patch for allowing prd command to work with sorted atoms

Some documentation fixes and IPython updates

.gitignore

@@ -0,0 +1,34 @@
+*~
+*.o
+*.so
+*.cu_o
+*.ptx
+*_ptx.h
+*.a
+*.d
+*.x
+*.exe
+*.dll
+*.pyc
+__pycache__
+
+Obj_*
+log.lammps
+log.cite
+*.bz2
+*.gz
+*.tar
+.*.swp
+*.orig
+*.rej
+.vagrant
+\#*#
+.#*
+
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db

doc/.gitignore

@@ -0,0 +1 @@
+/html

doc/Eqs/compute_dpd.tex

@@ -1,12 +0,0 @@
-\documentstyle[12pt]{article}
-\pagestyle{empty}
-\begin{document}
-
-\begin{eqnarray*}
-   U^{cond} = \displaystyle\sum_{i=1}^{N} u_{i}^{cond} \\ 
-   U^{mech} = \displaystyle\sum_{i=1}^{N} u_{i}^{mech} \\
-   U = \displaystyle\sum_{i=1}^{N} (u_{i}^{cond} + u_{i}^{mech}) \\
-   \theta_{avg} = (\frac{1}{N}\displaystyle\sum_{i=1}^{N} \frac{1}{\theta_{i}})^{-1} \\
-\end{eqnarray*}                           
-
-\end{document}

doc/Eqs/fix_ti_rs_force.tex

@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\usepackage{amsmath}
-
-\begin{document}
-
-$$
-  F_{\text{total}} = \lambda F_{\text{int}}
-$$
-
-\end{document}

doc/Eqs/fix_ti_rs_function_1.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  \lambda(\tau) = \lambda_i + \tau \left( \lambda_f - \lambda_i \right)
-$$
-
-\end{document}

doc/Eqs/fix_ti_rs_function_2.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  \lambda(\tau) = \frac{\lambda_i}{1 + \tau \left( \frac{\lambda_i}{\lambda_f} - 1 \right)}
-$$
-
-\end{document}

doc/Eqs/fix_ti_rs_function_3.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  \lambda(\tau) = \frac{\lambda_i}{ 1 + \log_2(1+\tau) \left( \frac{\lambda_i}{\lambda_f} - 1 \right)}
-$$
-
-\end{document}

doc/Eqs/fix_ti_spring_force.tex

@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\usepackage{amsmath}
-
-\begin{document}
-
-$$
-  F_{\text{total}} = \left( 1-\lambda \right) F_{\text{solid}} + \lambda F_{\text{harm}}
-$$
-
-\end{document}

doc/Eqs/improper_umbrella.tex

@@ -1,13 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=\frac{1}{2}K\left( \frac{1+cos\omega_0}{sin\omega_0}\right) ^2 \left( cos\omega - cos\omega_0\right) \qquad \omega_0 \neq 0^o
-$$
-
-$$
-E=K\left( 1-cos\omega\right)  \qquad \omega_0 = 0^o
-$$
-
-\end{document}

doc/Makefile

@@ -0,0 +1,126 @@
+# Makefile for LAMMPS documentation
+
+SHELL 	      = /bin/bash
+SHA1          = $(shell echo $USER-$PWD | python utils/sha1sum.py)
+BUILDDIR      = /tmp/lammps-docs-$(SHA1)
+RSTDIR        = $(BUILDDIR)/rst
+VENV          = $(BUILDDIR)/docenv
+TXT2RST       = $(VENV)/bin/txt2rst
+
+PYTHON        = $(shell which python3)
+
+ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 1)
+$(error Python3 was not found! Please check README.md for further instructions)
+endif
+
+ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 1)
+$(error virtualenv was not found! Please check README.md for further instructions)
+endif
+
+SOURCES=$(wildcard src/*.txt)
+OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
+
+.PHONY: help clean-all clean html pdf old venv
+
+# ------------------------------------------
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       create HTML doc pages in html dir"
+	@echo "  pdf        create Manual.pdf and Developer.pdf in this dir"
+	@echo "  old        create old-style HTML doc pages in old dir"
+	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
+	@echo "  clean      remove all intermediate RST files"
+	@echo "  clean-all  reset the entire build environment"
+	@echo "  txt2html   build txt2html tool"
+
+# ------------------------------------------
+
+clean-all:
+	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
+
+clean:
+	rm -rf $(RSTDIR)
+
+html: $(OBJECTS)
+	@(\
+		. $(VENV)/bin/activate ;\
+		cp -r src/* $(RSTDIR)/ ;\
+		sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
+		deactivate ;\
+	)
+	-rm html/searchindex.js
+	@rm -rf html/_sources
+	@rm -rf html/PDF
+	@rm -rf html/USER
+	@cp -r src/PDF html/PDF
+	@cp -r src/USER html/USER
+	@rm -rf html/PDF/.[sg]*
+	@rm -rf html/USER/.[sg]*
+	@rm -rf html/USER/*/.[sg]*
+	@rm -rf html/USER/*/*.[sg]*
+	@echo "Build finished. The HTML pages are in doc/html."
+
+pdf: utils/txt2html/txt2html.exe
+	@(\
+		cd src; \
+		../utils/txt2html/txt2html.exe -b *.txt; \
+		htmldoc --batch lammps.book;          \
+		for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
+			do grep -q $$s lammps.book || \
+			echo doc file $$s missing in src/lammps.book; done; \
+		rm *.html; \
+		cd Developer; \
+		pdflatex developer; \
+		pdflatex developer; \
+		mv developer.pdf ../../Developer.pdf; \
+	)
+
+old: utils/txt2html/txt2html.exe
+	@rm -rf old
+	@mkdir old; mkdir old/Eqs; mkdir old/JPG; mkdir old/PDF
+	@cd src; ../utils/txt2html/txt2html.exe -b *.txt; \
+	  mv *.html ../old; \
+	  cp Eqs/*.jpg ../old/Eqs; \
+	  cp JPG/* ../old/JPG; \
+	  cp PDF/* ../old/PDF;
+
+fetch:
+	@rm -rf html_www Manual_www.pdf Developer_www.pdf
+	@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
+	@curl -s -o Developer_www.pdf http://lammps.sandia.gov/doc/Developer.pdf
+	@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
+	@tar xzf lammps-doc.tar.gz
+	@rm -f lammps-doc.tar.gz
+
+txt2html: utils/txt2html/txt2html.exe
+
+# ------------------------------------------
+
+utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
+	g++ -O -Wall -o $@ $<
+
+$(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
+	@(\
+		mkdir -p $(RSTDIR) ; \
+		. $(VENV)/bin/activate ;\
+		txt2rst $< > $@ ;\
+		deactivate ;\
+	)
+
+$(VENV):
+	@( \
+		virtualenv -p $(PYTHON) $(VENV); \
+		. $(VENV)/bin/activate; \
+		pip install Sphinx; \
+		pip install sphinxcontrib-images; \
+		deactivate;\
+	)
+
+$(TXT2RST): $(VENV)
+	@( \
+		. $(VENV)/bin/activate; \
+		(cd utils/converters;\
+		python setup.py develop);\
+		deactivate;\
+	)

doc/Manual.html

@@ -1,457 +0,0 @@
-
-
-<!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>LAMMPS Documentation &mdash; LAMMPS documentation</title>
-  
-
-  
-  
-
-  
-
-  
-  
-    
-
-  
-
-  
-  
-    <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
-  
-
-  
-    <link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
-  
-
-  
-    <link rel="top" title="LAMMPS documentation" href="index.html"/>
-        <link rel="next" title="1. Introduction" href="Section_intro.html"/> 
-
-  
-  <script src="_static/js/modernizr.min.js"></script>
-
-</head>
-
-<body class="wy-body-for-nav" role="document">
-
-  <div class="wy-grid-for-nav">
-
-    
-    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
-      <div class="wy-side-nav-search">
-        
-
-        
-          <a href="#" class="icon icon-home"> LAMMPS
-        
-
-        
-        </a>
-
-        
-<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>
-
-        
-      </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 &amp; scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
-</ul>
-
-          
-        
-      </div>
-      &nbsp;
-    </nav>
-
-    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
-
-      
-      <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
-        <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-        <a href="#">LAMMPS</a>
-      </nav>
-
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-      
-      <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">
-        
-          
-            <a href="http://lammps.sandia.gov">Website</a>
-            <a href="Section_commands.html#comm">Commands</a>
-        
-      </li>
-  </ul>
-  <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="feb-2016-version">
-<h2>16 Feb 2016 version<a class="headerlink" href="#feb-2016-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 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>
-<ul class="simple">
-<li>If you browse the HTML doc pages on the LAMMPS WWW site, they always
-describe the most current version of LAMMPS.</li>
-<li>If you browse the HTML doc pages included in your tarball, they
-describe the version you have.</li>
-<li>The <a class="reference external" href="Manual.pdf">PDF file</a> on the WWW site or in the tarball is updated
-about once per month.  This is because it is large, and we don&#8217;t want
-it to be part of every patch.</li>
-<li>There is also a <a class="reference external" href="Developer.pdf">Developer.pdf</a> file in the doc
-directory, which describes the internal structure and algorithms of
-LAMMPS.</li>
-</ul>
-<p>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
-Simulator.</p>
-<p>LAMMPS is a classical molecular dynamics simulation code designed to
-run efficiently on parallel computers.  It was developed at Sandia
-National Laboratories, a US Department of Energy facility, with
-funding from the DOE.  It is an open-source code, distributed freely
-under the terms of the GNU Public License (GPL).</p>
-<p>The primary developers of LAMMPS are <a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, Aidan
-Thompson, and Paul Crozier who can be contacted at
-sjplimp,athomps,pscrozi at sandia.gov.  The <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> at
-<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a> has more information about the code and its
-uses.</p>
-<hr class="docutils" />
-<p>The LAMMPS documentation is organized into the following sections.  If
-you find errors or omissions in this manual or have suggestions for
-useful information to add, please send an email to the developers so
-we can improve the LAMMPS documentation.</p>
-<p>Once you are familiar with LAMMPS, you may want to bookmark <a class="reference internal" href="Section_commands.html#comm"><span>this page</span></a> at Section_commands.html#comm since
-it gives quick access to documentation for all LAMMPS commands.</p>
-<p><a class="reference external" href="Manual.pdf">PDF file</a> of the entire manual, generated by
-<a class="reference external" href="http://freecode.com/projects/htmldoc">htmldoc</a></p>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-features">1.2. LAMMPS features</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#lammps-non-features">1.3. LAMMPS non-features</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#open-source-distribution">1.4. Open source distribution</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_start.html#what-s-in-the-lammps-distribution">2.1. What&#8217;s in the LAMMPS distribution</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps">2.2. Making LAMMPS</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_start.html#making-lammps-with-optional-packages">2.3. Making LAMMPS with optional packages</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_start.html#building-lammps-via-the-make-py-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-dpd-package">4.20. USER-DPD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.21. USER-DRUDE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.22. USER-EFF package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.23. USER-FEP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-h5md-package">4.24. USER-H5MD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.25. USER-INTEL package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.26. USER-LB package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-mgpt-package">4.27. USER-MGPT package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.28. USER-MISC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.29. USER-MOLFILE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.30. USER-OMP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.31. USER-PHONON package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.32. USER-QMMM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.33. USER-QTB package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.34. USER-REAXC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smd-package">4.35. USER-SMD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smtbq-package">4.36. USER-SMTBQ package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.37. USER-SPH package</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#measuring-performance">5.1. Measuring performance</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#general-strategies">5.2. General strategies</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_accelerate.html#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#restarting-a-simulation">6.1. Restarting a simulation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#d-simulations">6.2. 2d simulations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#charmm-amber-and-dreiding-force-fields">6.3. CHARMM, AMBER, and DREIDING force fields</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#running-multiple-simulations-from-one-input-script">6.4. Running multiple simulations from one input script</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#multi-replica-simulations">6.5. Multi-replica simulations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#granular-models">6.6. Granular models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip3p-water-model">6.7. TIP3P water model</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#tip4p-water-model">6.8. TIP4P water model</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#spc-water-model">6.9. SPC water model</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#coupling-lammps-to-other-codes">6.10. Coupling LAMMPS to other codes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#visualizing-lammps-snapshots">6.11. Visualizing LAMMPS snapshots</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#triclinic-non-orthogonal-simulation-boxes">6.12. Triclinic (non-orthogonal) simulation boxes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#nemd-simulations">6.13. NEMD simulations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#finite-size-spherical-and-aspherical-particles">6.14. Finite-size spherical and aspherical particles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#output-from-lammps-thermo-dumps-computes-fixes-variables">6.15. Output from LAMMPS (thermo, dumps, computes, fixes, variables)</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#thermostatting-barostatting-and-computing-temperature">6.16. Thermostatting, barostatting, and computing temperature</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#walls">6.17. Walls</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#elastic-constants">6.18. Elastic constants</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#library-interface-to-lammps">6.19. Library interface to LAMMPS</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-thermal-conductivity">6.20. Calculating thermal conductivity</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-viscosity">6.21. Calculating viscosity</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#calculating-a-diffusion-coefficient">6.22. Calculating a diffusion coefficient</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#using-chunks-to-calculate-system-properties">6.23. Using chunks to calculate system properties</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#setting-parameters-for-the-kspace-style-pppm-disp-command">6.24. Setting parameters for the <code class="docutils literal"><span class="pre">kspace_style</span> <span class="pre">pppm/disp</span></code> command</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#polarizable-models">6.25. Polarizable models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#adiabatic-core-shell-model">6.26. Adiabatic core/shell model</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_howto.html#drude-induced-dipoles">6.27. Drude induced dipoles</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#amber2lmp-tool">9.1. amber2lmp tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#binary2txt-tool">9.2. binary2txt tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ch2lmp-tool">9.3. ch2lmp tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#chain-tool">9.4. chain tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#colvars-tools">9.5. colvars tools</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#createatoms-tool">9.6. createatoms tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#data2xmovie-tool">9.7. data2xmovie tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-database-tool">9.8. eam database tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eam-generate-tool">9.9. eam generate tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#eff-tool">9.10. eff tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#emacs-tool">9.11. emacs tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#fep-tool">9.12. fep tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#i-pi-tool">9.13. i-pi tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#ipp-tool">9.14. ipp tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#kate-tool">9.15. kate tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2arc-tool">9.16. lmp2arc tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#matlab-tool">9.19. matlab tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#micelle2d-tool">9.20. micelle2d tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#moltemplate-tool">9.21. moltemplate tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#msi2lmp-tool">9.22. msi2lmp tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#phonon-tool">9.23. phonon tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#python-tool">9.26. python tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#reax-tool">9.27. reax tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#restart2data-tool">9.28. restart2data tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#vim-tool">9.29. vim tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmgrace-tool">9.30. xmgrace tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_tools.html#xmovie-tool">9.31. xmovie tool</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#atom-styles">10.1. Atom styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#compute-styles">10.3. Compute styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-styles">10.4. Dump styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#dump-custom-output-options">10.5. Dump custom output options</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#fix-styles">10.6. Fix styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#input-script-commands">10.7. Input script commands</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#kspace-computations">10.8. Kspace computations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#minimization-styles">10.9. Minimization styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#pairwise-potentials">10.10. Pairwise potentials</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#region-styles">10.11. Region styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#body-styles">10.12. Body styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#variable-options">10.14. Variable options</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_modify.html#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_python.html#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_python.html#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_python.html#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_python.html#extending-python-with-mpi-to-run-in-parallel">11.5. Extending Python with MPI to run in parallel</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_python.html#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_python.html#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_python.html#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#common-problems">12.1. Common problems</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#reporting-bugs">12.2. Reporting bugs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error-warning-messages">12.3. Error &amp; warning messages</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#error">12.4. Errors:</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_errors.html#warnings">12.5. Warnings:</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="Section_history.html#coming-attractions">13.1. Coming attractions</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_history.html#past-versions">13.2. Past versions</a></li>
-</ul>
-</li>
-</ul>
-</div>
-</div>
-</div>
-<div class="section" id="indices-and-tables">
-<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
-<ul class="simple">
-<li><a class="reference internal" href="genindex.html"><span>Index</span></a></li>
-<li><a class="reference internal" href="search.html"><span>Search Page</span></a></li>
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doc/Manual.txt

@@ -1,304 +0,0 @@
-<!-- HTML_ONLY -->
-<HEAD>
-<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="16 Feb 2016 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 Documentation :c,h3
-16 Feb 2016 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).
-
-If you browse the HTML doc pages on the LAMMPS WWW site, they always
-describe the most current version of LAMMPS. :ulb,l
-
-If you browse the HTML doc pages included in your tarball, they
-describe the version you have. :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:
-   
-   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`
-* :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
-:ole
-
-:link(intro_1,Section_intro.html#intro_1)
-:link(intro_2,Section_intro.html#intro_2)
-:link(intro_3,Section_intro.html#intro_3)
-:link(intro_4,Section_intro.html#intro_4)
-:link(intro_5,Section_intro.html#intro_5)
-
-:link(start_1,Section_start.html#start_1)
-:link(start_2,Section_start.html#start_2)
-:link(start_3,Section_start.html#start_3)
-:link(start_4,Section_start.html#start_4)
-:link(start_5,Section_start.html#start_5)
-:link(start_6,Section_start.html#start_6)
-:link(start_7,Section_start.html#start_7)
-:link(start_8,Section_start.html#start_8)
-:link(start_9,Section_start.html#start_9)
-
-:link(cmd_1,Section_commands.html#cmd_1)
-:link(cmd_2,Section_commands.html#cmd_2)
-:link(cmd_3,Section_commands.html#cmd_3)
-:link(cmd_4,Section_commands.html#cmd_4)
-:link(cmd_5,Section_commands.html#cmd_5)
-
-:link(pkg_1,Section_packages.html#pkg_1)
-:link(pkg_2,Section_packages.html#pkg_2)
-
-:link(acc_1,Section_accelerate.html#acc_1)
-:link(acc_2,Section_accelerate.html#acc_2)
-:link(acc_3,Section_accelerate.html#acc_3)
-:link(acc_4,Section_accelerate.html#acc_4)
-
-:link(howto_1,Section_howto.html#howto_1)
-:link(howto_2,Section_howto.html#howto_2)
-:link(howto_3,Section_howto.html#howto_3)
-:link(howto_4,Section_howto.html#howto_4)
-:link(howto_5,Section_howto.html#howto_5)
-:link(howto_6,Section_howto.html#howto_6)
-:link(howto_7,Section_howto.html#howto_7)
-:link(howto_8,Section_howto.html#howto_8)
-:link(howto_9,Section_howto.html#howto_9)
-:link(howto_10,Section_howto.html#howto_10)
-:link(howto_11,Section_howto.html#howto_11)
-:link(howto_12,Section_howto.html#howto_12)
-:link(howto_13,Section_howto.html#howto_13)
-:link(howto_14,Section_howto.html#howto_14)
-:link(howto_15,Section_howto.html#howto_15)
-:link(howto_16,Section_howto.html#howto_16)
-:link(howto_17,Section_howto.html#howto_17)
-:link(howto_18,Section_howto.html#howto_18)
-:link(howto_19,Section_howto.html#howto_19)
-:link(howto_20,Section_howto.html#howto_20)
-:link(howto_21,Section_howto.html#howto_21)
-:link(howto_22,Section_howto.html#howto_22)
-:link(howto_23,Section_howto.html#howto_23)
-:link(howto_24,Section_howto.html#howto_24)
-:link(howto_25,Section_howto.html#howto_25)
-:link(howto_26,Section_howto.html#howto_26)
-:link(howto_27,Section_howto.html#howto_27)
-
-:link(mod_1,Section_modify.html#mod_1)
-:link(mod_2,Section_modify.html#mod_2)
-:link(mod_3,Section_modify.html#mod_3)
-:link(mod_4,Section_modify.html#mod_4)
-:link(mod_5,Section_modify.html#mod_5)
-:link(mod_6,Section_modify.html#mod_6)
-:link(mod_7,Section_modify.html#mod_7)
-:link(mod_8,Section_modify.html#mod_8)
-:link(mod_9,Section_modify.html#mod_9)
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-:link(mod_12,Section_modify.html#mod_12)
-:link(mod_13,Section_modify.html#mod_13)
-:link(mod_14,Section_modify.html#mod_14)
-:link(mod_15,Section_modify.html#mod_15)
-
-:link(py_1,Section_python.html#py_1)
-:link(py_2,Section_python.html#py_2)
-:link(py_3,Section_python.html#py_3)
-:link(py_4,Section_python.html#py_4)
-:link(py_5,Section_python.html#py_5)
-:link(py_6,Section_python.html#py_6)
-
-:link(err_1,Section_errors.html#err_1)
-:link(err_2,Section_errors.html#err_2)
-:link(err_3,Section_errors.html#err_3)
-
-:link(hist_1,Section_history.html#hist_1)
-:link(hist_2,Section_history.html#hist_2)
-<!-- END_HTML_ONLY -->
-
-</BODY>

doc/README

@@ -0,0 +1,96 @@
+LAMMPS Documentation
+
+Depending on how you obtained LAMMPS, this directory has 2 or 3
+sub-directories and optionally 2 PDF files:
+
+src             content files for LAMMPS documentation
+html            HTML version of the LAMMPS manual (see html/Manual.html)
+tools           tools and settings for building the documentation
+Manual.pdf      large PDF version of entire manual
+Developer.pdf   small PDF with info about how LAMMPS is structured
+
+If you downloaded LAMMPS as a tarball from the web site, all these
+directories and files should be included.
+
+If you downloaded LAMMPS from the public SVN or Git repositories, then
+the HTML and PDF files are not included.  Instead you need to create
+them, in one of three ways:
+
+(a) You can "fetch" the current HTML and PDF files from the LAMMPS web
+site.  Just type "make fetch".  This should create a html_www dir and
+Manual_www.pdf/Developer_www.pdf files.  Note that if new LAMMPS
+features have been added more recently than the date of your version,
+the fetched documentation will include those changes (but your source
+code will not, unless you update your local repository).
+
+(b) You can build the HTML and PDF files yourself, by typing "make
+html" followed by "make pdf".  Note that the PDF make requires the
+HTML files already exist.  This requires various tools including
+Sphinx, which the build process will attempt to download and install
+on your system, if not already available.  See more details below.
+
+(c) You can genererate an older, simpler, less-fancy style of HTML
+documentation by typing "make old".  This will create an "old"
+directory.  This can be useful if (b) does not work on your box for
+some reason, or you want to quickly view the HTML version of a doc
+page you have created or edited yourself within the src directory.
+E.g. if you are planning to submit a new feature to LAMMPS.
+
+----------------
+
+The generation of all documentation is managed by the Makefile in this
+dir.
+
+Options:
+
+make html         # generate HTML in html dir using Sphinx
+make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
+                  #   in this dir via htmldoc and pdflatex
+make old          # generate old-style HTML pages in old dir via txt2html
+make fetch        # fetch HTML doc pages and 2 PDF files from web site
+                  #   as a tarball and unpack into html dir and 2 PDFs
+make clean        # remove intermediate RST files created by HTML build
+make clean-all    # remove entire build folder and any cached data
+
+----------------
+
+Installing prerequisites for HTML build
+
+To run the HTML documention build toolchain, Python 3 and virtualenv
+have to be installed.  Here are instructions for common setups:
+
+# Ubuntu
+
+sudo apt-get install python-virtualenv
+
+# Fedora (up to version 21)
+# Red Hat Enterprise Linux or CentOS (up to version 7.x)
+
+sudo yum install python3-virtualenv
+
+# Fedora (since version 22)
+
+sudo dnf install python3-virtualenv
+
+# MacOS X
+
+## Python 3
+
+Download the latest Python 3 MacOS X package from
+https://www.python.org and install it.  This will install both Python
+3 and pip3.
+
+## virtualenv
+
+Once Python 3 is installed, open a Terminal and type
+
+pip3 install virtualenv
+
+This will install virtualenv from the Python Package Index.
+
+----------------
+
+Installing prerequisites for PDF build
+
+
+

doc/Scripts/correlate.py

@@ -1,89 +0,0 @@
-#!/usr/bin/env python
-"""
-  function: 
-    parse the block of thermo data in a lammps logfile and perform auto- and 
-    cross correlation of the specified column data.  The total sum of the 
-    correlation is also computed which can be converted to an integral by 
-    multiplying by the timestep. 
-  output:
-    standard output contains column data for the auto- & cross correlations 
-    plus the total sum of each. Note, only the upper triangle of the 
-    correlation matrix is computed.
-  usage: 
-    correlate.py [-c col] <-c col2> <-s max_correlation_time>  [logfile] 
-"""
-import sys
-import re
-import array
-
-# parse command line
-
-maxCorrelationTime = 0
-cols = array.array("I")
-nCols = 0
-args = sys.argv[1:]
-index = 0
-while index < len(args):
-  arg = args[index]
-  index += 1
-  if   (arg == "-c"):
-    cols.append(int(args[index])-1)
-    nCols += 1
-    index += 1
-  elif (arg == "-s"):
-    maxCorrelationTime = int(args[index])
-    index += 1
-  else :
-    filename = arg
-if (nCols < 1): raise RuntimeError, 'no data columns requested'
-data = [array.array("d")]
-for s in range(1,nCols)  : data.append( array.array("d") )
-
-# read data block from log file
-
-start = False
-input = open(filename)
-nSamples = 0
-pattern = re.compile('\d')
-line = input.readline()
-while line :
-  columns = line.split()
-  if (columns and pattern.match(columns[0])) :
-    for i in range(nCols): 
-      data[i].append( float(columns[cols[i]]) )
-    nSamples += 1
-    start = True
-  else :
-     if (start) : break
-  line = input.readline()
-print "# read :",nSamples," samples of ", nCols," data"
-if( maxCorrelationTime < 1): maxCorrelationTime = int(nSamples/2);
- 
-# correlate and integrate
-
-correlationPairs = []
-for i in range(0,nCols):
-  for j in range(i,nCols): # note only upper triangle of the correlation matrix
-    correlationPairs.append([i,j])
-header = "# "
-for k in range(len(correlationPairs)):
-  i = str(correlationPairs[k][0]+1)
-  j = str(correlationPairs[k][1]+1)
-  header += " C"+i+j+" sum_C"+i+j
-print header
-nCorrelationPairs = len(correlationPairs)
-sum = [0.0] * nCorrelationPairs
-for s in range(maxCorrelationTime)  :
-  correlation = [0.0] * nCorrelationPairs
-  nt = nSamples-s
-  for t in range(0,nt)  :
-    for p in range(nCorrelationPairs):
-      i = correlationPairs[p][0]
-      j = correlationPairs[p][1]
-      correlation[p] += data[i][t]*data[j][s+t]
-  output = ""
-  for p in range(0,nCorrelationPairs):
-    correlation[p] /= nt
-    sum[p] += correlation[p]
-    output += str(correlation[p]) + " " + str(sum[p]) + " "
-  print output

doc/Section_accelerate.html

@@ -1,642 +0,0 @@
-
-
-<!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>5. Accelerating LAMMPS performance &mdash; LAMMPS documentation</title>
-  
-
-  
-  
-
-  
-
-  
-  
-    
-
-  
-
-  
-  
-    <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
-  
-
-  
-    <link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
-  
-
-  
-    <link rel="top" title="LAMMPS documentation" href="index.html"/>
-        <link rel="next" title="6. How-to discussions" href="Section_howto.html"/>
-        <link rel="prev" title="4. Packages" href="Section_packages.html"/> 
-
-  
-  <script src="_static/js/modernizr.min.js"></script>
-
-</head>
-
-<body class="wy-body-for-nav" role="document">
-
-  <div class="wy-grid-for-nav">
-
-    
-    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
-      <div class="wy-side-nav-search">
-        
-
-        
-          <a href="Manual.html" class="icon icon-home"> LAMMPS
-        
-
-        
-        </a>
-
-        
-<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>
-
-        
-      </div>
-
-      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
-        
-          
-          
-              <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="">5. Accelerating LAMMPS performance</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#measuring-performance">5.1. Measuring performance</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#general-strategies">5.2. General strategies</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#examples">5.4.1. Examples</a></li>
-</ul>
-</li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
-</ul>
-
-          
-        
-      </div>
-      &nbsp;
-    </nav>
-
-    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
-
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-        <a href="Manual.html">LAMMPS</a>
-      </nav>
-
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-      <div class="wy-nav-content">
-        <div class="rst-content">
-          <div role="navigation" aria-label="breadcrumbs navigation">
-  <ul class="wy-breadcrumbs">
-    <li><a href="Manual.html">Docs</a> &raquo;</li>
-      
-    <li>5. Accelerating LAMMPS performance</li>
-      <li class="wy-breadcrumbs-aside">
-        
-          
-            <a href="http://lammps.sandia.gov">Website</a>
-            <a href="Section_commands.html#comm">Commands</a>
-        
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-  </ul>
-  <hr/>
-  
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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&#8217;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 &#8220;Communication&#8221; or &#8220;Other&#8221; 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 note">
-<p class="first admonition-title">Note</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>.</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, 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>
-</tbody>
-</table>
-<div class="line-block">
-<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, &lt;br&gt;
-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>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 note">
-<p class="first admonition-title">Note</p>
-<p class="last">With a few exceptions, you can build a single LAMMPS 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 &#8220;cuda&#8221; or &#8220;gpu&#8221; 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 &#8220;intel&#8221; 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 &#8220;offload&#8221; 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 &#8220;kk&#8221; 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 &#8220;native&#8221; mode.  The speed-up depends on a variety of
-factors, as discussed on the KOKKOS accelerator page.</li>
-<li>Styles with an &#8220;omp&#8221; 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 &#8220;opt&#8221; 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 &#8220;hybrid&#8221; 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 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>
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doc/Section_accelerate.txt

@@ -1,415 +0,0 @@
-"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)
-
-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
-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, OPT packages |
-re-build LAMMPS |
-  make machine |
-run a LAMMPS simulation |
-  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=|)
-
-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.
-
-NOTE: With a few exceptions, you can build a single LAMMPS 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 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.

doc/Section_example.html

@@ -1,401 +0,0 @@
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-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
-</ul>
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-            <a href="Section_commands.html#comm">Commands</a>
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-           <div itemprop="articleBody">
-            
-  <div class="section" id="example-problems">
-<h1>7. Example problems<a class="headerlink" href="#example-problems" title="Permalink to this headline">¶</a></h1>
-<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 &#8220;foo&#8221;.</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 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 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></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 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>
-<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
-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 class="reference internal" href="Section_start.html"><em>Section_start.html</em></a> file for more info about user
-packages.</p>
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doc/Section_example.txt

@@ -1,124 +0,0 @@
-"Previous Section"_Section_howto.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_perf.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-7. Example problems :h3
-
-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".
-
-For examples that use input data files, many of them were produced by
-"Pizza.py"_http://pizza.sandia.gov or setup tools described in the
-"Additional Tools"_Section_tools.html section of the LAMMPS
-documentation and provided with the LAMMPS distribution.
-
-If you uncomment the "dump"_dump.html command in the input script, a
-text dump file will be produced, which can be animated by various
-"visualization programs"_http://lammps.sandia.gov/viz.html.  It can
-also be animated using the xmovie tool described in the "Additional
-Tools"_Section_tools.html section of the LAMMPS documentation.
-
-If you uncomment the "dump image"_dump.html 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
-"dump image"_dump_image.html doc page.
-
-Animations of many of these examples can be viewed on the Movies
-section of the "LAMMPS WWW Site"_lws.
-
-These are the sample problems in the examples sub-directories:
-
-balance:  dynamic load balancing, 2d system
-body:     body particles, 2d system
-colloid:  big colloid particles in a small particle solvent, 2d system
-comb:	  models using the COMB potential
-crack:	  crack propagation in a 2d solid
-cuda:     use of the USER-CUDA package for GPU acceleration
-dipole:   point dipolar particles, 2d system
-dreiding: methanol via Dreiding FF
-eim:      NaCl using the EIM potential
-ellipse:  ellipsoidal particles in spherical solvent, 2d system
-flow:	  Couette and Poiseuille flow in a 2d channel
-friction: frictional contact of spherical asperities between 2d surfaces
-gpu:      use of the GPU package for GPU acceleration
-hugoniostat: Hugoniostat shock dynamics
-indent:	  spherical indenter into a 2d solid
-intel:    use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor
-kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
-line:     line segment particles in 2d rigid bodies
-meam:	  MEAM test for SiC and shear (same as shear examples)
-melt:	  rapid melt of 3d LJ system
-micelle:  self-assembly of small lipid-like molecules into 2d bilayers
-min:	  energy minimization of 2d LJ melt
-msst:	  MSST shock dynamics
-nb3b:     use of nonbonded 3-body harmonic pair style
-neb:	  nudged elastic band (NEB) calculation for barrier finding
-nemd:	  non-equilibrium MD of 2d sheared system
-obstacle: flow around two voids in a 2d channel
-peptide:  dynamics of a small solvated peptide chain (5-mer)
-peri:	  Peridynamic model of cylinder impacted by indenter
-pour:     pouring of granular particles into a 3d box, then chute flow
-prd:      parallel replica dynamics of vacancy diffusion in bulk Si
-qeq:      use of the QEQ pacakge for charge equilibration
-reax:     RDX and TATB models using the ReaxFF
-rigid:    rigid bodies modeled as independent or coupled
-shear:    sideways shear applied to 2d solid, with and without a void
-snap:     NVE dynamics for BCC tantalum crystal using SNAP potential
-srd:      stochastic rotation dynamics (SRD) particles as solvent
-tad:      temperature-accelerated dynamics of vacancy diffusion in bulk Si
-tri:      triangular particles in rigid bodies :tb(s=:)
-vashishta: models using the Vashishta potential
-
-Here is how you might run and visualize one of the sample problems:
-
-cd indent
-cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
-lmp_linux -in in.indent            # run the problem :pre
-
-Running the simulation produces the files {dump.indent} and
-{log.lammps}.  You can visualize the dump file as follows:
-
-../../tools/xmovie/xmovie -scale dump.indent :pre
-
-If you uncomment the "dump image"_dump_image.html 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
-"dump image"_dump_image.html doc page for more details.  E.g. this
-Imagemagick command would create a GIF file suitable for viewing in a
-browser.
-
-% convert -loop 1 *.jpg foo.gif :pre
-
-:line
-
-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.
-
-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.
-
-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.
-
-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
-"Section_start.html"_Section_start.html file for more info about user
-packages.

doc/Section_history.html

@@ -1,313 +0,0 @@
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-<li class="toctree-l1 current"><a class="current reference internal" href="">13. Future and history</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#coming-attractions">13.1. Coming attractions</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#past-versions">13.2. Past versions</a></li>
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-  <div class="section" id="future-and-history">
-<h1>13. Future and history<a class="headerlink" href="#future-and-history" title="Permalink to this headline">¶</a></h1>
-<p>This section lists features we plan to add to LAMMPS, features of
-previous versions of LAMMPS, and features of other parallel molecular
-dynamics codes our group has distributed.</p>
-<div class="line-block">
-<div class="line">13.1 <a class="reference internal" href="#hist-1"><span>Coming attractions</span></a></div>
-<div class="line">13.2 <a class="reference internal" href="#hist-2"><span>Past versions</span></a></div>
-<div class="line"><br /></div>
-</div>
-<div class="section" id="coming-attractions">
-<span id="hist-1"></span><h2>13.1. Coming attractions<a class="headerlink" href="#coming-attractions" title="Permalink to this headline">¶</a></h2>
-<p>The <a class="reference external" href="http://lammps.sandia.gov/future.html">Wish list link</a> on the
-LAMMPS WWW page gives a list of features we are hoping to add to
-LAMMPS in the future, including contact names of individuals you can
-email if you are interested in contributing to the developement or
-would be a future user of that feature.</p>
-<p>You can also send <a class="reference external" href="http://lammps.sandia.gov/authors.html">email to the developers</a> if you want to add
-your wish to the list.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="past-versions">
-<span id="hist-2"></span><h2>13.2. Past versions<a class="headerlink" href="#past-versions" title="Permalink to this headline">¶</a></h2>
-<p>LAMMPS development began in the mid 1990s under a cooperative research
-&amp; development agreement (CRADA) between two DOE labs (Sandia and LLNL)
-and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
-to develop a large-scale parallel classical MD code; the coding effort
-was led by Steve Plimpton at Sandia.</p>
-<p>After the CRADA ended, a final F77 version, LAMMPS 99, was
-released. As development of LAMMPS continued at Sandia, its memory
-management was converted to F90; a final F90 version was released as
-LAMMPS 2001.</p>
-<p>The current LAMMPS is a rewrite in C++ and was first publicly released
-as an open source code in 2004. It includes many new features beyond
-those in LAMMPS 99 or 2001. It also includes features from older
-parallel MD codes written at Sandia, namely ParaDyn, Warp, and
-GranFlow (see below).</p>
-<p>In late 2006 we began merging new capabilities into LAMMPS that were
-developed by Aidan Thompson at Sandia for his MD code GRASP, which has
-a parallel framework similar to LAMMPS. Most notably, these have
-included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF -
-and the associated charge-equilibration routines needed for ReaxFF.</p>
-<p>The <a class="reference external" href="http://lammps.sandia.gov/history.html">History link</a> on the
-LAMMPS WWW page gives a timeline of features added to the
-C++ open-source version of LAMMPS over the last several years.</p>
-<p>These older codes are available for download from the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW site</a>, except for Warp &amp; GranFlow which were primarily used
-internally.  A brief listing of their features is given here.</p>
-<p>LAMMPS 2001</p>
-<ul class="simple">
-<li>F90 + MPI</li>
-<li>dynamic memory</li>
-<li>spatial-decomposition parallelism</li>
-<li>NVE, NVT, NPT, NPH, rRESPA integrators</li>
-<li>LJ and Coulombic pairwise force fields</li>
-<li>all-atom, united-atom, bead-spring polymer force fields</li>
-<li>CHARMM-compatible force fields</li>
-<li>class 2 force fields</li>
-<li>3d/2d Ewald &amp; PPPM</li>
-<li>various force and temperature constraints</li>
-<li>SHAKE</li>
-<li>Hessian-free truncated-Newton minimizer</li>
-<li>user-defined diagnostics</li>
-</ul>
-<p>LAMMPS 99</p>
-<ul class="simple">
-<li>F77 + MPI</li>
-<li>static memory allocation</li>
-<li>spatial-decomposition parallelism</li>
-<li>most of the LAMMPS 2001 features with a few exceptions</li>
-<li>no 2d Ewald &amp; PPPM</li>
-<li>molecular force fields are missing a few CHARMM terms</li>
-<li>no SHAKE</li>
-</ul>
-<p>Warp</p>
-<ul class="simple">
-<li>F90 + MPI</li>
-<li>spatial-decomposition parallelism</li>
-<li>embedded atom method (EAM) metal potentials + LJ</li>
-<li>lattice and grain-boundary atom creation</li>
-<li>NVE, NVT integrators</li>
-<li>boundary conditions for applying shear stresses</li>
-<li>temperature controls for actively sheared systems</li>
-<li>per-atom energy and centro-symmetry computation and output</li>
-</ul>
-<p>ParaDyn</p>
-<ul class="simple">
-<li>F77 + MPI</li>
-<li>atom- and force-decomposition parallelism</li>
-<li>embedded atom method (EAM) metal potentials</li>
-<li>lattice atom creation</li>
-<li>NVE, NVT, NPT integrators</li>
-<li>all serial DYNAMO features for controls and constraints</li>
-</ul>
-<p>GranFlow</p>
-<ul class="simple">
-<li>F90 + MPI</li>
-<li>spatial-decomposition parallelism</li>
-<li>frictional granular potentials</li>
-<li>NVE integrator</li>
-<li>boundary conditions for granular flow and packing and walls</li>
-<li>particle insertion</li>
-</ul>
-</div>
-</div>
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doc/Section_history.txt

@@ -1,123 +0,0 @@
-"Previous Section"_Section_errors.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Manual.html :c
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-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-13. Future and history :h3
-
-This section lists features we plan to add to LAMMPS, features of
-previous versions of LAMMPS, and features of other parallel molecular
-dynamics codes our group has distributed.
-
-13.1 "Coming attractions"_#hist_1
-13.2 "Past versions"_#hist_2 :all(b)
-
-:line
-:line
-
-13.1 Coming attractions :h4,link(hist_1)
-
-The "Wish list link"_http://lammps.sandia.gov/future.html on the
-LAMMPS WWW page gives a list of features we are hoping to add to
-LAMMPS in the future, including contact names of individuals you can
-email if you are interested in contributing to the developement or
-would be a future user of that feature.
-
-You can also send "email to the
-developers"_http://lammps.sandia.gov/authors.html if you want to add
-your wish to the list.
-
-:line
-
-13.2 Past versions :h4,link(hist_2)
-
-LAMMPS development began in the mid 1990s under a cooperative research
-& development agreement (CRADA) between two DOE labs (Sandia and LLNL)
-and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
-to develop a large-scale parallel classical MD code; the coding effort
-was led by Steve Plimpton at Sandia.
-
-After the CRADA ended, a final F77 version, LAMMPS 99, was
-released. As development of LAMMPS continued at Sandia, its memory
-management was converted to F90; a final F90 version was released as
-LAMMPS 2001.
-
-The current LAMMPS is a rewrite in C++ and was first publicly released
-as an open source code in 2004. It includes many new features beyond
-those in LAMMPS 99 or 2001. It also includes features from older
-parallel MD codes written at Sandia, namely ParaDyn, Warp, and
-GranFlow (see below).
-
-In late 2006 we began merging new capabilities into LAMMPS that were
-developed by Aidan Thompson at Sandia for his MD code GRASP, which has
-a parallel framework similar to LAMMPS. Most notably, these have
-included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF -
-and the associated charge-equilibration routines needed for ReaxFF.
-
-The "History link"_http://lammps.sandia.gov/history.html on the 
-LAMMPS WWW page gives a timeline of features added to the
-C++ open-source version of LAMMPS over the last several years.
-
-These older codes are available for download from the "LAMMPS WWW
-site"_lws, except for Warp & GranFlow which were primarily used
-internally.  A brief listing of their features is given here.
-
-LAMMPS 2001
-    
-    F90 + MPI
-    dynamic memory
-    spatial-decomposition parallelism
-    NVE, NVT, NPT, NPH, rRESPA integrators
-    LJ and Coulombic pairwise force fields
-    all-atom, united-atom, bead-spring polymer force fields
-    CHARMM-compatible force fields
-    class 2 force fields
-    3d/2d Ewald & PPPM
-    various force and temperature constraints
-    SHAKE
-    Hessian-free truncated-Newton minimizer
-    user-defined diagnostics :ul
-
-LAMMPS 99
-    
-    F77 + MPI
-    static memory allocation
-    spatial-decomposition parallelism
-    most of the LAMMPS 2001 features with a few exceptions
-    no 2d Ewald & PPPM
-    molecular force fields are missing a few CHARMM terms
-    no SHAKE :ul
-
-Warp
-
-    F90 + MPI
-    spatial-decomposition parallelism
-    embedded atom method (EAM) metal potentials + LJ
-    lattice and grain-boundary atom creation
-    NVE, NVT integrators
-    boundary conditions for applying shear stresses
-    temperature controls for actively sheared systems
-    per-atom energy and centro-symmetry computation and output :ul
-
-ParaDyn
-
-    F77 + MPI
-    atom- and force-decomposition parallelism
-    embedded atom method (EAM) metal potentials
-    lattice atom creation
-    NVE, NVT, NPT integrators
-    all serial DYNAMO features for controls and constraints :ul
-
-GranFlow
-
-    F90 + MPI
-    spatial-decomposition parallelism
-    frictional granular potentials
-    NVE integrator
-    boundary conditions for granular flow and packing and walls
-    particle insertion :ul

doc/Section_intro.html

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-<li class="toctree-l1 current"><a class="current reference internal" href="">1. Introduction</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#what-is-lammps">1.1. What is LAMMPS</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#lammps-features">1.2. LAMMPS features</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#general-features">1.2.1. General features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#particle-and-model-types">1.2.2. Particle and model types</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#force-fields">1.2.3. Force fields</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#atom-creation">1.2.4. Atom creation</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#ensembles-constraints-and-boundary-conditions">1.2.5. Ensembles, constraints, and boundary conditions</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#integrators">1.2.6. Integrators</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#diagnostics">1.2.7. Diagnostics</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#output">1.2.8. Output</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#multi-replica-models">1.2.9. Multi-replica models</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#pre-and-post-processing">1.2.10. Pre- and post-processing</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#specialized-features">1.2.11. Specialized features</a></li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="#lammps-non-features">1.3. LAMMPS non-features</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#open-source-distribution">1.4. Open source distribution</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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-<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>
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-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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-  <div class="section" id="introduction">
-<h1>1. Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h1>
-<p>This section provides an overview of what LAMMPS can and can&#8217;t do,
-describes what it means for LAMMPS to be an open-source code, and
-acknowledges the funding and people who have contributed to LAMMPS
-over the years.</p>
-<div class="line-block">
-<div class="line">1.1 <a class="reference internal" href="#intro-1"><span>What is LAMMPS</span></a></div>
-<div class="line">1.2 <a class="reference internal" href="#intro-2"><span>LAMMPS features</span></a></div>
-<div class="line">1.3 <a class="reference internal" href="#intro-3"><span>LAMMPS non-features</span></a></div>
-<div class="line">1.4 <a class="reference internal" href="#intro-4"><span>Open source distribution</span></a></div>
-<div class="line">1.5 <a class="reference internal" href="#intro-5"><span>Acknowledgments and citations</span></a></div>
-<div class="line"><br /></div>
-</div>
-<div class="section" id="what-is-lammps">
-<span id="intro-1"></span><h2>1.1. What is LAMMPS<a class="headerlink" href="#what-is-lammps" title="Permalink to this headline">¶</a></h2>
-<p>LAMMPS is a classical molecular dynamics code that models an ensemble
-of particles in a liquid, solid, or gaseous state.  It can model
-atomic, polymeric, biological, metallic, granular, and coarse-grained
-systems using a variety of force fields and boundary conditions.</p>
-<p>For examples of LAMMPS simulations, see the Publications page of the
-<a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>
-<p>LAMMPS runs efficiently on single-processor desktop or laptop
-machines, but is designed for parallel computers.  It will run on any
-parallel machine that compiles C++ and supports the <a class="reference external" href="http://www-unix.mcs.anl.gov/mpi">MPI</a>
-message-passing library.  This includes distributed- or shared-memory
-parallel machines and Beowulf-style clusters.</p>
-<p>LAMMPS can model systems with only a few particles up to millions or
-billions.  See <a class="reference internal" href="Section_perf.html"><em>Section_perf</em></a> for information on
-LAMMPS performance and scalability, or the Benchmarks section of the
-<a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>
-<p>LAMMPS is a freely-available open-source code, distributed under the
-terms of the <a class="reference external" href="http://www.gnu.org/copyleft/gpl.html">GNU Public License</a>, which means you can use or
-modify the code however you wish.  See <a class="reference internal" href="#intro-4"><span>this section</span></a> for a
-brief discussion of the open-source philosophy.</p>
-<p>LAMMPS is designed to be easy to modify or extend with new
-capabilities, such as new force fields, atom types, boundary
-conditions, or diagnostics.  See <a class="reference internal" href="Section_modify.html"><em>Section_modify</em></a>
-for more details.</p>
-<p>The current version of LAMMPS is written in C++.  Earlier versions
-were written in F77 and F90.  See
-<a class="reference internal" href="Section_history.html"><em>Section_history</em></a> for more information on
-different versions.  All versions can be downloaded from the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>
-<p>LAMMPS was originally developed under a US Department of Energy CRADA
-(Cooperative Research and Development Agreement) between two DOE labs
-and 3 companies.  It is distributed by <a class="reference external" href="http://www.sandia.gov">Sandia National Labs</a>.
-See <a class="reference internal" href="#intro-5"><span>this section</span></a> for more information on LAMMPS funding and
-individuals who have contributed to LAMMPS.</p>
-<p>In the most general sense, LAMMPS integrates Newton&#8217;s equations of
-motion for collections of atoms, molecules, or macroscopic particles
-that interact via short- or long-range forces with a variety of
-initial and/or boundary conditions.  For computational efficiency
-LAMMPS uses neighbor lists to keep track of nearby particles.  The
-lists are optimized for systems with particles that are repulsive at
-short distances, so that the local density of particles never becomes
-too large.  On parallel machines, LAMMPS uses spatial-decomposition
-techniques to partition the simulation domain into small 3d
-sub-domains, one of which is assigned to each processor.  Processors
-communicate and store &#8220;ghost&#8221; atom information for atoms that border
-their sub-domain.  LAMMPS is most efficient (in a parallel sense) for
-systems whose particles fill a 3d rectangular box with roughly uniform
-density.  Papers with technical details of the algorithms used in
-LAMMPS are listed in <a class="reference internal" href="#intro-5"><span>this section</span></a>.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="lammps-features">
-<span id="intro-2"></span><h2>1.2. LAMMPS features<a class="headerlink" href="#lammps-features" title="Permalink to this headline">¶</a></h2>
-<p>This section highlights LAMMPS features, with pointers to specific
-commands which give more details.  If LAMMPS doesn&#8217;t have your
-favorite interatomic potential, boundary condition, or atom type, see
-<a class="reference internal" href="Section_modify.html"><em>Section_modify</em></a>, which describes how you can add
-it to LAMMPS.</p>
-<div class="section" id="general-features">
-<h3>1.2.1. General features<a class="headerlink" href="#general-features" title="Permalink to this headline">¶</a></h3>
-<ul class="simple">
-<li>runs on a single processor or in parallel</li>
-<li>distributed-memory message-passing parallelism (MPI)</li>
-<li>spatial-decomposition of simulation domain for parallelism</li>
-<li>open-source distribution</li>
-<li>highly portable C++</li>
-<li>optional libraries used: MPI and single-processor FFT</li>
-<li>GPU (CUDA and OpenCL), Intel(R) Xeon Phi(TM) coprocessors, and OpenMP support for many code features</li>
-<li>easy to extend with new features and functionality</li>
-<li>runs from an input script</li>
-<li>syntax for defining and using variables and formulas</li>
-<li>syntax for looping over runs and breaking out of loops</li>
-<li>run one or multiple simulations simultaneously (in parallel) from one script</li>
-<li>build as library, invoke LAMMPS thru library interface or provided Python wrapper</li>
-<li>couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both</li>
-</ul>
-</div>
-<div class="section" id="particle-and-model-types">
-<h3>1.2.2. Particle and model types<a class="headerlink" href="#particle-and-model-types" title="Permalink to this headline">¶</a></h3>
-<p>(<a class="reference internal" href="atom_style.html"><em>atom style</em></a> command)</p>
-<ul class="simple">
-<li>atoms</li>
-<li>coarse-grained particles (e.g. bead-spring polymers)</li>
-<li>united-atom polymers or organic molecules</li>
-<li>all-atom polymers, organic molecules, proteins, DNA</li>
-<li>metals</li>
-<li>granular materials</li>
-<li>coarse-grained mesoscale models</li>
-<li>finite-size spherical and ellipsoidal particles</li>
-<li>finite-size  line segment (2d) and triangle (3d) particles</li>
-<li>point dipole particles</li>
-<li>rigid collections of particles</li>
-<li>hybrid combinations of these</li>
-</ul>
-</div>
-<div class="section" id="force-fields">
-<h3>1.2.3. Force fields<a class="headerlink" href="#force-fields" title="Permalink to this headline">¶</a></h3>
-<p>(<a class="reference internal" href="pair_style.html"><em>pair style</em></a>, <a class="reference internal" href="bond_style.html"><em>bond style</em></a>,
-<a class="reference internal" href="angle_style.html"><em>angle style</em></a>, <a class="reference internal" href="dihedral_style.html"><em>dihedral style</em></a>,
-<a class="reference internal" href="improper_style.html"><em>improper style</em></a>, <a class="reference internal" href="kspace_style.html"><em>kspace style</em></a>
-commands)</p>
-<ul class="simple">
-<li>pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins,     Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated</li>
-<li>charged pairwise potentials: Coulombic, point-dipole</li>
-<li>manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM),     embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff,     REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic</li>
-<li>long-range interactions for charge, point-dipoles, and LJ dispersion:     Ewald, Wolf, PPPM (similar to particle-mesh Ewald)</li>
-<li>polarization models: <a class="reference internal" href="fix_qeq.html"><em>QEq</em></a>,     <a class="reference internal" href="Section_howto.html#howto-26"><span>core/shell model</span></a>,     <a class="reference internal" href="Section_howto.html#howto-27"><span>Drude dipole model</span></a></li>
-<li>charge equilibration (QEq via dynamic, point, shielded, Slater methods)</li>
-<li>coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO</li>
-<li>mesoscopic potentials: granular, Peridynamics, SPH</li>
-<li>electron force field (eFF, AWPMD)</li>
-<li>bond potentials: harmonic, FENE, Morse, nonlinear, class 2,     quartic (breakable)</li>
-<li>angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic,     class 2 (COMPASS)</li>
-<li>dihedral potentials: harmonic, CHARMM, multi-harmonic, helix,     class 2 (COMPASS), OPLS</li>
-<li>improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)</li>
-<li>polymer potentials: all-atom, united-atom, bead-spring, breakable</li>
-<li>water potentials: TIP3P, TIP4P, SPC</li>
-<li>implicit solvent potentials: hydrodynamic lubrication, Debye</li>
-<li>force-field compatibility with common CHARMM, AMBER, DREIDING,     OPLS, GROMACS, COMPASS options</li>
-<li>access to <a class="reference external" href="http://openkim.org">KIM archive</a> of potentials via     <a class="reference internal" href="pair_kim.html"><em>pair kim</em></a></li>
-<li>hybrid potentials: multiple pair, bond, angle, dihedral, improper     potentials can be used in one simulation</li>
-<li>overlaid potentials: superposition of multiple pair potentials</li>
-</ul>
-</div>
-<div class="section" id="atom-creation">
-<h3>1.2.4. Atom creation<a class="headerlink" href="#atom-creation" title="Permalink to this headline">¶</a></h3>
-<p>(<a class="reference internal" href="read_data.html"><em>read_data</em></a>, <a class="reference internal" href="lattice.html"><em>lattice</em></a>,
-<a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a>, <a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a>,
-<a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a>, <a class="reference internal" href="replicate.html"><em>replicate</em></a> commands)</p>
-<ul class="simple">
-<li>read in atom coords from files</li>
-<li>create atoms on one or more lattices (e.g. grain boundaries)</li>
-<li>delete geometric or logical groups of atoms (e.g. voids)</li>
-<li>replicate existing atoms multiple times</li>
-<li>displace atoms</li>
-</ul>
-</div>
-<div class="section" id="ensembles-constraints-and-boundary-conditions">
-<h3>1.2.5. Ensembles, constraints, and boundary conditions<a class="headerlink" href="#ensembles-constraints-and-boundary-conditions" title="Permalink to this headline">¶</a></h3>
-<p>(<a class="reference internal" href="fix.html"><em>fix</em></a> command)</p>
-<ul class="simple">
-<li>2d or 3d systems</li>
-<li>orthogonal or non-orthogonal (triclinic symmetry) simulation domains</li>
-<li>constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators</li>
-<li>thermostatting options for groups and geometric regions of atoms</li>
-<li>pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions</li>
-<li>simulation box deformation (tensile and shear)</li>
-<li>harmonic (umbrella) constraint forces</li>
-<li>rigid body constraints</li>
-<li>SHAKE bond and angle constraints</li>
-<li>Monte Carlo bond breaking, formation, swapping</li>
-<li>atom/molecule insertion and deletion</li>
-<li>walls of various kinds</li>
-<li>non-equilibrium molecular dynamics (NEMD)</li>
-<li>variety of additional boundary conditions and constraints</li>
-</ul>
-</div>
-<div class="section" id="integrators">
-<h3>1.2.6. Integrators<a class="headerlink" href="#integrators" title="Permalink to this headline">¶</a></h3>
-<p>(<a class="reference internal" href="run.html"><em>run</em></a>, <a class="reference internal" href="run_style.html"><em>run_style</em></a>, <a class="reference internal" href="minimize.html"><em>minimize</em></a> commands)</p>
-<ul class="simple">
-<li>velocity-Verlet integrator</li>
-<li>Brownian dynamics</li>
-<li>rigid body integration</li>
-<li>energy minimization via conjugate gradient or steepest descent relaxation</li>
-<li>rRESPA hierarchical timestepping</li>
-<li>rerun command for post-processing of dump files</li>
-</ul>
-</div>
-<div class="section" id="diagnostics">
-<h3>1.2.7. Diagnostics<a class="headerlink" href="#diagnostics" title="Permalink to this headline">¶</a></h3>
-<ul class="simple">
-<li>see the various flavors of the <a class="reference internal" href="fix.html"><em>fix</em></a> and <a class="reference internal" href="compute.html"><em>compute</em></a> commands</li>
-</ul>
-</div>
-<div class="section" id="output">
-<h3>1.2.8. Output<a class="headerlink" href="#output" title="Permalink to this headline">¶</a></h3>
-<p>(<a class="reference internal" href="dump.html"><em>dump</em></a>, <a class="reference internal" href="restart.html"><em>restart</em></a> commands)</p>
-<ul class="simple">
-<li>log file of thermodynamic info</li>
-<li>text dump files of atom coords, velocities, other per-atom quantities</li>
-<li>binary restart files</li>
-<li>parallel I/O of dump and restart files</li>
-<li>per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)</li>
-<li>user-defined system-wide (log file) or per-atom (dump file) calculations</li>
-<li>spatial and time averaging of per-atom quantities</li>
-<li>time averaging of system-wide quantities</li>
-<li>atom snapshots in native, XYZ, XTC, DCD, CFG formats</li>
-</ul>
-</div>
-<div class="section" id="multi-replica-models">
-<h3>1.2.9. Multi-replica models<a class="headerlink" href="#multi-replica-models" title="Permalink to this headline">¶</a></h3>
-<p><a class="reference internal" href="neb.html"><em>nudged elastic band</em></a>
-<a class="reference internal" href="prd.html"><em>parallel replica dynamics</em></a>
-<a class="reference internal" href="tad.html"><em>temperature accelerated dynamics</em></a>
-<a class="reference internal" href="temper.html"><em>parallel tempering</em></a></p>
-</div>
-<div class="section" id="pre-and-post-processing">
-<h3>1.2.10. Pre- and post-processing<a class="headerlink" href="#pre-and-post-processing" title="Permalink to this headline">¶</a></h3>
-<ul class="simple">
-<li>Various pre- and post-processing serial tools are packaged
-with LAMMPS; see these <a class="reference internal" href="Section_tools.html"><em>doc pages</em></a>.</li>
-<li>Our group has also written and released a separate toolkit called
-<a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a> which provides tools for doing setup, analysis,
-plotting, and visualization for LAMMPS simulations.  Pizza.py is
-written in <a class="reference external" href="http://www.python.org">Python</a> and is available for download from <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW site</a>.</li>
-</ul>
-</div>
-<div class="section" id="specialized-features">
-<h3>1.2.11. Specialized features<a class="headerlink" href="#specialized-features" title="Permalink to this headline">¶</a></h3>
-<p>These are LAMMPS capabilities which you may not think of as typical
-molecular dynamics options:</p>
-<ul class="simple">
-<li><a class="reference internal" href="balance.html"><em>static</em></a> and <a class="reference internal" href="fix_balance.html"><em>dynamic load-balancing</em></a></li>
-<li><a class="reference internal" href="body.html"><em>generalized aspherical particles</em></a></li>
-<li><a class="reference internal" href="fix_srd.html"><em>stochastic rotation dynamics (SRD)</em></a></li>
-<li><a class="reference internal" href="fix_imd.html"><em>real-time visualization and interactive MD</em></a></li>
-<li>calculate <a class="reference internal" href="compute_xrd.html"><em>virtual diffraction patterns</em></a></li>
-<li><a class="reference internal" href="fix_atc.html"><em>atom-to-continuum coupling</em></a> with finite elements</li>
-<li>coupled rigid body integration via the <a class="reference internal" href="fix_poems.html"><em>POEMS</em></a> library</li>
-<li><a class="reference internal" href="fix_qmmm.html"><em>QM/MM coupling</em></a></li>
-<li><a class="reference internal" href="fix_ipi.html"><em>path-integral molecular dynamics (PIMD)</em></a> and <a class="reference internal" href="fix_pimd.html"><em>this as well</em></a></li>
-<li>Monte Carlo via <a class="reference internal" href="fix_gcmc.html"><em>GCMC</em></a> and <a class="reference internal" href="fix_tfmc.html"><em>tfMC</em></a> and <code class="xref doc docutils literal"><span class="pre">atom</span> <span class="pre">swapping</span></code></li>
-<li><a class="reference internal" href="pair_dsmc.html"><em>Direct Simulation Monte Carlo</em></a> for low-density fluids</li>
-<li><a class="reference internal" href="pair_peri.html"><em>Peridynamics mesoscale modeling</em></a></li>
-<li><a class="reference internal" href="fix_lb_fluid.html"><em>Lattice Boltzmann fluid</em></a></li>
-<li><a class="reference internal" href="fix_tmd.html"><em>targeted</em></a> and <a class="reference internal" href="fix_smd.html"><em>steered</em></a> molecular dynamics</li>
-<li><a class="reference internal" href="fix_ttm.html"><em>two-temperature electron model</em></a></li>
-</ul>
-<hr class="docutils" />
-</div>
-</div>
-<div class="section" id="lammps-non-features">
-<span id="intro-3"></span><h2>1.3. LAMMPS non-features<a class="headerlink" href="#lammps-non-features" title="Permalink to this headline">¶</a></h2>
-<p>LAMMPS is designed to efficiently compute Newton&#8217;s equations of motion
-for a system of interacting particles.  Many of the tools needed to
-pre- and post-process the data for such simulations are not included
-in the LAMMPS kernel for several reasons:</p>
-<ul class="simple">
-<li>the desire to keep LAMMPS simple</li>
-<li>they are not parallel operations</li>
-<li>other codes already do them</li>
-<li>limited development resources</li>
-</ul>
-<p>Specifically, LAMMPS itself does not:</p>
-<ul class="simple">
-<li>run thru a GUI</li>
-<li>build molecular systems</li>
-<li>assign force-field coefficients automagically</li>
-<li>perform sophisticated analyses of your MD simulation</li>
-<li>visualize your MD simulation</li>
-<li>plot your output data</li>
-</ul>
-<p>A few tools for pre- and post-processing tasks are provided as part of
-the LAMMPS package; they are described in <a class="reference internal" href="Section_tools.html"><em>this section</em></a>.  However, many people use other codes or
-write their own tools for these tasks.</p>
-<p>As noted above, our group has also written and released a separate
-toolkit called <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a> which addresses some of the listed
-bullets.  It provides tools for doing setup, analysis, plotting, and
-visualization for LAMMPS simulations.  Pizza.py is written in
-<a class="reference external" href="http://www.python.org">Python</a> and is available for download from <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW site</a>.</p>
-<p>LAMMPS requires as input a list of initial atom coordinates and types,
-molecular topology information, and force-field coefficients assigned
-to all atoms and bonds.  LAMMPS will not build molecular systems and
-assign force-field parameters for you.</p>
-<p>For atomic systems LAMMPS provides a <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a>
-command which places atoms on solid-state lattices (fcc, bcc,
-user-defined, etc).  Assigning small numbers of force field
-coefficients can be done via the <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>, etc commands.
-For molecular systems or more complicated simulation geometries, users
-typically use another code as a builder and convert its output to
-LAMMPS input format, or write their own code to generate atom
-coordinate and molecular topology for LAMMPS to read in.</p>
-<p>For complicated molecular systems (e.g. a protein), a multitude of
-topology information and hundreds of force-field coefficients must
-typically be specified.  We suggest you use a program like
-<a class="reference external" href="http://www.scripps.edu/brooks">CHARMM</a> or <a class="reference external" href="http://amber.scripps.edu">AMBER</a> or other molecular builders to setup
-such problems and dump its information to a file.  You can then
-reformat the file as LAMMPS input.  Some of the tools in <a class="reference internal" href="Section_tools.html"><em>this section</em></a> can assist in this process.</p>
-<p>Similarly, LAMMPS creates output files in a simple format.  Most users
-post-process these files with their own analysis tools or re-format
-them for input into other programs, including visualization packages.
-If you are convinced you need to compute something on-the-fly as
-LAMMPS runs, see <a class="reference internal" href="Section_modify.html"><em>Section_modify</em></a> for a discussion
-of how you can use the <a class="reference internal" href="dump.html"><em>dump</em></a> and <a class="reference internal" href="compute.html"><em>compute</em></a> and
-<a class="reference internal" href="fix.html"><em>fix</em></a> commands to print out data of your choosing.  Keep in
-mind that complicated computations can slow down the molecular
-dynamics timestepping, particularly if the computations are not
-parallel, so it is often better to leave such analysis to
-post-processing codes.</p>
-<p>A very simple (yet fast) visualizer is provided with the LAMMPS
-package - see the <a class="reference internal" href="Section_tools.html#xmovie"><span>xmovie</span></a> tool in <a class="reference internal" href="Section_tools.html"><em>this section</em></a>.  It creates xyz projection views of
-atomic coordinates and animates them.  We find it very useful for
-debugging purposes.  For high-quality visualization we recommend the
-following packages:</p>
-<ul class="simple">
-<li><a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a></li>
-<li><a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a></li>
-<li><a class="reference external" href="http://pymol.sourceforge.net">PyMol</a></li>
-<li><a class="reference external" href="http://www.bmsc.washington.edu/raster3d/raster3d.html">Raster3d</a></li>
-<li><a class="reference external" href="http://www.openrasmol.org">RasMol</a></li>
-</ul>
-<p>Other features that LAMMPS does not yet (and may never) support are
-discussed in <a class="reference internal" href="Section_history.html"><em>Section_history</em></a>.</p>
-<p>Finally, these are freely-available molecular dynamics codes, most of
-them parallel, which may be well-suited to the problems you want to
-model.  They can also be used in conjunction with LAMMPS to perform
-complementary modeling tasks.</p>
-<ul class="simple">
-<li><a class="reference external" href="http://www.scripps.edu/brooks">CHARMM</a></li>
-<li><a class="reference external" href="http://amber.scripps.edu">AMBER</a></li>
-<li><a class="reference external" href="http://www.ks.uiuc.edu/Research/namd/">NAMD</a></li>
-<li><a class="reference external" href="http://www.emsl.pnl.gov/docs/nwchem/nwchem.html">NWCHEM</a></li>
-<li><a class="reference external" href="http://www.cse.clrc.ac.uk/msi/software/DL_POLY">DL_POLY</a></li>
-<li><a class="reference external" href="http://dasher.wustl.edu/tinker">Tinker</a></li>
-</ul>
-<p>CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
-modeling biological molecules.  CHARMM and AMBER use
-atom-decomposition (replicated-data) strategies for parallelism; NAMD
-and NWCHEM use spatial-decomposition approaches, similar to LAMMPS.
-Tinker is a serial code.  DL_POLY includes potentials for a variety of
-biological and non-biological materials; both a replicated-data and
-spatial-decomposition version exist.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="open-source-distribution">
-<span id="intro-4"></span><h2>1.4. Open source distribution<a class="headerlink" href="#open-source-distribution" title="Permalink to this headline">¶</a></h2>
-<p>LAMMPS comes with no warranty of any kind.  As each source file states
-in its header, it is a copyrighted code that is distributed free-of-
-charge, under the terms of the <a class="reference external" href="http://www.gnu.org/copyleft/gpl.html">GNU Public License</a> (GPL).  This
-is often referred to as open-source distribution - see
-<a class="reference external" href="http://www.gnu.org">www.gnu.org</a> or <a class="reference external" href="http://www.opensource.org">www.opensource.org</a> for more
-details.  The legal text of the GPL is in the LICENSE file that is
-included in the LAMMPS distribution.</p>
-<p>Here is a summary of what the GPL means for LAMMPS users:</p>
-<p>(1) Anyone is free to use, modify, or extend LAMMPS in any way they
-choose, including for commercial purposes.</p>
-<p>(2) If you distribute a modified version of LAMMPS, it must remain
-open-source, meaning you distribute it under the terms of the GPL.
-You should clearly annotate such a code as a derivative version of
-LAMMPS.</p>
-<p>(3) If you release any code that includes LAMMPS source code, then it
-must also be open-sourced, meaning you distribute it under the terms
-of the GPL.</p>
-<p>(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
-source file headers (including the copyright and GPL notices) should
-remain part of the code.</p>
-<p>In the spirit of an open-source code, these are various ways you can
-contribute to making LAMMPS better.  You can send email to the
-<a class="reference external" href="http://lammps.sandia.gov/authors.html">developers</a> on any of these
-items.</p>
-<ul class="simple">
-<li>Point prospective users to the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.  Mention it in
-talks or link to it from your WWW site.</li>
-<li>If you find an error or omission in this manual or on the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>, or have a suggestion for something to clarify or include,
-send an email to the
-<a class="reference external" href="http://lammps.sandia.gov/authors.html">developers</a>.</li>
-<li>If you find a bug, <a class="reference internal" href="Section_errors.html#err-2"><span>Section_errors 2</span></a>
-describes how to report it.</li>
-<li>If you publish a paper using LAMMPS results, send the citation (and
-any cool pictures or movies if you like) to add to the Publications,
-Pictures, and Movies pages of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>, with links
-and attributions back to you.</li>
-<li>Create a new Makefile.machine that can be added to the src/MAKE
-directory.</li>
-<li>The tools sub-directory of the LAMMPS distribution has various
-stand-alone codes for pre- and post-processing of LAMMPS data.  More
-details are given in <a class="reference internal" href="Section_tools.html"><em>Section_tools</em></a>.  If you write
-a new tool that users will find useful, it can be added to the LAMMPS
-distribution.</li>
-<li>LAMMPS is designed to be easy to extend with new code for features
-like potentials, boundary conditions, diagnostic computations, etc.
-<a class="reference internal" href="Section_modify.html"><em>This section</em></a> gives details.  If you add a
-feature of general interest, it can be added to the LAMMPS
-distribution.</li>
-<li>The Benchmark page of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> lists LAMMPS
-performance on various platforms.  The files needed to run the
-benchmarks are part of the LAMMPS distribution.  If your machine is
-sufficiently different from those listed, your timing data can be
-added to the page.</li>
-<li>You can send feedback for the User Comments page of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.  It might be added to the page.  No promises.</li>
-<li>Cash.  Small denominations, unmarked bills preferred.  Paper sack OK.
-Leave on desk.  VISA also accepted.  Chocolate chip cookies
-encouraged.</li>
-</ul>
-<hr class="docutils" />
-</div>
-<div class="section" id="acknowledgments-and-citations">
-<span id="intro-5"></span><h2>1.5. Acknowledgments and citations<a class="headerlink" href="#acknowledgments-and-citations" title="Permalink to this headline">¶</a></h2>
-<p>LAMMPS development has been funded by the <a class="reference external" href="http://www.doe.gov">US Department of Energy</a> (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
-programs and its <a class="reference external" href="http://www.sc.doe.gov/ascr/home.html">OASCR</a> and <a class="reference external" href="http://www.er.doe.gov/production/ober/ober_top.html">OBER</a> offices.</p>
-<p>Specifically, work on the latest version was funded in part by the US
-Department of Energy&#8217;s Genomics:GTL program
-(<a class="reference external" href="http://www.doegenomestolife.org">www.doegenomestolife.org</a>) under the <a class="reference external" href="http://www.genomes2life.org">project</a>, &#8220;Carbon
-Sequestration in Synechococcus Sp.: From Molecular Machines to
-Hierarchical Modeling&#8221;.</p>
-<p>The following paper describe the basic parallel algorithms used in
-LAMMPS.  If you use LAMMPS results in your published work, please cite
-this paper and include a pointer to the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>
-(<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a>):</p>
-<p>S. J. Plimpton, <strong>Fast Parallel Algorithms for Short-Range Molecular
-Dynamics</strong>, J Comp Phys, 117, 1-19 (1995).</p>
-<p>Other papers describing specific algorithms used in LAMMPS are listed
-under the <a class="reference external" href="http://lammps.sandia.gov/cite.html">Citing LAMMPS link</a> of
-the LAMMPS WWW page.</p>
-<p>The <a class="reference external" href="http://lammps.sandia.gov/papers.html">Publications link</a> on the
-LAMMPS WWW page lists papers that have cited LAMMPS.  If your paper is
-not listed there for some reason, feel free to send us the info.  If
-the simulations in your paper produced cool pictures or animations,
-we&#8217;ll be pleased to add them to the
-<a class="reference external" href="http://lammps.sandia.gov/pictures.html">Pictures</a> or
-<a class="reference external" href="http://lammps.sandia.gov/movies.html">Movies</a> pages of the LAMMPS WWW
-site.</p>
-<p>The core group of LAMMPS developers is at Sandia National Labs:</p>
-<ul class="simple">
-<li>Steve Plimpton, sjplimp at sandia.gov</li>
-<li>Aidan Thompson, athomps at sandia.gov</li>
-<li>Paul Crozier, pscrozi at sandia.gov</li>
-</ul>
-<p>The following folks are responsible for significant contributions to
-the code, or other aspects of the LAMMPS development effort.  Many of
-the packages they have written are somewhat unique to LAMMPS and the
-code would not be as general-purpose as it is without their expertise
-and efforts.</p>
-<ul class="simple">
-<li>Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM and USER-OMP packages</li>
-<li>Roy Pollock (LLNL), Ewald and PPPM solvers</li>
-<li>Mike Brown (ORNL), brownw at ornl.gov, GPU package</li>
-<li>Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential</li>
-<li>Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics</li>
-<li>Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion</li>
-<li>Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling</li>
-<li>Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD</li>
-<li>Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package</li>
-<li>Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field</li>
-<li>Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling</li>
-<li>Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF</li>
-<li>Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package</li>
-</ul>
-<p>As discussed in <a class="reference internal" href="Section_history.html"><em>Section_history</em></a>, LAMMPS
-originated as a cooperative project between DOE labs and industrial
-partners. Folks involved in the design and testing of the original
-version of LAMMPS were the following:</p>
-<ul class="simple">
-<li>John Carpenter (Mayo Clinic, formerly at Cray Research)</li>
-<li>Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)</li>
-<li>Steve Lustig (Dupont)</li>
-<li>Jim Belak (LLNL)</li>
-</ul>
-</div>
-</div>
-
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doc/Section_intro.txt

@@ -1,540 +0,0 @@
-"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_start.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-1. Introduction :h3
-
-This section provides an overview of what LAMMPS can and can't do,
-describes what it means for LAMMPS to be an open-source code, and
-acknowledges the funding and people who have contributed to LAMMPS
-over the years.
-
-1.1 "What is LAMMPS"_#intro_1
-1.2 "LAMMPS features"_#intro_2
-1.3 "LAMMPS non-features"_#intro_3
-1.4 "Open source distribution"_#intro_4
-1.5 "Acknowledgments and citations"_#intro_5 :all(b)
-
-:line
-:line
-
-1.1 What is LAMMPS :link(intro_1),h4
-
-LAMMPS is a classical molecular dynamics code that models an ensemble
-of particles in a liquid, solid, or gaseous state.  It can model
-atomic, polymeric, biological, metallic, granular, and coarse-grained
-systems using a variety of force fields and boundary conditions.
-
-For examples of LAMMPS simulations, see the Publications page of the
-"LAMMPS WWW Site"_lws.
-
-LAMMPS runs efficiently on single-processor desktop or laptop
-machines, but is designed for parallel computers.  It will run on any
-parallel machine that compiles C++ and supports the "MPI"_mpi
-message-passing library.  This includes distributed- or shared-memory
-parallel machines and Beowulf-style clusters.
-
-:link(mpi,http://www-unix.mcs.anl.gov/mpi)
-
-LAMMPS can model systems with only a few particles up to millions or
-billions.  See "Section_perf"_Section_perf.html for information on
-LAMMPS performance and scalability, or the Benchmarks section of the
-"LAMMPS WWW Site"_lws.
-
-LAMMPS is a freely-available open-source code, distributed under the
-terms of the "GNU Public License"_gnu, which means you can use or
-modify the code however you wish.  See "this section"_#intro_4 for a
-brief discussion of the open-source philosophy.
-
-:link(gnu,http://www.gnu.org/copyleft/gpl.html)
-
-LAMMPS is designed to be easy to modify or extend with new
-capabilities, such as new force fields, atom types, boundary
-conditions, or diagnostics.  See "Section_modify"_Section_modify.html
-for more details.
-
-The current version of LAMMPS is written in C++.  Earlier versions
-were written in F77 and F90.  See
-"Section_history"_Section_history.html for more information on
-different versions.  All versions can be downloaded from the "LAMMPS
-WWW Site"_lws.
-
-LAMMPS was originally developed under a US Department of Energy CRADA
-(Cooperative Research and Development Agreement) between two DOE labs
-and 3 companies.  It is distributed by "Sandia National Labs"_snl.
-See "this section"_#intro_5 for more information on LAMMPS funding and
-individuals who have contributed to LAMMPS.
-
-:link(snl,http://www.sandia.gov)
-
-In the most general sense, LAMMPS integrates Newton's equations of
-motion for collections of atoms, molecules, or macroscopic particles
-that interact via short- or long-range forces with a variety of
-initial and/or boundary conditions.  For computational efficiency
-LAMMPS uses neighbor lists to keep track of nearby particles.  The
-lists are optimized for systems with particles that are repulsive at
-short distances, so that the local density of particles never becomes
-too large.  On parallel machines, LAMMPS uses spatial-decomposition
-techniques to partition the simulation domain into small 3d
-sub-domains, one of which is assigned to each processor.  Processors
-communicate and store "ghost" atom information for atoms that border
-their sub-domain.  LAMMPS is most efficient (in a parallel sense) for
-systems whose particles fill a 3d rectangular box with roughly uniform
-density.  Papers with technical details of the algorithms used in
-LAMMPS are listed in "this section"_#intro_5.
-
-:line
-
-1.2 LAMMPS features :link(intro_2),h4
-
-This section highlights LAMMPS features, with pointers to specific
-commands which give more details.  If LAMMPS doesn't have your
-favorite interatomic potential, boundary condition, or atom type, see
-"Section_modify"_Section_modify.html, which describes how you can add
-it to LAMMPS.
-
-General features :h5
-
-  runs on a single processor or in parallel
-  distributed-memory message-passing parallelism (MPI)
-  spatial-decomposition of simulation domain for parallelism
-  open-source distribution
-  highly portable C++
-  optional libraries used: MPI and single-processor FFT
-  GPU (CUDA and OpenCL), Intel(R) Xeon Phi(TM) coprocessors, and OpenMP support for many code features
-  easy to extend with new features and functionality
-  runs from an input script
-  syntax for defining and using variables and formulas
-  syntax for looping over runs and breaking out of loops
-  run one or multiple simulations simultaneously (in parallel) from one script
-  build as library, invoke LAMMPS thru library interface or provided Python wrapper
-  couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
-
-Particle and model types :h5
-("atom style"_atom_style.html command)
-
-  atoms
-  coarse-grained particles (e.g. bead-spring polymers)
-  united-atom polymers or organic molecules
-  all-atom polymers, organic molecules, proteins, DNA
-  metals
-  granular materials
-  coarse-grained mesoscale models
-  finite-size spherical and ellipsoidal particles
-  finite-size  line segment (2d) and triangle (3d) particles
-  point dipole particles
-  rigid collections of particles
-  hybrid combinations of these :ul
-
-Force fields :h5
-("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, "kspace style"_kspace_style.html
-commands)
-
-  pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \
-    Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
-  charged pairwise potentials: Coulombic, point-dipole
-  manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
-    embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \
-    REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
-  long-range interactions for charge, point-dipoles, and LJ dispersion: \
-    Ewald, Wolf, PPPM (similar to particle-mesh Ewald)
-  polarization models: "QEq"_fix_qeq.html, \
-    "core/shell model"_Section_howto.html#howto_26, \
-    "Drude dipole model"_Section_howto.html#howto_27
-  charge equilibration (QEq via dynamic, point, shielded, Slater methods)
-  coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
-  mesoscopic potentials: granular, Peridynamics, SPH
-  electron force field (eFF, AWPMD)
-  bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
-    quartic (breakable)
-  angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \
-    class 2 (COMPASS)
-  dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \
-    class 2 (COMPASS), OPLS
-  improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)
-  polymer potentials: all-atom, united-atom, bead-spring, breakable
-  water potentials: TIP3P, TIP4P, SPC
-  implicit solvent potentials: hydrodynamic lubrication, Debye
-  force-field compatibility with common CHARMM, AMBER, DREIDING, \
-    OPLS, GROMACS, COMPASS options
-  access to "KIM archive"_http://openkim.org of potentials via \
-    "pair kim"_pair_kim.html
-  hybrid potentials: multiple pair, bond, angle, dihedral, improper \
-    potentials can be used in one simulation
-  overlaid potentials: superposition of multiple pair potentials :ul
-
-Atom creation :h5
-("read_data"_read_data.html, "lattice"_lattice.html,
-"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html,
-"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands)
-
-  read in atom coords from files
-  create atoms on one or more lattices (e.g. grain boundaries)
-  delete geometric or logical groups of atoms (e.g. voids)
-  replicate existing atoms multiple times
-  displace atoms :ul
-
-Ensembles, constraints, and boundary conditions :h5
-("fix"_fix.html command) 
-
-  2d or 3d systems
-  orthogonal or non-orthogonal (triclinic symmetry) simulation domains
-  constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
-  thermostatting options for groups and geometric regions of atoms
-  pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
-  simulation box deformation (tensile and shear)
-  harmonic (umbrella) constraint forces
-  rigid body constraints
-  SHAKE bond and angle constraints
-  Monte Carlo bond breaking, formation, swapping
-  atom/molecule insertion and deletion
-  walls of various kinds
-  non-equilibrium molecular dynamics (NEMD)
-  variety of additional boundary conditions and constraints :ul
-
-Integrators :h5
-("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands) 
-
-  velocity-Verlet integrator
-  Brownian dynamics
-  rigid body integration
-  energy minimization via conjugate gradient or steepest descent relaxation
-  rRESPA hierarchical timestepping
-  rerun command for post-processing of dump files :ul
-
-Diagnostics :h5
-
-  see the various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
-
-Output :h5
-("dump"_dump.html, "restart"_restart.html commands) 
-
-  log file of thermodynamic info
-  text dump files of atom coords, velocities, other per-atom quantities
-  binary restart files
-  parallel I/O of dump and restart files
-  per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
-  user-defined system-wide (log file) or per-atom (dump file) calculations
-  spatial and time averaging of per-atom quantities
-  time averaging of system-wide quantities
-  atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
-
-Multi-replica models :h5
-
-"nudged elastic band"_neb.html
-"parallel replica dynamics"_prd.html
-"temperature accelerated dynamics"_tad.html
-"parallel tempering"_temper.html
-
-Pre- and post-processing :h5
-
-Various pre- and post-processing serial tools are packaged
-with LAMMPS; see these "doc pages"_Section_tools.html. :ulb,l
-
-Our group has also written and released a separate toolkit called
-"Pizza.py"_pizza which provides tools for doing setup, analysis,
-plotting, and visualization for LAMMPS simulations.  Pizza.py is
-written in "Python"_python and is available for download from "the
-Pizza.py WWW site"_pizza. :l,ule
-
-:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
-:link(python,http://www.python.org)
-
-Specialized features :h5
-
-These are LAMMPS capabilities which you may not think of as typical
-molecular dynamics options:
-
-"static"_balance.html and "dynamic load-balancing"_fix_balance.html
-"generalized aspherical particles"_body.html
-"stochastic rotation dynamics (SRD)"_fix_srd.html
-"real-time visualization and interactive MD"_fix_imd.html
-calculate "virtual diffraction patterns"_compute_xrd.html
-"atom-to-continuum coupling"_fix_atc.html with finite elements
-coupled rigid body integration via the "POEMS"_fix_poems.html library
-"QM/MM coupling"_fix_qmmm.html
-"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html
-Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html and "atom swapping"_fix_swap.html
-"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
-"Peridynamics mesoscale modeling"_pair_peri.html
-"Lattice Boltzmann fluid"_fix_lb_fluid.html
-"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics
-"two-temperature electron model"_fix_ttm.html :ul
-
-:line
-
-1.3 LAMMPS non-features :link(intro_3),h4
-
-LAMMPS is designed to efficiently compute Newton's equations of motion
-for a system of interacting particles.  Many of the tools needed to
-pre- and post-process the data for such simulations are not included
-in the LAMMPS kernel for several reasons:
-
-the desire to keep LAMMPS simple
-they are not parallel operations
-other codes already do them
-limited development resources :ul
-
-Specifically, LAMMPS itself does not:
-
-run thru a GUI
-build molecular systems
-assign force-field coefficients automagically
-perform sophisticated analyses of your MD simulation
-visualize your MD simulation
-plot your output data :ul
-
-A few tools for pre- and post-processing tasks are provided as part of
-the LAMMPS package; they are described in "this
-section"_Section_tools.html.  However, many people use other codes or
-write their own tools for these tasks.
-
-As noted above, our group has also written and released a separate
-toolkit called "Pizza.py"_pizza which addresses some of the listed
-bullets.  It provides tools for doing setup, analysis, plotting, and
-visualization for LAMMPS simulations.  Pizza.py is written in
-"Python"_python and is available for download from "the Pizza.py WWW
-site"_pizza.
-
-LAMMPS requires as input a list of initial atom coordinates and types,
-molecular topology information, and force-field coefficients assigned
-to all atoms and bonds.  LAMMPS will not build molecular systems and
-assign force-field parameters for you.
-
-For atomic systems LAMMPS provides a "create_atoms"_create_atoms.html
-command which places atoms on solid-state lattices (fcc, bcc,
-user-defined, etc).  Assigning small numbers of force field
-coefficients can be done via the "pair coeff"_pair_coeff.html, "bond
-coeff"_bond_coeff.html, "angle coeff"_angle_coeff.html, etc commands.
-For molecular systems or more complicated simulation geometries, users
-typically use another code as a builder and convert its output to
-LAMMPS input format, or write their own code to generate atom
-coordinate and molecular topology for LAMMPS to read in.
-
-For complicated molecular systems (e.g. a protein), a multitude of
-topology information and hundreds of force-field coefficients must
-typically be specified.  We suggest you use a program like
-"CHARMM"_charmm or "AMBER"_amber or other molecular builders to setup
-such problems and dump its information to a file.  You can then
-reformat the file as LAMMPS input.  Some of the tools in "this
-section"_Section_tools.html can assist in this process.
-
-Similarly, LAMMPS creates output files in a simple format.  Most users
-post-process these files with their own analysis tools or re-format
-them for input into other programs, including visualization packages.
-If you are convinced you need to compute something on-the-fly as
-LAMMPS runs, see "Section_modify"_Section_modify.html for a discussion
-of how you can use the "dump"_dump.html and "compute"_compute.html and
-"fix"_fix.html commands to print out data of your choosing.  Keep in
-mind that complicated computations can slow down the molecular
-dynamics timestepping, particularly if the computations are not
-parallel, so it is often better to leave such analysis to
-post-processing codes.
-
-A very simple (yet fast) visualizer is provided with the LAMMPS
-package - see the "xmovie"_Section_tools.html#xmovie tool in "this
-section"_Section_tools.html.  It creates xyz projection views of
-atomic coordinates and animates them.  We find it very useful for
-debugging purposes.  For high-quality visualization we recommend the
-following packages:
-
-"VMD"_http://www.ks.uiuc.edu/Research/vmd
-"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
-"PyMol"_http://pymol.sourceforge.net
-"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
-"RasMol"_http://www.openrasmol.org :ul
-
-Other features that LAMMPS does not yet (and may never) support are
-discussed in "Section_history"_Section_history.html.
-
-Finally, these are freely-available molecular dynamics codes, most of
-them parallel, which may be well-suited to the problems you want to
-model.  They can also be used in conjunction with LAMMPS to perform
-complementary modeling tasks.
-
-"CHARMM"_charmm
-"AMBER"_amber
-"NAMD"_namd
-"NWCHEM"_nwchem
-"DL_POLY"_dlpoly
-"Tinker"_tinker :ul
-
-:link(charmm,http://www.scripps.edu/brooks)
-:link(amber,http://amber.scripps.edu)
-:link(namd,http://www.ks.uiuc.edu/Research/namd/)
-:link(nwchem,http://www.emsl.pnl.gov/docs/nwchem/nwchem.html)
-:link(dlpoly,http://www.cse.clrc.ac.uk/msi/software/DL_POLY)
-:link(tinker,http://dasher.wustl.edu/tinker)
-
-CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
-modeling biological molecules.  CHARMM and AMBER use
-atom-decomposition (replicated-data) strategies for parallelism; NAMD
-and NWCHEM use spatial-decomposition approaches, similar to LAMMPS.
-Tinker is a serial code.  DL_POLY includes potentials for a variety of
-biological and non-biological materials; both a replicated-data and
-spatial-decomposition version exist.
-
-:line
-
-1.4 Open source distribution :link(intro_4),h4
-
-LAMMPS comes with no warranty of any kind.  As each source file states
-in its header, it is a copyrighted code that is distributed free-of-
-charge, under the terms of the "GNU Public License"_gnu (GPL).  This
-is often referred to as open-source distribution - see
-"www.gnu.org"_gnuorg or "www.opensource.org"_opensource for more
-details.  The legal text of the GPL is in the LICENSE file that is
-included in the LAMMPS distribution.
-
-:link(gnuorg,http://www.gnu.org)
-:link(opensource,http://www.opensource.org)
-
-Here is a summary of what the GPL means for LAMMPS users:
-
-(1) Anyone is free to use, modify, or extend LAMMPS in any way they
-choose, including for commercial purposes.
-
-(2) If you distribute a modified version of LAMMPS, it must remain
-open-source, meaning you distribute it under the terms of the GPL.
-You should clearly annotate such a code as a derivative version of
-LAMMPS.
-
-(3) If you release any code that includes LAMMPS source code, then it
-must also be open-sourced, meaning you distribute it under the terms
-of the GPL.
-
-(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
-source file headers (including the copyright and GPL notices) should
-remain part of the code.
-
-In the spirit of an open-source code, these are various ways you can
-contribute to making LAMMPS better.  You can send email to the
-"developers"_http://lammps.sandia.gov/authors.html on any of these
-items.
-
-Point prospective users to the "LAMMPS WWW Site"_lws.  Mention it in
-talks or link to it from your WWW site. :ulb,l
-
-If you find an error or omission in this manual or on the "LAMMPS WWW
-Site"_lws, or have a suggestion for something to clarify or include,
-send an email to the
-"developers"_http://lammps.sandia.gov/authors.html. :l
-
-If you find a bug, "Section_errors 2"_Section_errors.html#err_2
-describes how to report it. :l
-
-If you publish a paper using LAMMPS results, send the citation (and
-any cool pictures or movies if you like) to add to the Publications,
-Pictures, and Movies pages of the "LAMMPS WWW Site"_lws, with links
-and attributions back to you. :l
-
-Create a new Makefile.machine that can be added to the src/MAKE
-directory. :l
-
-The tools sub-directory of the LAMMPS distribution has various
-stand-alone codes for pre- and post-processing of LAMMPS data.  More
-details are given in "Section_tools"_Section_tools.html.  If you write
-a new tool that users will find useful, it can be added to the LAMMPS
-distribution. :l
-
-LAMMPS is designed to be easy to extend with new code for features
-like potentials, boundary conditions, diagnostic computations, etc.
-"This section"_Section_modify.html gives details.  If you add a
-feature of general interest, it can be added to the LAMMPS
-distribution. :l
-
-The Benchmark page of the "LAMMPS WWW Site"_lws lists LAMMPS
-performance on various platforms.  The files needed to run the
-benchmarks are part of the LAMMPS distribution.  If your machine is
-sufficiently different from those listed, your timing data can be
-added to the page. :l
-
-You can send feedback for the User Comments page of the "LAMMPS WWW
-Site"_lws.  It might be added to the page.  No promises. :l
-
-Cash.  Small denominations, unmarked bills preferred.  Paper sack OK.
-Leave on desk.  VISA also accepted.  Chocolate chip cookies
-encouraged. :ule,l
-
-:line
-
-1.5 Acknowledgments and citations :h4,link(intro_5)
-
-LAMMPS development has been funded by the "US Department of
-Energy"_doe (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
-programs and its "OASCR"_oascr and "OBER"_ober offices.
-
-Specifically, work on the latest version was funded in part by the US
-Department of Energy's Genomics:GTL program
-("www.doegenomestolife.org"_gtl) under the "project"_ourgtl, "Carbon
-Sequestration in Synechococcus Sp.: From Molecular Machines to
-Hierarchical Modeling".
-
-:link(doe,http://www.doe.gov)
-:link(gtl,http://www.doegenomestolife.org)
-:link(ourgtl,http://www.genomes2life.org)
-:link(oascr,http://www.sc.doe.gov/ascr/home.html)
-:link(ober,http://www.er.doe.gov/production/ober/ober_top.html)
-
-The following paper describe the basic parallel algorithms used in
-LAMMPS.  If you use LAMMPS results in your published work, please cite
-this paper and include a pointer to the "LAMMPS WWW Site"_lws
-(http://lammps.sandia.gov):
-
-S. J. Plimpton, [Fast Parallel Algorithms for Short-Range Molecular
-Dynamics], J Comp Phys, 117, 1-19 (1995).
-
-Other papers describing specific algorithms used in LAMMPS are listed
-under the "Citing LAMMPS link"_http://lammps.sandia.gov/cite.html of
-the LAMMPS WWW page.
-
-The "Publications link"_http://lammps.sandia.gov/papers.html on the
-LAMMPS WWW page lists papers that have cited LAMMPS.  If your paper is
-not listed there for some reason, feel free to send us the info.  If
-the simulations in your paper produced cool pictures or animations,
-we'll be pleased to add them to the
-"Pictures"_http://lammps.sandia.gov/pictures.html or
-"Movies"_http://lammps.sandia.gov/movies.html pages of the LAMMPS WWW
-site.
-
-The core group of LAMMPS developers is at Sandia National Labs:
-
-Steve Plimpton, sjplimp at sandia.gov
-Aidan Thompson, athomps at sandia.gov
-Paul Crozier, pscrozi at sandia.gov :ul
-
-The following folks are responsible for significant contributions to
-the code, or other aspects of the LAMMPS development effort.  Many of
-the packages they have written are somewhat unique to LAMMPS and the
-code would not be as general-purpose as it is without their expertise
-and efforts.
-
-Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM and USER-OMP packages
-Roy Pollock (LLNL), Ewald and PPPM solvers
-Mike Brown (ORNL), brownw at ornl.gov, GPU package
-Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
-Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
-Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
-Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
-Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
-Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package
-Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
-Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
-Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
-Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package :ul
-
-As discussed in "Section_history"_Section_history.html, LAMMPS
-originated as a cooperative project between DOE labs and industrial
-partners. Folks involved in the design and testing of the original
-version of LAMMPS were the following:
-
-John Carpenter (Mayo Clinic, formerly at Cray Research)
-Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
-Steve Lustig (Dupont)
-Jim Belak (LLNL) :ul

doc/Section_modify.txt

@@ -1,768 +0,0 @@
- "Previous Section"_Section_tools.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Section_python.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-10. Modifying & extending LAMMPS :h3
-
-This section describes how to customize LAMMPS by modifying
-and extending its source code.
-
-10.1 "Atom styles"_#mod_1
-10.2 "Bond, angle, dihedral, improper potentials"_#mod_2
-10.3 "Compute styles"_#mod_3
-10.4 "Dump styles"_#mod_4
-10.5 "Dump custom output options"_#mod_5
-10.6 "Fix styles"_#mod_6 which include integrators, \
-     temperature and pressure control, force constraints, \
-     boundary conditions, diagnostic output, etc
-10.7 "Input script commands"_mod_7
-10.8 "Kspace computations"_#mod_8
-10.9 "Minimization styles"_#mod_9
-10.10 "Pairwise potentials"_#mod_10
-10.11 "Region styles"_#mod_11
-10.12 "Body styles"_#mod_12
-10.13 "Thermodynamic output options"_#mod_13
-10.14 "Variable options"_#mod_14
-10.15 "Submitting new features for inclusion in LAMMPS"_#mod_15 :all(b)
-
-LAMMPS is designed in a modular fashion so as to be easy to modify and
-extend with new functionality.  In fact, about 75% of its source code
-is files added in this fashion.
-
-In this section, changes and additions users can make are listed along
-with minimal instructions.  If you add a new feature to LAMMPS and
-think it will be of interest to general users, we encourage you to
-submit it to the developers for inclusion in the released version of
-LAMMPS.  Information about how to do this is provided
-"below"_#mod_14.
-
-The best way to add a new feature is to find a similar feature in
-LAMMPS and look at the corresponding source and header files to figure
-out what it does.  You will need some knowledge of C++ to be able to
-understand the hi-level structure of LAMMPS and its class
-organization, but functions (class methods) that do actual
-computations are written in vanilla C-style code and operate on simple
-C-style data structures (vectors and arrays).
-
-Most of the new features described in this section require you to
-write a new C++ derived class (except for exceptions described below,
-where you can make small edits to existing files).  Creating a new
-class requires 2 files, a source code file (*.cpp) and a header file
-(*.h).  The derived class must provide certain methods to work as a
-new option.  Depending on how different your new feature is compared
-to existing features, you can either derive from the base class
-itself, or from a derived class that already exists.  Enabling LAMMPS
-to invoke the new class is as simple as putting the two source
-files in the src dir and re-building LAMMPS.
-
-The advantage of C++ and its object-orientation is that all the code
-and variables needed to define the new feature are in the 2 files you
-write, and thus shouldn't make the rest of LAMMPS more complex or
-cause side-effect bugs.
-
-Here is a concrete example.  Suppose you write 2 files pair_foo.cpp
-and pair_foo.h that define a new class PairFoo that computes pairwise
-potentials described in the classic 1997 "paper"_#Foo by Foo, et al.
-If you wish to invoke those potentials in a LAMMPS input script with a
-command like
-
-pair_style foo 0.1 3.5 :pre
-
-then your pair_foo.h file should be structured as follows:
-
-#ifdef PAIR_CLASS
-PairStyle(foo,PairFoo)
-#else
-...
-(class definition for PairFoo)
-...
-#endif :pre
-
-where "foo" is the style keyword in the pair_style command, and
-PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h
-files.
-
-When you re-build LAMMPS, your new pairwise potential becomes part of
-the executable and can be invoked with a pair_style command like the
-example above.  Arguments like 0.1 and 3.5 can be defined and
-processed by your new class.
-
-As illustrated by this pairwise example, many kinds of options are
-referred to in the LAMMPS documentation as the "style" of a particular
-command.
-
-The instructions below give the header file for the base class that
-these styles are derived from.  Public variables in that file are ones
-used and set by the derived classes which are also used by the base
-class.  Sometimes they are also used by the rest of LAMMPS.  Virtual
-functions in the base class header file which are set = 0 are ones you
-must define in your new derived class to give it the functionality
-LAMMPS expects.  Virtual functions that are not set to 0 are functions
-you can optionally define.
-
-Additionally, new output options can be added directly to the
-thermo.cpp, dump_custom.cpp, and variable.cpp files as explained
-below.
-
-Here are additional guidelines for modifying LAMMPS and adding new
-functionality:
-
-Think about whether what you want to do would be better as a pre- or
-post-processing step.  Many computations are more easily and more
-quickly done that way. :ulb,l
-
-Don't do anything within the timestepping of a run that isn't
-parallel.  E.g. don't accumulate a bunch of data on a single processor
-and analyze it.  You run the risk of seriously degrading the parallel
-efficiency. :l
-
-If your new feature reads arguments or writes output, make sure you
-follow the unit conventions discussed by the "units"_units.html
-command. :l
-
-If you add something you think is truly useful and doesn't impact
-LAMMPS performance when it isn't used, send an email to the
-"developers"_http://lammps.sandia.gov/authors.html.  We might be
-interested in adding it to the LAMMPS distribution.  See further
-details on this at the bottom of this page. :l,ule
-
-:line
-:line
-
-10.1 Atom styles :link(mod_1),h4
-
-Classes that define an "atom style"_atom_style.html are derived from
-the AtomVec class and managed by the Atom class.  The atom style
-determines what attributes are associated with an atom.  A new atom
-style can be created if one of the existing atom styles does not
-define all the attributes you need to store and communicate with
-atoms.
-
-Atom_vec_atomic.cpp is a simple example of an atom style.
-
-Here is a brief description of methods you define in your new derived
-class.  See atom_vec.h for details.
-
-init: one time setup (optional)
-grow: re-allocate atom arrays to longer lengths (required)
-grow_reset: make array pointers in Atom and AtomVec classes consistent (required)
-copy: copy info for one atom to another atom's array locations (required)
-pack_comm: store an atom's info in a buffer communicated every timestep (required)
-pack_comm_vel: add velocity info to communication buffer (required)
-pack_comm_hybrid: store extra info unique to this atom style (optional)
-unpack_comm: retrieve an atom's info from the buffer (required)
-unpack_comm_vel: also retrieve velocity info (required)
-unpack_comm_hybrid: retreive extra info unique to this atom style (optional)
-pack_reverse: store an atom's info in a buffer communicating partial forces  (required)
-pack_reverse_hybrid: store extra info unique to this atom style (optional)
-unpack_reverse: retrieve an atom's info from the buffer (required)
-unpack_reverse_hybrid: retreive extra info unique to this atom style (optional)
-pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required)
-pack_border_vel: add velocity info to buffer (required)
-pack_border_hybrid: store extra info unique to this atom style (optional)
-unpack_border: retrieve an atom's info from the buffer (required)
-unpack_border_vel: also retrieve velocity info (required)
-unpack_border_hybrid: retreive extra info unique to this atom style (optional)
-pack_exchange: store all an atom's info to migrate to another processor (required)
-unpack_exchange: retrieve an atom's info from the buffer (required)
-size_restart: number of restart quantities associated with proc's atoms (required)
-pack_restart: pack atom quantities into a buffer (required)
-unpack_restart: unpack atom quantities from a buffer (required)
-create_atom: create an individual atom of this style (required)
-data_atom: parse an atom line from the data file (required)
-data_atom_hybrid: parse additional atom info unique to this atom style (optional)
-data_vel: parse one line of velocity information from data file (optional)
-data_vel_hybrid: parse additional velocity data unique to this atom style (optional)
-memory_usage: tally memory allocated by atom arrays (required) :tb(s=:)
-
-The constructor of the derived class sets values for several variables
-that you must set when defining a new atom style, which are documented
-in atom_vec.h.  New atom arrays are defined in atom.cpp.  Search for
-the word "customize" and you will find locations you will need to
-modify.
-
-NOTE: It is possible to add some attributes, such as a molecule ID, to
-atom styles that do not have them via the "fix
-property/atom"_fix_property_atom.html command.  This command also
-allows new custom attributes consisting of extra integer or
-floating-point values to be added to atoms.  See the "fix
-property/atom"_fix_property_atom.html doc page for examples of cases
-where this is useful and details on how to initialize, access, and
-output the custom values.
-
-New "pair styles"_pair_style.html, "fixes"_fix.html, or
-"computes"_compute.html can be added to LAMMPS, as discussed below.
-The code for these classes can use the per-atom properties defined by
-fix property/atom.  The Atom class has a find_custom() method that is
-useful in this context:
-
-int index = atom->find_custom(char *name, int &flag); :pre
-
-The "name" of a custom attribute, as specified in the "fix
-property/atom"_fix_property_atom.html command, is checked to verify
-that it exists and its index is returned.  The method also sets flag =
-0/1 depending on whether it is an integer or floating-point attribute.
-The vector of values associated with the attribute can then be
-accessed using the returned index as
-
-int *ivector = atom->ivector\[index\];
-double *dvector = atom->dvector\[index\]; :pre
-
-Ivector or dvector are vectors of length Nlocal = # of owned atoms,
-which store the attributes of individual atoms.
-
-:line
-
-10.2 Bond, angle, dihedral, improper potentials :link(mod_2),h4
-
-Classes that compute molecular interactions are derived from the Bond,
-Angle, Dihedral, and Improper classes.  New styles can be created to
-add new potentials to LAMMPS.
-
-Bond_harmonic.cpp is the simplest example of a bond style.  Ditto for
-the harmonic forms of the angle, dihedral, and improper style
-commands.
-
-Here is a brief description of common methods you define in your
-new derived class.  See bond.h, angle.h, dihedral.h, and improper.h
-for details and specific additional methods.
-
-init: check if all coefficients are set, calls {init_style} (optional)
-init_style: check if style specific conditions are met (optional)
-compute: compute the molecular interactions (required)
-settings: apply global settings for all types (optional)
-coeff: set coefficients for one type (required)
-equilibrium_distance: length of bond, used by SHAKE (required, bond only)
-equilibrium_angle: opening of angle, used by SHAKE (required, angle only)
-write & read_restart: writes/reads coeffs to restart files (required)
-single: force and energy of a single bond or angle (required, bond or angle only)
-memory_usage: tally memory allocated by the style (optional) :tb(s=:)
-
-:line
-
-10.3 Compute styles :link(mod_3),h4
-
-Classes that compute scalar and vector quantities like temperature
-and the pressure tensor, as well as classes that compute per-atom
-quantities like kinetic energy and the centro-symmetry parameter
-are derived from the Compute class.  New styles can be created
-to add new calculations to LAMMPS.
-
-Compute_temp.cpp is a simple example of computing a scalar
-temperature.  Compute_ke_atom.cpp is a simple example of computing
-per-atom kinetic energy.
-
-Here is a brief description of methods you define in your new derived
-class.  See compute.h for details.
-
-init: perform one time setup (required)
-init_list: neighbor list setup, if needed (optional)
-compute_scalar: compute a scalar quantity (optional)
-compute_vector: compute a vector of quantities (optional)
-compute_peratom: compute one or more quantities per atom (optional)
-compute_local: compute one or more quantities per processor (optional)
-pack_comm: pack a buffer with items to communicate (optional)
-unpack_comm: unpack the buffer (optional)
-pack_reverse: pack a buffer with items to reverse communicate (optional)
-unpack_reverse: unpack the buffer (optional)
-remove_bias: remove velocity bias from one atom (optional)
-remove_bias_all: remove velocity bias from all atoms in group (optional)
-restore_bias: restore velocity bias for one atom after remove_bias (optional)
-restore_bias_all: same as before, but for all atoms in group (optional)
-pair_tally_callback: callback function for {tally}-style computes (optional).
-memory_usage: tally memory usage (optional) :tb(s=:)
-
-Tally-style computes are a special case, as their computation is done
-in two stages: the callback function is registered with the pair style
-and then called from the Pair::ev_tally() function, which is called for
-each pair after force and energy has been computed for this pair. Then
-the tallied values are retrieved with the standard compute_scalar or
-compute_vector or compute_peratom methods. The USER-TALLY package
-provides {examples}_compute_tally.html for utilizing this mechanism.
-
-:line
-
-10.4 Dump styles :link(mod_4),h4
-10.5 Dump custom output options :link(mod_5),h4
-
-Classes that dump per-atom info to files are derived from the Dump
-class.  To dump new quantities or in a new format, a new derived dump
-class can be added, but it is typically simpler to modify the
-DumpCustom class contained in the dump_custom.cpp file.
-
-Dump_atom.cpp is a simple example of a derived dump class.
-
-Here is a brief description of methods you define in your new derived
-class.  See dump.h for details.
-
-write_header: write the header section of a snapshot of atoms
-count: count the number of lines a processor will output
-pack: pack a proc's output data into a buffer
-write_data: write a proc's data to a file :tb(s=:)
-
-See the "dump"_dump.html command and its {custom} style for a list of
-keywords for atom information that can already be dumped by
-DumpCustom.  It includes options to dump per-atom info from Compute
-classes, so adding a new derived Compute class is one way to calculate
-new quantities to dump.
-
-Alternatively, you can add new keywords to the dump custom command.
-Search for the word "customize" in dump_custom.cpp to see the
-half-dozen or so locations where code will need to be added.
-
-:line
-
-10.6 Fix styles :link(mod_6),h4
-
-In LAMMPS, a "fix" is any operation that is computed during
-timestepping that alters some property of the system.  Essentially
-everything that happens during a simulation besides force computation,
-neighbor list construction, and output, is a "fix".  This includes
-time integration (update of coordinates and velocities), force
-constraints or boundary conditions (SHAKE or walls), and diagnostics
-(compute a diffusion coefficient).  New styles can be created to add
-new options to LAMMPS.
-
-Fix_setforce.cpp is a simple example of setting forces on atoms to
-prescribed values.  There are dozens of fix options already in LAMMPS;
-choose one as a template that is similar to what you want to
-implement.
-
-Here is a brief description of methods you can define in your new
-derived class.  See fix.h for details.
-
-setmask: determines when the fix is called during the timestep (required)
-init: initialization before a run (optional)
-setup_pre_exchange: called before atom exchange in setup (optional)
-setup_pre_force: called before force computation in setup (optional)
-setup: called immediately before the 1st timestep and after forces are computed (optional)
-min_setup_pre_force: like setup_pre_force, but for minimizations instead of MD runs (optional)
-min_setup: like setup, but for minimizations instead of MD runs (optional)
-initial_integrate: called at very beginning of each timestep (optional)
-pre_exchange: called before atom exchange on re-neighboring steps (optional)
-pre_neighbor: called before neighbor list build (optional)
-pre_force: called before pair & molecular forces are computed (optional)
-post_force: called after pair & molecular forces are computed and communicated (optional)
-final_integrate: called at end of each timestep (optional)
-end_of_step: called at very end of timestep (optional)
-write_restart: dumps fix info to restart file (optional)
-restart: uses info from restart file to re-initialize the fix (optional)
-grow_arrays: allocate memory for atom-based arrays used by fix (optional)
-copy_arrays: copy atom info when an atom migrates to a new processor (optional)
-pack_exchange: store atom's data in a buffer (optional)
-unpack_exchange: retrieve atom's data from a buffer (optional)
-pack_restart: store atom's data for writing to restart file (optional)
-unpack_restart: retrieve atom's data from a restart file buffer (optional)
-size_restart: size of atom's data (optional)
-maxsize_restart: max size of atom's data (optional)
-setup_pre_force_respa: same as setup_pre_force, but for rRESPA (optional)
-initial_integrate_respa: same as initial_integrate, but for rRESPA (optional)
-post_integrate_respa: called after the first half integration step is done in rRESPA (optional)
-pre_force_respa: same as pre_force, but for rRESPA (optional)
-post_force_respa: same as post_force, but for rRESPA (optional)
-final_integrate_respa: same as final_integrate, but for rRESPA (optional)
-min_pre_force: called after pair & molecular forces are computed in minimizer (optional)
-min_post_force: called after pair & molecular forces are computed and communicated in minmizer (optional)
-min_store: store extra data for linesearch based minimization on a LIFO stack (optional)
-min_pushstore: push the minimization LIFO stack one element down (optional)
-min_popstore: pop the minimization LIFO stack one element up (optional)
-min_clearstore: clear minimization LIFO stack (optional)
-min_step: reset or move forward on line search minimization (optional)
-min_dof: report number of degrees of freedom {added} by this fix in minimization (optional)
-max_alpha: report maximum allowed step size during linesearch minimization (optional)
-pack_comm: pack a buffer to communicate a per-atom quantity (optional)
-unpack_comm: unpack a buffer to communicate a per-atom quantity (optional)
-pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity (optional)
-unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity (optional)
-dof: report number of degrees of freedom {removed} by this fix during MD (optional)
-compute_scalar: return a global scalar property that the fix computes (optional)
-compute_vector: return a component of a vector property that the fix computes (optional)
-compute_array: return a component of an array property that the fix computes (optional)
-deform: called when the box size is changed (optional)
-reset_target: called when a change of the target temperature is requested during a run (optional)
-reset_dt: is called when a change of the time step is requested during a run (optional)
-modify_param: called when a fix_modify request is executed (optional)
-memory_usage: report memory used by fix (optional)
-thermo: compute quantities for thermodynamic output (optional) :tb(s=:)
-
-Typically, only a small fraction of these methods are defined for a
-particular fix.  Setmask is mandatory, as it determines when the fix
-will be invoked during the timestep.  Fixes that perform time
-integration ({nve}, {nvt}, {npt}) implement initial_integrate() and
-final_integrate() to perform velocity Verlet updates.  Fixes that
-constrain forces implement post_force().
-
-Fixes that perform diagnostics typically implement end_of_step().  For
-an end_of_step fix, one of your fix arguments must be the variable
-"nevery" which is used to determine when to call the fix and you must
-set this variable in the constructor of your fix.  By convention, this
-is the first argument the fix defines (after the ID, group-ID, style).
-
-If the fix needs to store information for each atom that persists from
-timestep to timestep, it can manage that memory and migrate the info
-with the atoms as they move from processors to processor by
-implementing the grow_arrays, copy_arrays, pack_exchange, and
-unpack_exchange methods.  Similarly, the pack_restart and
-unpack_restart methods can be implemented to store information about
-the fix in restart files.  If you wish an integrator or force
-constraint fix to work with rRESPA (see the "run_style"_run_style.html
-command), the initial_integrate, post_force_integrate, and
-final_integrate_respa methods can be implemented.  The thermo method
-enables a fix to contribute values to thermodynamic output, as printed
-quantities and/or to be summed to the potential energy of the system.
-
-:line
-
-10.7 Input script commands :link(mod_7),h4
-
-New commands can be added to LAMMPS input scripts by adding new
-classes that have a "command" method.  For example, the create_atoms,
-read_data, velocity, and run commands are all implemented in this
-fashion.  When such a command is encountered in the LAMMPS input
-script, LAMMPS simply creates a class with the corresponding name,
-invokes the "command" method of the class, and passes it the arguments
-from the input script.  The command method can perform whatever
-operations it wishes on LAMMPS data structures.
-
-The single method your new class must define is as follows:
-
-command: operations performed by the new command :tb(s=:)
-
-Of course, the new class can define other methods and variables as
-needed.
-
-:line
-
-10.8 Kspace computations :link(mod_8),h4
-
-Classes that compute long-range Coulombic interactions via K-space
-representations (Ewald, PPPM) are derived from the KSpace class.  New
-styles can be created to add new K-space options to LAMMPS.
-
-Ewald.cpp is an example of computing K-space interactions.
-
-Here is a brief description of methods you define in your new derived
-class.  See kspace.h for details.
-
-init: initialize the calculation before a run
-setup: computation before the 1st timestep of a run
-compute: every-timestep computation
-memory_usage: tally of memory usage :tb(s=:)
-
-:line
-
-10.9 Minimization styles :link(mod_9),h4
-
-Classes that perform energy minimization derived from the Min class.
-New styles can be created to add new minimization algorithms to
-LAMMPS.
-
-Min_cg.cpp is an example of conjugate gradient minimization.
-
-Here is a brief description of methods you define in your new derived
-class.  See min.h for details.
-
-init: initialize the minimization before a run
-run: perform the minimization
-memory_usage: tally of memory usage :tb(s=:)
-
-:line
-
-10.10 Pairwise potentials :link(mod_10),h4
-
-Classes that compute pairwise interactions are derived from the Pair
-class.  In LAMMPS, pairwise calculation include manybody potentials
-such as EAM or Tersoff where particles interact without a static bond
-topology.  New styles can be created to add new pair potentials to
-LAMMPS.
-
-Pair_lj_cut.cpp is a simple example of a Pair class, though it
-includes some optional methods to enable its use with rRESPA.
-
-Here is a brief description of the class methods in pair.h:
-
-compute: workhorse routine that computes pairwise interactions
-settings: reads the input script line with arguments you define
-coeff: set coefficients for one i,j type pair
-init_one: perform initialization for one i,j type pair
-init_style: initialization specific to this pair style
-write & read_restart: write/read i,j pair coeffs to restart files
-write & read_restart_settings: write/read global settings to restart files
-single: force and energy of a single pairwise interaction between 2 atoms
-compute_inner/middle/outer: versions of compute used by rRESPA :tb(s=:)
-
-The inner/middle/outer routines are optional.
-
-:line
-
-10.11 Region styles :link(mod_11),h4
-
-Classes that define geometric regions are derived from the Region
-class.  Regions are used elsewhere in LAMMPS to group atoms, delete
-atoms to create a void, insert atoms in a specified region, etc.  New
-styles can be created to add new region shapes to LAMMPS.
-
-Region_sphere.cpp is an example of a spherical region.
-
-Here is a brief description of methods you define in your new derived
-class.  See region.h for details.
-
-match: determine whether a point is in the region :tb(s=:)
-
-:line
-
-10.11 Body styles :link(mod_12),h4
-
-Classes that define body particles are derived from the Body class.
-Body particles can represent complex entities, such as surface meshes
-of discrete points, collections of sub-particles, deformable objects,
-etc.
-
-See "Section_howto 14"_Section_howto.html#howto_14 of the manual for
-an overview of using body particles and the "body"_body.html doc page
-for details on the various body styles LAMMPS supports.  New styles
-can be created to add new kinds of body particles to LAMMPS.
-
-Body_nparticle.cpp is an example of a body particle that is treated as
-a rigid body containing N sub-particles.
-
-Here is a brief description of methods you define in your new derived
-class.  See body.h for details.
-
-data_body: process a line from the Bodies section of a data file
-noutrow: number of sub-particles output is generated for
-noutcol: number of values per-sub-particle output is generated for
-output: output values for the Mth sub-particle
-pack_comm_body: body attributes to communicate every timestep
-unpack_comm_body: unpacking of those attributes
-pack_border_body: body attributes to communicate when reneighboring is done
-unpack_border_body: unpacking of those attributes :tb(s=:)
-
-:line
-
-10.13 Thermodynamic output options :link(mod_13),h4
-
-There is one class that computes and prints thermodynamic information
-to the screen and log file; see the file thermo.cpp.
-
-There are two styles defined in thermo.cpp: "one" and "multi".  There
-is also a flexible "custom" style which allows the user to explicitly
-list keywords for quantities to print when thermodynamic info is
-output.  See the "thermo_style"_thermo_style.html command for a list
-of defined quantities.
-
-The thermo styles (one, multi, etc) are simply lists of keywords.
-Adding a new style thus only requires defining a new list of keywords.
-Search for the word "customize" with references to "thermo style" in
-thermo.cpp to see the two locations where code will need to be added.
-
-New keywords can also be added to thermo.cpp to compute new quantities
-for output.  Search for the word "customize" with references to
-"keyword" in thermo.cpp to see the several locations where code will
-need to be added.
-
-Note that the "thermo_style custom"_thermo.html command already allows
-for thermo output of quantities calculated by "fixes"_fix.html,
-"computes"_compute.html, and "variables"_variable.html.  Thus, it may
-be simpler to compute what you wish via one of those constructs, than
-by adding a new keyword to the thermo command.
-
-:line
-
-10.14 Variable options :link(mod_14),h4
-
-There is one class that computes and stores "variable"_variable.html
-information in LAMMPS; see the file variable.cpp.  The value
-associated with a variable can be periodically printed to the screen
-via the "print"_print.html, "fix print"_fix_print.html, or
-"thermo_style custom"_thermo_style.html commands.  Variables of style
-"equal" can compute complex equations that involve the following types
-of arguments:
-
-thermo keywords = ke, vol, atoms, ...
-other variables = v_a, v_myvar, ...
-math functions = div(x,y), mult(x,y), add(x,y), ...
-group functions = mass(group), xcm(group,x), ...
-atom values = x\[123\], y\[3\], vx\[34\], ...
-compute values = c_mytemp\[0\], c_thermo_press\[3\], ... :pre
-
-Adding keywords for the "thermo_style custom"_thermo_style.html command
-(which can then be accessed by variables) was discussed
-"here"_Section_modify.html#thermo on this page.
-
-Adding a new math function of one or two arguments can be done by
-editing one section of the Variable::evaulate() method.  Search for
-the word "customize" to find the appropriate location.
-
-Adding a new group function can be done by editing one section of the
-Variable::evaulate() method.  Search for the word "customize" to find
-the appropriate location.  You may need to add a new method to the
-Group class as well (see the group.cpp file).
-
-Accessing a new atom-based vector can be done by editing one section
-of the Variable::evaulate() method.  Search for the word "customize"
-to find the appropriate location.
-
-Adding new "compute styles"_compute.html (whose calculated values can
-then be accessed by variables) was discussed
-"here"_Section_modify.html#compute on this page.
-
-:line
-:line
-
-10.15 Submitting new features for inclusion in LAMMPS :link(mod_15),h4
-
-We encourage users to submit new features to "the
-developers"_http://lammps.sandia.gov/authors.html that they add to
-LAMMPS, especially if you think they will be of interest to other
-users.  If they are broadly useful we may add them as core files to
-LAMMPS or as part of a "standard package"_Section_start.html#start_3.
-Else we will add them as a user-contributed file or package.  Examples
-of user packages are in src sub-directories that start with USER.  The
-USER-MISC package is simply a collection of (mostly) unrelated single
-files, which is the simplest way to have your contribution quickly
-added to the LAMMPS distribution.  You can see a list of the both
-standard and user packages by typing "make package" in the LAMMPS src
-directory.
-
-Note that by providing us the files to release, you are agreeing to
-make them open-source, i.e. we can release them under the terms of the
-GPL, used as a license for the rest of LAMMPS.  See "Section
-1.4"_Section_intro.html#intro_4 for details.
-
-With user packages and files, all we are really providing (aside from
-the fame and fortune that accompanies having your name in the source
-code and on the "Authors page"_http://lammps.sandia.gov/authors.html
-of the "LAMMPS WWW site"_lws), is a means for you to distribute your
-work to the LAMMPS user community, and a mechanism for others to
-easily try out your new feature.  This may help you find bugs or make
-contact with new collaborators.  Note that you're also implicitly
-agreeing to support your code which means answer questions, fix bugs,
-and maintain it if LAMMPS changes in some way that breaks it (an
-unusual event).
-
-NOTE: If you prefer to actively develop and support your add-on
-feature yourself, then you may wish to make it available for download
-from your own website, as a user package that LAMMPS users can add to
-their copy of LAMMPS.  See the "Offsite LAMMPS packages and
-tools"_http://lammps.sandia.gov/offsite.html page of the LAMMPS web
-site for examples of groups that do this.  We are happy to advertise
-your package and web site from that page.  Simply email the
-"developers"_http://lammps.sandia.gov/authors.html with info about
-your package and we will post it there.
-
-The previous sections of this doc page describe how to add new "style"
-files of various kinds to LAMMPS.  Packages are simply collections of
-one or more new class files which are invoked as a new style within a
-LAMMPS input script.  If designed correctly, these additions typically
-do not require changes to the main core of LAMMPS; they are simply
-add-on files.  If you think your new feature requires non-trivial
-changes in core LAMMPS files, you'll need to "communicate with the
-developers"_http://lammps.sandia.gov/authors.html, since we may or may
-not want to make those changes.  An example of a trivial change is
-making a parent-class method "virtual" when you derive a new child
-class from it.
-
-Here are the steps you need to follow to submit a single file or user
-package for our consideration.  Following these steps will save both
-you and us time.  See existing files in packages in the src dir for
-examples.
-
-All source files you provide must compile with the most current
-version of LAMMPS. :ulb,l
-
-If you want your file(s) to be added to main LAMMPS or one of its
-standard packages, then it needs to be written in a style compatible
-with other LAMMPS source files.  This is so the developers can
-understand it and hopefully maintain it.  This basically means that
-the code accesses data structures, performs its operations, and is
-formatted similar to other LAMMPS source files, including the use of
-the error class for error and warning messages. :l
-
-If you want your contribution to be added as a user-contributed
-feature, and it's a single file (actually a *.cpp and *.h file) it can
-rapidly be added to the USER-MISC directory.  Send us the one-line
-entry to add to the USER-MISC/README file in that dir, along with the
-2 source files.  You can do this multiple times if you wish to
-contribute several individual features.  :l
-
-If you want your contribution to be added as a user-contribution and
-it is several related featues, it is probably best to make it a user
-package directory with a name like USER-FOO.  In addition to your new
-files, the directory should contain a README text file.  The README
-should contain your name and contact information and a brief
-description of what your new package does.  If your files depend on
-other LAMMPS style files also being installed (e.g. because your file
-is a derived class from the other LAMMPS class), then an Install.sh
-file is also needed to check for those dependencies.  See other README
-and Install.sh files in other USER directories as examples.  Send us a
-tarball of this USER-FOO directory. :l
-
-Your new source files need to have the LAMMPS copyright, GPL notice,
-and your name and email address at the top, like other
-user-contributed LAMMPS source files.  They need to create a class
-that is inside the LAMMPS namespace.  If the file is for one of the
-USER packages, including USER-MISC, then we are not as picky about the
-coding style (see above).  I.e. the files do not need to be in the
-same stylistic format and syntax as other LAMMPS files, though that
-would be nice for developers as well as users who try to read your
-code. :l
-
-You must also create a documentation file for each new command or
-style you are adding to LAMMPS.  This will be one file for a
-single-file feature.  For a package, it might be several files.  These
-are simple text files which we auto-convert to HTML.  Thus they must
-be in the same format as other *.txt files in the lammps/doc directory
-for similar commands and styles; use one or more of them as a starting
-point.  As appropriate, the text files can include links to equations
-(see doc/Eqs/*.tex for examples, we auto-create the associated JPG
-files), or figures (see doc/JPG for examples), or even additional PDF
-files with further details (see doc/PDF for examples).  The doc page
-should also include literature citations as appropriate; see the
-bottom of doc/fix_nh.txt for examples and the earlier part of the same
-file for how to format the cite itself.  The "Restrictions" section of
-the doc page should indicate that your command is only available if
-LAMMPS is built with the appropriate USER-MISC or USER-FOO package.
-See other user package doc files for examples of how to do this.  The
-txt2html tool we use to convert to HTML can be downloaded from "this
-site"_http://www.sandia.gov/~sjplimp/download.html, so you can perform
-the HTML conversion yourself to proofread your doc page. :l
-
-For a new package (or even a single command) you can include one or
-more example scripts.  These should run in no more than 1 minute, even
-on a single processor, and not require large data files as input.  See
-directories under examples/USER for examples of input scripts other
-users provided for their packages. :l
-
-If there is a paper of yours describing your feature (either the
-algorithm/science behind the feature itself, or its initial usage, or
-its implementation in LAMMPS), you can add the citation to the *.cpp
-source file.  See src/USER-EFF/atom_vec_electron.cpp for an example.
-A LaTeX citation is stored in a variable at the top of the file and a
-single line of code that references the variable is added to the
-constructor of the class.  Whenever a user invokes your feature from
-their input script, this will cause LAMMPS to output the citation to a
-log.cite file and prompt the user to examine the file.  Note that you
-should only use this for a paper you or your group authored.
-E.g. adding a cite in the code for a paper by Nose and Hoover if you
-write a fix that implements their integrator is not the intended
-usage.  That kind of citation should just be in the doc page you
-provide. :l,ule
-
-Finally, as a general rule-of-thumb, the more clear and
-self-explanatory you make your doc and README files, and the easier
-you make it for people to get started, e.g. by providing example
-scripts, the more likely it is that users will try out your new
-feature.
-
-:line
-:line
-
-:link(Foo)
-[(Foo)] Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997).

doc/Section_packages.txt

@@ -1,889 +0,0 @@
-"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.
-
-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. 
-
-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
-REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax,  lib/reax
-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-DPD, dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
-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-MGPT, fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, -
-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-SMTBQ, Second Moment Tight Binding - QEq potential, Salles & Maras & Politano & Tetot (4), "pair_style smtbq"_pair_smtbq.html, USER/smtbq, -, -
-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.
-
-(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).
-
-(4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
-Olivier Politano, and Robert Tetot (LAAS-CNRS, France).
-
-(4) The USER-DPD package was created by James Larentzos, Timothy
-Mattox, and John Brennan (Army Research Lab (ARL) and Engility Corp).
-
-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 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.
-
-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-DPD package :h4
-
-This package implements the dissipative particle dynamics (DPD) method
-under isothermal, isoenergetic, isobaric and isenthalpic conditions.
-The DPD equations of motion are integrated efficiently through the
-Shardlow splitting algorithm.
-
-See these doc pages and their related commands to get started:
-
-"compute dpd"_compute_dpd.html
-"compute dpd/atom"_compute_dpd_atom.html
-"fix_eos/cv"_fix_eos_table.html
-"fix_eos/table"_fix_eos_table.html
-"fix_shardlow"_fix_shardlow.html
-"pair_dpd/conservative"_pair_dpd_conservative.html
-"pair_dpd/fdt"_pair_dpd_fdt.html
-"pair_dpd/fdt/energy"_pair_dpd_fdt.html :ul
-
-There are example scripts for using this package in examples/USER/dpd.
-
-The people who created this package are James Larentzos
-(james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at
-engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil).
-Contact them 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-MGPT package :h4
-
-This package contains a fast implementation for LAMMPS of
-quantum-based MGPT multi-ion potentials.  The MGPT or model GPT method
-derives from first-principles DFT-based generalized pseudopotential
-theory (GPT) through a series of systematic approximations valid for
-mid-period transition metals with nearly half-filled d bands.  The
-MGPT method was originally developed by John Moriarty at Lawrence
-Livermore National Lab (LLNL).
-
-In the general matrix representation of MGPT, which can also be
-applied to f-band actinide metals, the multi-ion potentials are
-evaluated on the fly during a simulation through d- or f-state matrix
-multiplication, and the forces that move the ions are determined
-analytically.  The {mgpt} pair style in this package calculates forces
-and energies using an optimized matrix-MGPT algorithm due to Tomas
-Oppelstrup at LLNL.
-
-See this doc page to get started:
-
-"pair_style mgpt"_pair_mgpt.html
-
-The persons who created the USER-MGPT package are Tomas Oppelstrup
-(oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov)
-Contact them directly if you have any 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.
-
-:line
-
-USER-SMTBQ package :h4
-
-This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
-potential for the description of ionocovalent bonds in oxides.
-
-There are example scripts for using this package in
-examples/USER/smtbq.
-
-See this doc page to get started:
-
-"pair_style smtbq"_pair_smtbq.html
-
-The persons who created the USER-SMTBQ package are Nicolas Salles,
-Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at
-these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr.  Contact
-them directly if you have any questions.
-
-:line
-
-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.

doc/Section_perf.html

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-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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-            
-  <div class="section" id="performance-scalability">
-<h1>8. Performance &amp; scalability<a class="headerlink" href="#performance-scalability" title="Permalink to this headline">¶</a></h1>
-<p>LAMMPS performance on several prototypical benchmarks and machines is
-discussed on the Benchmarks page of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> where
-CPU timings and parallel efficiencies are listed.  Here, the
-benchmarks are described briefly and some useful rules of thumb about
-their performance are highlighted.</p>
-<p>These are the 5 benchmark problems:</p>
-<ol class="arabic simple">
-<li>LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55</li>
-</ol>
-<blockquote>
-<div>neighbors per atom), NVE integration</div></blockquote>
-<ol class="arabic simple">
-<li>Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ
-pairwise interactions with a 2^(1/6) sigma cutoff (5 neighbors per
-atom), NVE integration</li>
-<li>EAM = metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45
-neighbors per atom), NVE integration</li>
-<li>Chute = granular chute flow, frictional history potential with 1.1
-sigma cutoff (7 neighbors per atom), NVE integration</li>
-<li>Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force
-field with a 10 Angstrom LJ cutoff (440 neighbors per atom),
-particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT
-integration</li>
-</ol>
-<p>The input files for running the benchmarks are included in the LAMMPS
-distribution, as are sample output files.  Each of the 5 problems has
-32,000 atoms and runs for 100 timesteps.  Each can be run as a serial
-benchmarks (on one processor) or in parallel.  In parallel, each
-benchmark can be run as a fixed-size or scaled-size problem.  For
-fixed-size benchmarking, the same 32K atom problem is run on various
-numbers of processors.  For scaled-size benchmarking, the model size
-is increased with the number of processors.  E.g. on 8 processors, a
-256K-atom problem is run; on 1024 processors, a 32-million atom
-problem is run, etc.</p>
-<p>A useful metric from the benchmarks is the CPU cost per atom per
-timestep.  Since LAMMPS performance scales roughly linearly with
-problem size and timesteps, the run time of any problem using the same
-model (atom style, force field, cutoff, etc) can then be estimated.
-For example, on a 1.7 GHz Pentium desktop machine (Intel icc compiler
-under Red Hat Linux), the CPU run-time in seconds/atom/timestep for
-the 5 problems is</p>
-<table border="1" class="docutils">
-<colgroup>
-<col width="25%" />
-<col width="14%" />
-<col width="14%" />
-<col width="14%" />
-<col width="14%" />
-<col width="17%" />
-</colgroup>
-<tbody valign="top">
-<tr class="row-odd"><td>Problem:</td>
-<td>LJ</td>
-<td>Chain</td>
-<td>EAM</td>
-<td>Chute</td>
-<td>Rhodopsin</td>
-</tr>
-<tr class="row-even"><td>CPU/atom/step:</td>
-<td>4.55E-6</td>
-<td>2.18E-6</td>
-<td>9.38E-6</td>
-<td>2.18E-6</td>
-<td>1.11E-4</td>
-</tr>
-<tr class="row-odd"><td>Ratio to LJ:</td>
-<td>1.0</td>
-<td>0.48</td>
-<td>2.06</td>
-<td>0.48</td>
-<td>24.5</td>
-</tr>
-</tbody>
-</table>
-<p>The ratios mean that if the atomic LJ system has a normalized cost of
-1.0, the bead-spring chains and granular systems run 2x faster, while
-the EAM metal and solvated protein models run 2x and 25x slower
-respectively.  The bulk of these cost differences is due to the
-expense of computing a particular pairwise force field for a given
-number of neighbors per atom.</p>
-<p>Performance on a parallel machine can also be predicted from the
-one-processor timings if the parallel efficiency can be estimated.
-The communication bandwidth and latency of a particular parallel
-machine affects the efficiency.  On most machines LAMMPS will give
-fixed-size parallel efficiencies on these benchmarks above 50% so long
-as the atoms/processor count is a few 100 or greater - i.e. on 64 to
-128 processors.  Likewise, scaled-size parallel efficiencies will
-typically be 80% or greater up to very large processor counts.  The
-benchmark data on the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> gives specific examples on
-some different machines, including a run of 3/4 of a billion LJ atoms
-on 1500 processors that ran at 85% parallel efficiency.</p>
-</div>
-
-
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doc/Section_perf.txt

@@ -1,77 +0,0 @@
-"Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_tools.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-8. Performance & scalability :h3
-
-LAMMPS performance on several prototypical benchmarks and machines is
-discussed on the Benchmarks page of the "LAMMPS WWW Site"_lws where
-CPU timings and parallel efficiencies are listed.  Here, the
-benchmarks are described briefly and some useful rules of thumb about
-their performance are highlighted.
-
-These are the 5 benchmark problems:
-
-LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55
-neighbors per atom), NVE integration :olb,l
-
-Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ
-pairwise interactions with a 2^(1/6) sigma cutoff (5 neighbors per
-atom), NVE integration :l
-
-EAM = metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45
-neighbors per atom), NVE integration :l
-
-Chute = granular chute flow, frictional history potential with 1.1
-sigma cutoff (7 neighbors per atom), NVE integration :l
-
-Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force
-field with a 10 Angstrom LJ cutoff (440 neighbors per atom),
-particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT
-integration :ole,l
-
-The input files for running the benchmarks are included in the LAMMPS
-distribution, as are sample output files.  Each of the 5 problems has
-32,000 atoms and runs for 100 timesteps.  Each can be run as a serial
-benchmarks (on one processor) or in parallel.  In parallel, each
-benchmark can be run as a fixed-size or scaled-size problem.  For
-fixed-size benchmarking, the same 32K atom problem is run on various
-numbers of processors.  For scaled-size benchmarking, the model size
-is increased with the number of processors.  E.g. on 8 processors, a
-256K-atom problem is run; on 1024 processors, a 32-million atom
-problem is run, etc.
-
-A useful metric from the benchmarks is the CPU cost per atom per
-timestep.  Since LAMMPS performance scales roughly linearly with
-problem size and timesteps, the run time of any problem using the same
-model (atom style, force field, cutoff, etc) can then be estimated.
-For example, on a 1.7 GHz Pentium desktop machine (Intel icc compiler
-under Red Hat Linux), the CPU run-time in seconds/atom/timestep for
-the 5 problems is
-
-Problem:, LJ, Chain, EAM, Chute, Rhodopsin
-CPU/atom/step:, 4.55E-6, 2.18E-6, 9.38E-6, 2.18E-6, 1.11E-4
-Ratio to LJ:, 1.0, 0.48, 2.06, 0.48, 24.5 :tb(ea=c,ca1=r)
-
-The ratios mean that if the atomic LJ system has a normalized cost of
-1.0, the bead-spring chains and granular systems run 2x faster, while
-the EAM metal and solvated protein models run 2x and 25x slower
-respectively.  The bulk of these cost differences is due to the
-expense of computing a particular pairwise force field for a given
-number of neighbors per atom.
-
-Performance on a parallel machine can also be predicted from the
-one-processor timings if the parallel efficiency can be estimated.
-The communication bandwidth and latency of a particular parallel
-machine affects the efficiency.  On most machines LAMMPS will give
-fixed-size parallel efficiencies on these benchmarks above 50% so long
-as the atoms/processor count is a few 100 or greater - i.e. on 64 to
-128 processors.  Likewise, scaled-size parallel efficiencies will
-typically be 80% or greater up to very large processor counts.  The
-benchmark data on the "LAMMPS WWW Site"_lws gives specific examples on
-some different machines, including a run of 3/4 of a billion LJ atoms
-on 1500 processors that ran at 85% parallel efficiency.

doc/Section_python.txt

@@ -1,839 +0,0 @@
-"Previous Section"_Section_modify.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_errors.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-11. Python interface to LAMMPS :h3
-
-LAMMPS can work together with Python in two ways.  First, Python can
-wrap LAMMPS through the "LAMMPS library
-interface"_Section_howto.html#howto_19, so that a Python script can
-create one or more instances of LAMMPS and launch one or more
-simulations.  In Python lingo, this is "extending" Python with LAMMPS.
-
-Second, LAMMPS can use the Python interpreter, so that a LAMMPS input
-script can invoke Python code, and pass information back-and-forth
-between the input script and Python functions you write.  The Python
-code can also callback to LAMMPS to query or change its attributes.
-In Python lingo, this is "embedding" Python in LAMMPS.
-
-This section describes how to do both.
-
-11.1 "Overview of running LAMMPS from Python"_#py_1
-11.2 "Overview of using Python from a LAMMPS script"_#py_2 
-11.3 "Building LAMMPS as a shared library"_#py_3
-11.4 "Installing the Python wrapper into Python"_#py_4
-11.5 "Extending Python with MPI to run in parallel"_#py_5
-11.6 "Testing the Python-LAMMPS interface"_#py_6
-11.7 "Using LAMMPS from Python"_#py_7
-11.8 "Example Python scripts that use LAMMPS"_#py_8 :ul
-
-If you are not familiar with it, "Python"_http://www.python.org is a
-powerful scripting and programming language which can essentially do
-anything that faster, lower-level languages like C or C++ can do, but
-typically with much fewer lines of code.  When used in embedded mode,
-Python can perform operations that the simplistic LAMMPS input script
-syntax cannot.  Python can be also be used as a "glue" language to
-drive a program through its library interface, or to hook multiple
-pieces of software together, such as a simulation package plus a
-visualization package, or to run a coupled multiscale or multiphysics
-model.
-
-See "Section_howto 10"_Section_howto.html#howto_10 of the manual and
-the couple directory of the distribution for more ideas about coupling
-LAMMPS to other codes.  See "Section_howto
-19"_Section_howto.html#howto_19 for a description of the LAMMPS
-library interface provided in src/library.cpp and src/library.h, and
-how to extend it for your needs.  As described below, that interface
-is what is exposed to Python either when calling LAMMPS from Python or
-when calling Python from a LAMMPS input script and then calling back
-to LAMMPS from Python code.  The library interface is designed to be
-easy to add functions to.  Thus the Python interface to LAMMPS is also
-easy to extend as well.
-
-If you create interesting Python scripts that run LAMMPS or
-interesting Python functions that can be called from a LAMMPS input
-script, that you think would be useful to other users, please "email
-them to the developers"_http://lammps.sandia.gov/authors.html.  We can
-include them in the LAMMPS distribution.
-
-:line
-:line
-
-11.1 Overview of running LAMMPS from Python :link(py_1),h4
-
-The LAMMPS distribution includes a python directory with all you need
-to run LAMMPS from Python.  The python/lammps.py file wraps the LAMMPS
-library interface, with one wrapper function per LAMMPS library
-function.  This file makes it is possible to do the following either
-from a Python script, or interactively from a Python prompt: create
-one or more instances of LAMMPS, invoke LAMMPS commands or give it an
-input script, run LAMMPS incrementally, extract LAMMPS results, an
-modify internal LAMMPS variables.  From a Python script you can do
-this in serial or parallel.  Running Python interactively in parallel
-does not generally work, unless you have a version of Python that
-extends standard Python to enable multiple instances of Python to read
-what you type.
-
-To do all of this, you must first build LAMMPS as a shared library,
-then insure that your Python can find the python/lammps.py file and
-the shared library.  These steps are explained in subsequent sections
-11.3 and 11.4.  Sections 11.5 and 11.6 discuss using MPI from a
-parallel Python program and how to test that you are ready to use
-LAMMPS from Python.  Section 11.7 lists all the functions in the
-current LAMMPS library interface and how to call them from Python.
-
-Section 11.8 gives some examples of coupling LAMMPS to other tools via
-Python.  For example, LAMMPS can easily be coupled to a GUI or other
-visualization tools that display graphs or animations in real time as
-LAMMPS runs.  Examples of such scripts are inlcluded in the python
-directory.
-
-Two advantages of using Python to run LAMMPS are how concise the
-language is, and that it can be run interactively, enabling rapid
-development and debugging of programs.  If you use it to mostly invoke
-costly operations within LAMMPS, such as running a simulation for a
-reasonable number of timesteps, then the overhead cost of invoking
-LAMMPS thru Python will be negligible.
-
-The Python wrapper for LAMMPS uses the amazing and magical (to me)
-"ctypes" package in Python, which auto-generates the interface code
-needed between Python and a set of C interface routines for a library.
-Ctypes is part of standard Python for versions 2.5 and later.  You can
-check which version of Python you have installed, by simply typing
-"python" at a shell prompt.
-
-:line
-
-11.2 Overview of using Python from a LAMMPS script :link(py_2),h4
-
-NOTE: It is not currently possible to use the "python"_python.html
-command described in this section with Python 3, only with Python 2.
-The C API changed from Python 2 to 3 and the LAMMPS code is not
-compatible with both.
-
-LAMMPS has a "python"_python.html command which can be used in an
-input script to define and execute a Python function that you write
-the code for.  The Python function can also be assigned to a LAMMPS
-python-style variable via the "variable"_variable.html command.  Each
-time the variable is evaluated, either in the LAMMPS input script
-itself, or by another LAMMPS command that uses the variable, this will
-trigger the Python function to be invoked.
-
-The Python code for the function can be included directly in the input
-script or in an auxiliary file.  The function can have arguments which
-are mapped to LAMMPS variables (also defined in the input script) and
-it can return a value to a LAMMPS variable.  This is thus a mechanism
-for your input script to pass information to a piece of Python code,
-ask Python to execute the code, and return information to your input
-script.
-
-Note that a Python function can be arbitrarily complex.  It can import
-other Python modules, instantiate Python classes, call other Python
-functions, etc.  The Python code that you provide can contain more
-code than the single function.  It can contain other functions or
-Python classes, as well as global variables or other mechanisms for
-storing state between calls from LAMMPS to the function.
-
-The Python function you provide can consist of "pure" Python code that
-only performs operations provided by standard Python.  However, the
-Python function can also "call back" to LAMMPS through its
-Python-wrapped library interface, in the manner described in the
-previous section 11.1.  This means it can issue LAMMPS input script
-commands or query and set internal LAMMPS state.  As an example, this
-can be useful in an input script to create a more complex loop with
-branching logic, than can be created using the simple looping and
-brancing logic enabled by the "next"_next.html and "if"_if.html
-commands.
-
-See the "python"_python.html doc page and the "variable"_variable.html
-doc page for its python-style variables for more info, including
-examples of Python code you can write for both pure Python operations
-and callbacks to LAMMPS.
-
-To run pure Python code from LAMMPS, you only need to build LAMMPS
-with the PYTHON package installed:
-
-make yes-python
-make machine :pre
-
-Note that this will link LAMMPS with the Python library on your
-system, which typically requires several auxiliary system libraries to
-also be linked.  The list of these libraries and the paths to find
-them are specified in the lib/python/Makefile.lammps file.  You need
-to insure that file contains the correct information for your version
-of Python and your machine to successfully build LAMMPS.  See the
-lib/python/README file for more info.
-
-If you want to write Python code with callbacks to LAMMPS, then you
-must also follow the steps overviewed in the preceeding section (11.1)
-for running LAMMPS from Python.  I.e. you must build LAMMPS as a
-shared library and insure that Python can find the python/lammps.py
-file and the shared library.
-
-:line
-
-11.3 Building LAMMPS as a shared library :link(py_3),h4
-
-Instructions on how to build LAMMPS as a shared library are given in
-"Section_start 5"_Section_start.html#start_5.  A shared library is one
-that is dynamically loadable, which is what Python requires to wrap
-LAMMPS.  On Linux this is a library file that ends in ".so", not ".a".
-
-From the src directory, type
-
-make foo mode=shlib :pre
-
-where foo is the machine target name, such as linux or g++ or serial.
-This should create the file liblammps_foo.so in the src directory, as
-well as a soft link liblammps.so, which is what the Python wrapper will
-load by default.  Note that if you are building multiple machine
-versions of the shared library, the soft link is always set to the
-most recently built version.
-
-NOTE: If you are building LAMMPS with an MPI or FFT library or other
-auxiliary libraries (used by various packages), then all of these
-extra libraries must also be shared libraries.  If the LAMMPS
-shared-library build fails with an error complaining about this, see
-"Section_start 5"_Section_start.html#start_5 for more details.
-
-:line
-
-11.4 Installing the Python wrapper into Python :link(py_4),h4
-
-For Python to invoke LAMMPS, there are 2 files it needs to know about:
-
-python/lammps.py
-src/liblammps.so :ul
-
-Lammps.py is the Python wrapper on the LAMMPS library interface.
-Liblammps.so is the shared LAMMPS library that Python loads, as
-described above.
-
-You can insure Python can find these files in one of two ways:
-
-set two environment variables
-run the python/install.py script :ul
-
-If you set the paths to these files as environment variables, you only
-have to do it once.  For the csh or tcsh shells, add something like
-this to your ~/.cshrc file, one line for each of the two files:
-
-setenv PYTHONPATH $\{PYTHONPATH\}:/home/sjplimp/lammps/python
-setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
-
-If you use the python/install.py script, you need to invoke it every
-time you rebuild LAMMPS (as a shared library) or make changes to the
-python/lammps.py file.
-
-You can invoke install.py from the python directory as
-
-% python install.py \[libdir\] \[pydir\] :pre
-
-The optional libdir is where to copy the LAMMPS shared library to; the
-default is /usr/local/lib.  The optional pydir is where to copy the
-lammps.py file to; the default is the site-packages directory of the
-version of Python that is running the install script.
-
-Note that libdir must be a location that is in your default
-LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib.  And pydir must be a
-location that Python looks in by default for imported modules, like
-its site-packages dir.  If you want to copy these files to
-non-standard locations, such as within your own user space, you will
-need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables
-accordingly, as above.
-
-If the install.py script does not allow you to copy files into system
-directories, prefix the python command with "sudo".  If you do this,
-make sure that the Python that root runs is the same as the Python you
-run.  E.g. you may need to do something like
-
-% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre
-
-You can also invoke install.py from the make command in the src
-directory as
-
-% make install-python :pre
-
-In this mode you cannot append optional arguments.  Again, you may
-need to prefix this with "sudo".  In this mode you cannot control
-which Python is invoked by root.
-
-Note that if you want Python to be able to load different versions of
-the LAMMPS shared library (see "this section"_#py_5 below), you will
-need to manually copy files like liblammps_g++.so into the appropriate
-system directory.  This is not needed if you set the LD_LIBRARY_PATH
-environment variable as described above.
-
-:line
-
-11.5 Extending Python with MPI to run in parallel :link(py_5),h4
-
-If you wish to run LAMMPS in parallel from Python, you need to extend
-your Python with an interface to MPI.  This also allows you to
-make MPI calls directly from Python in your script, if you desire.
-
-There are several Python packages available that purport to wrap MPI
-as a library and allow MPI functions to be called from Python.
-
-These include
-
-"pyMPI"_http://pympi.sourceforge.net/
-"maroonmpi"_http://code.google.com/p/maroonmpi/
-"mpi4py"_http://code.google.com/p/mpi4py/
-"myMPI"_http://nbcr.sdsc.edu/forum/viewtopic.php?t=89&sid=c997fefc3933bd66204875b436940f16
-"Pypar"_http://code.google.com/p/pypar :ul
-
-All of these except pyMPI work by wrapping the MPI library and
-exposing (some portion of) its interface to your Python script.  This
-means Python cannot be used interactively in parallel, since they do
-not address the issue of interactive input to multiple instances of
-Python running on different processors.  The one exception is pyMPI,
-which alters the Python interpreter to address this issue, and (I
-believe) creates a new alternate executable (in place of "python"
-itself) as a result.
-
-In principle any of these Python/MPI packages should work to invoke
-LAMMPS in parallel and to make MPI calls themselves from a Python
-script which is itself running in parallel.  However, when I
-downloaded and looked at a few of them, their documentation was
-incomplete and I had trouble with their installation.  It's not clear
-if some of the packages are still being actively developed and
-supported.
-
-The packages Pypar and mpi4py have both been successfully tested with
-LAMMPS.  Pypar is simpler and easy to set up and use, but supports
-only a subset of MPI.  Mpi4py is more MPI-feature complete, but also a
-bit more complex to use.  As of version 2.0.0, mpi4py is the only
-python MPI wrapper that allows passing a custom MPI communicator to
-the LAMMPS constructor, which means one can easily run one or more
-LAMMPS instances on subsets of the total MPI ranks.
-
-:line
-
-Pypar requires the ubiquitous "Numpy package"_http://numpy.scipy.org
-be installed in your Python.  After launching Python, type
-
-import numpy :pre
-
-to see if it is installed.  If not, here is how to install it (version
-1.3.0b1 as of April 2009).  Unpack the numpy tarball and from its
-top-level directory, type
-
-python setup.py build
-sudo python setup.py install :pre
-
-The "sudo" is only needed if required to copy Numpy files into your
-Python distribution's site-packages directory.
-
-To install Pypar (version pypar-2.1.4_94 as of Aug 2012), unpack it
-and from its "source" directory, type
-
-python setup.py build
-sudo python setup.py install :pre
-
-Again, the "sudo" is only needed if required to copy Pypar files into
-your Python distribution's site-packages directory.
-
-If you have successully installed Pypar, you should be able to run
-Python and type
-
-import pypar :pre
-
-without error.  You should also be able to run python in parallel
-on a simple test script
-
-% mpirun -np 4 python test.py :pre
-
-where test.py contains the lines
-
-import pypar
-print "Proc %d out of %d procs" % (pypar.rank(),pypar.size()) :pre
-
-and see one line of output for each processor you run on.
-
-NOTE: To use Pypar and LAMMPS in parallel from Python, you must insure
-both are using the same version of MPI.  If you only have one MPI
-installed on your system, this is not an issue, but it can be if you
-have multiple MPIs.  Your LAMMPS build is explicit about which MPI it
-is using, since you specify the details in your lo-level
-src/MAKE/Makefile.foo file.  Pypar uses the "mpicc" command to find
-information about the MPI it uses to build against.  And it tries to
-load "libmpi.so" from the LD_LIBRARY_PATH.  This may or may not find
-the MPI library that LAMMPS is using.  If you have problems running
-both Pypar and LAMMPS together, this is an issue you may need to
-address, e.g. by moving other MPI installations so that Pypar finds
-the right one.
-
-:line
-
-To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it
-and from its main directory, type
-
-python setup.py build
-sudo python setup.py install :pre
-
-Again, the "sudo" is only needed if required to copy mpi4py files into
-your Python distribution's site-packages directory. To install with
-user privilege into the user local directory type
-
-python setup.py install --user :pre
-
-If you have successully installed mpi4py, you should be able to run
-Python and type
-
-from mpi4py import MPI :pre
-
-without error.  You should also be able to run python in parallel
-on a simple test script
-
-% mpirun -np 4 python test.py :pre
-
-where test.py contains the lines
-
-from mpi4py import MPI
-comm = MPI.COMM_WORLD
-print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size()) :pre
-
-and see one line of output for each processor you run on.
-
-NOTE: To use mpi4py and LAMMPS in parallel from Python, you must
-insure both are using the same version of MPI.  If you only have one
-MPI installed on your system, this is not an issue, but it can be if
-you have multiple MPIs.  Your LAMMPS build is explicit about which MPI
-it is using, since you specify the details in your lo-level
-src/MAKE/Makefile.foo file.  Mpi4py uses the "mpicc" command to find
-information about the MPI it uses to build against.  And it tries to
-load "libmpi.so" from the LD_LIBRARY_PATH.  This may or may not find
-the MPI library that LAMMPS is using.  If you have problems running
-both mpi4py and LAMMPS together, this is an issue you may need to
-address, e.g. by moving other MPI installations so that mpi4py finds
-the right one.
-
-:line
-
-11.6 Testing the Python-LAMMPS interface :link(py_6),h4
-
-To test if LAMMPS is callable from Python, launch Python interactively
-and type:
-
->>> from lammps import lammps
->>> lmp = lammps() :pre
-
-If you get no errors, you're ready to use LAMMPS from Python.  If the
-2nd command fails, the most common error to see is
-
-OSError: Could not load LAMMPS dynamic library :pre
-
-which means Python was unable to load the LAMMPS shared library.  This
-typically occurs if the system can't find the LAMMPS shared library or
-one of the auxiliary shared libraries it depends on, or if something
-about the library is incompatible with your Python.  The error message
-should give you an indication of what went wrong.
-
-You can also test the load directly in Python as follows, without
-first importing from the lammps.py file:
-
->>> from ctypes import CDLL
->>> CDLL("liblammps.so") :pre
-
-If an error occurs, carefully go thru the steps in "Section_start
-5"_Section_start.html#start_5 and above about building a shared
-library and about insuring Python can find the necessary two files
-it needs.
-
-[Test LAMMPS and Python in serial:] :h5
-
-To run a LAMMPS test in serial, type these lines into Python
-interactively from the bench directory:
-
->>> from lammps import lammps
->>> lmp = lammps()
->>> lmp.file("in.lj") :pre
-
-Or put the same lines in the file test.py and run it as
-
-% python test.py :pre
-
-Either way, you should see the results of running the in.lj benchmark
-on a single processor appear on the screen, the same as if you had
-typed something like:
-
-lmp_g++ -in in.lj :pre
-
-[Test LAMMPS and Python in parallel:] :h5
-
-To run LAMMPS in parallel, assuming you have installed the
-"Pypar"_Pypar package as discussed above, create a test.py file
-containing these lines:
-
-import pypar
-from lammps import lammps
-lmp = lammps()
-lmp.file("in.lj")
-print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp
-pypar.finalize() :pre
-
-To run LAMMPS in parallel, assuming you have installed the
-"mpi4py"_mpi4py package as discussed above, create a test.py file
-containing these lines:
-
-from mpi4py import MPI
-from lammps import lammps
-lmp = lammps()
-lmp.file("in.lj")
-me = MPI.COMM_WORLD.Get_rank()
-nprocs = MPI.COMM_WORLD.Get_size()
-print "Proc %d out of %d procs has" % (me,nprocs),lmp
-MPI.Finalize() :pre
-
-You can either script in parallel as:
-
-% mpirun -np 4 python test.py :pre
-
-and you should see the same output as if you had typed
-
-% mpirun -np 4 lmp_g++ -in in.lj :pre
-
-Note that if you leave out the 3 lines from test.py that specify Pypar
-commands you will instantiate and run LAMMPS independently on each of
-the P processors specified in the mpirun command.  In this case you
-should get 4 sets of output, each showing that a LAMMPS run was made
-on a single processor, instead of one set of output showing that
-LAMMPS ran on 4 processors.  If the 1-processor outputs occur, it
-means that Pypar is not working correctly.
-
-Also note that once you import the PyPar module, Pypar initializes MPI
-for you, and you can use MPI calls directly in your Python script, as
-described in the Pypar documentation.  The last line of your Python
-script should be pypar.finalize(), to insure MPI is shut down
-correctly.
-
-[Running Python scripts:] :h5
-
-Note that any Python script (not just for LAMMPS) can be invoked in
-one of several ways:
-
-% python foo.script
-% python -i foo.script
-% foo.script :pre
-
-The last command requires that the first line of the script be
-something like this:
-
-#!/usr/local/bin/python 
-#!/usr/local/bin/python -i :pre
-
-where the path points to where you have Python installed, and that you
-have made the script file executable:
-
-% chmod +x foo.script :pre
-
-Without the "-i" flag, Python will exit when the script finishes.
-With the "-i" flag, you will be left in the Python interpreter when
-the script finishes, so you can type subsequent commands.  As
-mentioned above, you can only run Python interactively when running
-Python on a single processor, not in parallel.
-
-:line
-:line
-
-11.7 Using LAMMPS from Python :link(py_7),h4
-
-As described above, the Python interface to LAMMPS consists of a
-Python "lammps" module, the source code for which is in
-python/lammps.py, which creates a "lammps" object, with a set of
-methods that can be invoked on that object.  The sample Python code
-below assumes you have first imported the "lammps" module in your
-Python script, as follows:
-
-from lammps import lammps :pre
-
-These are the methods defined by the lammps module.  If you look at
-the files src/library.cpp and src/library.h you will see that they
-correspond one-to-one with calls you can make to the LAMMPS library
-from a C++ or C or Fortran program.
-
-lmp = lammps()           # create a LAMMPS object using the default liblammps.so library
-                         4 optional args are allowed: name, cmdargs, ptr, comm
-lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
-lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
-lmp = lammps(name="g++")   # create a LAMMPS object using the liblammps_g++.so library
-lmp = lammps(name="g++",cmdargs=list)    # add LAMMPS command-line args, e.g. list = \["-echo","screen"\] :pre
-
-lmp.close()              # destroy a LAMMPS object :pre
-
-version = lmp.version()  # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902
-
-lmp.file(file)           # run an entire input script, file = "in.lj"
-lmp.command(cmd)         # invoke a single LAMMPS command, cmd = "run 100" :pre
-
-xlo = lmp.extract_global(name,type)  # extract a global quantity
-                                     # name = "boxxlo", "nlocal", etc
-				     # type = 0 = int
-				     #        1 = double :pre
-
-coords = lmp.extract_atom(name,type)      # extract a per-atom quantity
-                                          # name = "x", "type", etc
-				          # type = 0 = vector of ints
-				          #        1 = array of ints
-				          #        2 = vector of doubles
-				          #        3 = array of doubles :pre
-
-eng = lmp.extract_compute(id,style,type)  # extract value(s) from a compute
-v3 = lmp.extract_fix(id,style,type,i,j)   # extract value(s) from a fix
-                                          # id = ID of compute or fix
-					  # style = 0 = global data
-					  #	    1 = per-atom data
-					  #         2 = local data
-					  # type = 0 = scalar
-					  #	   1 = vector
-					  #        2 = array
-					  # i,j = indices of value in global vector or array :pre
-
-var = lmp.extract_variable(name,group,flag)  # extract value(s) from a variable
-	                                     # name = name of variable
-					     # group = group ID (ignored for equal-style variables)
-					     # flag = 0 = equal-style variable
-					     #        1 = atom-style variable :pre
-
-flag = lmp.set_variable(name,value)       # set existing named string-style variable to value, flag = 0 if successful
-natoms = lmp.get_natoms()                 # total # of atoms as int
-data = lmp.gather_atoms(name,type,count)  # return atom attribute of all atoms gathered into data, ordered by atom ID
-                                          # name = "x", "charge", "type", etc
-                                          # count = # of per-atom values, 1 or 3, etc
-lmp.scatter_atoms(name,type,count,data)   # scatter atom attribute of all atoms from data, ordered by atom ID
-                                          # name = "x", "charge", "type", etc
-                                          # count = # of per-atom values, 1 or 3, etc :pre
-
-:line
-
-The lines
-
-from lammps import lammps
-lmp = lammps() :pre
-
-create an instance of LAMMPS, wrapped in a Python class by the lammps
-Python module, and return an instance of the Python class as lmp.  It
-is used to make all subequent calls to the LAMMPS library.
-
-Additional arguments can be used to tell Python the name of the shared
-library to load or to pass arguments to the LAMMPS instance, the same
-as if LAMMPS were launched from a command-line prompt.
-
-If the ptr argument is set like this:
-
-lmp = lammps(ptr=lmpptr) :pre
-
-then lmpptr must be an argument passed to Python via the LAMMPS
-"python"_python.html command, when it is used to define a Python
-function that is invoked by the LAMMPS input script.  This mode of
-using Python with LAMMPS is described above in 11.2.  The variable
-lmpptr refers to the instance of LAMMPS that called the embedded
-Python interpreter.  Using it as an argument to lammps() allows the
-returned Python class instance "lmp" to make calls to that instance of
-LAMMPS.  See the "python"_python.html command doc page for examples
-using this syntax.
-
-Note that you can create multiple LAMMPS objects in your Python
-script, and coordinate and run multiple simulations, e.g.
-
-from lammps import lammps
-lmp1 = lammps()
-lmp2 = lammps()
-lmp1.file("in.file1")
-lmp2.file("in.file2") :pre
-
-The file() and command() methods allow an input script or single
-commands to be invoked.
-
-The extract_global(), extract_atom(), extract_compute(),
-extract_fix(), and extract_variable() methods return values or
-pointers to data structures internal to LAMMPS.
-
-For extract_global() see the src/library.cpp file for the list of
-valid names.  New names could easily be added.  A double or integer is
-returned.  You need to specify the appropriate data type via the type
-argument.
-
-For extract_atom(), a pointer to internal LAMMPS atom-based data is
-returned, which you can use via normal Python subscripting.  See the
-extract() method in the src/atom.cpp file for a list of valid names.
-Again, new names could easily be added.  A pointer to a vector of
-doubles or integers, or a pointer to an array of doubles (double **)
-or integers (int **) is returned.  You need to specify the appropriate
-data type via the type argument.
-
-For extract_compute() and extract_fix(), the global, per-atom, or
-local data calulated by the compute or fix can be accessed.  What is
-returned depends on whether the compute or fix calculates a scalar or
-vector or array.  For a scalar, a single double value is returned.  If
-the compute or fix calculates a vector or array, a pointer to the
-internal LAMMPS data is returned, which you can use via normal Python
-subscripting.  The one exception is that for a fix that calculates a
-global vector or array, a single double value from the vector or array
-is returned, indexed by I (vector) or I and J (array).  I,J are
-zero-based indices.  The I,J arguments can be left out if not needed.
-See "Section_howto 15"_Section_howto.html#howto_15 of the manual for a
-discussion of global, per-atom, and local data, and of scalar, vector,
-and array data types.  See the doc pages for individual
-"computes"_compute.html and "fixes"_fix.html for a description of what
-they calculate and store.
-
-For extract_variable(), an "equal-style or atom-style
-variable"_variable.html is evaluated and its result returned.
-
-For equal-style variables a single double value is returned and the
-group argument is ignored.  For atom-style variables, a vector of
-doubles is returned, one value per atom, which you can use via normal
-Python subscripting. The values will be zero for atoms not in the
-specified group.
-
-The get_natoms() method returns the total number of atoms in the
-simulation, as an int.
-
-The gather_atoms() method returns a ctypes vector of ints or doubles
-as specified by type, of length count*natoms, for the property of all
-the atoms in the simulation specified by name, ordered by count and
-then by atom ID.  The vector can be used via normal Python
-subscripting.  If atom IDs are not consecutively ordered within
-LAMMPS, a None is returned as indication of an error.
-
-Note that the data structure gather_atoms("x") returns is different
-from the data structure returned by extract_atom("x") in four ways.
-(1) Gather_atoms() returns a vector which you index as x\[i\];
-extract_atom() returns an array which you index as x\[i\]\[j\].  (2)
-Gather_atoms() orders the atoms by atom ID while extract_atom() does
-not.  (3) Gathert_atoms() returns a list of all atoms in the
-simulation; extract_atoms() returns just the atoms local to each
-processor.  (4) Finally, the gather_atoms() data structure is a copy
-of the atom coords stored internally in LAMMPS, whereas extract_atom()
-returns an array that effectively points directly to the internal
-data.  This means you can change values inside LAMMPS from Python by
-assigning a new values to the extract_atom() array.  To do this with
-the gather_atoms() vector, you need to change values in the vector,
-then invoke the scatter_atoms() method.
-
-The scatter_atoms() method takes a vector of ints or doubles as
-specified by type, of length count*natoms, for the property of all the
-atoms in the simulation specified by name, ordered by bount and then
-by atom ID.  It uses the vector of data to overwrite the corresponding
-properties for each atom inside LAMMPS.  This requires LAMMPS to have
-its "map" option enabled; see the "atom_modify"_atom_modify.html
-command for details.  If it is not, or if atom IDs are not
-consecutively ordered, no coordinates are reset.
-
-The array of coordinates passed to scatter_atoms() must be a ctypes
-vector of ints or doubles, allocated and initialized something like
-this:
-
-from ctypes import *
-natoms = lmp.get_natoms()
-n3 = 3*natoms
-x = (n3*c_double)()
-x\[0\] = x coord of atom with ID 1
-x\[1\] = y coord of atom with ID 1
-x\[2\] = z coord of atom with ID 1
-x\[3\] = x coord of atom with ID 2
-...
-x\[n3-1\] = z coord of atom with ID natoms
-lmp.scatter_coords("x",1,3,x) :pre
-
-Alternatively, you can just change values in the vector returned by
-gather_atoms("x",1,3), since it is a ctypes vector of doubles.
-
-:line 
-
-As noted above, these Python class methods correspond one-to-one with
-the functions in the LAMMPS library interface in src/library.cpp and
-library.h.  This means you can extend the Python wrapper via the
-following steps:
-
-Add a new interface function to src/library.cpp and
-src/library.h. :ulb,l
-
-Rebuild LAMMPS as a shared library. :l
-
-Add a wrapper method to python/lammps.py for this interface
-function. :l
-
-You should now be able to invoke the new interface function from a
-Python script.  Isn't ctypes amazing? :l,ule
-
-:line
-:line
-
-11.8 Example Python scripts that use LAMMPS :link(py_8),h4
-
-These are the Python scripts included as demos in the python/examples
-directory of the LAMMPS distribution, to illustrate the kinds of
-things that are possible when Python wraps LAMMPS.  If you create your
-own scripts, send them to us and we can include them in the LAMMPS
-distribution.
-
-trivial.py, read/run a LAMMPS input script thru Python,
-demo.py, invoke various LAMMPS library interface routines,
-simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp,
-split.py, same as simple.py but running in parallel on a subset of procs,
-gui.py, GUI go/stop/temperature-slider to control LAMMPS,
-plot.py, real-time temeperature plot with GnuPlot via Pizza.py,
-viz_tool.py, real-time viz via some viz package,
-vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2)
-
-:line
-
-For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
-with "gl" or "atomeye" or "pymol" or "vmd", depending on what
-visualization package you have installed. 
-
-Note that for GL, you need to be able to run the Pizza.py GL tool,
-which is included in the pizza sub-directory.  See the "Pizza.py doc
-pages"_pizza for more info:
-
-:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
-
-Note that for AtomEye, you need version 3, and there is a line in the
-scripts that specifies the path and name of the executable.  See the
-AtomEye WWW pages "here"_atomeye or "here"_atomeye3 for more details:
-
-http://mt.seas.upenn.edu/Archive/Graphics/A
-http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html :pre
-
-:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
-:link(atomeye3,http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html)
-
-The latter link is to AtomEye 3 which has the scriping
-capability needed by these Python scripts.
-
-Note that for PyMol, you need to have built and installed the
-open-source version of PyMol in your Python, so that you can import it
-from a Python script.  See the PyMol WWW pages "here"_pymol or
-"here"_pymolopen for more details:
-
-http://www.pymol.org
-http://sourceforge.net/scm/?type=svn&group_id=4546 :pre
-
-:link(pymol,http://www.pymol.org)
-:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546)
-
-The latter link is to the open-source version.
-
-Note that for VMD, you need a fairly current version (1.8.7 works for
-me) and there are some lines in the pizza/vmd.py script for 4 PIZZA
-variables that have to match the VMD installation on your system.
-
-:line
-
-See the python/README file for instructions on how to run them and the
-source code for individual scripts for comments about what they do.
-
-Here are screenshots of the vizplotgui_tool.py script in action for
-different visualization package options.  Click to see larger images:
-
-:image(JPG/screenshot_gl_small.jpg,JPG/screenshot_gl.jpg)
-:image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg)
-:image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg)
-:image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg)

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-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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-<li class="toctree-l1"><a class="reference internal" href="Section_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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-<li class="toctree-l1 current"><a class="current reference internal" href="">9. Additional tools</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#amber2lmp-tool">9.1. amber2lmp tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#binary2txt-tool">9.2. binary2txt tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#ch2lmp-tool">9.3. ch2lmp tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#chain-tool">9.4. chain tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#colvars-tools">9.5. colvars tools</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#createatoms-tool">9.6. createatoms tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#data2xmovie-tool">9.7. data2xmovie tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#eam-database-tool">9.8. eam database tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#eam-generate-tool">9.9. eam generate tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#eff-tool">9.10. eff tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#emacs-tool">9.11. emacs tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#fep-tool">9.12. fep tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#i-pi-tool">9.13. i-pi tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#ipp-tool">9.14. ipp tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#kate-tool">9.15. kate tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#lmp2arc-tool">9.16. lmp2arc tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#matlab-tool">9.19. matlab tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#micelle2d-tool">9.20. micelle2d tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#moltemplate-tool">9.21. moltemplate tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#msi2lmp-tool">9.22. msi2lmp tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#phonon-tool">9.23. phonon tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#python-tool">9.26. python tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#reax-tool">9.27. reax tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#restart2data-tool">9.28. restart2data tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#vim-tool">9.29. vim tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#xmgrace-tool">9.30. xmgrace tool</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#xmovie-tool">9.31. xmovie tool</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
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-<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="additional-tools">
-<h1>9. Additional tools<a class="headerlink" href="#additional-tools" title="Permalink to this headline">¶</a></h1>
-<p>LAMMPS is designed to be a computational kernel for performing
-molecular dynamics computations.  Additional pre- and post-processing
-steps are often necessary to setup and analyze a simulation.  A few
-additional tools are provided with the LAMMPS distribution and are
-described in this section.</p>
-<p>Our group has also written and released a separate toolkit called
-<a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a> which provides tools for doing setup, analysis,
-plotting, and visualization for LAMMPS simulations.  Pizza.py is
-written in <a class="reference external" href="http://www.python.org">Python</a> and is available for download from <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW site</a>.</p>
-<p>Note that many users write their own setup or analysis tools or use
-other existing codes and convert their output to a LAMMPS input format
-or vice versa.  The tools listed here are included in the LAMMPS
-distribution as examples of auxiliary tools.  Some of them are not
-actively supported by Sandia, as they were contributed by LAMMPS
-users.  If you have problems using them, we can direct you to the
-authors.</p>
-<p>The source code for each of these codes is in the tools sub-directory
-of the LAMMPS distribution.  There is a Makefile (which you may need
-to edit for your platform) which will build several of the tools which
-reside in that directory.  Some of them are larger packages in their
-own sub-directories with their own Makefiles.</p>
-<ul class="simple">
-<li><a class="reference internal" href="#amber"><span>amber2lmp</span></a></li>
-<li><a class="reference internal" href="#binary"><span>binary2txt</span></a></li>
-<li><a class="reference internal" href="#charmm"><span>ch2lmp</span></a></li>
-<li><a class="reference internal" href="#chain"><span>chain</span></a></li>
-<li><a class="reference internal" href="#colvars"><span>colvars</span></a></li>
-<li><a class="reference internal" href="#create"><span>createatoms</span></a></li>
-<li><a class="reference internal" href="#data"><span>data2xmovie</span></a></li>
-<li><a class="reference internal" href="#eamdb"><span>eam database</span></a></li>
-<li><a class="reference internal" href="#eamgn"><span>eam generate</span></a></li>
-<li><a class="reference internal" href="#eff"><span>eff</span></a></li>
-<li><a class="reference internal" href="#emacs"><span>emacs</span></a></li>
-<li><a class="reference internal" href="#fep"><span>fep</span></a></li>
-<li><a class="reference internal" href="fix_ipi.html#ipi"><span>i-pi</span></a></li>
-<li><a class="reference internal" href="#ipp"><span>ipp</span></a></li>
-<li><a class="reference internal" href="#kate"><span>kate</span></a></li>
-<li><a class="reference internal" href="#arc"><span>lmp2arc</span></a></li>
-<li><a class="reference internal" href="#cfg"><span>lmp2cfg</span></a></li>
-<li><a class="reference internal" href="#vmd"><span>lmp2vmd</span></a></li>
-<li><span class="xref std std-ref">matlab</span></li>
-<li><a class="reference internal" href="#micelle"><span>micelle2d</span></a></li>
-<li><a class="reference internal" href="#moltemplate"><span>moltemplate</span></a></li>
-<li><a class="reference internal" href="#msi"><span>msi2lmp</span></a></li>
-<li><a class="reference internal" href="#phonon"><span>phonon</span></a></li>
-<li><a class="reference internal" href="#polybond"><span>polymer bonding</span></a></li>
-<li><span class="xref std std-ref">pymol_asphere</span></li>
-<li><a class="reference internal" href="#pythontools"><span>python</span></a></li>
-<li><a class="reference internal" href="#reax"><span>reax</span></a></li>
-<li><a class="reference internal" href="#restart"><span>restart2data</span></a></li>
-<li><a class="reference internal" href="#vim"><span>vim</span></a></li>
-<li><a class="reference internal" href="#xmgrace"><span>xmgrace</span></a></li>
-<li><a class="reference internal" href="#xmovie"><span>xmovie</span></a></li>
-</ul>
-<hr class="docutils" />
-<div class="section" id="amber2lmp-tool">
-<span id="amber"></span><h2>9.1. amber2lmp tool<a class="headerlink" href="#amber2lmp-tool" title="Permalink to this headline">¶</a></h2>
-<p>The amber2lmp sub-directory contains two Python scripts for converting
-files back-and-forth between the AMBER MD code and LAMMPS.  See the
-README file in amber2lmp for more information.</p>
-<p>These tools were written by Keir Novik while he was at Queen Mary
-University of London.  Keir is no longer there and cannot support
-these tools which are out-of-date with respect to the current LAMMPS
-version (and maybe with respect to AMBER as well).  Since we don&#8217;t use
-these tools at Sandia, you&#8217;ll need to experiment with them and make
-necessary modifications yourself.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="binary2txt-tool">
-<span id="binary"></span><h2>9.2. binary2txt tool<a class="headerlink" href="#binary2txt-tool" title="Permalink to this headline">¶</a></h2>
-<p>The file binary2txt.cpp converts one or more binary LAMMPS dump file
-into ASCII text files.  The syntax for running the tool is</p>
-<div class="highlight-python"><div class="highlight"><pre>binary2txt file1 file2 ...
-</pre></div>
-</div>
-<p>which creates file1.txt, file2.txt, etc.  This tool must be compiled
-on a platform that can read the binary file created by a LAMMPS run,
-since binary files are not compatible across all platforms.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="ch2lmp-tool">
-<span id="charmm"></span><h2>9.3. ch2lmp tool<a class="headerlink" href="#ch2lmp-tool" title="Permalink to this headline">¶</a></h2>
-<p>The ch2lmp sub-directory contains tools for converting files
-back-and-forth between the CHARMM MD code and LAMMPS.</p>
-<p>They are intended to make it easy to use CHARMM as a builder and as a
-post-processor for LAMMPS. Using charmm2lammps.pl, you can convert an
-ensemble built in CHARMM into its LAMMPS equivalent.  Using
-lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files.</p>
-<p>See the README file in the ch2lmp sub-directory for more information.</p>
-<p>These tools were created by Pieter in&#8217;t Veld (pjintve at sandia.gov)
-and Paul Crozier (pscrozi at sandia.gov) at Sandia.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="chain-tool">
-<span id="chain"></span><h2>9.4. chain tool<a class="headerlink" href="#chain-tool" title="Permalink to this headline">¶</a></h2>
-<p>The file chain.f creates a LAMMPS data file containing bead-spring
-polymer chains and/or monomer solvent atoms.  It uses a text file
-containing chain definition parameters as an input.  The created
-chains and solvent atoms can strongly overlap, so LAMMPS needs to run
-the system initially with a &#8220;soft&#8221; pair potential to un-overlap it.
-The syntax for running the tool is</p>
-<div class="highlight-python"><div class="highlight"><pre>chain &lt; def.chain &gt; data.file
-</pre></div>
-</div>
-<p>See the def.chain or def.chain.ab files in the tools directory for
-examples of definition files.  This tool was used to create the
-system for the <a class="reference internal" href="Section_perf.html"><em>chain benchmark</em></a>.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="colvars-tools">
-<span id="colvars"></span><h2>9.5. colvars tools<a class="headerlink" href="#colvars-tools" title="Permalink to this headline">¶</a></h2>
-<p>The colvars directory contains a collection of tools for postprocessing
-data produced by the colvars collective variable library.
-To compile the tools, edit the makefile for your system and run &#8220;make&#8221;.</p>
-<p>Please report problems and issues the colvars library and its tools
-at: <a class="reference external" href="https://github.com/colvars/colvars/issues">https://github.com/colvars/colvars/issues</a></p>
-<p>abf_integrate:</p>
-<p>MC-based integration of multidimensional free energy gradient
-Version 20110511</p>
-<div class="highlight-python"><div class="highlight"><pre>Syntax: ./abf_integrate &lt; filename &gt; [-n &lt; nsteps &gt;] [-t &lt; temp &gt;] [-m [0|1] (metadynamics)] [-h &lt; hill_height &gt;] [-f &lt; variable_hill_factor &gt;]
-</pre></div>
-</div>
-<p>The LAMMPS interface to the colvars collective variable library, as
-well as these tools, were created by Axel Kohlmeyer (akohlmey at
-gmail.com) at ICTP, Italy.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="createatoms-tool">
-<span id="create"></span><h2>9.6. createatoms tool<a class="headerlink" href="#createatoms-tool" title="Permalink to this headline">¶</a></h2>
-<p>The tools/createatoms directory contains a Fortran program called
-createAtoms.f which can generate a variety of interesting crystal
-structures and geometries and output the resulting list of atom
-coordinates in LAMMPS or other formats.</p>
-<p>See the included Manual.pdf for details.</p>
-<p>The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="data2xmovie-tool">
-<span id="data"></span><h2>9.7. data2xmovie tool<a class="headerlink" href="#data2xmovie-tool" title="Permalink to this headline">¶</a></h2>
-<p>The file data2xmovie.c converts a LAMMPS data file into a snapshot
-suitable for visualizing with the <a class="reference internal" href="#xmovie"><span>xmovie</span></a> tool, as if it had
-been output with a dump command from LAMMPS itself.  The syntax for
-running the tool is</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">data2xmovie</span> <span class="p">[</span><span class="n">options</span><span class="p">]</span> <span class="o">&lt;</span> <span class="n">infile</span> <span class="o">&gt;</span> <span class="n">outfile</span>
-</pre></div>
-</div>
-<p>See the top of the data2xmovie.c file for a discussion of the options.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="eam-database-tool">
-<span id="eamdb"></span><h2>9.8. eam database tool<a class="headerlink" href="#eam-database-tool" title="Permalink to this headline">¶</a></h2>
-<p>The tools/eam_database directory contains a Fortran program that will
-generate EAM alloy setfl potential files for any combination of 16
-elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
-Zr.  The files can then be used with the <a class="reference internal" href="pair_eam.html"><em>pair_style eam/alloy</em></a> command.</p>
-<p>The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov,
-and is based on his paper:</p>
-<p>X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
-144113 (2004).</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="eam-generate-tool">
-<span id="eamgn"></span><h2>9.9. eam generate tool<a class="headerlink" href="#eam-generate-tool" title="Permalink to this headline">¶</a></h2>
-<p>The tools/eam_generate directory contains several one-file C programs
-that convert an analytic formula into a tabulated <a class="reference internal" href="pair_eam.html"><em>embedded atom method (EAM)</em></a> setfl potential file.  The potentials they
-produce are in the potentials directory, and can be used with the
-<a class="reference internal" href="pair_eam.html"><em>pair_style eam/alloy</em></a> command.</p>
-<p>The source files and potentials were provided by Gerolf Ziegenhain
-(gerolf at ziegenhain.com).</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="eff-tool">
-<span id="eff"></span><h2>9.10. eff tool<a class="headerlink" href="#eff-tool" title="Permalink to this headline">¶</a></h2>
-<p>The tools/eff directory contains various scripts for generating
-structures and post-processing output for simulations using the
-electron force field (eFF).</p>
-<p>These tools were provided by Andres Jaramillo-Botero at CalTech
-(ajaramil at wag.caltech.edu).</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="emacs-tool">
-<span id="emacs"></span><h2>9.11. emacs tool<a class="headerlink" href="#emacs-tool" title="Permalink to this headline">¶</a></h2>
-<p>The tools/emacs directory contains a Lips add-on file for Emacs that
-enables a lammps-mode for editing of input scripts when using Emacs,
-with various highlighting options setup.</p>
-<p>These tools were provided by Aidan Thompson at Sandia
-(athomps at sandia.gov).</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="fep-tool">
-<span id="fep"></span><h2>9.12. fep tool<a class="headerlink" href="#fep-tool" title="Permalink to this headline">¶</a></h2>
-<p>The tools/fep directory contains Python scripts useful for
-post-processing results from performing free-energy perturbation
-simulations using the USER-FEP package.</p>
-<p>The scripts were contributed by Agilio Padua (Universite Blaise
-Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.</p>
-<p>See README file in the tools/fep directory.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="i-pi-tool">
-<span id="ipi"></span><h2>9.13. i-pi tool<a class="headerlink" href="#i-pi-tool" title="Permalink to this headline">¶</a></h2>
-<p>The tools/i-pi directory contains a version of the i-PI package, with
-all the LAMMPS-unrelated files removed.  It is provided so that it can
-be used with the <a class="reference internal" href="fix_ipi.html"><em>fix ipi</em></a> command to perform
-path-integral molecular dynamics (PIMD).</p>
-<p>The i-PI package was created and is maintained by Michele Ceriotti,
-michele.ceriotti at gmail.com, to interface to a variety of molecular
-dynamics codes.</p>
-<p>See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
-<a class="reference internal" href="fix_ipi.html"><em>fix ipi</em></a> doc page for further details on running PIMD
-calculations with LAMMPS.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="ipp-tool">
-<span id="ipp"></span><h2>9.14. ipp tool<a class="headerlink" href="#ipp-tool" title="Permalink to this headline">¶</a></h2>
-<p>The tools/ipp directory contains a Perl script ipp which can be used
-to facilitate the creation of a complicated file (say, a lammps input
-script or tools/createatoms input file) using a template file.</p>
-<p>ipp was created and is maintained by Reese Jones (Sandia), rjones at
-sandia.gov.</p>
-<p>See two examples in the tools/ipp directory.  One of them is for the
-tools/createatoms tool&#8217;s input file.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="kate-tool">
-<span id="kate"></span><h2>9.15. kate tool<a class="headerlink" href="#kate-tool" title="Permalink to this headline">¶</a></h2>
-<p>The file in the tools/kate directory is an add-on to the Kate editor
-in the KDE suite that allow syntax highlighting of LAMMPS input
-scripts.  See the README.txt file for details.</p>
-<p>The file was provided by Alessandro Luigi Sellerio
-(alessandro.sellerio at ieni.cnr.it).</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="lmp2arc-tool">
-<span id="arc"></span><h2>9.16. lmp2arc tool<a class="headerlink" href="#lmp2arc-tool" title="Permalink to this headline">¶</a></h2>
-<p>The lmp2arc sub-directory contains a tool for converting LAMMPS output
-files to the format for Accelrys&#8217; Insight MD code (formerly
-MSI/Biosym and its Discover MD code).  See the README file for more
-information.</p>
-<p>This tool was written by John Carpenter (Cray), Michael Peachey
-(Cray), and Steve Lustig (Dupont).  John is now at the Mayo Clinic
-(jec at mayo.edu), but still fields questions about the tool.</p>
-<p>This tool was updated for the current LAMMPS C++ version by Jeff
-Greathouse at Sandia (jagreat at sandia.gov).</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="lmp2cfg-tool">
-<span id="cfg"></span><h2>9.17. lmp2cfg tool<a class="headerlink" href="#lmp2cfg-tool" title="Permalink to this headline">¶</a></h2>
-<p>The lmp2cfg sub-directory contains a tool for converting LAMMPS output
-files into a series of <a href="#id1"><span class="problematic" id="id2">*</span></a>.cfg files which can be read into the
-<a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualizer.  See
-the README file for more information.</p>
-<p>This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="lmp2vmd-tool">
-<span id="vmd"></span><h2>9.18. lmp2vmd tool<a class="headerlink" href="#lmp2vmd-tool" title="Permalink to this headline">¶</a></h2>
-<p>The lmp2vmd sub-directory contains a README.txt file that describes
-details of scripts and plugin support within the <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD package</a> for visualizing LAMMPS
-dump files.</p>
-<p>The VMD plugins and other supporting scripts were written by Axel
-Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="matlab-tool">
-<span id="matlab"></span><h2>9.19. matlab tool<a class="headerlink" href="#matlab-tool" title="Permalink to this headline">¶</a></h2>
-<p>The matlab sub-directory contains several <span class="xref std std-ref">MATLAB</span> scripts for
-post-processing LAMMPS output.  The scripts include readers for log
-and dump files, a reader for EAM potential files, and a converter that
-reads LAMMPS dump files and produces CFG files that can be visualized
-with the <a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a>
-visualizer.</p>
-<p>See the README.pdf file for more information.</p>
-<p>These scripts were written by Arun Subramaniyan at Purdue Univ
-(asubrama at purdue.edu).</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="micelle2d-tool">
-<span id="micelle"></span><h2>9.20. micelle2d tool<a class="headerlink" href="#micelle2d-tool" title="Permalink to this headline">¶</a></h2>
-<p>The file micelle2d.f creates a LAMMPS data file containing short lipid
-chains in a monomer solution.  It uses a text file containing lipid
-definition parameters as an input.  The created molecules and solvent
-atoms can strongly overlap, so LAMMPS needs to run the system
-initially with a &#8220;soft&#8221; pair potential to un-overlap it.  The syntax
-for running the tool is</p>
-<div class="highlight-python"><div class="highlight"><pre>micelle2d &lt; def.micelle2d &gt; data.file
-</pre></div>
-</div>
-<p>See the def.micelle2d file in the tools directory for an example of a
-definition file.  This tool was used to create the system for the
-<a class="reference internal" href="Section_example.html"><em>micelle example</em></a>.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="moltemplate-tool">
-<span id="moltemplate"></span><h2>9.21. moltemplate tool<a class="headerlink" href="#moltemplate-tool" title="Permalink to this headline">¶</a></h2>
-<p>The moltemplate sub-directory contains a Python-based tool for
-building molecular systems based on a text-file description, and
-creating LAMMPS data files that encode their molecular topology as
-lists of bonds, angles, dihedrals, etc.  See the README.TXT file for
-more information.</p>
-<p>This tool was written by Andrew Jewett (jewett.aij at gmail.com), who
-supports it.  It has its own WWW page at
-<a class="reference external" href="http://moltemplate.org">http://moltemplate.org</a>.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="msi2lmp-tool">
-<span id="msi"></span><h2>9.22. msi2lmp tool<a class="headerlink" href="#msi2lmp-tool" title="Permalink to this headline">¶</a></h2>
-<p>The msi2lmp sub-directory contains a tool for creating LAMMPS input
-data files from Accelrys&#8217; Insight MD code (formerly MSI/Biosym and
-its Discover MD code).  See the README file for more information.</p>
-<p>This tool was written by John Carpenter (Cray), Michael Peachey
-(Cray), and Steve Lustig (Dupont).  John is now at the Mayo Clinic
-(jec at mayo.edu), but still fields questions about the tool.</p>
-<p>This tool may be out-of-date with respect to the current LAMMPS and
-Insight versions.  Since we don&#8217;t use it at Sandia, you&#8217;ll need to
-experiment with it yourself.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="phonon-tool">
-<span id="phonon"></span><h2>9.23. phonon tool<a class="headerlink" href="#phonon-tool" title="Permalink to this headline">¶</a></h2>
-<p>The phonon sub-directory contains a post-processing tool useful for
-analyzing the output of the <a class="reference internal" href="fix_phonon.html"><em>fix phonon</em></a> command in
-the USER-PHONON package.</p>
-<p>See the README file for instruction on building the tool and what
-library it needs.  And see the examples/USER/phonon directory
-for example problems that can be post-processed with this tool.</p>
-<p>This tool was written by Ling-Ti Kong at Shanghai Jiao Tong
-University.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="polymer-bonding-tool">
-<span id="polybond"></span><h2>9.24. polymer bonding tool<a class="headerlink" href="#polymer-bonding-tool" title="Permalink to this headline">¶</a></h2>
-<p>The polybond sub-directory contains a Python-based tool useful for
-performing &#8220;programmable polymer bonding&#8221;.  The Python file
-lmpsdata.py provides a &#8220;Lmpsdata&#8221; class with various methods which can
-be invoked by a user-written Python script to create data files with
-complex bonding topologies.</p>
-<p>See the Manual.pdf for details and example scripts.</p>
-<p>This tool was written by Zachary Kraus at Georgia Tech.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="pymol-asphere-tool">
-<span id="pymol"></span><h2>9.25. pymol_asphere tool<a class="headerlink" href="#pymol-asphere-tool" title="Permalink to this headline">¶</a></h2>
-<p>The pymol_asphere sub-directory contains a tool for converting a
-LAMMPS dump file that contains orientation info for ellipsoidal
-particles into an input file for the <span class="xref std std-ref">PyMol visualization package</span>.</p>
-<p>Specifically, the tool triangulates the ellipsoids so they can be
-viewed as true ellipsoidal particles within PyMol.  See the README and
-examples directory within pymol_asphere for more information.</p>
-<p>This tool was written by Mike Brown at Sandia.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="python-tool">
-<span id="pythontools"></span><h2>9.26. python tool<a class="headerlink" href="#python-tool" title="Permalink to this headline">¶</a></h2>
-<p>The python sub-directory contains several Python scripts
-that perform common LAMMPS post-processing tasks, such as:</p>
-<ul class="simple">
-<li>extract thermodynamic info from a log file as columns of numbers</li>
-<li>plot two columns of thermodynamic info from a log file using GnuPlot</li>
-<li>sort the snapshots in a dump file by atom ID</li>
-<li>convert multiple <a class="reference internal" href="neb.html"><em>NEB</em></a> dump files into one dump file for viz</li>
-<li>convert dump files into XYZ, CFG, or PDB format for viz by other packages</li>
-</ul>
-<p>These are simple scripts built on <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a> modules.  See the
-README for more info on Pizza.py and how to use these scripts.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="reax-tool">
-<span id="reax"></span><h2>9.27. reax tool<a class="headerlink" href="#reax-tool" title="Permalink to this headline">¶</a></h2>
-<p>The reax sub-directory contains stand-alond codes that can
-post-process the output of the <a class="reference internal" href="fix_reax_bonds.html"><em>fix reax/bonds</em></a>
-command from a LAMMPS simulation using <a class="reference internal" href="pair_reax.html"><em>ReaxFF</em></a>.  See
-the README.txt file for more info.</p>
-<p>These tools were written by Aidan Thompson at Sandia.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="restart2data-tool">
-<span id="restart"></span><h2>9.28. restart2data tool<a class="headerlink" href="#restart2data-tool" title="Permalink to this headline">¶</a></h2>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">This tool is now obsolete and is not included in the current
-LAMMPS distribution.  This is becaues there is now a
-<a class="reference internal" href="write_data.html"><em>write_data</em></a> command, which can create a data file
-from within an input script.  Running LAMMPS with the &#8220;-r&#8221;
-<a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> as follows:</p>
-</div>
-<p>lmp_g++ -r restartfile datafile</p>
-<p>is the same as running a 2-line input script:</p>
-<p>read_restart restartfile
-write_data datafile</p>
-<p>which will produce the same data file that the restart2data tool used
-to create.  The following information is included in case you have an
-older version of LAMMPS which still includes the restart2data tool.</p>
-<p>The file restart2data.cpp converts a binary LAMMPS restart file into
-an ASCII data file.  The syntax for running the tool is</p>
-<div class="highlight-python"><div class="highlight"><pre>restart2data restart-file data-file (input-file)
-</pre></div>
-</div>
-<p>Input-file is optional and if specified will contain LAMMPS input
-commands for the masses and force field parameters, instead of putting
-those in the data-file.  Only a few force field styles currently
-support this option.</p>
-<p>This tool must be compiled on a platform that can read the binary file
-created by a LAMMPS run, since binary files are not compatible across
-all platforms.</p>
-<p>Note that a text data file has less precision than a binary restart
-file.  Hence, continuing a run from a converted data file will
-typically not conform as closely to a previous run as will restarting
-from a binary restart file.</p>
-<p>If a &#8220;%&#8221; appears in the specified restart-file, the tool expects a set
-of multiple files to exist.  See the <a class="reference internal" href="restart.html"><em>restart</em></a> and
-<a class="reference internal" href="write_restart.html"><em>write_restart</em></a> commands for info on how such sets
-of files are written by LAMMPS, and how the files are named.</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="vim-tool">
-<span id="vim"></span><h2>9.29. vim tool<a class="headerlink" href="#vim-tool" title="Permalink to this headline">¶</a></h2>
-<p>The files in the tools/vim directory are add-ons to the VIM editor
-that allow easier editing of LAMMPS input scripts.  See the README.txt
-file for details.</p>
-<p>These files were provided by Gerolf Ziegenhain (gerolf at
-ziegenhain.com)</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="xmgrace-tool">
-<span id="xmgrace"></span><h2>9.30. xmgrace tool<a class="headerlink" href="#xmgrace-tool" title="Permalink to this headline">¶</a></h2>
-<p>The files in the tools/xmgrace directory can be used to plot the
-thermodynamic data in LAMMPS log files via the xmgrace plotting
-package.  There are several tools in the directory that can be used in
-post-processing mode.  The lammpsplot.cpp file can be compiled and
-used to create plots from the current state of a running LAMMPS
-simulation.</p>
-<p>See the README file for details.</p>
-<p>These files were provided by Vikas Varshney (vv0210 at gmail.com)</p>
-<hr class="docutils" />
-</div>
-<div class="section" id="xmovie-tool">
-<span id="xmovie"></span><h2>9.31. xmovie tool<a class="headerlink" href="#xmovie-tool" title="Permalink to this headline">¶</a></h2>
-<p>The xmovie tool is an X-based visualization package that can read
-LAMMPS dump files and animate them.  It is in its own sub-directory
-with the tools directory.  You may need to modify its Makefile so that
-it can find the appropriate X libraries to link against.</p>
-<p>The syntax for running xmovie is</p>
-<div class="highlight-python"><div class="highlight"><pre>xmovie [options] dump.file1 dump.file2 ...
-</pre></div>
-</div>
-<p>If you just type &#8220;xmovie&#8221; you will see a list of options.  Note that
-by default, LAMMPS dump files are in scaled coordinates, so you
-typically need to use the -scale option with xmovie.  When xmovie runs
-it opens a visualization window and a control window.  The control
-options are straightforward to use.</p>
-<p>Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he
-spent a summer at Sandia.  It displays 2d projections of a 3d domain.
-While simple in design, it is an amazingly fast program that can
-render large numbers of atoms very quickly.  It&#8217;s a useful tool for
-debugging LAMMPS input and output and making sure your simulation is
-doing what you think it should.  The animations on the Examples page
-of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW site</a> were created with xmovie.</p>
-<p>I&#8217;ve lost contact with Mike, so I hope he&#8217;s comfortable with us
-distributing his great tool!</p>
-</div>
-</div>
-
-
-           </div>
-          </div>
-          <footer>
-  
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doc/Section_tools.txt

@@ -1,566 +0,0 @@
-"Previous Section"_Section_perf.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Section_modify.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-9. Additional tools :h3
-
-LAMMPS is designed to be a computational kernel for performing
-molecular dynamics computations.  Additional pre- and post-processing
-steps are often necessary to setup and analyze a simulation.  A few
-additional tools are provided with the LAMMPS distribution and are
-described in this section.
-
-Our group has also written and released a separate toolkit called
-"Pizza.py"_pizza which provides tools for doing setup, analysis,
-plotting, and visualization for LAMMPS simulations.  Pizza.py is
-written in "Python"_python and is available for download from "the
-Pizza.py WWW site"_pizza.
-
-:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
-:link(python,http://www.python.org)
-
-Note that many users write their own setup or analysis tools or use
-other existing codes and convert their output to a LAMMPS input format
-or vice versa.  The tools listed here are included in the LAMMPS
-distribution as examples of auxiliary tools.  Some of them are not
-actively supported by Sandia, as they were contributed by LAMMPS
-users.  If you have problems using them, we can direct you to the
-authors.
-
-The source code for each of these codes is in the tools sub-directory
-of the LAMMPS distribution.  There is a Makefile (which you may need
-to edit for your platform) which will build several of the tools which
-reside in that directory.  Some of them are larger packages in their
-own sub-directories with their own Makefiles.
-
-"amber2lmp"_#amber
-"binary2txt"_#binary
-"ch2lmp"_#charmm
-"chain"_#chain
-"colvars"_#colvars
-"createatoms"_#create
-"data2xmovie"_#data
-"eam database"_#eamdb
-"eam generate"_#eamgn
-"eff"_#eff
-"emacs"_#emacs
-"fep"_#fep
-"i-pi"_#ipi
-"ipp"_#ipp
-"kate"_#kate
-"lmp2arc"_#arc
-"lmp2cfg"_#cfg
-"lmp2vmd"_#vmd
-"matlab"_#matlab
-"micelle2d"_#micelle
-"moltemplate"_#moltemplate
-"msi2lmp"_#msi
-"phonon"_#phonon
-"polymer bonding"_#polybond
-"pymol_asphere"_#pymol
-"python"_#pythontools
-"reax"_#reax
-"restart2data"_#restart
-"vim"_#vim
-"xmgrace"_#xmgrace
-"xmovie"_#xmovie :ul
-
-:line
-
-amber2lmp tool :h4,link(amber)
-
-The amber2lmp sub-directory contains two Python scripts for converting
-files back-and-forth between the AMBER MD code and LAMMPS.  See the
-README file in amber2lmp for more information.
-
-These tools were written by Keir Novik while he was at Queen Mary
-University of London.  Keir is no longer there and cannot support
-these tools which are out-of-date with respect to the current LAMMPS
-version (and maybe with respect to AMBER as well).  Since we don't use
-these tools at Sandia, you'll need to experiment with them and make
-necessary modifications yourself.
-
-:line
-
-binary2txt tool :h4,link(binary)
-
-The file binary2txt.cpp converts one or more binary LAMMPS dump file
-into ASCII text files.  The syntax for running the tool is
-
-binary2txt file1 file2 ... :pre
-
-which creates file1.txt, file2.txt, etc.  This tool must be compiled
-on a platform that can read the binary file created by a LAMMPS run,
-since binary files are not compatible across all platforms.
-
-:line
-
-ch2lmp tool :h4,link(charmm)
-
-The ch2lmp sub-directory contains tools for converting files
-back-and-forth between the CHARMM MD code and LAMMPS. 
-
-They are intended to make it easy to use CHARMM as a builder and as a
-post-processor for LAMMPS. Using charmm2lammps.pl, you can convert an
-ensemble built in CHARMM into its LAMMPS equivalent.  Using
-lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files.
-
-See the README file in the ch2lmp sub-directory for more information.
-
-These tools were created by Pieter in't Veld (pjintve at sandia.gov)
-and Paul Crozier (pscrozi at sandia.gov) at Sandia.
-
-:line
-
-chain tool :h4,link(chain)
-
-The file chain.f creates a LAMMPS data file containing bead-spring
-polymer chains and/or monomer solvent atoms.  It uses a text file
-containing chain definition parameters as an input.  The created
-chains and solvent atoms can strongly overlap, so LAMMPS needs to run
-the system initially with a "soft" pair potential to un-overlap it.
-The syntax for running the tool is
-
-chain < def.chain > data.file :pre
-
-See the def.chain or def.chain.ab files in the tools directory for
-examples of definition files.  This tool was used to create the
-system for the "chain benchmark"_Section_perf.html.
-
-:line
-
-colvars tools :h4,link(colvars)
-
-The colvars directory contains a collection of tools for postprocessing
-data produced by the colvars collective variable library.
-To compile the tools, edit the makefile for your system and run "make".
-
-Please report problems and issues the colvars library and its tools
-at: https://github.com/colvars/colvars/issues
-
-abf_integrate:
-
-MC-based integration of multidimensional free energy gradient
-Version 20110511
-
-Syntax: ./abf_integrate < filename > \[-n < nsteps >\] \[-t < temp >\] \[-m \[0|1\] (metadynamics)\] \[-h < hill_height >\] \[-f < variable_hill_factor >\] :pre
-
-The LAMMPS interface to the colvars collective variable library, as
-well as these tools, were created by Axel Kohlmeyer (akohlmey at
-gmail.com) at ICTP, Italy.
-
-:line
-
-createatoms tool :h4,link(create)
-
-The tools/createatoms directory contains a Fortran program called
-createAtoms.f which can generate a variety of interesting crystal
-structures and geometries and output the resulting list of atom
-coordinates in LAMMPS or other formats.
-
-See the included Manual.pdf for details.
-
-The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
-
-:line
-
-data2xmovie tool :h4,link(data)
-
-The file data2xmovie.c converts a LAMMPS data file into a snapshot
-suitable for visualizing with the "xmovie"_#xmovie tool, as if it had
-been output with a dump command from LAMMPS itself.  The syntax for
-running the tool is
-
-data2xmovie \[options\] < infile > outfile :pre
-
-See the top of the data2xmovie.c file for a discussion of the options.
-
-:line
-
-eam database tool :h4,link(eamdb)
-
-The tools/eam_database directory contains a Fortran program that will
-generate EAM alloy setfl potential files for any combination of 16
-elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
-Zr.  The files can then be used with the "pair_style
-eam/alloy"_pair_eam.html command.
-
-The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov,
-and is based on his paper:
-
-X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
-144113 (2004).
-
-:line
-
-eam generate tool :h4,link(eamgn)
-
-The tools/eam_generate directory contains several one-file C programs
-that convert an analytic formula into a tabulated "embedded atom
-method (EAM)"_pair_eam.html setfl potential file.  The potentials they
-produce are in the potentials directory, and can be used with the
-"pair_style eam/alloy"_pair_eam.html command.
-
-The source files and potentials were provided by Gerolf Ziegenhain
-(gerolf at ziegenhain.com).
-
-:line
-
-eff tool :h4,link(eff)
-
-The tools/eff directory contains various scripts for generating
-structures and post-processing output for simulations using the
-electron force field (eFF).
-
-These tools were provided by Andres Jaramillo-Botero at CalTech
-(ajaramil at wag.caltech.edu).
-
-:line
-
-emacs tool :h4,link(emacs)
-
-The tools/emacs directory contains a Lips add-on file for Emacs that
-enables a lammps-mode for editing of input scripts when using Emacs,
-with various highlighting options setup.
-
-These tools were provided by Aidan Thompson at Sandia
-(athomps at sandia.gov).
-
-:line
-
-fep tool :h4,link(fep)
-
-The tools/fep directory contains Python scripts useful for
-post-processing results from performing free-energy perturbation
-simulations using the USER-FEP package.
-
-The scripts were contributed by Agilio Padua (Universite Blaise
-Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.
-
-See README file in the tools/fep directory.
-
-:line
-
-i-pi tool :h4,link(ipi)
-
-The tools/i-pi directory contains a version of the i-PI package, with
-all the LAMMPS-unrelated files removed.  It is provided so that it can
-be used with the "fix ipi"_fix_ipi.html command to perform
-path-integral molecular dynamics (PIMD).
-
-The i-PI package was created and is maintained by Michele Ceriotti,
-michele.ceriotti at gmail.com, to interface to a variety of molecular
-dynamics codes.
-
-See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
-"fix ipi"_fix_ipi.html doc page for further details on running PIMD
-calculations with LAMMPS.
-
-:line
-
-ipp tool :h4,link(ipp)
-
-The tools/ipp directory contains a Perl script ipp which can be used
-to facilitate the creation of a complicated file (say, a lammps input
-script or tools/createatoms input file) using a template file.
-
-ipp was created and is maintained by Reese Jones (Sandia), rjones at
-sandia.gov.
-
-See two examples in the tools/ipp directory.  One of them is for the
-tools/createatoms tool's input file.
-
-:line
-
-kate tool :h4,link(kate)
-
-The file in the tools/kate directory is an add-on to the Kate editor
-in the KDE suite that allow syntax highlighting of LAMMPS input
-scripts.  See the README.txt file for details.
-
-The file was provided by Alessandro Luigi Sellerio
-(alessandro.sellerio at ieni.cnr.it).
-
-:line
-
-lmp2arc tool :h4,link(arc)
-
-The lmp2arc sub-directory contains a tool for converting LAMMPS output
-files to the format for Accelrys' Insight MD code (formerly
-MSI/Biosym and its Discover MD code).  See the README file for more
-information.
-
-This tool was written by John Carpenter (Cray), Michael Peachey
-(Cray), and Steve Lustig (Dupont).  John is now at the Mayo Clinic
-(jec at mayo.edu), but still fields questions about the tool.
-
-This tool was updated for the current LAMMPS C++ version by Jeff
-Greathouse at Sandia (jagreat at sandia.gov).
-
-:line
-
-lmp2cfg tool :h4,link(cfg)
-
-The lmp2cfg sub-directory contains a tool for converting LAMMPS output
-files into a series of *.cfg files which can be read into the
-"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A visualizer.  See
-the README file for more information.
-
-This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
-
-:line
-
-lmp2vmd tool :h4,link(vmd)
-
-The lmp2vmd sub-directory contains a README.txt file that describes
-details of scripts and plugin support within the "VMD
-package"_http://www.ks.uiuc.edu/Research/vmd for visualizing LAMMPS
-dump files.
-
-The VMD plugins and other supporting scripts were written by Axel
-Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.
-
-:line
-
-matlab tool :h4,link(matlab)
-
-The matlab sub-directory contains several "MATLAB"_matlab scripts for
-post-processing LAMMPS output.  The scripts include readers for log
-and dump files, a reader for EAM potential files, and a converter that
-reads LAMMPS dump files and produces CFG files that can be visualized
-with the "AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
-visualizer.
-
-See the README.pdf file for more information.
-
-These scripts were written by Arun Subramaniyan at Purdue Univ
-(asubrama at purdue.edu).
-
-:link(matlab,http://www.mathworks.com)
-
-:line
-
-micelle2d tool :h4,link(micelle)
-
-The file micelle2d.f creates a LAMMPS data file containing short lipid
-chains in a monomer solution.  It uses a text file containing lipid
-definition parameters as an input.  The created molecules and solvent
-atoms can strongly overlap, so LAMMPS needs to run the system
-initially with a "soft" pair potential to un-overlap it.  The syntax
-for running the tool is
-
-micelle2d < def.micelle2d > data.file :pre
-
-See the def.micelle2d file in the tools directory for an example of a
-definition file.  This tool was used to create the system for the
-"micelle example"_Section_example.html.
-
-:line
-
-moltemplate tool :h4,link(moltemplate)
-
-The moltemplate sub-directory contains a Python-based tool for
-building molecular systems based on a text-file description, and
-creating LAMMPS data files that encode their molecular topology as
-lists of bonds, angles, dihedrals, etc.  See the README.TXT file for
-more information.
-
-This tool was written by Andrew Jewett (jewett.aij at gmail.com), who
-supports it.  It has its own WWW page at
-"http://moltemplate.org"_http://moltemplate.org.
-
-:line
-
-msi2lmp tool :h4,link(msi)
-
-The msi2lmp sub-directory contains a tool for creating LAMMPS input
-data files from Accelrys' Insight MD code (formerly MSI/Biosym and
-its Discover MD code).  See the README file for more information.
-
-This tool was written by John Carpenter (Cray), Michael Peachey
-(Cray), and Steve Lustig (Dupont).  John is now at the Mayo Clinic
-(jec at mayo.edu), but still fields questions about the tool.
-
-This tool may be out-of-date with respect to the current LAMMPS and
-Insight versions.  Since we don't use it at Sandia, you'll need to
-experiment with it yourself.
-
-:line
-
-phonon tool :h4,link(phonon)
-
-The phonon sub-directory contains a post-processing tool useful for
-analyzing the output of the "fix phonon"_fix_phonon.html command in
-the USER-PHONON package.
-
-See the README file for instruction on building the tool and what
-library it needs.  And see the examples/USER/phonon directory
-for example problems that can be post-processed with this tool.
-
-This tool was written by Ling-Ti Kong at Shanghai Jiao Tong
-University.
-
-:line
-
-polymer bonding tool :h4,link(polybond)
-
-The polybond sub-directory contains a Python-based tool useful for
-performing "programmable polymer bonding".  The Python file
-lmpsdata.py provides a "Lmpsdata" class with various methods which can
-be invoked by a user-written Python script to create data files with
-complex bonding topologies.
-
-See the Manual.pdf for details and example scripts.
-
-This tool was written by Zachary Kraus at Georgia Tech.
-
-:line
-
-pymol_asphere tool :h4,link(pymol)
-
-The pymol_asphere sub-directory contains a tool for converting a
-LAMMPS dump file that contains orientation info for ellipsoidal
-particles into an input file for the "PyMol visualization
-package"_pymol.
-
-:link(pymol,http://pymol.sourceforge.net)
-
-Specifically, the tool triangulates the ellipsoids so they can be
-viewed as true ellipsoidal particles within PyMol.  See the README and
-examples directory within pymol_asphere for more information.
-
-This tool was written by Mike Brown at Sandia.
-
-:line
-
-python tool :h4,link(pythontools)
-
-The python sub-directory contains several Python scripts
-that perform common LAMMPS post-processing tasks, such as:
-
-extract thermodynamic info from a log file as columns of numbers
-plot two columns of thermodynamic info from a log file using GnuPlot
-sort the snapshots in a dump file by atom ID
-convert multiple "NEB"_neb.html dump files into one dump file for viz
-convert dump files into XYZ, CFG, or PDB format for viz by other packages :ul
-
-These are simple scripts built on "Pizza.py"_pizza modules.  See the
-README for more info on Pizza.py and how to use these scripts.
-
-:line
-
-reax tool :h4,link(reax)
-
-The reax sub-directory contains stand-alond codes that can
-post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
-command from a LAMMPS simulation using "ReaxFF"_pair_reax.html.  See
-the README.txt file for more info.
-
-These tools were written by Aidan Thompson at Sandia.
-
-:line
-
-restart2data tool :h4,link(restart)
-
-NOTE: This tool is now obsolete and is not included in the current
-LAMMPS distribution.  This is becaues there is now a
-"write_data"_write_data.html command, which can create a data file
-from within an input script.  Running LAMMPS with the "-r"
-"command-line switch"_Section_start.html#start_7 as follows:
-
-lmp_g++ -r restartfile datafile
-
-is the same as running a 2-line input script:
-
-read_restart restartfile
-write_data datafile
-
-which will produce the same data file that the restart2data tool used
-to create.  The following information is included in case you have an
-older version of LAMMPS which still includes the restart2data tool.
-
-The file restart2data.cpp converts a binary LAMMPS restart file into
-an ASCII data file.  The syntax for running the tool is
-
-restart2data restart-file data-file (input-file) :pre
-
-Input-file is optional and if specified will contain LAMMPS input
-commands for the masses and force field parameters, instead of putting
-those in the data-file.  Only a few force field styles currently
-support this option.
-
-This tool must be compiled on a platform that can read the binary file
-created by a LAMMPS run, since binary files are not compatible across
-all platforms.
-
-Note that a text data file has less precision than a binary restart
-file.  Hence, continuing a run from a converted data file will
-typically not conform as closely to a previous run as will restarting
-from a binary restart file.
-
-If a "%" appears in the specified restart-file, the tool expects a set
-of multiple files to exist.  See the "restart"_restart.html and
-"write_restart"_write_restart.html commands for info on how such sets
-of files are written by LAMMPS, and how the files are named.
-
-:line
-
-vim tool :h4,link(vim)
-
-The files in the tools/vim directory are add-ons to the VIM editor
-that allow easier editing of LAMMPS input scripts.  See the README.txt
-file for details.
-
-These files were provided by Gerolf Ziegenhain (gerolf at
-ziegenhain.com)
-
-:line
-
-xmgrace tool :h4,link(xmgrace)
-
-The files in the tools/xmgrace directory can be used to plot the
-thermodynamic data in LAMMPS log files via the xmgrace plotting
-package.  There are several tools in the directory that can be used in
-post-processing mode.  The lammpsplot.cpp file can be compiled and
-used to create plots from the current state of a running LAMMPS
-simulation.
-
-See the README file for details.
-
-These files were provided by Vikas Varshney (vv0210 at gmail.com)
-
-:line
-
-xmovie tool :h4,link(xmovie)
-
-The xmovie tool is an X-based visualization package that can read
-LAMMPS dump files and animate them.  It is in its own sub-directory
-with the tools directory.  You may need to modify its Makefile so that
-it can find the appropriate X libraries to link against.
-
-The syntax for running xmovie is
-
-xmovie \[options\] dump.file1 dump.file2 ... :pre
-
-If you just type "xmovie" you will see a list of options.  Note that
-by default, LAMMPS dump files are in scaled coordinates, so you
-typically need to use the -scale option with xmovie.  When xmovie runs
-it opens a visualization window and a control window.  The control
-options are straightforward to use.
-
-Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he
-spent a summer at Sandia.  It displays 2d projections of a 3d domain.
-While simple in design, it is an amazingly fast program that can
-render large numbers of atoms very quickly.  It's a useful tool for
-debugging LAMMPS input and output and making sure your simulation is
-doing what you think it should.  The animations on the Examples page
-of the "LAMMPS WWW site"_lws were created with xmovie.
-
-I've lost contact with Mike, so I hope he's comfortable with us
-distributing his great tool!