKED_SCALAR)) {
+ compute->compute_scalar();
+ compute->invoked_flag |= INVOKED_SCALAR;
+ }
+ scalar = compute->scalar;
+ } else {
+ if (!(compute->invoked_flag & INVOKED_VECTOR)) {
+ compute->compute_vector();
+ compute->invoked_flag |= INVOKED_VECTOR;
+ }
+ scalar = compute->vector[argindex[i]-1];
+ }
+
+ // access fix fields, guaranteed to be ready
+
+ } else if (which[i] == FIX) {
+ if (argindex[i] == 0)
+ scalar = modify->fix[m]->compute_scalar();
+ else
+ scalar = modify->fix[m]->compute_vector(argindex[i]-1);
+
+ // evaluate equal-style variable
+
+ } else if (which[i] == VARIABLE)
+ scalar = input->variable->compute_equal(m);
+
+ values[i] = scalar;
+ }
+
+ // fistindex = index in values ring of earliest time sample
+
+ nvalid += nevery;
+ modify->addstep_compute(nvalid);
+
+ // calculate all Cij() enabled by latest values
+
+ accumulate();
+ if (ntimestep % nfreq) return;
+
+ // output result to file
+ evaluate();
+
+ if (fp && me == 0) {
+ if(overwrite) fseek(fp,filepos,SEEK_SET);
+ fprintf(fp,"# Timestep: " BIGINT_FORMAT "\n", ntimestep);
+ for (unsigned int i=0;i<npcorr;++i) {
+ fprintf(fp, "%lg ", t[i]*update->dt);
+ for (unsigned int j=0;j<npair;++j) {
+ fprintf(fp, "%lg ", f[j][i]);
+ }
+ fprintf(fp, "\n");
+ }
+ fflush(fp);
+ if (overwrite) {
+ long fileend = ftell(fp);
+ if (fileend > 0) ftruncate(fileno(fp),fileend);
+ }
+ }
+
+ return;
+
+}
+
+void FixAveCorrelateLong::evaluate() {
+ unsigned int jm=0;
+
+ // First correlator
+ for (unsigned int j=0;j<p;++j) {
+ if (ncorrelation[0][j] > 0) {
+ t[jm] = j;
+ for (int i=0;i<npair;++i)
+ f[i][jm] = correlation[i][0][j]/ncorrelation[0][j];
+ ++jm;
+ }
+ }
+
+ // Subsequent correlators
+ for (int k=1;k<kmax;++k) {
+ for (int j=dmin;j<p;++j) {
+ if (ncorrelation[k][j]>0) {
+ t[jm] = j * pow((double)m, k);
+ for (int i=0;i<npair;++i)
+ f[i][jm] = correlation[i][k][j] / ncorrelation[k][j];
+ ++jm;
+ }
+ }
+ }
+
+ npcorr = jm;
+}
+
+
+/* ----------------------------------------------------------------------
+ accumulate correlation data using more recently added values
+------------------------------------------------------------------------- */
+
+void FixAveCorrelateLong::accumulate()
+{
+ int i,j,ipair;
+
+ //printf("DEBUG %i %i\n", nvalues, npair);
+
+ if (type == AUTO) {
+ for (i=0; i<nvalues;i++) add(i,values[i]);
+ } else if (type == UPPER) {
+ ipair = 0;
+ for (i=0;i<nvalues;i++)
+ for (j=i+1;j<nvalues;j++) add(ipair++,values[i],values[j]);
+ } else if (type == LOWER) {
+ ipair = 0;
+ for (i=0;i<nvalues;i++)
+ for (j=0;j<i;j++) add(ipair++,values[i],values[j]);
+ } else if (type == AUTOUPPER) {
+ ipair = 0;
+ for (i=0;i<nvalues;i++)
+ for (j=i;j<nvalues;j++) {
+ if (i==j) add(ipair++,values[i]);
+ else add(ipair++,values[i],values[j]);
+ }
+ } else if (type == AUTOLOWER) {
+ ipair = 0;
+ for (i=0;i<nvalues;i++)
+ for (j=0;j<=i;j++) {
+ if (i==j) add(ipair++,values[i]);
+ else add(ipair++,values[i],values[j]);
+ }
+ } else if (type == FULL) {
+ ipair = 0;
+ for (i=0;i<nvalues;i++)
+ for (j=0;j<nvalues;j++) {
+ if (i==j) add(ipair++,values[i]);
+ else add(ipair++,values[i],values[j]);
+ }
+ }
+}
+
+
+/* ----------------------------------------------------------------------
+ Add a scalar value to the autocorrelator k of pair i
+------------------------------------------------------------------------- */
+void FixAveCorrelateLong::add(const int i, const double w, const unsigned int k){
+ // If we exceed the correlator side, the value is discarded
+ if (k == numcorrelators) return;
+ if (k > kmax) kmax=k;
+
+ // Insert new value in shift array
+ shift[i][k][insertindex[k]] = w;
+
+ // Add to accumulator and, if needed, add to next correlator
+ accumulator[i][k] += w;
+ if (i==0) ++naccumulator[k];
+ if (naccumulator[k]==m) {
+ add(i,accumulator[i][k]/m, k+1);
+ accumulator[i][k]=0;
+ if (i==npair-1) naccumulator[k]=0;
+ }
+
+ // Calculate correlation function
+ unsigned int ind1=insertindex[k];
+ if (k==0) { // First correlator is different
+ int ind2=ind1;
+ for (unsigned int j=0;j<p;++j) {
+ if (shift[i][k][ind2] > -1e10) {
+ correlation[i][k][j]+= shift[i][k][ind1]*shift[i][k][ind2];
+ if (i==0) ++ncorrelation[k][j];
+ }
+ --ind2;
+ if (ind2<0) ind2+=p;
+ }
+ } else {
+ int ind2=ind1-dmin;
+ for (unsigned int j=dmin;j<p;++j) {
+ if (ind2<0) ind2+=p;
+ if (shift[i][k][ind2] > -1e10) {
+ correlation[i][k][j]+= shift[i][k][ind1]*shift[i][k][ind2];
+ if (i==0) ++ncorrelation[k][j];
+ }
+ --ind2;
+ }
+ }
+
+ if (i==npair-1) {
+ ++insertindex[k];
+ if (insertindex[k]==p) insertindex[k]=0;
+ }
+}
+
+
+/* ----------------------------------------------------------------------
+ Add 2 scalar values to the cross-correlator k of pair i
+------------------------------------------------------------------------- */
+void FixAveCorrelateLong::add(const int i, const double wA, const double wB,
+ const unsigned int k) {
+ if (k == numcorrelators) return;
+ if (k > kmax) kmax=k;
+
+ shift[i][k][insertindex[k]] = wA;
+ shift2[i][k][insertindex[k]] = wB;
+
+ accumulator[i][k] += wA;
+ accumulator2[i][k] += wB;
+ if (i==0) ++naccumulator[k];
+ if (naccumulator[k]==m) {
+ add(i,accumulator[i][k]/m, accumulator2[i][k]/m,k+1);
+ accumulator[i][k]=0;
+ accumulator2[i][k]=0;
+ if (i==npair-1) naccumulator[k]=0;
+ }
+
+ unsigned int ind1=insertindex[k];
+ if (k==0) {
+ int ind2=ind1;
+ for (unsigned int j=0;j<p;++j) {
+ if (shift[i][k][ind2] > -1e10) {
+ correlation[i][k][j]+= shift[i][k][ind1]*shift2[i][k][ind2];
+ if (i==0) ++ncorrelation[k][j];
+ }
+ --ind2;
+ if (ind2<0) ind2+=p;
+ }
+ }
+ else {
+ int ind2=ind1-dmin;
+ for (unsigned int j=dmin;j<p;++j) {
+ if (ind2<0) ind2+=p;
+ if (shift[i][k][ind2] > -1e10) {
+ correlation[i][k][j]+= shift[i][k][ind1]*shift2[i][k][ind2];
+ if (i==0) ++ncorrelation[k][j];
+ }
+ --ind2;
+ }
+ }
+
+ if (i==npair-1) {
+ ++insertindex[k];
+ if (insertindex[k]==p) insertindex[k]=0;
+ }
+}
+
+
+/* ----------------------------------------------------------------------
+ nvalid = next step on which end_of_step does something
+ this step if multiple of nevery, else next multiple
+ startstep is lower bound
+------------------------------------------------------------------------- */
+
+bigint FixAveCorrelateLong::nextvalid()
+{
+ bigint nvalid = update->ntimestep;
+ if (startstep > nvalid) nvalid = startstep;
+ if (nvalid % nevery) nvalid = (nvalid/nevery)*nevery + nevery;
+ return nvalid;
+}
+
+
+/* ----------------------------------------------------------------------
+ memory_usage
+------------------------------------------------------------------------- */
+double FixAveCorrelateLong::memory_usage() {
+ // shift: npair x numcorrelators x p
+ // shift2: npair x numcorrelators x p
+ // correlation: npair x numcorrelators x p
+ // accumulator: npair x numcorrelators
+ // accumulator2: npair x numcorrelators
+ // ncorrelation: numcorrelators x p
+ // naccumulator: numcorrelators
+ // insertindex: numcorrelators
+ // t: numcorrelators x p
+ // f: npair x numcorrelators x p
+ double bytes = (4*npair*numcorrelators*p + 2*npair*numcorrelators
+ + numcorrelators*p)*sizeof(double)
+ + numcorrelators*p*sizeof(unsigned long int)
+ + 2*numcorrelators*sizeof(unsigned int);
+ return bytes;
+}
+
+/* ----------------------------------------------------------------------
+ Write Restart data to restart file
+------------------------------------------------------------------------- */
+// Save everything except t and f
+void FixAveCorrelateLong::write_restart(FILE *fp) {
+ if (me == 0) {
+ int nsize = 3*npair*numcorrelators*p + 2*npair*numcorrelators
+ + numcorrelators*p + 2*numcorrelators + 6;
+ int n=0;
+ double *list;
+ memory->create(list,nsize,"correlator:list");
+ list[n++]=npair;
+ list[n++]=numcorrelators;
+ list[n++]=p;
+ list[n++]=m;
+ list[n++]=nvalid;
+ list[n++]=nvalid_last;
+ for (int i=0;i<npair;i++)
+ for (int j=0;j<numcorrelators;j++) {
+ for (int k=0;k<p;k++) {
+ list[n++]=shift[i][j][k];
+ list[n++]=shift2[i][j][k];
+ list[n++]=correlation[i][j][k];
+ }
+ list[n++]=accumulator[i][j];
+ list[n++]=accumulator2[i][j];
+ }
+ for (int i=0;i<numcorrelators;i++) {
+ for (int j=0;j<p;j++) list[n++]=ncorrelation[i][j];
+ list[n++]=naccumulator[i];
+ list[n++]=insertindex[i];
+ }
+
+ int size = n*sizeof(double);
+ fwrite(&size,sizeof(int),1,fp);
+ fwrite(list,sizeof(double),n,fp);
+ memory->destroy(list);
+ }
+}
+
+
+/* ----------------------------------------------------------------------
+ use state info from restart file to restart the Fix
+------------------------------------------------------------------------- */
+void FixAveCorrelateLong::restart(char *buf)
+{
+ int n = 0;
+ double *list = (double *) buf;
+ int npairin = static_cast<int> (list[n++]);
+ int numcorrelatorsin = static_cast<int> (list[n++]);
+ int pin = static_cast<int> (list[n++]);
+ int min = static_cast<int> (list[n++]);
+ nvalid = static_cast<int> (list[n++]);
+ nvalid_last = static_cast<int> (list[n++]);
+
+ if ((npairin!=npair) || (numcorrelatorsin!=numcorrelators)
+ || (pin!=p) || (min!=m))
+ error->all(FLERR,"Fix ave/correlate/long: restart and input data are different");
+
+ for (int i=0;i<npair;i++)
+ for (int j=0;j<numcorrelators;j++) {
+ for (int k=0;k<p;k++) {
+ shift[i][j][k] = list[n++];
+ shift2[i][j][k] = list[n++];
+ correlation[i][j][k] = list[n++];
+ }
+ accumulator[i][j] = list[n++];
+ accumulator2[i][j] = list[n++];
+ }
+ for (int i=0;i<numcorrelators;i++) {
+ for (int j=0;j<p;j++)
+ ncorrelation[i][j] = static_cast<unsigned long int>(list[n++]);
+ naccumulator[i] = static_cast<unsigned int> (list[n++]);
+ insertindex[i] = static_cast<unsigned int> (list[n++]);
+ }
+}
diff --git a/src/USER-MISC/fix_ave_correlate_long.h b/src/USER-MISC/fix_ave_correlate_long.h
new file mode 100644
index 000000000..49e840e89
--- /dev/null
+++ b/src/USER-MISC/fix_ave_correlate_long.h
@@ -0,0 +1,152 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(ave/correlate/long,FixAveCorrelateLong)
+
+#else
+
+#ifndef LMP_FIX_AVE_CORRELATE_LONG_H
+#define LMP_FIX_AVE_CORRELATE_LONG_H
+
+#include "stdio.h"
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixAveCorrelateLong : public Fix {
+ public:
+ FixAveCorrelateLong(class LAMMPS *, int, char **);
+ ~FixAveCorrelateLong();
+ int setmask();
+ void init();
+ void setup(int);
+ void end_of_step();
+
+ void write_restart(FILE *);
+ void restart(char *);
+ double memory_usage();
+
+ double *t; // Time steps for result arrays
+ double **f; // Result arrays
+ unsigned int npcorr;
+
+ private:
+ // NOT OPTIMAL: shift2 and accumulator2 only needed in cross-correlations
+ double ***shift, *** shift2;
+ double ***correlation;
+ double **accumulator, **accumulator2;
+ unsigned long int **ncorrelation;
+ unsigned int *naccumulator;
+ unsigned int *insertindex;
+
+ unsigned int numcorrelators; // Recommended 20
+ unsigned int p; // Points per correlator (recommended 16)
+ unsigned int m; // Num points for average (recommended 2; p mod m = 0)
+ unsigned int dmin; // Min distance between ponts for correlators k>0; dmin=p/m
+
+ unsigned int length; // Length of result arrays
+ unsigned int kmax; // Maximum correlator attained during simulation
+
+ int me,nvalues;
+ int nfreq;
+ bigint nvalid,nvalid_last;
+ int *which,*argindex,*value2index;
+ char **ids;
+ FILE *fp;
+
+ int type,startstep,overwrite;
+ long filepos;
+
+ int npair; // number of correlation pairs to calculate
+ double *values;
+
+ void accumulate();
+ void evaluate();
+ bigint nextvalid();
+
+ void add(const int i, const double w, const unsigned int k = 0);
+ void add(const int i, const double wA, const double wB, const unsigned int k = 0);
+
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Cannot open fix ave/correlate/long file %s
+
+The specified file cannot be opened. Check that the path and name are
+correct.
+
+E: Compute ID for fix ave/correlate/long does not exist
+
+Self-explanatory.
+
+E: Fix ave/correlate/long compute does not calculate a scalar
+
+Self-explanatory.
+
+E: Fix ave/correlate/long compute does not calculate a vector
+
+Self-explanatory.
+
+E: Fix ave/correlate/long compute vector is accessed out-of-range
+
+The index for the vector is out of bounds.
+
+E: Fix ID for fix ave/correlate/long does not exist
+
+Self-explanatory.
+
+E: Fix ave/correlate/long fix does not calculate a scalar
+
+Self-explanatory.
+
+E: Fix ave/correlate/long fix does not calculate a vector
+
+Self-explanatory.
+
+E: Fix ave/correlate/long fix vector is accessed out-of-range
+
+The index for the vector is out of bounds.
+
+E: Fix for fix ave/correlate/long not computed at compatible time
+
+Fixes generate their values on specific timesteps. Fix ave/correlate/long
+is requesting a value on a non-allowed timestep.
+
+E: Variable name for fix ave/correlate/long does not exist
+
+Self-explanatory.
+
+E: Fix ave/correlate/long variable is not equal-style variable
+
+Self-explanatory.
+
+E: Invalid timestep reset for fix ave/correlate/long
+
+Resetting the timestep has invalidated the sequence of timesteps this
+fix needs to process.
+
+*/
diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp
index 08701982e..3b2730001 100644
--- a/src/compute_msd_chunk.cpp
+++ b/src/compute_msd_chunk.cpp
@@ -1,264 +1,265 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "string.h"
#include "compute_msd_chunk.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute_chunk_atom.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute msd/chunk command");
array_flag = 1;
size_array_cols = 4;
size_array_rows = 0;
size_array_rows_variable = 1;
extarray = 0;
// ID of compute chunk/atom
int n = strlen(arg[3]) + 1;
idchunk = new char[n];
strcpy(idchunk,arg[3]);
init();
massproc = masstotal = NULL;
com = comall = cominit = NULL;
msd = NULL;
firstflag = 1;
}
/* ---------------------------------------------------------------------- */
ComputeMSDChunk::~ComputeMSDChunk()
{
delete [] idchunk;
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(com);
memory->destroy(comall);
memory->destroy(cominit);
memory->destroy(msd);
}
/* ---------------------------------------------------------------------- */
void ComputeMSDChunk::init()
{
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for compute msd/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute msd/chunk does not use chunk/atom compute");
}
/* ----------------------------------------------------------------------
compute initial COM for each chunk
only once on timestep compute is defined, when firstflag = 1
------------------------------------------------------------------------- */
void ComputeMSDChunk::setup()
{
if (!firstflag) return;
compute_array();
firstflag = 0;
for (int i = 0; i < nchunk; i++) {
cominit[i][0] = comall[i][0];
cominit[i][1] = comall[i][1];
cominit[i][2] = comall[i][2];
msd[i][0] = msd[i][1] = msd[i][2] = msd[i][3] = 0.0;
}
}
/* ---------------------------------------------------------------------- */
void ComputeMSDChunk::compute_array()
{
int index;
double massone;
double unwrap[3];
invoked_array = update->ntimestep;
// compute chunk/atom assigns atoms to chunk IDs
// extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
int n = cchunk->setup_chunks();
cchunk->compute_ichunk();
int *ichunk = cchunk->ichunk;
// first time call, allocate per-chunk arrays
// thereafter, require nchunk remain the same
if (firstflag) {
nchunk = n;
size_array_rows = nchunk;
allocate();
+ size_array_rows = nchunk;
} else if (n != nchunk)
error->all(FLERR,"Compute msd/chunk nchunk is not static");
// zero local per-chunk values
for (int i = 0; i < nchunk; i++) {
massproc[i] = 0.0;
com[i][0] = com[i][1] = com[i][2] = 0.0;
}
// compute current COM for each chunk
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
imageint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
domain->unmap(x[i],image[i],unwrap);
massproc[index] += massone;
com[index][0] += unwrap[0] * massone;
com[index][1] += unwrap[1] * massone;
com[index][2] += unwrap[2] * massone;
}
MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < nchunk; i++) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
comall[i][2] /= masstotal[i];
}
// MSD is difference between current and initial COM
// cominit does not yet exist when called first time from setup()
if (firstflag) return;
double dx,dy,dz;
for (int i = 0; i < nchunk; i++) {
dx = comall[i][0] - cominit[i][0];
dy = comall[i][1] - cominit[i][1];
dz = comall[i][2] - cominit[i][2];
msd[i][0] = dx*dx;
msd[i][1] = dy*dy;
msd[i][2] = dz*dz;
msd[i][3] = dx*dx + dy*dy + dz*dz;
}
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods insure vector/array size is locked for Nfreq epoch
by passing lock info along to compute chunk/atom
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
increment lock counter
------------------------------------------------------------------------- */
void ComputeMSDChunk::lock_enable()
{
cchunk->lockcount++;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void ComputeMSDChunk::lock_disable()
{
int icompute = modify->find_compute(idchunk);
if (icompute >= 0) {
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
cchunk->lockcount--;
}
}
/* ----------------------------------------------------------------------
calculate and return # of chunks = length of vector/array
------------------------------------------------------------------------- */
int ComputeMSDChunk::lock_length()
{
nchunk = cchunk->setup_chunks();
return nchunk;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void ComputeMSDChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
cchunk->lock(fixptr,startstep,stopstep);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void ComputeMSDChunk::unlock(Fix *fixptr)
{
cchunk->unlock(fixptr);
}
/* ----------------------------------------------------------------------
one-time allocate of per-chunk arrays
------------------------------------------------------------------------- */
void ComputeMSDChunk::allocate()
{
memory->create(massproc,nchunk,"msd/chunk:massproc");
memory->create(masstotal,nchunk,"msd/chunk:masstotal");
memory->create(com,nchunk,3,"msd/chunk:com");
memory->create(comall,nchunk,3,"msd/chunk:comall");
memory->create(cominit,nchunk,3,"msd/chunk:cominit");
memory->create(msd,nchunk,4,"msd/chunk:msd");
array = msd;
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeMSDChunk::memory_usage()
{
double bytes = (bigint) nchunk * 2 * sizeof(double);
bytes += (bigint) nchunk * 3*3 * sizeof(double);
bytes += (bigint) nchunk * 4 * sizeof(double);
return bytes;
}
diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp
index 56a3538f5..d5ae80c07 100644
--- a/src/fix_adapt.cpp
+++ b/src/fix_adapt.cpp
@@ -1,570 +1,586 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "fix_adapt.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "modify.h"
#include "force.h"
#include "pair.h"
#include "pair_hybrid.h"
#include "kspace.h"
#include "fix_store.h"
#include "input.h"
#include "variable.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{PAIR,KSPACE,ATOM};
enum{DIAMETER,CHARGE};
/* ---------------------------------------------------------------------- */
FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
if (narg < 5) error->all(FLERR,"Illegal fix adapt command");
nevery = force->inumeric(FLERR,arg[3]);
if (nevery < 0) error->all(FLERR,"Illegal fix adapt command");
dynamic_group_allow = 1;
create_attribute = 1;
// count # of adaptations
nadapt = 0;
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) {
if (iarg+6 > narg) error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 6;
} else if (strcmp(arg[iarg],"kspace") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 2;
} else if (strcmp(arg[iarg],"atom") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 3;
} else break;
}
if (nadapt == 0) error->all(FLERR,"Illegal fix adapt command");
adapt = new Adapt[nadapt];
// parse keywords
nadapt = 0;
diamflag = 0;
chgflag = 0;
iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) {
if (iarg+6 > narg) error->all(FLERR,"Illegal fix adapt command");
adapt[nadapt].which = PAIR;
int n = strlen(arg[iarg+1]) + 1;
adapt[nadapt].pstyle = new char[n];
strcpy(adapt[nadapt].pstyle,arg[iarg+1]);
n = strlen(arg[iarg+2]) + 1;
adapt[nadapt].pparam = new char[n];
strcpy(adapt[nadapt].pparam,arg[iarg+2]);
force->bounds(arg[iarg+3],atom->ntypes,
adapt[nadapt].ilo,adapt[nadapt].ihi);
force->bounds(arg[iarg+4],atom->ntypes,
adapt[nadapt].jlo,adapt[nadapt].jhi);
if (strstr(arg[iarg+5],"v_") == arg[iarg+5]) {
n = strlen(&arg[iarg+5][2]) + 1;
adapt[nadapt].var = new char[n];
strcpy(adapt[nadapt].var,&arg[iarg+5][2]);
} else error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 6;
} else if (strcmp(arg[iarg],"kspace") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
adapt[nadapt].which = KSPACE;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
int n = strlen(&arg[iarg+1][2]) + 1;
adapt[nadapt].var = new char[n];
strcpy(adapt[nadapt].var,&arg[iarg+1][2]);
} else error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 2;
} else if (strcmp(arg[iarg],"atom") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix adapt command");
adapt[nadapt].which = ATOM;
if (strcmp(arg[iarg+1],"diameter") == 0) {
adapt[nadapt].aparam = DIAMETER;
diamflag = 1;
} else if (strcmp(arg[iarg+1],"charge") == 0) {
adapt[nadapt].aparam = CHARGE;
chgflag = 1;
} else error->all(FLERR,"Illegal fix adapt command");
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
adapt[nadapt].var = new char[n];
strcpy(adapt[nadapt].var,&arg[iarg+2][2]);
} else error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 3;
} else break;
}
// optional keywords
resetflag = 0;
scaleflag = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"reset") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
if (strcmp(arg[iarg+1],"no") == 0) resetflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) resetflag = 1;
else error->all(FLERR,"Illegal fix adapt command");
iarg += 2;
} else if (strcmp(arg[iarg],"scale") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
if (strcmp(arg[iarg+1],"no") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) scaleflag = 1;
else error->all(FLERR,"Illegal fix adapt command");
iarg += 2;
} else error->all(FLERR,"Illegal fix adapt command");
}
// allocate pair style arrays
int n = atom->ntypes;
for (int m = 0; m < nadapt; m++)
if (adapt[m].which == PAIR)
memory->create(adapt[m].array_orig,n+1,n+1,"adapt:array_orig");
id_fix_diam = id_fix_chg = NULL;
}
/* ---------------------------------------------------------------------- */
FixAdapt::~FixAdapt()
{
for (int m = 0; m < nadapt; m++) {
delete [] adapt[m].var;
if (adapt[m].which == PAIR) {
delete [] adapt[m].pstyle;
delete [] adapt[m].pparam;
memory->destroy(adapt[m].array_orig);
}
}
delete [] adapt;
// check nfix in case all fixes have already been deleted
if (id_fix_diam && modify->nfix) modify->delete_fix(id_fix_diam);
if (id_fix_chg && modify->nfix) modify->delete_fix(id_fix_chg);
delete [] id_fix_diam;
delete [] id_fix_chg;
}
/* ---------------------------------------------------------------------- */
int FixAdapt::setmask()
{
int mask = 0;
mask |= PRE_FORCE;
mask |= POST_RUN;
mask |= PRE_FORCE_RESPA;
return mask;
}
/* ----------------------------------------------------------------------
if need to restore per-atom quantities, create new fix STORE styles
------------------------------------------------------------------------- */
void FixAdapt::post_constructor()
{
if (!resetflag) return;
if (!diamflag && !chgflag) return;
// new id = fix-ID + FIX_STORE_ATTRIBUTE
// new fix group = group for this fix
id_fix_diam = NULL;
id_fix_chg = NULL;
char **newarg = new char*[5];
newarg[1] = group->names[igroup];
newarg[2] = (char *) "STORE";
newarg[3] = (char *) "1";
newarg[4] = (char *) "1";
if (diamflag) {
int n = strlen(id) + strlen("_FIX_STORE_DIAM") + 1;
id_fix_diam = new char[n];
strcpy(id_fix_diam,id);
strcat(id_fix_diam,"_FIX_STORE_DIAM");
newarg[0] = id_fix_diam;
modify->add_fix(5,newarg);
fix_diam = (FixStore *) modify->fix[modify->nfix-1];
if (fix_diam->restart_reset) fix_diam->restart_reset = 0;
else {
double *vec = fix_diam->vstore;
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) vec[i] = radius[i];
else vec[i] = 0.0;
}
}
}
if (chgflag) {
int n = strlen(id) + strlen("_FIX_STORE_CHG") + 1;
id_fix_chg = new char[n];
strcpy(id_fix_chg,id);
strcat(id_fix_chg,"_FIX_STORE_CHG");
newarg[0] = id_fix_chg;
modify->add_fix(5,newarg);
fix_chg = (FixStore *) modify->fix[modify->nfix-1];
if (fix_chg->restart_reset) fix_chg->restart_reset = 0;
else {
double *vec = fix_chg->vstore;
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) vec[i] = q[i];
else vec[i] = 0.0;
}
}
}
delete [] newarg;
}
/* ---------------------------------------------------------------------- */
void FixAdapt::init()
{
int i,j;
// allow a dynamic group only if ATOM attribute not used
if (group->dynamic[igroup])
for (int i = 0; i < nadapt; i++)
if (adapt[i].which == ATOM)
error->all(FLERR,"Cannot use dynamic group with fix adapt atom");
// setup and error checks
anypair = 0;
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
ad->ivar = input->variable->find(ad->var);
if (ad->ivar < 0)
error->all(FLERR,"Variable name for fix adapt does not exist");
if (!input->variable->equalstyle(ad->ivar))
error->all(FLERR,"Variable for fix adapt is invalid style");
if (ad->which == PAIR) {
anypair = 1;
Pair *pair = NULL;
+ // if ad->pstyle has trailing sub-style annotation ":N",
+ // strip it for pstyle arg to pair_match() and set nsub = N
+ // this should work for appended suffixes as well
+
+ int n = strlen(ad->pstyle) + 1;
+ char *pstyle = new char[n];
+ strcpy(pstyle,ad->pstyle);
+
+ char *cptr;
+ int nsub = 0;
+ if (cptr = strchr(pstyle,':')) {
+ *cptr = '\0';
+ nsub = force->inumeric(FLERR,cptr+1);
+ }
+
if (lmp->suffix_enable) {
- int len = 2 + strlen(ad->pstyle) + strlen(lmp->suffix);
+ int len = 2 + strlen(pstyle) + strlen(lmp->suffix);
char *psuffix = new char[len];
-
- strcpy(psuffix,ad->pstyle);
+ strcpy(psuffix,pstyle);
strcat(psuffix,"/");
strcat(psuffix,lmp->suffix);
- pair = force->pair_match(psuffix,1);
+ pair = force->pair_match(psuffix,1,nsub);
delete[] psuffix;
}
- if (pair == NULL) pair = force->pair_match(ad->pstyle,1);
+ if (pair == NULL) pair = force->pair_match(pstyle,1,nsub);
if (pair == NULL) error->all(FLERR,"Fix adapt pair style does not exist");
void *ptr = pair->extract(ad->pparam,ad->pdim);
if (ptr == NULL)
error->all(FLERR,"Fix adapt pair style param not supported");
ad->pdim = 2;
if (ad->pdim == 0) ad->scalar = (double *) ptr;
if (ad->pdim == 2) ad->array = (double **) ptr;
// if pair hybrid, test that ilo,ihi,jlo,jhi are valid for sub-style
if (ad->pdim == 2 && (strcmp(force->pair_style,"hybrid") == 0 ||
strcmp(force->pair_style,"hybrid/overlay") == 0)) {
PairHybrid *pair = (PairHybrid *) force->pair;
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
- if (!pair->check_ijtype(i,j,ad->pstyle))
+ if (!pair->check_ijtype(i,j,pstyle))
error->all(FLERR,"Fix adapt type pair range is not valid for "
"pair hybrid sub-style");
}
+ delete [] pstyle;
+
} else if (ad->which == KSPACE) {
if (force->kspace == NULL)
error->all(FLERR,"Fix adapt kspace style does not exist");
kspace_scale = (double *) force->kspace->extract("scale");
} else if (ad->which == ATOM) {
if (ad->aparam == DIAMETER) {
if (!atom->radius_flag)
error->all(FLERR,"Fix adapt requires atom attribute diameter");
}
if (ad->aparam == CHARGE) {
if (!atom->q_flag)
error->all(FLERR,"Fix adapt requires atom attribute charge");
}
}
}
// make copy of original pair array values
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
if (ad->which == PAIR && ad->pdim == 2) {
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array_orig[i][j] = ad->array[i][j];
}
}
// fixes that store initial per-atom values
if (id_fix_diam) {
int ifix = modify->find_fix(id_fix_diam);
if (ifix < 0) error->all(FLERR,"Could not find fix adapt storage fix ID");
fix_diam = (FixStore *) modify->fix[ifix];
}
if (id_fix_chg) {
int ifix = modify->find_fix(id_fix_chg);
if (ifix < 0) error->all(FLERR,"Could not find fix adapt storage fix ID");
fix_chg = (FixStore *) modify->fix[ifix];
}
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixAdapt::setup_pre_force(int vflag)
{
change_settings();
}
/* ---------------------------------------------------------------------- */
void FixAdapt::setup_pre_force_respa(int vflag, int ilevel)
{
if (ilevel < nlevels_respa-1) return;
setup_pre_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixAdapt::pre_force(int vflag)
{
if (nevery == 0) return;
if (update->ntimestep % nevery) return;
change_settings();
}
/* ---------------------------------------------------------------------- */
void FixAdapt::pre_force_respa(int vflag, int ilevel, int)
{
if (ilevel < nlevels_respa-1) return;
pre_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixAdapt::post_run()
{
if (resetflag) restore_settings();
}
/* ----------------------------------------------------------------------
change pair,kspace,atom parameters based on variable evaluation
------------------------------------------------------------------------- */
void FixAdapt::change_settings()
{
int i,j;
// variable evaluation may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
double value = input->variable->compute_equal(ad->ivar);
// set global scalar or type pair array values
if (ad->which == PAIR) {
if (ad->pdim == 0) {
if (scaleflag) *ad->scalar = value * ad->scalar_orig;
else *ad->scalar = value;
} else if (ad->pdim == 2) {
if (scaleflag)
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array[i][j] = value*ad->array_orig[i][j];
else
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array[i][j] = value;
}
// set kspace scale factor
} else if (ad->which == KSPACE) {
*kspace_scale = value;
// set per atom values, also make changes for ghost atoms
} else if (ad->which == ATOM) {
// reset radius from diameter
// also scale rmass to new value
if (ad->aparam == DIAMETER) {
int mflag = 0;
if (atom->rmass_flag) mflag = 1;
double density;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (mflag == 0) {
for (i = 0; i < nall; i++)
if (mask[i] & groupbit)
radius[i] = 0.5*value;
} else {
for (i = 0; i < nall; i++)
if (mask[i] & groupbit) {
density = rmass[i] / (4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i]);
radius[i] = 0.5*value;
rmass[i] = 4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i] * density;
}
}
} else if (ad->aparam == CHARGE) {
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
for (i = 0; i < nall; i++)
if (mask[i] & groupbit) q[i] = value;
}
}
}
modify->addstep_compute(update->ntimestep + nevery);
// re-initialize pair styles if any PAIR settings were changed
// this resets other coeffs that may depend on changed values,
// and also offset and tail corrections
if (anypair) force->pair->reinit();
// reset KSpace charges if charges have changed
if (chgflag && force->kspace) force->kspace->qsum_qsq();
}
/* ----------------------------------------------------------------------
restore pair,kspace,atom parameters to original values
------------------------------------------------------------------------- */
void FixAdapt::restore_settings()
{
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
if (ad->which == PAIR) {
if (ad->pdim == 0) *ad->scalar = ad->scalar_orig;
else if (ad->pdim == 2) {
for (int i = ad->ilo; i <= ad->ihi; i++)
for (int j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array[i][j] = ad->array_orig[i][j];
}
} else if (ad->which == KSPACE) {
*kspace_scale = 1.0;
} else if (ad->which == ATOM) {
if (diamflag) {
double density;
double *vec = fix_diam->vstore;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
density = rmass[i] / (4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i]);
radius[i] = vec[i];
rmass[i] = 4.0*MY_PI/3.0 * radius[i]*radius[i]*radius[i] * density;
}
}
if (chgflag) {
double *vec = fix_chg->vstore;
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) q[i] = vec[i];
}
}
}
if (anypair) force->pair->reinit();
if (chgflag && force->kspace) force->kspace->qsum_qsq();
}
/* ----------------------------------------------------------------------
initialize one atom's storage values, called when atom is created
------------------------------------------------------------------------- */
void FixAdapt::set_arrays(int i)
{
if (fix_diam) fix_diam->vstore[i] = atom->radius[i];
if (fix_chg) fix_chg->vstore[i] = atom->q[i];
}
diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp
index 730b247cd..92da3e33c 100644
--- a/src/fix_nh.cpp
+++ b/src/fix_nh.cpp
@@ -1,2300 +1,2302 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Mark Stevens (SNL), Aidan Thompson (SNL)
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "math.h"
#include "fix_nh.h"
#include "math_extra.h"
#include "atom.h"
#include "force.h"
#include "group.h"
#include "comm.h"
#include "neighbor.h"
#include "irregular.h"
#include "modify.h"
#include "fix_deform.h"
#include "compute.h"
#include "kspace.h"
#include "update.h"
#include "respa.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define DELTAFLIP 0.1
#define TILTMAX 1.5
enum{NOBIAS,BIAS};
enum{NONE,XYZ,XY,YZ,XZ};
enum{ISO,ANISO,TRICLINIC};
/* ----------------------------------------------------------------------
NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion
---------------------------------------------------------------------- */
FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal fix nvt/npt/nph command");
restart_global = 1;
dynamic_group_allow = 1;
time_integrate = 1;
scalar_flag = 1;
vector_flag = 1;
global_freq = 1;
extscalar = 1;
extvector = 0;
// default values
pcouple = NONE;
drag = 0.0;
allremap = 1;
id_dilate = NULL;
mtchain = mpchain = 3;
nc_tchain = nc_pchain = 1;
mtk_flag = 1;
deviatoric_flag = 0;
nreset_h0 = 0;
eta_mass_flag = 1;
omega_mass_flag = 0;
etap_mass_flag = 0;
flipflag = 1;
// turn on tilt factor scaling, whenever applicable
dimension = domain->dimension;
scaleyz = scalexz = scalexy = 0;
if (domain->yperiodic && domain->xy != 0.0) scalexy = 1;
if (domain->zperiodic && dimension == 3) {
if (domain->yz != 0.0) scaleyz = 1;
if (domain->xz != 0.0) scalexz = 1;
}
// set fixed-point to default = center of cell
fixedpoint[0] = 0.5*(domain->boxlo[0]+domain->boxhi[0]);
fixedpoint[1] = 0.5*(domain->boxlo[1]+domain->boxhi[1]);
fixedpoint[2] = 0.5*(domain->boxlo[2]+domain->boxhi[2]);
// used by FixNVTSllod to preserve non-default value
mtchain_default_flag = 1;
tstat_flag = 0;
double t_period = 0.0;
double p_period[6];
for (int i = 0; i < 6; i++) {
p_start[i] = p_stop[i] = p_period[i] = p_target[i] = 0.0;
p_flag[i] = 0;
}
// process keywords
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
tstat_flag = 1;
t_start = force->numeric(FLERR,arg[iarg+1]);
t_target = t_start;
t_stop = force->numeric(FLERR,arg[iarg+2]);
t_period = force->numeric(FLERR,arg[iarg+3]);
if (t_start < 0.0 || t_stop <= 0.0)
error->all(FLERR,
"Target temperature for fix nvt/npt/nph cannot be 0.0");
iarg += 4;
} else if (strcmp(arg[iarg],"iso") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
pcouple = XYZ;
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
p_period[0] = p_period[1] = p_period[2] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
p_start[2] = p_stop[2] = p_period[2] = 0.0;
p_flag[2] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
pcouple = NONE;
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
p_period[0] = p_period[1] = p_period[2] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
p_start[2] = p_stop[2] = p_period[2] = 0.0;
p_flag[2] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"tri") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
pcouple = NONE;
scalexy = scalexz = scaleyz = 0;
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
p_period[0] = p_period[1] = p_period[2] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
p_start[3] = p_start[4] = p_start[5] = 0.0;
p_stop[3] = p_stop[4] = p_stop[5] = 0.0;
p_period[3] = p_period[4] = p_period[5] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[3] = p_flag[4] = p_flag[5] = 1;
if (dimension == 2) {
p_start[2] = p_stop[2] = p_period[2] = 0.0;
p_flag[2] = 0;
p_start[3] = p_stop[3] = p_period[3] = 0.0;
p_flag[3] = 0;
p_start[4] = p_stop[4] = p_period[4] = 0.0;
p_flag[4] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"x") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[0] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = force->numeric(FLERR,arg[iarg+2]);
p_period[0] = force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = 1;
deviatoric_flag = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[1] = force->numeric(FLERR,arg[iarg+1]);
p_stop[1] = force->numeric(FLERR,arg[iarg+2]);
p_period[1] = force->numeric(FLERR,arg[iarg+3]);
p_flag[1] = 1;
deviatoric_flag = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
p_period[2] = force->numeric(FLERR,arg[iarg+3]);
p_flag[2] = 1;
deviatoric_flag = 1;
iarg += 4;
if (dimension == 2)
error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
} else if (strcmp(arg[iarg],"yz") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[3] = force->numeric(FLERR,arg[iarg+1]);
p_stop[3] = force->numeric(FLERR,arg[iarg+2]);
p_period[3] = force->numeric(FLERR,arg[iarg+3]);
p_flag[3] = 1;
deviatoric_flag = 1;
scaleyz = 0;
iarg += 4;
if (dimension == 2)
error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
} else if (strcmp(arg[iarg],"xz") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[4] = force->numeric(FLERR,arg[iarg+1]);
p_stop[4] = force->numeric(FLERR,arg[iarg+2]);
p_period[4] = force->numeric(FLERR,arg[iarg+3]);
p_flag[4] = 1;
deviatoric_flag = 1;
scalexz = 0;
iarg += 4;
if (dimension == 2)
error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
} else if (strcmp(arg[iarg],"xy") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[5] = force->numeric(FLERR,arg[iarg+1]);
p_stop[5] = force->numeric(FLERR,arg[iarg+2]);
p_period[5] = force->numeric(FLERR,arg[iarg+3]);
p_flag[5] = 1;
deviatoric_flag = 1;
scalexy = 0;
iarg += 4;
} else if (strcmp(arg[iarg],"couple") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
if (strcmp(arg[iarg+1],"xyz") == 0) pcouple = XYZ;
else if (strcmp(arg[iarg+1],"xy") == 0) pcouple = XY;
else if (strcmp(arg[iarg+1],"yz") == 0) pcouple = YZ;
else if (strcmp(arg[iarg+1],"xz") == 0) pcouple = XZ;
else if (strcmp(arg[iarg+1],"none") == 0) pcouple = NONE;
else error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"drag") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
drag = force->numeric(FLERR,arg[iarg+1]);
if (drag < 0.0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"dilate") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
if (strcmp(arg[iarg+1],"all") == 0) allremap = 1;
else {
allremap = 0;
delete [] id_dilate;
int n = strlen(arg[iarg+1]) + 1;
id_dilate = new char[n];
strcpy(id_dilate,arg[iarg+1]);
int idilate = group->find(id_dilate);
if (idilate == -1)
error->all(FLERR,"Fix nvt/npt/nph dilate group ID does not exist");
}
iarg += 2;
} else if (strcmp(arg[iarg],"tchain") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
mtchain = force->inumeric(FLERR,arg[iarg+1]);
// used by FixNVTSllod to preserve non-default value
mtchain_default_flag = 0;
if (mtchain < 1) error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"pchain") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
mpchain = force->inumeric(FLERR,arg[iarg+1]);
if (mpchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"mtk") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
if (strcmp(arg[iarg+1],"yes") == 0) mtk_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) mtk_flag = 0;
else error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"tloop") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
nc_tchain = force->inumeric(FLERR,arg[iarg+1]);
if (nc_tchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"ploop") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
nc_pchain = force->inumeric(FLERR,arg[iarg+1]);
if (nc_pchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"nreset") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
nreset_h0 = force->inumeric(FLERR,arg[iarg+1]);
if (nreset_h0 < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"scalexy") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
if (strcmp(arg[iarg+1],"yes") == 0) scalexy = 1;
else if (strcmp(arg[iarg+1],"no") == 0) scalexy = 0;
else error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"scalexz") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
if (strcmp(arg[iarg+1],"yes") == 0) scalexz = 1;
else if (strcmp(arg[iarg+1],"no") == 0) scalexz = 0;
else error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"scaleyz") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
if (strcmp(arg[iarg+1],"yes") == 0) scaleyz = 1;
else if (strcmp(arg[iarg+1],"no") == 0) scaleyz = 0;
else error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"flip") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
if (strcmp(arg[iarg+1],"yes") == 0) flipflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) flipflag = 0;
else error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"fixedpoint") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
fixedpoint[0] = force->numeric(FLERR,arg[iarg+1]);
fixedpoint[1] = force->numeric(FLERR,arg[iarg+2]);
fixedpoint[2] = force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else error->all(FLERR,"Illegal fix nvt/npt/nph command");
}
// error checks
if (dimension == 2 && (p_flag[2] || p_flag[3] || p_flag[4]))
error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
if (dimension == 2 && (pcouple == YZ || pcouple == XZ))
error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
if (dimension == 2 && (scalexz == 1 || scaleyz == 1 ))
error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
if (pcouple == XYZ && (p_flag[0] == 0 || p_flag[1] == 0))
error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings");
if (pcouple == XYZ && dimension == 3 && p_flag[2] == 0)
error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings");
if (pcouple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings");
if (pcouple == YZ && (p_flag[1] == 0 || p_flag[2] == 0))
error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings");
if (pcouple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings");
// require periodicity in tensile dimension
if (p_flag[0] && domain->xperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph on a non-periodic dimension");
if (p_flag[1] && domain->yperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph on a non-periodic dimension");
if (p_flag[2] && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph on a non-periodic dimension");
// require periodicity in 2nd dim of off-diagonal tilt component
if (p_flag[3] && domain->zperiodic == 0)
error->all(FLERR,
"Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
if (p_flag[4] && domain->zperiodic == 0)
error->all(FLERR,
"Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
if (p_flag[5] && domain->yperiodic == 0)
error->all(FLERR,
"Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
if (scaleyz == 1 && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph "
"with yz scaling when z is non-periodic dimension");
if (scalexz == 1 && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph "
"with xz scaling when z is non-periodic dimension");
if (scalexy == 1 && domain->yperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph "
"with xy scaling when y is non-periodic dimension");
if (p_flag[3] && scaleyz == 1)
error->all(FLERR,"Cannot use fix nvt/npt/nph with "
"both yz dynamics and yz scaling");
if (p_flag[4] && scalexz == 1)
error->all(FLERR,"Cannot use fix nvt/npt/nph with "
"both xz dynamics and xz scaling");
if (p_flag[5] && scalexy == 1)
error->all(FLERR,"Cannot use fix nvt/npt/nph with "
"both xy dynamics and xy scaling");
if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5]))
error->all(FLERR,"Can not specify Pxy/Pxz/Pyz in "
"fix nvt/npt/nph with non-triclinic box");
if (pcouple == XYZ && dimension == 3 &&
(p_start[0] != p_start[1] || p_start[0] != p_start[2] ||
p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] ||
p_period[0] != p_period[1] || p_period[0] != p_period[2]))
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
if (pcouple == XYZ && dimension == 2 &&
(p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
p_period[0] != p_period[1]))
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
if (pcouple == XY &&
(p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
p_period[0] != p_period[1]))
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
if (pcouple == YZ &&
(p_start[1] != p_start[2] || p_stop[1] != p_stop[2] ||
p_period[1] != p_period[2]))
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
if (pcouple == XZ &&
(p_start[0] != p_start[2] || p_stop[0] != p_stop[2] ||
p_period[0] != p_period[2]))
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
if ((tstat_flag && t_period <= 0.0) ||
(p_flag[0] && p_period[0] <= 0.0) ||
(p_flag[1] && p_period[1] <= 0.0) ||
(p_flag[2] && p_period[2] <= 0.0) ||
(p_flag[3] && p_period[3] <= 0.0) ||
(p_flag[4] && p_period[4] <= 0.0) ||
(p_flag[5] && p_period[5] <= 0.0))
error->all(FLERR,"Fix nvt/npt/nph damping parameters must be > 0.0");
// set pstat_flag and box change and restart_pbc variables
+ pre_exchange_flag = 0;
pstat_flag = 0;
+ pstyle = ISO;
+
for (int i = 0; i < 6; i++)
if (p_flag[i]) pstat_flag = 1;
if (pstat_flag) {
if (p_flag[0] || p_flag[1] || p_flag[2]) box_change_size = 1;
if (p_flag[3] || p_flag[4] || p_flag[5]) box_change_shape = 1;
no_change_box = 1;
if (allremap == 0) restart_pbc = 1;
- }
- // pstyle = TRICLINIC if any off-diagonal term is controlled -> 6 dof
- // else pstyle = ISO if XYZ coupling or XY coupling in 2d -> 1 dof
- // else pstyle = ANISO -> 3 dof
+ // pstyle = TRICLINIC if any off-diagonal term is controlled -> 6 dof
+ // else pstyle = ISO if XYZ coupling or XY coupling in 2d -> 1 dof
+ // else pstyle = ANISO -> 3 dof
- if (p_flag[3] || p_flag[4] || p_flag[5]) pstyle = TRICLINIC;
- else if (pcouple == XYZ || (dimension == 2 && pcouple == XY)) pstyle = ISO;
- else pstyle = ANISO;
+ if (p_flag[3] || p_flag[4] || p_flag[5]) pstyle = TRICLINIC;
+ else if (pcouple == XYZ || (dimension == 2 && pcouple == XY)) pstyle = ISO;
+ else pstyle = ANISO;
- // pre_exchange only required if flips can occur due to shape changes
+ // pre_exchange only required if flips can occur due to shape changes
- pre_exchange_flag = 0;
- if (flipflag && (p_flag[3] || p_flag[4] || p_flag[5])) pre_exchange_flag = 1;
- if (flipflag && (domain->yz != 0.0 || domain->xz != 0.0 || domain->xy != 0.0))
- pre_exchange_flag = 1;
+ if (flipflag && (p_flag[3] || p_flag[4] || p_flag[5])) pre_exchange_flag = 1;
+ if (flipflag && (domain->yz != 0.0 || domain->xz != 0.0 || domain->xy != 0.0))
+ pre_exchange_flag = 1;
+ }
// convert input periods to frequencies
t_freq = 0.0;
p_freq[0] = p_freq[1] = p_freq[2] = p_freq[3] = p_freq[4] = p_freq[5] = 0.0;
if (tstat_flag) t_freq = 1.0 / t_period;
if (p_flag[0]) p_freq[0] = 1.0 / p_period[0];
if (p_flag[1]) p_freq[1] = 1.0 / p_period[1];
if (p_flag[2]) p_freq[2] = 1.0 / p_period[2];
if (p_flag[3]) p_freq[3] = 1.0 / p_period[3];
if (p_flag[4]) p_freq[4] = 1.0 / p_period[4];
if (p_flag[5]) p_freq[5] = 1.0 / p_period[5];
// Nose/Hoover temp and pressure init
size_vector = 0;
if (tstat_flag) {
int ich;
eta = new double[mtchain];
// add one extra dummy thermostat, set to zero
eta_dot = new double[mtchain+1];
eta_dot[mtchain] = 0.0;
eta_dotdot = new double[mtchain];
for (ich = 0; ich < mtchain; ich++) {
eta[ich] = eta_dot[ich] = eta_dotdot[ich] = 0.0;
}
eta_mass = new double[mtchain];
size_vector += 2*2*mtchain;
}
if (pstat_flag) {
omega[0] = omega[1] = omega[2] = 0.0;
omega_dot[0] = omega_dot[1] = omega_dot[2] = 0.0;
omega_mass[0] = omega_mass[1] = omega_mass[2] = 0.0;
omega[3] = omega[4] = omega[5] = 0.0;
omega_dot[3] = omega_dot[4] = omega_dot[5] = 0.0;
omega_mass[3] = omega_mass[4] = omega_mass[5] = 0.0;
if (pstyle == ISO) size_vector += 2*2*1;
else if (pstyle == ANISO) size_vector += 2*2*3;
else if (pstyle == TRICLINIC) size_vector += 2*2*6;
if (mpchain) {
int ich;
etap = new double[mpchain];
// add one extra dummy thermostat, set to zero
etap_dot = new double[mpchain+1];
etap_dot[mpchain] = 0.0;
etap_dotdot = new double[mpchain];
for (ich = 0; ich < mpchain; ich++) {
etap[ich] = etap_dot[ich] =
etap_dotdot[ich] = 0.0;
}
etap_mass = new double[mpchain];
size_vector += 2*2*mpchain;
}
if (deviatoric_flag) size_vector += 1;
}
nrigid = 0;
rfix = NULL;
if (pre_exchange_flag) irregular = new Irregular(lmp);
else irregular = NULL;
// initialize vol0,t0 to zero to signal uninitialized
// values then assigned in init(), if necessary
vol0 = t0 = 0.0;
}
/* ---------------------------------------------------------------------- */
FixNH::~FixNH()
{
if (copymode) return;
delete [] id_dilate;
delete [] rfix;
delete irregular;
// delete temperature and pressure if fix created them
if (tflag) modify->delete_compute(id_temp);
delete [] id_temp;
if (tstat_flag) {
delete [] eta;
delete [] eta_dot;
delete [] eta_dotdot;
delete [] eta_mass;
}
if (pstat_flag) {
if (pflag) modify->delete_compute(id_press);
delete [] id_press;
if (mpchain) {
delete [] etap;
delete [] etap_dot;
delete [] etap_dotdot;
delete [] etap_mass;
}
}
}
/* ---------------------------------------------------------------------- */
int FixNH::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= THERMO_ENERGY;
mask |= INITIAL_INTEGRATE_RESPA;
mask |= FINAL_INTEGRATE_RESPA;
if (pre_exchange_flag) mask |= PRE_EXCHANGE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixNH::init()
{
// recheck that dilate group has not been deleted
if (allremap == 0) {
int idilate = group->find(id_dilate);
if (idilate == -1)
error->all(FLERR,"Fix nvt/npt/nph dilate group ID does not exist");
dilate_group_bit = group->bitmask[idilate];
}
// ensure no conflict with fix deform
if (pstat_flag)
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
(p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) ||
(p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5]))
error->all(FLERR,"Cannot use fix npt and fix deform on "
"same component of stress tensor");
}
// set temperature and pressure ptrs
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Temperature ID for fix nvt/npt does not exist");
temperature = modify->compute[icompute];
if (temperature->tempbias) which = BIAS;
else which = NOBIAS;
if (pstat_flag) {
icompute = modify->find_compute(id_press);
if (icompute < 0)
error->all(FLERR,"Pressure ID for fix npt/nph does not exist");
pressure = modify->compute[icompute];
}
// set timesteps and frequencies
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dthalf = 0.5 * update->dt;
dt4 = 0.25 * update->dt;
dt8 = 0.125 * update->dt;
dto = dthalf;
p_freq_max = 0.0;
if (pstat_flag) {
p_freq_max = MAX(p_freq[0],p_freq[1]);
p_freq_max = MAX(p_freq_max,p_freq[2]);
if (pstyle == TRICLINIC) {
p_freq_max = MAX(p_freq_max,p_freq[3]);
p_freq_max = MAX(p_freq_max,p_freq[4]);
p_freq_max = MAX(p_freq_max,p_freq[5]);
}
pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain);
}
if (tstat_flag)
tdrag_factor = 1.0 - (update->dt * t_freq * drag / nc_tchain);
// tally the number of dimensions that are barostatted
// set initial volume and reference cell, if not already done
if (pstat_flag) {
pdim = p_flag[0] + p_flag[1] + p_flag[2];
if (vol0 == 0.0) {
if (dimension == 3) vol0 = domain->xprd * domain->yprd * domain->zprd;
else vol0 = domain->xprd * domain->yprd;
h0_inv[0] = domain->h_inv[0];
h0_inv[1] = domain->h_inv[1];
h0_inv[2] = domain->h_inv[2];
h0_inv[3] = domain->h_inv[3];
h0_inv[4] = domain->h_inv[4];
h0_inv[5] = domain->h_inv[5];
}
}
boltz = force->boltz;
nktv2p = force->nktv2p;
if (force->kspace) kspace_flag = 1;
else kspace_flag = 0;
if (strstr(update->integrate_style,"respa")) {
nlevels_respa = ((Respa *) update->integrate)->nlevels;
step_respa = ((Respa *) update->integrate)->step;
dto = 0.5*step_respa[0];
}
// detect if any rigid fixes exist so rigid bodies move when box is remapped
// rfix[] = indices to each fix rigid
delete [] rfix;
nrigid = 0;
rfix = NULL;
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->rigid_flag) nrigid++;
if (nrigid) {
rfix = new int[nrigid];
nrigid = 0;
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->rigid_flag) rfix[nrigid++] = i;
}
}
/* ----------------------------------------------------------------------
compute T,P before integrator starts
------------------------------------------------------------------------- */
void FixNH::setup(int vflag)
{
// t_target is needed by NPH and NPT in compute_scalar()
// If no thermostat or using fix nphug,
// t_target must be defined by other means.
if (tstat_flag && strcmp(style,"nphug") != 0) {
compute_temp_target();
} else if (pstat_flag) {
// t0 = reference temperature for masses
// cannot be done in init() b/c temperature cannot be called there
// is b/c Modify::init() inits computes after fixes due to dof dependence
// guesstimate a unit-dependent t0 if actual T = 0.0
// if it was read in from a restart file, leave it be
if (t0 == 0.0) {
t0 = temperature->compute_scalar();
if (t0 == 0.0) {
if (strcmp(update->unit_style,"lj") == 0) t0 = 1.0;
else t0 = 300.0;
}
}
t_target = t0;
}
if (pstat_flag) compute_press_target();
t_current = temperature->compute_scalar();
tdof = temperature->dof;
if (pstat_flag) {
if (pstyle == ISO) pressure->compute_scalar();
else pressure->compute_vector();
couple();
pressure->addstep(update->ntimestep+1);
}
// masses and initial forces on thermostat variables
if (tstat_flag) {
eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq);
for (int ich = 1; ich < mtchain; ich++)
eta_mass[ich] = boltz * t_target / (t_freq*t_freq);
for (int ich = 1; ich < mtchain; ich++) {
eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1] -
boltz * t_target) / eta_mass[ich];
}
}
// masses and initial forces on barostat variables
if (pstat_flag) {
double kt = boltz * t_target;
double nkt = atom->natoms * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
if (pstyle == TRICLINIC) {
for (int i = 3; i < 6; i++)
if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
}
// masses and initial forces on barostat thermostat variables
if (mpchain) {
etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max);
for (int ich = 1; ich < mpchain; ich++)
etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max);
for (int ich = 1; ich < mpchain; ich++)
etap_dotdot[ich] =
(etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] -
boltz * t_target) / etap_mass[ich];
}
}
}
/* ----------------------------------------------------------------------
1st half of Verlet update
------------------------------------------------------------------------- */
void FixNH::initial_integrate(int vflag)
{
// update eta_press_dot
if (pstat_flag && mpchain) nhc_press_integrate();
// update eta_dot
if (tstat_flag) {
compute_temp_target();
nhc_temp_integrate();
}
// need to recompute pressure to account for change in KE
// t_current is up-to-date, but compute_temperature is not
// compute appropriately coupled elements of mvv_current
if (pstat_flag) {
if (pstyle == ISO) {
temperature->compute_scalar();
pressure->compute_scalar();
} else {
temperature->compute_vector();
pressure->compute_vector();
}
couple();
pressure->addstep(update->ntimestep+1);
}
if (pstat_flag) {
compute_press_target();
nh_omega_dot();
nh_v_press();
}
nve_v();
// remap simulation box by 1/2 step
if (pstat_flag) remap();
nve_x();
// remap simulation box by 1/2 step
// redo KSpace coeffs since volume has changed
if (pstat_flag) {
remap();
if (kspace_flag) force->kspace->setup();
}
}
/* ----------------------------------------------------------------------
2nd half of Verlet update
------------------------------------------------------------------------- */
void FixNH::final_integrate()
{
nve_v();
// re-compute temp before nh_v_press()
// only needed for temperature computes with BIAS on reneighboring steps:
// b/c some biases store per-atom values (e.g. temp/profile)
// per-atom values are invalid if reneigh/comm occurred
// since temp->compute() in initial_integrate()
if (which == BIAS && neighbor->ago == 0)
t_current = temperature->compute_scalar();
if (pstat_flag) nh_v_press();
// compute new T,P after velocities rescaled by nh_v_press()
// compute appropriately coupled elements of mvv_current
t_current = temperature->compute_scalar();
tdof = temperature->dof;
if (pstat_flag) {
if (pstyle == ISO) pressure->compute_scalar();
else pressure->compute_vector();
couple();
pressure->addstep(update->ntimestep+1);
}
if (pstat_flag) nh_omega_dot();
// update eta_dot
// update eta_press_dot
if (tstat_flag) nhc_temp_integrate();
if (pstat_flag && mpchain) nhc_press_integrate();
}
/* ---------------------------------------------------------------------- */
void FixNH::initial_integrate_respa(int vflag, int ilevel, int iloop)
{
// set timesteps by level
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
dthalf = 0.5 * step_respa[ilevel];
// outermost level - update eta_dot and omega_dot, apply to v
// all other levels - NVE update of v
// x,v updates only performed for atoms in group
if (ilevel == nlevels_respa-1) {
// update eta_press_dot
if (pstat_flag && mpchain) nhc_press_integrate();
// update eta_dot
if (tstat_flag) {
compute_temp_target();
nhc_temp_integrate();
}
// recompute pressure to account for change in KE
// t_current is up-to-date, but compute_temperature is not
// compute appropriately coupled elements of mvv_current
if (pstat_flag) {
if (pstyle == ISO) {
temperature->compute_scalar();
pressure->compute_scalar();
} else {
temperature->compute_vector();
pressure->compute_vector();
}
couple();
pressure->addstep(update->ntimestep+1);
}
if (pstat_flag) {
compute_press_target();
nh_omega_dot();
nh_v_press();
}
nve_v();
} else nve_v();
// innermost level - also update x only for atoms in group
// if barostat, perform 1/2 step remap before and after
if (ilevel == 0) {
if (pstat_flag) remap();
nve_x();
if (pstat_flag) remap();
}
// if barostat, redo KSpace coeffs at outermost level,
// since volume has changed
if (ilevel == nlevels_respa-1 && kspace_flag && pstat_flag)
force->kspace->setup();
}
/* ---------------------------------------------------------------------- */
void FixNH::final_integrate_respa(int ilevel, int iloop)
{
// set timesteps by level
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
dthalf = 0.5 * step_respa[ilevel];
// outermost level - update eta_dot and omega_dot, apply via final_integrate
// all other levels - NVE update of v
if (ilevel == nlevels_respa-1) final_integrate();
else nve_v();
}
/* ---------------------------------------------------------------------- */
void FixNH::couple()
{
double *tensor = pressure->vector;
if (pstyle == ISO)
p_current[0] = p_current[1] = p_current[2] = pressure->scalar;
else if (pcouple == XYZ) {
double ave = 1.0/3.0 * (tensor[0] + tensor[1] + tensor[2]);
p_current[0] = p_current[1] = p_current[2] = ave;
} else if (pcouple == XY) {
double ave = 0.5 * (tensor[0] + tensor[1]);
p_current[0] = p_current[1] = ave;
p_current[2] = tensor[2];
} else if (pcouple == YZ) {
double ave = 0.5 * (tensor[1] + tensor[2]);
p_current[1] = p_current[2] = ave;
p_current[0] = tensor[0];
} else if (pcouple == XZ) {
double ave = 0.5 * (tensor[0] + tensor[2]);
p_current[0] = p_current[2] = ave;
p_current[1] = tensor[1];
} else {
p_current[0] = tensor[0];
p_current[1] = tensor[1];
p_current[2] = tensor[2];
}
// switch order from xy-xz-yz to Voigt
if (pstyle == TRICLINIC) {
p_current[3] = tensor[5];
p_current[4] = tensor[4];
p_current[5] = tensor[3];
}
}
/* ----------------------------------------------------------------------
change box size
remap all atoms or dilate group atoms depending on allremap flag
if rigid bodies exist, scale rigid body centers-of-mass
------------------------------------------------------------------------- */
void FixNH::remap()
{
int i;
double oldlo,oldhi;
double expfac;
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *h = domain->h;
// omega is not used, except for book-keeping
for (int i = 0; i < 6; i++) omega[i] += dto*omega_dot[i];
// convert pertinent atoms and rigid bodies to lamda coords
if (allremap) domain->x2lamda(nlocal);
else {
for (i = 0; i < nlocal; i++)
if (mask[i] & dilate_group_bit)
domain->x2lamda(x[i],x[i]);
}
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->deform(0);
// reset global and local box to new size/shape
// this operation corresponds to applying the
// translate and scale operations
// corresponding to the solution of the following ODE:
//
// h_dot = omega_dot * h
//
// where h_dot, omega_dot and h are all upper-triangular
// 3x3 tensors. In Voigt notation, the elements of the
// RHS product tensor are:
// h_dot = [0*0, 1*1, 2*2, 1*3+3*2, 0*4+5*3+4*2, 0*5+5*1]
//
// Ordering of operations preserves time symmetry.
double dto2 = dto/2.0;
double dto4 = dto/4.0;
double dto8 = dto/8.0;
// off-diagonal components, first half
if (pstyle == TRICLINIC) {
if (p_flag[4]) {
expfac = exp(dto8*omega_dot[0]);
h[4] *= expfac;
h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= expfac;
}
if (p_flag[3]) {
expfac = exp(dto4*omega_dot[1]);
h[3] *= expfac;
h[3] += dto2*(omega_dot[3]*h[2]);
h[3] *= expfac;
}
if (p_flag[5]) {
expfac = exp(dto4*omega_dot[0]);
h[5] *= expfac;
h[5] += dto2*(omega_dot[5]*h[1]);
h[5] *= expfac;
}
if (p_flag[4]) {
expfac = exp(dto8*omega_dot[0]);
h[4] *= expfac;
h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= expfac;
}
}
// scale diagonal components
// scale tilt factors with cell, if set
if (p_flag[0]) {
oldlo = domain->boxlo[0];
oldhi = domain->boxhi[0];
expfac = exp(dto*omega_dot[0]);
domain->boxlo[0] = (oldlo-fixedpoint[0])*expfac + fixedpoint[0];
domain->boxhi[0] = (oldhi-fixedpoint[0])*expfac + fixedpoint[0];
}
if (p_flag[1]) {
oldlo = domain->boxlo[1];
oldhi = domain->boxhi[1];
expfac = exp(dto*omega_dot[1]);
domain->boxlo[1] = (oldlo-fixedpoint[1])*expfac + fixedpoint[1];
domain->boxhi[1] = (oldhi-fixedpoint[1])*expfac + fixedpoint[1];
if (scalexy) h[5] *= expfac;
}
if (p_flag[2]) {
oldlo = domain->boxlo[2];
oldhi = domain->boxhi[2];
expfac = exp(dto*omega_dot[2]);
domain->boxlo[2] = (oldlo-fixedpoint[2])*expfac + fixedpoint[2];
domain->boxhi[2] = (oldhi-fixedpoint[2])*expfac + fixedpoint[2];
if (scalexz) h[4] *= expfac;
if (scaleyz) h[3] *= expfac;
}
// off-diagonal components, second half
if (pstyle == TRICLINIC) {
if (p_flag[4]) {
expfac = exp(dto8*omega_dot[0]);
h[4] *= expfac;
h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= expfac;
}
if (p_flag[3]) {
expfac = exp(dto4*omega_dot[1]);
h[3] *= expfac;
h[3] += dto2*(omega_dot[3]*h[2]);
h[3] *= expfac;
}
if (p_flag[5]) {
expfac = exp(dto4*omega_dot[0]);
h[5] *= expfac;
h[5] += dto2*(omega_dot[5]*h[1]);
h[5] *= expfac;
}
if (p_flag[4]) {
expfac = exp(dto8*omega_dot[0]);
h[4] *= expfac;
h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
h[4] *= expfac;
}
}
domain->yz = h[3];
domain->xz = h[4];
domain->xy = h[5];
// tilt factor to cell length ratio can not exceed TILTMAX in one step
if (domain->yz < -TILTMAX*domain->yprd ||
domain->yz > TILTMAX*domain->yprd ||
domain->xz < -TILTMAX*domain->xprd ||
domain->xz > TILTMAX*domain->xprd ||
domain->xy < -TILTMAX*domain->xprd ||
domain->xy > TILTMAX*domain->xprd)
error->all(FLERR,"Fix npt/nph has tilted box too far in one step - "
"periodic cell is too far from equilibrium state");
domain->set_global_box();
domain->set_local_box();
// convert pertinent atoms and rigid bodies back to box coords
if (allremap) domain->lamda2x(nlocal);
else {
for (i = 0; i < nlocal; i++)
if (mask[i] & dilate_group_bit)
domain->lamda2x(x[i],x[i]);
}
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->deform(1);
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixNH::write_restart(FILE *fp)
{
int nsize = size_restart_global();
double *list;
memory->create(list,nsize,"nh:list");
pack_restart_data(list);
if (comm->me == 0) {
int size = nsize * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),nsize,fp);
}
memory->destroy(list);
}
/* ----------------------------------------------------------------------
calculate the number of data to be packed
------------------------------------------------------------------------- */
int FixNH::size_restart_global()
{
int nsize = 2;
if (tstat_flag) nsize += 1 + 2*mtchain;
if (pstat_flag) {
nsize += 16 + 2*mpchain;
if (deviatoric_flag) nsize += 6;
}
return nsize;
}
/* ----------------------------------------------------------------------
pack restart data
------------------------------------------------------------------------- */
int FixNH::pack_restart_data(double *list)
{
int n = 0;
list[n++] = tstat_flag;
if (tstat_flag) {
list[n++] = mtchain;
for (int ich = 0; ich < mtchain; ich++)
list[n++] = eta[ich];
for (int ich = 0; ich < mtchain; ich++)
list[n++] = eta_dot[ich];
}
list[n++] = pstat_flag;
if (pstat_flag) {
list[n++] = omega[0];
list[n++] = omega[1];
list[n++] = omega[2];
list[n++] = omega[3];
list[n++] = omega[4];
list[n++] = omega[5];
list[n++] = omega_dot[0];
list[n++] = omega_dot[1];
list[n++] = omega_dot[2];
list[n++] = omega_dot[3];
list[n++] = omega_dot[4];
list[n++] = omega_dot[5];
list[n++] = vol0;
list[n++] = t0;
list[n++] = mpchain;
if (mpchain) {
for (int ich = 0; ich < mpchain; ich++)
list[n++] = etap[ich];
for (int ich = 0; ich < mpchain; ich++)
list[n++] = etap_dot[ich];
}
list[n++] = deviatoric_flag;
if (deviatoric_flag) {
list[n++] = h0_inv[0];
list[n++] = h0_inv[1];
list[n++] = h0_inv[2];
list[n++] = h0_inv[3];
list[n++] = h0_inv[4];
list[n++] = h0_inv[5];
}
}
return n;
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixNH::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
int flag = static_cast<int> (list[n++]);
if (flag) {
int m = static_cast<int> (list[n++]);
if (tstat_flag && m == mtchain) {
for (int ich = 0; ich < mtchain; ich++)
eta[ich] = list[n++];
for (int ich = 0; ich < mtchain; ich++)
eta_dot[ich] = list[n++];
} else n += 2*m;
}
flag = static_cast<int> (list[n++]);
if (flag) {
omega[0] = list[n++];
omega[1] = list[n++];
omega[2] = list[n++];
omega[3] = list[n++];
omega[4] = list[n++];
omega[5] = list[n++];
omega_dot[0] = list[n++];
omega_dot[1] = list[n++];
omega_dot[2] = list[n++];
omega_dot[3] = list[n++];
omega_dot[4] = list[n++];
omega_dot[5] = list[n++];
vol0 = list[n++];
t0 = list[n++];
int m = static_cast<int> (list[n++]);
if (pstat_flag && m == mpchain) {
for (int ich = 0; ich < mpchain; ich++)
etap[ich] = list[n++];
for (int ich = 0; ich < mpchain; ich++)
etap_dot[ich] = list[n++];
} else n+=2*m;
flag = static_cast<int> (list[n++]);
if (flag) {
h0_inv[0] = list[n++];
h0_inv[1] = list[n++];
h0_inv[2] = list[n++];
h0_inv[3] = list[n++];
h0_inv[4] = list[n++];
h0_inv[5] = list[n++];
}
}
}
/* ---------------------------------------------------------------------- */
int FixNH::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"temp") == 0) {
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
if (tflag) {
modify->delete_compute(id_temp);
tflag = 0;
}
delete [] id_temp;
int n = strlen(arg[1]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(arg[1]);
if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,
"Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != 0 && comm->me == 0)
error->warning(FLERR,"Temperature for fix modify is not for group all");
// reset id_temp of pressure to new temperature ID
if (pstat_flag) {
icompute = modify->find_compute(id_press);
if (icompute < 0)
error->all(FLERR,"Pressure ID for fix modify does not exist");
modify->compute[icompute]->reset_extra_compute_fix(id_temp);
}
return 2;
} else if (strcmp(arg[0],"press") == 0) {
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
if (!pstat_flag) error->all(FLERR,"Illegal fix_modify command");
if (pflag) {
modify->delete_compute(id_press);
pflag = 0;
}
delete [] id_press;
int n = strlen(arg[1]) + 1;
id_press = new char[n];
strcpy(id_press,arg[1]);
int icompute = modify->find_compute(arg[1]);
if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID");
pressure = modify->compute[icompute];
if (pressure->pressflag == 0)
error->all(FLERR,"Fix_modify pressure ID does not compute pressure");
return 2;
}
return 0;
}
/* ---------------------------------------------------------------------- */
double FixNH::compute_scalar()
{
int i;
double volume;
double energy;
double kt = boltz * t_target;
double lkt_press = kt;
int ich;
if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
else volume = domain->xprd * domain->yprd;
energy = 0.0;
// thermostat chain energy is equivalent to Eq. (2) in
// Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117
// Sum(0.5*p_eta_k^2/Q_k,k=1,M) + L*k*T*eta_1 + Sum(k*T*eta_k,k=2,M),
// where L = tdof
// M = mtchain
// p_eta_k = Q_k*eta_dot[k-1]
// Q_1 = L*k*T/t_freq^2
// Q_k = k*T/t_freq^2, k > 1
if (tstat_flag) {
energy += ke_target * eta[0] + 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0];
for (ich = 1; ich < mtchain; ich++)
energy += kt * eta[ich] + 0.5*eta_mass[ich]*eta_dot[ich]*eta_dot[ich];
}
// barostat energy is equivalent to Eq. (8) in
// Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117
// Sum(0.5*p_omega^2/W + P*V),
// where N = natoms
// p_omega = W*omega_dot
// W = N*k*T/p_freq^2
// sum is over barostatted dimensions
if (pstat_flag) {
for (i = 0; i < 3; i++)
if (p_flag[i])
energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] +
p_hydro*(volume-vol0) / (pdim*nktv2p);
if (pstyle == TRICLINIC) {
for (i = 3; i < 6; i++)
if (p_flag[i])
energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i];
}
// extra contributions from thermostat chain for barostat
if (mpchain) {
energy += lkt_press * etap[0] + 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0];
for (ich = 1; ich < mpchain; ich++)
energy += kt * etap[ich] +
0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich];
}
// extra contribution from strain energy
if (deviatoric_flag) energy += compute_strain_energy();
}
return energy;
}
/* ----------------------------------------------------------------------
return a single element of the following vectors, in this order:
eta[tchain], eta_dot[tchain], omega[ndof], omega_dot[ndof]
etap[pchain], etap_dot[pchain], PE_eta[tchain], KE_eta_dot[tchain]
PE_omega[ndof], KE_omega_dot[ndof], PE_etap[pchain], KE_etap_dot[pchain]
PE_strain[1]
if no thermostat exists, related quantities are omitted from the list
if no barostat exists, related quantities are omitted from the list
ndof = 1,3,6 degrees of freedom for pstyle = ISO,ANISO,TRI
------------------------------------------------------------------------- */
double FixNH::compute_vector(int n)
{
int ilen;
if (tstat_flag) {
ilen = mtchain;
if (n < ilen) return eta[n];
n -= ilen;
ilen = mtchain;
if (n < ilen) return eta_dot[n];
n -= ilen;
}
if (pstat_flag) {
if (pstyle == ISO) {
ilen = 1;
if (n < ilen) return omega[n];
n -= ilen;
} else if (pstyle == ANISO) {
ilen = 3;
if (n < ilen) return omega[n];
n -= ilen;
} else {
ilen = 6;
if (n < ilen) return omega[n];
n -= ilen;
}
if (pstyle == ISO) {
ilen = 1;
if (n < ilen) return omega_dot[n];
n -= ilen;
} else if (pstyle == ANISO) {
ilen = 3;
if (n < ilen) return omega_dot[n];
n -= ilen;
} else {
ilen = 6;
if (n < ilen) return omega_dot[n];
n -= ilen;
}
if (mpchain) {
ilen = mpchain;
if (n < ilen) return etap[n];
n -= ilen;
ilen = mpchain;
if (n < ilen) return etap_dot[n];
n -= ilen;
}
}
double volume;
double kt = boltz * t_target;
double lkt_press = kt;
int ich;
if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
else volume = domain->xprd * domain->yprd;
if (tstat_flag) {
ilen = mtchain;
if (n < ilen) {
ich = n;
if (ich == 0)
return ke_target * eta[0];
else
return kt * eta[ich];
}
n -= ilen;
ilen = mtchain;
if (n < ilen) {
ich = n;
if (ich == 0)
return 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0];
else
return 0.5*eta_mass[ich]*eta_dot[ich]*eta_dot[ich];
}
n -= ilen;
}
if (pstat_flag) {
if (pstyle == ISO) {
ilen = 1;
if (n < ilen)
return p_hydro*(volume-vol0) / nktv2p;
n -= ilen;
} else if (pstyle == ANISO) {
ilen = 3;
if (n < ilen) {
if (p_flag[n])
return p_hydro*(volume-vol0) / (pdim*nktv2p);
else
return 0.0;
}
n -= ilen;
} else {
ilen = 6;
if (n < ilen) {
if (n > 2) return 0.0;
else if (p_flag[n])
return p_hydro*(volume-vol0) / (pdim*nktv2p);
else
return 0.0;
}
n -= ilen;
}
if (pstyle == ISO) {
ilen = 1;
if (n < ilen)
return pdim*0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
n -= ilen;
} else if (pstyle == ANISO) {
ilen = 3;
if (n < ilen) {
if (p_flag[n])
return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
else return 0.0;
}
n -= ilen;
} else {
ilen = 6;
if (n < ilen) {
if (p_flag[n])
return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
else return 0.0;
}
n -= ilen;
}
if (mpchain) {
ilen = mpchain;
if (n < ilen) {
ich = n;
if (ich == 0) return lkt_press * etap[0];
else return kt * etap[ich];
}
n -= ilen;
ilen = mpchain;
if (n < ilen) {
ich = n;
if (ich == 0)
return 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0];
else
return 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich];
}
n -= ilen;
}
if (deviatoric_flag) {
ilen = 1;
if (n < ilen)
return compute_strain_energy();
n -= ilen;
}
}
return 0.0;
}
/* ---------------------------------------------------------------------- */
void FixNH::reset_target(double t_new)
{
t_target = t_start = t_stop = t_new;
}
/* ---------------------------------------------------------------------- */
void FixNH::reset_dt()
{
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dthalf = 0.5 * update->dt;
dt4 = 0.25 * update->dt;
dt8 = 0.125 * update->dt;
dto = dthalf;
// If using respa, then remap is performed in innermost level
if (strstr(update->integrate_style,"respa"))
dto = 0.5*step_respa[0];
if (pstat_flag)
pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain);
if (tstat_flag)
tdrag_factor = 1.0 - (update->dt * t_freq * drag / nc_tchain);
}
/* ----------------------------------------------------------------------
extract thermostat properties
------------------------------------------------------------------------- */
void *FixNH::extract(const char *str, int &dim)
{
dim=0;
if (strcmp(str,"t_target") == 0) {
return &t_target;
} else if (strcmp(str,"mtchain") == 0) {
return &mtchain;
}
dim=1;
if (strcmp(str,"eta") == 0) {
return η
}
return NULL;
}
/* ----------------------------------------------------------------------
perform half-step update of chain thermostat variables
------------------------------------------------------------------------- */
void FixNH::nhc_temp_integrate()
{
int ich;
double expfac;
double kecurrent = tdof * boltz * t_current;
// Update masses, to preserve initial freq, if flag set
if (eta_mass_flag) {
eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq);
for (int ich = 1; ich < mtchain; ich++)
eta_mass[ich] = boltz * t_target / (t_freq*t_freq);
}
if (eta_mass[0] > 0.0)
eta_dotdot[0] = (kecurrent - ke_target)/eta_mass[0];
else eta_dotdot[0] = 0.0;
double ncfac = 1.0/nc_tchain;
for (int iloop = 0; iloop < nc_tchain; iloop++) {
for (ich = mtchain-1; ich > 0; ich--) {
expfac = exp(-ncfac*dt8*eta_dot[ich+1]);
eta_dot[ich] *= expfac;
eta_dot[ich] += eta_dotdot[ich] * ncfac*dt4;
eta_dot[ich] *= tdrag_factor;
eta_dot[ich] *= expfac;
}
expfac = exp(-ncfac*dt8*eta_dot[1]);
eta_dot[0] *= expfac;
eta_dot[0] += eta_dotdot[0] * ncfac*dt4;
eta_dot[0] *= tdrag_factor;
eta_dot[0] *= expfac;
factor_eta = exp(-ncfac*dthalf*eta_dot[0]);
nh_v_temp();
// rescale temperature due to velocity scaling
// should not be necessary to explicitly recompute the temperature
t_current *= factor_eta*factor_eta;
kecurrent = tdof * boltz * t_current;
if (eta_mass[0] > 0.0)
eta_dotdot[0] = (kecurrent - ke_target)/eta_mass[0];
else eta_dotdot[0] = 0.0;
for (ich = 0; ich < mtchain; ich++)
eta[ich] += ncfac*dthalf*eta_dot[ich];
eta_dot[0] *= expfac;
eta_dot[0] += eta_dotdot[0] * ncfac*dt4;
eta_dot[0] *= expfac;
for (ich = 1; ich < mtchain; ich++) {
expfac = exp(-ncfac*dt8*eta_dot[ich+1]);
eta_dot[ich] *= expfac;
eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1]
- boltz * t_target)/eta_mass[ich];
eta_dot[ich] += eta_dotdot[ich] * ncfac*dt4;
eta_dot[ich] *= expfac;
}
}
}
/* ----------------------------------------------------------------------
perform half-step update of chain thermostat variables for barostat
scale barostat velocities
------------------------------------------------------------------------- */
void FixNH::nhc_press_integrate()
{
int ich,i;
double expfac,factor_etap,kecurrent;
double kt = boltz * t_target;
double lkt_press = kt;
// Update masses, to preserve initial freq, if flag set
if (omega_mass_flag) {
double nkt = atom->natoms * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
if (pstyle == TRICLINIC) {
for (int i = 3; i < 6; i++)
if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
}
}
if (etap_mass_flag) {
if (mpchain) {
etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max);
for (int ich = 1; ich < mpchain; ich++)
etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max);
for (int ich = 1; ich < mpchain; ich++)
etap_dotdot[ich] =
(etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] -
boltz * t_target) / etap_mass[ich];
}
}
kecurrent = 0.0;
for (i = 0; i < 3; i++)
if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
if (pstyle == TRICLINIC) {
for (i = 3; i < 6; i++)
if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
}
etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0];
double ncfac = 1.0/nc_pchain;
for (int iloop = 0; iloop < nc_pchain; iloop++) {
for (ich = mpchain-1; ich > 0; ich--) {
expfac = exp(-ncfac*dt8*etap_dot[ich+1]);
etap_dot[ich] *= expfac;
etap_dot[ich] += etap_dotdot[ich] * ncfac*dt4;
etap_dot[ich] *= pdrag_factor;
etap_dot[ich] *= expfac;
}
expfac = exp(-ncfac*dt8*etap_dot[1]);
etap_dot[0] *= expfac;
etap_dot[0] += etap_dotdot[0] * ncfac*dt4;
etap_dot[0] *= pdrag_factor;
etap_dot[0] *= expfac;
for (ich = 0; ich < mpchain; ich++)
etap[ich] += ncfac*dthalf*etap_dot[ich];
factor_etap = exp(-ncfac*dthalf*etap_dot[0]);
for (i = 0; i < 3; i++)
if (p_flag[i]) omega_dot[i] *= factor_etap;
if (pstyle == TRICLINIC) {
for (i = 3; i < 6; i++)
if (p_flag[i]) omega_dot[i] *= factor_etap;
}
kecurrent = 0.0;
for (i = 0; i < 3; i++)
if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
if (pstyle == TRICLINIC) {
for (i = 3; i < 6; i++)
if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
}
etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0];
etap_dot[0] *= expfac;
etap_dot[0] += etap_dotdot[0] * ncfac*dt4;
etap_dot[0] *= expfac;
for (ich = 1; ich < mpchain; ich++) {
expfac = exp(-ncfac*dt8*etap_dot[ich+1]);
etap_dot[ich] *= expfac;
etap_dotdot[ich] =
(etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] - boltz*t_target) /
etap_mass[ich];
etap_dot[ich] += etap_dotdot[ich] * ncfac*dt4;
etap_dot[ich] *= expfac;
}
}
}
/* ----------------------------------------------------------------------
perform half-step barostat scaling of velocities
-----------------------------------------------------------------------*/
void FixNH::nh_v_press()
{
double factor[3];
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
factor[0] = exp(-dt4*(omega_dot[0]+mtk_term2));
factor[1] = exp(-dt4*(omega_dot[1]+mtk_term2));
factor[2] = exp(-dt4*(omega_dot[2]+mtk_term2));
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
v[i][0] *= factor[0];
v[i][1] *= factor[1];
v[i][2] *= factor[2];
if (pstyle == TRICLINIC) {
v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
v[i][1] += -dthalf*v[i][2]*omega_dot[3];
}
v[i][0] *= factor[0];
v[i][1] *= factor[1];
v[i][2] *= factor[2];
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
v[i][0] *= factor[0];
v[i][1] *= factor[1];
v[i][2] *= factor[2];
if (pstyle == TRICLINIC) {
v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
v[i][1] += -dthalf*v[i][2]*omega_dot[3];
}
v[i][0] *= factor[0];
v[i][1] *= factor[1];
v[i][2] *= factor[2];
temperature->restore_bias(i,v[i]);
}
}
}
}
/* ----------------------------------------------------------------------
perform half-step update of velocities
-----------------------------------------------------------------------*/
void FixNH::nve_v()
{
double dtfm;
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm*f[i][0];
v[i][1] += dtfm*f[i][1];
v[i][2] += dtfm*f[i][2];
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm*f[i][0];
v[i][1] += dtfm*f[i][1];
v[i][2] += dtfm*f[i][2];
}
}
}
}
/* ----------------------------------------------------------------------
perform full-step update of positions
-----------------------------------------------------------------------*/
void FixNH::nve_x()
{
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// x update by full step only for atoms in group
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
}
/* ----------------------------------------------------------------------
perform half-step thermostat scaling of velocities
-----------------------------------------------------------------------*/
void FixNH::nh_v_temp()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
v[i][0] *= factor_eta;
v[i][1] *= factor_eta;
v[i][2] *= factor_eta;
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
v[i][0] *= factor_eta;
v[i][1] *= factor_eta;
v[i][2] *= factor_eta;
temperature->restore_bias(i,v[i]);
}
}
}
}
/* ----------------------------------------------------------------------
compute sigma tensor
needed whenever p_target or h0_inv changes
-----------------------------------------------------------------------*/
void FixNH::compute_sigma()
{
// if nreset_h0 > 0, reset vol0 and h0_inv
// every nreset_h0 timesteps
if (nreset_h0 > 0) {
int delta = update->ntimestep - update->beginstep;
if (delta % nreset_h0 == 0) {
if (dimension == 3) vol0 = domain->xprd * domain->yprd * domain->zprd;
else vol0 = domain->xprd * domain->yprd;
h0_inv[0] = domain->h_inv[0];
h0_inv[1] = domain->h_inv[1];
h0_inv[2] = domain->h_inv[2];
h0_inv[3] = domain->h_inv[3];
h0_inv[4] = domain->h_inv[4];
h0_inv[5] = domain->h_inv[5];
}
}
// generate upper-triangular half of
// sigma = vol0*h0inv*(p_target-p_hydro)*h0inv^t
// units of sigma are are PV/L^2 e.g. atm.A
//
// [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ] [ 0 - - ]
// [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ] [ 5 1 - ]
// [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ] [ 4 3 2 ]
sigma[0] =
vol0*(h0_inv[0]*((p_target[0]-p_hydro)*h0_inv[0] +
p_target[5]*h0_inv[5]+p_target[4]*h0_inv[4]) +
h0_inv[5]*(p_target[5]*h0_inv[0] +
(p_target[1]-p_hydro)*h0_inv[5]+p_target[3]*h0_inv[4]) +
h0_inv[4]*(p_target[4]*h0_inv[0]+p_target[3]*h0_inv[5] +
(p_target[2]-p_hydro)*h0_inv[4]));
sigma[1] =
vol0*(h0_inv[1]*((p_target[1]-p_hydro)*h0_inv[1] +
p_target[3]*h0_inv[3]) +
h0_inv[3]*(p_target[3]*h0_inv[1] +
(p_target[2]-p_hydro)*h0_inv[3]));
sigma[2] =
vol0*(h0_inv[2]*((p_target[2]-p_hydro)*h0_inv[2]));
sigma[3] =
vol0*(h0_inv[1]*(p_target[3]*h0_inv[2]) +
h0_inv[3]*((p_target[2]-p_hydro)*h0_inv[2]));
sigma[4] =
vol0*(h0_inv[0]*(p_target[4]*h0_inv[2]) +
h0_inv[5]*(p_target[3]*h0_inv[2]) +
h0_inv[4]*((p_target[2]-p_hydro)*h0_inv[2]));
sigma[5] =
vol0*(h0_inv[0]*(p_target[5]*h0_inv[1]+p_target[4]*h0_inv[3]) +
h0_inv[5]*((p_target[1]-p_hydro)*h0_inv[1]+p_target[3]*h0_inv[3]) +
h0_inv[4]*(p_target[3]*h0_inv[1]+(p_target[2]-p_hydro)*h0_inv[3]));
}
/* ----------------------------------------------------------------------
compute strain energy
-----------------------------------------------------------------------*/
double FixNH::compute_strain_energy()
{
// compute strain energy = 0.5*Tr(sigma*h*h^t) in energy units
double* h = domain->h;
double d0,d1,d2;
d0 =
sigma[0]*(h[0]*h[0]+h[5]*h[5]+h[4]*h[4]) +
sigma[5]*( h[1]*h[5]+h[3]*h[4]) +
sigma[4]*( h[2]*h[4]);
d1 =
sigma[5]*( h[5]*h[1]+h[4]*h[3]) +
sigma[1]*( h[1]*h[1]+h[3]*h[3]) +
sigma[3]*( h[2]*h[3]);
d2 =
sigma[4]*( h[4]*h[2]) +
sigma[3]*( h[3]*h[2]) +
sigma[2]*( h[2]*h[2]);
double energy = 0.5*(d0+d1+d2)/nktv2p;
return energy;
}
/* ----------------------------------------------------------------------
compute deviatoric barostat force = h*sigma*h^t
-----------------------------------------------------------------------*/
void FixNH::compute_deviatoric()
{
// generate upper-triangular part of h*sigma*h^t
// units of fdev are are PV, e.g. atm*A^3
// [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ] [ 0 - - ]
// [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ] [ 5 1 - ]
// [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ] [ 4 3 2 ]
double* h = domain->h;
fdev[0] =
h[0]*(sigma[0]*h[0]+sigma[5]*h[5]+sigma[4]*h[4]) +
h[5]*(sigma[5]*h[0]+sigma[1]*h[5]+sigma[3]*h[4]) +
h[4]*(sigma[4]*h[0]+sigma[3]*h[5]+sigma[2]*h[4]);
fdev[1] =
h[1]*( sigma[1]*h[1]+sigma[3]*h[3]) +
h[3]*( sigma[3]*h[1]+sigma[2]*h[3]);
fdev[2] =
h[2]*( sigma[2]*h[2]);
fdev[3] =
h[1]*( sigma[3]*h[2]) +
h[3]*( sigma[2]*h[2]);
fdev[4] =
h[0]*( sigma[4]*h[2]) +
h[5]*( sigma[3]*h[2]) +
h[4]*( sigma[2]*h[2]);
fdev[5] =
h[0]*( sigma[5]*h[1]+sigma[4]*h[3]) +
h[5]*( sigma[1]*h[1]+sigma[3]*h[3]) +
h[4]*( sigma[3]*h[1]+sigma[2]*h[3]);
}
/* ----------------------------------------------------------------------
compute target temperature and kinetic energy
-----------------------------------------------------------------------*/
void FixNH::compute_temp_target()
{
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
t_target = t_start + delta * (t_stop-t_start);
ke_target = tdof * boltz * t_target;
}
/* ----------------------------------------------------------------------
compute hydrostatic target pressure
-----------------------------------------------------------------------*/
void FixNH::compute_press_target()
{
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
p_hydro = 0.0;
for (int i = 0; i < 3; i++)
if (p_flag[i]) {
p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);
p_hydro += p_target[i];
}
p_hydro /= pdim;
if (pstyle == TRICLINIC)
for (int i = 3; i < 6; i++)
p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);
// if deviatoric, recompute sigma each time p_target changes
if (deviatoric_flag) compute_sigma();
}
/* ----------------------------------------------------------------------
update omega_dot, omega
-----------------------------------------------------------------------*/
void FixNH::nh_omega_dot()
{
double f_omega,volume;
if (dimension == 3) volume = domain->xprd*domain->yprd*domain->zprd;
else volume = domain->xprd*domain->yprd;
if (deviatoric_flag) compute_deviatoric();
mtk_term1 = 0.0;
if (mtk_flag) {
if (pstyle == ISO) {
mtk_term1 = tdof * boltz * t_current;
mtk_term1 /= pdim * atom->natoms;
} else {
double *mvv_current = temperature->vector;
for (int i = 0; i < 3; i++)
if (p_flag[i])
mtk_term1 += mvv_current[i];
mtk_term1 /= pdim * atom->natoms;
}
}
for (int i = 0; i < 3; i++)
if (p_flag[i]) {
f_omega = (p_current[i]-p_hydro)*volume /
(omega_mass[i] * nktv2p) + mtk_term1 / omega_mass[i];
if (deviatoric_flag) f_omega -= fdev[i]/(omega_mass[i] * nktv2p);
omega_dot[i] += f_omega*dthalf;
omega_dot[i] *= pdrag_factor;
}
mtk_term2 = 0.0;
if (mtk_flag) {
for (int i = 0; i < 3; i++)
if (p_flag[i])
mtk_term2 += omega_dot[i];
mtk_term2 /= pdim * atom->natoms;
}
if (pstyle == TRICLINIC) {
for (int i = 3; i < 6; i++) {
if (p_flag[i]) {
f_omega = p_current[i]*volume/(omega_mass[i] * nktv2p);
if (deviatoric_flag)
f_omega -= fdev[i]/(omega_mass[i] * nktv2p);
omega_dot[i] += f_omega*dthalf;
omega_dot[i] *= pdrag_factor;
}
}
}
}
/* ----------------------------------------------------------------------
if any tilt ratios exceed limits, set flip = 1 and compute new tilt values
do not flip in x or y if non-periodic (can tilt but not flip)
this is b/c the box length would be changed (dramatically) by flip
if yz tilt exceeded, adjust C vector by one B vector
if xz tilt exceeded, adjust C vector by one A vector
if xy tilt exceeded, adjust B vector by one A vector
check yz first since it may change xz, then xz check comes after
if any flip occurs, create new box in domain
image_flip() adjusts image flags due to box shape change induced by flip
remap() puts atoms outside the new box back into the new box
perform irregular on atoms in lamda coords to migrate atoms to new procs
important that image_flip comes before remap, since remap may change
image flags to new values, making eqs in doc of Domain:image_flip incorrect
------------------------------------------------------------------------- */
void FixNH::pre_exchange()
{
double xprd = domain->xprd;
double yprd = domain->yprd;
// flip is only triggered when tilt exceeds 0.5 by DELTAFLIP
// this avoids immediate re-flipping due to tilt oscillations
double xtiltmax = (0.5+DELTAFLIP)*xprd;
double ytiltmax = (0.5+DELTAFLIP)*yprd;
int flipxy,flipxz,flipyz;
flipxy = flipxz = flipyz = 0;
if (domain->yperiodic) {
if (domain->yz < -ytiltmax) {
domain->yz += yprd;
domain->xz += domain->xy;
flipyz = 1;
} else if (domain->yz >= ytiltmax) {
domain->yz -= yprd;
domain->xz -= domain->xy;
flipyz = -1;
}
}
if (domain->xperiodic) {
if (domain->xz < -xtiltmax) {
domain->xz += xprd;
flipxz = 1;
} else if (domain->xz >= xtiltmax) {
domain->xz -= xprd;
flipxz = -1;
}
if (domain->xy < -xtiltmax) {
domain->xy += xprd;
flipxy = 1;
} else if (domain->xy >= xtiltmax) {
domain->xy -= xprd;
flipxy = -1;
}
}
int flip = 0;
if (flipxy || flipxz || flipyz) flip = 1;
if (flip) {
domain->set_global_box();
domain->set_local_box();
domain->image_flip(flipxy,flipxz,flipyz);
double **x = atom->x;
imageint *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
domain->x2lamda(atom->nlocal);
irregular->migrate_atoms();
domain->lamda2x(atom->nlocal);
}
}
/* ----------------------------------------------------------------------
memory usage of Irregular
------------------------------------------------------------------------- */
double FixNH::memory_usage()
{
double bytes = 0.0;
if (irregular) bytes += irregular->memory_usage();
return bytes;
}
diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp
index d854410b4..08aa7c9f9 100644
--- a/src/fix_wall_region.cpp
+++ b/src/fix_wall_region.cpp
@@ -1,361 +1,363 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "fix_wall_region.h"
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "region.h"
#include "force.h"
#include "lattice.h"
#include "update.h"
#include "output.h"
#include "respa.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{LJ93,LJ126,COLLOID,HARMONIC};
/* ---------------------------------------------------------------------- */
FixWallRegion::FixWallRegion(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 8) error->all(FLERR,"Illegal fix wall/region command");
scalar_flag = 1;
vector_flag = 1;
size_vector = 3;
global_freq = 1;
extscalar = 1;
extvector = 1;
// parse args
iregion = domain->find_region(arg[3]);
if (iregion == -1)
error->all(FLERR,"Region ID for fix wall/region does not exist");
int n = strlen(arg[3]) + 1;
idregion = new char[n];
strcpy(idregion,arg[3]);
if (strcmp(arg[4],"lj93") == 0) style = LJ93;
else if (strcmp(arg[4],"lj126") == 0) style = LJ126;
else if (strcmp(arg[4],"colloid") == 0) style = COLLOID;
else if (strcmp(arg[4],"harmonic") == 0) style = HARMONIC;
else error->all(FLERR,"Illegal fix wall/region command");
epsilon = force->numeric(FLERR,arg[5]);
sigma = force->numeric(FLERR,arg[6]);
cutoff = force->numeric(FLERR,arg[7]);
if (cutoff <= 0.0) error->all(FLERR,"Fix wall/region cutoff <= 0.0");
eflag = 0;
ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
}
/* ---------------------------------------------------------------------- */
FixWallRegion::~FixWallRegion()
{
delete [] idregion;
}
/* ---------------------------------------------------------------------- */
int FixWallRegion::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixWallRegion::init()
{
// set index and check validity of region
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all(FLERR,"Region ID for fix wall/region does not exist");
// error checks for style COLLOID
// insure all particles in group are extended particles
if (style == COLLOID) {
if (!atom->sphere_flag)
error->all(FLERR,"Fix wall/region colloid requires atom style sphere");
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int flag = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (radius[i] == 0.0) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall)
error->all(FLERR,"Fix wall/region colloid requires extended particles");
}
// setup coefficients for each style
if (style == LJ93) {
coeff1 = 6.0/5.0 * epsilon * pow(sigma,9.0);
coeff2 = 3.0 * epsilon * pow(sigma,3.0);
coeff3 = 2.0/15.0 * epsilon * pow(sigma,9.0);
coeff4 = epsilon * pow(sigma,3.0);
double rinv = 1.0/cutoff;
double r2inv = rinv*rinv;
double r4inv = r2inv*r2inv;
offset = coeff3*r4inv*r4inv*rinv - coeff4*r2inv*rinv;
} else if (style == LJ126) {
coeff1 = 48.0 * epsilon * pow(sigma,12.0);
coeff2 = 24.0 * epsilon * pow(sigma,6.0);
coeff3 = 4.0 * epsilon * pow(sigma,12.0);
coeff4 = 4.0 * epsilon * pow(sigma,6.0);
double r2inv = 1.0/(cutoff*cutoff);
double r6inv = r2inv*r2inv*r2inv;
offset = r6inv*(coeff3*r6inv - coeff4);
} else if (style == COLLOID) {
coeff1 = -4.0/315.0 * epsilon * pow(sigma,6.0);
coeff2 = -2.0/3.0 * epsilon;
coeff3 = epsilon * pow(sigma,6.0)/7560.0;
coeff4 = epsilon/6.0;
double rinv = 1.0/cutoff;
double r2inv = rinv*rinv;
double r4inv = r2inv*r2inv;
offset = coeff3*r4inv*r4inv*rinv - coeff4*r2inv*rinv;
}
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixWallRegion::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
/* ---------------------------------------------------------------------- */
void FixWallRegion::min_setup(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixWallRegion::post_force(int vflag)
{
int i,m,n;
double rinv,fx,fy,fz,tooclose;
- eflag = 0;
- ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
-
double **x = atom->x;
double **f = atom->f;
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
Region *region = domain->regions[iregion];
region->prematch();
int onflag = 0;
// region->match() insures particle is in region or on surface, else error
// if returned contact dist r = 0, is on surface, also an error
// in COLLOID case, r <= radius is an error
+ // initilize ewall after region->prematch(),
+ // so a dynamic region can access last timestep values
+
+ eflag = 0;
+ ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (!region->match(x[i][0],x[i][1],x[i][2])) {
onflag = 1;
continue;
}
if (style == COLLOID) tooclose = radius[i];
else tooclose = 0.0;
n = region->surface(x[i][0],x[i][1],x[i][2],cutoff);
for (m = 0; m < n; m++) {
if (region->contact[m].r <= tooclose) {
onflag = 1;
continue;
} else rinv = 1.0/region->contact[m].r;
if (style == LJ93) lj93(region->contact[m].r);
else if (style == LJ126) lj126(region->contact[m].r);
else if (style == COLLOID) colloid(region->contact[m].r,radius[i]);
else harmonic(region->contact[m].r);
ewall[0] += eng;
fx = fwall * region->contact[m].delx * rinv;
fy = fwall * region->contact[m].dely * rinv;
fz = fwall * region->contact[m].delz * rinv;
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
ewall[1] -= fx;
ewall[2] -= fy;
ewall[3] -= fz;
}
}
if (onflag) error->one(FLERR,"Particle outside surface of region "
"used in fix wall/region");
}
/* ---------------------------------------------------------------------- */
void FixWallRegion::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixWallRegion::min_post_force(int vflag)
{
post_force(vflag);
}
/* ----------------------------------------------------------------------
energy of wall interaction
------------------------------------------------------------------------- */
double FixWallRegion::compute_scalar()
{
// only sum across procs one time
if (eflag == 0) {
MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world);
eflag = 1;
}
return ewall_all[0];
}
/* ----------------------------------------------------------------------
components of force on wall
------------------------------------------------------------------------- */
double FixWallRegion::compute_vector(int n)
{
// only sum across procs one time
if (eflag == 0) {
MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world);
eflag = 1;
}
return ewall_all[n+1];
}
/* ----------------------------------------------------------------------
LJ 9/3 interaction for particle with wall
compute eng and fwall = magnitude of wall force
------------------------------------------------------------------------- */
void FixWallRegion::lj93(double r)
{
double rinv = 1.0/r;
double r2inv = rinv*rinv;
double r4inv = r2inv*r2inv;
double r10inv = r4inv*r4inv*r2inv;
fwall = coeff1*r10inv - coeff2*r4inv;
eng = coeff3*r4inv*r4inv*rinv - coeff4*r2inv*rinv - offset;
}
/* ----------------------------------------------------------------------
LJ 12/6 interaction for particle with wall
compute eng and fwall = magnitude of wall force
------------------------------------------------------------------------- */
void FixWallRegion::lj126(double r)
{
double rinv = 1.0/r;
double r2inv = rinv*rinv;
double r6inv = r2inv*r2inv*r2inv;
fwall = r6inv*(coeff1*r6inv - coeff2) * rinv;
eng = r6inv*(coeff3*r6inv - coeff4) - offset;
}
/* ----------------------------------------------------------------------
colloid interaction for finite-size particle of rad with wall
compute eng and fwall = magnitude of wall force
------------------------------------------------------------------------- */
void FixWallRegion::colloid(double r, double rad)
{
double new_coeff2 = coeff2*rad*rad*rad;
double diam = 2.0*rad;
double rad2 = rad*rad;
double rad4 = rad2*rad2;
double rad8 = rad4*rad4;
double delta2 = rad2 - r*r;
double rinv = 1.0/delta2;
double r2inv = rinv*rinv;
double r4inv = r2inv*r2inv;
double r8inv = r4inv*r4inv;
fwall = coeff1*(rad8*rad + 27.0*rad4*rad2*rad*pow(r,2.0)
+ 63.0*rad4*rad*pow(r,4.0)
+ 21.0*rad2*rad*pow(r,6.0))*r8inv - new_coeff2*r2inv;
double r2 = 0.5*diam - r;
double rinv2 = 1.0/r2;
double r2inv2 = rinv2*rinv2;
double r4inv2 = r2inv2*r2inv2;
double r3 = r + 0.5*diam;
double rinv3 = 1.0/r3;
double r2inv3 = rinv3*rinv3;
double r4inv3 = r2inv3*r2inv3;
eng = coeff3*((-3.5*diam+r)*r4inv2*r2inv2*rinv2
+ (3.5*diam+r)*r4inv3*r2inv3*rinv3) -
coeff4*((-diam*r+r2*r3*(log(-r2)-log(r3)))*
(-rinv2)*rinv3) - offset;
}
/* ----------------------------------------------------------------------
harmonic interaction for particle with wall
compute eng and fwall = magnitude of wall force
------------------------------------------------------------------------- */
void FixWallRegion::harmonic(double r)
{
double dr = cutoff - r;
fwall = 2.0*epsilon*dr;
eng = epsilon*dr*dr;
}
diff --git a/src/force.cpp b/src/force.cpp
index aa70874ad..f51b0c181 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -1,1020 +1,1023 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "string.h"
#include "ctype.h"
#include "force.h"
#include "style_bond.h"
#include "style_angle.h"
#include "style_dihedral.h"
#include "style_improper.h"
#include "style_pair.h"
#include "style_kspace.h"
#include "atom.h"
#include "comm.h"
#include "pair.h"
#include "pair_hybrid.h"
#include "pair_hybrid_overlay.h"
#include "bond.h"
#include "bond_hybrid.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
/* ---------------------------------------------------------------------- */
Force::Force(LAMMPS *lmp) : Pointers(lmp)
{
newton = newton_pair = newton_bond = 1;
special_lj[0] = special_coul[0] = 1.0;
special_lj[1] = special_lj[2] = special_lj[3] = 0.0;
special_coul[1] = special_coul[2] = special_coul[3] = 0.0;
special_angle = special_dihedral = 0;
special_extra = 0;
dielectric = 1.0;
pair = NULL;
bond = NULL;
angle = NULL;
dihedral = NULL;
improper = NULL;
kspace = NULL;
char *str = (char *) "none";
int n = strlen(str) + 1;
pair_style = new char[n];
strcpy(pair_style,str);
bond_style = new char[n];
strcpy(bond_style,str);
angle_style = new char[n];
strcpy(angle_style,str);
dihedral_style = new char[n];
strcpy(dihedral_style,str);
improper_style = new char[n];
strcpy(improper_style,str);
kspace_style = new char[n];
strcpy(kspace_style,str);
// fill pair map with pair styles listed in style_pair.h
pair_map = new std::map<std::string,PairCreator>();
#define PAIR_CLASS
#define PairStyle(key,Class) \
(*pair_map)[#key] = &pair_creator<Class>;
#include "style_pair.h"
#undef PairStyle
#undef PAIR_CLASS
}
/* ---------------------------------------------------------------------- */
Force::~Force()
{
delete [] pair_style;
delete [] bond_style;
delete [] angle_style;
delete [] dihedral_style;
delete [] improper_style;
delete [] kspace_style;
if (pair) delete pair;
if (bond) delete bond;
if (angle) delete angle;
if (dihedral) delete dihedral;
if (improper) delete improper;
if (kspace) delete kspace;
pair = NULL;
bond = NULL;
angle = NULL;
dihedral = NULL;
improper = NULL;
kspace = NULL;
delete pair_map;
}
/* ---------------------------------------------------------------------- */
void Force::init()
{
qqrd2e = qqr2e/dielectric;
if (kspace) kspace->init(); // kspace must come before pair
if (pair) pair->init(); // so g_ewald is defined
if (bond) bond->init();
if (angle) angle->init();
if (dihedral) dihedral->init();
if (improper) improper->init();
}
/* ----------------------------------------------------------------------
create a pair style, called from input script or restart file
------------------------------------------------------------------------- */
void Force::create_pair(const char *style, int trysuffix)
{
delete [] pair_style;
if (pair) delete pair;
int sflag;
pair = new_pair(style,trysuffix,sflag);
store_style(pair_style,style,sflag);
}
/* ----------------------------------------------------------------------
generate a pair class
if trysuffix = 1, try first with suffix1/2 appended
return sflag = 0 for no suffix added, 1 or 2 for suffix1/2 added
------------------------------------------------------------------------- */
Pair *Force::new_pair(const char *style, int trysuffix, int &sflag)
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->suffix) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix);
if (pair_map->find(estyle) != pair_map->end()) {
PairCreator pair_creator = (*pair_map)[estyle];
return pair_creator(lmp);
}
}
if (lmp->suffix2) {
sflag = 2;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix2);
if (pair_map->find(estyle) != pair_map->end()) {
PairCreator pair_creator = (*pair_map)[estyle];
return pair_creator(lmp);
}
}
}
sflag = 0;
if (strcmp(style,"none") == 0) return NULL;
if (pair_map->find(style) != pair_map->end()) {
PairCreator pair_creator = (*pair_map)[style];
return pair_creator(lmp);
}
error->all(FLERR,"Unknown pair style");
return NULL;
}
/* ----------------------------------------------------------------------
one instance per pair style in style_pair.h
------------------------------------------------------------------------- */
template <typename T>
Pair *Force::pair_creator(LAMMPS *lmp)
{
return new T(lmp);
}
/* ----------------------------------------------------------------------
return ptr to Pair class if matches word or matches hybrid sub-style
if exact, then style name must be exact match to word
if not exact, style name must contain word
- return NULL if no match or multiple sub-styles match
+ if nsub > 0, match Nth hybrid sub-style
+ return NULL if no match or if nsub=0 and multiple sub-styles match
------------------------------------------------------------------------- */
-Pair *Force::pair_match(const char *word, int exact)
+Pair *Force::pair_match(const char *word, int exact, int nsub)
{
int iwhich,count;
if (exact && strcmp(pair_style,word) == 0) return pair;
else if (!exact && strstr(pair_style,word)) return pair;
else if (strstr(pair_style,"hybrid/overlay")) {
PairHybridOverlay *hybrid = (PairHybridOverlay *) pair;
count = 0;
for (int i = 0; i < hybrid->nstyles; i++)
if ((exact && strcmp(hybrid->keywords[i],word) == 0) ||
(!exact && strstr(hybrid->keywords[i],word))) {
iwhich = i;
count++;
+ if (nsub == count) return hybrid->styles[iwhich];
}
if (count == 1) return hybrid->styles[iwhich];
} else if (strstr(pair_style,"hybrid")) {
PairHybrid *hybrid = (PairHybrid *) pair;
count = 0;
for (int i = 0; i < hybrid->nstyles; i++)
if ((exact && strcmp(hybrid->keywords[i],word) == 0) ||
(!exact && strstr(hybrid->keywords[i],word))) {
iwhich = i;
count++;
+ if (nsub == count) return hybrid->styles[iwhich];
}
if (count == 1) return hybrid->styles[iwhich];
}
return NULL;
}
/* ----------------------------------------------------------------------
create a bond style, called from input script or restart file
------------------------------------------------------------------------- */
void Force::create_bond(const char *style, int trysuffix)
{
delete [] bond_style;
if (bond) delete bond;
int sflag;
bond = new_bond(style,trysuffix,sflag);
store_style(bond_style,style,sflag);
}
/* ----------------------------------------------------------------------
generate a bond class, fist with suffix appended
------------------------------------------------------------------------- */
Bond *Force::new_bond(const char *style, int trysuffix, int &sflag)
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->suffix) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix);
if (0) return NULL;
#define BOND_CLASS
#define BondStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp);
#include "style_bond.h"
#undef BondStyle
#undef BOND_CLASS
}
if (lmp->suffix2) {
sflag = 2;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix2);
if (0) return NULL;
#define BOND_CLASS
#define BondStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp);
#include "style_bond.h"
#undef BondStyle
#undef BOND_CLASS
}
}
sflag = 0;
if (strcmp(style,"none") == 0) return NULL;
#define BOND_CLASS
#define BondStyle(key,Class) \
else if (strcmp(style,#key) == 0) return new Class(lmp);
#include "style_bond.h"
#undef BOND_CLASS
else error->all(FLERR,"Unknown bond style");
return NULL;
}
/* ----------------------------------------------------------------------
return ptr to current bond class or hybrid sub-class if matches style
------------------------------------------------------------------------- */
Bond *Force::bond_match(const char *style)
{
if (strcmp(bond_style,style) == 0) return bond;
else if (strcmp(bond_style,"hybrid") == 0) {
BondHybrid *hybrid = (BondHybrid *) bond;
for (int i = 0; i < hybrid->nstyles; i++)
if (strcmp(hybrid->keywords[i],style) == 0) return hybrid->styles[i];
}
return NULL;
}
/* ----------------------------------------------------------------------
create an angle style, called from input script or restart file
------------------------------------------------------------------------- */
void Force::create_angle(const char *style, int trysuffix)
{
delete [] angle_style;
if (angle) delete angle;
int sflag;
angle = new_angle(style,trysuffix,sflag);
store_style(angle_style,style,sflag);
}
/* ----------------------------------------------------------------------
generate an angle class
------------------------------------------------------------------------- */
Angle *Force::new_angle(const char *style, int trysuffix, int &sflag)
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->suffix) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix);
if (0) return NULL;
#define ANGLE_CLASS
#define AngleStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp);
#include "style_angle.h"
#undef AngleStyle
#undef ANGLE_CLASS
}
if (lmp->suffix2) {
sflag = 2;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix);
if (0) return NULL;
#define ANGLE_CLASS
#define AngleStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp);
#include "style_angle.h"
#undef AngleStyle
#undef ANGLE_CLASS
}
}
sflag = 0;
if (strcmp(style,"none") == 0) return NULL;
#define ANGLE_CLASS
#define AngleStyle(key,Class) \
else if (strcmp(style,#key) == 0) return new Class(lmp);
#include "style_angle.h"
#undef ANGLE_CLASS
else error->all(FLERR,"Unknown angle style");
return NULL;
}
/* ----------------------------------------------------------------------
create a dihedral style, called from input script or restart file
------------------------------------------------------------------------- */
void Force::create_dihedral(const char *style, int trysuffix)
{
delete [] dihedral_style;
if (dihedral) delete dihedral;
int sflag;
dihedral = new_dihedral(style,trysuffix,sflag);
store_style(dihedral_style,style,sflag);
}
/* ----------------------------------------------------------------------
generate a dihedral class
------------------------------------------------------------------------- */
Dihedral *Force::new_dihedral(const char *style, int trysuffix, int &sflag)
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->suffix) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix);
if (0) return NULL;
#define DIHEDRAL_CLASS
#define DihedralStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp);
#include "style_dihedral.h"
#undef DihedralStyle
#undef DIHEDRAL_CLASS
}
if (lmp->suffix2) {
sflag = 2;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix2);
if (0) return NULL;
#define DIHEDRAL_CLASS
#define DihedralStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp);
#include "style_dihedral.h"
#undef DihedralStyle
#undef DIHEDRAL_CLASS
}
}
sflag = 0;
if (strcmp(style,"none") == 0) return NULL;
#define DIHEDRAL_CLASS
#define DihedralStyle(key,Class) \
else if (strcmp(style,#key) == 0) return new Class(lmp);
#include "style_dihedral.h"
#undef DihedralStyle
#undef DIHEDRAL_CLASS
else error->all(FLERR,"Unknown dihedral style");
return NULL;
}
/* ----------------------------------------------------------------------
create an improper style, called from input script or restart file
------------------------------------------------------------------------- */
void Force::create_improper(const char *style, int trysuffix)
{
delete [] improper_style;
if (improper) delete improper;
int sflag;
improper = new_improper(style,trysuffix,sflag);
store_style(improper_style,style,sflag);
}
/* ----------------------------------------------------------------------
generate a improper class
------------------------------------------------------------------------- */
Improper *Force::new_improper(const char *style, int trysuffix, int &sflag)
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->suffix) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix);
if (0) return NULL;
#define IMPROPER_CLASS
#define ImproperStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp);
#include "style_improper.h"
#undef ImproperStyle
#undef IMPROPER_CLASS
}
if (lmp->suffix2) {
sflag = 2;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix2);
if (0) return NULL;
#define IMPROPER_CLASS
#define ImproperStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp);
#include "style_improper.h"
#undef ImproperStyle
#undef IMPROPER_CLASS
}
}
sflag = 0;
if (strcmp(style,"none") == 0) return NULL;
#define IMPROPER_CLASS
#define ImproperStyle(key,Class) \
else if (strcmp(style,#key) == 0) return new Class(lmp);
#include "style_improper.h"
#undef IMPROPER_CLASS
else error->all(FLERR,"Unknown improper style");
return NULL;
}
/* ----------------------------------------------------------------------
return ptr to current improper class or hybrid sub-class if matches style
------------------------------------------------------------------------- */
Improper *Force::improper_match(const char *style)
{
if (strcmp(improper_style,style) == 0) return improper;
else if (strcmp(improper_style,"hybrid") == 0) {
ImproperHybrid *hybrid = (ImproperHybrid *) bond;
for (int i = 0; i < hybrid->nstyles; i++)
if (strcmp(hybrid->keywords[i],style) == 0) return hybrid->styles[i];
}
return NULL;
}
/* ----------------------------------------------------------------------
new kspace style
------------------------------------------------------------------------- */
void Force::create_kspace(int narg, char **arg, int trysuffix)
{
delete [] kspace_style;
if (kspace) delete kspace;
int sflag;
kspace = new_kspace(narg,arg,trysuffix,sflag);
store_style(kspace_style,arg[0],sflag);
if (comm->style == 1 && !kspace_match("ewald",0))
error->all(FLERR,
"Cannot yet use KSpace solver with grid with comm style tiled");
}
/* ----------------------------------------------------------------------
generate a kspace class
------------------------------------------------------------------------- */
KSpace *Force::new_kspace(int narg, char **arg, int trysuffix, int &sflag)
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->suffix) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",arg[0],lmp->suffix);
if (0) return NULL;
#define KSPACE_CLASS
#define KSpaceStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp,narg-1,&arg[1]);
#include "style_kspace.h"
#undef KSpaceStyle
#undef KSPACE_CLASS
}
if (lmp->suffix2) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",arg[0],lmp->suffix2);
if (0) return NULL;
#define KSPACE_CLASS
#define KSpaceStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp,narg-1,&arg[1]);
#include "style_kspace.h"
#undef KSpaceStyle
#undef KSPACE_CLASS
}
}
sflag = 0;
if (strcmp(arg[0],"none") == 0) return NULL;
#define KSPACE_CLASS
#define KSpaceStyle(key,Class) \
else if (strcmp(arg[0],#key) == 0) return new Class(lmp,narg-1,&arg[1]);
#include "style_kspace.h"
#undef KSPACE_CLASS
else error->all(FLERR,"Unknown kspace style");
return NULL;
}
/* ----------------------------------------------------------------------
return ptr to Kspace class if matches word
if exact, then style name must be exact match to word
if not exact, style name must contain word
return NULL if no match
------------------------------------------------------------------------- */
KSpace *Force::kspace_match(const char *word, int exact)
{
if (exact && strcmp(kspace_style,word) == 0) return kspace;
else if (!exact && strstr(kspace_style,word)) return kspace;
return NULL;
}
/* ----------------------------------------------------------------------
store style name in str allocated here
if sflag = 0, no suffix
if sflag = 1/2, append suffix or suffix2 to style
------------------------------------------------------------------------- */
void Force::store_style(char *&str, const char *style, int sflag)
{
if (sflag) {
char estyle[256];
if (sflag == 1) sprintf(estyle,"%s/%s",style,lmp->suffix);
else sprintf(estyle,"%s/%s",style,lmp->suffix2);
int n = strlen(estyle) + 1;
str = new char[n];
strcpy(str,estyle);
} else {
int n = strlen(style) + 1;
str = new char[n];
strcpy(str,style);
}
}
/* ----------------------------------------------------------------------
set special bond values
------------------------------------------------------------------------- */
void Force::set_special(int narg, char **arg)
{
if (narg == 0) error->all(FLERR,"Illegal special_bonds command");
// defaults, but do not reset special_extra
special_lj[1] = special_lj[2] = special_lj[3] = 0.0;
special_coul[1] = special_coul[2] = special_coul[3] = 0.0;
special_angle = special_dihedral = 0;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"amber") == 0) {
if (iarg+1 > narg) error->all(FLERR,"Illegal special_bonds command");
special_lj[1] = 0.0;
special_lj[2] = 0.0;
special_lj[3] = 0.5;
special_coul[1] = 0.0;
special_coul[2] = 0.0;
special_coul[3] = 5.0/6.0;
iarg += 1;
} else if (strcmp(arg[iarg],"charmm") == 0) {
if (iarg+1 > narg) error->all(FLERR,"Illegal special_bonds command");
special_lj[1] = 0.0;
special_lj[2] = 0.0;
special_lj[3] = 0.0;
special_coul[1] = 0.0;
special_coul[2] = 0.0;
special_coul[3] = 0.0;
iarg += 1;
} else if (strcmp(arg[iarg],"dreiding") == 0) {
if (iarg+1 > narg) error->all(FLERR,"Illegal special_bonds command");
special_lj[1] = 0.0;
special_lj[2] = 0.0;
special_lj[3] = 1.0;
special_coul[1] = 0.0;
special_coul[2] = 0.0;
special_coul[3] = 1.0;
iarg += 1;
} else if (strcmp(arg[iarg],"fene") == 0) {
if (iarg+1 > narg) error->all(FLERR,"Illegal special_bonds command");
special_lj[1] = 0.0;
special_lj[2] = 1.0;
special_lj[3] = 1.0;
special_coul[1] = 0.0;
special_coul[2] = 1.0;
special_coul[3] = 1.0;
iarg += 1;
} else if (strcmp(arg[iarg],"lj/coul") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal special_bonds command");
special_lj[1] = special_coul[1] = numeric(FLERR,arg[iarg+1]);
special_lj[2] = special_coul[2] = numeric(FLERR,arg[iarg+2]);
special_lj[3] = special_coul[3] = numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"lj") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal special_bonds command");
special_lj[1] = numeric(FLERR,arg[iarg+1]);
special_lj[2] = numeric(FLERR,arg[iarg+2]);
special_lj[3] = numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"coul") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal special_bonds command");
special_coul[1] = numeric(FLERR,arg[iarg+1]);
special_coul[2] = numeric(FLERR,arg[iarg+2]);
special_coul[3] = numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"angle") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal special_bonds command");
if (strcmp(arg[iarg+1],"no") == 0) special_angle = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) special_angle = 1;
else error->all(FLERR,"Illegal special_bonds command");
iarg += 2;
} else if (strcmp(arg[iarg],"dihedral") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal special_bonds command");
if (strcmp(arg[iarg+1],"no") == 0) special_dihedral = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) special_dihedral = 1;
else error->all(FLERR,"Illegal special_bonds command");
iarg += 2;
} else if (strcmp(arg[iarg],"extra") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal special_bonds command");
special_extra = atoi(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal special_bonds command");
}
for (int i = 1; i <= 3; i++)
if (special_lj[i] < 0.0 || special_lj[i] > 1.0 ||
special_coul[i] < 0.0 || special_coul[i] > 1.0)
error->all(FLERR,"Illegal special_bonds command");
if (special_extra < 0) error->all(FLERR,"Illegal special_bonds command");
}
/* ----------------------------------------------------------------------
compute bounds implied by numeric str with a possible wildcard asterik
1 = lower bound, nmax = upper bound
5 possibilities:
(1) i = i to i, (2) * = nmin to nmax,
(3) i* = i to nmax, (4) *j = nmin to j, (5) i*j = i to j
return nlo,nhi
------------------------------------------------------------------------- */
void Force::bounds(char *str, int nmax, int &nlo, int &nhi, int nmin)
{
char *ptr = strchr(str,'*');
if (ptr == NULL) {
nlo = nhi = atoi(str);
} else if (strlen(str) == 1) {
nlo = nmin;
nhi = nmax;
} else if (ptr == str) {
nlo = nmin;
nhi = atoi(ptr+1);
} else if (strlen(ptr+1) == 0) {
nlo = atoi(str);
nhi = nmax;
} else {
nlo = atoi(str);
nhi = atoi(ptr+1);
}
if (nlo < nmin || nhi > nmax || nlo > nhi)
error->all(FLERR,"Numeric index is out of bounds");
}
/* ----------------------------------------------------------------------
compute bounds implied by numeric str with a possible wildcard asterik
1 = lower bound, nmax = upper bound
5 possibilities:
(1) i = i to i, (2) * = nmin to nmax,
(3) i* = i to nmax, (4) *j = nmin to j, (5) i*j = i to j
return nlo,nhi
------------------------------------------------------------------------- */
void Force::boundsbig(char *str, bigint nmax, bigint &nlo, bigint &nhi,
bigint nmin)
{
char *ptr = strchr(str,'*');
if (ptr == NULL) {
nlo = nhi = ATOBIGINT(str);
} else if (strlen(str) == 1) {
nlo = nmin;
nhi = nmax;
} else if (ptr == str) {
nlo = nmin;
nhi = ATOBIGINT(ptr+1);
} else if (strlen(ptr+1) == 0) {
nlo = ATOBIGINT(str);
nhi = nmax;
} else {
nlo = ATOBIGINT(str);
nhi = ATOBIGINT(ptr+1);
}
if (nlo < nmin || nhi > nmax || nlo > nhi)
error->all(FLERR,"Numeric index is out of bounds");
}
/* ----------------------------------------------------------------------
read a floating point value from a string
generate an error if not a legitimate floating point value
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
double Force::numeric(const char *file, int line, char *str)
{
if (!str)
error->all(file,line,"Expected floating point parameter "
"in input script or data file");
int n = strlen(str);
if (n == 0)
error->all(file,line,"Expected floating point parameter "
"in input script or data file");
for (int i = 0; i < n; i++) {
if (isdigit(str[i])) continue;
if (str[i] == '-' || str[i] == '+' || str[i] == '.') continue;
if (str[i] == 'e' || str[i] == 'E') continue;
error->all(file,line,"Expected floating point parameter "
"in input script or data file");
}
return atof(str);
}
/* ----------------------------------------------------------------------
read an integer value from a string
generate an error if not a legitimate integer value
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
int Force::inumeric(const char *file, int line, char *str)
{
if (!str)
error->all(file,line,
"Expected integer parameter in input script or data file");
int n = strlen(str);
if (n == 0)
error->all(file,line,
"Expected integer parameter in input script or data file");
for (int i = 0; i < n; i++) {
if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue;
error->all(file,line,
"Expected integer parameter in input script or data file");
}
return atoi(str);
}
/* ----------------------------------------------------------------------
read a big integer value from a string
generate an error if not a legitimate integer value
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
bigint Force::bnumeric(const char *file, int line, char *str)
{
if (!str)
error->all(file,line,
"Expected integer parameter in input script or data file");
int n = strlen(str);
if (n == 0)
error->all(file,line,
"Expected integer parameter in input script or data file");
for (int i = 0; i < n; i++) {
if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue;
error->all(file,line,
"Expected integer parameter in input script or data file");
}
return ATOBIGINT(str);
}
/* ----------------------------------------------------------------------
read a tag integer value from a string
generate an error if not a legitimate integer value
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
tagint Force::tnumeric(const char *file, int line, char *str)
{
if (!str)
error->all(file,line,
"Expected integer parameter in input script or data file");
int n = strlen(str);
if (n == 0)
error->all(file,line,
"Expected integer parameter in input script or data file");
for (int i = 0; i < n; i++) {
if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue;
error->all(file,line,
"Expected integer parameter in input script or data file");
}
return ATOTAGINT(str);
}
/* ----------------------------------------------------------------------
open a potential file as specified by name
if fails, search in dir specified by env variable LAMMPS_POTENTIALS
------------------------------------------------------------------------- */
FILE *Force::open_potential(const char *name)
{
FILE *fp;
if (name == NULL) return NULL;
// attempt to open file directly
// if successful, return ptr
fp = fopen(name,"r");
if (fp) {
if (comm->me == 0) potential_date(fp,name);
rewind(fp);
return fp;
}
// try the environment variable directory
const char *path = getenv("LAMMPS_POTENTIALS");
if (path == NULL) return NULL;
const char *pot = potential_name(name);
if (pot == NULL) return NULL;
size_t len1 = strlen(path);
size_t len2 = strlen(pot);
char *newpath = new char[len1+len2+2];
strcpy(newpath,path);
#if defined(_WIN32)
newpath[len1] = '\\';
newpath[len1+1] = 0;
#else
newpath[len1] = '/';
newpath[len1+1] = 0;
#endif
strcat(newpath,pot);
fp = fopen(newpath,"r");
if (fp) {
if (comm->me == 0) potential_date(fp,name);
rewind(fp);
}
delete [] newpath;
return fp;
}
/* ----------------------------------------------------------------------
strip off leading part of path, return just the filename
------------------------------------------------------------------------- */
const char *Force::potential_name(const char *path)
{
const char *pot;
if (path == NULL) return NULL;
#if defined(_WIN32)
// skip over the disk drive part of windows pathnames
if (isalpha(path[0]) && path[1] == ':')
path += 2;
#endif
for (pot = path; *path != '\0'; ++path) {
#if defined(_WIN32)
if ((*path == '\\') || (*path == '/')) pot = path + 1;
#else
if (*path == '/') pot = path + 1;
#endif
}
return pot;
}
/* ----------------------------------------------------------------------
read first line of potential file
if has DATE field, print following word
------------------------------------------------------------------------- */
void Force::potential_date(FILE *fp, const char *name)
{
char line[MAXLINE];
char *ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) return;
char *word;
word = strtok(line," \t\n\r\f");
while (word) {
if (strcmp(word,"DATE:") == 0) {
word = strtok(NULL," \t\n\r\f");
if (word == NULL) return;
if (screen)
fprintf(screen,"Reading potential file %s with DATE: %s\n",name,word);
if (logfile)
fprintf(logfile,"Reading potential file %s with DATE: %s\n",name,word);
return;
}
word = strtok(NULL," \t\n\r\f");
}
}
/* ----------------------------------------------------------------------
memory usage of force classes
------------------------------------------------------------------------- */
bigint Force::memory_usage()
{
bigint bytes = 0;
if (pair) bytes += static_cast<bigint> (pair->memory_usage());
if (bond) bytes += static_cast<bigint> (bond->memory_usage());
if (angle) bytes += static_cast<bigint> (angle->memory_usage());
if (dihedral) bytes += static_cast<bigint> (dihedral->memory_usage());
if (improper) bytes += static_cast<bigint> (improper->memory_usage());
if (kspace) bytes += static_cast<bigint> (kspace->memory_usage());
return bytes;
}
diff --git a/src/force.h b/src/force.h
index a3fca5102..54b661268 100644
--- a/src/force.h
+++ b/src/force.h
@@ -1,168 +1,168 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_FORCE_H
#define LMP_FORCE_H
#include "pointers.h"
#include "stdio.h"
#include <map>
#include <string>
namespace LAMMPS_NS {
class Force : protected Pointers {
public:
double boltz; // Boltzmann constant (eng/degree-K)
double hplanck; // Planck's constant (energy-time)
double mvv2e; // conversion of mv^2 to energy
double ftm2v; // conversion of ft/m to velocity
double mv2d; // conversion of mass/volume to density
double nktv2p; // conversion of NkT/V to pressure
double qqr2e; // conversion of q^2/r to energy
double qe2f; // conversion of qE to force
double vxmu2f; // conversion of vx dynamic-visc to force
double xxt2kmu; // conversion of xx/t to kinematic-visc
double dielectric; // dielectric constant
double qqrd2e; // q^2/r to energy w/ dielectric constant
double e_mass; // electron mass
double hhmrr2e; // conversion of (hbar)^2/(mr^2) to energy
double mvh2r; // conversion of mv/hbar to distance
// hbar = h/(2*pi)
double angstrom; // 1 angstrom in native units
double femtosecond; // 1 femtosecond in native units
double qelectron; // 1 electron charge abs() in native units
int newton,newton_pair,newton_bond; // Newton's 3rd law settings
class Pair *pair;
char *pair_style;
typedef Pair *(*PairCreator)(LAMMPS *);
std::map<std::string,PairCreator> *pair_map;
class Bond *bond;
char *bond_style;
class Angle *angle;
char *angle_style;
class Dihedral *dihedral;
char *dihedral_style;
class Improper *improper;
char *improper_style;
class KSpace *kspace;
char *kspace_style;
// index [0] is not used in these arrays
double special_lj[4]; // 1-2, 1-3, 1-4 prefactors for LJ
double special_coul[4]; // 1-2, 1-3, 1-4 prefactors for Coulombics
int special_angle; // 0 if defined angles are ignored
// 1 if only weight 1,3 atoms if in an angle
int special_dihedral; // 0 if defined dihedrals are ignored
// 1 if only weight 1,4 atoms if in a dihedral
int special_extra; // extra space for added bonds
Force(class LAMMPS *);
~Force();
void init();
void create_pair(const char *, int);
class Pair *new_pair(const char *, int, int &);
- class Pair *pair_match(const char *, int);
+ class Pair *pair_match(const char *, int, int nsub=0);
void create_bond(const char *, int);
class Bond *new_bond(const char *, int, int &);
class Bond *bond_match(const char *);
void create_angle(const char *, int);
class Angle *new_angle(const char *, int, int &);
void create_dihedral(const char *, int);
class Dihedral *new_dihedral(const char *, int, int &);
void create_improper(const char *, int);
class Improper *new_improper(const char *, int, int &);
class Improper *improper_match(const char *);
void create_kspace(int, char **, int);
class KSpace *new_kspace(int, char **, int, int &);
class KSpace *kspace_match(const char *, int);
void store_style(char *&, const char *, int);
void set_special(int, char **);
void bounds(char *, int, int &, int &, int nmin=1);
void boundsbig(char *, bigint, bigint &, bigint &, bigint nmin=1);
double numeric(const char *, int, char *);
int inumeric(const char *, int, char *);
bigint bnumeric(const char *, int, char *);
tagint tnumeric(const char *, int, char *);
FILE *open_potential(const char *);
const char *potential_name(const char *);
void potential_date(FILE *, const char *);
bigint memory_usage();
private:
template <typename T> static Pair *pair_creator(LAMMPS *);
};
}
#endif
/* ERROR/WARNING messages:
E: Unknown pair style
The choice of pair style is unknown.
E: Unknown bond style
The choice of bond style is unknown.
E: Unknown angle style
The choice of angle style is unknown.
E: Unknown dihedral style
The choice of dihedral style is unknown.
E: Unknown improper style
The choice of improper style is unknown.
E: Cannot yet use KSpace solver with grid with comm style tiled
This is current restriction in LAMMPS.
E: Unknown kspace style
The choice of kspace style is unknown.
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Numeric index is out of bounds
A command with an argument that specifies an integer or range of
integers is using a value that is less than 1 or greater than the
maximum allowed limit.
*/
diff --git a/src/output.cpp b/src/output.cpp
index 8c16cbfee..44892f5bd 100644
--- a/src/output.cpp
+++ b/src/output.cpp
@@ -1,822 +1,822 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "output.h"
#include "style_dump.h"
#include "atom.h"
#include "neighbor.h"
#include "input.h"
#include "variable.h"
#include "comm.h"
#include "update.h"
#include "group.h"
#include "domain.h"
#include "thermo.h"
#include "modify.h"
#include "compute.h"
#include "force.h"
#include "dump.h"
#include "write_restart.h"
#include "accelerator_cuda.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 1
/* ----------------------------------------------------------------------
initialize all output
------------------------------------------------------------------------- */
Output::Output(LAMMPS *lmp) : Pointers(lmp)
{
// create default computes for temp,pressure,pe
char **newarg = new char*[4];
newarg[0] = (char *) "thermo_temp";
newarg[1] = (char *) "all";
newarg[2] = (char *) "temp";
modify->add_compute(3,newarg,1);
newarg[0] = (char *) "thermo_press";
newarg[1] = (char *) "all";
newarg[2] = (char *) "pressure";
newarg[3] = (char *) "thermo_temp";
modify->add_compute(4,newarg,1);
newarg[0] = (char *) "thermo_pe";
newarg[1] = (char *) "all";
newarg[2] = (char *) "pe";
modify->add_compute(3,newarg,1);
delete [] newarg;
// create default Thermo class
newarg = new char*[1];
newarg[0] = (char *) "one";
thermo = new Thermo(lmp,1,newarg);
delete [] newarg;
thermo_every = 0;
var_thermo = NULL;
ndump = 0;
max_dump = 0;
every_dump = NULL;
next_dump = NULL;
last_dump = NULL;
var_dump = NULL;
ivar_dump = NULL;
dump = NULL;
restart_flag = restart_flag_single = restart_flag_double = 0;
restart_every_single = restart_every_double = 0;
last_restart = -1;
restart1 = restart2a = restart2b = NULL;
var_restart_single = var_restart_double = NULL;
restart = NULL;
}
/* ----------------------------------------------------------------------
free all memory
------------------------------------------------------------------------- */
Output::~Output()
{
if (thermo) delete thermo;
delete [] var_thermo;
memory->destroy(every_dump);
memory->destroy(next_dump);
memory->destroy(last_dump);
for (int i = 0; i < ndump; i++) delete [] var_dump[i];
memory->sfree(var_dump);
memory->destroy(ivar_dump);
for (int i = 0; i < ndump; i++) delete dump[i];
memory->sfree(dump);
delete [] restart1;
delete [] restart2a;
delete [] restart2b;
delete [] var_restart_single;
delete [] var_restart_double;
delete restart;
}
/* ---------------------------------------------------------------------- */
void Output::init()
{
thermo->init();
if (var_thermo) {
ivar_thermo = input->variable->find(var_thermo);
if (ivar_thermo < 0)
error->all(FLERR,"Variable name for thermo every does not exist");
if (!input->variable->equalstyle(ivar_thermo))
error->all(FLERR,"Variable for thermo every is invalid style");
}
for (int i = 0; i < ndump; i++) dump[i]->init();
for (int i = 0; i < ndump; i++)
if (every_dump[i] == 0) {
ivar_dump[i] = input->variable->find(var_dump[i]);
if (ivar_dump[i] < 0)
error->all(FLERR,"Variable name for dump every does not exist");
if (!input->variable->equalstyle(ivar_dump[i]))
error->all(FLERR,"Variable for dump every is invalid style");
}
if (restart_flag_single && restart_every_single == 0) {
ivar_restart_single = input->variable->find(var_restart_single);
if (ivar_restart_single < 0)
error->all(FLERR,"Variable name for restart does not exist");
if (!input->variable->equalstyle(ivar_restart_single))
error->all(FLERR,"Variable for restart is invalid style");
}
if (restart_flag_double && restart_every_double == 0) {
ivar_restart_double = input->variable->find(var_restart_double);
if (ivar_restart_double < 0)
error->all(FLERR,"Variable name for restart does not exist");
if (!input->variable->equalstyle(ivar_restart_double))
error->all(FLERR,"Variable for restart is invalid style");
}
}
/* ----------------------------------------------------------------------
perform output for setup of run/min
do dump first, so memory_usage will include dump allocation
do thermo last, so will print after memory_usage
memflag = 0/1 for printing out memory usage
------------------------------------------------------------------------- */
void Output::setup(int memflag)
{
bigint ntimestep = update->ntimestep;
// perform dump at start of run only if:
// current timestep is multiple of every and last dump not >= this step
// this is first run after dump created and firstflag is set
// note that variable freq will not write unless triggered by firstflag
// set next_dump to multiple of every or variable value
// set next_dump_any to smallest next_dump
// wrap dumps that invoke computes and variable eval with clear/add
// if dump not written now, use addstep_compute_all() since don't know
// what computes the dump write would invoke
// if no dumps, set next_dump_any to last+1 so will not influence next
int writeflag;
if (ndump && update->restrict_output == 0) {
for (int idump = 0; idump < ndump; idump++) {
if (dump[idump]->clearstep || every_dump[idump] == 0)
modify->clearstep_compute();
writeflag = 0;
if (every_dump[idump] && ntimestep % every_dump[idump] == 0 &&
last_dump[idump] != ntimestep) writeflag = 1;
if (last_dump[idump] < 0 && dump[idump]->first_flag == 1) writeflag = 1;
if (writeflag) {
dump[idump]->write();
last_dump[idump] = ntimestep;
}
if (every_dump[idump])
next_dump[idump] =
(ntimestep/every_dump[idump])*every_dump[idump] + every_dump[idump];
else {
bigint nextdump = static_cast<bigint>
(input->variable->compute_equal(ivar_dump[idump]));
if (nextdump <= ntimestep)
error->all(FLERR,"Dump every variable returned a bad timestep");
next_dump[idump] = nextdump;
}
if (dump[idump]->clearstep || every_dump[idump] == 0) {
if (writeflag) modify->addstep_compute(next_dump[idump]);
else modify->addstep_compute_all(next_dump[idump]);
}
if (idump) next_dump_any = MIN(next_dump_any,next_dump[idump]);
else next_dump_any = next_dump[0];
}
} else next_dump_any = update->laststep + 1;
// do not write restart files at start of run
// set next_restart values to multiple of every or variable value
// wrap variable eval with clear/add
// if no restarts, set next_restart to last+1 so will not influence next
if (restart_flag && update->restrict_output == 0) {
if (restart_flag_single) {
if (restart_every_single)
next_restart_single =
(ntimestep/restart_every_single)*restart_every_single +
restart_every_single;
else {
bigint nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_single));
if (nextrestart <= ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
next_restart_single = nextrestart;
}
} else next_restart_single = update->laststep + 1;
if (restart_flag_double) {
if (restart_every_double)
next_restart_double =
(ntimestep/restart_every_double)*restart_every_double +
restart_every_double;
else {
bigint nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_double));
if (nextrestart <= ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
next_restart_double = nextrestart;
}
} else next_restart_double = update->laststep + 1;
next_restart = MIN(next_restart_single,next_restart_double);
} else next_restart = update->laststep + 1;
// print memory usage unless being called between multiple runs
if (memflag) memory_usage();
// set next_thermo to multiple of every or variable eval if var defined
// insure thermo output on last step of run
// thermo may invoke computes so wrap with clear/add
modify->clearstep_compute();
thermo->header();
thermo->compute(0);
last_thermo = ntimestep;
if (var_thermo) {
next_thermo = static_cast<bigint>
(input->variable->compute_equal(ivar_thermo));
if (next_thermo <= ntimestep)
error->all(FLERR,"Thermo every variable returned a bad timestep");
} else if (thermo_every) {
next_thermo = (ntimestep/thermo_every)*thermo_every + thermo_every;
next_thermo = MIN(next_thermo,update->laststep);
} else next_thermo = update->laststep;
modify->addstep_compute(next_thermo);
// next = next timestep any output will be done
next = MIN(next_dump_any,next_restart);
next = MIN(next,next_thermo);
}
/* ----------------------------------------------------------------------
perform all output for this timestep
only perform output if next matches current step and last output doesn't
do dump/restart before thermo so thermo CPU time will include them
------------------------------------------------------------------------- */
void Output::write(bigint ntimestep)
{
// next_dump does not force output on last step of run
// wrap dumps that invoke computes or eval of variable with clear/add
// download data from GPU if necessary
if (next_dump_any == ntimestep) {
if (lmp->cuda && !lmp->cuda->oncpu) lmp->cuda->downloadAll();
for (int idump = 0; idump < ndump; idump++) {
if (next_dump[idump] == ntimestep) {
if (dump[idump]->clearstep || every_dump[idump] == 0)
modify->clearstep_compute();
if (last_dump[idump] != ntimestep) {
dump[idump]->write();
last_dump[idump] = ntimestep;
}
if (every_dump[idump]) next_dump[idump] += every_dump[idump];
else {
bigint nextdump = static_cast<bigint>
(input->variable->compute_equal(ivar_dump[idump]));
if (nextdump <= ntimestep)
error->all(FLERR,"Dump every variable returned a bad timestep");
next_dump[idump] = nextdump;
}
if (dump[idump]->clearstep || every_dump[idump] == 0)
modify->addstep_compute(next_dump[idump]);
}
if (idump) next_dump_any = MIN(next_dump_any,next_dump[idump]);
else next_dump_any = next_dump[0];
}
}
// next_restart does not force output on last step of run
// for toggle = 0, replace "*" with current timestep in restart filename
// download data from GPU if necessary
// eval of variable may invoke computes so wrap with clear/add
if (next_restart == ntimestep) {
if (lmp->cuda && !lmp->cuda->oncpu) lmp->cuda->downloadAll();
if (next_restart_single == ntimestep) {
char *file = new char[strlen(restart1) + 16];
char *ptr = strchr(restart1,'*');
*ptr = '\0';
sprintf(file,"%s" BIGINT_FORMAT "%s",restart1,ntimestep,ptr+1);
*ptr = '*';
if (last_restart != ntimestep) restart->write(file);
delete [] file;
if (restart_every_single) next_restart_single += restart_every_single;
else {
modify->clearstep_compute();
bigint nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_single));
if (nextrestart <= ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
next_restart_single = nextrestart;
modify->addstep_compute(next_restart_single);
}
}
if (next_restart_double == ntimestep) {
if (last_restart != ntimestep) {
if (restart_toggle == 0) {
restart->write(restart2a);
restart_toggle = 1;
} else {
restart->write(restart2b);
restart_toggle = 0;
}
}
if (restart_every_double) next_restart_double += restart_every_double;
else {
modify->clearstep_compute();
bigint nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_double));
if (nextrestart <= ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
next_restart_double = nextrestart;
modify->addstep_compute(next_restart_double);
}
}
last_restart = ntimestep;
next_restart = MIN(next_restart_single,next_restart_double);
}
// insure next_thermo forces output on last step of run
// thermo may invoke computes so wrap with clear/add
if (next_thermo == ntimestep) {
modify->clearstep_compute();
if (last_thermo != ntimestep) thermo->compute(1);
last_thermo = ntimestep;
if (var_thermo) {
next_thermo = static_cast<bigint>
(input->variable->compute_equal(ivar_thermo));
if (next_thermo <= ntimestep)
error->all(FLERR,"Thermo every variable returned a bad timestep");
} else if (thermo_every) next_thermo += thermo_every;
else next_thermo = update->laststep;
next_thermo = MIN(next_thermo,update->laststep);
modify->addstep_compute(next_thermo);
}
// next = next timestep any output will be done
next = MIN(next_dump_any,next_restart);
next = MIN(next,next_thermo);
}
/* ----------------------------------------------------------------------
force a snapshot to be written for all dumps
called from PRD and TAD
------------------------------------------------------------------------- */
void Output::write_dump(bigint ntimestep)
{
for (int idump = 0; idump < ndump; idump++) {
dump[idump]->write();
last_dump[idump] = ntimestep;
}
}
/* ----------------------------------------------------------------------
force restart file(s) to be written
called from PRD and TAD
------------------------------------------------------------------------- */
void Output::write_restart(bigint ntimestep)
{
if (restart_flag_single) {
char *file = new char[strlen(restart1) + 16];
char *ptr = strchr(restart1,'*');
*ptr = '\0';
sprintf(file,"%s" BIGINT_FORMAT "%s",restart1,ntimestep,ptr+1);
*ptr = '*';
restart->write(file);
delete [] file;
}
if (restart_flag_double) {
if (restart_toggle == 0) {
restart->write(restart2a);
restart_toggle = 1;
} else {
restart->write(restart2b);
restart_toggle = 0;
}
}
last_restart = ntimestep;
}
/* ----------------------------------------------------------------------
timestep is being changed, called by update->reset_timestep()
reset next timestep values for dumps, restart, thermo output
reset to smallest value >= new timestep
if next timestep set by variable evaluation,
eval for ntimestep-1, so current ntimestep can be returned if needed
no guarantee that variable can be evaluated for ntimestep-1
if it depends on computes, but live with that rare case for now
------------------------------------------------------------------------- */
void Output::reset_timestep(bigint ntimestep)
{
next_dump_any = MAXBIGINT;
for (int idump = 0; idump < ndump; idump++) {
if (every_dump[idump]) {
next_dump[idump] = (ntimestep/every_dump[idump])*every_dump[idump];
if (next_dump[idump] < ntimestep) next_dump[idump] += every_dump[idump];
} else {
- // ivar_dump may not be initialized.
+ // ivar_dump may not be initialized
if (ivar_dump[idump] < 0) {
ivar_dump[idump] = input->variable->find(var_dump[idump]);
if (ivar_dump[idump] < 0)
error->all(FLERR,"Variable name for dump every does not exist");
if (!input->variable->equalstyle(ivar_dump[idump]))
error->all(FLERR,"Variable for dump every is invalid style");
}
modify->clearstep_compute();
update->ntimestep--;
bigint nextdump = static_cast<bigint>
(input->variable->compute_equal(ivar_dump[idump]));
if (nextdump < ntimestep)
error->all(FLERR,"Dump every variable returned a bad timestep");
update->ntimestep++;
next_dump[idump] = nextdump;
modify->addstep_compute(next_dump[idump]);
}
next_dump_any = MIN(next_dump_any,next_dump[idump]);
}
if (restart_flag_single) {
if (restart_every_single) {
next_restart_single =
(ntimestep/restart_every_single)*restart_every_single;
if (next_restart_single < ntimestep)
next_restart_single += restart_every_single;
} else {
modify->clearstep_compute();
update->ntimestep--;
bigint nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_single));
if (nextrestart < ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
update->ntimestep++;
next_restart_single = nextrestart;
modify->addstep_compute(next_restart_single);
}
} else next_restart_single = update->laststep + 1;
if (restart_flag_double) {
if (restart_every_double) {
next_restart_double =
(ntimestep/restart_every_double)*restart_every_double;
if (next_restart_double < ntimestep)
next_restart_double += restart_every_double;
} else {
modify->clearstep_compute();
update->ntimestep--;
bigint nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_double));
if (nextrestart < ntimestep)
error->all(FLERR,"Restart variable returned a bad timestep");
update->ntimestep++;
next_restart_double = nextrestart;
modify->addstep_compute(next_restart_double);
}
} else next_restart_double = update->laststep + 1;
next_restart = MIN(next_restart_single,next_restart_double);
if (var_thermo) {
modify->clearstep_compute();
update->ntimestep--;
next_thermo = static_cast<bigint>
(input->variable->compute_equal(ivar_thermo));
if (next_thermo < ntimestep)
error->all(FLERR,"Thermo_modify every variable returned a bad timestep");
update->ntimestep++;
next_thermo = MIN(next_thermo,update->laststep);
modify->addstep_compute(next_thermo);
} else if (thermo_every) {
next_thermo = (ntimestep/thermo_every)*thermo_every;
if (next_thermo < ntimestep) next_thermo += thermo_every;
next_thermo = MIN(next_thermo,update->laststep);
} else next_thermo = update->laststep;
next = MIN(next_dump_any,next_restart);
next = MIN(next,next_thermo);
}
/* ----------------------------------------------------------------------
add a Dump to list of Dumps
------------------------------------------------------------------------- */
void Output::add_dump(int narg, char **arg)
{
if (narg < 5) error->all(FLERR,"Illegal dump command");
// error checks
for (int idump = 0; idump < ndump; idump++)
if (strcmp(arg[0],dump[idump]->id) == 0)
error->all(FLERR,"Reuse of dump ID");
int igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"Could not find dump group ID");
if (force->inumeric(FLERR,arg[3]) <= 0)
error->all(FLERR,"Invalid dump frequency");
// extend Dump list if necessary
if (ndump == max_dump) {
max_dump += DELTA;
dump = (Dump **)
memory->srealloc(dump,max_dump*sizeof(Dump *),"output:dump");
memory->grow(every_dump,max_dump,"output:every_dump");
memory->grow(next_dump,max_dump,"output:next_dump");
memory->grow(last_dump,max_dump,"output:last_dump");
var_dump = (char **)
memory->srealloc(var_dump,max_dump*sizeof(char *),"output:var_dump");
memory->grow(ivar_dump,max_dump,"output:ivar_dump");
}
- // make certain that per-dump data is properly initialized to suitable default values
+ // initialize per-dump data to suitable default values
every_dump[ndump] = 0;
last_dump[ndump] = -1;
var_dump[ndump] = NULL;
ivar_dump[ndump] = -1;
// create the Dump
if (0) return; // dummy line to enable else-if macro expansion
#define DUMP_CLASS
#define DumpStyle(key,Class) \
else if (strcmp(arg[2],#key) == 0) dump[ndump] = new Class(lmp,narg,arg);
#include "style_dump.h"
#undef DUMP_CLASS
else error->all(FLERR,"Unknown dump style");
every_dump[ndump] = force->inumeric(FLERR,arg[3]);
if (every_dump[ndump] <= 0) error->all(FLERR,"Illegal dump command");
last_dump[ndump] = -1;
var_dump[ndump] = NULL;
ndump++;
}
/* ----------------------------------------------------------------------
modify parameters of a Dump
------------------------------------------------------------------------- */
void Output::modify_dump(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal dump_modify command");
// find which dump it is
int idump;
for (idump = 0; idump < ndump; idump++)
if (strcmp(arg[0],dump[idump]->id) == 0) break;
if (idump == ndump) error->all(FLERR,"Cound not find dump_modify ID");
dump[idump]->modify_params(narg-1,&arg[1]);
}
/* ----------------------------------------------------------------------
delete a Dump from list of Dumps
------------------------------------------------------------------------- */
void Output::delete_dump(char *id)
{
// find which dump it is and delete it
int idump;
for (idump = 0; idump < ndump; idump++)
if (strcmp(id,dump[idump]->id) == 0) break;
if (idump == ndump) error->all(FLERR,"Could not find undump ID");
delete dump[idump];
delete [] var_dump[idump];
// move other dumps down in list one slot
for (int i = idump+1; i < ndump; i++) {
dump[i-1] = dump[i];
every_dump[i-1] = every_dump[i];
next_dump[i-1] = next_dump[i];
last_dump[i-1] = last_dump[i];
var_dump[i-1] = var_dump[i];
ivar_dump[i-1] = ivar_dump[i];
}
ndump--;
}
/* ----------------------------------------------------------------------
set thermo output frequency from input script
------------------------------------------------------------------------- */
void Output::set_thermo(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal thermo command");
if (strstr(arg[0],"v_") == arg[0]) {
delete [] var_thermo;
int n = strlen(&arg[0][2]) + 1;
var_thermo = new char[n];
strcpy(var_thermo,&arg[0][2]);
} else {
thermo_every = force->inumeric(FLERR,arg[0]);
if (thermo_every < 0) error->all(FLERR,"Illegal thermo command");
}
}
/* ----------------------------------------------------------------------
new Thermo style
------------------------------------------------------------------------- */
void Output::create_thermo(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal thermo_style command");
// don't allow this so that dipole style can safely allocate inertia vector
if (domain->box_exist == 0)
error->all(FLERR,"Thermo_style command before simulation box is defined");
// warn if previous thermo had been modified via thermo_modify command
if (thermo->modified && comm->me == 0)
error->warning(FLERR,"New thermo_style command, "
"previous thermo_modify settings will be lost");
// set thermo = NULL in case new Thermo throws an error
delete thermo;
thermo = NULL;
thermo = new Thermo(lmp,narg,arg);
}
/* ----------------------------------------------------------------------
setup restart capability for single or double output files
if only one filename and it contains no "*", then append ".*"
------------------------------------------------------------------------- */
void Output::create_restart(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal restart command");
int every = 0;
int varflag = 0;
if (strstr(arg[0],"v_") == arg[0]) varflag = 1;
else every = force->inumeric(FLERR,arg[0]);
if (!varflag && every == 0) {
if (narg != 1) error->all(FLERR,"Illegal restart command");
restart_flag = restart_flag_single = restart_flag_double = 0;
last_restart = -1;
delete restart;
restart = NULL;
delete [] restart1;
delete [] restart2a;
delete [] restart2b;
restart1 = restart2a = restart2b = NULL;
delete [] var_restart_single;
delete [] var_restart_double;
var_restart_single = var_restart_double = NULL;
return;
}
if (narg < 2) error->all(FLERR,"Illegal restart command");
int nfile = 0;
if (narg % 2 == 0) nfile = 1;
else nfile = 2;
if (nfile == 1) {
restart_flag = restart_flag_single = 1;
if (varflag) {
delete [] var_restart_single;
int n = strlen(&arg[0][2]) + 1;
var_restart_single = new char[n];
strcpy(var_restart_single,&arg[0][2]);
restart_every_single = 0;
} else restart_every_single = every;
int n = strlen(arg[1]) + 3;
restart1 = new char[n];
strcpy(restart1,arg[1]);
if (strchr(restart1,'*') == NULL) strcat(restart1,".*");
}
if (nfile == 2) {
restart_flag = restart_flag_double = 1;
if (varflag) {
delete [] var_restart_double;
int n = strlen(&arg[0][2]) + 1;
var_restart_double = new char[n];
strcpy(var_restart_double,&arg[0][2]);
restart_every_double = 0;
} else restart_every_double = every;
restart_toggle = 0;
int n = strlen(arg[1]) + 3;
restart2a = new char[n];
strcpy(restart2a,arg[1]);
n = strlen(arg[2]) + 1;
restart2b = new char[n];
strcpy(restart2b,arg[2]);
}
// check for multiproc output and an MPI-IO filename
// if 2 filenames, must be consistent
int multiproc;
if (strchr(arg[1],'%')) multiproc = comm->nprocs;
else multiproc = 0;
if (nfile == 2) {
if (multiproc && !strchr(arg[2],'%'))
error->all(FLERR,"Both restart files must use % or neither");
if (!multiproc && strchr(arg[2],'%'))
error->all(FLERR,"Both restart files must use % or neither");
}
int mpiioflag;
if (strstr(arg[1],".mpi")) mpiioflag = 1;
else mpiioflag = 0;
if (nfile == 2) {
if (mpiioflag && !strstr(arg[2],".mpi"))
error->all(FLERR,"Both restart files must use MPI-IO or neither");
if (!mpiioflag && strstr(arg[2],".mpi"))
error->all(FLERR,"Both restart files must use MPI-IO or neither");
}
// setup output style and process optional args
delete restart;
restart = new WriteRestart(lmp);
int iarg = nfile+1;
restart->multiproc_options(multiproc,mpiioflag,narg-iarg,&arg[iarg]);
}
/* ----------------------------------------------------------------------
sum and print memory usage
result is only memory on proc 0, not averaged across procs
------------------------------------------------------------------------- */
void Output::memory_usage()
{
bigint bytes = 0;
bytes += atom->memory_usage();
bytes += neighbor->memory_usage();
bytes += comm->memory_usage();
bytes += update->memory_usage();
bytes += force->memory_usage();
bytes += modify->memory_usage();
for (int i = 0; i < ndump; i++) bytes += dump[i]->memory_usage();
double mbytes = bytes/1024.0/1024.0;
if (comm->me == 0) {
if (screen)
fprintf(screen,"Memory usage per processor = %g Mbytes\n",mbytes);
if (logfile)
fprintf(logfile,"Memory usage per processor = %g Mbytes\n",mbytes);
}
}
diff --git a/src/version.h b/src/version.h
index 04b0c2166..c4415eb1b 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "5 Oct 2015"
+#define LAMMPS_VERSION "22 Oct 2015"