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<HTML>
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<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="24 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.">
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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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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
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&nbsp;
</nav>
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<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
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<a href="#">LAMMPS</a>
</nav>
<HR>
<H1></H1>
<CENTER><H3>LAMMPS Documentation
</H3></CENTER>
<CENTER><H4>24 Oct 2015 version
</H4></CENTER>
<H4>Version info:
</H4>
<P>The LAMMPS "version" is the date when it was released, such as 1 May
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="#">Docs</a> &raquo;</li>
<li>LAMMPS Documentation</li>
<li class="wy-breadcrumbs-aside">
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<a href="Section_commands.html#comm">Commands</a>
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<hr/>
<div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
<a href="Section_intro.html" class="btn btn-neutral float-right" title="1. Introduction" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
</div>
</div>
<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 &#8220;version&#8221; 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
@ -65,428 +174,300 @@ 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>
</OL>
<!-- 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&#8217;s in the LAMMPS distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps">2.2. Making LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps-with-optional-packages">2.3. Making LAMMPS with optional packages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-via-the-make-py-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-mgpt-package">4.26. USER-MGPT package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.27. USER-MISC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.28. USER-MOLFILE package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.29. USER-OMP package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.30. USER-PHONON package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.31. USER-QMMM package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.32. USER-QTB package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.33. USER-REAXC package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smd-package">4.34. USER-SMD package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smtbq-package">4.35. USER-SMTBQ package</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.36. USER-SPH package</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#measuring-performance">5.1. Measuring performance</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#general-strategies">5.2. General strategies</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#restarting-a-simulation">6.1. Restarting a simulation</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#d-simulations">6.2. 2d simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#charmm-amber-and-dreiding-force-fields">6.3. CHARMM, AMBER, and DREIDING force fields</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#running-multiple-simulations-from-one-input-script">6.4. Running multiple simulations from one input script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#granular-models">6.6. Granular models</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip3p-water-model">6.7. TIP3P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip4p-water-model">6.8. TIP4P water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#spc-water-model">6.9. SPC water model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#nemd-simulations">6.13. NEMD simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#finite-size-spherical-and-aspherical-particles">6.14. Finite-size spherical and aspherical particles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#output-from-lammps-thermo-dumps-computes-fixes-variables">6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#walls">6.17. Walls</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#elastic-constants">6.18. Elastic constants</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-viscosity">6.21. Calculating viscosity</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#using-chunks-to-calculate-system-properties">6.23. Using chunks to calculate system properties</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#setting-parameters-for-the-kspace-style-pppm-disp-command">6.24. Setting parameters for the <code class="docutils literal"><span class="pre">kspace_style</span> <span class="pre">pppm/disp</span></code> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#polarizable-models">6.25. Polarizable models</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#binary2txt-tool">9.2. binary2txt tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ch2lmp-tool">9.3. ch2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#chain-tool">9.4. chain tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#colvars-tools">9.5. colvars tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#createatoms-tool">9.6. createatoms tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#data2xmovie-tool">9.7. data2xmovie tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-database-tool">9.8. eam database tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-generate-tool">9.9. eam generate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eff-tool">9.10. eff tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#fep-tool">9.12. fep tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#i-pi-tool">9.13. i-pi tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ipp-tool">9.14. ipp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#kate-tool">9.15. kate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2arc-tool">9.16. lmp2arc tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#matlab-tool">9.19. matlab tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#micelle2d-tool">9.20. micelle2d tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#moltemplate-tool">9.21. moltemplate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#msi2lmp-tool">9.22. msi2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#phonon-tool">9.23. phonon tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#python-tool">9.26. python tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#reax-tool">9.27. reax tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#restart2data-tool">9.28. restart2data tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#vim-tool">9.29. vim tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmgrace-tool">9.30. xmgrace tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmovie-tool">9.31. xmovie tool</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#atom-styles">10.1. Atom styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#compute-styles">10.3. Compute styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-styles">10.4. Dump styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-custom-output-options">10.5. Dump custom output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#fix-styles">10.6. Fix styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#input-script-commands">10.7. Input script commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#kspace-computations">10.8. Kspace computations</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#minimization-styles">10.9. Minimization styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#region-styles">10.11. Region styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#body-styles">10.12. Body styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#variable-options">10.14. Variable options</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#extending-python-with-mpi-to-run-in-parallel">11.5. Extending Python with MPI to run in parallel</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_python.html#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#common-problems">12.1. Common problems</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#reporting-bugs">12.2. Reporting bugs</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error-warning-messages">12.3. Error &amp; warning messages</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error">12.4. Errors:</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#warnings">12.5. Warnings:</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a><ul>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#coming-attractions">13.1. Coming attractions</a></li>
<li class="toctree-l2"><a class="reference internal" href="Section_history.html#past-versions">13.2. Past versions</a></li>
</ul>
</li>
</ul>
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<META NAME="docnumber" CONTENT="26 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>
@ -21,7 +21,7 @@
<H1></H1>
LAMMPS-ICMS Documentation :c,h3
24 Oct 2015 version :c,h4
26 Oct 2015 version :c,h4
Version info: :h4
@ -100,7 +100,7 @@ it gives quick access to documentation for all LAMMPS commands.
.. toctree::
:maxdepth: 2
:numbered: // comment
:numbered:
Section_intro
Section_start
@ -120,8 +120,8 @@ it gives quick access to documentation for all LAMMPS commands.
Indices and tables
==================
* :ref:`genindex` // comment
* :ref:`search` // comment
* :ref:`genindex`
* :ref:`search`
END_RST -->

19
doc/displace_atoms.html
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@ -138,6 +138,7 @@
<pre class="literal-block">
<em>move</em> args = delx dely delz
delx,dely,delz = distance to displace in each dimension (distance units)
any of delx,dely,delz can be a variable (see below)
<em>ramp</em> args = ddim dlo dhi dim clo chi
ddim = <em>x</em> or <em>y</em> or <em>z</em>
dlo,dhi = displacement distance between dlo and dhi (distance units)
@ -174,7 +175,23 @@ on a lattice. For example, in a shear simulation, an initial strain
can be imposed on the system. Or two groups of atoms can be brought
into closer proximity.</p>
<p>The <em>move</em> style displaces the group of atoms by the specified 3d
distance.</p>
displacement vector. Any of the 3 quantities defining the vector
components can be specified as an equal-style or atom-style
<a class="reference internal" href="variable.html"><em>variable</em></a>. If the value is a variable, it should be
specified as v_name, where name is the variable name. In this case,
the variable will be evaluated, and its value(s) used for the
displacement(s). The scale factor implied by the <em>units</em> keyword will
also be applied to the variable result.</p>
<p>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. Atom-style variables can specify the same formulas as
equal-style variables but can also include per-atom values, such as
atom coordinates or per-atom values read from a file. Note that if
the variable references other <a class="reference internal" href="compute.html"><em>compute</em></a> or <a class="reference internal" href="fix.html"><em>fix</em></a>
commands, those values must be up-to-date for the current timestep.
See the &#8220;Variable Accuracy&#8221; section of the <a class="reference internal" href="variable.html"><em>variable</em></a>
doc page for more details.</p>
<p>The <em>ramp</em> style displaces atoms a variable amount in one dimension
depending on the atom&#8217;s coordinate in a (possibly) different
dimension. For example, the second example command displaces atoms in

20
doc/displace_atoms.txt
View File

@ -16,6 +16,7 @@ group-ID = ID of group of atoms to displace :ulb,l
style = {move} or {ramp} or {random} or {rotate} :l
{move} args = delx dely delz
delx,dely,delz = distance to displace in each dimension (distance units)
any of delx,dely,delz can be a variable (see below)
{ramp} args = ddim dlo dhi dim clo chi
ddim = {x} or {y} or {z}
dlo,dhi = displacement distance between dlo and dhi (distance units)
@ -48,7 +49,24 @@ can be imposed on the system. Or two groups of atoms can be brought
into closer proximity.
The {move} style displaces the group of atoms by the specified 3d
distance.
displacement vector. Any of the 3 quantities defining the vector
components can be specified as an equal-style or atom-style
"variable"_variable.html. If the value is a variable, it should be
specified as v_name, where name is the variable name. In this case,
the variable will be evaluated, and its value(s) used for the
displacement(s). The scale factor implied by the {units} keyword will
also be applied to the variable result.
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. Atom-style variables can specify the same formulas as
equal-style variables but can also include per-atom values, such as
atom coordinates or per-atom values read from a file. Note that if
the variable references other "compute"_compute.html or "fix"_fix.html
commands, those values must be up-to-date for the current timestep.
See the "Variable Accuracy" section of the "variable"_variable.html
doc page for more details.
The {ramp} style displaces atoms a variable amount in one dimension
depending on the atom's coordinate in a (possibly) different

4
doc/doc2/Manual.html.html
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@ -3,7 +3,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="23 Oct 2015 version">
<META NAME="docnumber" CONTENT="26 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>
@ -21,7 +21,7 @@
<P><CENTER><H3>LAMMPS Documentation
</H3></CENTER>
<CENTER><H4>23 Oct 2015 version
<CENTER><H4>26 Oct 2015 version
</H4></CENTER>
<H4>Version info:
</H4>

20
doc/doc2/displace_atoms.html
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@ -21,6 +21,7 @@
<PRE> <I>move</I> args = delx dely delz
delx,dely,delz = distance to displace in each dimension (distance units)
any of delx,dely,delz can be a variable (see below)
<I>ramp</I> args = ddim dlo dhi dim clo chi
ddim = <I>x</I> or <I>y</I> or <I>z</I>
dlo,dhi = displacement distance between dlo and dhi (distance units)
@ -55,7 +56,24 @@ can be imposed on the system. Or two groups of atoms can be brought
into closer proximity.
</P>
<P>The <I>move</I> style displaces the group of atoms by the specified 3d
distance.
displacement vector. Any of the 3 quantities defining the vector
components can be specified as an equal-style or atom-style
<A HREF = "variable.html">variable</A>. If the value is a variable, it should be
specified as v_name, where name is the variable name. In this case,
the variable will be evaluated, and its value(s) used for the
displacement(s). The scale factor implied by the <I>units</I> keyword will
also be applied to the variable result.
</P>
<P>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. Atom-style variables can specify the same formulas as
equal-style variables but can also include per-atom values, such as
atom coordinates or per-atom values read from a file. Note that if
the variable references other <A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A>
commands, those values must be up-to-date for the current timestep.
See the "Variable Accuracy" section of the <A HREF = "variable.html">variable</A>
doc page for more details.
</P>
<P>The <I>ramp</I> style displaces atoms a variable amount in one dimension
depending on the atom's coordinate in a (possibly) different

23
doc/doc2/timestep.html
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@ -25,9 +25,11 @@ timestep 0.003
<P><B>Description:</B>
</P>
<P>Set the timestep size for subsequent molecular dynamics simulations.
See the <A HREF = "units.html">units</A> command for a discussion of time units.
The default value for the timestep also depends on the choice of units
for the simulation; see the default values below.
See the <A HREF = "units.html">units</A> command for the time units associated with
each choice of units that LAMMPS supports.
</P>
<P>The default value for the timestep size also depends on the choice of
units for the simulation; see the default values below.
</P>
<P>When the <A HREF = "run_style.html">run style</A> is <I>respa</I>, dt is the timestep for
the outer loop (largest) timestep.
@ -41,9 +43,16 @@ the outer loop (largest) timestep.
</P>
<P><B>Default:</B>
</P>
timestep = 0.005 tau for units = lj<BR>
timestep = 1.0 fmsec for units = real<BR>
timestep = 0.001 psec for units = metal<BR>
timestep = 1.0e-8 sec (10 nsec) for units = si or cgs <BR>
<DIV ALIGN=left ><TABLE BORDER=1 >
<TR ALIGN="center"><TD >choice of <A HREF = "units.html">units</A> </TD><TD > time units </TD><TD > default timestep size</TD></TR>
<TR ALIGN="center"><TD >lj </TD><TD > tau </TD><TD > 0.005 tau</TD></TR>
<TR ALIGN="center"><TD >real </TD><TD > fmsec </TD><TD > 1.0 fmsec</TD></TR>
<TR ALIGN="center"><TD >metal </TD><TD > psec </TD><TD > 0.001 psec</TD></TR>
<TR ALIGN="center"><TD >si </TD><TD > sec </TD><TD > 1.0e-8 sec (10 nsec)</TD></TR>
<TR ALIGN="center"><TD >cgs </TD><TD > sec </TD><TD > 1.0e-8 sec (10 nsec)</TD></TR>
<TR ALIGN="center"><TD >electron </TD><TD > fmsec </TD><TD > 0.001 fmsec</TD></TR>
<TR ALIGN="center"><TD >micro </TD><TD > usec </TD><TD > 2.0 usec</TD></TR>
<TR ALIGN="center"><TD >nano </TD><TD > nsec </TD><TD > 0.00045 nsec
</TD></TR></TABLE></DIV>
</HTML>

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59
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@ -145,9 +145,10 @@ timestep 0.003
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Set the timestep size for subsequent molecular dynamics simulations.
See the <a class="reference internal" href="units.html"><em>units</em></a> command for a discussion of time units.
The default value for the timestep also depends on the choice of units
for the simulation; see the default values below.</p>
See the <a class="reference internal" href="units.html"><em>units</em></a> command for the time units associated with
each choice of units that LAMMPS supports.</p>
<p>The default value for the timestep size also depends on the choice of
units for the simulation; see the default values below.</p>
<p>When the <a class="reference internal" href="run_style.html"><em>run style</em></a> is <em>respa</em>, dt is the timestep for
the outer loop (largest) timestep.</p>
</div>
@ -163,13 +164,51 @@ the outer loop (largest) timestep.</p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<div class="line-block">
<div class="line">timestep = 0.005 tau for units = lj</div>
<div class="line">timestep = 1.0 fmsec for units = real</div>
<div class="line">timestep = 0.001 psec for units = metal</div>
<div class="line">timestep = 1.0e-8 sec (10 nsec) for units = si or cgs</div>
<div class="line"><br /></div>
</div>
<table border="1" class="docutils">
<colgroup>
<col width="48%" />
<col width="18%" />
<col width="34%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>choice of <a class="reference internal" href="units.html"><em>units</em></a></td>
<td>time units</td>
<td>default timestep size</td>
</tr>
<tr class="row-even"><td>lj</td>
<td>tau</td>
<td>0.005 tau</td>
</tr>
<tr class="row-odd"><td>real</td>
<td>fmsec</td>
<td>1.0 fmsec</td>
</tr>
<tr class="row-even"><td>metal</td>
<td>psec</td>
<td>0.001 psec</td>
</tr>
<tr class="row-odd"><td>si</td>
<td>sec</td>
<td>1.0e-8 sec (10 nsec)</td>
</tr>
<tr class="row-even"><td>cgs</td>
<td>sec</td>
<td>1.0e-8 sec (10 nsec)</td>
</tr>
<tr class="row-odd"><td>electron</td>
<td>fmsec</td>
<td>0.001 fmsec</td>
</tr>
<tr class="row-even"><td>micro</td>
<td>usec</td>
<td>2.0 usec</td>
</tr>
<tr class="row-odd"><td>nano</td>
<td>nsec</td>
<td>0.00045 nsec</td>
</tr>
</tbody>
</table>
</div>
</div>

21
doc/timestep.txt
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@ -22,9 +22,11 @@ timestep 0.003 :pre
[Description:]
Set the timestep size for subsequent molecular dynamics simulations.
See the "units"_units.html command for a discussion of time units.
The default value for the timestep also depends on the choice of units
for the simulation; see the default values below.
See the "units"_units.html command for the time units associated with
each choice of units that LAMMPS supports.
The default value for the timestep size also depends on the choice of
units for the simulation; see the default values below.
When the "run style"_run_style.html is {respa}, dt is the timestep for
the outer loop (largest) timestep.
@ -38,7 +40,12 @@ the outer loop (largest) timestep.
[Default:]
timestep = 0.005 tau for units = lj
timestep = 1.0 fmsec for units = real
timestep = 0.001 psec for units = metal
timestep = 1.0e-8 sec (10 nsec) for units = si or cgs :all(b)
choice of "units"_units.html : time units : default timestep size
lj : tau : 0.005 tau
real : fmsec : 1.0 fmsec
metal : psec : 0.001 psec
si : sec : 1.0e-8 sec (10 nsec)
cgs : sec : 1.0e-8 sec (10 nsec)
electron : fmsec : 0.001 fmsec
micro : usec : 2.0 usec
nano : nsec : 0.00045 nsec :tb(s=:,a=l,ea=c)

55
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@ -0,0 +1,55 @@
MGPT multi-ion potentials: Mo5.2 (Mo, version 5.2)
Author: John A. Moriarty
Potential data files: Mo5.2.mgpt.parmin Mo5.2.mgpt.potin
Volume mesh for potential data, with x = (vol/vol0)**(1/3):
x vol/vol0 vol(au) rws(au) dens(g/cc) dens/dens0
1.080 1.260 132.396 3.16176 8.120 0.794
1.070 1.225 128.752 3.13248 8.350 0.816
1.060 1.191 125.176 3.10321 8.589 0.840
1.050 1.158 121.666 3.07393 8.837 0.864
1.040 1.125 118.223 3.04465 9.094 0.889
1.030 1.093 114.846 3.01538 9.361 0.915
1.020 1.061 111.533 2.98610 9.639 0.942
1.010 1.030 108.285 2.95683 9.929 0.971
1.000 1.000 105.100 2.92755 10.229 1.000
0.990 0.970 101.978 2.89828 10.543 1.031
0.980 0.941 98.919 2.86900 10.869 1.062
0.970 0.913 95.922 2.83973 11.208 1.096
0.960 0.885 92.986 2.81045 11.562 1.130
0.950 0.857 90.110 2.78117 11.931 1.166
0.940 0.831 87.294 2.75190 12.316 1.204
0.930 0.804 84.538 2.72262 12.718 1.243
0.920 0.779 81.840 2.69335 13.137 1.284
0.910 0.754 79.200 2.66407 13.575 1.327
0.900 0.729 76.618 2.63480 14.032 1.372
0.890 0.705 74.092 2.60552 14.510 1.419
0.880 0.681 71.623 2.57625 15.011 1.467
0.870 0.659 69.209 2.54697 15.534 1.519
0.860 0.636 66.849 2.51770 16.083 1.572
0.850 0.614 64.545 2.48842 16.657 1.628
0.840 0.593 62.293 2.45914 17.259 1.687
Corresponding T = 0 bcc pressure range: -37 GPa to 418 GPa
General references to MGPT potentials:
J. A. Moriarty, Phys. Rev. B 42, 1609 (1990) and 49, 12431 (1994).
J. A. Moriarty, L. X. Benedict, J. N. Glosli, R. Q. Hood, D. A. Orlikowski, M. V. Patel,
P. Soderlind, F. H. Streitz, M. Tang, and L. H. Yang, J. Mater. Res. 21, 563 (2006).
Specific references to Mo5.2 potentials:
J. A. Moriarty, L. X. Benedict, J. N. Glosli, R. Q. Hood, D. A. Orlikowski, M. V. Patel,
P. Soderlind, F. H. Streitz, M. Tang, and L. H. Yang, J. Mater. Res. 21, 563 (2006).
L. H. Yang, M. Tang, and J. A. Moriarty, in Dislocations in Solids, Vol. 16, edited by
J. P. Hirth and L. Kubin (Elsevier, Amsterdam, 2010), p. 1.

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@ -0,0 +1,2 @@
0.84 1.08 0.01 105.10
6.00 -4.00 1.00 0.00 2

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@ -0,0 +1,49 @@
MGPT multi-ion potentials: Ta4 (Ta, version 4)
Author: John A. Moriarty
Potential data files: Ta4.mgpt.parmin Ta4.mgpt.potin
Volume mesh for potential data, with x = (vol/vol0)**(1/3):
x vol/vol0 vol(au) rws(au) dens(g/cc) dens/dens0
1.080 1.260 153.181 3.31924 13.237 0.794
1.060 1.191 144.828 3.25777 14.001 0.840
1.040 1.125 136.783 3.19631 14.824 0.889
1.020 1.061 129.043 3.13484 15.714 0.942
1.000 1.000 121.600 3.07337 16.675 1.000
0.980 0.941 114.449 3.01190 17.717 1.062
0.960 0.885 107.584 2.95044 18.848 1.130
0.940 0.831 100.999 2.88897 20.077 1.204
0.920 0.779 94.688 2.82750 21.415 1.284
0.900 0.729 88.646 2.76603 22.874 1.372
0.880 0.681 82.867 2.70457 24.470 1.467
0.860 0.636 77.344 2.64310 26.217 1.572
0.840 0.593 72.073 2.58163 28.134 1.687
0.820 0.551 67.046 2.52016 30.244 1.814
0.800 0.512 62.259 2.45870 32.569 1.953
0.780 0.475 57.706 2.39723 35.139 2.107
0.760 0.439 53.379 2.33576 37.987 2.278
Corresponding T = 0 bcc pressure range: -29 GPa to 780 GPa
General references to MGPT potentials:
J. A. Moriarty, Phys. Rev. B 42, 1609 (1990) and 49, 12431 (1994).
J. A. Moriarty, L. X. Benedict, J. N. Glosli, R. Q. Hood, D. A. Orlikowski, M. V. Patel,
P. Soderlind, F. H. Streitz, M. Tang, and L. H. Yang, J. Mater. Res. 21, 563 (2006).
Specific references to Ta4 potentials:
J. A. Moriarty, J. F. Belak, R. E. Rudd, P. Soderlind, F. H. Streitz, and L. H. Yang,
J. Phys.: Condens. Matter 14, 2825 (2002).
L. H. Yang, P. Soderlind, and J. A. Moriarty, Philos. Mag. A 81, 1355 (2001).
L. H. Yang, M. Tang, and J. A. Moriarty, in Dislocations in Solids, Vol. 16, edited by
J. P. Hirth and L. Kubin (Elsevier, Amsterdam, 2010), p. 1.

2
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@ -0,0 +1,2 @@
0.76 1.08 0.02 121.60
6.00 -4.00 1.00 0.00 2

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@ -0,0 +1,57 @@
MGPT multi-ion potentials: Ta6.8x (Ta, version 6.8x)
Author: John A. Moriarty
Potential data files: Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin
Volume mesh for potential data, with x = (vol/vol0)**(1/3):
x vol/vol0 vol(au) rws(au) dens(g/cc) dens/dens0
1.080 1.260 153.181 3.31924 13.237 0.794
1.070 1.225 148.965 3.28851 13.612 0.816
1.060 1.191 144.828 3.25777 14.001 0.840
1.050 1.158 140.767 3.22704 14.405 0.864
1.040 1.125 136.783 3.19631 14.824 0.889
1.030 1.093 132.876 3.16557 15.260 0.915
1.020 1.061 129.043 3.13484 15.714 0.942
1.010 1.030 125.285 3.10410 16.185 0.971
1.000 1.000 121.600 3.07337 16.675 1.000
0.990 0.970 117.988 3.04264 17.186 1.031
0.980 0.941 114.449 3.01190 17.717 1.062
0.970 0.913 110.981 2.98117 18.271 1.096
0.960 0.885 107.584 2.95044 18.848 1.130
0.950 0.857 104.257 2.91970 19.449 1.166
0.940 0.831 100.999 2.88897 20.077 1.204
0.930 0.804 97.810 2.85824 20.731 1.243
0.920 0.779 94.688 2.82750 21.415 1.284
0.910 0.754 91.634 2.79677 22.128 1.327
0.900 0.729 88.646 2.76603 22.874 1.372
0.890 0.705 85.724 2.73530 23.654 1.419
0.880 0.681 82.867 2.70457 24.470 1.467
0.870 0.659 80.074 2.67383 25.323 1.519
0.860 0.636 77.344 2.64310 26.217 1.572
0.850 0.614 74.678 2.61237 27.153 1.628
0.840 0.593 72.073 2.58163 28.134 1.687
0.830 0.572 69.529 2.55090 29.164 1.749
0.820 0.551 67.046 2.52016 30.244 1.814
0.810 0.531 64.623 2.48943 31.378 1.882
0.800 0.512 62.259 2.45870 32.569 1.953
Corresponding T = 0 bcc pressure range: -30 GPa to 422 GPa
General references to MGPT potentials:
J. A. Moriarty, Phys. Rev. B 42, 1609 (1990) and 49, 12431 (1994).
J. A. Moriarty, L. X. Benedict, J. N. Glosli, R. Q. Hood, D. A. Orlikowski, M. V. Patel,
P. Soderlind, F. H. Streitz, M. Tang, and L. H. Yang, J. Mater. Res. 21, 563 (2006).
Specific references to Ta6.8x potentials:
J. A. Moriarty and J. B. Haskins, Phys. Rev. B 90, 054113 (2014).
J. B. Haskins, J. A. Moriarty, and R. Q. Hood, Phys. Rev. B 86, 224104 (2012).

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@ -0,0 +1,2 @@
0.80 1.08 0.01 121.60
6.00 -4.00 1.00 0.00 2

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@ -0,0 +1,56 @@
MGPT multi-ion potentials: V6.1 (V, version 6.1)
Author: John A. Moriarty
Potential data files: V6.1.mgpt.parmin V6.1.mgpt.potin
Volume mesh for potential data, with x = (vol/vol0)**(1/3):
x vol/vol0 vol(au) rws(au) dens(g/cc) dens/dens0
1.080 1.260 117.443 3.03794 4.861 0.794
1.070 1.225 114.211 3.00981 4.998 0.816
1.060 1.191 111.038 2.98168 5.141 0.840
1.050 1.158 107.925 2.95355 5.289 0.864
1.040 1.125 104.871 2.92543 5.443 0.889
1.030 1.093 101.875 2.89730 5.604 0.915
1.020 1.061 98.936 2.86917 5.770 0.942
1.010 1.030 96.055 2.84104 5.943 0.971
1.000 1.000 93.230 2.81291 6.123 1.000
0.990 0.970 90.461 2.78478 6.311 1.031
0.980 0.941 87.747 2.75665 6.506 1.062
0.970 0.913 85.089 2.72852 6.709 1.096
0.960 0.885 82.484 2.70039 6.921 1.130
0.950 0.857 79.933 2.67226 7.142 1.166
0.940 0.831 77.435 2.64413 7.372 1.204
0.930 0.804 74.990 2.61601 7.612 1.243
0.920 0.779 72.597 2.58788 7.863 1.284
0.910 0.754 70.255 2.55975 8.126 1.327
0.900 0.729 67.965 2.53162 8.399 1.372
0.890 0.705 65.724 2.50349 8.686 1.419
0.880 0.681 63.534 2.47536 8.985 1.467
0.870 0.659 61.392 2.44723 9.299 1.519
0.860 0.636 59.300 2.41910 9.627 1.572
0.850 0.614 57.255 2.39097 9.971 1.628
0.840 0.593 55.258 2.36284 10.331 1.687
Corresponding T = 0 bcc pressure range: -23 GPa to 233 GPa
General references to MGPT potentials:
J. A. Moriarty, Phys. Rev. B 42, 1609 (1990) and 49, 12431 (1994).
J. A. Moriarty, L. X. Benedict, J. N. Glosli, R. Q. Hood, D. A. Orlikowski, M. V. Patel,
P. Soderlind, F. H. Streitz, M. Tang, and L. H. Yang, J. Mater. Res. 21, 563 (2006).
Specific references to V6.1 potentials:
J. A. Moriarty, J. N. Glosli, R. Q. Hood, J. E. Klepeis, D. A. Orlikowski, P. Soderlind,
and L. H. Yang, in TMS Annual Meeting Supplemental Proceedings Volume I: Materials
Processing and Properties (TMS, Warrendale, PA, 2008), p. 313.
L. H. Yang, M. Tang, and J. A. Moriarty, in Dislocations in Solids, Vol. 16, edited by
J. P. Hirth and L. Kubin (Elsevier, Amsterdam, 2010), p. 1.

2
potentials/V6.1.mgpt.parmin Normal file
View File

@ -0,0 +1,2 @@
0.84 1.08 0.01 93.23
6.00 -4.00 1.00 0.00 2

9701
potentials/V6.1.mgpt.potin Normal file
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File diff suppressed because it is too large Load Diff

11
src/KOKKOS/verlet_kokkos.cpp
View File

@ -58,17 +58,6 @@ void VerletKokkos::setup()
fprintf(screen," Unit style : %s\n", update->unit_style);
fprintf(screen," Current step: " BIGINT_FORMAT "\n", update->ntimestep);
fprintf(screen," Time step : %g\n", update->dt);
if (update->max_wall > 0) {
char outtime[128];
double totalclock = update->max_wall;
int seconds = fmod(totalclock,60.0);
totalclock = (totalclock - seconds) / 60.0;
int minutes = fmod(totalclock,60.0);
int hours = (totalclock - minutes) / 60.0;
sprintf(outtime," Max walltime: "
"%d:%02d:%02d\n", hours, minutes, seconds);
fputs(outtime,screen);
}
}
update->setupflag = 1;

16
src/USER-INTEL/verlet_intel.cpp
View File

@ -102,17 +102,6 @@ void VerletIntel::setup()
fprintf(screen," Unit style : %s\n", update->unit_style);
fprintf(screen," Current step: " BIGINT_FORMAT "\n", update->ntimestep);
fprintf(screen," Time step : %g\n", update->dt);
if (update->max_wall > 0) {
char outtime[128];
double totalclock = update->max_wall;
int seconds = fmod(totalclock,60.0);
totalclock = (totalclock - seconds) / 60.0;
int minutes = fmod(totalclock,60.0);
int hours = (totalclock - minutes) / 60.0;
sprintf(outtime," Max walltime: "
"%d:%02d:%02d\n", hours, minutes, seconds);
fputs(outtime,screen);
}
}
update->setupflag = 1;
@ -282,10 +271,6 @@ void VerletIntel::run(int n)
else sortflag = 0;
for (int i = 0; i < n; i++) {
if (update->time_expired()) {
update->nsteps = i;
return;
}
ntimestep = ++update->ntimestep;
ev_set(ntimestep);
@ -346,7 +331,6 @@ void VerletIntel::run(int n)
timer->stamp(Timer::MODIFY);
}
if (pair_compute_flag) {
force->pair->compute(eflag,vflag);
timer->stamp(Timer::PAIR);

76
src/displace_atoms.cpp
View File

@ -26,6 +26,9 @@
#include "random_park.h"
#include "error.h"
#include "force.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -34,7 +37,17 @@ enum{MOVE,RAMP,RANDOM,ROTATE};
/* ---------------------------------------------------------------------- */
DisplaceAtoms::DisplaceAtoms(LAMMPS *lmp) : Pointers(lmp) {}
DisplaceAtoms::DisplaceAtoms(LAMMPS *lmp) : Pointers(lmp)
{
mvec = NULL;
}
/* ---------------------------------------------------------------------- */
DisplaceAtoms::~DisplaceAtoms()
{
memory->destroy(mvec);
}
/* ---------------------------------------------------------------------- */
@ -53,9 +66,9 @@ void DisplaceAtoms::command(int narg, char **arg)
// group and style
int igroup = group->find(arg[0]);
igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find displace_atoms group ID");
int groupbit = group->bitmask[igroup];
groupbit = group->bitmask[igroup];
int style = -1;
if (strcmp(arg[1],"move") == 0) style = MOVE;
@ -85,25 +98,12 @@ void DisplaceAtoms::command(int narg, char **arg)
}
else xscale = yscale = zscale = 1.0;
// move atoms by 3-vector
// move atoms by 3-vector or specified variable(s)
if (style == MOVE) {
double delx = xscale*force->numeric(FLERR,arg[2]);
double dely = yscale*force->numeric(FLERR,arg[3]);
double delz = zscale*force->numeric(FLERR,arg[4]);
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
x[i][0] += delx;
x[i][1] += dely;
x[i][2] += delz;
}
}
move(0,arg[2],xscale);
move(1,arg[3],yscale);
move(2,arg[4],zscale);
}
// move atoms in ramped fashion
@ -286,6 +286,42 @@ void DisplaceAtoms::command(int narg, char **arg)
}
}
/* ----------------------------------------------------------------------
move atoms either by specified numeric displacement or variable evaluation
------------------------------------------------------------------------- */
void DisplaceAtoms::move(int idim, char *arg, double scale)
{
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (strstr(arg,"v_") != arg) {
double delta = scale*force->numeric(FLERR,arg);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) x[i][idim] += delta;
} else {
int n = strlen(&arg[2]) + 1;
char *vstr = new char[n];
strcpy(vstr,&arg[2]);
int ivar = input->variable->find(vstr);
if (ivar < 0)
error->all(FLERR,"Variable name for displace_atoms does not exist");
if (input->variable->equalstyle(ivar)) {
double delta = scale * input->variable->compute_equal(ivar);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) x[i][idim] += delta;
} else if (input->variable->atomstyle(ivar)) {
if (mvec == NULL) memory->create(mvec,nlocal,"displace_atoms:mvec");
input->variable->compute_atom(ivar,igroup,mvec,1,0);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) x[i][idim] += scale*mvec[i];
} else error->all(FLERR,"Variable for displace_atoms is invalid style");
}
}
/* ----------------------------------------------------------------------
parse optional parameters at end of displace_atoms input line
------------------------------------------------------------------------- */

5
src/displace_atoms.h
View File

@ -27,10 +27,15 @@ namespace LAMMPS_NS {
class DisplaceAtoms : protected Pointers {
public:
DisplaceAtoms(class LAMMPS *);
~DisplaceAtoms();
void command(int, char **);
private:
int igroup,groupbit;
int scaleflag;
double *mvec;
void move(int, char *, double);
void options(int, char **);
};

4
src/fix_addforce.cpp
View File

@ -112,7 +112,7 @@ FixAddForce::FixAddForce(LAMMPS *lmp, int narg, char **arg) :
force_flag = 0;
foriginal[0] = foriginal[1] = foriginal[2] = foriginal[3] = 0.0;
maxatom = atom->nmax;
maxatom = 1;
memory->create(sforce,maxatom,4,"addforce:sforce");
}
@ -371,6 +371,6 @@ double FixAddForce::compute_vector(int n)
double FixAddForce::memory_usage()
{
double bytes = 0.0;
if (varflag == ATOM) bytes = atom->nmax*4 * sizeof(double);
if (varflag == ATOM) bytes = maxatom*4 * sizeof(double);
return bytes;
}

4
src/fix_setforce.cpp
View File

@ -99,7 +99,7 @@ FixSetForce::FixSetForce(LAMMPS *lmp, int narg, char **arg) :
force_flag = 0;
foriginal[0] = foriginal[1] = foriginal[2] = 0.0;
maxatom = atom->nmax;
maxatom = 1;
memory->create(sforce,maxatom,3,"setforce:sforce");
}
@ -342,6 +342,6 @@ double FixSetForce::compute_vector(int n)
double FixSetForce::memory_usage()
{
double bytes = 0.0;
if (varflag == ATOM) bytes = atom->nmax*3 * sizeof(double);
if (varflag == ATOM) bytes = maxatom*3 * sizeof(double);
return bytes;
}

2
src/version.h
View File

@ -1 +1 @@
#define LAMMPS_VERSION "24 Oct 2015"
#define LAMMPS_VERSION "26 Oct 2015"